Summary statistics of the sequence assembly generated from Cichorium intybus.
\r\n\t
",isbn:"978-1-83968-760-0",printIsbn:"978-1-83968-759-4",pdfIsbn:"978-1-83968-761-7",doi:null,price:0,priceEur:0,priceUsd:0,slug:null,numberOfPages:0,isOpenForSubmission:!1,hash:"cc49d6034d85f8f2e2890c6acc3cc629",bookSignature:"Dr. Abhijit Biswas",publishedDate:null,coverURL:"https://cdn.intechopen.com/books/images_new/10285.jpg",keywords:"Mott Insulators, Semi Metals, Polycrystals, Single Crystals, Electronic Properties, Magnetic Properties, PLD, MBE, Topological Insulators, Topological Hall Effect, Devices Applications, Catalysis",numberOfDownloads:null,numberOfWosCitations:0,numberOfCrossrefCitations:null,numberOfDimensionsCitations:null,numberOfTotalCitations:null,isAvailableForWebshopOrdering:!0,dateEndFirstStepPublish:"September 9th 2020",dateEndSecondStepPublish:"October 7th 2020",dateEndThirdStepPublish:"December 6th 2020",dateEndFourthStepPublish:"February 24th 2021",dateEndFifthStepPublish:"April 25th 2021",remainingDaysToSecondStep:"5 months",secondStepPassed:!0,currentStepOfPublishingProcess:5,editedByType:null,kuFlag:!1,biosketch:"A pioneering researcher in the field of tailoring metal oxide crystal surfaces and growth as well as engineering of thin films for various emergent phenomena and energy applications. Dr. Biswas received his Ph.D. from POSTECH, South Korea.",coeditorOneBiosketch:null,coeditorTwoBiosketch:null,coeditorThreeBiosketch:null,coeditorFourBiosketch:null,coeditorFiveBiosketch:null,editors:[{id:"194151",title:"Dr.",name:"Abhijit",middleName:null,surname:"Biswas",slug:"abhijit-biswas",fullName:"Abhijit Biswas",profilePictureURL:"https://mts.intechopen.com/storage/users/194151/images/system/194151.png",biography:"Dr. Abhijit Biswas is a research associate at the Indian Institute of Science Education and Research (IISER) Pune, in India. His research goal is to design and synthesize highest quality epitaxial heterostructures and superlattices, to play with their internal degrees of freedom to exploit the structure–property relationships, in order to find the next-generation multi-functional materials, in view of applications and of fundamental interest. His current research interest ranges from growth of novel perovskite oxides to non-oxides epitaxial films, down to its ultra-thin limit, to observe unforeseeable phenomena. He is also engaged in the growth of high quality epitaxial layered carbides and two-dimensional non-oxide thin films, to exploit the strain, dimension, and quantum confinement effect. His recent work also includes the metal-insulator transitions and magneto-transport phenomena in strong spin-orbit coupled epitaxial perovskite oxide thin films by reducing dimensionality as well as strain engineering. He is also extremely interested in the various energy related environment friendly future technological applications of thin films. In his early research career, he had also extensively worked on the tailoring of metal oxide crystal surfaces to obtain the atomic flatness with single terminating layer. Currently, he is also serving as a reviewer of several reputed peer-review journals.\nDr. Biswas received his B.Sc. in Physics from Kalyani University, followed by M.Sc in Physics (specialization in experimental condensed matter physics) from Indian Institute of Technology (IIT), Bombay. His Ph.D., also in experimental condensed matter physics, was awarded by POSTECH, South Korea for his work on the transport phenomena in perovskite oxide thin films. Before moving back to India as a national post-doctoral fellow, he was a post-doc at POSTECH working in the field of growth and characterizations of strong spin-orbit coupled metal oxide thin films.",institutionString:"Indian Institute of Science Education and Research Pune",position:null,outsideEditionCount:0,totalCites:0,totalAuthoredChapters:"2",totalChapterViews:"0",totalEditedBooks:"0",institution:{name:"Indian Institute of Science Education and Research Pune",institutionURL:null,country:{name:"India"}}}],coeditorOne:null,coeditorTwo:null,coeditorThree:null,coeditorFour:null,coeditorFive:null,topics:[{id:"20",title:"Physics",slug:"physics"}],chapters:null,productType:{id:"1",title:"Edited Volume",chapterContentType:"chapter",authoredCaption:"Edited by"},personalPublishingAssistant:{id:"205697",firstName:"Kristina",lastName:"Kardum Cvitan",middleName:null,title:"Ms.",imageUrl:"https://mts.intechopen.com/storage/users/205697/images/5186_n.jpg",email:"kristina.k@intechopen.com",biography:"As an Author Service Manager my responsibilities include monitoring and facilitating all publishing activities for authors and editors. From chapter submission and review, to approval and revision, copyediting and design, until final publication, I work closely with authors and editors to ensure a simple and easy publishing process. I maintain constant and effective communication with authors, editors and reviewers, which allows for a level of personal support that enables contributors to fully commit and concentrate on the chapters they are writing, editing, or reviewing. I assist authors in the preparation of their full chapter submissions and track important deadlines and ensure they are met. I help to coordinate internal processes such as linguistic review, and monitor the technical aspects of the process. As an ASM I am also involved in the acquisition of editors. 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Venkateswarlu",coverURL:"https://cdn.intechopen.com/books/images_new/371.jpg",editedByType:"Edited by",editors:[{id:"58592",title:"Dr.",name:"Arun",surname:"Shanker",slug:"arun-shanker",fullName:"Arun Shanker"}],productType:{id:"1",chapterContentType:"chapter",authoredCaption:"Edited by"}},{type:"book",id:"878",title:"Phytochemicals",subtitle:"A Global Perspective of Their Role in Nutrition and Health",isOpenForSubmission:!1,hash:"ec77671f63975ef2d16192897deb6835",slug:"phytochemicals-a-global-perspective-of-their-role-in-nutrition-and-health",bookSignature:"Venketeshwer Rao",coverURL:"https://cdn.intechopen.com/books/images_new/878.jpg",editedByType:"Edited by",editors:[{id:"82663",title:"Dr.",name:"Venketeshwer",surname:"Rao",slug:"venketeshwer-rao",fullName:"Venketeshwer Rao"}],productType:{id:"1",chapterContentType:"chapter",authoredCaption:"Edited by"}},{type:"book",id:"4816",title:"Face Recognition",subtitle:null,isOpenForSubmission:!1,hash:"146063b5359146b7718ea86bad47c8eb",slug:"face_recognition",bookSignature:"Kresimir Delac and Mislav Grgic",coverURL:"https://cdn.intechopen.com/books/images_new/4816.jpg",editedByType:"Edited by",editors:[{id:"528",title:"Dr.",name:"Kresimir",surname:"Delac",slug:"kresimir-delac",fullName:"Kresimir Delac"}],productType:{id:"1",chapterContentType:"chapter",authoredCaption:"Edited by"}}]},chapter:{item:{type:"chapter",id:"49516",title:"Toward a First High-quality Genome Draft for Marker-assisted Breeding in Leaf Chicory, Radicchio (Cichorium intybus L.)",doi:"10.5772/61747",slug:"toward-a-first-high-quality-genome-draft-for-marker-assisted-breeding-in-leaf-chicory-radicchio-cich",body:'The common Italian name of Radicchio was adopted in recent years by all the most internationally used languages and indicates a highly differentiated group of chicories, with red or variegated leaves. Radicchio (Cichorium intybus subsp. intybus var. foliosum L.) is currently one of the most important leaf chicories, used mainly as a component for fresh salads but also very often cooked and prepared differently according to local traditions and alimentary habits [1]. This plant species belongs to the Asteraceae family and includes several cultivar groups whose commercial food products are the leaves, namely Witloof, Pain de sucre, and Catalogne, as well as several types of Radicchio.
From the reproductive point of view, Radicchio is prevalently allogamous, due to an efficient sporophytic self-incompatibility system, proterandry and gametophytic competition favoring allo-pollen grains and tubes [1]. Probably known by the Egyptians and used as food and/or medicinal plants by the ancient Greeks and Romans, this species gradually underwent a process of naturalization and domestication in Europe during the past few centuries. This plant has become part of both natural and agricultural environments of Italy. Currently, among the different biotypes of leaf chicories, the so-called Radicchio of Chioggia, native to and very extensively grown in northeastern Italy, is the Radicchio cultivar acquiring more and more commercial interest worldwide. In Italy, the Radicchio of Chioggia is cultivated on a total area of approximately 16–18,000 ha, half of which is in the Veneto region, with a total production of approximately 270,000 tons (more than 60% obtained using professional seeds), reaching an overall turnover of approximately € 10,000,000 per year.
Grown plant materials are usually represented by landraces or their directly derived synthetics that are known to possess a high variation and adaptation to the natural and anthropological environment where they originated from and are still cultivated. These populations are characterized by high-quality traits and have been maintained or even improved over the years by local farmers through phenotypical selection according to their own criteria and more recently by seed companies through genotypical selection following intercross or polycross schemes combined with progeny tests to obtain populations showing superior DUS scores for both agronomic and commercial traits. The breeding programs currently underway by local firms and regional institutions exploit the best landraces and aim to isolate individuals amenable for use as parents for the constitution of narrow genetic base synthetic varieties and/or to select inbred lines suitable for the production of heterotic F1 hybrids [2]. In recent years, phenotypic evaluation trials are increasingly assisted by genotypic selection procedures through the use of molecular markers scattered throughout the genome. In fact, marker-assisted breeding allows the identification of the parental individuals or the inbred lines showing the best general or specific combining ability in order to breed synthetics and hybrids, respectively.
