Fine mapping and RNA-Seq unravels candidate genes for a major QTL controlling multiple fiber quality traits at the T1 region in upland cottonReport as inadecuate

Fine mapping and RNA-Seq unravels candidate genes for a major QTL controlling multiple fiber quality traits at the T1 region in upland cotton - Download this document for free, or read online. Document in PDF available to download.

BMC Genomics

, 17:295

Plant genomics


BackgroundImproving fiber quality is a major challenge in cotton breeding, since the molecular basis of fiber quality traits is poorly understood. Fine mapping and candidate gene prediction of quantitative trait loci QTL controlling cotton fiber quality traits can help to elucidate the molecular basis of fiber quality. In our previous studies, one major QTL controlling multiple fiber quality traits was identified near the T1 locus on chromosome 6 in Upland cotton.

ResultsTo finely map this major QTL, the F2 population with 6975 individuals was established from a cross between Yumian 1 and a recombinant inbred line RIL118 selected from a recombinant inbred line population T586 × Yumian 1. The QTL was mapped to a 0.28-cM interval between markers HAU2119 and SWU2302. The QTL explained 54.7 % LOD = 222.3, 40.5 % LOD = 145.0, 50.0 % LOD = 194.3 and 30.1 % LOD = 100.4 of phenotypic variation with additive effects of 2.78, −0.43, 2.92 and 1.90 units for fiber length, micronaire, strength and uniformity, respectively. The QTL region corresponded to a 2.7-Mb interval on chromosome 10 in the G. raimondii genome sequence and a 5.3-Mb interval on chromosome A06 in G. hirsutum. The fiber of Yumian 1 was much longer than that of RIL118 from 3 DPA to 7 DPA. RNA-Seq of ovules at 0 DPA and fibers at 5 DPA from Yumian 1 and RIL118 showed four genes in the QTL region of the G. raimondii genome to be extremely differentially expressed. RT-PCR analysis showed three genes in the QTL region of the G. hirsutum genome to behave similarly.

ConclusionsThis study mapped a major QTL influencing four fiber quality traits to a 0.28-cM interval and identified three candidate genes by RNA-Seq and RT-PCR analysis. Integration of fine mapping and RNA-Seq is a powerful strategy to uncover candidates for QTL in large genomes.

KeywordsFiber quality Trichome Fine mapping Quantitative trait loci QTL RNA-Seq Gossypium hirsutum L. AbbreviationsDPAdays post-anthesis

FEfiber elongation

FLfiber length

FMfiber micronaire reading

FPKMfragments per kilo base of exon per million fragments mapped

FSfiber strength

FUuniformity ratio

KEGGKyoto encyclopedia of genes and genomes

LODlog of odds ratio

MASmarker-assisted selection

QTLquantitative trait loci

RILrecombinant inbred line

RNA-seqhigh-throughput sequencing of RNA

RT-PCRreal-time quantitative PCR

Electronic supplementary materialThe online version of this article doi:10.1186-s12864-016-2605-6 contains supplementary material, which is available to authorized users.

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Author: Dexin Liu - Jian Zhang - Xueying Liu - Wenwen Wang - Dajun Liu - Zhonghua Teng - Xiaomei Fang - Zhaoyun Tan - Shiyi Tang


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