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Mapping and verification of grain shape QTLs based on high-throughput SNP markers in rice

Chen, Junxiao, Zhou, Hao, Gu, Yuan, Xia, Duo, Wu, Bian, Gao, Guanjun, Zhang, Qinglu, He, Yuqing
Molecular breeding 2019 v.39 no.3 pp. 42
chromosome mapping, chromosomes, genetic resources, genotyping, grain yield, quantitative trait loci, rice, seed size, single nucleotide polymorphism
Grain shape is an important trait that determines appearance quality in rice. In order to dissect the genetic basis of this complex trait, we constructed an F₂ and derived F₂:₃ lines from a cross between a long-grain variety and one with an intermediate grain length. The F₂ population was genotyped by the RICE6K array to construct a high-density linkage map. A total of 30 quantitative trait loci (QTL) for grain shape were detected over 2 years. A major QTL cluster on chromosome 7 had a strong effect on grain length and width, consistent with the effect of GL7/GW7. The other QTLs, qGL2, qGW2, and qGL12, had large effects on grain shape and were detected in both years. The effects of four QTL on seed size as well as grain yield were then validated by using BC₁F₆ populations derived from selected F₃ plants with residual heterozygous genotypes on each QTL region. Our study indicated that the SNP array was an efficient genotyping method for QTL mapping, and the novel QTL, qGW2 and qGL12, provided insight into the genetic basis of grain shape as well as additional genetic resources for developing elite rice varieties.