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Hindawi Publishing Corporation International Journal of Plant Genomics Volume 2008, Article ID 742304, 20 pages doi:10.1155/2008/742304 Review Article 1 2 3, 4 3 Hong-Bin Zhang, Yaning Li, Baohua Wang, and Peng W. Chee Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA Department of Plant Pathology, Biological Control Center of Plant Diseases and Plant Pests of Hebei Province, Agricultural University of Hebei, Baoding 071001, China Molecular Cotton Breeding Laboratory, University of Georgia, Tifton, GA 31793, USA School of Life Sciences, Nantong University, Nantong 226007, China Correspondence should be addressed to Hong-Bin Zhang, firstname.lastname@example.org Received 27 June 2007; Accepted 10 October 2007 Recommended by P. K. Gupta Genome research promises to promote continued and enhanced plant genetic improvement. As a world’s leading crop and a model system for studies of many biological processes, genomics research of cottons has advanced rapidly in the past few years. This article presents a comprehensive review on the recent advances of cotton genomics research. The reviewed areas include DNA markers, genetic maps, mapped genes and QTLs, ESTs, microarrays, gene expression proﬁling, BAC and BIBAC libraries, physical mapping, genome sequencing, and applications of genomic tools in cotton breeding. Analysis of the current status of each of the genome research areas suggests that the areas of physical mapping, QTL ﬁne mapping, genome sequencing, nonﬁber and nonovule EST development, gene expression proﬁling, and association studies between gene expression and ﬁber trait performance should be emphasized currently and in near future to accelerate utilization of the genomics research achievements for enhancing cotton genetic improvement. Copyright © 2008 Hong-Bin Zhang et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 1. INTRODUCTION ton, Extra Long Staple Cotton, American Pima, or Egyp- tian Cotton, contributes 8% of the world’s cotton; and G. Cottons (Gossypium spp.) belong to the genus Gossypium of herbaceum, also known as Levant Cotton, and G. arboreum, the family Malvaceae. Gossypium consists of 45–50 species, also known as Tree Cotton, together provide 2% of the with 40–45 being diploids (2n = 26) and 5 being allote- world’s cotton. traploids (2n = 52). The species are grouped into eight Cottons are not only a world’s leading textile ﬁber and genome groups, designated A through G and K, on the basis oilseed crop, but also a crop that is of signiﬁcance for foil of chromosome pairing aﬃnities . At the tetraploid level, energy and bioengergy production. Although cottons are there are ﬁve species, designated (AD) through (AD) for native to tropics and subtropics naturally, including the 1 5 their genome constitutions. Phylogenetic analyses clustered Americas, Africa and Asia, they are cultivated in nearly the diploid species of Gossypium into two major lineages, 100 countries. India, China, USA, and Pakistan are the top including the 13 D-genome species lineage and the 30∼32 four cotton growing countries, accounting for approxi- A-, B-, E-, F-, C-, G-, and K-genome species lineage, and the mately 2/3 of the world’s cotton (http://www.ers.usda.gov/ polyploid species into one lineage, that is, the 5 AD-genome Brieﬁng/Cotton/trade.htm). According to the Food and species lineage (Figure 1;). Agriculture Organization (FAO) of the United Nations Of the Gossypium species, four are cultivated in agricul- (http://www.fao.org), the cotton planting area reached ture, including two allotetraploids (G. hirsutum and G. bar- about 35 million hectares and the total world’s cotton badense) and two diploids (G. herbaceum and G. arboreum). production had a record of about 23 million metric tones Gossypium hirsutum, also known as Upland cotton, Long Sta- in 2004/2005. Cotton products include ﬁbers and seeds ple Cotton, or Mexican Cotton, produces over 90% of the that have a variety of uses. Cotton ﬁbers sustain one of the world’s cotton; G. barbadense, also known as Sea Island Cot- world’s largest industries, the textile industry, for wearing 2 International Journal of Plant Genomics AD-genome allopolyploids, 5 species, New world, 2347∼2489 Mb/1C G. barbadense (AD) G. hirsutum (AD) G. darwinii (AD) G. tomentosum (AD) G. mustelinum (AD) 1∼2MYA A-genome diploids, D-genome diploids, 13 species, 2species, Africa, New world, 841∼934 Mb/1C 1667∼1746 Mb/1C F-genome diploid, 1 species, Africa, 1311 Mb/1C B-genome diploid, 3 species, Africa, 1345∼1359 Mb/1C E-genome diploid, +7 species, Africa-Arabia, 1496∼1663 Mb/1C C-genome diploid, 2 species, Australia, 1951∼2015 Mb/1C G-genome diploid, 3 species, Australia, 1756∼1834 Mb/1C K-genome diploid, 12 species, Australia, 2450∼2778 Mb/1C 5∼10 MYA Figure 1: Phylogeny and evolution of Gossypium species. The phylogenetic data is from Wendel and Cronn , the genome sizes are from Hendrix and Stewart , and genomic designations follow Endrizzi et al.  and Percival . The species in bold face are cultivated. MYA: million years ago. apparel, home furnishings, and medical supplies, whereas polyploidization and single-celled biological processes. The cottonseeds are widely used for food oil, animal feeds, genomes of angiosperm plants vary over 1000 folds in size, and industrial materials (such as soap). Cottonseed oil is ranging from 100 to >100,000 Mb/1C (haploid) . It has ranked ﬁfth in production and consumption volume among long been recognized that polyploidy is a common, promi- all vegetable oils in the past decades, accounting for 8% nent, ongoing, and dynamic process of genome organization, of the world’s vegetable oil consumption. The business function diversiﬁcation, and evolution in angiosperms . stimulated by cotton is hundreds of billion dollars in the The genomes of most angiosperms are thought to have in- world. In the USA alone, for instance, the annual cotton curred one or more polyploidization events during evolu- business revenue exceeds $120 billion (Agricultural Statistics tion . Studieshavedemonstratedthatgenomedoubling Board 1999; National Cotton Council of America, http:// has also been signiﬁcant in the evolutionary history of all www.cotton.org/news/releases/2003/cotton-trade.cfm). vertebrates and in many other eukaryotes [9–12]. It is esti- Moreover, nearly a billion barrels of petroleum worldwide mated that about 70% of the ﬂowering plant species are poly- are used in every year to synthesize artiﬁcial “synthetic” ploids. For instance, of the world-leading ﬁeld, forage, hor- ﬁbers. Further improvement of cotton ﬁbers in yield and ticultural, and environmental crops, many are contributed quality will replace or signiﬁcantly reduce the consumption by polyploid species, such as cotton, wheat, soybean, pota- of fossil oil for synthetic ﬁber production, thus being saved toes, canola, sugarcane, Brassica, oats, peanut, tobacco, rose, for energy production. Finally, cottonseed oil, the main coﬀee, and banana. Therefore, studies of both genome size by-product of cotton ﬁber production, could be potentially evolution and polyploidization have long attracted the inter- used as biofuel. ests of scientists in diﬀerent disciplines. Nevertheless, much In addition to their economic importance, cottons are remains to be learned. Examples include impacts of poly- an excellent model system for several important biologi- ploidization on genome size, genome organization, gene du- cal studies, including plant genome size evolution, plant plication and function, and gene family evolution; the role of G. raimondii (D ) G. klotzschianum (D ) 3-k G. davidsonii (D ) 3-d G. thurberi (D ) G. trilobum (D ) G. lobatum (D ) G. aridum (D ) G. laxum (D ) G. schwendimanii (D ) G. armourianum (D ) 2-1 G. harknessii (D ) 2-2 G. turneri (D ) G. gossypioides (D ) G. arboreum (A ) G. herbaceum (A ) 1 Hong-Bin Zhang et al. 3 transposable elements in structural and regulatory gene evo- chromosome addition and substitution lines . These cy- lution and gene functions; and mechanisms and functional togenetic stocks are unique and valuable not only for cotton signiﬁcance of rapid genome changes. genetics research, but also for deciphering the ramiﬁcations Cottons have several advantages over other polyploid of polyploidization on genome organization, function, and complexes for plant genome size and polyploidization stud- evolution. ies. First, the genome sizes of 37 of the 45∼50 Gossyp- Cotton ﬁber is an excellent single-celled model system ium species, including all