Development of weed competitive rice (Oryza sativa L.) cultivars and identification of QTLs governing weed competitive ability

Breeding for new rice cultivars with weed competitive ability traits provides a new strategy for integrated weed management. Determination of the complexity of mechanisms and agro-morphological traits that confer weed competitiveness at the QTL level will fast-forward breeding efforts for weed competitiveness at the QTL level will fast-forward breeding efforts for weed competitive rice. Four populations of Green Super Rice (GSR) IR2 introgression lines (ILs) were tested to identify suitable donor and recurrent parent for weed competitiveness and to standardize the weed competitive ability traits in rice. GSR IR2-6 population, derived from a cross between Weed Tolerant Rice 1 (recurrent parent) and Y134 (donor parent), was selected as the best population and was advanced for phenotypic evaluations in dry season 2014. The ILs of GSR IR2-6 population were analyzed and compared to the parents and checks in upland non-weedy, upland weedy, lowland weedy, and screenhouse conditions and tested for seed germination and seedling vigor. Across conditions, 21 lines were selected as the most promising ILs with superior and weed competitive ability traits. Two sets of 167 GSR IR 2-6 (BC1F5) ILs, originally selected for weed competitiveness and grain quality traits, were used to map quantitative trait loci (QTL) for weed competitive ability traits in rice using Single Nucleotide Polymorphism (SNP) markers. The SNP analysis identified 114 QTLs for different traits related to weed competitiveness, in which 29 QTLs were identified for seed germination and early vigor, 15 QTLs for seedling vigor, 12 QTLs for canopy characteristics, and 58 QTLs for maturity and yield-related traits. Among the traits, 40 of QTLs were discovered for number of panicles, 10 for percent spikelet fertility, 8 for first count of germination, 6 for number of leaves at 7 DAS, 5 for total dry weight, 4 for percent germination, 4 for number of tillers, and 4 for number of filled grains. Seven QTLs were identified for secondary traits, 4 for vigor index and 3 for weed tolerance index (panicle number, flag leaf width and flag leaf length). A total of 19 SNP markers were associated with two or more QTLs. A total of 31 QTLs across chromosomes 1-12 (except 8 and 9) have desirable alleles donated by the recurrent parent WTR 1, while 83 QTLs distributed on all chromosomes have desirable alleles contributed by the donor parent Y134. These QTLs need to be further studied, and molecular pyramiding of these QTLs would permit the development of superior weed competitive varieties for aerobic rice systems.