Radicchio, like the other leaf chicories, is diploid (2n=2x=18) and is characterized by an estimated haploid genome size of approximately 1.3 Gb. In recent years, three distinct saturated molecular linkage maps were constructed for leaf chicories, covering approximately 1,200 cM [3-5]. Its linkage groups were mainly based on neutral SSR markers, but many EST-derived SNP markers were also mapped. A method for genotyping elite breeding stocks of Radicchio, both local and modern varieties, assaying mapped SSR marker loci possibly linked to EST-rich regions and scoring PIC>0.5, was recently developed using multiplex PCRs [6]. Here, we are dealing with a research and development project aimed at sequencing and annotating the first draft of the leaf chicory genome as we believe it will have an extraordinary impact from both scientific and economic points of view. Indeed, the availability of the first genome sequence for this plant species will provide a powerful tool to be exploited in the identification of markers associated with or genes responsible for relevant agronomic traits, influencing crop productivity and product quality. As an example, data and knowhow produced in this research project will be useful for detailed studies of the genetic control of male-sterility and self-incompatibility in this species.
The plant material that we used for the sequencing of the leaf chicory genome belongs to the Radicchio of Chioggia type, specifically to the male fertile inbred line named SEG111. This type was chosen as the most suitable accession based on the following criteria: i) the commercial relevance of the variety of origin; ii) the availability of clonal materials; iii) robust phenotypic and genotypic characterization; iv) a high degree of homozygosity (80%); and v) high breeding value as pollen parent of F1 hybrids. Sequencing reactions of the genomic DNA library were performed with Illumina HiSeq and MySeq platforms to combine the high number of reads originated by the former with the longer sequences produced by the latter. Here, we report original data from the bioinformatic assembly of the first genome draft of Radicchio, along with the most relevant findings that emerged from an extensive de novo gene prediction and in silico functional annotation of more than 18,000 unigenes. Analyses were performed according to established computational biology protocols by taking advantage of the publically available reference transcriptome data for Cichorium intybus [7]. The main preliminary findings on the genome organization and gene composition of Radicchio are presented, and the potentials of newly annotated expressed sequences and diagnostic microsatellite markers in breeding programs are critically discussed.
Plant materials used for the sequencing belong to a variety of commercial relevance of the Radicchio of Chioggia type. The clone chosen derives from the inbred line SEG111 and shows a degree of homozygosity equal to 80% [6]. In particular, this clone was obtained by several cycles of selfing from plants yearly selected on the basis of a robust phenotypic and genotypic characterization, being also characterized by high-quality agronomic traits on farm and the ability to be easily cloned in vitro.
DNA was isolated from 150 mg of fresh leaf tissue using a CTAB-based protocol [8]. The eventual contamination of RNA was avoided with an RNase A (Sigma-Aldrich) treatment. DNA samples were eluted in 80–100 μL of 0.1× TE buffer (100 mM Tris-HCl 1, 0.1 mM EDTA, pH=8). The integrity of the extracted DNA samples was estimated through electrophoresis in 0.8% agarose/1× TAE gels containing 1× SYBR Safe DNA Gel Stain (Life Technologies, USA). The purity and quantity of the DNA extracts were assessed with a NanoDrop spectrophotometer (Thermo Scientific, USA). Then, 1 μg of high-quality DNA was used for library preparation with the TruSeq DNA Sample Preparation chemistry (Illumina). Sequencing reactions were performed with the Illumina platforms: HiSeq (1 lane, 2 × 100 bp) and MySeq (1 lane, 2 × 300 bp).
All high-quality reads generated from the two sequencing reactions were assembled in a single reference genome. Assemblies were attempted with three pieces of software: i) Velvet [9]; ii) SPAdes [10]; and iii) CLC Genomics Workbench 6.5 (Qiagen). The average coverage was estimated for the run HiSeq by calculating the frequency distribution of 25-mers [11].
To annotate all assembled contigs, a BLASTX-based approach was used to compare the C. intybus sequences to a subset of the NR protein collection that was made by focusing on the clade pentapetalae [12]. Moreover, the GI identifiers of the best BLASTX hits, having E-value ≤1.0E-15 and similarity ≥70%, were mapped to the UniprotKB protein database [13] to extract Gene Ontology annotations [14] and KEGG terms [15] for functional annotations. Further enrichment of enzyme annotations was made with the BLAST2GO software v1.3.3 using the function “direct GO to Enzyme annotation”. The BLAST2GO software v1.3.3 [16, 17] was used to reduce the complexity of the data and perform basic statistics on ontological annotations, as reported by Galla et al. [18].
SSRs were detected among the 522.301 contigs via MISA [19]. The parameters were adjusted to identify perfect and complex mono-, di-, tri-, tetra-, penta-, and hexanucleotide motifs with a minimum of 49, 13, 9, 8, 8, and 8 repeats, respectively. Repeated elements were detected with a BLASTN-based approach using a PGSB Repeat Element Database in all blast searches [20]. The parameters set for the identification of Transposable Elements (TEs) were: reward 1, penalty 1, gap_open 2, gap_extend 2, word_size 9, dust no. An E-value cutoff of 1.0E-9 was adopted to filter the BLAST results.
Two public C. intybus transcriptomes CHI-2418 and CHI-Witloof originally developed from plant seedlings [7] corresponding to a wild accession of leaf chicory and a cultivated variety of witloof, respectively, were mapped to the reference genome using the CLC Genomics Workbench V7.02 (Qiagen). Mappings were performed with default mapping parameters, including mismatch cost: 2; insertion cost: 3; deletion cost: 3; length fraction: 0.5; and similarity fraction: 0.8. Non-specific matches were ignored and not included in the annotation tracks. For nucleotide variant analysis, the appropriate reference masking options were used to map transcriptome reads selectively over the sequences annotated as CDS or TEs. The variant detection analysis was done by using the Basic Variant Detection tool of the CLC Genomics Workbench V7.02 (Qiagen) with default parameters. As general filters, positions with coverage above 100,000 were not considered. Base quality filters were turned on and set to default parameters. All variants included in homopolymer regions with minimum length of 3nt, and with frequency below 0.8 were also removed from the dataset. As coverage and count filters, all variants with a minimum count lower than 20 were discarded.
To obtain the first genome draft of leaf chicory, a single genomic library produced from the inbred line SEG111 was sequenced using the Illumina MySeq and HiSeq platforms. Here, we report the genome assembly results derived from the CLC Genomic Workbench assembly output. Figure 1 describes the frequency distribution of 25-mers in the HiSeq data.
Frequency distribution of 25-mers in the HiSeq data (logarithmic scale for both axes)
The data shown suggest that the average coverage in the HiSeq run is approximately 21×. Additionally, the curve indicates that a certain number of sequences are present with a relatively high frequency within the genome. This might indicate that repeated elements are relatively abundant within the genome. As a consequence, the estimated size of the assembled genome draft is 760 Mb.
We obtained 58,392,530 and 389,385,400 raw reads through the MySeq and HiSeq platforms, respectively. The de novo assembly of the two datasets in a unique reference genome draft assembled 724,009,424 nucleotides into 522,301 contigs (Table 1). The maximum contig length was equal to 379,698 bp, whereas the minimum contig length was set to 200 bp, with an average contig length of 1,386 bp. Overall statistics are summarized in Table 1.
Total number of contigs | \n\t\t\t522,301 | \n\t\t
Total No. of assembled nucleotides (nt) | \n\t\t\t724,009,424 | \n\t\t
GC percentage | \n\t\t\t34.8% | \n\t\t
Average contig length (bp) | \n\t\t\t1,386 | \n\t\t
Minimum contig length (bp) | \n\t\t\t200 | \n\t\t
Maximum contig length (bp) | \n\t\t\t379,698 | \n\t\t
N75 | \n\t\t\t1,051 | \n\t\t
N50 | \n\t\t\t3,131 | \n\t\t
Summary statistics of the sequence assembly generated from Cichorium intybus.
The length distribution of the contig size, expressed in base pairs, is reported in Figure 2.
Distribution of length of contigs for leaf chicory
As much as 68.9% of the recovered sequences are contained within a length spanning from 200 nt to 999 nt. The interval length ranging between 1,000 nt and 2,999 nt is represented by 19.7% of the assembled contigs, whereas the proportion of contigs whose length is higher or equal to 3,000 nt corresponds to 11.5%.
We searched the genome sequence assembly for TEs and estimated their abundance using a BLASTN strategy. The proportion of base pairs annotated as TEs out of the total amount of assembled nucleotides was equal to 6.3% (Table 2).
