Identification of significant SNPs and candidate loci for blast disease resistance via GWAS and population structure analysis in ARC panel of Oryza sativa.

IF 3.4 3区生物学 Q1 PLANT SCIENCES

Physiology and Molecular Biology of Plants Pub Date : 2024-10-01 Epub Date: 2024-10-26 DOI:10.1007/s12298-024-01518-6

Parinda Barua, Munmi Phukon, Sunita Munda, Vipin Ranga, R Sruthi, Jyoti Lekha Borah, Janardan Das, Pompi Dutta, Ashok Bhattacharyya, Mahendra Kumar Modi, Sanjay Kumar Chetia

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引用次数: 0

Abstract

Pyricularia (syn. Magnaporthe) oryzae is responsible for the blast disease in rice resulting in a greater extent of yield loss. However, some of the cultivars of rice have the ability to survive this devastating infection due to the presence of R (resistance) genes. Therefore, genome wide association study (GWAS) was undertaken using a panel of 400 rice landraces (ARC panel) and a set of filtered 38,723 single nucleotide polymorphisms (SNPs). The highest SNPs were mapped to chromosome 1 with a number of 4332 SNPs and lowest (2252) in chromosome 12. The ARC panel was evaluated phenotypically which revealed that 6% of the selected cultivars has resistance to rice blast disease with SES score of 1. The majority of the resistant cultivars belong to the group Asra of the panel. The population structure analysis was executed wherein three genetic subpopulations were identified namely RC1, RC2, RC3 and an admixture population constituting 48 accessions. Further, GWAS detected 15 significant association signal with P value in the range of 1.03E-05 to 1.03E-04, effect ranged from - 1.18 to 1.06, phenotypic variance explained was from 0 to 7.14%, R² of 0.047 to 0.058, and minor allele frequency of 0.107 to 0.444. Eleven (Os01g39980, Os01g56130, Os01g67100, Os01g67110, Os03g41030, Os04g33310, Os07g42104, Os09g06464, Os09g08920, Os09g38800, Os12g37680) out of these 15 significant associations were identified as the candidate loci for the blast resistance in rice that will serve as an important genetic resistance source to be introgressed into an elite rice line in future breeding programs for deciphering blast resistance in rice. The GWAS study presented in this article helped to uncover significant gene regions which encode proteins to resist blast infection in rice plant. This is the first report on the GWAS analysis for blast resistance in unique landraces of rice from Northeast India employing single nucleotide polymorphism.

Supplementary information: The online version contains supplementary material available at 10.1007/s12298-024-01518-6.

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通过基因组分析和种群结构分析，鉴定抗稻瘟病的重要 SNPs 和候选位点。

Pyricularia (syn. Magnaporthe) oryzae 是水稻稻瘟病的致病菌，会造成较大的产量损失。然而，由于存在 R（抗性）基因，一些水稻栽培品种有能力在这种毁灭性感染中存活下来。因此，研究人员利用 400 个水稻品种（ARC 品种）和一组经过筛选的 38,723 个单核苷酸多态性（SNPs）进行了全基因组关联研究（GWAS）。最高的 SNPs 映射在 1 号染色体上，有 4332 个 SNPs，最低的（2252 个）映射在 12 号染色体上。对 ARC 群体进行了表型评估，结果表明 6% 的入选品种对稻瘟病具有抗性，SES 得分为 1。通过种群结构分析，确定了三个遗传亚群，即 RC1、RC2、RC3 和一个由 48 个品种组成的混合群。此外，GWAS 发现了 15 个显著的关联信号，P 值范围在 1.03E-05 至 1.03E-04，效应范围在-1.18 至 1.06 之间，表型变异解释率在 0 至 7.14%之间，R2 在 0.047 至 0.058 之间，小等位基因频率在 0.107 至 0.444 之间。11个等位基因（Os01g39980、Os01g56130、Os01g67100、Os01g67110、Os03g41030、Os04g33310、Os07g42104、Os09g06464、Os09g08920、Os09g38800、在这 15 个显著相关位点中，Os03g41030、Os04g33310、Os07g42104、Os09g06464、Os09g08920、Os09g38800 和 Os12g37680 被确定为水稻抗稻瘟病的候选位点。本文介绍的 GWAS 研究有助于发现编码水稻抗稻瘟病蛋白的重要基因区域。这是首次报道利用单核苷酸多态性对印度东北部水稻独特陆稻品种的稻瘟病抗性进行 GWAS 分析：在线版本包含补充材料，见 10.1007/s12298-024-01518-6。

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来源期刊

Physiology and Molecular Biology of Plants PLANT SCIENCES-

CiteScore

7.10

自引率

0.00%

发文量

126

期刊介绍： Founded in 1995, Physiology and Molecular Biology of Plants (PMBP) is a peer reviewed monthly journal co-published by Springer Nature. It contains research and review articles, short communications, commentaries, book reviews etc., in all areas of functional plant biology including, but not limited to plant physiology, biochemistry, molecular genetics, molecular pathology, biophysics, cell and molecular biology, genetics, genomics and bioinformatics. Its integrated and interdisciplinary approach reflects the global growth trajectories in functional plant biology, attracting authors/editors/reviewers from over 98 countries.