Genetic diversity, linkage disequilibrium, and association mapping analyses of Gossypium barbadense L. germplasm

Abstract

Limited polymorphism and narrow genetic base, due to genetic bottleneck through historic domestication, highlight a need for comprehensive characterization and utilization of existing genetic diversity in cotton germplasm collections. In this study, 288 worldwide Gossypium barbadense L. cotton germplasm accessions were evaluated in two diverse environments (Uzbekistan and USA). These accessions were assessed for genetic diversity, population structure, linkage disequilibrium (LD), and LD-based association mapping (AM) of fiber quality traits using 108 genome-wide simple sequence repeat (SSR) markers. Analyses revealed structured population characteristics and a high level of intra-variability (67.2%) and moderate interpopulation differentiation (32.8%). Eight percent and 4.3% of markers revealed LD in the genome of the G. barbadense at critical values of r2 ≥ 0.1 and r2 ≥ 0.2, respectively. The LD decay was on average 24.8 cM at the threshold of r2 ≥ 0.05. LD retained on average distance of 3.36 cM at the threshold of r2 ≥ 0.1. Based on the phenotypic evaluations in the two diverse environments, 100 marker loci revealed a strong association with major fiber quality traits using mixed linear model (MLM) based association mapping approach. Fourteen marker loci were found to be consistent with previously identified quantitative trait loci (QTLs), and 86 were found to be new unreported marker loci. Our results provide insights into the breeding history and genetic relationship of G. barbadense germplasm and should be helpful for the improvement of cotton cultivars using molecular breeding and omics-based technologies.

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

“…A total of 47 (i.e., 48%) and 50 (i.e., 52%) SSR markers were located over all the 13 chromosomes of A- and D-genome each, respectively. A total of 293 different alleles were amplified by the present panel of SSRs, ranging from 2 to 5 alleles per marker with an average value of 3.020 alleles per marker, which is lower than as reported by Abdullaev et al (2017) and Baytar et al (2017) . The results for the number of alleles for markers depend on the panel of germplasm, but these are also highly affected even by the methods used for screening of results like PAGE, AGE, MAZE, micro-capillary, etc.…”

“…These markers could be used in other studies too for the screening of lint-and fiber-related traits. SSR markers have shown similar linkage and pleiotropic effect in previous studies of Abdullaev et al (2017), Rahman (2017), andZhang et al (2020). Use of these markers showing linkage and pleiotropic effect in cotton will be very helpful in the screening of progenies in crop improvement programs specific to yield and other yield attributing traits.…”

“…In this study, they detected 30 markers associated with fiber-related traits based on 98 simple sequence repeat (SSR) markers using 56 G. arboreum genotypes. Afterward, a number of attempts have been made even using next-generation sequencing (NGS) to find the MTA for various agronomic traits ( Cai et al, 2014 ; Mei et al, 2017 ; Dong C. et al, 2018 ; Ali et al, 2020 ; Zhang et al, 2020 ), fiber quality traits ( Nie et al, 2016 ; Abdullaev et al, 2017 ; Ademe et al, 2017 ; Iqbal and Rahman, 2017 ; Dong C. G. et al, 2018 ; Huang et al, 2018 ), and biotic/abiotic stress tolerance ( Wang et al, 2016 ; Zhao et al, 2016 ; Baytar et al, 2017 ; Sun et al, 2019 ) using molecular marker-based approach exhausting different germplasm of Gossypium sp. Though association studies based on SNP through genotyping by sequencing (GBS) and NGS are more promising and more efficient than SSR, the cost of sequencing makes this technique not readily available for researchers in undeveloped and developing countries, while easy accessibility of PCR thermo-cycler and SSR markers has kept their importance in the research field.…”

Genome-wide association study of agronomic traits in bread wheat reveals novel putative alleles for future breeding programs

“…Selection, recombination, mutation, genetic drift, mating systems and population relatedness are all major factors, which influence linkage disequilibrium [37–39]. The fact that varieties show significantly overall higher LD compared to landraces, in particular in the D genome, is likely the result of selection during breeding for important agronomic traits [40, 41].…”

Examining two sets of introgression lines across multiple environments reveals background-independent and stably expressed quantitative trait loci of fiber quality in cotton

“…In the past 20 years, researchers have identified a large number of QTLs related to fiber quality in G. barbadense using interspecific segregating populations of G. hirsutum × G. barbadense or natural populations of G. barbadense (Abdullaev et al 2017;Said et al 2015a), but most of the mapping populations are early segregating populations of G. hirsutum × G. barbadense such as F 2 populations (Jiang et al 1998;Kohel et al 2001;Lin et al 2005;Mei et al 2004;Paterson et al 2003), F 2:3 populations (He et al 2007) and early backcross generation populations (BC 1 , BC 2 , BC 2 S 1 ) (Lacape et al 2005;Shi et al 2015. A few mapping populations are recombinant inbred line (RIL) populations (Lacape et al 2009(Lacape et al , 2010 or backcross introgression line (BIL) populations (Nie et al 2015;Yu et al 2013), as well as natural populations of G. barbadense (Abdullaev et al 2017;Wang et al 2013a). Due to the complex background of these mapping populations, it is difficult to accurately identify and precisely locate QTLs (Islam et al 2016).…”