Summary of the content of Uzbekistan cotton germplasm collections
Uzbekistan, the northernmost cotton growing country, is the sixth largest cotton producer and the second largest cotton exporter in the world  with annual production of 0.85-1.0 million metric tons of fibre valued at ~US$0.9 to 1.2 billion [1; 2]. Cotton is grown in ~30% of all lands available for crop cultivation in the country. Uzbekistan's cotton lint fibre yield was close to the world average of 753 kg/ha in 2010/11  and was estimated at 804 kg/ha in 2012/13 and 812 kg/ha in 2013/14 [1; 5].
Cotton farming is affected by commonly observed cotton pathogens and pests, as well as major environmental stress factors (salinity, drought, heat, etc.) that greatly impacts the quality and yield characteristics of cotton cultivars. Therefore, the major objectives of the cotton breeding programs of Uzbekistan are the improvement of cotton fibre quality, lint yield, agronomic productivity, maturity,and resistance to various diseases, pests and abiotic stresses. During the past century of cotton production Uzbekistan prioritized and promoted cotton research and farming methods that resulted in increased cotton farming expertise, and the breeding of highly adapted, very-early maturing cotton cultivars suitable to be grown in the northern latitudes and arid zones [6; 7; 8]. This led to the development of a large number of cotton germplasm resources, which are being preserved and maintained for cotton genetics and breeding research that target current and future needs of the cotton improvement for different soil-climatic regions of Uzbekistan [1; 2; 3; 8].
Aspects of Uzbekistan cotton germplasm resources including the content, distribution, descriptions, characterizations, utilization, genetic and molecular diversity, maintenance, and ongoing and prospective research previously have been highlighted in several documents [2; 3; 7; 8; 9; 10]. In this chapter, we provide a detailed inventory of the Uzbekistan cotton germplasm collection, review previous reports and add updated information including the development and characterization of novel germplasm resources.
2. History and development of Uzbekistan cotton collection
The past century of cotton production in Uzbekistan has developed well-established cotton research programs and distinguished cotton scientists who initiated and devoted themselves to collecting important materials for cotton research. As highlighted in previous reports [3; 8] the cotton germplasm collection initiative was began by Drs. N. I. Vavilov and F. M. Mauer in 1930 in the former Soviet Union. Subsequently, Uzbekistan cotton germplasm founder and leader Dr. A. Abdullaev and his group expanded this initiative and established a collection of Uzbekistan germplasm materials through the (1) coordination of scientific efforts of continuous selection of cultivated cotton varieties, (2) continuation of collecting and preserving wild cotton species and landraces from centres of origin during many scientific expeditions, and (3) germplasm exchange worldwide.
According to Abdullaev et al. , several expeditions to Central Asia, Afghanistan, China, India, Turkey, Iran, Korea and Japan to obtain germplasm were made during 1920-1930, Dr. N. I. Vavilov, P. M. Jukovsky and Dr. F. M. Mauer, and in 1950s Dr. D. V. Ter-Avanesyan. In later periods from 1974 to 1998, Dr. A. Abdullaev visited to Mexico, Peru, China, India and Sri-Lanka, Australia and Pakistan and obtained germplasm. These historic scientific expeditions enriched Uzbekistan collection with Old World (Afro-Asian and Indian) diploid cottons (
The Uzbekistan collection has been periodically enriched as a result of germplasm exchanges with collections worldwide. In the most recent exchanges within the framework of USDA-Uzbekistan Cooperation programs, approximately ~ 1000
3. Content of Uzbekistan cotton germplasm collection
3.1. Main collections
The main cotton germplasm collections are being historically preserved at the research centres and institutions of the Academy of Sciences of Uzbekistan (ASUz), Ministry of Agriculture and Water Resources of Uzbekistan (MAWR), and the biology department of the National University (NU) of Uzbekistan. Table 1 summarizes and highlights the general content and description of cotton germplasm resources of these main collections. These collections maintain cultivars, wild and primitive, predomesticated landraces, hybrids breeding and genetic stocks, cytogenetic and mutant lines of widely cultivated allotetraploids(
|Genetic stocks of inbred and RI lines||771||-||-||-||-||771|
|Association mapping individuals||986||286||-||-||-||1272|
|Nested association mapping cross combination||20||-||-||-||-||20|
|F1 to F4 generation families||260||-||-||-||-||260|
|Tissue culture derived (T1-6)||1444||1444|
|Hybrids (F1-6 and BC1-5) with local cultivars||1852||1852|
|MAS – F1-2 and BC2-4 families||51||14||65|
|MAS gene pyramiding families||24||24|
