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

Genetic map and QTL peak map of cotton chromosome 06 from 360 F2 plants in 2011
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Fig2: Genetic map and QTL peak map of cotton chromosome 06 from 360 F2 plants in 2011

Mentions: Based on the genetic map and the QTL region for fiber quality traits [37, 43], thirteen newly developed SSR markers from G. raimondii reference genome [10] showed polymorphism between Yumian 1 and RIL118 (Additional file 6). The newly identified SSR markers and SSR markers previously mapped on chromosome 6 were used to genotype 360 F2 individuals randomly selected from the 2011 F2 population, with a total of 116 loci (115 SSR and T1) mapped on chromosome 6. The genetic map covered 133.1 cM (Fig. 2). The QTL controlling four fiber quality traits was located in the confidence interval between MUCS114 and MUSS099, and 19 markers co-segregated with T1 (Fig. 2 and Table. 1). The QTL explained 59.3 % (LOD = 62.6), 45.7 % (LOD = 42.6), 36.4 % (LOD = 31.6) and 53.8 % (LOD = 52.43) of phenotypic variation, with additive effects of 2.78, −0.43, 1.90 and 2.92 for FL, FM, FU and FS, respectively.Fig. 2


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)

Genetic map and QTL peak map of cotton chromosome 06 from 360 F2 plants in 2011
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig2: Genetic map and QTL peak map of cotton chromosome 06 from 360 F2 plants in 2011
Mentions: Based on the genetic map and the QTL region for fiber quality traits [37, 43], thirteen newly developed SSR markers from G. raimondii reference genome [10] showed polymorphism between Yumian 1 and RIL118 (Additional file 6). The newly identified SSR markers and SSR markers previously mapped on chromosome 6 were used to genotype 360 F2 individuals randomly selected from the 2011 F2 population, with a total of 116 loci (115 SSR and T1) mapped on chromosome 6. The genetic map covered 133.1 cM (Fig. 2). The QTL controlling four fiber quality traits was located in the confidence interval between MUCS114 and MUSS099, and 19 markers co-segregated with T1 (Fig. 2 and Table. 1). The QTL explained 59.3 % (LOD = 62.6), 45.7 % (LOD = 42.6), 36.4 % (LOD = 31.6) and 53.8 % (LOD = 52.43) of phenotypic variation, with additive effects of 2.78, −0.43, 1.90 and 2.92 for FL, FM, FU and FS, respectively.Fig. 2

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