\n\t\t\t\tKey\n\t\t\t | \n\t\t\t\n\t\t\t\tClassification\n\t\t\t | \n\t\t\t\n\t\t\t\tNumber\n\t\t\t | \n\t\t\t\n\t\t\t\tAbundance (%)\n\t\t\t | \n\t\t\t\n\t\t\t\tLength (bp)\n\t\t\t | \n\t\t\t\n\t\t\t\tPercentage over the assembled genome\n\t\t\t | \n\t\t
\n\t\t\t\t02.01\n\t\t\t | \n\t\t\tClass I retroelement | \n\t\t\t273 | \n\t\t\t0.19 | \n\t\t\t85,241 | \n\t\t\t0.012% | \n\t\t
\n\t\t\t\t02.01.01\n\t\t\t | \n\t\t\tLTR Retrotransposon | \n\t\t\t82,260 | \n\t\t\t56.55 | \n\t\t\t19,658,874 | \n\t\t\t2.715% | \n\t\t
\n\t\t\t\t02.01.01.05\n\t\t\t | \n\t\t\tTy1/copia | \n\t\t\t35,802 | \n\t\t\t24.61 | \n\t\t\t17,519,102 | \n\t\t\t2.420% | \n\t\t
\n\t\t\t\t02.01.01.10\n\t\t\t | \n\t\t\tTy3/gypsy | \n\t\t\t23,651 | \n\t\t\t16.26 | \n\t\t\t7,121,605 | \n\t\t\t0.984% | \n\t\t
\n\t\t\t\t02.01.02\n\t\t\t | \n\t\t\tnon-LTR Retrotransposon | \n\t\t\t354 | \n\t\t\t0.24 | \n\t\t\t106,259 | \n\t\t\t0.015% | \n\t\t
\n\t\t\t\t02.05\n\t\t\t | \n\t\t\tClass II: DNA Transposon | \n\t\t\t1,976 | \n\t\t\t1.36 | \n\t\t\t713,119 | \n\t\t\t0.098% | \n\t\t
\n\t\t\t\t02\n\t\t\t | \n\t\t\tUnclassified mobile element | \n\t\t\t861 | \n\t\t\t0.59 | \n\t\t\t199,301 | \n\t\t\t0.028% | \n\t\t
\n\t\t\t\t10 / 90 / 99\n\t\t\t | \n\t\t\tHigh Copy Number Genes and additional attributes | \n\t\t\t283 | \n\t\t\t0.19 | \n\t\t\t51,577 | \n\t\t\t0.007% | \n\t\t
\n\t\t\t\tTotal\n\t\t\t | \n\t\t\t\n\t\t\t | 145,462 | \n\t\t\t100.0 | \n\t\t\t45,455,078 | \n\t\t\t6.278% | \n\t\t
Classification statistics of transposable elements (TEs) in Radicchio genome draft assembly.
The retroelements were the most abundant elements (>97% of the total). Within the major class of retroelements, Long Terminal Repeat (LTR) retrotransposons proved to be the dominant class (56.55%) in the leaf chicory genome. Moreover, the Copia-type (24.61%) and the Gypsy-type (16.26%) appeared to be the most abundant LTR retrotransposons. A total of 273 (0.2%) elements were annotated as retroelements, but they lacked the assignation to a specific class based on sequence similarity and conservation. Non-LTR retrotransposons were detected to a very low extent (0.24%). Less than 2% of the total repeat elements were annotated as DNA transposons.
Overall, we identified 66,785 SSR containing regions. As many as 52,186 and 11,501 sequences proved to contain one or more microsatellites, respectively. These numbers included 1,226 mononucleotide SSR motifs (which were no longer taken into account for further computations). We found a total number of di- or multinucleotide SSR motifs equaling 65,559.
The most common SSR elements were those showing a dinucleotide motif (89.0%), followed by trinucleotide (7.1%) and tetranucleotide (3.0%) ones. Microsatellites revealing a pentanucleotide and hexanucleotide motif were less than 1.0% of the total. Overall data are summarized in Table 3.
\n\t\t\t\tType of motif\n\t\t\t | \n\t\t\t\n\t\t\t\tRange of repeat numbers\n\t\t\t | \n\t\t\t\n\t\t\t\tTotal No.\n\t\t\t | \n\t\t\t\n\t\t\t\tPercentage (%)\n\t\t\t | \n\t\t|||
\n\t\t\t | \n\t\t\t\t8-12\n\t\t\t | \n\t\t\t\n\t\t\t\t13-17\n\t\t\t | \n\t\t\t\n\t\t\t\t18-22\n\t\t\t | \n\t\t\t\n\t\t\t\t>22\n\t\t\t | \n\t\t\t\n\t\t\t | \n\t\t |
\n\t\t\t\tDi-nucleotide\n\t\t\t | \n\t\t\t0 | \n\t\t\t8,333 | \n\t\t\t7,100 | \n\t\t\t42,913 | \n\t\t\t58,346 | \n\t\t\t89.0 | \n\t\t
\n\t\t\t\tTri-nucleotide\n\t\t\t | \n\t\t\t1,822 | \n\t\t\t1,769 | \n\t\t\t762 | \n\t\t\t321 | \n\t\t\t4,674 | \n\t\t\t7.1 | \n\t\t
\n\t\t\t\tTetra-nucleotide\n\t\t\t | \n\t\t\t1,114 | \n\t\t\t475 | \n\t\t\t205 | \n\t\t\t202 | \n\t\t\t1,996 | \n\t\t\t3.0 | \n\t\t
\n\t\t\t\tPenta-nucleotide\n\t\t\t | \n\t\t\t69 | \n\t\t\t23 | \n\t\t\t0 | \n\t\t\t2 | \n\t\t\t94 | \n\t\t\t0.1 | \n\t\t
\n\t\t\t\tHexa-nucleotide\n\t\t\t | \n\t\t\t359 | \n\t\t\t80 | \n\t\t\t8 | \n\t\t\t2 | \n\t\t\t449 | \n\t\t\t0.7 | \n\t\t
\n\t\t\t\tTotal\n\t\t\t | \n\t\t\t3,364 | \n\t\t\t10,680 | \n\t\t\t8,075 | \n\t\t\t43,440 | \n\t\t\t\n\t\t\t | \n\t\t |
\n\t\t\t\tPercentage (%)\n\t\t\t | \n\t\t\t5.1 | \n\t\t\t16.3 | \n\t\t\t12.3 | \n\t\t\t66.3 | \n\t\t\t\n\t\t\t | \n\t\t |
Number of SSRs detected in the Radicchio genome draft assembly. For each type of motif, the number of SSRs identified in the range of repeated numbers is reported. Albeit present in the genome, mono-nucleotide SSRs were not considered in this analysis.
Functional annotation of the assembled contigs was performed with a BLASTX approach, according to which all contig sequences were used to query different public protein databases (Table 4).
\n\t\t\t\tPublic database\n\t\t\t | \n\t\t\t\n\t\t\t\tNo. of Hits (gene models)\n\t\t\t | \n\t\t\t\n\t\t\t\tNo. of C. intybus contigs\n\t\t\t | \n\t\t
\n\t\t\t\tNR \n\t\t\t | \n\t\t\t38,782 | \n\t\t\t80,862 | \n\t\t
\n\t\t\t\tArabidopsis\n\t\t\t | \n\t\t\t16,689 | \n\t\t\t50,417 | \n\t\t
\n\t\t\t\tGO\n\t\t\t | \n\t\t\t14,073 | \n\t\t\t45,381 | \n\t\t
\n\t\t\t\tKEGG\n\t\t\t | \n\t\t\t4,512 | \n\t\t\t22,273 | \n\t\t
Summary statistics of functional annotations for leaf chicory genome sequences in public protein databases. As for the NR database, only the protein sequences from the clade pentapetalae of eudicots were considered. The Arabidopsis proteome used in all BLAST analysis was TAIR10.
The database enclosing all public protein sequences belonging to the pentapetalae clade of the eudicots, which includes the sub-clades of rosids and asterids to which leaf chicory belongs, provided a total of 38,782 hits. The proteome of Arabidopsis thaliana alone scored 16,689 hits when an E-value cutoff of 1.0E-15 was applied for the screening of the most reliable BLASTX hits.
Two public C. intybus transcriptomes originally developed from plant seedlings and provided by UC DAVIS, the Compositae Genome Project (CHI-2418 and CHI-Witloof) [7] were mapped to the reference genome using the appropriate mapping function of the CLC Genomics Workbench.
By doing so, we were able to map 76.5% and 78.0% of the sequences, respectively. Data derived from the mapping of two C. intybus transcriptomes were used to integrate the annotation of the assembled contigs. BLAST and mapping data integration increased the BLAST-based annotation with an additional set of 1,995 contigs.
Arabidopsis matches were used to retrieve both GO and KEGG annotations from public databases. We could finally assign one or multiple GO terms to 45,381 leaf chicory genome contigs. The analysis performed against the GO illustrate 14,073 genes annotated with terms belonging to one or multiple vocabularies. Of these, 24,634 contigs were annotated for their putative biological process, 39,118 contigs were related to a molecular function, and 37,561 contigs were associated to a specific cellular component. Figure 3 shows the fine distribution of the 14,073 hits caught by our Radicchio contigs from the TAIR database according to the aforementioned three GO categories.
Venn diagram showing the fine distribution according to GO terms of the 14,073 A. thaliana hits matching our leaf chicory contigs
Among all the terms underlined by the GO vocabulary for the biological process, our investigations were focused on terms related to the response to biotic and abiotic stresses (Figure 4), hormonal responses (Figure 5), and flower and seed development (Figure 6). Of the 15 most interesting processes for molecular breeding in leaf chicory, 7 and 8 were linked to biotic and abiotic stresses, respectively (see Figure 4). The ontological terms were assigned to 2,388 and 3,844 genome contigs, respectively.
Number of C. intybus genomic contigs for response to biotic (the first 7) and abiotic (the last 8) stress
The computational analysis for the identification of SSR elements within these contigs unveiled 495 motifs linked to biotic stresses and 841 motifs associated with abiotic stresses. Among the biotic stresses, the most abundant gene ontology (GO) term was GO:0042742, which corresponds to the “defense response to bacterium” and shows a match with 667 genome contigs containing 135 microsatellites. Concerning the abiotic stresses, the GO term assigned with the higher frequency was GO:0009651, which accounts for processes related to “response to salt stress” and matches 1,028 genome contigs containing 249 microsatellites.
Data of hormonal responses and processes of flower and seed development are reported in Figures 5 and 6. The analysis for hormonal responses noted nine different GO terms, for a total of 3,344 genome contigs, and 833 SSR elements linked to these sequences and terms. In particular, the term “response to jasmonic acid stimulus” (GO:0009753) was the most represented, with 478 matches with different genome contigs, including 118 SSR motifs (Figure 5).
