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Genetic dissection of drought resistance based on root traits at the bud 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 196 loci significantly associated with drought stress based on root traits. Candidate genes identified in the regions of these loci include homologs of known drought resistance genes in A. thaliana.

Abstract

Drought is the main abiotic constraint of the production of common bean. Improved adaptation to drought environments has become a main goal of crop breeding due to the increasing scarcity of water that will occur in the future. The overall objective of our study was to identify genomic regions associated with drought resistance based on root traits using genome-wide association analysis. A natural population of 438 common bean accessions was evaluated for root traits: root surface area, root average diameter, root volume, total root length, taproot length, lateral root number, root dry weight, lateral root length, special root weight/length, using seed germination pouches under drought conditions and in well-watered environments. The coefficient of variation ranged from 11.24% (root average diameter) to 38.19% (root dry weight) in the well-watered environment and from 9.61% (root average diameter) to 39.05% (lateral root length) under drought stress. A whole-genome resequencing-derived SNP dataset revealed 196 loci containing 230 candidate SNPs associated with drought resistance. Seventeen candidate SNPs were simultaneously associated with more than two traits. Forty-one loci were simultaneously associated with more than two traits, and eleven loci were colocated with loci previously reported to be related to drought resistance. Candidate genes of the associated loci included the ABA-responsive element-binding protein family, MYB, NAC, the protein kinase superfamily, etc. These results revealed promising alleles linked to drought resistance or root traits, providing insights into the genetic basis of drought resistance and roots, which will be useful for common bean improvement.

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Availability of data and material

Data supporting the current study can be obtained by contacting the corresponding author (wangshumin@caas.cn).

Code availability

Not applicable.

Abbreviations

GWAS:

Genome-wide association study

SNP:

Single nucleotide polymorphisms

CHR:

Chromosome

LD:

Linkage disequilibrium

QTL:

Quantitative trait loci

ABA:

Abscisic acid

RSA:

Root surface area

RAD:

Root average diameter

RV:

Root volume

TRL:

Total root length

TL:

Taproot length

LRN:

Lateral root number

RDW:

Root dry weight

LRL:

Lateral root length

SRL:

Special root weight/length

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Funding

This work was supported by grants from the National Key R & D Program of China (2018YFD1000700/2018YFD1000704), the Ministry of Agriculture of China [the earmarked fund for the China Agriculture Research System (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, Jing Wu & Shumin Wang

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  1. Lei Wu
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L W, YJ C performed QTL analysis and characterized candidate genes. L W, LF W, J W and SM W designed and conducted the field experiments and generated phenotype data. L W, YJ C and J W wrote and finalized the manuscript. SM W planned and organized this study, and co-wrote the manuscript. All authors contributed to and approved the final manuscript.

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Correspondence to Shumin Wang.

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Communicated by Janila Pasupuleti.

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Wu, L., Chang, Y., Wang, L. et al. Genetic dissection of drought resistance based on root traits at the bud stage in common bean. Theor Appl Genet 134, 1047–1061 (2021). https://doi.org/10.1007/s00122-020-03750-6

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