The Sikkim-Himalaya represents one of the unique reservoirs of rice genetic resources in India owing to the presence of a large number of landraces adapted to extreme climatic and edaphic conditions. This valuable gene pool is now under threat due to the introduction of high-yielding varieties, wanting suitable genetic intervention for enhancing their productivity, and thus economic viability. Development of lodging resistant, high-yielding varieties tolerant to soil acidity through association mapping aided marker-assisted breeding programmes can help achieve this in a fast and efficient manner. But this requires information on genetic diversity, population structure, etc., of the germplasm collection, which is strikingly lacking. We, therefore, characterized a set of 53 rice landraces from Sikkim to address the above issues. The results revealed moderate diversity, poor divergence and high gene flow in our germplasm collection attesting its utility as an association mapping panel. Further, a total of 115 putative marker-trait associations (P < 0.05, R2 ≥ 10%) were obtained using the general linear model and mixed linear models of which 25 were identical in both. Some of the associated markers were positioned in those regions where Qualitative Trait Loci have been previously identified in rice, providing credence to our results. The resources generated from this study will benefit the rice breeders from this region and elsewhere for targeting the yield and related traits, in addition to conservation efforts by the interested researchers.

中文翻译：

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锡金-喜马拉雅地区水稻（Oryza sativa L.）地方品种的遗传多样性及其在全基因组关联分析中的应用

由于存在大量适应极端气候和土壤条件的地方品种，锡金-喜马拉雅地区是印度独特的水稻遗传资源库之一。由于高产品种的引入，这个宝贵的基因库现在正面临威胁，需要合适的基因干预来提高它们的生产力，从而提高经济可行性。通过关联绘图辅助标记辅助育种计划开发抗倒伏、耐土壤酸度的高产品种可以帮助以快速有效的方式实现这一目标。但这需要种质资源收集的遗传多样性、种群结构等方面的信息，而这些信息明显缺乏。因此，我们对来自锡金的 53 个水稻地方品种进行了表征，以解决上述问题。结果显示，我们的种质资源库中的多样性适中、差异性差和基因流动性高，证明了其作为关联作图面板的实用性。此外，共有 115 个推定的标记-性状关联（磷< 0.05,R2≥ 10%）是使用一般线性模型和混合线性模型获得的，其中 25 个是相同的。一些相关标记位于先前已在水稻中鉴定出定性性状基因座的那些区域，这为我们的结果提供了依据。除了感兴趣的研究人员的保护工作外，这项研究产生的资源将使该地区和其他地方的水稻育种者受益，以瞄准产量和相关性状。