Genomic regions and candidate genes selected during the breeding of rice in Vietnam.
Genomic regions and candidate genes selected during the breeding of rice in Vietnam.
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越南水稻育种过程中选择的基因组区域和候选基因。
DOI：
10.1111/eva.13433
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发表时间：
2022-07
影响因子：
4.1
通讯作者：
中科院分区：
文献类型：
--
作者：
越南拥有适应各种条件的水稻地方品种的丰富多样性，这构成了品种持续改进的多样性来源。我们以前在越南水稻中发现了一个强大的种群结构，它被捕获在五个籼稻和四个粳稻亚群中，包括一个偏远的籼稻-5组。在这里，我们利用这种强大的分化和672个本地水稻基因组来识别越南水稻育种过程中选择的基因组区域和基因。我们确定了等位基因频率（XP‐ ST）和群体分化评分（F ST）的显着扭曲模式，这是由本地亚群之间的选择压力差异造成的，后来用GWAS先前在同一面板中确定的QTL对其进行了注释。我们特别关注了外围的Indica-5亚群，因为它可能具有新奇和差异进化，我们注释了52个选定的区域，占水稻基因组的8.1%。我们在这些区域中注释了4576个基因，并选择了65个候选基因作为有前途的育种目标，其中几个含有非同义替换的等位基因。我们的研究结果突出了传统越南地方品种之间的基因组差异，这可能是适应多种环境条件和区域烹饪偏好在一个非常多样化的国家的产物。我们还验证了这种基因组扫描方法的适用性，以确定潜在的区域窝藏新的基因座和等位基因，以培育新一代的可持续和有弹性的水稻。
Vietnam harnesses a rich diversity of rice landraces adapted to a range of conditions, which constitute a largely untapped source of diversity for the continuous improvement of cultivars. We previously identified a strong population structure in Vietnamese rice, which is captured in five Indica and four Japonica subpopulations, including an outlying Indica‐5 group. Here, we leveraged that strong differentiation and 672 native rice genomes to identify genomic regions and genes putatively selected during the breeding of rice in Vietnam. We identified significant distorted patterns in allele frequency (XP‐CLR) and population differentiation scores (F ST) resulting from differential selective pressures between native subpopulations, and later annotated them with QTLs previously identified by GWAS in the same panel. We particularly focussed on the outlying Indica‐5 subpopulation because of its likely novelty and differential evolution, where we annotated 52 selected regions, which represented 8.1% of the rice genome. We annotated the 4576 genes in these regions and selected 65 candidate genes as promising breeding targets, several of which harboured alleles with nonsynonymous substitutions. Our results highlight genomic differences between traditional Vietnamese landraces, which are likely the product of adaption to multiple environmental conditions and regional culinary preferences in a very diverse country. We also verified the applicability of this genome scanning approach to identify potential regions harbouring novel loci and alleles to breed a new generation of sustainable and resilient rice.
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影响因子：
18
作者：
Gutaker, Rafal M.;Groen, Simon C.;Purugganan, Michael D.
通讯作者：
Purugganan, Michael D.
DOI：
10.1016/j.tig.2017.04.002
发表时间：
2017-06
期刊：
Trends in genetics : TIG
影响因子：
--
作者：
Hartfield M;Bataillon T;Glémin S
通讯作者：
Glémin S
影响因子：
7
作者：
Chen, Hua;Patterson, Nick;Reich, David
通讯作者：
Reich, David
影响因子：
1.2
作者：
Cingolani, Pablo;Platts, Adrian;Ruden, Douglas M.
通讯作者：
Ruden, Douglas M.
影响因子：
4.9
作者：
Delteil, Amandine;Blein, Melisande;Morel, Jean-Benoit
通讯作者：
Morel, Jean-Benoit