Crop domestication processes: a suite of procedures performed by humans to domesticate plants for food production.
Cassava (Manihot esculenta Crantz) provides a staple food source for millions of people in tropical and subtropical world regions. Brazil is the major center of diversification for species of the Manihot, and a center for domestication of the cultivated species originated from wild ancestral M. esculenta subsp. flabellifolia. Genetic breeding of cassava depends on landraces. Molecular phylogenetic technologies used to study genetic traits selected by mankind in crops, are likely to predict proposed “domestication syndrome.” Phylogenetic trees use DNA sequences alignment to infer on gene historical events. A study on regulatory and structural complexity that dictates gene/protein function, will add non-sequence information to predict a more complete understanding of functional evolution. Transcriptional profile contains critical information on when and where a gene is manifested. These regulatory properties could explain functional genes diversity achieved within gene families across closely related species such as cassava and its ancestor. Microarray technologies measure transcriptional response of gene to a given environmental or genetic factor. Integration of genomic and transcriptomic data provides more detailed picture of molecular evolution. This chapter describes comprehensive study using the wild relative of cassava ancestor, recognition of natural morphological trait changes during domestication, and gene expression of cassava storage root.
- M. esculenta subsp flabellifolia
- M. esculenta subsp esculenta
- domestication syndrome
- genetic diversity
- gene expression
Although obtaining space for the intentional cultivation of edible plants often starts with the clearing of forests and modification of landscapes, it was the ability to domesticate plants that made agriculture possible in the first place. Domestication consists of a set of consecutive stages that begins with the original set of plant traits and evolves through the increase in selection frequency for desirable traits (the domestication traits). In the genus
|Domestication index||Other crops||Cassava|
|Removal of the forest||Yes||Yes|
|Seed dispersion at campground||High/low||Refractive|
|Discarded undesirable genotype||None/low||Low|
2. Cassava wild relatives and the ancestral species
Mexico and Brazil are considered two relevant centers of diversification for
3. Domestication as evolutionary processes
Phylogenetic techniques used for determining the molecular evolution of a crop have relied predominantly on sequence information to model the evolutionary history that determines plant speciation and domestication. Phylogenetic trees are based on alignment of DNA or protein sequences, from which evolutionary distances between genes can be inferred. However, transcriptional behavior of a gene is poorly represented by DNA sequence data alone. A gene’s transcriptional profile may contain critical functions, including when and where a gene is expressed, and the conditions under which gene expression is manifested. This chapter addresses questions on how function transcriptional profiles vary due to changes in the environment (light intensity) and due to genetic diversity of landraces and commercial breed varieties.
3.1. Molecular evolution of a crop species
Factors involved in regulation of expressed genes or gene sets could be crucial in explaining the key functional differences between related genes whose function, during selection (natural and artificial), cannot be distinguished from DNA sequence alone [11, 12, 13, 14, 15, 16, 17, 18, 19]. Attempts to predict expression patterns of genes using sequence information  have typically been limited by the complexity and diversity of factors influencing genes. Thus, sequence-based prediction of a gene’s regulation remains a premature goal. However, transcriptomic approaches, for example, using microarray chip or RNA-Seq technology, allow for a direct, quantitative measurement of global transcriptional responses to a given environmental or genetic factor and are useful experimental sources for obtaining large-scale gene expression data [21, 22]. Genomic data sets spanning a wide selection of the cassava ancestor (
3.2. Differentially expressed genes
A cDNA microarray chip designed for Euphorbiaceae  was probed with total RNA extracted from storage root (31 samples total) of cassava with diverse storage root traits. This chapter documents a total of 569 genes which were identified as differentially expressed (
3.3. Ontology and functional classification of differentially expressed genes (DEG)
Analysis of the DEG identified 22 distinct groups among gene ontologies and functional classifications. The groups (Figure 4) highlighted in yellow (i.e., “Protein with Binding Function or Cofactor Requirement,” “Regulation of Metabolism and Protein Function,” and “Cellular Transport, Transport Facilities and Transport Routes”) were targeted to elucidate candidate genes involved in regulation of these key pathway networks.
