Despite rapidly decreasing costs and innovative technologies, sequencing of angiosperm genomes is not yet undertaken lightly. Generating larger amounts of sequence data more quickly does not address the difficulties of sequencing and assembling complex genomes de novo. The cotton (Gossypium spp.) genomes represent a challenging case. To this end, a coalition of cotton genome scientists has developed a strategy for sequencing the cotton genomes, which will vastly expand opportunities for cotton research and improvement worldwide.

The narrow genetic base of cultivated cotton germplasm is hindering the cotton productivity worldwide. Although potential genetic diversity exists in Gossypium genus, it is largely 'underutilized' due to photoperiodism and the lack of innovative tools to overcome such challenges. The application of linkage disequilibrium (LD)-based association mapping is an alternative powerful molecular tool to dissect and exploit the natural genetic diversity conserved within cotton germplasm collections, greatly accelerating still 'lagging' cotton marker-assisted selection (MAS) programs. However, the extent of genome-wide linkage disequilibrium (LD) has not been determined in cotton. We report the extent of genome-wide LD and association mapping of fiber quality traits by using a 95 core set of microsatellite markers in a total of 285 exotic Gossypium hirsutum accessions, comprising of 208 landrace stocks and 77 photoperiodic variety accessions. We demonstrated the existence of useful genetic diversity within exotic cotton germplasm. In this germplasm set, 11-12% of SSR loci pairs revealed a significant LD. At the significance threshold (r(2)>/=0.1), a genome-wide average of LD declines within the genetic distance at <10 cM in the landrace stocks germplasm and >30 cM in variety germplasm. Genome wide LD at r(2)>/=0.2 was reduced on average to approximately 1-2 cM in the landrace stock germplasm and 6-8 cM in variety germplasm, providing evidence of the potential for association mapping of agronomically important traits in cotton. We observed significant population structure and relatedness in assayed germplasm. Consequently, the application of the mixed liner model (MLM), considering both kinship (K) and population structure (Q) detected between 6% and 13% of SSR markers associated with the main fiber quality traits in cotton. Our results highlight for the first time the feasibility and potential of association mapping, with consideration of the population structure and stratification existing in cotton germplasm resources. The number of SSR markers associated with fiber quality traits in diverse cotton germplasm, which broadly covered many historical meiotic events, should be useful to effectively exploit potentially new genetic variation by using MAS programs.

Cotton is the world's leading cash crop, but it lags behind other major crops for marker-assisted breeding due to limited polymorphisms and a genetic bottleneck through historic domestication. This underlies a need for characterization, tagging, and utilization of existing natural polymorphisms in cotton germplasm collections. Here we report genetic diversity, population characteristics, the extent of linkage disequilibrium (LD), and association mapping of fiber quality traits using 202 microsatellite marker primer pairs in 335 G. hirsutum germplasm grown in two diverse environments, Uzbekistan and Mexico. At the significance threshold (r (2) >or= 0.1), a genome-wide average of LD extended up to genetic distance of 25 cM in assayed cotton variety accessions. Genome wide LD at r (2) >or= 0.2 was reduced to approximately 5-6 cM, providing evidence of the potential for association mapping of agronomically important traits in cotton. Results suggest linkage, selection, inbreeding, population stratification, and genetic drift as the potential LD-generating factors in cotton. In two environments, an average of ~20 SSR markers was associated with each main fiber quality traits using a unified mixed liner model (MLM) incorporating population structure and kinship. These MLM-derived significant associations were confirmed in general linear model and structured association test, accounting for population structure and permutation-based multiple testing. Several common markers, showing the significant associations in both Uzbekistan and Mexican environments, were determined. Between 7 and 43% of the MLM-derived significant associations were supported by a minimum Bayes factor at 'moderate to strong' and 'strong to very strong' evidence levels, suggesting their usefulness for marker-assisted breeding programs and overall effectiveness of association mapping using cotton germplasm resources.