eight genomes and polyploidy for studies of many single-celled biological processes, par- species, have been determined and shown to vary ex- ticularly cell expansion and cellulose biosynthesis. Cotton tremely signiﬁcantly (; Figure 1). At the diploid level, the ﬁbers are unicellular, unbranched, simple trichomes that dif- genome sizes vary by three folds, ranging from 885 Mb/1C ferentiate from the protoderm of developing seeds. There are in the D-genome species to 2,572 Mb/1C in the K-genome probably over one-half million quasi-synchronously elongat- species. Within each lineage, the genome sizes vary most ing ﬁbers in each boll or ovary. Although all plant cells extend in the A+F+B+E+C+G+K lineage, ranging from 1,311 to to some degree during development and diﬀerentiation, cot- 2,778 Mb/1C with a diﬀerence of 1,467 Mb (110.2%); second tonﬁbers canreach up to 5.0 cminlengthinsomegenotypes, in the D-genome lineage, ranging from 841 to 934 Mb/1C being among the longest cells. Therefore, they oﬀer a unique with a diﬀerence of 93 Mb (10.5%); and least in the poly- opportunity to study cell expansion at the single cell level. ploidy lineage, ranging from 2,347 to 2,489 Mb/1C with a Cellulose is a major component of the cell walls of all higher diﬀerence of 142 Mb (5.9%). Variations were also observed plants, constituting perhaps the largest component of plant within a species. For instance, within G. hirsutum, the vari- biomass, with an estimated annual world production of 100 ation (n = 5) was from 2,347 to 2,489 Mb/1C, diﬀering million metric tons. The ﬁber cell wall of cottons consists of by 142 Mb (5.9%) while within G. arboreum, the variation >90% cellulose. Therefore, cotton ﬁber cells have long been (n = 5) was from 1,677 to 1,746 Mb/1C, diﬀering by 69 Mb used as a model system to study cellulose biosynthesis  (4.0%). that is the basis for biomass-based bioenergy production. Second, the evolutionary history of the allotetraploid species of Gossypium has been established (Figure 1), espe- 2. ADVANCES IN COTTON GENOMICS RESEARCH cially for the two cultivated AD-genome cottons, G. hir- sutum and G. barbadense, and their closely related diploid Genome research has been demonstrated to be promising progenitors, G. herbaceum (A ), G. arboreum (A ), G. rai- for continued and enhanced crop plant genetic improve- 1 2 mondii (D ), and G. gossypioides (D ). TheA-genomespecies ment. Therefore, eﬀorts have been made in cotton genome 5 6 are African-Asian in origin, whereas the D-genome species research, especially development of genomic resources and are endemic to the New World subtropics, primarily Mex- tools for basic and applied genetics, genomics, and breeding ico. Following the transoceanic dispersal of an A-genome research. These resources and tools include diﬀerent types taxon to the New World, hybridization between the immi- of DNA markers such as restriction fragment length poly- grant A-genome taxon and a local D-genome taxon led to morphism (RFLP), randomly ampliﬁed polymorphic DNA the origin and evolution of the New World allopolyploids (RAPD), ampliﬁed fragment length polymorphism (AFLP), (AD-genome) [13, 14]. Subsequent to the polyploidization resistance gene analogs (RGA), sequence-related ampliﬁed event, the allopolyploids radiated into three sublineages , polymorphism (SRAP), simple sequence repeat (SSR) or mi- among which included are the world’s commercially most crosatellites, DNA marker-based genetic linkage maps, QTLs important species, G. hirsutum and G. barbadense. Studies and genes for the traits important to agriculture, expressed showed that the A subgenome of the AD-genome-cultivated sequence tags (ESTs), arrayed large-insert bacterial artiﬁcial cottons is the most closely related to the genome of the ex- chromosome (BAC) and plant-transformation-competent tant diploid G. herbaceum (A ); the D subgenome of binary BAC (BIBAC) libraries, and genome-wide, cDNA-, or the AD-genome-cultivated cottons is the most closely re- unigene EST-based microarrays. Eﬀorts are also being made lated to the genome of the extant diploid, G. raimondii (D ) to develop the genome-wide, BAC/BIBAC-based integrated or G. gossypioides (D ); and the cytoplasm of the AD- physical and genetic maps, and sequence the genomes of genome-cultivated cottons is the most closely related to that the key cotton species. However, compared with other major of the extant diploids G. herbaceum (A )and G. arboreum crops, such as rice, maize, and soybean, the genome research (A )[14, 17]. Sequence analysis and paleontological record of cottons is far behind, mainly due to the limited funds al- suggest that the A-genome and the D-genome groups di- located to the species. Summarized below are the major ad- verged from a common ancestor 5–10 million years ago, and vances achieved recently in cotton genomics research. that the two diverged diploid genomes became reunited in a common nucleus to form the polyploid cottons, via allopoly- 2.1. DNA markers and molecular linkage maps ploidization, in the mid-Pleistocene, or 1-2 million years ago [14, 15, 18, 19]. Genetic maps constructed in the Gossypium species and the Finally, as in the wheat polyploid complex, cottons have types of markers used are listed in Table 1.Asinmostplant a long history of research at the cytological level. A wealth of species, the early application of DNA markers in cotton ge- cytogenetic stocks has been developed, including artiﬁcially nomic research has been in the form of RFLPs. It is, there- synthesized AD-genome polyploids between the A-genome fore, not surprising that the ﬁrst molecular linkage map of and D-genome diploid species  as well as individual the Gossypium species was constructed from an interspeciﬁc 4 International Journal of Plant Genomics G. hirsutum × G. barbadense F population based on RFLPs BAC subcloning as described by Lichtenzveig et al. . Cur- . The map contained 705 loci that were assembled into rently, a total of approximately 5,484 SSRs have been devel- 41 linkage groups and spanned 4,675 cM. This map later oped in cotton (; http://www.cottonmarker.org). was further advanced by Rong et al.  that comprised The development of a large number of ESTs (see below) 2,584 loci at 1.74-cM intervals and covered all 13 home- provides a good source of PCR-based primers for targeting ologous chromosomes of the allotetraploid cottons, repre- SSRs [92, 95, 96]. Taliercio et al.  sequenced ESTs repre- senting the most complete genetic map of the Gossypium to senting a variety of tissues and treatments with SSRs identi- date. Many of the DNA probes of the map were also mapped ﬁed among the ESTs. Their results indicated that these SSRs in crosses of the D-genome diploid species G. trilobum × could potentially map the genes represented by the ESTs. G. raimondii  and the A-genome diploid species G. ar- Guo et al.  examined the transferability of 207 G. ar- boreum × G. herbaceum . Detailed comparative analysis boreum-derived EST-SSR primer pairs among 25 diﬀerent of the relationship of gene orders between the tetraploid AD- diploid accessions from 23 species representing 7 Gossypium subgenomes with the maps of the A and D diploid genomes genomes. Their results demonstrated that the transferability has revealed intriguing insights on the organization, trans- of EST-SSR markers among these diploid species could as- mission and evolution of the Gossypium genomes. sist the introgression of genes into cultivated cotton species Because RFLPs are labor-intensive and require large especially by molecular tagging of the important genes ex- amounts of DNA, tedious blot hybridization and autoradio- isting in these diploid species. Guo et al.  also developed graphic methods, polymerase chain reaction (PCR)-based 2,218 EST-SSRs, with 1,554 from G. raimondii-derived ESTs DNA marker methods have come into vogue. Several types and 754 from G. hirsutum-derived ESTs. By integrating these of PCR-based DNA markers have been utilized in cotton new EST-SSRs to enhance the genetic map constructed by genome research. Methods, such as RAPD, AFLP, RGA, and Han et al. , the present SSR-based genetic map consists SRAP, oﬀer an excellent opportunity to scan enormous num- of 1,790 loci in 26 linkage groups and covers 3,425.8 cM with bers of DNA loci rapidly, often targeting the DNA elements an average distance between markers of 1.91 cM. This SSR- that are rapidly-evolving and therefore, are more likely to based high-density map contains 71.96% functional marker contain loci diﬀering among genotypes. Kohel