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

Liu D, Zhang J, Liu X, Wang W, Liu D, Teng Z, Fang X, Tan Z, Tang S, Yang J, Zhong J, Zhang Z - BMC Genomics (2016)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, 400716, Chongqing, People's Republic of China.

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.

No MeSH data available.


Related in: MedlinePlus

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
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Fig4: 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

Mentions: To assess and facilitate genetic mapping, all SSR markers on the genetic map were used to do Blastn searches against G. raimondii and G. hirsutum genome sequences [10, 14]. All markers could be aligned to the reference genomes, as shown in Fig. 4c, 4d and Additional file 7. The 0.28-cM genetic interval corresponded to a 2.7-Mb physical distance on chromosome 10 in the G. raimondii genome and a 4.4-Mb physical distance on chromosome A06 in the G. hirsutum genome. Compared to the genome-wide averages of 0.33 Mb per cM for G. raimondii and 0.6 Mb per cM for G. hirsutum [10, 46], this result suggested that recombination suppression occurred in the region where the QTL located.Fig. 4


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

Liu D, Zhang J, Liu X, Wang W, Liu D, Teng Z, Fang X, Tan Z, Tang S, Yang J, Zhong J, Zhang Z - BMC Genomics (2016)

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
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4837631&req=5

Fig4: 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
Mentions: To assess and facilitate genetic mapping, all SSR markers on the genetic map were used to do Blastn searches against G. raimondii and G. hirsutum genome sequences [10, 14]. All markers could be aligned to the reference genomes, as shown in Fig. 4c, 4d and Additional file 7. The 0.28-cM genetic interval corresponded to a 2.7-Mb physical distance on chromosome 10 in the G. raimondii genome and a 4.4-Mb physical distance on chromosome A06 in the G. hirsutum genome. Compared to the genome-wide averages of 0.33 Mb per cM for G. raimondii and 0.6 Mb per cM for G. hirsutum [10, 46], this result suggested that recombination suppression occurred in the region where the QTL located.Fig. 4

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, 400716, Chongqing, People's Republic of China.

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.

No MeSH data available.


Related in: MedlinePlus