Analysis of genetic diversity, population structure and linkage disequilibrium in elite cotton (Gossypium L.) germplasm in India

Abstract

An understanding of the level of genetic diversity is a prerequisite for designing efficient breeding programs. Fifty-one cultivars of four cotton species (Gossypium hirsutum, G. barbadense, G. herbaceum and G. arboreum) representing core collections at four major cotton research stations with a wide range of eco-geographical regions in India were examined for the level of genetic diversity, distinct subpopulations and the level of linkage disequilibrium (LD) using 1100 amplified fragment length polymorphism (AFLP) markers with 16 primer pairs combinations. The AFLP markers enabled a reliable assessment of inter- and intra-specific genetic variability with a heterogeneous genetic structure. Higher genetic diversity was noticed in G. herbaceum, followed by G. arboreum. The genetic diversity in tetraploid cotton species was found to be less than that in the diploid species. The genotypes VAGAD, RAHS14, IPS187, 221 557, Jayhellar of G. herbaceum and 551, DLSA17, 221 566 of G. arboreum were identified as the most diverse parents, useful for quantitative trait loci (QTL) analysis in diploid cotton. Similarly, LRA 5166, AS3 and MCU5 of G. hirsutum and B1, B3, Suvin of G. barbadense were most diverse to develop mapping populations for fibre quality. The internal transcribed spacer sequences were sufficient to resolve different species and subspecies of diploid cotton. Low level of genome-wide LD was detected in the entire collection (r2 = 0.07) as well as within the four species (r2 = 0.11–0.15). A strong agreement was noticed between the clusters constructed on the basis of morphological and genotyping data.

Marker-trait association study for sucrose and yield contributing traits in sugarcane (Saccharum spp. hybrid)

“…Sugarcane exhibits a rare case where a limited pool of progenitor lines (utilized to develop modern breeding materials) and less number of breeding cycles have resulted in extensive LD blocks across the genome (Raboin et al 2008), and thus, a high density of markers may not be required in sugarcane to detect MTA (Wei et al 2006). In a similar study, Jena et al (2011) reported an increase in LD levels within a sub-population in cotton and opined that this could be due to strong selection pressure leading to non-random distribution of haplotypes at the genomic level. In a deeper agreement to this theory, Tian et al (2008) stated that genetic heterogeneity in the association panel may limit the power of the model, and that the use of population substructure information in genome-wide association studies (GWAS) was able to increase the homogeneity within the sub-groups ultimately decrease type II errors.…”

Large‐scale resource development in Gossypium hirsutum L. by 454 sequencing of genic‐enriched libraries from six diverse genotypes

“…We selected six diverse G. hirsutum genotypes (JKC703, JKC725, JKC737, JKC770, MCU5 and LRA5166; Table S1) on the basis of their genetic diversity as observed in amplified fragment length polymorphism (AFLP) analysis (Jena et al ., ). These genotypes are commonly used in breeding programme for varietal and mapping population development, and hence, identification of markers such as single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) will be directly applicable.…”

Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array

“…Diverse resources within other worldwide cotton germplasm collections have also been characterized with molecular markers, primarily SSRs [ 7 , 12 – 14 ]. Additionally, elite cultivars from breeding programs are often genotyped to enable molecular comparisons of cultivars, known pedigrees, and the respective breeding germplasm resources in specific countries and growing regions [ 15 – 20 ]. The accumulation of knowledge regarding genetic differences is especially useful when combined with knowledge of differences in phenotypes because it allows breeders and other researchers to generate segregating populations of increased usefulness by choosing parents with complementary phenotypic traits and genetic distinctiveness.…”