et al.  loci, of which 87.11% are EST-SSR loci. constructed a genetic map based on a population derived DNA sequences derived from clone end sequencing of from an interspeciﬁc cross between Texas Marker-1 (TM- BAC libraries provide yet another resource for SSR marker 1) (G. hirsutum) and 3–79 (G. barbadense)inwhich atotal development. In addition to the uses as genetic markers, SSRs of 355 DNA markers (216 RFLPs and 139 RAPDs) were as- developed from BAC-end sequences provide the possibility sembled into 50 linkage groups, covering 4,766 cM. Brubaker to eﬃciently integrate the genetic and physical maps of cot- and Brown  presented the ﬁrst AFLP genetic linkage ton. Frelichowski et al.  developed 1,316 PCR primer map for the Gossypium G-genome that was constructed from pairs to ﬂank SSR motif sequences from 2,603 new BAC- an interspeciﬁc G. nelsonii × G. australe population. The end genomic sequences developed from G. hirsutum Acala AFLP genetic linkage maps were used to identify G-genome “Maxxa.” An interspeciﬁc recombinant inbred population chromosome-speciﬁc molecular markers, which, in turn, was used to map 433 marker loci in 46 linkage groups with a were used to track the ﬁdelity and frequency of G. australe total genetic distance of 2,126.3 cM and an average distance chromosome transmission in a G. hirsutum × G. australe between loci of 4.9 cM which covered approximately 45% of hexaploid bridging family. the cotton genome. Advent of SSR or microsatellite markers has brought To overcome the paucity of a particular type of DNA a new, user-friendly, and highly polymorphic class of ge- markers, genetic maps were developed by incorporating dif- netic markers for cotton. The latter feature is especially use- ferent classes of markers. For example, Lacape et al. con- ful to the cultivated Upland cotton due to its low intraspe- structed a combined RFLP-SSR-AFLP map based on an in- ciﬁc polymorphism. SSRs are PCR-based markers, usually terspeciﬁc G. hirsutum × G. barbadense backcross popula- codominant, well dispersed throughout the genome, easily tion of 75 BC plants. The map consists of 888 loci that or- shared between labs via ﬂanking primer sequences, and well dered into 37 linkage groups and spanning 4,400 cM. This portable from one population to another . Reddy et al. map was updated, mostly with new SSR markers, to con-  suggested that the total pool of SSRs present in the cot- tain 1,160 loci that spanned 5,519 cM with an average dis- ton genome is suﬃciently abundant to satisfy the require- tance between loci of 4.8 cM . Mei et al.  developed a ments of extensive genome mapping and marker-assisted se- genetic map using an interspeciﬁc G. hirsutum and G. bar- lection (MAS). Liu et al.  reported the assignment of badense F population that contained 392 genetic loci, in- SSRs to cotton chromosomes by making use of aneuploid cluding AFLPs, SSRs, and RFLPs, and mapped into 42 linkage stocks. SSRs have been widely employed in genetic diversity groups that spanned 3,287 cM, thus covering approximately analyses of cotton [87–90] and several genetic linkage maps 70% of the cotton genome. Lin et al.  constructed a link- based mostly on SSRs have now been developed [37–41]. age map of tetraploid cotton using SRAPs, SSRs, and RAPDs Several methods have been pursued to develop SSR to screen an interspeciﬁc G. hirsutum × G. barbadense F markers in cottons, including analysis of SSR-enriched small- population. A total of 566 loci were assembled into 41 link- insert genomic DNA libraries [29, 85, 86, 91], SSR mining ages that covered 5,141.8 cM with a mean interlocus space from ESTs (see below; [35, 38, 39, 92], and large-insert BAC of 9.08 cM. He et al.  constructed a more detailed cotton derivation by end sequence analysis  or SSR-containing mapwiththissameF population  using SSRs, SRAP, 2 Hong-Bin Zhang et al. 5 Table 1: Genetic maps constructed for Gossypium species. (a) (b) Marker type Total loci Map distance Population Cross type References AFLP 176 773 cM F2 GN × GAU  AFLP 213 931 cM F2 GN × GAU  AFLP, SSR, and RFLP 392 3,287 cM F2 GH × GB  AFLP, SSR, and RFLP 888 4,400 cM BC1 GH × GB  AFLP, SSR, and RFLP 1,160 5,519 cM BC1 GH × GB  RFLP 275 1,147 cM F2 GAR × GHE  RFLP 284 1,503 cM F2 and F3 GH × GH  RFLP 589 4,259 cM F2 GH × GTO  RFLP 705 4,675 cM F2 GH × GB  RFLP 763 1,493 cM F2 GT × GR  RFLP 2,584 4,448 cM F2 GH × GB  RFLP and RAPD 355 4,766 cM F2 GH × GB  SRAP 237 3,031 cM F2 GH × GB  SRAP, SSR, and RAPD 566 5,142 cM F2 GH × GB  SRAP, SSR, RAPD and REMAP 1,029 5,472 cM F2 GH × GB  SSR 193 1,277 cM RIL GH × GB  SSR 433 2,126 cM RIL GH × GB  SSR 442 4,331 cM BC1 GH × GB  SSR 444 3,263 cM DH GH × GB  SSR 624 5,644 cM BC1 GH × GB  SSR 907 5,060 cM BC1 GH × GB  SSR 1,790 3,426 cM BC1 GH × GB  SSR and RAPD 489 3,315 cM DH GH × GB  (a) RIL = recombinant inbred line, and DH = doubled haploid. (b) GH = G. hirsutum,GB = G. barbadense,GTO = G. tomentosum,GR = G. raimondii,GAR = G. arboretum,GHE = G. herbaceum,GN = G. nelsonii,and GAU = G. australe. RAPD, and retrotransposon-microsatellite ampliﬁed poly- into discrete classes in the segregating progenies. Over 200 morphisms (REMAPs). One thousand twenty nine loci were qualitative traits have been identiﬁed in either the diploid mapped to 26 linkage groups that extended for 5,472.3 cM (G. arboreum and G. herbaceum) or tetraploid (mostly in with an average distance between loci of 5.32 cM. The linkage G. hirsutum and G. barbadense)species . Examples of groups of the genetic maps have been assigned to their corre- such traits include leaf shape, pollen color, leaf color, lint sponding chromosomes by using the available cotton aneu- color, pubescent, bract shape, and so on. Because many ploid stocks [21, 23] and ﬂuorescent in situ hybridization us- qualitative traits are either morphological mutants that have ing mapped genetic marker-containing BACs as probes . arisen through spontaneous mutation, irradiation, or from natural variation between species in interspeciﬁc hybrids, they have little utility in crop improvement. Consequently, 2.2. Gene and QTL mapping there have been little eﬀorts in mapping qualitative traits onto the molecular genetic map. Qualitative traits that Although molecular linkage maps have contributed greatly have been mapped using molecular markers were recently to our understanding of the evolution and organization of summarized in . Many of these traits were mapped not the cotton genomes, a primary purpose of the map construc- as the main objective but as a tool for aligning the various tion is to provide a common point of reference for locating linkage groups to chromosomes assigned by the classical the genes aﬀecting qualitative and quantitative traits. DNA map. Noteworthy exceptions include those that are related markers that are associated with genes conferring important to agricultural productivity and quality of cotton and can be agronomic traits that are costly or laborious to measure broadly grouped into four categories: genes for leaf shape, will provide a less costly and yet more dependable means ﬁber development, resistant to disease and insect pests, and of selection for identifying desirable progenies in breeding fertility restoration . programs. Mapping quantitative traits Mapping qualitative traits Qualitative or simple Mendelian inherited traits are traits of Quantitative traits are traits of individuals that diﬀer as to individuals that diﬀer as to kind and not of degree, typically degree and not of kind, typically considered as interactions controlled by single genes and the phenotypic variation falls of multiple loci, tend to exhibit continuous variation in a 6 International Journal of Plant Genomics Table 2: QTLs or genes identiﬁed for various traits in cottons. Traits/genes Parental materials Reference Resistance to the bacterial blight pathogen Empire B2/B3/B2b6, S295 and Pima S-7  Resistance to the bacterial blight pathogen CS50 and Pima S-7  Density of leaf and stem trichomes Pima S-7 and Empire B2b6  Fiber quality and yield CAMD-E and Sea Island Seaberry  Agronomic and ﬁber traits MARCABUCAG8US-1-88 and HS46  Cotton leaf morphology and other traits Seaberry and Deltapine 61 with morphological mutants  Productivity and quality Siv’on and F-177  Physiological variables and crop productivity Siv’on and F-177  Fiber quality TM-1 and 3-79  Yield components, ﬁber, ﬂowering date, et al. TM-1 and 3-79  Rf1 fertility-restoring gene CMS and the restoring lines  Fiber quality Siv’on and F-177  Fiber strength 7235 and TM-1  Rf1 fertility-restoring gene XiangyuanA, ZMS12A, Sumian16A and 0-613-2R  Fiber-related traits Acala-44 and Pima S-7  Agronomic and ﬁber quality traits MD5678ne and Prema  Fiber and yield traits MARCABUCAG8US-1-88, HS46, MD5678ne et al.  