Favorable pleiotropic loci for fiber yield and quality in upland cotton (Gossypium hirsutum)

Pengpeng Wang,Xiaoli Geng,Junling Sun,Zhen Peng,Shoupu He,Zhaoe Pan,Baoyin Pang,Gaofei Sun,Liru Wang,Yinhua Jia,Wenfang Gong,Xiongming Du

doi:10.1038/s41598-021-95629-9

Abstract

Upland cotton (Gossypium hirsutum L.) is an important economic crop for renewable textile fibers. However, the simultaneous improvement of yield and fiber quality in cotton is difficult as the linkage drag. Compared with breaking the linkage drag, identification of the favorable pleiotropic loci on the genome level by genome-wide association study (GWAS) provides a new way to improve the yield and fiber quality simultaneously. In our study restriction-site-associated DNA sequencing (RAD-seq) was used to genotype 316 cotton accessions. Eight major traits in three categories including yield, fiber quality and maturation were investigated in nine environments (3 sites × 3 years). 231 SNPs associated with these eight traits (− log10(P) > 5.27) were identified, located in 27 genomic regions respectively by linkage disequilibrium analysis. Further analysis showed that four genomic regions (the region 1, 6, 8 and 23) held favorable pleiotropic loci and 6 candidate genes were identified. Through genotyping, 14 elite accessions carrying the favorable loci on four pleiotropic regions were identified. These favorable pleiotropic loci and elite genotypes identified in this study will be utilized to improve the yield and fiber quality simultaneously in future cotton breeding.

Highlights

Abbreviations boll weight (BW) Boll weight seed index (SI) Seed index lint percentage (LP) Lint percentage fiber length (FL) Fiber length fiber strength (FS) Fiber strength fiber elongation (FE) Fiber elongation MIC Micronaire flowering data (FD) Flowering data genome-wide association study (GWAS) Genome-wide association study linkage disequilibrium (LD) Linkage disequilibrium restriction-site-associated DNA sequencing (RAD-seq) Restriction-site-associated DNA sequencing CV Coefficient of variation BLUP Best Linear Unbiased Prediction CA Central Asia region YR Yellow River region US United States YZR Yangtze River region other places (OTH) Other regions
Our work aimed to identify favorable pleiotropic loci associated with fiber quality and yield, and accessions carrying these pleiotropic loci
The Coefficient of variation (CV) of fiber yield was bigger than fiber quality (Additional file 1: Table S2), indicting the dispersion degree of fiber quality was lower than fiber yield

Summary

Introduction

Abbreviations BW Boll weight SI Seed index LP Lint percentage FL Fiber length FS Fiber strength FE Fiber elongation MIC Micronaire FD Flowering data GWAS Genome-wide association study LD Linkage disequilibrium RAD-seq Restriction-site-associated DNA sequencing CV Coefficient of variation BLUP Best Linear Unbiased Prediction CA Central Asia region YR Yellow River region US United States YZR Yangtze River region OTH Other regions. Unfavorable associations between the gene of interest and other characteristics may be found; for example, the introduction of a tobacco mosaic virus (TMV) resistance gene resulted in a yield decrease in tobacco because of pleiotropy of the gene and/or linkage d rag[19]. This phenomenon has been found in other crops. Linkage drag makes it difficult to transfer favorable traits from G. barbadense to G. hirsutum[4], and significantly limits the simultaneous improvement of yield and fiber quality in G. hirsutum[8,9]. The relationship between fiber quality and yield has changed from linkage drag to favorable linkage, the molecular mechanism underlying this change has never been reported

Methods

Results

Conclusion