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Dissecting yield-associated loci in super hybrid rice by resequencing recombinant inbred lines and improving parental genome sequences

Significance Hybrid rice developed in China has been contributing greatly to the world’s food production. The pioneer super hybrid rice developed by crossing 93–11 and Peiai 64s, Liang–You–Pei–Jiu has been widely grown in China and other Asia-Pacific regions for its high yield. Here, the quality genome sequences for both parental lines were presented and updated, and a high-resolution map of genome-wide graphic genotypes was constructed by deep resequencing a core population of 132 Liang–You–Pei–Jiu recombinant inbred lines. A series of yield-associated loci were fine-mapped, and two of them were delimited to regions each covering one candidate gene with the large recombinant inbred line population. The study provided an ideal platform for molecular breeding by quantitative trait loci cloning in rice. The growing world population and shrinkage of arable land demand yield improvement of rice, one of the most important staple crops. To elucidate the genetic basis of yield and uncover its associated loci in rice, we resequenced the core recombinant inbred lines of Liang–You–Pei–Jiu, the widely cultivated super hybrid rice, and constructed a high-resolution linkage map. We detected 43 yield-associated quantitative trait loci, of which 20 are unique. Based on the high-density physical map, the genome sequences of paternal variety 93–11 and maternal cultivar PA64s of Liang–You–Pei–Jiu were significantly improved. The large recombinant inbred line population combined with plentiful high-quality single nucleotide polymorphisms and insertions/deletions between parental genomes allowed us to fine-map two quantitative trait loci, qSN8 and qSPB1, and to identify days to heading8 and lax panicle1 as candidate genes, respectively. The quantitative trait locus qSN8 was further confirmed to be days to heading8 by a complementation test. Our study provided an ideal platform for molecular breeding by targeting and dissecting yield-associated loci in rice.