Resistance to Verticillium wilt Pima S-7 and Acala 44  Fiber elongation Tamcot 2111 and Pima S6  Fiber length, length uniformity, and short ﬁber content Tamcot 2111 and Pima S6  Fiber ﬁneness and micronaire (MIC) Tamcot 2111 and Pima S6  Li1, Li2, N1, Fbl, n2, sma-4(ha), and sma-4(fz) Pima S-7, Li1, Li2, N1, Fbl,n2, SMA4, A1-97  Leaf morphology TMS-22 and WT936  Leaf morphological traits and chlorophyll content TM-1 and Hai 7124  Fiber quality traits TM1 and Pima 3-79  Leaf and stem pubescence Guazuncho 2 and VH8-4602  Fiber quality Guazuncho 2 and VH8  Lint percentage and ﬁber quality traits Yumian 1 and T586  Fiber traits Handan208 and Pima90  Fiber yield and yield components Handan 208 and Pima 90  Fiber quality and yield component Handan 208 and Pima 90  Fiber traits 7235, TM-1, HS427-10, PD6992 and SM3  Root-knot nematode resistance gene M-120 RNR and Pima S-6  Fiber and yield component traits 7235 and TM-1  Fiber quality and yield components 7235 and TM-1  Root-knot nematode resistance gene (rkn1) Acala SJ-2, Acala NemX, and Pima S-7  Root-knot nematode resistance gene (rkn1) Acala SJ-2 and Acala NemX  Root-knot nematode resistance gene Resistant near isoline and susceptible near isoline  Lint percentage and morphological marker genes TM-1 and T586  Fiber-related traits TM-1 and 3-79  Yield, yield component and ﬁber quality Near-isogenicBC5S1 chromosome substitution lines, TM-1  Plant architecture traits Zhongmiansuo12 and 8891  Fiber quality traits Zhongmiansuo12 and 8891  Yield and yield-component traits Zhongmiansuo12 and 8891  Interspeciﬁc cross. segregating population, and are readily subjected to varia- identiﬁed in cotton include yield and yield components, ﬁber tion of environments. With the increased availability of DNA quality, plant architecture, resistance to diseases such as bac- markersfor useincottongenetic mapconstructioninthe terial blight and Verticillium wilt, resistance to pests like root- last ten years, activities in identifying and locating quanti- knot nematode, and ﬂowering date. A list of QTLs mapped tative trait loci (QTLs) have blossomed. QTLs that have been in cotton is presented in Table 2. Hong-Bin Zhang et al. 7 Table 3: Upland cotton BAC and BIBAC libraries that have been published or are accessible to the public (as of May 2007). Mean insert References/locations where (a) Genotype No. of clones Genome equivalents Vector Cloning site size (kb) libraries are available Tamcot HQ95 51,353 2.3x pBeloBAC11 HindIII 93 http://hbz7.tamu.edu Auburn 623 44,160 2.7x pBeloBAC11 BamHI 140 http://hbz7.tamu.edu Texas Marker-1 76,800 4.4x pCLD04541 BamHI 130 http://hbz7.tamu.edu Texas Marker-1 76,800 6.0x pECBAC1 EcoRI 175 http://hbz7.tamu.edu Maxxa 129,024 8.3x pCUGI-1 HindIII 137  0-613-2R 97,825 5.7x pIndigoBAC-5 HindIII 130  (a) The vectors, pBeloBAC11 (Kim et al. ), pECBAC1 (Frijters et al. ), pCUGI-1 , and pIndigoBAC-5 (http://www.epibio.com/item.asp?ID=328), are BAC vectors whereas pCLD04541 is plant-transformation-competent BIBAC vector (http://www.jic.bbsrc.ac.uk/staﬀ/ian-bancroft/vectorspage.htm;) that can be directly transformed into cotton plants via Agrobacterium. Table 4: Summary of ESTs of major crops available in GenBank (as of April 27, 2007). (a) Species Genome No. of ESTs Cotton and related species (Gossypium species): G. hirsutum (Upland cotton) (AADD) 177,154 G. raimondii D D 63,577 5 5 G. arboreum A A 39,232 2 2 G. barbadense (Sea Island) (AADD) 1,023 G. herbaceum var. africanum A A 247 1 1 Total: 281,233 Rice and Related Species (Oryza species): O. sativa (rice) AA 1,211,447 O. minuta BBCC 5,760 O. grandiglumis CCDD 128 Total: 1,217,335 Maize and Related Species (Zea species): Z. mays (maize) 1,161,241 Total: 1,161,241 Wheat and Related Species (Triticum and Aegilops species): T. aestivum (wheat) AABBDD 1,050,131 T. monococcum AA 10,139 T. turgidum ssp. durum AABB 8,924 T. turgidum AABB 1,938 Ae. speltoides BB 4,315 Ae. tauschii DD 116 Total: 1,075,563 Soybean and Related Species (Glycine species): G. max (soybean) GG 371,817 G. soja GG 18,511 G. clandestina A A 931 1 1 Total: 391,259 (a) There is no relationship in the genome letter designation between genera, but there is a relationship in the genome letter designation between species within a genus, the species with the same genome letter being closely related. Several noteworthy ﬁndings have come out of QTL map- ing of tetraploid cottons has resulted in ﬁber with a higher ping in cotton. First, in tetraploid cottons, although the D- quality than those achieved by parallel improvement of the subgenome was derived from an ancestor that does not pro- A-genome diploid cottons which produce spinnable ﬁbers. duce spinnable ﬁbers, many QTLs inﬂuencing ﬁber quality The merger of the A- and D-genomes in tetraploid cot- traits were detected on the D-subgenome . For exam- tons, where each genome has a diﬀerent evolutionary his- ple, Jiang et al.  pointed out that D-subgenome QTLs tory, may have oﬀered unique avenues for phenotypic re- may partly explain the fact that domestication and breed- sponse to selection. Second, numerous studies have shown 8 International Journal of Plant Genomics Table 5: Summary of cotton ESTs (as of May 2007). Genotypes Library name Tissues used No. of ESTs No. of unigenes Authors References Gossypium arboreum (A ): 7- to 10-dpa ﬁbers Wing et al. AKA8401 GA-Ea 46,603 (normalized) Arpat et al.  Subtotal 46,603 13,947 G. Raimondii (D ): Whole seedlings GN34 GR Ea 33,671 Udall et al. with 1st true leaves −3-dpa buds to GN34 GR-Eb 33,061 Udall et al. +3-dpa bolls Subtotal 68,732 G. hirsutum (AD ): 8- to 10-dpa boll Coker 312 GH MD 1,144 Allen (irrigated) 8- to 10-dpa boll Coker 312 GH MDDS 1,238 Allen (drought stressed) 15- to 20-dpa boll Coker 312 GH LDI 1,799 Allen & Payton (irrigated) 15- to 20-dpa boll Coker 312 GH LDDI 1,409 Allen & Payton (drought stressed) Acala Maxxa GH BNL 5-dpa ﬁbers 8,022 Blewitt & Burr  0- to 5-dpa ovule and Xu-142 GH FOX 7,997 Gou & Chen 1- to 22-dpa ﬁbers 2nd versus 1st primary Haigler & Deltapine 90 GH SCW 7,385 ﬁbers Wilkerson Zhongmian 12 GH SUO 0-dpa ovules 1,240 Suo & Xue Deltapine 16 GH-CHX −3- to 0-dpa ovules 7,631 Wu & Dennis Deltapine 16 GH OCF 0-dpa ovules 867 Wu and Dennis 0-dpa ovules Deltapine 16 GH ON 5,903 Wu & Dennis (normalized) Stv 7A gl GH ECT 18 h etiolated seedlings 2,880 Chapman Delta emerald GH CRH Root and hypocotyls 1,464 Dowd & McFadden RH tissues infected with Dowd & Delta emerald GH CFUS 820 Fusarium oxysporum McFadden Faivre-Nitschke Sicot GH LSL S9i leaves, late season 1,810 & Dennis Coker 312 GH SDL Seedlings (control) 1,918 Klueva et al. Seedlings (drought Coker 312 GH SDLD 1,142 Klueva & Nguyen stressed) Seedling (chilling Coker 312 GH SDCH 576 Klueva & Nguyen stressed) Deltapine 16 GH IME Immature embryo 1,536 Liu & Dennis Leaf 8, 14, 20, 30, 45, Im216 GH IMX 1,134 Patil et al. 60 hpi Xanthomonas Leaf 8 + 14 hpi AcB4Blnb7 GH ACXE 647 Phillips et al. Xanthomonas Leaf 20 + 30 hpi AcB4Blnb7 GH ACXM 1,328 Phillips et al. Xanthomonas Leaf 45 + 60 hpi AcB4Blnb7 GH ACXL 862 Phillips et al. Xanthomonas Hong-Bin Zhang et al. 9 Table 5: Continued. Genotypes Library name Tissues used No. of ESTs No. of unigenes Authors References T25 GH pAR Leaves 1,230 Trolinder DES119 GH STEM Mature stem 8,643 Taliercio DP62 GH ECOT Etiolated cotyledon 2,772 Ni & Trelease 91-D-92 GH CBAZ Ball abscission zone 1,306 Wan & Wing (a) 185,198 51,107  Texas Marker-1 GH TMO −3- to 3-dpa ovules 32,789 8,540 Chen  −1 (TM-1) Not available 5- to 10-dpa ﬁbers 29,992 12,992 Zhu Xuzhou 142  (Xu-142) Subtotal 132,644 Total 247,979 (a) The number was the sum of numbers of all ESTs above the line including those of G. arboreum, G. raimondii and G. hirsutum . Of the 247,979 cotton ESTs, 187,014 (75.4%) were from developing ﬁbers or ovules whereas 160,965 (24.6%) from nonﬁber or nonovule organs. that QTLs occur in clusters genetically in the cotton genome [27, 46, 55, 56, 76, 106]. Ulloa et al.  suggested the pos- Random BACs sible existence of highly recombined regions in the cotton genome with abundant putative genes. QTL clusters might exert their multiple functions to compensate for a numerical deﬁciency, expanding their roles in cotton growth and devel- 200 kb opment . Finally, the position and eﬀect of QTLs for ﬁber 150 kb quality are not comparable in diﬀerent populations and en- 100 kb vironments evaluated [60, 106]. This suggests that QTL stud- 50 kb ies conducted thus far have detected only a small number of loci for ﬁber growth and development and that additional QTLs remain to be discovered [58, 59]. Furthermore, because quantitative traits are readily subjected to variation of envi- ronments, mapping eﬀorts of these traits need to be pursued in multiple environments including years and locations. Figure 2: BACs randomly selected from the TM-1/Eco RI BAC li- brary (see Table 3; C. Scheuring and H.