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Identification of candidate genes for fiber length quantitative trait loci through RNA-Seq and linkage and physical mapping in cotton

Overview of attention for article published in BMC Genomics, May 2017
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Title
Identification of candidate genes for fiber length quantitative trait loci through RNA-Seq and linkage and physical mapping in cotton
Published in
BMC Genomics, May 2017
DOI 10.1186/s12864-017-3812-5
Pubmed ID
Authors

Xihua Li, Man Wu, Guoyuan Liu, Wenfeng Pei, Honghong Zhai, Jiwen Yu, Jinfa Zhang, Shuxun Yu

Abstract

Cotton (Gossypium spp.) fibers are single-celled elongated trichomes, the molecular aspects of genetic variation in fiber length (FL) among genotypes are currently unknown. In this study, two backcross inbred lines (BILs), i.e., NMGA-062 ("Long") and NMGA-105 ("Short") with 32.1 vs. 27.2 mm in FL, respectively, were chosen to perform RNA-Seq on developing fibers at 10 days post anthesis (DPA). The two BILs differed in 4 quantitative trait loci (QTL) for FL and were developed from backcrosses between G. hirsutum as the recurrent parent and G. barbadense. In total, 51.7 and 54.3 million reads were obtained and assembled to 49,508 and 49,448 transcripts in the two genotypes, respectively. Of 1551 differentially expressed genes (DEGs) between the two BILs, 678 were up-regulated and 873 down-regulated in "Long"; and 703 SNPs were identified in 339 DEGs. Further physical mapping showed that 8 DEGs were co-localized with the 4 FL QTL identified in the BIL population containing the two BILs. Four SNP markers in 3 DEGs that showed significant correlations with FL were developed. Among the three candidate genes encoding for proline-rich protein, D-cysteine desulfhydrase, and thaumatin-like protein, a SNP of thaumatin-like protein gene showed consistent correlations with FL across all testing environments. This study represents one of the first investigations of positional candidate gene approach of QTL in cotton in integrating transcriptome and SNP identification based on RNA-Seq with linkage and physical mapping of QTL and genes, which will facilitate eventual cloning and identification of genes responsible for FL QTL. The candidate genes may serve as the foundation for further in-depth studies of the molecular mechanism of natural variation in fiber elongation.

Twitter Demographics

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Mendeley readers

The data shown below were compiled from readership statistics for 24 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 24 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 8 33%
Student > Master 6 25%
Researcher 4 17%
Student > Doctoral Student 1 4%
Professor 1 4%
Other 2 8%
Unknown 2 8%
Readers by discipline Count As %
Agricultural and Biological Sciences 11 46%
Biochemistry, Genetics and Molecular Biology 7 29%
Business, Management and Accounting 1 4%
Computer Science 1 4%
Social Sciences 1 4%
Other 1 4%
Unknown 2 8%

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 23 January 2018.
All research outputs
#11,026,478
of 12,406,609 outputs
Outputs from BMC Genomics
#6,439
of 7,352 outputs
Outputs of similar age
#227,635
of 269,901 outputs
Outputs of similar age from BMC Genomics
#5
of 7 outputs
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