粳稻嵌套关联图谱群体:开发、特征描述及在全基因组关联研究中的应用

IF 5.4 Q1 PLANT SCIENCES Current Plant Biology Pub Date : 2024-10-18 DOI:10.1016/j.cpb.2024.100401
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引用次数: 0

摘要

多亲本制图群体在剖析数量性状和快速鉴定遗传决定因素方面具有巨大潜力。我们建立了一个粳稻嵌套关联作图群体 KNU_NAM,该群体由 880 个品系组成,这些品系来自 10 个著名品种的近交系重组(RIL)家族和韩国优良品种 "新东真"。KNU_NAM 的遗传特征发现了 48,159 个多态 SNPs,家系数从 18,787 个到 42,578 个不等,平均每个家系有 30,019 个 SNPs。对 KNU_NAM 的进一步分子多样性分析表明,种群结构缩小,遗传多样性广泛。对五个形态性状的全基因组关联研究(GWAS)发现了 47 个显著的标记-性状关联(MTAs),其中 18 个 MTAs 位于 9 号染色体上。对该区域的连锁不平衡(LD)区块分析发现了 15 个单倍型,并确定了与圆锥花序结构相关的五个关键基因:OsDEP1、OsEATB、OsLGD1 和 OsSPL18。此外,第 7 号染色体上的两个非同义 MTA 位于 OsPRR37/Ghd7.1 的外显子上,该基因与株高、头期和每圆锥花序的粒数有关。对这些热点区域单倍型的进一步表型表现分析表明,这些单倍型在目标性状上存在显著差异。该研究验证了 KNU_NAM 和 GWAS 在水稻育种计划中用于高分辨率遗传图谱的潜力,强调了这些群体在提高水稻遗传多样性和改进性状选择方面的实用性。
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Nested association mapping population in japonica rice: Development, characterization, and application in genome-wide association studies
Multiparental mapping populations hold great potential for dissecting quantitative traits and rapidly identifying genetic determinants. We developed a japonica nested association mapping population, KNU_NAM, comprising 880 lines derived from ten recombinant inbred lines (RILs) families of prominent varieties and the elite Korean variety Shindongjin. Genetic characterization of KNU_NAM revealed 48,159 polymorphic SNPs, with family counts ranging from 18,787 to 42,578 and an average of 30,019 SNPs per family. Further molecular diversity analysis of KNU_NAM indicated reduced population structure and broad genetic diversity. Genome-wide association studies (GWAS) on five morphological traits identified 47 significant marker-trait associations (MTAs), with a set of 18 MTAs located on chromosome 9. Linkage disequilibrium (LD) block analysis of this region revealed 15 haplotypes and identified five key genes associated with panicle architecture: OsDEP1, OsEATB, OsLGD1, and OsSPL18. Additionally, two non-synonymous MTAs on chromosome 7 were located on the exon of OsPRR37/Ghd7.1, a gene associated with plant height, heading date, and grain number per panicle. Further phenotypic performance analysis of haplotypes from these hotspot regions revealed significant differences in the targeted traits. The study validates the potential of KNU_NAM and GWAS for high-resolution genetic mapping in rice breeding programs, highlighting the utility of these populations for enhancing genetic diversity and improving trait selection in rice.
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来源期刊
Current Plant Biology
Current Plant Biology Agricultural and Biological Sciences-Plant Science
CiteScore
10.90
自引率
1.90%
发文量
32
审稿时长
50 days
期刊介绍: Current Plant Biology aims to acknowledge and encourage interdisciplinary research in fundamental plant sciences with scope to address crop improvement, biodiversity, nutrition and human health. It publishes review articles, original research papers, method papers and short articles in plant research fields, such as systems biology, cell biology, genetics, epigenetics, mathematical modeling, signal transduction, plant-microbe interactions, synthetic biology, developmental biology, biochemistry, molecular biology, physiology, biotechnologies, bioinformatics and plant genomic resources.
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