Cotton germplasm collection of the Institute of Genetics and Plant Experimental Biology (IG&PEB) of the ASUz, founded and headed by academician and Prof. Abdumavlyan Abdullaev, preserves a total of 7,500 cotton accessions. The collection specifically aims to gather, maintain, and study wild cotton species, primitive, pre-domesticated landraces and domesticated genotypes from entire
MAWR has two distinctive cotton collections: one is preserved at the UzSRICBSP, another is in the Uzbek Research Institute of Plant Industry (UzRIPI), which was a Central Asian branch of All Union scientific-research institute after N.I. Vavilov. The UzSRICBSP collection preserves more than 12,000 cotton accessions from primary and secondary gene pools and refereed to as “breeding” germplasm resources that resulted from continuous breeding and selection efforts of the institute's scientists as well as cotton germplasm exchange efforts . Geographically, this collection represents 107 countries of origin for cotton accessions . The uniqueness of UzSRICBSP collection is its wide representation and coverage of cultivar germplasm developed and collected over the past century from worldwide breeding efforts. This collection also maintains synthetic tetraploid, pentaploid and octoploid hybrids [7; 16]. There are small differences in germplasm accession numbers reported here (Table 1) and by Ibragimov et al. . However, our inventory is based on the latest information obtained from this collection (Dr. H. Saydaliev, a germplasm curator of the UzSRICBSP, personal communication).
The UzRIPI cotton collection has contents similar to those of the IG&PEB collection and preserves a total of over 6,000 accessions (Table 1) from primary and secondary gene pools as well as accessions of other gene pools of wild species. Among all the collections, UzRIPI cotton collection is the richest resource for primitive, and pre-domesticated landrace stocks for all
The NU collection is tasked with maintaining of a total about 1200 germplasm resources that include 771 genetic stocks and recombinant inbred lines, formed during study of key cotton traits and mutations [3; 17; 18]. Additionally, the NU collection has a unique set of over 400 cytogenetics stocks primarily derived from radio-mutagenesis of a single genotype of
3.2. Novel resources
Efforts focused on genetic mapping of important traits, application of marker-assisted breeding as an aid for contemporary breeding, and the development of cotton tissue culture-based transgenomics programs and their integration into conventional cotton improvement efforts have resulted in the creation and collection of novel germplasm resources in Uzbekistan. These novel germplasm resources were developed in the past decade by scientists of Centre of Genomics and Bioinformatics (CGB), ASUz, MAWR, and “UzcottonIndustry association” within the framework of international collaborations and government funding [1; 21; 22]. The CGB collection with over 5,000 germplasm resources (Table 1) includes (i) panels of association mapping and nested-association mapping populations [22; 23; 24], (ii) hybrids and recombinant inbred lines (F1-4) derived from the combination of sexual top crosses between 9 commercialized Uzbek cotton cultivars and 16 different chromosome substituted lines (CS-B) [25; 26; 27; 28; 29], (iii) germplasm resources developed through marker-assisted selection (MAS) programs that bear novel quantitative trait loci (QTL) loci mobilized from unique donors to the genetic background of commercial Uzbek cotton cultivars via molecular markers, and (iv) tissue culture-derived, genetically modified (GM) germplasm and their hybrids to local cultivars that bear RNA interference (RNAi), synthetic hairpin oligonucleotides, anti-sense, or overexpression genetic constructs for
It is noteworthy to mention that association mapping individuals (Table 1) were selected from the IG&PEB collection and re-grown at the Mexico Winter Nursery of USDA-ARS by Drs. Russel Kohel and John Yu, (cotton germplasm Unit of USDA-ARS at College Station,Texas) for phenotypic evaluations and seed increase. Increased seeds grown at the Mexican environment kindly were sent back to Uzbekistan by Dr. Richard Percy (USDA cotton germplasm curator) and currently backed-up at the CGB and IG&PEB collections. Additionally, chromosome substituted (CS-B) lines were received within the frame of USDA-Uzbekistan Cooperation Programs, kindly provided by Dr. David Stelly (Texas A&M University), Dr. Sukumar Saha and Dr. Johnie Jenkins, USDA-ARS, Starkville, Mississippi, and now are preserved in both CGB and IGPEB collections. CGB scientists in collaboration with USDA partners are developing CS-B specific chromosome substituted recombinant inbred lines (CSRILs) in the background of important Uzbekistan cultivars. Further, development of cotton tissue culture and trangenomics efforts , and the mobilization of useful genetic constructs into commercialized cultivars has created novel germplasm resources, useful for cotton improvement and helpful to address many problems associated with improving and boosting yield and quality [1; 22; 32].
