Anaerobic germination (AG) is an important trait for direct-seeded rice (DSR) to be successful. Rice usually has low germination under anaerobic conditions, which leads to a poor crop stand in DSR when rain occurs after seeding. The ability of rice to germinate under water reduces the risk of poor crop stand. Further, this allows the use of water as a method of weed control. The identification of the genetic factors leading to high anaerobic germination is required to develop improved DSR varieties. In the present study, two BC1F2:3 mapping families involving a common parent with anaerobic germination potential, Kalarata, an indica landrace, and two recurrent parents, NSIC Rc222 and NSIC Rc238, were used. Phenotyping was done under two environmental conditions and genotyping was carried out through the KASP SNP genotyping platform. A total of 185 and 189 individuals genotyped with 170 and 179 polymorphic SNPs were used for QTL analysis for the two populations, Kalarata/NSIC Rc238 and Kalarata/NSIC Rc222, respectively. A total of five QTLs on chromosomes 3, 5, 6, 7, and 8 for survival (SUR) and four QTLs on chromosomes 1, 3 (two locations), and 7 for the trait seedling height (SH) across the populations and over the screening conditions were identified. Except for the QTLs on chromosomes 5 and 8, the parent with AG potential, Kalarata, contributed all the other QTLs. Among the five QTLs for SUR, the second-largest QTL (qSUR6-1) was novel for AG potential in rice, showing a stable expression in terms of genetic background and screening conditions explaining 11.96% to 16.01% of the phenotypic variation. The QTL for SH (qSH1-1) was also novel. Considering different genetic backgrounds and different screening conditions, the QTLs identified for the trait SUR explained phenotypic variation in the range of 57.60% to 73.09% while that for the trait SH ranged from 13.53% to 34.30%.

中文翻译：

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水稻稳定无氧萌发背后的遗传学破译：表型，QTL鉴定和相互作用分析。

厌氧萌发（AG）是直接播种水稻（DSR）成功的重要特征。水稻通常在厌氧条件下发芽率低，导致播种后下雨时，DSR的农作物收成不好。水稻在水中发芽的能力降低了作物歉收的风险。此外，这允许使用水作为除草方法。要开发改良的DSR品种，需要鉴定导致高厌氧发芽的遗传因素。在本研究中，使用了两个BC1F2：3作图族，涉及一个具有厌氧发芽潜力的普通亲本，印度Ka种Kalarata，以及两个亲本，NSIC Rc222和NSIC Rc238。在两种环境条件下进行表型分型，并通过KASP SNP基因分型平台进行基因分型。分别对Kalarata / NSIC Rc238和Kalarata / NSIC Rc222这两个种群的185和189个具有170和179个多态性SNP基因型的个体进行了QTL分析。在整个种群及以上种群中，第3、5、6、7和8号染色体上共有5个QTL用于生存（SUR），第1、3号染色体上具有4个QTL（两个位置），而对于整个种群及以上种群的性状苗高（SH）则为7个确定筛选条件。除了5号和8号染色体上的QTL外，具有AG潜力的亲本Kalarata贡献了所有其他QTL。在五个SUR的QTL中，第二大QTL（qSUR6-1）具有水稻AG潜力，在遗传背景和筛选条件方面表现出稳定的表达，解释了11.96％至16.01％的表型变异。SH（qSH1-1）的QTL也很新颖。