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.
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Data availability
The original contributions presented in this study are included in the article/Supplementary Material, and further inquiries can be directed to the corresponding author. Raw sequencing data of genome re-sequencing are available in the Genome Sequence Archive (https://bigd.big.ac.cn/gsa/) with Bio-project IDs PRJCA002835 and PRJCA002836. All the materials in this study are available upon request.
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Funding
This work was supported by the National Nature Science Foundation of China (Grant Nos. 31972498 and 32172662). The computations in this paper were run on the bioinformatics computing platform of the National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University.
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Pan Yuan, Haijiang Liu, and Lei Shi designed the research, reviewed the writing, and drafted the manuscript. Pan Yuan, Haijiang Liu, and Xiaohua Wang participated the experiments. John P. Hammond participated in the manuscript revision.
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ESM 1
Fig. S1. Correlation of eight root related traits at low phosphorus supplies. (DOCX 257 kb)
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Fig. S2. The LD decay of an association panel of B. napus. (DOCX 45 kb)
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Fig. S3. Population structure of an association panel of B. napus with K from 2 to 8. (DOCX 135 kb)
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Fig. S4. The kinship of an association panel of 370 B. napus accessions. (DOCX 175 kb)
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Fig. S5. Distribution of linkage disequilibrium block sizes across all chromosomes. (DOCX 63 kb)
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Table S1. List of 370 accessions of B. napus used in the study. (XLSX 20 kb)
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Table S2. Primers used for qRT-PCR. (XLSX 9 kb)
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Table S3. Root related traits at low phosphorus supplies in an association panel of B. napus. (XLSX 30 kb)
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Table S4. AMOVA analysis between the K = 4 assigned populations in Brassica napus. (XLSX 9 kb)
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Table S5. Linkage disequilibrium block in this study. (XLSX 28730 kb)
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Table S6. Significant SNP loci for root related traits of B. napus by genome wide association study at low phosphorus supplies. (XLSX 12 kb)
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Table S7. LD blocks harboring significant SNPs associated with RSA. (XLSX 12 kb)
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Table S8. Candidate genes within LD decay value up and down the lead SNPs (chrA06_19934701, chrC03_3535476 and chrC07_42348526) for root related traits. (XLSX 43 kb)
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Table S9. Comparison of SNPs detected by WGR for RSA in this study with previously identified SNPs by 60 K SNP chip for RSA at a low phosphorus supply. (XLSX 10 kb)
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Yuan, P., Liu, H., Wang, X. et al. Genome-wide association study reveals candidate genes controlling root system architecture under low phosphorus supply at seedling stage in Brassica napus. Mol Breeding 43, 63 (2023). https://doi.org/10.1007/s11032-023-01411-2
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DOI: https://doi.org/10.1007/s11032-023-01411-2