Number of C. intybus genomic contigs for hormonal response
Results of the GO term annotation of genome contigs according to the flower and seed developmental processes are reported in Figure 6.
Number of C. intybus genomic contigs for flower and seed (only the last 3) development
The flower development process was embraced by selecting nine ontological terms, whereas three terms were assigned to seed development and seed germination. A total of 2,162 contigs were annotated with GO terms related to flower development; 496 of these were also annotated for the presence of one or multiple SSRs. In particular, the term “pollen development” (GO:0009555) was the most abundant, with 655 contigs containing 153 SSR motifs.
As far as the seed development process is concerned, we annotated 1,182 contigs linked to this GO term, 273 of which co-localized with one or multiple SSRs. Among these, the most abundant ontological term was “embryo development ending in seed dormancy” (GO:0009793) as it is assigned to 771 contigs, co-localizing with 171 SSR elements.
Using the Kyoto Encyclopaedia of Genes and Genomes database (http://www.genome.jp/kegg/), a total of 22,273 contigs enabled the mapping of 795 enzymes to 157 metabolic pathways. Among the metabolic pathways with the highest number of mapped reads, we found fructose and mannose metabolism (418 gene models matched), phenylpropanoid biosynthesis (415 gene models matched) and tryptophan metabolism (380 gene models matched). The biosynthetic pathway of flavonoid biosynthesis, described in map:00941, is relevant as the biosynthesis of flavonoid is directly connected to the synthesis of anthocyanin (Figure 7), whose accumulation contributes to the pigmentation of leaf chicories. This map includes 236 gene models that were assigned to 14 unique enzymes, including CHS (CHALCONE SYNTHASE), CHI (CHALCONE ISOMERASE), and ANS (ANTHOCYANIDIN SYNTHASE), among others.
KEGG pathway for flavonoid biosynthesis (Map:00941)
KEGG data related to a number of selected metabolic pathways were exploited to find SSR regions potentially associated with highly valuable phenotypes in this plant species. The number of SSRs putatively linked to the most interesting phenotypic traits with breeding values in leaf chicory is displayed in Table 5.
\n\t\t\t\tKEGG map ID\n\t\t\t | \n\t\t\t\n\t\t\t\tMetabolic pathway\n\t\t\t | \n\t\t\t\n\t\t\t\tCharacteristic\n\t\t\t | \n\t\t\t\n\t\t\t\tNo. of SSRs\n\t\t\t | \n\t\t
map00909 | \n\t\t\tSesquiterpenoid and triterpenoid biosynthesis | \n\t\t\tBitter taste | \n\t\t\t107 | \n\t\t
map00053 | \n\t\t\tAscorbate and aldarate metabolism | \n\t\t\tVitamin C content | \n\t\t\t172 | \n\t\t
map00940 | \n\t\t\tPhenylpropanoid biosynthesis | \n\t\t\tLeaf color | \n\t\t\t281 | \n\t\t
map00941 | \n\t\t\tFlavonoid biosynthesis | \n\t\t\tLeaf color | \n\t\t\t173 | \n\t\t
map00942 | \n\t\t\tAnthocyanin biosynthesis | \n\t\t\tLeaf color | \n\t\t\t180 | \n\t\t
map00943 | \n\t\t\tIsoflavonoid biosynthesis | \n\t\t\tLeaf color | \n\t\t\t5 | \n\t\t
map00944 | \n\t\t\tFlavone and flavonol biosynthesis | \n\t\t\tLeaf color | \n\t\t\t128 | \n\t\t
map00040 | \n\t\t\tPentose and glucuronate interconversions | \n\t\t\tResponse to cold | \n\t\t\t96 | \n\t\t
map00051 | \n\t\t\tFructose and mannose metabolism | \n\t\t\tResponse to cold | \n\t\t\t259 | \n\t\t
map00052 | \n\t\t\tGalactose metabolism | \n\t\t\tResponse to cold | \n\t\t\t31 | \n\t\t
map00061 | \n\t\t\tFatty acid biosynthesis | \n\t\t\tResponse to cold | \n\t\t\t39 | \n\t\t
map00260 | \n\t\t\tGlycine, serine and threonine metabolism | \n\t\t\tResponse to cold | \n\t\t\t60 | \n\t\t
map00290 | \n\t\t\tValine, leucine and isoleucine biosynthesis | \n\t\t\tResponse to cold | \n\t\t\t13 | \n\t\t
map00330 | \n\t\t\tArginine and proline metabolism | \n\t\t\tResponse to cold | \n\t\t\t55 | \n\t\t
map00410 | \n\t\t\tbeta-Alanine metabolism | \n\t\t\tResponse to cold | \n\t\t\t16 | \n\t\t
map00480 | \n\t\t\tGlutathione metabolism | \n\t\t\tResponse to cold | \n\t\t\t48 | \n\t\t
map00500 | \n\t\t\tStarch and sucrosa metabolism | \n\t\t\tResponse to cold | \n\t\t\t164 | \n\t\t
map00561 | \n\t\t\tGlycerolipid metabolism | \n\t\t\tResponse to cold | \n\t\t\t159 | \n\t\t
map00564 | \n\t\t\tGlycerophospholipid metabolism | \n\t\t\tResponse to cold | \n\t\t\t124 | \n\t\t
map00592 | \n\t\t\talpha-Linolenic acid metabolism | \n\t\t\tResponse to cold | \n\t\t\t66 | \n\t\t
map00710 | \n\t\t\tCalvin cycle | \n\t\t\tResponse to cold | \n\t\t\t28 | \n\t\t
map00780 | \n\t\t\tBiotin metabolism | \n\t\t\tResponse to cold | \n\t\t\t18 | \n\t\t
map00960 | \n\t\t\tTropane, piperidine and pyridine alkaloid biosynthesis | \n\t\t\tResponse to cold | \n\t\t\t97 | \n\t\t
Number of SSRs located in contig sequences annotated for the presence of proteins with known enzymatic activity in relevant metabolic pathways for the breeding of leaf chicory.
Considering the overall grouping of selected metabolic pathways, we identified many microsatellite sequences putatively linked to important traits, according to their potential effect on plant characteristics. For instance, 107 SSRs were linked to bitter taste, 172 SSRs were associated with vitamin C biosynthesis and metabolism, and 767 SSRs located in sequence contigs encoding enzymes of the flavonoid and anthocyanin biosynthetic pathways, thus potentially associated with the leaf color. The most represented characteristic is the response to cold. For this trait, we analyzed 16 different metabolic pathways that altogether led to the selection of 1,273 microsatellites potentially associated with one or multiple genes actively involved in the plant response to cold eventually, but not exclusively, through the accumulation of sugar.
We also performed the calling of nucleotide variants. Stringent quality criteria were used for discriminating sequence variations from sequencing errors and mutations introduced during cDNA synthesis. Only sequence variations with mapping quality scores over the established thresholds were annotated, leading to the identification of 123,943 and 121,086 variants that were present only in the leaf chicory transcriptome CHI-2418 (wild type) or the Witloof transcriptome CHI-Witloof (cultivated type), respectively. A total of 119,729 variants were shared by both C. intybus transcriptomes. The average number of variants per contig ranged from 9.5 to 10.5 in the two assemblies (Table 6), yielding one single variation per 100 bp in both cases.
\n\t\t\t | \n\t\t\t\tRadicchio CDS – 29,175 contigs\n\t\t\t | \n\t\t\t\n\t\t\t\tRadicchio TEs – 122,745 contigs\n\t\t\t | \n\t\t||||
\n\t\t\t | \n\t\t\t\tCHI-2418\n\t\t\t | \n\t\t\t\n\t\t\t\tCHI-Witloof\n\t\t\t | \n\t\t\t\n\t\t\t\tShared\n\t\t\t | \n\t\t\t\n\t\t\t\tCHI-2418\n\t\t\t | \n\t\t\t\n\t\t\t\tCHI-Witloof\n\t\t\t | \n\t\t\t\n\t\t\t\tShared\n\t\t\t | \n\t\t
\n\t\t\t\tNo. contigs\n\t\t\t | \n\t\t\t12,725 | \n\t\t\t12,739 | \n\t\t\t11,419 | \n\t\t\t2,016 | \n\t\t\t1,924 | \n\t\t\t1,554 | \n\t\t
\n\t\t\t\tNo. variants\n\t\t\t | \n\t\t\t123,843 | \n\t\t\t121,086 | \n\t\t\t119,729 | \n\t\t\t10,662 | \n\t\t\t10,651 | \n\t\t\t10,246 | \n\t\t
\n\t\t\t\tNo. variants/contigs\n\t\t\t | \n\t\t\t9.75 | \n\t\t\t9.52 | \n\t\t\t10.52 | \n\t\t\t5.29 | \n\t\t\t5.54 | \n\t\t\t6.61 | \n\t\t
\n\t\t\t\tNo. variants/100 bp\n\t\t\t | \n\t\t\t0.99 (1.14) | \n\t\t\t0.98 (1.14) | \n\t\t\t1.14 (2.05) | \n\t\t\t3.26 (3.64) | \n\t\t\t3.16 (3.50) | \n\t\t\t5.42 (8.88) | \n\t\t
\n\t\t\t\tSNVs\n\t\t\t | \n\t\t\t115,678 | \n\t\t\t113,049 | \n\t\t\t107,255 | \n\t\t\t9,532 | \n\t\t\t9,605 | \n\t\t\t9,006 | \n\t\t
\n\t\t\t\tMNVs\n\t\t\t | \n\t\t\t5,367 | \n\t\t\t5,439 | \n\t\t\t8,475 | \n\t\t\t507 | \n\t\t\t441 | \n\t\t\t261 | \n\t\t
\n\t\t\t\tInsertions\n\t\t\t | \n\t\t\t2,044 | \n\t\t\t2,036 | \n\t\t\t2,166 | \n\t\t\t556 | \n\t\t\t552 | \n\t\t\t714 | \n\t\t
\n\t\t\t\tDeletions\n\t\t\t | \n\t\t\t754 | \n\t\t\t562 | \n\t\t\t1,833 | \n\t\t\t67 | \n\t\t\t53 | \n\t\t\t265 | \n\t\t
Summary statistics of nucleotide variants restricted to gemonic regions of Radicchio annotated as CDS and Transposable Elements. Nucleotide variants were detected by using the transcriptomes CHI-2418 (wild type leaf chicory) and CHI-Witloof (cultivated Witloof type). For each transcriptome, the number of contigs displaying one or multiple variants, the number of variants and the number of variants per contigs are indicated. The number of variants per 100bp is also reported. Variants present in both transcriptomes are indicated as shared.
