Submergence damage to rice was reported as one of the major problems in rainfed lowland areas where the water remains. This study assessed the submergence tolerance of core collection during the seedling stage of the rice using dry seeds. Also, genome-wide association study (GWAS) combined with principal component analysis (PCA) and kinship matrix analysis was performed to identify quantitative trait loci (QTL) for submergence tolerance. Through this GWAS analysis, nine lead SNPs were confirmed to be associated with submergence tolerance, and a linkage disequilibrium (LD) decay analysis identified the 230 kb exploratory range for the detection of QTLs and candidate genes. Nine QTL were detected, on chromosomes 3 (
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Flooding often occurs during the vegetative stage in freshwater swamps and rainfed lowlands, and therefore submergence tolerant rice varieties are needed. This study was aimed at evaluating rice lines to submergence stress. The experiments were conducted at Indonesian Center for Rice Research (ICRR) experimental station in Sukamandi, Subang, West Java, each in different environmental conditions: (1) submergence condition, which was conducted in a submergence pool and (2) optimal condition, which was conducted in the irrigation field. Ninety-five lines and four check varieties, namely Inpari 30 Ciherang Sub1, IR42, Limboto, and IR20 were used. An augmented design with five blocks was followed in each environment. Three selection methods were used: (1) selection based on survival rate and vigor, (2) selection based on productivity under submergence and sensitivity index on productivity character, (3) selection based on the weighted selection index using sensitivity index variables of morphological and agronomic characters. The clustergram analysis with heatmaps method was used to compile of three previous selection methods to facilitate scientist in clarifying tolerant and sensitive lines. There were eighteen lines selected as tolerant to submergence stress, i.e., line no. 9, 15, 34, 46, 47, 48, 49, 50, 53, 55, 56, 57, 59, 60, 61, 62, 89, and 90. These lines are considered promising for breeding improved rice varieties tolerant to submergence.
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The
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The increased severity and frequency of flooding is causing greater yield reductions in most rice-growing areas. To address this, popular cultivars were improved through introgression of
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