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

Content Provider	Springer Nature : BioMed Central
Author	Liu, Dexin Zhang, Jian Liu, Xueying Wang, Wenwen Liu, Dajun Teng, Zhonghua Fang, Xiaomei Tan, Zhaoyun Tang, Shiyi Yang, Jinghong Zhong, Jianwei Zhang, Zhengsheng
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.
Related Links	https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/s12864-016-2605-6.pdf
Ending Page	13
Page Count	13
Starting Page	1
File Format	HTM / HTML
ISSN	14712164
DOI	10.1186/s12864-016-2605-6
Journal	BMC Genomics
Issue Number	1
Volume Number	17
Language	English
Publisher	BioMed Central
Publisher Date	2016-04-19
Access Restriction	Open
Subject Keyword	Life Sciences Microarrays Proteomics Animal Genetics and Genomics Microbial Genetics and Genomics Plant Genetics and Genomics Fiber quality Trichome Fine mapping Quantitative trait loci (QTL) RNA-Seq Gossypium hirsutum L
Content Type	Text
Resource Type	Article
Subject	Biotechnology Genetics
Journal Impact Factor	3.5/2023
5-Year Journal Impact Factor	4.1/2023

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