Construction of a High‐Density Genetic Map and Its Application to QTL Identification for Fiber Strength in Upland Cotton

Abstract

Cotton (Gossypium sp.) is an important worldwide cash crop that provides a competitive renewable natural fiber supply for the demands of textile industry. The development of new textile technologies and the improvement of living standards increase the demands for both fiber quantity and fiber quality. ‘0–153’ is an upland cotton cultivar with excellent fiber quality derived from Asiatic cotton sources, especially with regards to fiber strength. To identify quantitative trait loci (QTLs) for fiber strength in this line, a recombinant inbred line population consisting of 196 lines was developed from a cross between it and ‘sGK9708’. A genetic linkage map consisting of 2393 loci was constructed using this recombinant inbred line population, with single nucleotide polymorphism (SNP) markers from the IntlCottonSNPConsortium_70k chip. Quantitative trait loci for fiber strength were detected across 11 environments using both single‐environment and combined multiple‐environment models. A total of 63 QTLs controlling fiber strength were detected by the single‐environment model. Sixteen QTLs were identified by the combined multiple‐environment model. These QTLs could make a contribution to the improvement of fiber quality via marker‐assisted selection and provide useful information for QTL fine mapping and functional gene research activities as well.

Genome mapping and molecular markers identification for yield, yield component and fibre quality traits in tetraploid cotton

“…But in the present study, a higher percentage of polymorphic SNP markers were mapped on D‐genome (799) than the A‐genome (631). This indicates that higher marker density is present on D‐genome than A‐genome, which is also evident in the map reported by Zhang et al (). In this study, we constructed the genetic map with 1,430 SNP markers spanning 3,149.8 cM.…”

“…The large number of SNP markers detected in different cotton species (Byers, Harker, Yourstone, Maughan, & Udall, ; Van Deynze et al, ; Gore et al, ; Hulse‐Kemp, Ashrafi, et al, ; Hulse‐Kemp et al, ; Islam, Thyssen, Jenkins, & Fang, ; Lacape et al, ; Rai et al, ; Zhu, Spriggs, Taylor, Llewellyn, & Wilson, ) have helped the cotton researchers in genome‐based identification and mapping of QTL. Till now, only a few mapping studies in cotton have been based on SNP markers (Gore et al, ; Kumar et al, ; Li et al, ; Yu et al, ; Zhang et al, ). An international collaborative effort has developed the CottonSNP63k Illumina Infinium genotyping assay and genotyping these SNP markers in interspecific and intraspecific cotton F 2 populations (Hulse‐Kemp, Lemm, et al, ).…”

“…Gore et al () have also previously reported 28 major QTL explaining phenotypic variation of 14%–22% for 10 agronomic and fibre quality traits in a recombinant inbred mapping population derived from a cross between TM‐1 ( G. hirsutum ) and NM24016, an elite G. hirsutum line with stabilized introgression from G. barbadense. Zhang et al () detected 63 QTL in a single environment and 16 QTL in multiple environments for fibre strength in intraspecific RILs of upland cotton.…”

Quantitative Trait Locus Mapping for Verticillium wilt Resistance in an Upland Cotton Recombinant Inbred Line Using SNP-Based High Density Genetic Map

“…A high-density genetic map constructed with single nucleotide polymorphisms (SNPs) based on CottonSNP70K chip (Zhang et al, 2017) and simple sequence repeats (SSRs; Sun et al, 2012) was used for the QTLs identification (Supplementary Table 1). The SNPs and SSRs were screened and excluded after several steps based on the following criteria: the SNPs that did not show three clearly defined clusters (AA, BB, and AB); second, the SNPs that their genotypes in one or both of the parents showed heterozygosis; third, the SNPs that had no polymorphism between parents; fourth, the SNPs and SSRs for which genotyping data were missing in more than 40% of the 196 RILs; and finally, the SNPs and SSRs with a significant segregation distortion ( P < 0.001).…”

“…The map spanned a total distance of 2,856.73 cM with 26 linkage groups, all of which were allocated into chromosomes of cotton genome, and an average marker interval of 1.20 cM. The quality criteria assessments of the genetic linkage map indicated that the segregation distortion of mapped markers was low (34.78% of the mapped markers showed distorted segregation) and that the collinearity of SNP and SSR markers between the genetic and physical maps had a sufficient consistency with their locations on both maps across the whole genome (Zhang et al, 2017). …”