**3. Content of Uzbekistan cotton germplasm collection**

#### **3.1. Main collections**

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

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

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 continu‐ ous 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)

According to Abdullaev et al. [8], 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 expedi‐ tions enriched Uzbekistan collection with Old World (Afro-Asian and Indian) diploid cottons (*G. herbaceum* and *G. arboreum*), and a number of wild, exotic and cultivated tetraploid and

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 *G. hirsutum* exotic and varietal accessions were exchanged with the US cotton germplasm collection [11; 12]. Annually, 100-120 cotton accessions from the collection of Uzbek Research Institute of Cotton Breeding and Seed Production (UzSRICBSP) are exchanged with world centres. During the period of 2001-2003, the Institute received 990 accessions from and sent 260 cotton accessions to the US

soil-climatic regions of Uzbekistan [1; 2; 3; 8].

290 World Cotton Germplasm Resources

germplasm exchange worldwide.

diploid cottons around the world [8].

cotton germplasm collection [7].

development and characterization of novel germplasm resources.

**2. History and development of Uzbekistan cotton collection**

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 allotetra‐ ploids(*G. hirsutum* and *G. barbadense*) representing the primary gene pool, and two cultivated Asian diploids (*G. herbaceum* and *G. arboreum*) representing the secondary gene pool. Although some redundancy of accessions maintained by collections could be possible and is a subject for future comparative inventory work, each collection has its own specifici‐ ties and has been formed according to distinctive research efforts conducted by the scientists of these institutions for past decades.



collection, also referred to as "wild collection", was formed as a result of scientific expeditions to the centres of origin of *Gossypium* species and a 50 years of research efforts by IG&PEB scientists and research programs. IG&PEB cotton collection maintains more than 40 wild A-to G and K-genome *Gossypium* species [2; 3; 8] and targets the study of the taxonomy, phylogeny, evolution, hybridization compatibility, and introgression of wild germplasm for breeding purposes, all of which make the collection unique compared to others. The detailed descrip‐ tion, content, geographic coverage and history of *G. hirsutum* and *G. barbadense* germplasm development in Uzbekistan were discussed by Abdullaev et al., 2013, where authors report the representation of 4 continents, ~33 geographic regions and ~103 countries by the IG&PEB collection [8].There are a large number di-and tri-genomic hybrids and their diploid and allotetraploid progenies recovered from tedious sexual crosses within and/or between wild, primitive and domesticated genotypes within different gene pools [13; 14; Dr. Rizaeva, personal communication]. Some of examples such as tri-genomic hybrids were highlighted in

Cotton Germplasm Collection of Uzbekistan http://dx.doi.org/10.5772/58590 293

MAWR has two distinctive cotton collections: one is preserved at the UzSRICBSP, anoth‐ er 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 [16]. Geographically, this collection represents 107 countries of origin for cotton acces‐ sions [7]. The uniqueness of UzSRICBSP collection is its wide representation and cover‐ age 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. [7]. However, our inventory is based on the latest information obtained from this collection (Dr. H. Saydaliev, a germplasm curator

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 *Gossypium* gene pools in the country. However, there is a need to conduct comparative reinventory between UzRIPI and IG&PEB collection to identify the distinctive versus redundant germplasm accessions. Because UZRIPI was the Central Asian branch of All Union scientificresearch institute after N.I. Vavilov some level of redundancies to Russian VIR collection is

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 *G.*

previous reports [14; 15].

of the UzSRICBSP, personal communication).

expected that requires future study.

**Table 1.** Summary of the content of Uzbekistan cotton germplasm collections

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 *Gossypium* genus. The IG&PEB cotton germplasm collection, also referred to as "wild collection", was formed as a result of scientific expeditions to the centres of origin of *Gossypium* species and a 50 years of research efforts by IG&PEB scientists and research programs. IG&PEB cotton collection maintains more than 40 wild A-to G and K-genome *Gossypium* species [2; 3; 8] and targets the study of the taxonomy, phylogeny, evolution, hybridization compatibility, and introgression of wild germplasm for breeding purposes, all of which make the collection unique compared to others. The detailed descrip‐ tion, content, geographic coverage and history of *G. hirsutum* and *G. barbadense* germplasm development in Uzbekistan were discussed by Abdullaev et al., 2013, where authors report the representation of 4 continents, ~33 geographic regions and ~103 countries by the IG&PEB collection [8].There are a large number di-and tri-genomic hybrids and their diploid and allotetraploid progenies recovered from tedious sexual crosses within and/or between wild, primitive and domesticated genotypes within different gene pools [13; 14; Dr. Rizaeva, personal communication]. Some of examples such as tri-genomic hybrids were highlighted in previous reports [14; 15].

