Germplasm and Genetic Stocks

The U.S. Cotton Germplasm Collection is the largest publicly available cotton collection worldwide, serving as a rich resource for cotton improvement and genetic research. The collection faces two major challenges: meeting the steadily increasing demand for seed and information from the germplasm collection in the face of static or decreasing budget resources, and improving the management and knowledge database of the collection. Reducing bottlenecks and streamlining operations is one approach to better handle the workload. Barcoding the collection and harvested samples, integrating with electronic counting scales, and improvements in cultural practices are ways to shorten times to produce and process seed. Collection of standardized morphological descriptors and field notes with electronic field tablets and collecting digital images in formats that are readily shared with the cotton community have been instituted to improve the collection database. Digital images are obtained to document reference vouchers and provide detailed examples of morphological descriptors used to characterize the collection. A more comprehensive, up to date, and interactive database is an expected outcome with our goal of improving the utility, management, and presentation of the collection for both the curator and user. This is also the prerequisite for scientific study of the collection (e.g. molecular markers), recruiting collaboration/feedback on observations of the collection, and comparisons with worldwide cotton collections for optimum use and conservation of Gossypium.

Salinity resistance and differential gene expression associated with salinity in cotton germplasm were studied, according to the large scale of saline area in China and its negative significant effects on the cotton production. The salinity-resisted genes and their differential expression were studied under the stress of NaCl on cotton. There found, under the NaCl stress, 1644 genes differentially expressed from the salinity-sensitive cotton and only 817genes differentially expressed from the salinity-resisted cotton. The differential expressed genes could be divided into five groups according to the expressed levels by the cluster analysis. Two genes were excavated by gene chips and SSH librarys, cloned by RACE and RT-PCR, named GhPTAC and GhGnT separately. Salt-resistant related expression analysis studied for the two genes by Real-time PCR. More in-depth researches for GhGnT gene were studied by GFP sub-cellular localization and yeast expression technology. The full length cDNA sequences of GhPTAC and GhGnT were obtained by RACE technology combined with RT-PCR. The full length of GhPTAC is 1564bp, including 5'-UTR 41bp, complete ORF 1038bp and 3'-UTR 485bp, which encodes a polypeptide of 345 amino acids. The full length of GhGnT is 2140bp, including 5'-UTR 587bp, complete ORF 1353bp, 3'-UTR 200bp, and PolyA 27bp, which encodes a polypeptide of 450 amino acids.

Genetically improved cottonseed with high protein content and low or no gossypol content could be suitably processed for human and animal consumption. In the present study, quantitative trait loci (QTL) associated with the genetic effects including QTL main effects and QTL × environment interaction effects from tetroploid maternal plant genome and tetroploid embryo genome were simultaneously identified for protein and gossypol contents of cottonseeds. This is to help understand the QTL and QTL × environment interactions from embryo and maternal genomes for these two traits, and provide more effective information for their improvement in cottonseed through maker-assisted selection. The experiment was carried out on an immortal F2 population comprising 376 lines obtained among 188 recombinant inbred lines (RILs) derived from a cross between parents HS46 and MARKCBUCAG8US-1-88, grown in 2009 and 2010. Twelve QTL for protein content (PC) and ten for gossypol content (GC) were detected using a genetic linkage map comprising 388 molecular markers. Among them, five QTL for gossypol content and six QTL for protein content were found in two different environments, explaining 62.95 and 58.52% of phenotypic variances, respectively. A total of nine QTL were associated with these two traits, which were subsequently mapped to chromosome 3, 5, 6, 15, 18, 22 and 25. Six of these QTL were also found to have environmental interaction effects. The results from this study could be very useful in adopting effect strategies for protein improvement and gossyopol elimination in cottonseeds.

Cultivated Upland cotton (Gossypium hirsutum) has very low genetic diversity. Therefore, to differentiate closely-related cotton cultivars or to conduct a genome-wide association-based molecular breeding project requires a large number of polymorphic markers with good genome coverage. In this study, 1555 mapped simple sequence repeat (SSR) markers were screened for their polymorphisms within elite Upland cotton. Out of 925 polymorphic markers, 448 were selected to form the highly informative marker set. Seventy-five multiplex PCR bins were designed to amplify these markers. The 448 markers were used to genotype 193 elite Upland cotton cultivars from 26 countries. These markers revealed 1590 alleles belonging to 732 loci that covered the genome. The average polymorphism information content of the polymorphic loci was 0.287, and all sampled cultivars could be differentiated using this set of markers. Intra-cultivar polymorphism was mainly due to heterogeneity and present in most cultivars. No clear population structure was observed among the sampled cultivars, an indication that very few contributing ancestors were involved in the creation of modern Upland cotton cultivars around the world and that extensive blending of the variability present had occurred. However, some grouping was possible; allowing the sampled cultivars to be classified into nine groups. Clustering results were largely congruent with the breeding history and pedigrees of the cultivars. The marker set developed here along with their profiles in elite Upland cotton will provide cotton scientists with very useful information and efficient tools in their genetic and breeding studies.

A core set of SSR markers were employed to develop accession profiles and analyze genetic relationships among 2,254 plant introductions of cotton (Gossypium spp.) including wild species, landraces, and adapted cultivars from around the world as represented in the US Cotton Germplasm Collection. Eight diploid genomes representing 28 species and 272 accessions along with one tetraploid genome representing six species and 1,982 accessions were genotyped with a set of 104 SSR markers. These SSRs are evenly distributed throughout the genome with two markers per chromosome arm. Due to bulking of ten individuals and amplification of duplicated homeologous loci, SSRs could not be reliably scored as co-dominant markers. Instead, the results were scored as a dominant (AFLP-type) marker system. A total of 1,702 polymerase chain reaction fragments (bands) were scored and all were found to be polymorphic across this set of accessions. The tetraploid accessions had more polymorphic bands (79.8%) than the diploid accessions (13.6%). The overall PIC value was 0.077 and ranged from 0.003 in the F diploid genome represented by G. longicalyx to 0.073 in the AD tetraploid genome represented by six species. Molecular characterization efforts continue with multivariate analysis of genetic relationships between individual accessions, species, and genomes. This molecular information will be further analyzed and used in the identification of species-specific alleles, documentation of introgression, creation of core subsets, and identification of misclassified or duplicated accessions. Altogether, these analyses will provide a more comprehensive knowledge of molecular diversity that is necessary to facilitate the most effective utilization and the greatest efficiency in maintenance of the US Cotton Germplasm Collection.