3.4. Exploratory pathway networks and candidate regulatory genes
The program Pathway Studio  was used to conduct subanalysis (SNEA) to identify potential regulatory networks from transcriptome data obtained in this study and available databases, as previously described [36, 37, 38, 39, 40, 41, 42]. The results on statistics (shown in Tables 2 and 3) and visualization of gene networks (shown in Figures 5 and 6) took into consideration three types of molecular interaction mechanisms (expression target, protein binding, and protein modification).
|Name||Gene set root||Entities||Neighbors||p-Value|
|Binding partners (protein interaction)||PHYB||9||8||0.0004|
|Binding partners (protein interaction)||PHYB||9||8||0.0063|
|Binding partners (protein interaction)||PHYB||9||8||0.0006|
|Binding partners (protein interaction)||PHYB||9||8||0.0008|
|Binding partners (protein interaction)||PHYB||9||8||0.0006|
|Common to all genotype||Landrace (pink)||Landrace (||Commercial cv. (white)||Landrace (yellow)||World core collection (white)|
These results indicate node operating gene/hub, edge genes which are regulated (activated or silenced), and their expression level—increased abundance (blue color) or decreased abundance (pink color) among genes visualized in the pathways; regulatory genes such as transcription factors and other gene products modulating functionality (protein binding and modification) were observed. The node/hub gene regulates the network and genes, while on the edge are regulatory genes of a particular network. Table 4 summarizes the list of nodes/hubs in the networks unique to each class of landraces based on comparisons to the cassava ancestor and the cv. IAC 12-829.
|Gene abbreviation||Gene name||ATG number||Function (from www.arabidopsis.org)|
|14-3-3||14-3-3 family protein||14-3-3 proteins are a family of conserved regulatory molecules that are expressed in all eukaryotic cells. 14–3-3 proteins have the ability to bind a multitude of functionally diverse signaling proteins, including kinases, phosphatases, and transmembrane receptors. More than 200 signaling proteins have been reported as 14–3-3 ligands|
|ABI1||ABA INSENSITIVE 1||AT4G26080||Involved in abscisic acid (ABA) signal transduction|
|AP1||APETALA1||AT1G69120||Floral homeotic gene encoding a MADS domain protein homologous to SRF transcription factors. Specifies floral meristem and sepal identity|
|AXR3||AUXIN RESISTANT 3||AT1G04250||Transcription regulator acting as repressor of auxin-inducible gene expression|
|BRI1||BRASSINOSTEROID INSENSITIVE 1||AT4G39400||Encodes a plasma membrane-localized leucine-rich repeat receptor kinase involved in brassinosteroid signal transduction. BRI1 appears to be involved in the autonomous pathway that regulates the transition to flowering, primarily through its effects on FLC expression levels|
|COP1||CONSTITUTIVE PHOTOMORPHOGENIC 1||AT2G32950||Represses photomorphogenesis and induces skotomorphogenesis in the dark|
|CRY1||CRYPTOCHROME 1||AT4G08920||A flavin-type blue-light photoreceptor with ATP-binding and autophosphorylation activity. Functions in perception of blue/green ratio of light|
|CTR1||CONSTITUTIVE TRIPLE RESPONSE 1||AT5G03730||Homologous to the RAF family of serine/threonine protein kinases. Negative regulator in the ethylene signal transduction pathway|
|EIN2||ETHYLENE INSENSITIVE 2||AT5G03280||Involved in ethylene signal transduction. Acts downstream of CTR1|
|FLC||FLOWERING LOCUS C||AT5G10140||Transcription factor that functions as a repressor of floral transition and contributes to temperature compensation of the circadian clock|
|LSD1||LESION SIMULATING DISEASE 1||AT4G20380||LSD1 monitors a superoxide-dependent signal and negatively regulates a plant cell death pathway|
|PHYA||PHYTOCHROME A||AT1G09570||Light-labile cytoplasmic red/far-red light photoreceptor involved in the regulation of photomorphogenesis|
|PHYB||PHYTOCHROME B||AT2G18790||Red/far-red photoreceptor involved in the regulation of de-etiolation|
|PRL1||PLEIOTROPIC REGULATORY LOCUS 1||AT4G15900||Mutations confer hypersensitivity to glucose and sucrose and augment sensitivity to cytokinin, ethylene, ABA, and auxin|
|SCF||Skp, Cullin, F-box containing complex||A multi-protein E3 ubiquitin ligase complex catalyzing the ubiquitination of proteins destined for proteasomal degradation|
|SLY1||SLEEPY1||AT4G24210||F-box protein that is involved in GA signaling. Component of E3 ubiquitin complex. Interacts with DELLA proteins|
|TIR1||TRANSPORT INHIBITOR RESPONSE 1||AT3G62980||Encodes an auxin receptor that mediates auxin-regulated transcription. It contains leucine-rich repeats and an F-box and interacts with ASK1, ASK2, and AtCUL1 to form SCF-TIR1, an SCF ubiquitin ligase complex|
