Genome wide association study identifies donors and candidate genes underlying QTLs for resistance to sheath blight in a collection of Oryza nivara (Sharma et Shastry) accessions

IF 1.6 3区农林科学 Q2 AGRONOMY

Euphytica Pub Date : 2024-03-28 DOI:10.1007/s10681-024-03325-2

{"title":"Genome wide association study identifies donors and candidate genes underlying QTLs for resistance to sheath blight in a collection of Oryza nivara (Sharma et Shastry) accessions","authors":"","doi":"10.1007/s10681-024-03325-2","DOIUrl":null,"url":null,"abstract":"<h3>Abstract</h3> <p>Sheath blight is an emerging disease of rice that appears in rice production areas worldwide. A total of 294 <em>O. nivara</em> accessions along with susceptible check PR114, the cultivated rice, were screened against sheath blight under field conditions for three consecutive years. Based on screening, 15 accessions were identified that showed moderate resistance reaction to sheath blight across the years. However, none of the accession showed highly resistant reaction. Sheath blight resistance was found to be quantitative controlled based on near normal distribution of lesion length. These 15 accessions further showed same level of resistance in detached tiller culture method and are proposed as the candidate donors for resistance to sheath blight, to be used in rice breeding programme. Further Multi locus-GWAS implemented using the 3VmrMLM model in 294 <em>O. nivara</em> accessions using 22,261 SNPs identified 11 marker-trait associations (MTAs) on 8 different chromosomes with the LOD score ranging from 3.34 to 20.58, while 10 out of 11 significant showed significant statistical difference based on Kruskal–Wallis test. Based on the LD decay in the panel, an interval of ± 300 kb of each significant MTA was investigated to identify candidate genes governing resistance to sheath blight. Among 11 QTL regions, a total of 19 candidate genes were found to be differentially expressed in response to the sheath blight pathogen based on in-depth <em>in silico </em>analysis, including those encoding lignin biosynthesis proteins, calcineurin B, thaumatin proteins, protein kinase domains, NBS-LRR domains, and cytochrome P450 oxidoreductases. The study highlighted 15 sheath blight resistant donors along with 10 QTL regions and 19 candidate genes that will provide a platform for understanding genetic basis of sheath blight resistance in rice.</p>","PeriodicalId":11803,"journal":{"name":"Euphytica","volume":"43 1","pages":""},"PeriodicalIF":1.6000,"publicationDate":"2024-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Euphytica","FirstCategoryId":"97","ListUrlMain":"https://doi.org/10.1007/s10681-024-03325-2","RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"AGRONOMY","Score":null,"Total":0}

引用次数: 0

Abstract

Sheath blight is an emerging disease of rice that appears in rice production areas worldwide. A total of 294 O. nivara accessions along with susceptible check PR114, the cultivated rice, were screened against sheath blight under field conditions for three consecutive years. Based on screening, 15 accessions were identified that showed moderate resistance reaction to sheath blight across the years. However, none of the accession showed highly resistant reaction. Sheath blight resistance was found to be quantitative controlled based on near normal distribution of lesion length. These 15 accessions further showed same level of resistance in detached tiller culture method and are proposed as the candidate donors for resistance to sheath blight, to be used in rice breeding programme. Further Multi locus-GWAS implemented using the 3VmrMLM model in 294 O. nivara accessions using 22,261 SNPs identified 11 marker-trait associations (MTAs) on 8 different chromosomes with the LOD score ranging from 3.34 to 20.58, while 10 out of 11 significant showed significant statistical difference based on Kruskal–Wallis test. Based on the LD decay in the panel, an interval of ± 300 kb of each significant MTA was investigated to identify candidate genes governing resistance to sheath blight. Among 11 QTL regions, a total of 19 candidate genes were found to be differentially expressed in response to the sheath blight pathogen based on in-depth in silico analysis, including those encoding lignin biosynthesis proteins, calcineurin B, thaumatin proteins, protein kinase domains, NBS-LRR domains, and cytochrome P450 oxidoreductases. The study highlighted 15 sheath blight resistant donors along with 10 QTL regions and 19 candidate genes that will provide a platform for understanding genetic basis of sheath blight resistance in rice.

查看原文本刊更多论文

全基因组关联研究确定了Oryza nivara (Sharma et Shastry)登录品系中抗鞘枯病QTLs的供体和候选基因

摘要鞘枯病是一种新出现的水稻病害，在世界各地的水稻产区都有发生。连续三年在田间条件下对 294 个 O. nivara 品种和易感对照 PR114（栽培稻）进行了鞘枯病抗性筛选。根据筛选结果，确定了 15 个品种在各年对鞘枯病表现出中等抗性。然而，没有一个品种表现出高度抗性。根据病斑长度的近似正态分布，发现鞘枯病的抗性是定量控制的。这 15 个品种在离体分蘖培养法中进一步表现出相同的抗性水平，因此被建议作为抗鞘枯病的候选供体，用于水稻育种计划。此外，利用 3VmrMLM 模型对 294 个 O. nivara 接种的 22,261 个 SNPs 进行了多位点-GWAS，在 8 条不同的染色体上发现了 11 个标记-性状关联（MTAs），其 LOD 分从 3.34 到 20.58 不等，而根据 Kruskal-Wallis 检验，11 个显著位点中有 10 个表现出显著的统计差异。根据面板中的 LD 衰减，研究了每个显著 MTA 的 ± 300 kb 区间，以确定抗鞘枯病的候选基因。在 11 个 QTL 区域中，根据深入的硅学分析，共发现 19 个候选基因在对鞘枯病病原体的反应中存在差异表达，其中包括编码木质素生物合成蛋白、钙调素 B、thaumatin 蛋白、蛋白激酶结构域、NBS-LRR 结构域和细胞色素 P450 氧化还原酶的基因。该研究强调了 15 个抗鞘枯病供体以及 10 个 QTL 区域和 19 个候选基因，这将为了解水稻抗鞘枯病的遗传基础提供一个平台。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

Euphytica 农林科学-农艺学

CiteScore

3.80

自引率

5.30%

发文量

157

审稿时长

4.5 months

期刊介绍： Euphytica is an international journal on theoretical and applied aspects of plant breeding. It publishes critical reviews and papers on the results of original research related to plant breeding. The integration of modern and traditional plant breeding is a growing field of research using transgenic crop plants and/or marker assisted breeding in combination with traditional breeding tools. The content should cover the interests of researchers directly or indirectly involved in plant breeding, at universities, breeding institutes, seed industries, plant biotech companies and industries using plant raw materials, and promote stability, adaptability and sustainability in agriculture and agro-industries.