The vast majority of variants were Single Nucleotide Variants (SNVs), whereas Multi Nucleotide Variants (MNVs), Insertions, and Deletions were found to a considerably lower extent (Table 6). On average, the proportion of SNVs and MNVs was comparable in the CDS and TE contigs and equal to about 90% and 5%, respectively.
Among all contigs annotated as TEs, those characterized by the presence of one or multiple variants were 10,662 and 10,651 for the two transcriptomes (Table 6). The average number of variants per contig was equal to 5.3 and 5.5. Despite the relatively low abundance of polymorphic residues in these regions, the average number of variants per 100 bp was equal to 3.3 and 3.2. Single Nucleotide Polymorphisms (SNPs) were by far the most abundant type of variants in TEs as well as in CDS regions (Table 6). In particular, transversions and transitions were on average 37% (ranging from 35.6% and 37.8%) and 63% (ranging from 62.2% and 64.4%) of the point mutations, respectively. The total number of nonsynonymous SNPs calculated with the reference transcriptomes was equal to 13,559 (10.9%) and 11,197 (9.2%) for wild-type leaf chicory and cultivated Witloof accessions, respectively.
Here, we report the uncovering of the first draft of the Radicchio genome. This highly relevant discovery was achieved by combining the recent advancement of next-generation sequencing technologies on the public side with the significant investment of financial resources in research and development on the private side.
Currently, conventional agronomic-based selection methods are supported by molecular marker-assisted breeding schemes. In recent years, we have demonstrated that the constitution of F1 hybrids is not only feasible in a small experimental scheme but also realizable and profitable on a large commercial scale (e.g., registered CPVO varieties TT4070/F1, TT5010/F1, TT5070/F1, and TT4010/F1 in progress). F1 hybrids are varieties manifesting heterosis, or hybrid vigor, which refers to the phenomenon in which highly heterozygous progeny plants obtained by crossing genetically divergent inbred or pure lines exhibit greater biomass, faster speed of development, higher resistance to pests and better adaptation to environmental stresses than the two homozygous parents. Critical steps of an applicative breeding program are the production of parental inbreds. Two highly relevant factors in this context are the selection of self-compatible genotypes, to be used as pollen donors, and the identification of male-sterile genotypes, to be used as seed parents in large-scale crosses [21, 22].
It is worth mentioning that there are several reasons why the constitution of F1 hybrids is a strategic choice for a seed company. First, the crop yield of modern F1 hybrid varieties is usually much higher than that of traditional OP or synthetic varieties. Second, the uniformity of F1 populations and the way to legally protect their parental lines allow a seed company to adopt a plant breeder’s rights, promoting genetic research and development programs that are very expensive and require many years. Finally, the need for breeding hybrid varieties also promotes the preservation of local varieties because the selection of appropriate inbred or pure lines as parents in pairwise cross-combinations requires the exploration and exploitation of germplasm resources. Our expectation is that F1 hybrid varieties will be bred and adopted with increasing frequency in Radicchio. Consequently, we invested in the sequencing and annotation of the first draft of the leaf chicory genome as it will have an extraordinary impact from both scientific and economic points of view. Indeed, the availability of the first genome sequence for this plant species will provide a powerful tool to be exploited in the identification of markers associated with or genes responsible for relevant agronomic traits, influencing crop productivity and product quality. As an example, data and knowhow produced in this research project will be capitalized on in subsequent years to plan and develop basic studies and applied research on male-sterility and self-incompatibility in this species.
The availability of high-quality sequencing platforms (i.e., Illumina) on the one hand, and specific and high-performing software for genome data assembly and gene set analysis on the other, made this project feasible. High-quality genomic DNA libraries were used for sequencing reactions performed with the Illumina platforms HiSeq and MySeq, originating a total of 197 million (mln) short reads and 29 mln longer sequences passing quality filters, respectively, which were then bioinformatically assembled to obtain the first genome draft. On the basis of this strategy, the genome draft of leaf chicory is composed of approximately 500,000 contigs, forming approximately 720 Mb. Based on the distribution of 25-mer frequencies, we estimated that the genome coverage is close to 25X. The same distribution also indicates that a significant part of the genome might be composed of highly repeated elements, as indicated by the number of k-mers that appears to be present with high frequency.
Nucleotide variant calling for the Radicchio genome showed comparable number of polymorphisms in the pairwise comparisons with the two publically available transcriptomes, originally developed from seedlings of two leaf chicory accessions (i.e., wild and cultivated types). The total number of variants discovered in the CDS regions was shown to be approximately 10 times higher than the ones found in the TEs. This result might be a consequence of low expression, or silencing, of numerous transposable elements at the level of plant seedlings, as indicated by the finding that the mapping of the two transcriptomes to the reference genome failed to align sequences to about 98% of the contigs annotated as TEs. Noteworthy, the number of variations per 100 base pairs was significantly higher in the TEs than in the CSD sequences. This result might be explained by the accumulation of mutations in noncoding sequences, as most of the TEs are.
Overall, Single Nucleotide Variants (SNVs) were the most common variants compared with In/Del mutations. Since SNP mutations very often result in silent mutations, their high proportion in the CDS regions was an expected result. In/Del mutations that usually occur in silenced or functionally disrupted genes, along with noncoding regions, were found at a low rate in CDS regions.
TEs were found to occur, at least in one copy, in the 23.50% of the 522,301 contigs that constitute our chicory genome draft assembly. Retrotransposons proved to be the most abundant elements in the Radicchio genome. This finding is in agreement with data from previous studies [23-26]. It is worth mentioning that Copia-type elements were more abundant than Gypsy-type elements, forming the predominant subclass of LTR retrotransposons.
Although the amount of TEs of the totally assembled sequences was much lower than that reported for other species, the class ratio of the TE types corresponds to that found in previous studies [23-26]. Our estimate of TEs in leaf chicory is equal to 6.28% of the contigs length, which is much lower than amounts reported for soybean (59%), pigeonpea (52%), alfalfa (27%), trefoil (34%), and chickpea (40%) [25, 27-30]. One of the reasons could be that our BLAST strategy chosen to find repeated elements in the genome was less efficient than specific software (e.g., RepeatScout and RepeatMasker [31, 32]). Another reason could be the lack of TEs in the assembled portion of the Radicchio genome due to the low complexity of these repeated DNA regions.
The BLAST strategy with the nonredundant (NR) pentapetalae protein database produced the best output in terms of similarity with our contigs. This is undoubtedly due to the availability of large collections of sequences from species taxonomically related to leaf chicory, such as Beta vulgaris, Helianthus annuus, and Lactuca sativa, among others. Unfortunately, the depth of annotation of these recently sequenced genomes is frequently not comparable to that of the long-studied Arabidopsis thaliana. Although BLAST results obtained by querying the NR database proved to be highly informative in terms of the number of hits producing alignments with significant e-value, the annotation of the leaf chicory assembled contigs was more successful when the A. thaliana database was used alone. Therefore, a possible alternative for future enrichment of the current annotation state would imply the use of software (e.g., Blast2GO) that could extract the annotation codes from multiple BLAST hits, provide the appropriate specificity cutoff, and assign the mapped GO terms to the original query.
Our choice to use the TAIR10 database to annotate our sequence contigs led to the annotation of a large number of assembled sequences and provided precious information concerning the putative process, or eventually, the metabolic pathways in which genes are putatively active.
The ability to annotate a certain number of sequences is not only exclusively dictated by the length and quality of the query sequences but also by their match with orthologous sequences that need to be annotated in depth.
This would be the case of annotations for metabolic pathways not actively studied or present in A. thaliana and for processes whose study is hampered by biological or physical circumstances. This might explain some discrepancies in annotations for male and female gametogenesis (Figure 6). From the graph, it is easy to understand the large discrepancy between the number of contigs presented for the term “Megagametogenesis” (GO:0009561), just 107, and the term “Pollen development” (GO:0009555), cited in the results as the most prevalent (more than six times that of megagametogenesis). We can suppose that this difference might not be due to a real difference in the number of genes involved in these two reproductive processes but rather to the lower number of genes known to be involved in female sporogenesis and gametogenesis.
Similarly, enzymes involved in the biosynthesis of germacren-type sesquiterpenoids, such as the germacrene-A synthase (EC:4.2.3.23), which are responsible for the biosynthesis of lactones associated with bitter taste in leaf chicory, are not known or properly characterized in A. thaliana.
