Resequencing of 683 common bean genotypes identifies yield component trait associations across a north–south cline

Abstract

We conducted a large-scale genome-wide association study evaluation of 683 common bean accessions, including landraces and breeding lines, grown over 3 years and in four environments across China, ranging in latitude from 18.23° to 45.75° N, with different planting dates and abiotic or biotic stresses. A total of 505 loci were associated with yield components, of which seed size, flowering time and harvest maturity traits were stable across years and environments. Some loci aligned with candidate genes controlling these traits. Yield components were observed to have strong associations with a gene-rich region on the long arm of chromosome 1. Manipulation of seed size, through selection of seed length versus seed width and height, was deemed possible, providing a genome-based means to select for important yield components. This study shows that evaluation of large germplasm collections across north–south geographic clines is useful in the detection of marker associations that determine grain yield in pulses.

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Fig. 1: Diversity in 683 common bean accessions.
Fig. 2: Diagram of SNPs found by resequencing of 683 common bean accessions.
Fig. 3: Summary of MTAs identified.
Fig. 4: A genetic locus for anthracnose resistance on chr. 1.

Data availability

All genomic sequence data sets for genetic diversity analysis and GWAS are available from NCBI under BioProject accession no. PRJNA515107. Genomic variant and genotypic data can be downloaded from https://doi.org/10.5281/zenodo.3236786

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Acknowledgements

We thank X. Zheng and J. Liu at the Chinese Academy of Agricultural Sciences and W. Liu at the China Agricultural University for useful comments on the manuscript and discussions. This work was supported by grants from the National Key R&D Program of China (nos. 2018YFD1000700 and 2018YFD1000704), the National Natural Science Foundation of China (no. 31471559), the Ministry of Agriculture of China (fund earmarked for the China Agriculture Research System, no. CARS-08), the Evans Allen fund at Tennessee State University (no. TENX-07), the Agricultural Science and Technology Innovation Program of CAAS and the Youth Talent Plan of CAAS (to J.F.).

Author information

J.W., L. Wang and S. Wang contributed genetic material. J.W., S. Wang and M.W.B. contributed to generation of whole-genome resequencing data. J.W., J. F., J. Zhang, S.X. and H.Z. worked on GWAS and population genetics analysis. J.W., L. Wang, J.C., S. Wei, S.Z., Y.T., M.C., J. Zhu, L.L., Q.G., C.L., L. Wu., X.L., X.W., Q.W., Z.W. and M.W.B. performed phenotyping, data analysis and/or figure design. J.W., M.W.B. and S. Wang wrote and finalized the manuscript, with advice from J.F. J.W. and S. Wang conceived and designed the study. All authors read and approved the paper.

Correspondence to Matthew W. Blair or Shumin Wang.

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Extended data

Extended Data Fig. 1 Venn diagram distribution of unique single nucleotide polymorphisms (SNPs) among common bean breeding lines (BL) and landraces (L).

Venn diagram distribution of unique single nucleotide polymorphisms (SNPs) among common bean breeding lines (BL) and landraces (L). a) the Chinese national collection (China in text) or from b) outside of China (non-China in text) from whole genome re-sequencing (WGRS).

Extended Data Fig. 2 Population structure and dendograms based on single nucleotide polymorphisms (SNPs) from whole genome re-sequencing (WGRS).

Population structure and dendograms based on single nucleotide polymorphisms (SNPs) from whole genome re-sequencing (WGRS). a, sub-population identity based on K=6 number in STRUCTURE. b, dendogram with seed colors indicated. c, dendogram with distribution of phaseolin type indicated.

Extended Data Fig. 3 Comparison of synonymous and non-synonymous SNPs from genes found in 1 mega base-pair (Mbp) sliding windows across each chromosome of the entire sequenced Phaseolus vulgaris L.

Comparison of synonymous and non-synonymous SNPs from genes found in 1 mega base-pair (Mbp) sliding windows across each chromosome of the entire sequenced Phaseolus vulgaris L. genome found during common bean whole genome re-sequencing (WGRS). Each chromosome diagram shows the overall values for breeding line (blue color) versus landrace (orange color) for all accessions.

Extended Data Fig. 4 Nucleotide polymorphisms of three haplotypes of the Auxin transport gene homolog, Phvul.001G202000, identified from 658 common bean accessions during single nucleotide polymorphism (SNP) analysis of whole genome re-sequencing (WGRS) data.

Nucleotide polymorphisms of three haplotypes of the Auxin transport gene homolog, Phvul.001G202000, identified from 658 common bean accessions during single nucleotide polymorphism (SNP) analysis of whole genome re-sequencing (WGRS) data. Black boxes represent coding regions, black lines represent the introns.

Extended Data Fig. 5 Number of identified marker trait associations (MTA) loci for each of 15 characteristics measured on the entire set of Chinese and Non-China genotypes of Andean and Mesoamerican common beans used in the re-sequencing study.

Number of identified marker trait associations (MTA) loci for each of 15 characteristics measured on the entire set of Chinese and Non-China genotypes of Andean and Mesoamerican common beans used in the re-sequencing study. Number of MTAs for each characteristic are indicated at ends of the vertical bars.

Extended Data Fig. 6 Box plot for seed length, seed height, seed width and days to maturity of common bean in the genome wide association study (GWAS) conducted here.

Box plot for seed length, seed height, seed width and days to maturity of common bean in the genome wide association study (GWAS) conducted here. The different color of boxes represent genotype of the most significant signal. Center line, median; box limits, upper and lower quartiles; whiskers, 1.5× the interquartile range; points, outliers. Environments means phenotype evaluated by three years and four locations, three years are 2014(14), 2015(15) and 2016(16); four locations are HA (Harbin), NY (Nanyang), BIJ (Bijie) and HN (Hainan). (a) seed length, Chr.2: 47,022,865 bp (b) seed height, Chr.2: 47,025,271 bp (c) seed width, Chr.5: 32,508,462 bp (d) days to flower, Chr.1: 45,498,766 bp.

Extended Data Fig. 7 The strongest association signal for growth habit (2015BIJ) of Chr.1 (45,791,065 bp).

The strongest association signal for growth habit (2015BIJ) of Chr.1 (45,791,065 bp). The red dot indicate the strongest association signal. The black pentagons represent the predicted genes, and the arrows indicate the relative orientation. I to V represent five predicted genes (I, Phvul.001G189000; II, Phvul.001G189100; III, Phvul.001G189200; IV, Phvul.001G189300; V, Phvul.001G189400).

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Wu, J., Wang, L., Fu, J. et al. Resequencing of 683 common bean genotypes identifies yield component trait associations across a north–south cline. Nat Genet 52, 118–125 (2020). https://doi.org/10.1038/s41588-019-0546-0

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