North Eastern part of India such as Assam is inundated by flood every year where the farmers are forced to grow the traditional tall deep-water rice. Genetic improvement of this type of rice is slow because of insufficient knowledge about their genetic architecture and population structure. In the present investigation, the genetic diversity architecture of 94 deep-water rice genotypes of Assam and association mapping strategy was, for the first time, applied to determine the significant SNPs and genes for deep-water rice. These genotypes are known for their unique elongation ability under deep-water condition. The anaerobic germination (AG) related trait-associated genes identified here can provide affluent resources for rice breeding especially in flood-prone areas. We investigated the genome-wide association studies (GWAS) using 50 K rice genic SNP chip across 94 deep-water rice genotypes collected from different flood-prone districts/villages of Assam. Population structure and diversity analysis revealed that these genotypes were stratified into four sub-populations. Using GWAS approach, 20 significant genes were identified and found to be associated with AG-related traits. Of them, two most relevant genes (OsXDH1and SSXT) have been identified which explain phenotypic variability (R² > 20%) in the population. These genes were located in Chr 3 (LOC_Os03g31550) which encodes for enzyme xanthine dehydrogenase 1(OsXDH1) and in Chr 12 (LOC_Os12g31350) which encodes for SSXT family protein. Both of these genes were found to be associated with anaerobic response index (increase in the coleoptile length under water in anaerobic condition with respect to control), respectively. Interestingly, OsXDH1is involved in purine catabolism pathway and acts as a scavenger of reactive oxygen species in plants, whereas SSXT is GRF1-interacting factor 3. These two candidate genes associated with AG of deep-water rice have been found to be reported for the first time. Thus, this study provides a greater resource for breeders not only for improvement of deep-water rice, but also for AG tolerant variety useful for direct-seeded rice in flood-affected areas.

印度东北部（例如阿萨姆邦）每年都被洪水淹没，农民被迫种植传统的高深水稻米。由于对水稻的遗传结构和种群结构了解不足，因此这种水稻的遗传改良进展缓慢。在本研究中，首次将94种阿萨姆邦深水稻基因型的遗传多样性结构和关联作图策略用于确定深水稻的重要SNP和基因。这些基因型以其在深水条件下的独特延伸能力而闻名。此处鉴定的与厌氧萌发（AG）相关的性状相关基因可以为水稻育种提供丰富的资源，特别是在易发洪水地区。我们调查了使用50 K水稻基因SNP芯片的全基因组关联研究（GWAS），该芯片跨越了从阿萨姆邦易发洪水地区/村庄收集的94种深水水稻基因型。人口结构和多样性分析表明，这些基因型被分为四个亚群。使用GWAS方法，鉴定出20个重要基因，并发现它们与AG相关性状相关。其中，两个最相关的基因（已经鉴定出OsXDH1和SSXT，它们可以解释群体中的表型变异性（R ²  > 20％）。这些基因位于编码黄嘌呤脱氢酶1（OsXDH1）的Chr 3（LOC_Os03g31550）和编码SSXT家族蛋白的Chr 12（LOC_Os12g31350）中。发现这两个基因分别与厌氧反应指数相关（相对于对照，在厌氧条件下水中胚芽鞘长度的增加）。有趣的是，OsXDH1参与嘌呤分解代谢途径，并充当植物中活性氧的清除剂，而SSXT是GRF1相互作用因子3。这两个与深水稻的AG相关的候选基因已被首次报道。因此，这项研究不仅为育种者提供了更大的资源，不仅用于改良深水稻，而且还为在洪灾地区用于直接播种水稻的耐AG品种提供了更多的资源。