|WAVE1||WISKOTT-ALDRICH SYNDROME PROTEIN FAMILY VERPROLIN HOMOLOGOUS PROTEIN 1||AT2G34150||Encodes a member of the SCAR family. These proteins are part of a WAVE complex. The SCAR subunit activates the ARP2/ARP3 complex which in turn acts as a nucleator for actin filaments|
3.5. Identification of regulatory gene sets
Exploratory pathways network common among cassava ancestor (
The removal of ancestral cassava from a shaded forest environment would be expected to alter regulatory networks and pathways involved in light perception and signaling, as highlighted in Figure 5 (Panel C) and Figure 6 (Panel A) (the Brazilian collection). Further, altering light quantity and quality or selection for storage root traits during the domestication process also appears to have differentially impacted gibberellic acid (GA) signaling regulation of DELLAs, as indicated by Figure 5 (Panel C) (GAI) and Figure 6 (Panel B) (SLY1, RGA1, RGL2, GAI). These alterations are likely to have impacted known regulatory networks involving interactions between DELLAs and PIF3/PIF4 [39, 40]. Because light perception (lack of shade) would be expected to reduce the positive impact that GA signaling has on inhibiting DELLA, the function of DELLAs in reduced GA-induced elongation likely resulted in dwarfed and bushy phenotypes [41, 42]. In aboveground photosynthesizing tissues, shifts in expression of genes linked to the GA/DELLA regulatory pathway would also be expected to result in shifts between skotomorphogenesis and photomorphogenesis  and, potentially, reduced flowering as illustrated in Figures 2 and 7. However, in the underground storage root of cassava, altered regulation of DELLAs may have played some role in the shift observed from a fibrous type to a storage root type, as also illustrated in Figures 2 and 7. DELLAs have been reported to impact auxin signaling pathways, and, possibly, DELLA’s impact on auxin via jasmonic acid (JA) regulation involving JAZ1 and MYC2, as reviewed by , could be involved in this process (Figure 7). Further, DELLA and SCARECROW (SCR, see Figure 5
4. Synthesis and conclusions
This study highlighted some key factors influencing the fate of gene function in relation to cassava domestication syndrome traits including (1) landscape alterations resulting in sunlight exposure (alteration of light quality and quantity) in early stages of the domestication process of cassava crop due to removal of forest; (2) natural selective pressure, due to high light intensity under open-field cultivation leading to an edible cassava storage root; (3) artificial selective pressure (man selecting edible plant parts), due to harvest of plants showing storage root formation; and (4) artificial selective pressure (man involuntarily selecting plant traits such as plants with low flowering set in relation to the ancestor). Additionally, the data presented in the present study also allowed, for the first time, to propose a hormonal regulating model (Figure 7) on the involvement of GA/DELLA and Auxin/Jasmonate in cassava domestication traits. It appears that domestication of cassava originated with the removal of ancestral
As our understanding of gene expression evolution improves, it should become possible to infer protein function into approaches focused on the use of proteomics technologies . Ancestral protein functions can be estimated using this approach, and efforts to annotate current genes/proteins will benefit from knowledge of the behavior and factors influencing gene expression profiles. Ultimately, gene expression profiles should be equally integrated with structure and sequence to predict and assist in annotating protein function and evolution directly on the genome sequence of the ancestor and cultivated species.
Technological advances have aided our ability to rapidly and affordably obtain and compare transcriptomes from within and across plant species. As presented in this chapter, we compare the global transcriptomes from storage root of various landraces and cultivars of domesticated cassava and ancestral
Source of funds
National Nature Science Foundation of China (NSFC grant number 31271776).
We would like to acknowledge the financial support provided by the Rockefeller Foundation (RF96010#25 and RF9707#26 in the search for landrace diversity); Conselho Nacional de Desenvolvimento Cientifica e Tecnológico – CNPq (grant #480410.2001-1 for functional genomic work); Programa Nacional de Pesquisa em Biotecnologia – CENARGEN (Project Nº 1 060302058 for carbohydrate analysis); IAEA (contract #13188 for funds supplied to gene expression analysis); National Nature Science Foundation of China (NSFC grant #31271776), and NSFC-CGIAR International (Regional) Cooperation and Exchange Programs (grant #31361140366) for genome proteome sequences, and this publication.