Identification of Loci and Candidate Genes Responsible for Fiber Length in Upland Cotton (Gossypium hirsutum L.) via Association Mapping and Linkage Analyses.

Chi Zhang,Qibao Liu,Shuxun Yu,Jianqin Huang,Hengling Wei,Libei Li,Hantao Wang,Lijiao Gu

doi:10.3389/fpls.2019.00053

Abstract

Fiber length (FL) is an important fiber quality trait in cotton. Although many fiber quality quantitative trait loci (QTL) responsible for FL have been identified, most cannot be applied to breeding programs, mainly due to unstable environments or large confidence intervals. In this study, we combined a genome-wide association study (GWAS) and linkage mapping to identify and validate high-quality QTLs responsible for FL. For the GWAS, we developed 93,250 high-quality single-nucleotide polymorphism (SNP) markers based on 355 accessions, and the FL was measured in eight different environments. For the linkage mapping, we constructed an F2 population from two extreme accessions. The high-density linkage maps spanned 3,848.29 cM, with an average marker interval of 1.41 cM. In total, 14 and 13 QTLs were identified in the association and linkage mapping analyses, respectively. Most importantly, a major QTL on chromosome D03 identified in both populations explained more than 10% of the phenotypic variation (PV). Furthermore, we found that a sucrose synthesis-related gene (Gh_D03G1338) was associated with FL in this QTL region. The RNA-seq data showed that Gh_D03G1338 was highly expressed during the fiber development stage, and the qRT-PCR analysis showed significant expression differences between the long fiber and short fiber varieties. These results suggest that Gh_D03G1338 may determine cotton fiber elongation by regulating the synthesis of sucrose. Favorable QTLs and candidate genes should be useful for increasing fiber quality in cotton breeding.

Highlights

Cotton (Gossypium L.) is one of the most important cash crops and is extensively cultivated in more than 80 countries, having an annual global economic impact of approximately $500 billion and accounting for 2.5% of arable land worldwide (Chen et al, 2007)
The broad-sense heritability (h2) in the eight environments was estimated to be relatively high at 81%, suggesting that the Fiber length (FL) was mainly controlled by genetic factors and was less affected by environmental effects
The high Pearson’s correlations and stable heritability indicated that much of the FL variance was genetically controlled in the populations and suitable for a genome-wide association study (GWAS) analysis and quantitative trait loci (QTL) mapping

Summary

Introduction

Cotton (Gossypium L.) is one of the most important cash crops and is extensively cultivated in more than 80 countries, having an annual global economic impact of approximately $500 billion and accounting for 2.5% of arable land worldwide (Chen et al, 2007). FL is one of the most important and highly heritable fiber quality traits in cotton (Jamshed et al, 2016) and is directly related to its spinning performance, as longer fibers are typically better for manufacturing fine yarns. Over the last few decades, FL has been successfully used for genetic analysis, such as QTL mapping and association analysis, and more than 490 QTLs for FL have been reported (Said et al, 2015). Huang et al (2017) employed association mapping techniques, which are different from biparental linkage mapping, using 1,1975 high-quality SNP markers in a set of 503 upland cotton accessions and identified 11 highly favorable SNP alleles for FL. A better understanding of the genetic architecture of FL could help breeders develop varieties with longer fibers

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Results

Conclusion