4. Storage, maintenance and funding
The above-mentioned main collections and novel germplasm resources are stored and maintained in each institution and managed separately by its scientists. The IG&PEB, UzSRICBSP, and NU collections are stored under room temperature conditions (20-25°C) and there is no facility available for cold storage of germplasm accessions [3; 8]. In contrast, UzRIPI  and CGB collections are stored in short term (under+4°C) cold room facilities that were established as a result of government and international funding (in the case of UzRIPI, . No long term cold storage (-20 or-80 °C) facilities, requiring attention and investment, are available for any of the germplasm collections in Uzbekistan, as highlighted by Campbell et al.  and Abdullaev et al. .
Germplasm accession seeds are preserved according to commonly practised procedures used over the decades of germplasm maintenance efforts in each collection. For instance, according to previous reports  germplasm seeds are ginned and put into paper bags with a label of catalogue number, accession name, year of collection and origin. Paper bags also contain “
Consequently, germplasm resources, in particular those without short term cold room facility, are scheduled for seed renewal every 8-10 years under forced self-pollination in the open field conditions . Each organization has its own, but very similar protocols, schemes of planting, growing and evaluating germplasm (see  for detailed protocol for IG&PEB cotton collection), government research grants and field extension stations with up to 8-10 staff working on germplasm maintenance. During a seed renewal year, accessions of re-grown germplasm are phenotypically evaluated for major agronomic and morpho-biological and fibre quality traits [3; 8].
Germplasm evaluation records from each collection are maintained as a hard copy catalogue book that contains all descriptions about accessions (origin, year, collector, collected sites, seed renewal, etc), and data from the past 50 years of evaluations [e.g. 34] In UzRIPI, there is a “Unified Council for Mutual Economic Assistance (COMECON) list of descriptors for the species
As reported by Campbell et al. , all germplasm related activities and maintenance of the Uzbekistan cotton collections are funded by the Committee for Coordination of Science and Technology Development under the Cabinet of Ministry of Uzbekistan, MAWR, and ASUz where funds are given as competitive research and “a unique facility” maintenance grants. Moreover, each institution receives international grants for projects that utilize the germplasm resources, and therefore, budget funding for germplasm related works .
5. Sharing and exchange
As highlighted in the recent reports by Campbell et al.  and Abdullaev et al. , all existing cotton germplasm resources, deposited and preserved in the country, are available for cotton researchers, breeders, and students who are conducting the cotton research. Written requests should be addressed to the directors of institutions, and should describe the purpose of the germplasm usage and specify the amount of seeds requested. Directors of institutions, with approval and on the responsibility of germplasm curators, grant the distribution of requested germplasm. If a specific germplasm with commercial interest is requested, a bi-lateral agreements are sought defining the condition of sharing that varies according institutions' internal regulations. All granted requests are registered in the germplasm exchange book of the collection.
Previously, germplasm requested by foreign institutions were officially sent under a standard “research purposes only” Material Transfer Agreement (MTA) and accompanied by proper phytosanitary certificates upon approval of the National Coordinator of Plant Genetic Resources (PGR) of Uzbekistan and responsible offices at the MAWR. Presently, any genetic and biological material sharing is granted by approval of Committee for Coordination of Science and Technology Development under the Cabinet of Ministry of Uzbekistan with “a research purpose only” MTA.