-B. Zhang, unpublished). BAC DNA was isolated, digested with NotI, and run on a pulsed- 2.3. BAC and BIBAC resources ﬁeld gel. Large-insert BAC and BIBAC libraries have been demon- strated essential and desirable for advanced genomics and genetics research [107–111]. Because of their low-level chimerism, readily amenability to high-throughput puriﬁ- braries have been developed for several genotypes of Upland cation of cloned insert DNA, and high stability in the host cotton, G. hirsutum (Table 3). As of May 1, 2007, at least six BAC and BIBAC libraries have been developed and made cell [83, 112, 113], BACs and BIBACs have quickly assumed a central position in genome research. BAC and BIBAC li- available to the public. These libraries were constructed from braries have widely been used in many research areas of ge- ﬁve genotypes of Upland cotton, including Tamcot HQ95, nomics and molecular biology, including whole-genome or Auburn 623, TM-1, Maxxa, and 0-613-2R, in four BAC vec- chromosome physical mapping [110, 114–128], large-scale tors and one Agrobacterum-mediated, plant-transformation- genome sequencing [129–133], positional cloning of genes competent BIBAC vector with three restriction enzymes. and QTLs (for review, see ), isolation and characteriza- The libraries have average insert sizes ranging from 93 to tion of structural and regulatory genes [135, 136], long-range 175 kb and each have a genome coverage ranging from 2.3 to genome analysis [135, 136], organization and evolution of 8.3x genome equivalents, collectively covering >21x haploid multigene families , and cytologically physical mapping genomes of the polyploid cotton (Figure 2). Moreover, BAC . libraries have also been constructed for several other Gossyp- BAC libraries have been developed for a number of ium species, including G. barbadense (Pima S6), G. arboreum species, including plants, animals, insects, and microbes (AKA8401), G. raimindii,and G. longicalyx (A.H. Paterson, and made available to the public (http://hbz7.tamu.edu; pers. communication). These BAC and BIBAC libraries pro- http://bacpac.chori.org; http://www.genome.clemson.edu). vide resources essential for advanced genomics and genetics To facilitate cotton genome research, BAC and BIBAC li- research of cottons. λ ladder λ ladder 10 International Journal of Plant Genomics 2.4. ESTs, microarrays, and gene expression proﬁling there is also a signiﬁcant bias in the number of ESTs. Cot- ton ﬁber development is classiﬁed into four clearly character- ESTs ized, but overlapping stages, including ﬁber initiation (−3- to 5 dpa), elongation (5–25 dpa), secondary cell wall deposi- Cloning and sequencing of expressed gene sequence tags tion (15–45 dpa), and maturation/dehydration (45–70 dpa) (see Figure 3). All of the 187,080 ﬁber ESTs were generated (ESTs) by single sequencing pass from one or both ends of cDNA clones have been widely used to rapidly dis- from the ﬁbers or ﬁber-bearing ovules collected from the ﬁrst cover and characterize genes in a large-scale and high- three stages with 43.6% from the initiation stage, 46.5% from the elongation stage, and 5.7% from the secondary cell wall throughput manner. As have been done in many other plant and animal species of biological and/or econom- deposition stage. It is apparent that the number of ﬁber ESTs ical importance, signiﬁcant eﬀorts have been made to from the secondary cell wall deposition stage is much smaller generate ESTs in cottons. As of April 27, 2007, 281,233 than that of either initiation or elongation stage. Although ESTs have been available for the Gossypium species in the initiation and elongation stages are of signiﬁcance for the GenBank (Table 4; http://www.ncbi.nlm.nih.gov/dbEST). Of number of ﬁbers per seed and ﬁber length, the secondary cell these ESTs, 178,177 were from the polyploid cultivated cot- wall deposition stage is crucial to ﬁber strength. Of the 60,899 tons with 177,154 (63.0%) from G. hirsutum and 1,023 nonﬁber/nonovule ESTs, 66.0% were from seedlings, 14.2% from stems, and 2.4% from roots. (<1.0%) from G. barbadnese while 103,056 were from the related diploid species with 39,232 (13.9%) from G. ar- ThecottonESTshavebeenusedinseveral aspects, in- boreum (A ), 63,577 (22.6%) from G. raimondii (D ), and cluding development of genome-wide cotton microarrays 2 5 (see below), mining of SSRs (see above) and study of poly- 247 (<1.0%) from G. herbaceum (A ). This number of cot- ton ESTs, compared with that of ﬁve years ago, has been sig- ploidization. The development of the signiﬁcant numbers niﬁcantly increased, due to several large EST projects funded of ESTs from the cultivated tetraploid cotton, G. hirsutum [100–104]. Nevertheless, when compared with those of other [(AADD) ], and its closely related diploid species, G. ar- major crop species such as rice, maize, wheat, and soybean, boreum (A A )and G. raimondii (D D ) (see Table 5)made 1 1 5 5 it possible to compare the transcriptomes among the three the number of the cotton ESTs is very low, only being about one-forth of those of rice, maize, or wheat (Table 4). species. Udall et al.  comparatively analyzed 31,424, Table 5 summaries 247,979 ESTs of cottons published 68,732, and 69,853 ESTs derived from G. arboreum, G. rai- mondii,and G. hirsutum, respectively. Although the compar- [100, 102–104]. These ESTs were collectively generated from 32 cDNA libraries constructed from mRNA isolated from 18 ison was signiﬁcantly aﬀected by the tissue sources and de- genotypes of three species, G. hirsutum, G. arboreum, and G velopmental status, they identiﬁed the putative homoeologs raimondii, by one-pass sequencing of cDNA clones from one among the four genomes, A, D, A ,and D . This information 1 5 (3 or 5 end) or both ends. They were generated from 12 dif- is useful for our understanding of how the cotton genomes ferent organs, including developing ﬁbers, seedlings, buds, function and evolve during the courses of speciation, domes- bolls, ovules, roots, hypocotyls, immature embryos, leaves, tication, plant breeding, and polyploidization. stems, and cotyledons. Some of the ESTs were generated from plants growing under biotic or abiotic stress conditions Microarray such as drought, chilling, and pathogens. By analyzing ap- proximately 185,000 ESTs from both ﬁbers/ovules (124,299 Microarray has been a technology that is widely used in ESTs) and nonﬁber/ovule tissues (60,899 ESTs) of G. hirsu- many aspects of genomics research, including gene discovery, tum, G. arboreum and G. raimondii,Udall et al.ob- gene expression proﬁling, mutation assay, high-throughput tained 51,107 unigenes. A few months later, Yang et al.  genetic mapping, gene expression mapping (eQTL map- analyzed their 32,789 ESTs generated from −3- to +3-dpa ping), and comparative genome analysis. It involves roboti- ﬁbers of Upland cotton cv. TM-1, along with 211,397 cotton cally printing tens of thousands of cDNA amplicons or gene- ESTs downloaded from GenBank (as of April 2006), resulting speciﬁc long (70 mers) oligonucleotides as array elements on in 55,673 unigenes and updating The Institute of Genomic a chemically-coated glass slide, followed by hybridizing the Research Cotton Gene Index version 6 (CGI6) into CGI7 array with one or more ﬂuorescent-labeled cDNA or cRNA (http://www.tigr.org). The unigene EST number may pro- targets derived from mRNA isolated from particular tissues, vide a reasonable estimation about the number of expressed organs, or cells. Therefore, it allows the simultaneous mon- genes in the cotton genomes. Of the unigene set, those de- itoring of the expression/activities of all genes arrayed on rived from ﬁbers or ﬁber-bearing ovules suggest the number the array in a single hybridization experiment. To facilitate of genes potentially involved in ﬁber development and ge- cotton genomics research, microarrays have been developed netic complexity of ﬁber traits. from the cotton ESTs (Table 5)inseveral laboratories world- A predominant feature of the cotton