Another fundamental finding of our study is the large number of SSR markers that were found in the assembled contigs. We can affirm that the leaf chicory genome shows an unexpected number and distribution of repeated sequences. Submitting our Radicchio draft to MISA software, we were able to reveal such a number of potential SSR markers. It is therefore interesting that we were able to link a reasonably large number of microsatellites to each item here presented for both GO terms and KEGG maps. In the results, we presented only a small selection of important characteristics that could be utilized in marker-assisted selection and breeding programs in Radicchio. Together with SSRs, thousands of sequences that could be used in Single Nucleotide Polymorphism (SNP) analysis were associated to fundamental biosynthetic pathways or metabolism enzymes. This is a crucial starting point for modern breeding in leaf chicories.
It is noteworthy that further studies must be conducted to determine whether and how these potential markers could be exploited in molecular breeding programs. As a final step, gene prediction and annotation were also performed according to established computational biology protocols by taking advantage of the reference transcriptome data publically available for Cichorium intybus L. These sequences allowed us to learn the number, sequence, and role of the ~25.000 genes of the Radicchio’s genome. This finding represents an important achievement for Italian agriculture genetics as a whole and opens new perspectives in both basic and applied research programs in Radicchio. It will have great impacts, potentials, and advantages in terms of breeding methods and tools useful for the constitution and protection of new varieties. Information obtained by the sequencing of the genome will be exploitable to detect and dissect the chromosomal regions where the genetic factors that control the expression of important agronomic and qualitative traits are located in Radicchio.
Modern marker-assisted breeding (MAB) technology based on traditional methods using molecular markers such as SSRs and SNPs, without relations to genetic modification (GM) techniques, will now be planned and adopted for breeding of vigorous and uniform F1 hybrids combining quality, uniformity, and productivity traits in the same genotypes.
In conclusion, our study will contribute to increase and reinforce the reliability of Italian seed firms and local activities of the Veneto region associated with the cultivation and commercialization of Radicchio plant varieties and food products; the seed market of this species will have the chance to become highly professional and more competitive at the national and international levels. To uncover the sequence of a given genome means to gain a robust scientific background and technological knowhow, which in short time can play a crucial role in addressing and solving issues related to the cultivation and protection of modern Radicchio varieties. In fact, we are confident that our efforts will extend the current knowledge of the genome organization and gene composition of leaf chicories, which is crucial in the development of new tools and diagnostic markers useful for our breeding strategies, and allow researchers for more focused studies on chromosome regions controlling relevant agronomic traits of Radicchio. In addition, conducting novel research programs for the preservation and valorization of the biodiversity, still present in the Radicchio germplasm of the Veneto region, is very important and accomplished through the genetic characterization of the most locally dominant and historically important landraces using sequenced genome information of Radicchio presented in this work.
Recently, a white1 mother of a white, 3 year old son told me she was planning to talk to her son soon about race and so, given my scholarship in race and parenting [1], she’d want to have a conversation with me before she brought it up because she did not know what to say. She went on to note that her son’s best friend was Black, and she was so glad that her son had not brought up the race of his friend because “he just doesn’t notice race.” As she related this, I sensed a touch of pride from this mother that her small son did not see race.
Even though this mother seemed self-assured that her child had never heard or seen a racist or racially discriminate comment or action, I explained to her that children as young as her son not only can see color or race difference, but they are already forming social meaning and value based on that difference. The white mother’s face turned grim as I mentioned that oftentimes children, even though they are starting to think about race, learn from their white parents that it is rude or embarrassing to point out someone’s race. It is this taboo avoidance, as much if not more, than her son not noticing race that could be why her son had said nothing within earshot of his parents about his friend’s or his own race or color.
In this critical theoretical essay, I discuss literature related to white parenting and racialization as well as draw on autoethnographic mother writing [1, 2, 3], to show how whiteness is passed down intergenerationally particularly in the United States. Autoethnographic mother writing is a methodology that draws on motherscholars’ experiences and observations rooted in their roles as both mother and having been mothered [1, 2]. Although autoethnographic mother writing is radically specific [3], it is rich with lived experience and sense-making. By pairing this methodology with other existing scholarship related to whiteness and parenting, this essay offers practical anti-racist explanations and strategies immersed in theory, research, and narrative.
This essay also falls within a larger body of scholarly work known as Critical Race Parenting or ParentCrit [1, 4, 5, 6, 7, 8, 9]. ParentCrit falls within Critical Race Theory work as it applies to parenting children within racial realism and to be critically conscious. For Parents of Color and/or white parents of Children of Color, ParentCrit often focuses on parenting to teach self-love and how to combat racism in parenting Children of Color [4, 5, 7, 8]. For white parents, it often involves reflection on and combating whiteness in oneself and in one’s white or white-presenting children [1, 6, 9]. Yet, one of the tenets of ParentCrit is the continued learning and growing toward social justice in both parent and child [10], as well the way that this growth happens in relationship with parent and child [1].
Given this, the essay focuses on intergenerational whiteness in the midst neoliberal movements that insist that race is no longer socially significant [11] and where color evasive [12] stances twist the words of those working to increase critical consciousness around race and instead call them racist for even bringing up the word “race.” I end by offering several strategies for parents wanting to disrupt the cycle of whiteness in their parenting and in so doing, begin to reverse the complicity of most white parenting with white supremacy.
Before moving into this discussion, it is helpful to give starting definitions of whiteness and neoliberalism, although this essay delves into different dynamics of both. I define whiteness as a sociopolitical ideology, held mostly by white people, that is used to normalize and promote white supremacism [13]. Whiteness is embedded in systems through traditions and spoken and unspoken rules that privilege [14] or immunize [15] white people, protecting them from the racialized violence that is the reality for People of Color. This includes white people retaining amassed wealth particularly from ancestors who stole land from Native peoples or profited from African enslavement, access to quality education, and exemption to discrimination, microaggressions and larger acts of aggression due to race.
Whiteness is not a static phenomenon. White people constantly evolve their performances of whiteness to best normalize and uphold it and white supremacy [16]. Given this, one of the latest flavors of whiteness, particularly in the United States lies in white post-racial and neoliberal belief systems. Giroux shows how the racism of today or new racism [11, 17] is entwined with neoliberalism, and demonstrates how this neoliberalism is an individualistic endeavor, focused on free market that, in its pursuit toward these, has relied on pretense and a color evasive political project that denies how race and racism work in our world, particularly to benefit white people. Instead, neoliberalism and its users have adapted a language that explains white beneficiaries as meritorious and uses a cultural racism [17] to blame People of Color for their own disenfranchisement.
In the 1950s, Black Pscyhologists, Kenneth and Mamie Clark [18] conducted a series of experiments studying how children interpreted race. In these experiments, children of different races were presented with two dolls, a Black doll with black hair and a white doll with yellow hair. The children were then asked a series of questions, like which doll is beautiful, which doll is the good doll, or which is the bad doll. Most of the children, regardless of the child’s race chose the white doll when asked which was beautiful, and similarly most children chose the white doll when asked which was the good doll and, conversely, the Black doll when asked which was the bad doll. The Clarks at the time used their research to demonstrate the damage to self-identity and self-esteem of Black children in the then segregated US school system. The Clarks even testified compellingly in the Brown v. Board of Education (1954) case [19] in support of school desegregation.
The Clarks’ doll study was significant in the way that it showed that not only did small children recognize race, but they also made social value judgments based on race at that same young age. Although the Clarks’ original studies were published in the 1940s and 1950s, similar experiments with children’s perceptions of race have since been replicated, with results being similarly troubling [20, 21]. One significant difference is that Black children identify the Black doll as the bad one to a lesser extent [21], perhaps signaling improved self-image for those Black children whose parents diligently provide them with dolls, books, toys, etc. that are positive representations of Black people and Black culture. However, white children in the 1950s and today in the US, despite the national rhetoric touting a post-racial society where color no longer matters, still tend to make value judgments based on race that favor white people [20, 22]. But, why? Most children in the US today have grown up with a Black President, they have seen Doc McStuffins on TV, they have worn Black Panther costumes for Halloween. Certainly, these Black role models have had some impact on children’s racial values. So, why would a white boy wearing a t-shirt with the latest Spider-verse Spiderman character (a Black, Latinx boy) still say the Black doll is bad [20, 22]?
Thandeka, a Black scholar and Theologian wrote the book Learning to Be White, [23] published in 1999. In the book, she describes how white parents pass down whiteness to their white children or “teach them to be white” by withholding love or shaming their children when those children engage with Children of Color. For instance, white parents berating their children for playing with the Black child next door or refusing to talk to their child when they show up at home dating a Person of Color are examples of the punishment some white parents impart when their white children do not keep to their own. All of these subtle and not-so-subtle reprimands of white parents signal to their white children that if they have relationships with People of Color, the cost will be the ending of their relationship with their parents. Thandeka describes this withholding of love or this race-conditioned love as akin to child abuse, and shows the damage done to white children, as they are groomed to be the next generation of whiteness keepers.
Thandeka captures the white parenting process and also touches on how white people teach themselves to avoid thinking of themselves as white or even part of a racialized system. White people tend to think that race is something possessed by People of Color. It is in this belief that white people then begin to found the normalization of whiteness. Things that are white are normal; everything else is different, diverse, exotic, strange…race. Thandeka describes a game she created where she invites white people for a week to identify each person they talk about as white (if they are), e.g., My white neighbor, Sally, stopped by for a cup of coffee with my white friend, Angie, and all of our white kids played out back. Thandeka relates how none of the white people she invites to play this game can manage to do it for more than a day. They all find themselves embarrassed or shamed to racialize themselves and other white people and cannot stand the looks of disdain from other whites when they are breaking this cardinal rule of never racializing whites and, in so doing, maintaining the normalization of whiteness.
