Genome-wide association reveals genetic variation of lint yield components under salty field conditions in cotton (Gossypium hirsutum L.)

Fenglei Sun,Wenwei Gao,Xiaohui Song,Sen Hou,Wangzhen Guo,Quanjia Chen,Dayong Zhang,Guozhong Zhu,Zhiyong Ni,Na Liu,Yajie Huang

doi:10.1186/s12870-019-2187-y

Fenglei Sun, Wenwei Gao + Show 9 more

Open Access

https://doi.org/10.1186/s12870-019-2187-y

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Abstract

BackgroundSalinity is one of the most significant environmental factors limiting the productivity of cotton. However, the key genetic components responsible for the reduction in cotton yield in saline-alkali soils are still unclear.ResultsHere, we evaluated three main components of lint yield, single boll weight (SBW), lint percentage (LP) and boll number per plant (BNPP), across 316 G. hirsutum accessions under four salt conditions over two years. Phenotypic analysis indicated that LP was unchanged under different salt conditions, however BNPP decreased significantly and SBW increased slightly under high salt conditions. Based on 57,413 high-quality single nucleotide polymorphisms (SNPs) and genome-wide association study (GWAS) analysis, a total of 42, 91 and 25 stable quantitative trait loci (QTLs) were identified for SBW, LP and BNPP, respectively. Phenotypic and QTL analysis suggested that there was little correlation among the three traits. For LP, 8 stable QTLs were detected simultaneously in four different salt conditions, while fewer repeated QTLs for SBW or BNPP were identified. Gene Ontology (GO) analysis indicated that their regulatory mechanisms were also quite different. Via transcriptome profile data, we detected that 10 genes from the 8 stable LP QTLs were predominantly expressed during fiber development. Further, haplotype analyses found that a MYB gene (GhMYB103), with the two SNP variations in cis-regulatory and coding regions, was significantly correlated with lint percentage, implying a crucial role in lint yield. We also identified that 40 candidate genes from BNPP QTLs were salt-inducible. Genes related to carbohydrate metabolism and cell structure maintenance were rich in plants grown in high salt conditions, while genes related to ion transport were active in plants grown in low salt conditions, implying different regulatory mechanisms for BNPP at high and low salt conditions.ConclusionsThis study provides a foundation for elucidating cotton salt tolerance mechanisms and contributes gene resources for developing upland cotton varieties with high yields and salt stress tolerance.

Highlights

Salinity is one of the most significant environmental factors limiting the productivity of cotton
Phenotypic variation of lint yield components under salt conditions single boll weight (SBW), lint percentage (LP) and boll number per plant (BNPP) were measured in 316 upland cotton accessions (Additional file 1: Table S1) grown under four different salt conditions (Additional file 2: Figure S1A and Additional file 3: Table S2)
The average values of SBW, LP and BNPP traits ranged from 5.28 g to 6.84 g (Additional file 4: Table S3), 37.89 to 40.39% (Additional file 5: Table S4) and 5.01 to 7.74 (Additional file 6: Table S5) under the four different salt conditions, respectively

Summary

Introduction

Salinity is one of the most significant environmental factors limiting the productivity of cotton. Salinity is one of the most significant environmental factors limiting the productivity of crop plants [1]. In addition to using physical and chemical methods to reduce salt content, screening or breeding high-salt-tolerant crops by modern molecular means is an economic and effective way to solve the present situation. Cotton (Gossypium spp.) could be used for soil reclamation as a pioneer crop of saline-alkali land due to its high salt tolerance [9]. Discovering the limiting factors and identifying the genes involved in the salttolerance response pathway is an effective way to increase cotton yield

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