Genome-Wide SNP Linkage Mapping and QTL Analysis for Fiber Quality and Yield Traits in the Upland Cotton Recombinant Inbred Lines Population

Abstract

It is of significance to discover genes related to fiber quality and yield traits and tightly linked markers for marker-assisted selection (MAS) in cotton breeding. In this study, 188 F8 recombinant inbred lines (RILs), derived from a intraspecific cross between HS46 and MARCABUCAG8US-1-88 were genotyped by the cotton 63K single nucleotide polymorphism (SNP) assay. Field trials were conducted in Sanya, Hainan Province, during the 2014–2015 cropping seasons under standard conditions. Results revealed significant differences (P < 0.05) among RILs, environments and replications for fiber quality and yield traits. Broad-sense heritabilities of all traits including fiber length, fiber uniformity, micronaire, fiber elongation, fiber strength, boll weight, and lint percentage ranged from 0.26 to 0.66. A 1784.28 cM (centimorgans) linkage map, harboring 2618 polymorphic SNP markers, was constructed, which had 0.68 cM per marker density. Seventy-one quantitative trait locus (QTLs) for fiber quality and yield traits were detected on 21 chromosomes, explaining 4.70∼32.28% phenotypic variance, in which 16 were identified as stable QTLs across two environments. Meanwhile, 12 certain regions were investigated to be involved in the control of one (hotspot) or more (cluster) traits, mainly focused on Chr05, Chr09, Chr10, Chr14, Chr19, and Chr20. Nineteen pairs of epistatic QTLs (e-QTLs) were identified, of which two pairs involved in two additive QTLs. These additive QTLs, e-QTLs, and QTL clusters were tightly linked to SNP markers, which may serve as target regions for map-based cloning, gene discovery, and MAS in cotton breeding.

A genome‐wide association study of early‐maturation traits in upland cotton based on the CottonSNP80K array

“…The first SNP chip for cotton, the CottonSNP63K array (Illumina, USA), was developed in 2015, allowing assays for 45,104 putative intra‐specific SNP markers for use within the cultivated cotton species G. hirsutum L. and 17,954 putative inter‐specific SNP markers for use with crosses of other cotton species with G. hirsutum (Hulse‐Kemp et al ). To date, the chip has been used in a diversity analysis of cotton germplasm (Hinze et al ), high‐density linkage mapping and QTL analysis (Hulse‐Kemp et al ; Li et al ), and GWASs of yield components and fiber quality traits (Gapare et al ; Sun et al ). Compared with CottonSNP63K, the second cotton SNP chip, CottonSNP80K, is particularly useful for comprehensively dissecting the genetic architecture of agronomically important traits in upland cotton because the SNP loci in the CottonSNP80K array benefited from the whole‐genome sequencing of G. hirsutum acc.…”

Deciphering Genetic Architecture of Adventitious Root and Related Shoot Traits in Populus Using QTL Mapping and RNA-Seq Data

“…Classical quantitative genetics hypothesize that the presence of QTL clusters and hotspots is ascribed to the very close linkage of genes in certain regions of the genome [26,27]. The QTL cluster refers to multiple different traits related to a QTL, and the QTL hotspot refers to multiple QTLs of the same trait distributed within the 20 cM region [28].…”

QTL and genetic analysis controlling fiber quality traits using paternal backcross population in Upland Cotton

“…A number of QTLs were located on Chr 5, Chr 19 and Chr 21 (Said et al 2013, 2015). For fiber quality, the most QTLs were detected based on mapping in recombinant inbred lines (RIL) populations of Upland cotton (Wu et al 2009; Sun et al 2012; Ning et al 2014; Tan et al 2014; Shang et al 2015; Tang et al 2015; Zhang et al 2015b; Jamshed et al 2016; Li et al 2016). However, RIL population can be only used to dissect additive and additive × additive effects and not to dissect dominance and dominance-related genetic effects because lacking of heterozygous genotypes.…”

“…In Wang’s work (2016), two markers of NAU5530 and CIR099 flanking qFL-c19-2 , qFU-LG3-1 and qFS-LG3 were same in Shang’s work (2016d). Using a map of single nucleotide polymorphism (SNP) markers, one fiber length hotspot on Chr 5 carrying three QTLs was observed (Li et al 2016). Additionally, four potential candidate genes for fiber length on Chr Dt7 were found using genotyping by sequencing by genome-wide association studies (GWAS) (Su et al 2016).…”