Genetic diversity and population structure in the US Upland cotton (Gossypium hirsutum L.)

Abstract

Genetic diversity and population structure in the US Upland cotton was established and core sets of allelic richness were identified for developing association mapping populations in cotton. Elite plant breeding programs could likely benefit from the unexploited standing genetic variation of obsolete cultivars without the yield drag typically associated with wild accessions. A set of 381 accessions comprising 378 Upland (Gossypium hirsutum L.) and 3 G. barbadense L. accessions of the United States cotton belt were genotyped using 120 genome-wide SSR markers to establish the genetic diversity and population structure in tetraploid cotton. These accessions represent more than 100 years of Upland cotton breeding in the United States. Genetic diversity analysis identified a total of 546 alleles across 141 marker loci. Twenty-two percent of the alleles in Upland accessions were unique, specific to a single accession. Population structure analysis revealed extensive admixture and identified five subgroups corresponding to Southeastern, Midsouth, Southwest, and Western zones of cotton growing areas in the United States, with the three accessions of G. barbadense forming a separate cluster. Phylogenetic analysis supported the subgroups identified by STRUCTURE. Average genetic distance between G. hirsutum accessions was 0.195 indicating low levels of genetic diversity in Upland cotton germplasm pool. The results from both population structure and phylogenetic analysis were in agreement with pedigree information, although there were a few exceptions. Further, core sets of different sizes representing different levels of allelic richness in Upland cotton were identified. Establishment of genetic diversity, population structure, and identification of core sets from this study could be useful for genetic and genomic analysis and systematic utilization of the standing genetic variation in Upland cotton.

Modifications to a LATE MERISTEM IDENTITY1 gene are responsible for the major leaf shapes of Upland cotton ( Gossypium hirsutum L.)

“…A 538-member diversity panel was used for association mapping and genomewide association studies. This panel consisted of the 384-member cotton diversity panel (39), plus 154 wild and landrace accessions, all of which were obtained from USDA Cotton Germplasm Collection (Dataset S1). Two sets of isolines were used in fine-mapping and/or in gene expression and VIGS studies, a BC 8 set that included all four leaf shapes in the Stoneville 213 background (40) and a BC 3 pair of normal and okra in the Stoneville 7A background (41).…”

“…The association mapping population consisted of the 384-member elite cotton diversity panel (39) and 154 wild and landrace accessions of tetraploid cotton, some of which were sensitive to long-day photoperiod conditions. Of this population, a diversity panel of 447 photoperiod insensitive lines were grown under summer field conditions in Clayton, North Carolina, whereas the 91 photoperiod-sensitive accessions were grown in 10-inch single pots in the greenhouse under short-day conditions.…”

Optimal use of SSR markers for varietal identification of upland cotton

“…Polymorphic primer pairs were distributed along 22 of the 26 amphidiploid cotton chromosomes; these markers were equally distributed on the chromosomes of both Lacape et al (2007), and seems to contradict a previous belief that the D genome would be more diverse than the A genome (Adams & Wendel, 2004 The cultivated cotton race, G. hirsutum race latifolium, is less diverse than the other races (Bertini et al, 2006). Lacape et al (2007) found a relatively low dissimilarity value of 0.20 within latifolium genotypes, but greater than when measured in other DNA marker studies, including those with RFLP (Brubaker & Wendel, 1994) or SSRs (Rungis et al, 2005;Tyagi et al, 2014). A decrease in the diversity of cultivated genotypes, when compared to the wild ones, is mostly related to the selection for crop domestication, which may be accompanied by a dispersal bottleneck (Van de Wouw et al, 2010).…”

Genetic diversity of Turkish commercial cotton varieties revealed by molecular markers and fiber quality traits

“…PCA indicated the relationships of genotypes in a more meaningful form showing that PCA should be used along with the dendrogram to gain a better understanding of relationships among genotypes. A recent study on the establishment of genetic diversity, population structure, and identification of core sets of allelic richness in US Upland cotton indicated average genetic distance between G. hirsutum accessions with low levels of genetic diversity in the Upland cotton germplasm pool (Tyagi et al, 2014). Although there are many studies on genetic diversity of cotton cultivars, only some of the recent studies have analyzed Turkish cotton varieties for genetic variability.…”