Thandeka does elucidate multiple elements of whiteness and the intergenerational passing on of whiteness in her book. And, what she describes is still very much at play in many white families. However, her book was written over 20 years ago, and what critical whiteness scholars show, is that whiteness and white tactics evolve to best uphold white supremacy. [13, 16, 24] Whiteness is slippery in the way that it’s hard to get a handle on. As soon as you think you have nailed down how whiteness is operating, whites have already morphed how they perform and maintain it. As soon as you have developed an antiracist training to confront the problem of whiteness, white people have already taken a diversity training and are employing the same language to instead promote white norms. My point is that Thandeka, at the time of her book’s writing could not foresee how white neoliberal parents of the next generation were going to mold the principles of whiteness they’d learned from their parents. When these younger neoliberal parents were raised by the Baby Boomers, it was socially acceptable in many white communities to forbid your child to play with the Black kid next door. Today, in many places, this is not socially acceptable. So, white parents (often unconsciously) employ a more tactful maintenance of whiteness, one that no one can call you racist for. This leads to a whiteness performance that creates a scapegoat of racist Uncle Donald at the holiday dinner table while quietly allowing today’s white parents to go about affirming white norms and superiority with their children, all the while assuring themselves that they and their children aren’t racist.
Thandeka captured the shame that white people have when asked to racialize themselves and acknowledge their whiteness, but in addition to whites’ aversion to identifying their own race, today’s neoliberal white parent also does not want to identify anyone else’s race; it’s uncouth. Beverly Tatum, in her book, Why Are All the Black Kids Sitting Together in the Cafeteria: And Other Conversations About Race, [25] points out that white people consider race talk taboo. She remarks on how white people tend to whisper that a person is Black or Latinx as if identifying the race or ethnicity of a Person of Color is an insult or a dirty secret that nobody dare say. This taboo of identifying anyone’s race is rooted in early colonization and enslavement where white people, and particularly white women taught themselves to fear Black people, and particularly Black men. Black Psychologist, Frantz Fanon, in his book Black Skin, White Masks [26] vividly describes a moment of walking down the street in Martinique, when a white child points at him and cries to his mother, “Look, a negro!” His mother gasps and pulls her son to the other side of the street and out of harm’s way. Fanon analyzes this action and names the fear behind both the white child’s utterance and his mother’s response. This illustration although written about in the 1950s feels uncannily relevant today. A white child, particularly one who has not been around People of Color because he/she was raised in a white suburban enclave, upon first seeing a Black person, points and says in a loud voice, “Mommy, look that person is Black!” The white mother then swiftly teaches the child the race taboo by shushing the child, getting embarrassed, or even scolding the child for identifying something new they are seeing – race [1]. Although, as Tatum discusses, there is nothing negative about identifying a Person of Color’s physical attributes, the white mother out of embarrassment, and perhaps deep-rooted fear or disdain tries to distance herself from the Person of Color the child has pointed out. But, even though these may be deep-rooted racist reactions to a Person of Color, today’s nice white neoliberal parent instead rationalizes their reaction because their child has not intuited the cardinal rule of color evasion, which the parent justifies is all about equality [1].
Sociologist, Eduardo Bonilla-Silva identified this white neoliberal race evasion in his book, Racism Without Racists: Color-Blind Racism and the Persistence of Racial Inequality in America. [17] Although Bonilla-Silva coins this phenomenon as “color-blind racism,” I opt for an expression that does not use ableist language as recommended by Annamma, Jackson, and Morrison [12]. I refer to this concept as color evasive racism or color evasion. Bonilla-Silva’s book is based on interviews with white adults. Through these, he identifies several ways that white people employ color evasion. These include making false justifications for the evidence of racism that do not sound explicitly racist, for instance describing gentrification and racial segregation of schools as being a natural result of people just wanting to be around people who are like them. Bonilla-Silva also identifies what he describes as “abstract liberalism,” which gets at the heart of color evasion. White people, when asked a question about race often default to “Oh, I don’t even see race.” Or, as Bonilla-Silva showed, when asked about affirmative action, i.e., preferences for people from under-represented racial groups in higher education or the job market, white people would often say they were against it because they thought everyone should be treated equally. Of course, this abstract liberalism sounds nice. How can you call the person speaking racist when they have just said they want everyone to be treated equally? Yet, this nice, color evasive talk is perpetuating racism in the way that it denies the lived reality of People of Color and instead blames their disenfranchisement on People of Color, themselves.
It will come as no surprise then, that these same white adults, use the same color evasive approaches if and when they teach their children about race. The white parents focused on in Thandeka’s book are in no uncertain terms telling their white children to stop playing with Kids of Color, if they want to remain in the family. But, currently, there is a growing crop of neoliberal parents who are avoiding conversations about race with their children, but if their child asks a question about race or color, white parents resort to canned abstract liberalism, assuring their kids that everybody is equal and color does not matter.
Years ago, I was conducting research with focus groups of white kindergartners in the rural Midwest of the United States. I had their white teacher read them several multicultural picture books and then asked the children a series of question about the books. I wanted to know how white children in a mostly white setting understood race and culture through the books. As we began the study, the kindergarten teacher went off script. She asked all of the children to hold out their hands. A plentitude of beige, pinkish, and peachy little hands all reached into the circle where the teacher also held out her hand. “Are we all the same color?” she asked. “No,” replied most of the kids, identifying freckles or the slight variations of shade in their hands. “That’s right!” congratulated the teacher, “we all have different color skin, but we’re still all the same!” I remember thinking at the time that this teacher might as well have concluded her mini race lesson with, “So, there’s no reason for us to ever talk about color or race again!”
As mentioned, one of the core problems with teaching white children to be color evasive is that color evasion ignores the reality of racism and white supremacism. While the color evasive parent will read children’s books about Martin Luther King Jr. to their children, particularly on MLK day, most of those books read as though when the ‘white only’ signs came down racism ended and today we are all treated equally. Racism, as it were, is a thing of the past and a thing of the US south. This is the message that well-intentioned, neoliberal white parents teach the next generation about race. And this serves white families well, as they continue to normalize themselves and their dominant narratives. This is also why we frequently see white college students demonstrating what Robin DiAngelo refers to as white fragility [27] when they are first confronted with the racial realities of People of Color in a course that deals with race. Or a white student is assigned a roommate who is a Person of Color and not willing to go along with the shallow color evasive framework the now white young adult has embraced and managed not to question [22], in part cause they knew how upset their white family would get if they went and brought up a nasty topic like race.
I titled this chapter, “Racist Babies?” to get at the paradox of whiteness in parenting, which is this: Although we know kids see race and make value judgments about it, children are not born racist. White children are parented into racism. Yet, given how whites have constructed whiteness norms within their families, the first time a child makes an observation about race, the parent is shocked at the audacity of their child breaking the taboo and worries that the child is racist instead of examining themselves and how whiteness is at work [28] in their parenting.
White neoliberal parents tend to avoid conversations about race with children. They do this possibly because they are in denial that race and racism are real and relevant. Perhaps they do not know what to say about race and are uncomfortable breaking the race taboo that they were raised to uphold. Or, maybe they think their children will just naturally grow up to “do the right thing.” These same parents are thrown into upheaval the first time their child makes a comment on or asks a question about race. This is when, as a race scholar and white mother, my nice, white neoliberal friends come to me and explain that their child is racist and can I recommend some good kids’ books that will teach their children to not be racist? One white friend’s child did not like his brown-skinned swim instructor. One child pointed at a Black woman, saying she looked like a brownie. Neither of these statements are inherently racist. These white children are noticing skin color and trying to make sense of it, particularly when they have not been around many People of Color previously. My own child, when he began a new preschool class, declared that he did not like one of his teachers. “Which teacher don’t you like?” I asked. “The Black one,” he answered. I’ll admit, even as a person who studies race and whiteness in parenting, I was taken aback with my 4 year old’s comment. But, I was careful not to scold him for identifying race, which we had discussed. “You don’t like Ms. Andrea?” I clarified, identifying his teacher who I’d noted was the most strict, and as he had identified had the darkest skin of all of his teachers. We then went on to have a conversation where I encouraged him to learn all of his teachers’ names and also began a conversation about racism and how white people treat Black and Brown people unfairly. “That’s why it’s super important for us as white people to respect Black and Brown people and especially our teachers by knowing their names,” I concluded.
To be honest, on the fly, I’m not sure how well I articulated any of this or how much my son understood. But, what is important is that I continue to have conversations with my children about race and racism to ensure that we are not participating in color evasive racism. This also allows me to continue to guide my children’s interpretations and understanding of race and racism as they grow. Although I have a leg up on many white parents given that I am a researcher of race, racism, and whiteness, it is still crucial for all white parents, including me, to continue our work to understand how whiteness is working in ourselves, in our partners, and in our children.
Below, I offer some ParentCrit strategies, particularly for white parents who are working to parent critically conscious, socially just people, and are they themselves working to be the same. It’s important to note that parenting is not the only influence that children receive that teach them about race. Certainly, a child’s experience at school, in social settings, and with various media also convey messages about race to white children and Children of Color. When we as parents work with our children to develop a critical consciousness around systems of oppression, we must be working with them to interpret, critique, and dismantle those systems whether they manifest in their classroom or in their Saturday morning cartoons.
The United States is highly racially segregated in our neighborhoods, schools, workplaces, etc. This is not coincidental or natural. It is by design [29]. Historical and current processes and legacies have continued to disenfranchise People of Color in the United States and maintain white privilege and power. Systems such as redlining and gentrification to mass incarceration and school privatization go to work every day to keep most white Americans in their bubble.
