Identification of Candidate Cotton Genes Associated With Fiber Length Through Quantitative Trait Loci Mapping and RNA-Sequencing Using a Chromosome Segment Substitution Line.

Quanwei Lu,Yuzhen Shi,Jiajia Feng,Xianghui Xiao,Juwu Gong,Youlu Yuan,Pengtao Li,Renhai Peng,Yan Zhao

doi:10.3389/fpls.2021.796722

Abstract

Fiber length is an important determinant of fiber quality, and it is a quantitative multi-genic trait. Identifying genes associated with fiber length is of great importance for efforts to improve fiber quality in the context of cotton breeding. Integrating transcriptomic information and details regarding candidate gene regions can aid in candidate gene identification. In the present study, the CCRI45 line and a chromosome segment substitution line (CSSL) with a significantly higher fiber length (MBI7747) were utilized to establish F2 and F2:3 populations. Using a high-density genetic map published previously, six quantitative trait loci (QTLs) associated with fiber length and two QTLs associated with fiber strength were identified on four chromosomes. Within these QTLs, qFL-A07-1, qFL-A12-2, qFL-A12-5, and qFL-D02-1 were identified in two or three environments and confirmed by a meta-analysis. By integrating transcriptomic data from the two parental lines and through qPCR analyses, four genes associated with these QTLs including Cellulose synthase-like protein D3 (CSLD3, GH_A12G2259 for qFL-A12-2), expansin-A1 (EXPA1, GH_A12G1972 for qFL-A12-5), plasmodesmata callose-binding protein 3 (PDCB3, GH_A12G2014 for qFL-A12-5), and Polygalacturonase (At1g48100, GH_D02G0616 for qFL-D02-1) were identified as promising candidate genes associated with fiber length. Overall, these results offer a robust foundation for further studies regarding the molecular basis for fiber length and for efforts to improve cotton fiber quality.

Highlights

Cotton (Gossypium spp.) is an important cash crop and the most commonly planted form of renewable textile fiber in the world
We have identified multiple chromosome segment substitution line (CSSL) within a population of 332 CSSLs derived from the Hai1 line, a conventional cultivar of G. barbadense with a donor parent with high fiber quality, and the recurrent parental line CCRI45, a widely grown upland cotton cultivar with a high yield bred by the Institute of Cotton Research (ICR), the Chinese Academy of Agricultural Sciences (CAAS) Anyang, Henan Province (Shi et al, 2020)
Chromosome segment substitution lines have the same or similar genetic backgrounds to those of receptor parental lines, Studies of these CSSLs can separate QTLs based on specific qualitative findings, and the effect values associated with individual genotypes can be accurately assessed within the segregation population

Summary

Introduction

Cotton (Gossypium spp.) is an important cash crop and the most commonly planted form of renewable textile fiber in the world. Introgressing novel genetic material associated with fiber length and strength from G. barbadense into G. hirsutum may offer valuable opportunities to improve Upland cotton fiber quality. Many quantitative trait loci (QTLs) associated with fiber quality and yields have been identified through the crossing of G. hirsutum and G. barbadense (Said et al, 2015; Abdullaev et al, 2017), with most such interspecific mapping having been performed using F2 (Jiang et al, 1998; Kohel et al, 2001; Paterson et al, 2003; Mei et al, 2004; Lin et al, 2005), F2:3 (He et al, 2012), BC1, BC2, and BC2S1 populations (Shi et al, 2020). CSSLs have been successfully employed for studies of rice and tomato plants (Illa-Berenguer et al, 2015), and recent reports have demonstrated their promise in the context of cotton breeding analyses (Wang et al, 2008; Yang and Li, 2009; Peng et al, 2012)

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Conclusion