Genetic linkage maps play fundamental roles in understanding genome structure, explaining genome formation events during evolution, and discovering the genetic bases of important traits. A high-density cotton (Gossypium spp.) genetic map was developed using representative sets of simple sequence repeat (SSR) and the first public set of single nucleotide polymorphism (SNP) markers to genotype 186 recombinant inbred lines (RILs) derived from an interspecific cross between Gossypium hirsutum L. (TM-1) and G. barbadense L. (3-79). The genetic map comprised 2072 loci (1825 SSRs and 247 SNPs) and covered 3380 centiMorgan (cM) of the cotton genome (AD) with an average marker interval of 1.63 cM. The allotetraploid cotton genome produced equivalent recombination frequencies in its two subgenomes (At and Dt). Of the 2072 loci, 1138 (54.9%) were mapped to 13 At-subgenome chromosomes, covering 1726.8 cM (51.1%), and 934 (45.1%) mapped to 13 Dt-subgenome chromosomes, covering 1653.1 cM (48.9%). The genetically smallest homeologous chromosome pair was Chr. 04 (A04) and 22 (D04), and the largest was Chr. 05 (A05) and 19 (D05). Duplicate loci between and within homeologous chromosomes were identified that facilitate investigations of chromosome translocations. The map augments evidence of reciprocal rearrangement between ancestral forms of Chr. 02 and 03 versus segmental homeologs 14 and 17 as centromeric regions show homeologous between Chr. 02 (A02) and 17 (D02), as well as between Chr. 03 (A03) and 14 (D03). This research represents an important foundation for studies on polyploid cottons, including germplasm characterization, gene discovery, and genome sequence assembly.

Chromosome identities were assigned to 15 linkage groups of the RFLP joinmap developed from four intraspecific cotton (Gossypium hirsutum L.) populations with different genetic backgrounds (Acala, Delta, and Texas Plains). The linkage groups were assigned to chromosomes by deficiency analysis of probes in the previously published joinmap, based on genomic DNA from hypoaneuploid chromosome substitution lines. These findings were integrated with QTL identification for multiple fiber and yield traits. Overall results revealed the presence of 63 QTLs on five different chromosomes of the A subgenome (chromosomes-03, -07, -09, -10, and -12) and 29 QTLs on the three different D subgenome (chromosomes-14 Lo, -20, and the long arm of -26). Linkage group-1 (chromosome-03) harbored 26 QTLs, covering 117 cM with 54 RFLP loci. Linkage group-2, (the long arm of chromosome-26) harbored 19 QTLs, covering 77.6 cM with 27 RFLP loci. Approximately 49% of the putative 92 QTLs for agronomic and fiber quality traits were placed on the above two major joinmap linkage groups, which correspond to just two different chromosomes, indicating that cotton chromosomes may have islands of high and low meiotic recombination like some other eukaryotic organisms. In addition, it reveals highly recombined and putative gene abundant regions in the cotton genome. QTLs for fiber quality traits in certain regions are located between two RFLP markers with an average of less than one cM (approximately 0.4-0.6 Mb) and possibly represent targets for map-based cloning. Identification of chromosomal location of RFLP markers common to different intra- and interspecific-populations will facilitate development of portable framework markers, as well as genetic and physical mapping of the cotton genome.

Interspecific chromosome substitution is among the most powerful means of introgression and steps toward quantitative trait locus (QTL) identification. By reducing the genetic ''noise'' from other chromosomes, it greatly empowers the detection of genetic effects by specific chromosomes on quantitative traits. Here, we report on such results for 14 cotton lines (CS-B) with specific chromosomes or chromosome arms from G. barbadense L. substituted into G. hirsutum and chromosome-specific F 2 families. Boll size, lint percentage, micronaire, 2.5% span length, elongation, strength, and yield were measured by replicated field experiments in five diverse environments and analyzed under an additive-dominance (AD) genetic model with genotype and environment interaction. Additive effects were significant for all traits and dominance effects were significant for all traits except 2.5% span length. CS-B25 had additive effects increasing fiber strength and fiber length and decreasing micronaire. CS-B16 and CS-B18 had additive effects related to reduced yields. The results point toward specific chromosomes of G. barbadense 3-79 as the probable locations of the genes that significantly affect quantitative traits of importance. Our results provided a scope to analyze individual chromosomes of the genome in homozygous and heterozygous conditions and thus detected novel effects of alleles controlling important QTL.

The cultivated Gossypium spp. (cotton) represents the single most important, natural fiber crop in the world. In addition to its fiber, the oil and protein portion of the cottonseed also represents significant economic value. To protect the worldwide economic value of cotton fiber and cotton byproducts, coordinated efforts to collect and maintain cotton genetic resources have increased over the last 100 yr. The classified genetic resources of cotton are extensive and include five tetraploid species in the primary gene pool, 20 diploid species in the secondary gene pool, and 25 diploid species in the tertiary gene pool. This report provides information on the status and contents of eight major cotton germplasm collections present across the world. Based on the findings of this report, a number of classified Gossypium species are not maintained in these collections, and several are underrepresented and vulnerable to extinction. This report presents several critical challenges and opportunities facing international efforts to enhance and preserve the world's Gossypium genetic resources. Multinational communication and collaboration are essential to protect, secure, and evaluate the global cotton germplasm resources. Without global, collaborative efforts, the rarest and most unique cotton germplasm resources are vulnerable to extinction.

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