6. Characterization and utilization of the collection
Detailed evaluation, characterization, and cataloguing of germplasm accessions in the collections are very important to the utility of the collections by the local and world cotton research community interested in using ‘candidate’ accessions for breeding purposes. As mentioned above, during the periodic renewal of seed of germplasm accessions to maintain the collection, accessions are evaluated and characterized for the major characteristics and traits useful for both biodiversity estimates and cotton improvement. Each collection has its independent programs and objectives toward this goal; therefore, there was a need to develop a unified germplasm evaluation methodology and descriptors [11; 12].
6.1. Cotton germplasm descriptor and database
In UzRIPI, there is a computerized “CAC-DB” database for plant germplasm resources developed for Central Asian and Transcaucasian countries using Microsoft FoxPro [36; 37]. In this database, the principle information systems of the International Centre for Agricultural Research in the Dry Areas (ICARDA) and the N.I. Vavilov Research Institute of Plant Industry (VIR) is used. Major characteristics for the entire cotton collection of the UZRIPI as well as UzSRICBSP have been described in an electronic catalogue in Microsoft Excel (Dr. Fyzulla Abdullaev, germplasm specialist of the UzSRICBSP, personal communication).
Within the framwork of USDA-Uzbekistan cooperation programs, CGB scientists in collaboration with IG&PEB colleagues and cotton germplasm Unit staff worked on updating the cotton cataloguing system. Scientists suggested the use of a modified version of the “Descriptor for Cotton” which was originally developed and approved by IPGRI in 1985 (http://www/ipgri/cgiar.org). After considering recommendations from more recent descriptors for plant germplasm resources (e.g., Descriptor for Groundnuts-1992; and Descriptor for Pistachio-2002) and consulting with IG&PEB germplasm curator and leaders (Dr. Abdumavlyan Abdullaev and Dr. Sofiya Rizaeva), some modifications were introduced to the “Descriptor for Cotton-1985” of IPGRI. In the modified descriptors, two categories: “characterization and preliminary evaluation” and “further characterization and evaluation” were combined into one category “characterization and evaluation” because of the lack of preliminary information for accessions that were brought from abroad to the IG&PEB collection. New sub-categories, such as 1) cotton boll size, and 2) natural leaf defoliation properties were introduced; in “Susceptibility to biotic stresses” diseases and disease sources, specific to Uzbekistan, were introduced. At present, about 1,000 Upland germplasm accessions have been characterized for main agronomic, fibre quality properties and molecular diversity [12; 23; 24] using the modified “Descriptor for Cotton-1985” [Table 2; 8].
|1||SCIENTIFIC NAME||Latin name||Name of genus, species, subspecies etc. (ex.: |
|2||ACCESSION NAME||Name of line or cultivar||Ex.: TM-1, 3-79|
|3||ACCESSION NUMBER||Number of accession in collection catalogue||Ex.: 1, 2, 3…|
|4||ORIGIN||Place of sample origin||Collection, author/scientist, country etc.|
|5||YEAR||Year of acceptance to collection||YYYY|
|6||RENEWAL||Last time of seeds renewal||DD.MM.YYYY|
|7||HOMOGENIETY||Not uniform||0||Homogeneity of cotton germplasm population|
|8||GROW HABIT||Prostrate||3||Growth of habit (Bush shape)|
|9||ANTOCYAN||Weak||0||Colour of the plant in general|
|Not became brown||3|
|10||STEM HAIRINESS||Naked||1||Hairiness of the plant stem|
|11||LEAF HAIRINES||As above||Hairiness of the leaves|
|13||LOBE NUMB||Numeric||Number of leaf lobe|
|14||EMERGENCE||Numeric||Days to emergence of cotton seedlings|