Although this allows most white children in the US to be surrounded by other white children, white teachers, and white community, Families of Color are forced to navigate the white world to participate in systems such as economic, education, medicine, law, etc. Thus, white children raised in white enclaves develop an understanding of their white identities and their whiteness as normal, which Children of Color do not have the luxury of doing [30]. This allows for white children to then see anything that is not within these white norms as different, weird, exotic, or even deviant or bad.
Once, after I had offered a community training on ‘dismantling whiteness,’ I had a white father approach me. He and his wife were upper class and white and were raising their two biological children in a wealthy white suburb. We were discussing white children and their understanding of race, and he said, “My 7 year old, Skyler, said to me yesterday, ‘Dad, why are all Black people famous?’” Upon sharing this, he offered me an incredulous look in which I think he expected me to share in his utter confusion. “Does he know any Black people?” I asked. The man furrowed his brow, and said, “No, just those he sees on TV.” After describing the painfully obvious connection between his child thinking all Black people were famous and how it was because he only saw Black people on TV, I went on to discuss the importance of children having relationships and engaging with racially diverse communities so as not to stereotype People of Color. The father nodded, but then added, “It’s just that our neighborhood is so white.” With that, he shrugged and our conversation ended. This Dad could not envision making choices about where his family lived or learned that considered his children’s critical consciousness and racial awareness. Subsequently, his white son was learning about Black people from TV. This meant that the source of his son’s race knowledge was and would continue to be formed by mass media, and all the racist stereotypes therein. The intergenerational whiteness was being almost perfectly maintained in this nice, white, neoliberal family.
My point here is that environment matters when you want to raise critically conscious, socially just children. Within the higher education Affirmative Action2 struggle, those defending Affirmative Action have argued about the importance of a Critical Mass of Students of Color within the college classroom. They argue that this critical mass is important for all students to have a rich and diverse college experience. Part of this idea is that if you have only one or two Students of Color in an otherwise all-white classroom, the white students are more likely to tokenize and stereotype the few Students of Color. This argument fairly suggests that white college students upon meeting a Student of Color (often one of the first People of Color they have met) are likely to make sweeping generalizations about an entire racial group based on the experiences with that one Person of Color. Thus, a critical mass is achieved when there is enough diversity in the diversity (coded as People of Color) [31].
I bring this up, because if knowing and working with People of Color is actually important to the white neoliberal groups that largely serve as the leadership, faculty, staff, and students of predominantly white institutions of higher education, why is it not important to raise those same white children in community with People of Color? My point is that, of course, environment is crucial in raising critically conscious, socially just children and families.
When I began talking with my first child at three about race, I was shocked at how color evasive my descriptions were. Things like “People have different skin colors but we’re all the same” or describing racism as “People treating people with other skin colors bad,” just fell out of my mouth. I was quick to correct myself, particularly on the latter comment to say “When white people treat people with Black or Brown skin bad…” But, horrified, I stumbled through conversations while my preschooler quickly lost interest in my race lessons. I realized that like any good educator, I needed to plan out what I wanted my child to understand and then back track to identify and teach the building blocks to that concept. I wanted my kids to understand racism at the individual but also the systemic levels and I also wanted them to confront it when they saw it.
I started by identifying key concepts, equating race with skin color while simultaneously reading books and talking about the US enslavement of Africans and the stealing of native lands. I then introduced the concept of racism. This worked as a good transition. When my son understood race and also the history of race in the US, particularly around enslavement, it was easier to show how racism only went in one direction, given that white people had historically created the concept of race and used it to steal rights and power [32]. Yet, my previous research helped me understand that white kids often understand racism as happening only in the past and only in the south. So, I also offered my children examples of racism, including those from the news or even comments or things I noticed. We would discuss police shootings of Black people. We would discuss how racism was working in our leaders’ justification of separating Latinx children from their parents at the US/Mexican border. My partner and I and our friends would discuss race and racism openly in front of the kids, whether or not they were paying attention. These ongoing race conversations not only helped my children build their understanding of race and racism, but it also gave them permission and even encouragement to bring up race topics and to ask questions of their own.
As a critical race scholar, I was laser focused on my white-presenting boys’ understanding race and racism. When they would talk about gender or something being a girls’ toy, I would say little more than “There is no such thing as a girls’ toy.” Shortly after my oldest son began public elementary school, a fourth grade Latinx boy within our school district died by suicide shortly after he had come out as gay. Immediately, all of the heteronormative and gender-binary school traditions that I had kept quiet about became urgent to correct. As I saw it, the public school system of which we were part was scapegoating children as bullies and letting themselves off the hook for all of the practices that said “you (cisgender conforming child) are normal, and you (nonconforming child) do not belong and deserve your isolation.” These practices included the lining up after the school bell by binary gender, no bathroom options for trans or gender nonconforming students, and allowing the gender policing of children (e.g., teasing a boy who used a pink crayon).
Interestingly, we had family friends who were laser-focused on gender and LGBTIQ+ issues to the detriment of discussions of other systems of oppression, including race. I think it’s difficult for parents who hold multiple forms of privilege and dominant identities to hold these all together at the same time, whereas parents who combat multiple forms of oppression, do not have the luxury of isolating one with their children. Indeed, intersectionality is meant to combat the rendering of queer Black women as invisible [33, 34] Reading Audre Lorde’s words [35] makes this clear. She simultaneously holds her identities as mother, scholar, Black, woman, and lesbian as she navigates raising her Black children. There is no moment where she forgets that she and her children are Black or that she is raising her children as a lesbian woman. She holds them all and navigates them simultaneously.
This is not the case for white, heteronormative parents. So, we must do the work to understand how these systems of white supremacism, patriarchy, classism, heteronormativity, ableism, etc. are all working simultaneously for or against our children. Holding our understanding, oppression, and dominance together as we raise our kids, and not letting one system or another go because they will not oppress our kids directly today is vital. The point here is that we cannot teach anybody, including our children, how any system of oppression really works without understanding and offering an intersectional approach. We cannot fully understand white supremacy without understanding patriarchy, nor can we understand patriarchy without ableism, or ableism without classism and so on. So, as we work to build critical consciousness in our children, we must not set aside any part of the story.
It feels like new kids’ movies come out by the week these days, and, luckily, there is generally a critique of each new film. I actually included my racial critique of Zootopia in a 2018 article [1], showing how it drew on white saviority, racial stereotypes, and color evasive racism to form its storyline. By most accounts, children’s movies seem to be getting better and more thoughtful. For example, consider the 1995 Disney film, Pocahontas, along with its stereotyping of indigenous people as noble or savage with the 2017 Pixar film Coco, which is a beautiful and thoughtful depiction of a Mexican story.
Yet, when we take a comprehensive look at child media we still see the same problematic depictions of race, i.e., racial stereotypes, color evasions, and other racial fictions. For instance, while the first Frozen movie, happily avoided race by making every notable character in it lily white, Frozen II tried to make up for it by depicting a racially ambiguous indigenous group that was having their way of life stolen by an unambiguously white king. While this may have paralleled the settler colonialist history and stolen lands of the United States, the movie ends with the two white granddaughters of the colonizer-king saving the day, the land, and restoring justice, which included one of the white sisters (Elsa) becoming queen over the indigenous peoples and land.
The point I want to make here is that I do not think we should keep children from seeing the latest Disney or Pixar film, but we should be diligent about critiquing storylines and messages within media with our kids. We should be deconstructing both the explicit and hidden messages in children’s movies with our kids. This demonstrates to them that they cannot take what they see at face value even in their seemingly morally resplendent movies. When we describe what we see in the movies and critical interpretations of the media our children are watching, they learn to not only question what they see and understand, but learn that it’s important to do so. Soon enough, we will not need to bring up racist stereotypes or white savior storylines in the movies our children are watching; pretty soon, they’ll catch it and point it out before we do.
These discussions also reinforce that race talk is okay and encouraged. My white-presenting son received a Black Panther costume as a gift from his grandparents around Halloween last year. Although he already had planned to be a video game character for trick or treating, he told me he thought he might wear his Black Panther costume to school. My son’s school is made-up of mostly Black and Brown students, and I worried about my son co-opting one of the few Black heroes available to Kids of Color.
“I actually don’t think you should wear your Black Panther costume out of the house,” I said to my son.” “Why not?” he asked. “Well, because Black Panther is a Black super hero, and because of racism, there aren’t a lot of Black super heroes that look like Black and Brown kids. But there are a whole bunch that look more like you, so I think we should treat Black Panther as a special super hero that just Black and Brown kids get to dress up as at school.” “Ok,” my son resolved quickly, “I think I’ll be a Harry Potter character for school then.” “Perfect!” I said.
When we normalize race and racism conversations with our children, we build their skills and critical consciousness. In Beverly Tatum’s book [25], she mentions a white kid that asked her Black son if his skin was brown because he drank too much chocolate milk. Children, including white children, are trying to make sense of their world and their social interactions. They pick up on who gets included and who does not, on who’s considered beautiful, and who is not, on who’s considered smart and who is not. If we do not advise them in this sense making process, we should not then be surprised when, in the next round of doll studies they tell us that the white doll is good and beautiful and the Black doll is bad.
White parents have got to set aside their fear of race talk, shrug off the taboo, and educate themselves on how race works in the US and how they and their white skin are normalized and privileged. Only then can we educate the next generation of children to resist whiteness and make strides toward equity and justice, instead of just reframing whiteness to trick ourselves as we raise the next generation of racist babies.
I dedicate this chapter to my children and those of the next generation. May we invest in you critical consciousness and social justice, along with our hopes and dreams.
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