EST set is the sig- wide. niﬁcant preference of their tissue sources for ﬁber or ﬁber- The ﬁrst batch of cotton microarrays was fabricated from bearing ovules than other organs. Of the 247,979 ESTs listed 70-mers oligos designed from the 7–10 dpa ﬁber nonredun- in Table 5, 187,080 (75.4%) were from developing ﬁbers or dant (NR) or unigene ESTs of G. arboreum (Table 5)(; ﬁber-bearing ovules while only 60,899 (24.6%) were from http://cottongenomecenter.ucdavis.edu/microarrays.asp). nonﬁber and nonovule organs. Within each of the two cate- Each microarray consists of 12,227 elements corresponding gories, ﬁber/ﬁber-bearing ovules and nonﬁber/ovule organs, to 12,227 NR ﬁber ESTs, with a duplicate of each element. Hong-Bin Zhang et al. 11 Flowers and balls Fibers under microscopes Maturation Elongation Fiber developmental 2 cell wall deposition stages Initiation −30 5 10 15 20 25 70 Days post anthesis (dpa) Figure 3: Cotton ﬁber development and corresponding morphogenesis stages (according to [138, 139]). The initiation stage is characterized by the enlargement and protrusion of epidermal cells from the ovular surface; during the elongation stage the cells expend in polar directions with a rate of >2 mm/day; during the secondary cell wall deposition stage celluloses are synthesized rapidly until the ﬁbers contain ∼90% of cellulose; and at the maturation stages minerals accumulate in the ﬁbers and the ﬁbers dehydrate. Using the microarrays, Arpat et al.  compared the 142 and using the amplicons of the EST clones as the ar- expression of the genes between 10-dpa ﬁbers at elongation ray elements. The microarrays each consist of 11,962 uniEST or primary cell wall synthesis stage and 24-dpa ﬁbers at elements. Using the microarrays, Shi et al. compara- secondary cell wall disposition stage (see Figure 3). The tively studied the wild-type Xuzhou 142 versus its fuzzless- expression of ﬁber genes was found to change dynamically lintless (ﬂ) mutation using the RNAs isolated from the ovules from elongation or primary cell wall to secondary cell wall at stages of 0-, 3-, 5-, 10-, 15-, and 20-dpa. It was found that biogenesis, with 2,553 of the ﬁber genes being signiﬁcantly ethylene biosynthesis is one of the most signiﬁcantly upreg- downregulated and 81 being signiﬁcantly upregulated. ulated biochemical pathways during ﬁber elongation. Sim- This result suggests that the expression of ﬁber genes is ilarly, Wu et al.  also fabricated a set of microarrays stage-speciﬁc or cell expansion-associated. Annotation of from amplicons of 10,410 cDNA clones derived from −3- the genes upregulated in the secondary cell wall synthesis to 0-dpa ovules of the Upland cotton cv. DP16 (see Table 5, relative to the primary cell wall biogenesis showed that Wu & Dennis). The arrays were analyzed with RNAs isolated most of the genes felt in three major functional categories, from 0-dpa whole ovules, outer integument, and inner in- energy/metabolism, cell structure, organization and biogen- tegument/nucellus of ﬁve lintless mutation lines against the esis, and cytoskeleton. This ﬁnding is consistent with the fact wild-type DP16. Of the 10,410 gene elements on the array, 60 of massive cellulose synthesis and cell wall biogenesis during to 243 were found to signiﬁcantly diﬀerentially express be- this stage. The ﬁber gene microarrays have been updated tween each pair of the wild type and mutant when the array was hybridized with the RNAs isolated from the 0-dpa whole recently by incorporating nearly 10,000 gene elements designed from the ﬁber and ovary ESTs of the tetraploid ovules. Of these diﬀerentially expressed genes, 70.6% were cultivated cotton, G. hirsutum (Table 5; T.A. Wilkins, pers. upregulated and 29.4% downregulated in the ﬁber mutant, communication). The current ﬁber microarrays each slide suggesting that the mutation caused not only gene down- consist of four duplicated arrays with 22,406 60-mers oligo regulation, but also gene upregulation. However, when the elements per array and a duplicate of each element (see, whole ovule was dissected into three layers, outer integu- e.g., Figure 4). The new version of ﬁber gene arrays covers ment, inner integument, and nucellus, of which cotton ﬁbers 100% of the ﬁber ESTs of diploid cotton and 65% of the develop from the epidermal cells of the outer integument, ﬁber ESTs of the tetraploid cultivated cotton, G. hirsutum and analyzed with the outer integument against the inner in- that are available in GenBank, thus representing the most tegument and the nucellus, the number of the genes down- comprehensive coverage of the cotton ﬁber genes. The regulated in the mutants was reduced to 13. These include elements are printed on a slide in a randomized manner an Myb transcription factor, a putative homeodomain pro- instead of the conventional ordered manner. The fabrication tein, a cyclin D gene, and some ﬁber-expressed structural and of four duplicated arrays per slide and randomized printing metabolic genes, suggesting that these genes may be involved design have signiﬁcantly minimized the systematic problems in the process of ﬁber initiation. that are frequently encountered in the conventional array In summary, three batches of EST- or cDNA-based cot- design (one array per slide and ordered printing), thus ton microarrays were fabricated from ﬁber genes of either further enhancing the reproducibility and accuracy of the cultivated tetraploid cotton, G. hirsutum [104, 140], or cul- microarray analysis results. tivated diploid cotton, G. arboreum . Using the mi- Recently, several additional batches of EST- or cDNA- croarrays, the expression of the ﬁber genes was proﬁled based microarrays with diﬀerent formats and elements have and comparatively analyzed at ﬁber initiation stage , been reported in cotton [102, 104, 140]. Shi et al. re- elongation stage [100, 104], and secondary cell wall depo- ported the fabrication of microarrays from unigene ESTs de- sition stage . However, the expression of other cot- rived from 5–10 dpa ovules of the Upland cotton cv. Xuzhou ton genes such as those from nonﬁber and nonovary tissues 12 International Journal of Plant Genomics remains to proﬁle. To ﬁll this gap, another two batches of of Georgia (Athens, Georgia) is also working toward devel- long oligo-based microarrays have been developed. The ﬁrst opment of a whole-genome BAC-based physical map of the batch contains approximately 21,000 gene elements per ar- diploid species, G. raimondii (A.H.Paterson, pers.commu- ray (http://cotton.agtec.uga.edu/CottonFiber/pages/mcriar- nication). Given the importance of physical maps for mod- ray/Array.aspx). These genes were from 52 cDNA libraries ern genome research, there is no doubt that development of a constructed from a variety of tissues and organs in a robust integrated physical/genetic map will greatly promote range of conditions, including drought stress and pathogen advanced genomics research of cottons and related species challenges, and represents tetraploid (G. hirsutum) and its (also see below). diploid relatives (G. arboreum and G. raimondii). Of the 21,000 genes, approximately one-forth were from ﬁber genes 2.6. Genome sequencing and three-forth were from nonﬁber and nonovary tissues (J. A. Udall, pers. communication). The second batch contains 38,716 gene elements per array. Of the gene elements, 22,409 Sequence maps represent the most-ﬁne physical maps of are designed from ﬁber ESTs and 16,307 from nonﬁber ESTs genomes . They provide not only physical positions of (T.A. Wilkins, pers. communication). There is no doubt that and distances between genes and other components consti- these versions of cotton microarrays will provide new tools tuting a genome , but also their sequences and putative for comprehensive functional and comparative genomics re- functions inferred from the sequences. Therefore, develop- search of cottons. ment of a complete genome sequence map of a species will signiﬁcantly promote genomics research of the species in a variety of aspects. Because of this reason, the whole genomes 2.5. Physical mapping of several plant and animal species have been sequenced. In Whole-genome, BAC- and/or BIBAC-based, integrated plants, the genomes of two model species, Arabidopsis  physical/genetic maps have played a central role in genomics and rice , have been completely sequenced and the research of humans, plants, animals, and microbes [110, genomes of several other species, including Medicago trun- 123, 127]. This is because they provide central platforms catula (http://www.medicago.org), Lotus japonicus (http:// for many areas, if not all, of modern genomics research, www.kazusa.or.jp/lotus), tomato (http://www.sgn.cornell including large-scale transcript or gene mapping, region- .edu/about/tomato sequencing.pl), maize (http://www.mai- targeted marker development for ﬁne mapping and MAS zegenome.org), and soybean (http://genome.purdue.edu/ of genes and QTLs, map-based gene/QTL cloning, local- isgc/Tsukuba07/ISGC report Apr2007.htm), are currently and whole-genome comparative analysis, genome sequenc- being sequenced. ing, and functional analysis of DNA sequences and com- However, there is only a limited amount of genomic se- ponent network. Therefore, whole-genome, BAC/BIBAC- quences available for cotton and related species in GenBank. based, integrated physical/genetic maps have been developed A major source of the genomic sequences of Gossypium for a number of plant and animal species. In plants, whole- species was from Hawkins et al. . To understand the genome BAC physical maps have been developed for sev- underlying genome size variation and evolution of Gossyp- eral species, including Arabidopsis [114, 118], indica rice ium species, Hawkins et al. constructed whole-genome , japonica rice , soybean , and maize . shotgun libraries for G. raimondii (D D ), G. herbaceum 5 5 However, whole-genome physical maps of cottons have only (A A ), G. exiguum (KK), and the species that was used 1 1 been initiated in several laboratories. One is the labora- as the outgroup species for phylogenetic analysis of the tory of H.-B. Zhang, Texas A&M University, College Station Gossypium species, Gossypioides kirkii,witheachspecies (Texas, USA). This laboratory is developing a whole-genome library containing 1920–10,368 clones. From each of the BAC/BIBAC physical map of the Upland cotton cv. TM-1 four shotgun libraries, 1,464–6,747 clones were sequenced, by using the latest physical mapping technology [123, 126]. together covering a total length of 11.4 Mb. Annotation of these clone sequences and estimation of the copy number The project was a collaborative eﬀort among the laborato- ries of H.-B. Zhang, R. J. Kohel, USDA/ARS, College Sta- of each type of the sequences suggested that diﬀerential tion (Texas, USA) (who provided a part of the fund for the lineage-speciﬁc ampliﬁcation of transposable elements is re- project), and D. M. Stelly, Texas A&M University (Texas, sponsible for genome size variation in the Gossypium species. USA). Nearly 120,000 (∼7.3x) BIBACs and BACs selected Moreover, G. raimondii has been selected recently by the from the TM-1 BIBAC and BAC libraries (see Table 3)have DOE Joint Genome Institute, U.S. Department of Energy to been ﬁngerprinted and a draft BAC/BIBAC contig map has be sequenced for genomic study of cotton and related species been constructed. The draft physical map consists of 5,088 (http://www.jgi.doe.gov/sequencing/cspseqplans2007.html). contigs collectively spanning approximately 2,300 Mb of the At the ﬁrst phase of the sequencing project, a whole-genome 2,400 Mb Upland genome (unpublished). Currently, addi- shotgun library covering about 1x of the G. raimondii tional clones (to reach about 10x genome coverage clones) genome will be sequenced. While this number is far from the are being analyzed. Furthermore, because the Upland cot- genome coverage of clones (>6x) that is needed to assemble ton is an allotetraploid which makes the physical map con- the sequence map of the genome, it will provide the ﬁrst struction more complicated, several approaches are being glimpse into the cotton genome and useful information for used to sort the map contigs according to their origin of sequencing the entire genomes of this and other cotton key subgenomes. The laboratory of A. H. Paterson, University species eﬃciently. Hong-Bin Zhang et al. 13 3. APPLICATIONS OF GENOMIC TOOLS IN trait indicates that maximum genetic gain will require breed- COTTON GENETIC IMPROVEMENT ing eﬀorts that target each trait. Lacape et al. performed QTL analysis of 11 ﬁber properties in BC ,BC ,and BC S 1 2 2 1 One of the major goals of genome research is to use the ge- backcross generations derived from the cross between G. hir- nomic tools developed to promote or assist continued crop sutum “Guazuncho 2” and G. barbadense “VH8.” They de- genetic improvement. In cottons, the development of the tected 15, 12, 21, and 16 QTLs for length, strength, ﬁne- genomic resources and tools has allowed addressing many ness, and color, respectively, in one or more populations. signiﬁcantly scientiﬁc questions that are impossible to do The results showed that favorable alleles came from the G. so before. These include, but not limited to, construction barbadense parent for the majority of QTLs, and cases of of genome-wide genetic maps (Table 1), identiﬁcation and colocalization of QTLs for diﬀerent traits were more fre- mapping of genes and loci controlling traits underlying qual- quent than isolated positioning. Taking these QTL-rich chro- itative and quantitative inheritance (Table 2), determination mosomal regions into consideration, they identiﬁed 19 re- of mechanisms of cotton genome evolution, and identiﬁca- gions on 15 diﬀerent chromosomes as target regions for tion and determination of genes that are involved in cotton the marker-assisted introgression strategy. The availability of ﬁber initiation, elongation, and secondary cell wall biogene- DNA markers linked to G. barbadense QTLs promises to as- sis. The genomic resources and tools could be used to pro- sist breeders in transferring and maintaining valuable traits mote or facilitate cotton genetic improvement in numerous from exotic sources during cultivar development. ways. Marker-assisted selection (MAS) is likely one of the most important and practical applications at present time Cytoplasmic male sterility and in near future. The MAS technology could oﬀer many potential beneﬁts to a breeding program. For instance, DNA In cotton, cytoplasmic male sterility conditioned by the D8 linked to a gene of interest could be utilized in early genera- alloplasm (CMS-D8) is independently restored to fertility by tion of breeding cycle to improve the eﬃciency of selection. its speciﬁc D8 restorer (D8R) and by the D2 restorer (D2R) This approach has a particular advantage when screening for that was developed for the D2 cytoplasmic male sterile allo- phenotypes in which the selection is expensive or diﬃcult to plasm (CMS-D2). Zhang and Stewart  concluded that perform, as is the case involving recessive or multiple genes, the two restorer loci are nonallelic, but are tightly linked with seasonal or geographical considerations, and late expression an average genetic distance of 0.93 cM. The D2 restorer gene of the phenotype . However, application of MAS in cot- is redesignated as Rf1,and Rf2 is assigned to the D8 restorer ton breeding programs is still in its infancy as the major eﬀort gene. The identiﬁcation of molecular markers closely linked of cotton genome research in the past has been on the devel- to restorer genes of the cytoplasmic male sterile could fa- opment of genomic resources and tools for the eventual goal cilitate the development of parental lines for hybrid cotton. of enhanced cotton genetic improvement. Guo et al.  found that one RAPD marker fragment, des- ignated OPV-15(300), was closely linked with the fertility- restoring gene Rf1. Zhang and Stewart  identiﬁed RAPD Fiber quality markers linked to the restorer gene and, furthermore, con- verted the three RAPD markers into reliable and genome- Zhang et al. useda G. anomalum introgression line 7235 with good ﬁber quality properties to identify molec- speciﬁc sequence tagged site (STS) markers. Liu et al.  ular markers linked to ﬁber-strength QTLs. A major QTL, determined that the Rf1 locus is located on the long arm QTLFS1, was detected at the Nanjing and Hainan ﬁeld loca- of chromosome 4. Two RAPD and three SSR markers were tions (China) and College Station, Texas, (USA). This QTL identiﬁed to be closely linked to the Rf1 gene. These mark- was associated with eight markers and explained more than ers are restorer-speciﬁc and should be useful in MAS for de- 30% of the phenotypic variation. QTLFS1 was ﬁrst thought veloping restorer parental lines. Yin et al.  further con- to be mapped to chromosome 10, however, further study structed a high-resolution genetic map of Rf1 containing 13 markers in a genetic distance of 0.9 cM. They constructed a showed that this QTL was located on LGD03 . Guo et al.  