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GWAS 在不同小麦预育种质中揭示了 4D 染色体上对检疫性疾病卡那尔叶斑病的一个新的抗性位点。

GWAS revealed a novel resistance locus on chromosome 4D for the quarantine disease Karnal bunt in diverse wheat pre-breeding germplasm.

机构信息

International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45, El Batán, Texcoco, C.P. 56237, México.

Geneshifters, 222 Mary Jena Lane, Pullman, WA, 99163, USA.

出版信息

Sci Rep. 2020 Apr 7;10(1):5999. doi: 10.1038/s41598-020-62711-7.

DOI:10.1038/s41598-020-62711-7
PMID:32265455
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7138846/
Abstract

This study was initiated to identify genomic regions conferring resistance to Karnal Bunt (KB) disease in wheat through a genome-wide association study (GWAS) on a set of 179 pre-breeding lines (PBLs). A GWAS of 6,382 high-quality DArTseq SNPs revealed 15 significant SNPs (P-value <10) on chromosomes 2D, 3B, 4D and 7B that were associated with KB resistance in individual years. In particular, two SNPs (chromosome 4D) had the maximum R values: SNP 1114200 | F | 0-63:T > C at 1.571 cM and R of 12.49% and SNP 1103052 | F | 0-61:C > A at 1.574 cM and R of 9.02%. These two SNPs displayed strong linkage disequilibrium (LD). An in silico analysis of SNPs on chromosome 4D identified two candidate gene hits, TraesCS4D02G352200 (TaNox8; an NADPH oxidase) and TraesCS4D02G350300 (a rhomboid-like protein belonging to family S54), with SNPs 1103052 | F | 0-61:C > A and 1101835 | F | 0-5:C > A, respectively, both of which function in biotic stress tolerance. The epistatic interaction analysis revealed significant interactions among 4D and 7B loci. A pedigree analysis of confirmed resistant PBLs revealed that Aegilops species is one of the parents and contributed the D genome in these resistant PBLs. These identified lines can be crossed with any elite cultivar across the globe to incorporate novel KB resistance identified on 4B.

摘要

本研究旨在通过对 179 个预育种系（PBL）进行全基因组关联研究（GWAS），鉴定小麦对卡纳尔布伦特病（KB）的抗性基因组区域。对 6382 个高质量 DArTseq SNP 的 GWAS 显示，在第 2D、3B、4D 和 7B 染色体上有 15 个与个体年份 KB 抗性相关的显著 SNP（P 值<10）。特别是两个 SNP（4D 染色体）具有最大的 R 值：SNP 1114200 | F | 0-63：T>C 在 1.571 cM 处，R 值为 12.49%，SNP 1103052 | F | 0-61：C>A 在 1.574 cM 处，R 值为 9.02%。这两个 SNP 显示出强烈的连锁不平衡（LD）。对 4D 染色体上 SNP 的计算机分析确定了两个候选基因，TraesCS4D02G352200（TaNox8；一种 NADPH 氧化酶）和 TraesCS4D02G350300（一种属于 S54 家族的类菱形蛋白），SNP 1103052 | F | 0-61：C>A 和 1101835 | F | 0-5：C>A，分别位于 SNP 1103052 | F | 0-61：C>A 和 1101835 | F | 0-5：C>A，它们都在生物胁迫耐受中发挥作用。上位性互作分析显示 4D 和 7B 位点之间存在显著的互作。对已确认抗性 PBL 的系谱分析表明，Aegilops 种是亲本之一，在这些抗性 PBL 中贡献了 D 基因组。这些鉴定的系谱可以与全球任何优良品种杂交，以纳入在 4B 上发现的新的 KB 抗性。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1443/7138846/8e831ed5afad/41598_2020_62711_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1443/7138846/ab38a51b387b/41598_2020_62711_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1443/7138846/27c07fe94c60/41598_2020_62711_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1443/7138846/826bb8028590/41598_2020_62711_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1443/7138846/b46fb4f33c5d/41598_2020_62711_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1443/7138846/8e831ed5afad/41598_2020_62711_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1443/7138846/ab38a51b387b/41598_2020_62711_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1443/7138846/27c07fe94c60/41598_2020_62711_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1443/7138846/826bb8028590/41598_2020_62711_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1443/7138846/b46fb4f33c5d/41598_2020_62711_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1443/7138846/8e831ed5afad/41598_2020_62711_Fig5_HTML.jpg

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