Genome-wide association study reveals candidate genes controlling root system architecture under low phosphorus supply at seedling stage in Brassica napus

Pan Yuan; Haijiang Liu; Xiaohua Wang; John P Hammond; Lei Shi

doi:10.1007/s11032-023-01411-2

Genome-wide association study reveals candidate genes controlling root system architecture under low phosphorus supply at seedling stage in Brassica napus

Mol Breed. 2023 Jul 28;43(8):63. doi: 10.1007/s11032-023-01411-2. eCollection 2023 Aug.

Authors

Pan Yuan^{1

2}, Haijiang Liu^{1

2}, Xiaohua Wang³, John P Hammond⁴, Lei Shi^{1

2}

Affiliations

¹ National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China.
² Key Lab of Cultivated Land Conservation, Ministry of Agriculture and Rural Affairs/Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070 China.
³ College of Agriculture and Forestry Science, Linyi University, Linyi, 276000 China.
⁴ School of Agriculture, Policy and Development, University of Reading, Reading, RG6 6AR UK.

PMID: 37521313
PMCID: PMC10382450 (available on 2024-07-28)
DOI: 10.1007/s11032-023-01411-2

Abstract

Optimal root system architecture (RSA) is essential for vigorous growth and yield in crops. Plants have evolved adaptive mechanisms in response to low phosphorus (LP) stress, and one of those is changes in RSA. Here, more than five million single-nucleotide polymorphisms (SNPs) obtained from whole-genome re-sequencing data (WGR) of an association panel of 370 oilseed rape (Brassica napus L.) were used to conduct a genome-wide association study (GWAS) of RSA traits of the panel at LP in "pouch and wick" system. Fifty-two SNPs were forcefully associated with lateral root length (LRL), total root length (TRL), lateral root density (LRD), lateral root number (LRN), mean lateral root length (MLRL), and root dry weight (RDW) at LP. There were significant correlations between phenotypic variation and the number of favorable alleles of the associated loci on chromosomes A06 (chrA06_20030601), C03 (chrC03_3535483), and C07 (chrC07_42348561), respectively. Three candidate genes (BnaA06g29270D, BnaC03g07130D, and BnaC07g43230D) were detected by combining transcriptome, candidate gene association analysis, and haplotype analysis. Cultivar carrying "CCGC" at BnaA06g29270DHap1, "CAAT" at BnaC03g07130DHap1, and "ATC" at BnaC07g43230DHap1 had greater LRL, LRN, and RDW than lines carrying other haplotypes at LP supply. The RSA of a cultivar harboring the three favorable haplotypes was further confirmed by solution culture experiments. These findings define exquisite insights into genetic architectures underlying B. napus RSA at LP and provide valuable gene resources for root breeding.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-023-01411-2.

Keywords: Genome-wide association study (GWAS); Haplotype analysis; Low phosphorus supply; Oilseed rape (B. napus L.); Root system architecture (RSA).

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