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

Abstract

Background: Improving 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.

Results: To 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.

Conclusions: This 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.

Keywords: Fiber quality; Fine mapping; Gossypium hirsutum L.; Quantitative trait loci (QTL); RNA-Seq; Trichome.

Fig. 1

Phenotypeof trichome and fiber traits in G. hirsutum RIL118 and Yumian 1. a,c, e and g indicate plant, stem, leaf and fiber of RIL118; b, d, f and h indicate plant, stem, leaf and fiber of Yumian 1. Scale bars:1 mm (b-e)

Fig. 2

Genetic map and QTL peak map of cotton chromosome 06 from 360 F₂ plants in 2011

Fig. 3

Genetic map of the QTL region and trace of the log probabilities for the four fiber quality traits. The genetic map and QTL identification come from 1440 F₂ plants in 2011. The genetic distances between adjacent markers are shown to the left of chromosomes

Fig. 4

a Graphical genotypes and fiber quality traits for recombinants derived from 6975 individuals. White, black and gray bars represent genotypes of Yumian 1, RIL118and heterozygotes, respectively. b The genetic map (cM) for the QTL region. c The physical locations (Mb) of markers and genes on chromosome 10 of the G. raimondii genome sequence and on d chromosome A06 of the G. hirsutum TM-1 genome sequence. The physical distances of the chromosomes on the plots are represented by cells of different sizes according to the ratio of the chromosome lengths. The candidate genes suggested by RNA-Seq are highlighted with black squares. The figures in turn indicate genes from the G. hirsutum genome: GhA06G1256, GhA06G1277, GhA06G1301 and GhA06G1313. The figures with # in turn indicate genes from the G. raimondii genome: Gorai.010G174800, Gorai.010G177300, Gorai.010G180100 and Gorai.010G181500. The same number of genes indicates the analogous gene of the reference genome

Fig. 5

Phenotype valuation during early fiber development. a: Scanning electron microscope mages of the +1 DPA ovule; b, c and d: Anatomy microscope images of the +3, +5, +7 DPA fiber. Scanning electron microscope images were taken at a similar position in the middle of ovules. Scale bars: 200 μm (a); Scale bars: 1 mm (b); Scale bars: 2.5 mm (c, d)

Fig. 6

Venn diagram showing the number of differentially expressed genes in ovules and fibers. a b Differentially expressed genes between RIL118 and Yuan 1 on 0 DPA ovule and 5DPA fiber; c The expression of regulated genes were significantly different between two joint time points (P-value < 0.05 and fold change > 1)

Fig. 7

RT-PCR expression of the differentially expressed genes in leaf and during fiber development of RIL118 and Yumian1. All data were normalized to the expression level of actin. Error bars indicate standard deviation of three biological replicates