|15||SEEDENERGY %||Numeric||The energy required for seed germination|
|16||SEEDTERM %||Seed energy in thermostat (%)||Numeric||The energy required for seed germination in thermostat|
|17||BRHGHT (HS)||Numeric||Height of the first fruit branch in cm.|
|18||BRANCHTYPE||Branching Type||Distance of first sympodial fruit branch from first fruit brunch in cm|
|19||HIEGHT (cm)||Numeric||Plant height in cm.|
|20||MONO||Numeric||Number of monopodia|
|21||SYMP||Numeric||Number of sympodia|
|22||STEAMNODE||Numeric||Number of total stem nodes|
|Sensitivity to day/night length|
|27||FLOWERING||Numeric||Days to 50% of plants flowering|
|28||OPENING||Numeric||Days to 50% of bolls opening|
|Level of Boll opening|
|31||BOLL NUM||Numeric||Number of boll|
|32||BOLL WEIGHT||Boll weight (g)||Numeric||Average weight in grams of a 10 boll sample|
|33||LOCULES NUM||Numeric||Locules per boll|
|34||SEED WEIGHT||Numeric||Weight of 100 seeds in grams (could be applied to cultivated plants only)|
|Fuzz grade (amount of fuzz on seeds)|
|38||fibre LENGHT||Numeric||fibre length in millimeter|
|39||T0||fibre strength (g/tex)||Numeric||The fibre strength of a bundle of fibres measured on a Stelometre with the jaws holding the fibre bundle tightly apprised. Measured in grams force per tex.|
|40||MIC||Micronaire||Numeric||The fitness of the sample taken from the ginned lint measured by the Micronaire and expressed in standard curvilinear micronaire units|
|41||UI%||Numeric||fibre maturity in %|
|42||YELLOWNESS||fibre yellowness||Numeric||Hunter's B value, a measure of increasing yellowness of the cotton, taken with a Nickerson-Hunter colourimeter|
|43||REFLECT||Reflectance (RD)||Numeric||A measure of the percentage of reflectance on a Nickerson-Hunter colourimeter. The higher the value the lighter the cotton.|
|44||LINT||Lint (yield) percentage||Numeric||The weight of lint ginned from sample of seed cotton expressed as percentage of the weight of seed cotton|
|45||LINT INDEX||Numeric||The weight of lint from 100 seed in gram|
|46||ELO||The percentage of fibre elongation||Numeric||The percentage of elongation at break of the centre 1/8 each of the fibre bundle measured for T1 strength on the Stelometer|
|47||CGRD||Numeric||colour grade of fibre|
|48||AREA||Area of seed in %||Numeric||Seed covered area with fibre|
|49||DISEASE RES||Highly Resistant (≥86% -100%)||1||Percentage of plants Resistant to pests/insects or phytopathogen (fungi, bacteria, virus etc.)|
|Highly susceptible (1%-30%)||5|
|50||ENVRES||Special resistance to environmental conditions||As above||Resistance to salt, drought, low water, temperature etc.|
6.2. Germplasm characterization and utilization
Cotton germplasm Units of each collection work extensively on characterization of their own germplasm resources within the framework of various projects. IG&PEB cotton germplasm Unit scientists, as mentioned above, investigate the evolution, taxonomy, phylogeny, hybridization compatibility, usage and introgression of wild germplasm. On the basis of investigations of the gene pools from IG&PEB collection, Abdullaev et al.  updated the Mauer taxonomy system for
Being a breeding collection of cultivated cottons in Uzbekistan, the UzSRICBSP researchers mainly use their collection to study genetics of various agronomic traits and disease resistance aspects of germplasm accessions during the variety development process [7; 16]. The NU collection, in particular the genetic stocks and cytogenetic stocks has been characterized in detail for the genetic traits  and cytogenetic aberrations [19; 20; 42]. The unique cytogenetic collection preserved at the NU also is being characterized using molecular markers and identification of chromosome specificities of the monosomics is in progress (Dr. Marina Sanamyan, personal communication).
