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. 2013 Aug 27;110(35):14492-7.
doi: 10.1073/pnas.1306579110. Epub 2013 Aug 12.

Dissecting Yield-Associated Loci in Super Hybrid Rice by Resequencing Recombinant Inbred Lines and Improving Parental Genome Sequences

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Free PMC article

Dissecting Yield-Associated Loci in Super Hybrid Rice by Resequencing Recombinant Inbred Lines and Improving Parental Genome Sequences

Zhen-Yu Gao et al. Proc Natl Acad Sci U S A. .
Free PMC article

Abstract

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.

Keywords: Oryza sativa; QTL dissection; genome sequence update.

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1.
Fig. 1.
Schematic overview of the parents–RIL system construction and the map of genome-wide graphic genotypes. (A) SNP markers were developed between PA64s and 93–11, at which point each RIL was genotyped. A map of genome-wide graphic genotypes with high resolution was constructed to dissect QTL. (B) Improved genome sequence assembly of both parents, including gap filling and base-error correction. (C) Graphic genotypes of 132 RILs were identified by a sliding window approach along each chromosome. Different colors represent different genotypes: purple, 93–11; sapphire, PA64s; maroon, heterozygous blocks.
Fig. 2.
Fig. 2.
Concentric circles showing different features of the PA64s genome using the Circos program (36). (A) Sequence coverage of transposable elements (TEs) with all identified intact elements in PA64s. (B) Density of annotated genes counted per 0.5-MB sliding window. (C and D) Graphical view of the collinear blocks of genome sequence in PA64s compared with Nipponbare (C) and with 93–11 (D). (E) Density of single-base errors per 0.5-Mb sliding window. (F) The distribution of filled gaps.
Fig. 3.
Fig. 3.
The positions of QTLs located on each chromosome. The number on the left of each chromosome is the marker’s genetic distance (cM). The red patterns represent phenotypes collected in Hainan, the blue ones those in Hangzhou, and the green ones represent reported QTL. The texts of different shapes are abbreviations of different phenotypes: ETN, effective tiller number; GL, grain length; GW, grain width; HD, heading date; PH, plant height; PL, panicle length; PPB, primary panicle branch number; PY, yield per plant; SN, spikelet number per panicle; SPB, secondary panicle branch number; SS, seed set; TGW, 1,000-grain weight. The gradual change of colors represents different LOD values.
Fig. 4.
Fig. 4.
(A) Fine-mapping of qSN8. The qSN8 locus was mapped between the SNP markers SNP8-45 and SNP8-47 on Chr08, and was covered by three discontinuous BACs. The qSN8 locus was narrowed down to a 9.83-kb genomic region between SNP marker SNP1 and InDel marker IND1. T→C, 93–11 (C) to PA64s (T) at 873 from A+1TG in DTH8. 8 bp Del, 8 bp deletion (TATCATTG) at 471–478-bp from A+1TG in PA64s. (B) Fine-mapping of qSPB1. The qSPB1 locus was mapped between the SNP markers SNP1-308 and SNP1-309 on Chr01, and was covered by three BAC contigs. The qSPB1 locus was narrowed down to a 2.50-kb genomic DNA region between the SNP markers SNP2 and SNP3. A→C, 93–11 (A) to PA64s (C) at +222 from A+1TG in LAX1. The numerals indicate those of recombinants identified from 1,708 RIL lines. All lines displayed are the recombinants from the RIL population. Closed boxes indicate the coding sequence. The white and black bars denote the molecular marker genotype of PA64s and 93–11, respectively.
Fig. 5.
Fig. 5.
Genetic complementation test. (A) Schematic structure of the complementation construct pCAMBIA1300-DTH8, containing the entire DTH8 gene, the 2,627-bp upstream sequence, and the 234-bp downstream sequence. (B) Comparison of plant height of the DTH8 transformants and PA64s at the mature stage. (Scale bar 10 cm.) (C) Comparison of panicle of the DTH8 transformants and PA64s. (Scale bar, 5 cm.) From left to right are PA64s, T1-1, T1-2, and T1-3.

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