showed that the speciﬁc SCAR4311920 marker could physical map for the Rf1 locus and enclosed the possible loca- be applied to large-scale screening for the presence or ab- tion of the Rf1 gene to a minimum of two BAC clones span- ning an interval of approximately 100 kb between two clones, sence of this major ﬁber strength QTL in breeding popu- lations. The DNA markers tightly linked to this QTL could designated as 081-05K and 052-01N. Work to isolate the Rf1 be useful for developing commercial cultivars with enhanced gene in cotton is now in progress. ﬁber length properties . Wang et al.  identiﬁed a stable ﬁber length QTL, qFL- Resistance to diseases and insect pests D2-1, simultaneously in four environments in Xiangzamian 2. The high degree of stability suggests this QTL might be Breeding for disease resistance is of great importance in cot- particularly valuable for use in MAS programs. Chee et al. ton breeding program. To facilitate analysis, cloning, and  dissected the molecular basis of genetic variation gov- manipulation of the genes conferring resistance to diﬀer- erning 15 parameters that reﬂect ﬁber length by applying ent pathogens, including bacteria, fungi, viruses, and nema- a detailed RFLP map to 3,662 BC F plants from 24 inde- todes, He et al.  isolated and characterized the family 3 2 pendently derived BC families utilizing G. barbadense as the of nucleotide-banding site-leucine-rich repeat (NBS-LRR)- donor parent. The discovery of many QTLs unique to each encoding genes or resistance gene analogues (RGAs) in the 14 International Journal of Plant Genomics Upland cotton cv. Auburn 634 genome. Genetic mapping of a sample (21 genes) of the RGAs indicated that the gene fam- ily resides on a limited number of the cotton AD-genome chromosomes with those from a single subfamily tending to cluster on the cotton genetic map and more RGAs in the A subgenome than in the D subgenome. Of the 16 RGAs mapped, two happened to be comapped with the cotton bac- terial blight resistance QTLs previously mapped by Wright et al. . Since nearly 80% of the genes (>40 genes) cloned to date that confer resistance to bacteria, fungi, viruses, and Figure 4: Comparative analysis of the expression of ﬁber genes in 10-dpa ﬁbers between G. hirsutum and G. barbadense (M. Goebel, nematodes are contributed by the NBS-LRR gene family, the M. Alabady, C.W. Smith, T. A. Wilkins and H.-B. Zhang, unpub- cotton RGAs of the NBS-LRR family have provided valuable lished). The cotton ﬁber microarrays are available in the laboratory tools for cloning, characterization, and manipulation of the of T. A. Wilkins, Texas Tech University (Texas, USA). One of the resistant genes to diﬀerent pathogens and pests in cottons. four arrays printed on a single slide is shown. Root-knot nematodes (RKN), Meloidogyne incognita,can cause severe yield loss in cotton. Wang et al.  identiﬁed one SSR marker CIR316 on the linkage group A03 tightly linked to a major RKN resistant gene (rkn1) in the resistant plant biology in general and to cotton in particular. Never- cultivar G. hirsutum “Aacla NemX.” In a companion study, theless, many eﬀorts are needed to further develop the re- a bulked segregant analysis (BSA) combined with AFLP was sources and tools and to make the tools readily usable in ap- used to identify additional molecular markers linked to rkn1 plications in order to fully and eﬀectively use them in cotton . An AFLP marker linked to rkn1 designated as GHACC1 genetic improvement and biology research. In particular, the was converted to a cleaved ampliﬁed polymorphic sequence following areas of cotton genomics research should be em- (CAPS) marker. These two markers have potential for uti- phasized. lization in MAS. Shen et al.  identiﬁed RFLP markers on (i) Development of whole-genome BAC/BIBAC-based, in- chromosome 7 and chromosome 11 showing signiﬁcant as- tegrated physical maps of cottons. There is no whole-genome, sociation with RKN resistance from the Auburn 634 source, robust BAC/BIBAC-based, integrated physical/genetic map adiﬀerent source of resistant germplasm than Acala NemX. that has been developed for cottons. The maps should be The association was further conﬁrmed by detection of a mi- developed for at least two species of Gossypium. One is nor and a major dominant QTL on chromosomes 7 and 11, the Upland cotton that produces >90% of the world’s cot- respectively, using SSR markers. Ynturi et al.  identiﬁed ton whereas the other is G. raimondii, the species hav- two SSR markers which together accounted for 31% of the ing the smallest genome among all Gossypium species, variation in galling index. The marker BNL 3661 is mapped thus likely having highest density of genes. This research to the short arm of chromosome 14 while BNL 1231 to the is emphasized because it has been proven in model and long arm of chromosome 11. The association of two diﬀer- other species, including Arabidopsis,rice, Drosophila,human, ent chromosomes with RKN resistance suggests at least two mouse, and chicken, that whole-genome integrated physi- genes are involved in resistance to RKN. cal/genetic maps provide powerful platforms and “freeways” Bacterial blight caused by the pathogen Xanthomonas for many, if not all, modern genetics and genomics research campestris pv. malvacearum (Xcm) is another economically ([110, 123, 127]; see above). These include not only genome important disease in cotton. Wright et al.  and Rungi sequencing (see below), but also development of closely et al.  both used mapped RFLP markers to investigate linked, user-friendly DNA markers for any region or loci of the chromosomal location of genes conferring resistance to the genome, ﬁne QTL and gene mapping (see below), map- the bacterial blight pathogen. The mapping data suggest that based gene/QTL cloning, and high-throughput and high- the resistance locus segregates with a marker on chromo- resolution transcript (unigene EST) mapping . Devel- some 14 known to be linked to the broad-spectrum B12 re- opment of the integrated physical maps will allow rapidly sistance gene originally from African cotton cultivars. AFLPs and eﬃciently integrating all existing genetic maps, mapped and SSRs were also used to search for novel markers linked genes and QTLs, and BAC and BIBAC resources and cotton to the Xcm resistance locus to facilitate introgression of this unigene ESTs, and accelerate the eﬃciency and reduce the trait into G. barbadense through MAS. cost of research in all areas by manifold. (ii) QTL ﬁne mapping. Many genes and QTLs that are important to cotton ﬁber yield ﬁber quality, and biotic and 4. CONCLUDING REMARKS abiotic stresses have been genetically mapped, but two prob- A signiﬁcant amount of genomic resources and tools has lems are apparent. The ﬁrst one is that almost all of the QTLs been available in cottons though cotton genomics research were mapped using F ,BC , or early segregating generations 2 1 is far behind those of other major crops such as rice, maize, in a single or a limited number of environments (Table 2). wheat, and soybean. These resources and tools have allowed Since quantitative traits are readily subjected to environmen- identifying and mapping many genes and QTLs of impor- tal variation, the mapping results using the early generations tance to cotton ﬁber quality, ﬁber yield, and biotic and abi- in a single or a limited number of environments would vary otic stresses and addressing several signiﬁcant questions to from experiments to experiments [59, 60, 106]. The other Hong-Bin Zhang et al. 15 problem is that the genetic distances between DNA markers sisting in cotton breeding. The genes that are involved in ﬁber and most of the QTLs are too far to be used for MAS. There- initiation [104, 140], elongation [100, 104], and secondary fore, it is of signiﬁcance to ﬁne map the QTLs using large and cell wall deposition  have been identiﬁed from several advanced generation or homozygous populations, such as genotypes of cottons, but it is unknown about what the up- RILs and DHs, in multiple environments, and closely linked or downregulation, or active expression of ﬁber genes at a de- DNA markers, for which advantage of integrated physical velopmental stage and organ means to ﬁnal ﬁber yield and/or maps could be taken. In addition to accurate mapping of the quality. For instance, does the active expression of a gene at QTLs and development of DNA markers that are well-suited ﬁber elongation stage in ﬁber suggest longer ﬁbers? 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