**Germplasm type** *G. hirsutum G. barbadense G. arboreum G. herbaceum*

Genetic stocks of inbred

292 World Cotton Germplasm Resources

Association mapping

Nested association mapping cross combination

Hybrids (F1-6 and BC1-5) with

MAS gene pyramiding

local cultivars

families

individuals

and RI lines

**National University of Uzbekistan (NUUz)**

**Cytogenetic stocks/Mutants** Primary monosomics 94 - - - - 94 Tertiary monosomics 22 - - - - 22 Monotelodisomics 20 - - - - 20 Monoisodisomics 4 - - - - 4 Haploids 4 - - - - 4 Disynaptics 31 - - - - 31 Translocations 235 - - - - 235

Total 1181 0 0 0 0 1181 **Centre of Genomics and Bioinformatics, ASUz, MAWR, and "UzCottonIndustry" association Mapping panels**

**Chromosome substitution line hybrids** F1 to F4 generation families 260 - - - - 260 CSUZ-RILs individuals 301 - - - - 301 **Transformed lines** Tissue culture derived (T1-6) 1444 1444

**MAS-derived germplasm** MAS – F1-2 and BC2-4 families51 14 65

Total 4938 286 0 0 14 5238 Grand total 24571 4190 1623 1292 937 32580

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 *Gossypium* genus. The IG&PEB cotton germplasm

**Table 1.** Summary of the content of Uzbekistan cotton germplasm collections

771 - - - - 771

986 286 - - - 1272

20 - - - - 20

1852 1852

24 24

**Other species**

**Total**

0

MAWR has two distinctive cotton collections: one is preserved at the UzSRICBSP, anoth‐ er 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 [16]. Geographically, this collection represents 107 countries of origin for cotton acces‐ sions [7]. The uniqueness of UzSRICBSP collection is its wide representation and cover‐ age 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. [7]. 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 *Gossypium* gene pools in the country. However, there is a need to conduct comparative reinventory between UzRIPI and IG&PEB collection to identify the distinctive versus redundant germplasm accessions. Because UZRIPI was the Central Asian branch of All Union scientificresearch institute after N.I. Vavilov some level of redundancies to Russian VIR collection is expected that requires future study.

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 *G.* *hirsutum* line L-458 [19; 20]. Readers can find detailed description of Uzbekistan's cytogenetic cotton collection in this book.

**4. Storage, maintenance and funding**

al. [3] and Abdullaev et al. [8].

traits [3; 8].

regenerated lines.

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, UzS‐ RICBSP, 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 [33] 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, [33]. 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

Cotton Germplasm Collection of Uzbekistan http://dx.doi.org/10.5772/58590 295

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 [8] 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 "*the weight of seeds (50 g or 100 g individual or total pick respectively*") and "*bags are stored in special metal boxes (30 x 11 cm) and boxes are placed in wooden-cases"* [8]. Other collections follow similar storage procedure with some modifications in types of storage boxes and variations in labelling of bags. Since 2003, after the reconstruction of the building for germplasm resources at UZRIPI,

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 [3]. Each organization has its own, but very similar protocols, schemes of planting, growing and evaluating germplasm (see [8] for detailed protocol for IG&PEB cotton collec‐ tion), 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

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 *Gossypium L* [35]. IG&PEB has started using modified "Cotton descriptor" of International Plant Genetic Resource Institution [see below for detail description; 3; 8]. Moreover, data records on germplasm accession characteristics and description are being currently entered into electronic Microsoft database formats (personal communications with germplasm heads of all collections). All cotton collections also have their own green‐ house facilities to vegetatively maintain [7; 8] wild and primitive accessions, unique multigenomic hybrids, mutants, and cytogenetics stocks as well as transformed and somatically

cotton germplasm seed have been stored in plastic containers [33].

#### **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 culturebased transgenomics programs and their integration into conventional cotton improve‐ ment 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 "UzcottonIn‐ dustry 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 devel‐ oped 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 con‐ structs for *de novo* characterized genes and sequence signatures in the CGB laboratories [1; 22; 30; 31; 32].

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 Sta‐ tion,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, Mississip‐ pi, and now are preserved in both CGB and IGPEB collections. CGB scientists in collabora‐ tion 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 [21], 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 associat‐ ed with improving and boosting yield and quality [1; 22; 32].