Cotton germplasm resources were the foundation to develop highly adapted, disease resistant and superior agronomic quality cotton cultivars for Uzbekistan that were highlighted in a number of past reports [2; 3; 6; 8; 10]. In particular, forecasting the benefit of utilization of wild cotton germplasm accessions in conventional breeding of cotton in early 1960s by germplasm leaders, Drs. F. Mauer and A. Abdullaev [3; 8; 43] boosted the new variety development in Uzbekistan that provided timely responses to cotton production problems in the country. Over the past several decades, Uzbekistan breeders have developed more than 200 new cotton cultivars highly adapted  to the different soil-climatic regions of Uzbekistan, with high resistance characteristics to the major cotton diseases and pests, having high-yield and better fibre qualities [6; 7; 8; 44]. It is noteworthy to highlight here that the major accomplishment of Uzbekistan cotton breeders for the past century of efforts was the development of very early-maturing and productive cotton cultivars with 105-120 days of vegetation period, which made cotton growing suitable and profitable in the northern latitudes like Uzbekistan. This was only possible because of the existence and efficient exploitation of cotton germplasm resources that should be highlighted and valued as Uzbekistan's cotton breeders greatest commitment.
Further, as highlighted in recent reports [3; 8; 21] with the advances in cotton sciences and the development and application of modern molecular genetics tools and approaches for plant germplasm analysis , initial efforts by Uzbekistan scientist to characterize a selected global set of ~1000
Efforts also identified several SSR markers associated with main fibre quality traits along with donor accessions, bearing “golden” QTLs useful for MAS programs [23; 24]. As a result, a successful MAS program has been established in Uzbekistan that facilitated to mobilize novel haplotypes of important fibre quality QTLs from donor accessions preserved in cotton germplasm collection to commercial cultivars. In that fibre trait-associated DNA markers were used as a tool to manipulate the transfer of QTLs during a genetic hybridization [38; 46; 47].
The MAS program, extensively utilized during past decade in Uzbekistan that involved several donor (germplasm accessions) and recipient (commercial cultivars) germplasm not only improved and developed novel MAS cultivars through mobilization of novel untapped loci but also created novel germplasm resources useful for cotton breeders and future cotton breeding [Table 1; 10; 38; 46; 47]. Several first generation MAS-derived cultivars were developed and submitted for State Variety Testing Committee of Uzbekistan for future commercialization that are being field-trailed for improved agronomic and fibre qualities across the Uzbekistan regions. Moreover, as a ongoing effort, Uzbekistan researchers initiated a gene-pyramiding approach to combine major fibre quality traits into single genotype of several commercial Upland cotton cultivars of Uzbekistan using these effective molecular markers as a breeding tool and donor genotypes from cotton germplasm collections [38; 46; 47].
As a continuation of efforts to characterize cotton germplasm resources at the molecular level, about 300
Use of cotton germplasm resources and their characterization at the molecular level further helped us to select the most diverse
Currently, genotyping of additional cotton germplasm accessions from major collections using widely available SSR markers is in progress that will help to characterize and organize the entire cotton germplasm resources of Uzbekistan. In perspective, we also aim to apply novel molecular tools such as SNP platforms and genotyping-by-sequencing (GBS) technologies to better characterize the selected cotton germplasm resources, AM and NAM panels that require additional funding, coordinated efforts and international collaborations.
Due to the importance of cotton production for the country and the historic expertise on cotton farming and production developed during the past century, Uzbekistan has prioritized and promoted the breeding programs, leading to a collection of one of the richest cotton germplasm resources in the world. Developed and maintained by several leading cotton research institutions in Uzbekistan, cotton germplasm collections preserve over 25,000 major cotton germplasm accessions of
Although each cotton collection has its own specific goals and objectives for preserved materials, there is a huge need for conducting joint re-inventory for clarification of redundancies between some of collections. There is a need for building short-term and long term cold storage rooms for all collections available in the country to better preserve the collection for future generations and cotton production. Moreover, although initial efforts have been made, coordinated efforts are needed to create a unified electronic database to systematize the germplasm records for all collections that will help for better utilization of the accessions in the breeding programs.
There are over 5,000 novel germplasm resources that were developed for past decade of collaborative efforts on molecular genetic characterization of cotton germplasm resources and establishment of modern MAS and GM programs. The modern cotton genomics and bioinformatics programs in combination with conventional cotton breeding efforts will further enhance the characterization and utilization as well as efficient documentation and systematization of the germplasm resources in Uzbekistan.
We thank the Uzbekistan government for continual funding support for cotton germplasm collections and research. We acknowledge the Office of International Research Programs (OIRP) of the United States Department of Agriculture (USDA) and USA partner laboratories for the financial support of cotton germplasm related works through project P120/P120a.