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The aquaporin gene PvXIP1;2 conferring drought resistance identified by GWAS at seedling stage in common bean

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Abstract

Key message

A whole-genome resequencing-derived SNP dataset used for genome-wide association analysis revealed 12 loci significantly associated with drought stress based on survival rate after drought stress at seedling stage. We further confirmed the drought-related function of an aquaporin gene (PvXIP1;2) located at Locus_10.

Abstract

A variety of adverse conditions, including drought stress, severely affect common bean production. Molecular breeding for drought resistance has been proposed as an effective and practical way to improve the drought resistance of common bean. A genome-wide association analysis was conducted to identify drought-related loci based on survival rates at the seedling stage using a natural population consisting of 400 common bean accessions and 3,832,340 SNPs. The coefficient of variation ranged from 40.90 to 56.22% for survival rates in three independent experiments. A total of 12 associated loci containing 89 significant SNPs were identified for survival rates at the seedling stage. Four loci overlapped in the region of the QTLs reported to be associated with drought resistance. According to the expression profiles, gene annotations and references of the functions of homologous genes in Arabidopsis, 39 genes were considered potential candidate genes selected from 199 genes annotated within all associated loci. A stable locus (Locus_10) was identified on chromosome 11, which contained LEA, aquaporin, and proline-rich protein genes. We further confirmed the drought-related function of an aquaporin (PvXIP1;2) located at Locus_10 by expression pattern analysis, phenotypic analysis of PvXIP1;2-overexpressing Arabidopsis and Agrobacterium rhizogenes-mediated hairy root transformation systems, indicating that the association results can facilitate the efficient identification of genes related to drought resistance. These loci and their candidate genes provide a foundation for crop improvement via breeding for drought resistance in common bean.

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Availability of data and material

The data supporting the findings of this study are available from the corresponding author (Jing Wu) upon request.

Abbreviations

GWASs:

Genome-wide association studies

IL:

Ion leakage

MDA:

Malondialdehyde

QTLs:

Quantitative trait loci

RIL:

Recombinant inbred line

RWC:

Relative water content

SNPs:

Single nucleotide polymorphisms

SR:

Survival rate

WT:

Wild-type

RAPD:

Random amplified polymorphic DNA

LG:

Linkage group

AFLP:

Amplified fragment length polymorphism

SSR:

Simple sequence repeat

CMLM:

Compressed mixed linear model

PC:

Principal component

LD:

Linkage disequilibrium

ABA:

Abscisic acid

CV:

Coefficient of variation

XIP:

X-intrinsic protein

MS:

Murashige and Skoog

RT-qPCR:

Quantitative real-time reverse transcription-polymerase chain reaction

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Funding

This work was supported by grants from the National Key R&D Program of China (Nos. 2018YFD1000700 and 2018YFD1000704), Supported by China Agriculture Research System of MOF and MARA- Food Legumes (CARS-08), the Agricultural Science and Technology Innovation Program of CAAS.

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  1. Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China

    Lei Wu, Yujie Chang, Lanfen Wang, Shumin Wang & Jing Wu

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  1. Lei Wu
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  2. Yujie Chang
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  3. Lanfen Wang
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  4. Shumin Wang
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  5. Jing Wu
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LW and JW designed the project. LW conducted the main experiments. YC, LFW and SW participated in data analysis. LW, SW and JW wrote the manuscript.

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Correspondence to Jing Wu.

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Wu, L., Chang, Y., Wang, L. et al. The aquaporin gene PvXIP1;2 conferring drought resistance identified by GWAS at seedling stage in common bean. Theor Appl Genet 135, 485–500 (2022). https://doi.org/10.1007/s00122-021-03978-w

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