Genetic Diversity and Population Structure in the Landrace Accessions of Gossypium hirsutum

Abstract

In this study, genetic diversity and population structure was assessed in a set of 185 Gossypium hirsutum L. landrace accessions, collected mainly from Central America during the mid‐1900s using genomewide simple sequence repeat (SSR) markers. Genotyping the diversity panel using 122 SSRs detected 143 marker loci. A total of 819 alleles were identified across 143 markers loci, and out of these, 23.3% were unique alleles, observed only in one accession. Average genetic distance between accessions was 0.36, suggesting higher levels of genetic variation present in the cotton tropical landrace germplasm. Using Bayesian model‐based structure analysis, five major subgroups were identified that roughly corresponded to the geographical origins of accessions. Substantial admixture was observed as accessions from different geographical locations were grouped together. Results from phylogenetic analysis, principal component analysis, and analysis of molecular variance supported clustering based on STRUCTURE analysis. Pairwise kinship estimates suggested that most of the accessions were unrelated. Finally, core sets representing various levels of allelic richness were identified using POWERMARKER. Assessing genetic diversity, population structure, and identifying the core sets in the landraces will facilitate the utilization of unexploited tropical genetic diversity towards developing improved cotton cultivars.

Identification of Novel Marker–Trait Associations for Lint Yield Contributing Traits in Upland Cotton (Gossypium hirsutum L.) Using SSRs

“…Genotypes that were highly diverse at the molecular level too will give a more heterotic effect in their F 1 hybrids. Results are in accordance with previous reports as genotypes or lines from different origins showed higher genetic distance as compared with genotypes of origin ( Fang et al, 2013 ; Mei et al, 2013 ; Nie et al, 2016 ; Kaur et al, 2017 ). Though the panel of genotypes in the current study is limited to Indian origin only, still it has enough diversity to proceed further.…”

“…The reason for a smaller number of significant clusters might be the same geographical origin of most of the genotypes in the present study and close ancestral history. Mei et al (2013); Cai et al (2014), andSong et al (2019) reported the highest likelihood score at K = 2 and obtained clusters with large germplasms grouping into two clusters, while Jena et al (2012), Tyagi et al (2014), Badigannavar and Myers (2015), Kaur et al (2017), andSeyoum et al (2018) reported likelihood score at K = 3 or more and clustered the genotype panels accordingly. Significant linkage was obtained for 151 marker pairs (3.24%) at r 2 ≥ 0.1 and for 514 markers pairs (11.04%) at r 2 ≥ 0.05, which were similar to results as reported in previous studies by Cai et al (2014), Li et al (2016), Iqbal and Rahman (2017).…”

Genetic dissection of an allotetraploid interspecific CSSLs guides interspecific genetics and breeding in cotton

“…4 Cotton Research Institute, Shihezi Academy of Agriculture Science, Shihezi, Xinjiang 832003, China. 5 Key Laboratory of Oasis Ecology Agricultural of Xinjiang Bingtuan, Agricultural College, Shihezi University, Shihezi, Xinjiang 832003, China. 6 Institute of Industrial Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang 830091, China.…”

“…These two tetraploid (2n = 4x = 52) cotton species both share the common progenitors, which formed by a natural hybridization between A genome and D genome 1-2 million years ago [1][2][3]. The G. hirsutum (Gh), known as Upland cotton, contributed over 95% of cotton fiber yield by its wide adaptation and high yield [4,5]. Because of the long process of domestication and selection bottlenecks, the elite Upland cotton has a narrow genetic base and limited genetic diversity [3].…”

Genetic analysis of the transition from wild to domesticated cotton (G. hirsutumL.)

“…These are distinguished from domesticated and feral forms by their short, coarse, brown fibers, as well as their sprawling growth habit, photoperiod sensitivity, and seed dormancy requirements, among others ( Figure 1). Results from molecular marker analyses, including allozymes (Wendel and Albert 1992), restriction fragment length polymorphisms (RFLPs) (Brubaker and Wendel 1994), simple sequence repeats (SSRs) (Liu and Wendel 2002;Zhang et al 2011;Tyagi et al 2014;Zhao et al 2015;Kaur et al 2017;McCarty et al 2018), SNP arrays (Hinze et al 2017;Cai et al 2017;Ai et al 2017), and next-generation sequencing (Reddy et al 2017;Fang et al 2017c;Ma et al 2018) have quantified genetic diversity and aspects of population structure among wild, feral, and domesticated stocks of the species, as well as the allopolyploid origin of the species. Notably, the allopolyploid origin of G. hirsutum includes a diploid species with no spinnable fiber, i.e., the paternal parent derived from the fiberless Mesoamerican "D-genome" clade.…”