Fixation of hybrid sterility genes and favorable alleles of key yield-related genes with dominance contribute to the high yield of the Yongyou series of intersubspecific hybrid rice

Alexander, 2009, Fast model-based estimation of ancestry in unrelated individuals, Genome Res., 19, 1655, 10.1101/gr.094052.109 Ashikari, 2005, Cytokinin oxidase regulates rice grain production, Science, 309, 741, 10.1126/science.1113373 Bradbury, 2007, TASSEL: software for association mapping of complex traits in diverse samples, Bioinformatics, 23, 2633, 10.1093/bioinformatics/btm308 Bruce, 1910, The mendelian theory of heredity and the augmentation of vigor, Science, 32, 627, 10.1126/science.32.827.627.b Chang, 2015, Second-generation PLINK: rising to the challenge of larger and richer datasets, GigaScience, 4, 7, 10.1186/s13742-015-0047-8 Chen, 2014, Male sterility and fertility restoration in crops, Annu. Rev. Plant Biol., 65, 579, 10.1146/annurev-arplant-050213-040119 Danecek, 2021, Twelve years of SAMtools and BCFtools, GigaScience, 10, giab008, 10.1093/gigascience/giab008 East, 1908, Inbreeding in corn, Rep. Conn. Agric. Exp. Stn., 1907, 419 Elshire, 2011, A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species, PLoS ONE, 6, e19379, 10.1371/journal.pone.0019379 Fan, 2006, GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein, Theor. Appl. Genet., 112, 1164, 10.1007/s00122-006-0218-1 Gonda, 2019, Sequencing-based bin map construction of a tomato mapping population, facilitating high-resolution quantitative trait loci detection, Plant Genome, 12, 180010, 10.3835/plantgenome2018.02.0010 Hu, 2018, A novel QTL qTGW3 encodes the GSK3/SHAGGY-like kinase OsGSK5/OsSK41 that interacts with OsARF4 to negatively regulate grain size and weight in rice, Mol. Plant, 11, 736, 10.1016/j.molp.2018.03.005 Hua, 2003, Single-locus heterotic effects and dominance by dominance interactions can adequately explain the genetic basis of heterosis in an elite rice hybrid, Proc. Natl. Acad. Sci. U. S. A., 100, 2574, 10.1073/pnas.0437907100 Huang, 2016, Genomic architecture of heterosis for yield traits in rice, Nature, 537, 629, 10.1038/nature19760 Huang, 2015, Genomic analysis of hybrid rice varieties reveals numerous superior alleles that contribute to heterosis, Nat. Commun., 6, 6258, 10.1038/ncomms7258 Huo, 2017, NOG1 increases grain production in rice, Nat. Commun., 8, 1497, 10.1038/s41467-017-01501-8 Jakobsson, 2007, CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure, Bioinformatics, 23, 1801, 10.1093/bioinformatics/btm233 Jones, 1917, Dominance of linked factors as a means of accounting for heterosis, Genetics, 2, 466, 10.1093/genetics/2.5.466 Kosambi, 1943, The estimation of map distances from recombination values, Ann. Eugen., 12, 172, 10.1111/j.1469-1809.1943.tb02321.x Krieger, 2010, The flowering gene SINGLE FLOWER TRUSS drives heterosis for yield in tomato, Nat. Genet., 42, 459, 10.1038/ng.550 Li, 2016, Integrated analysis of phenome, genome, and transcriptome of hybrid rice uncovered multiple heterosis-related loci for yield increase, Proc. Natl. Acad. Sci. U. S. A., 113, E6026, 10.1073/pnas.1610115113 Li, 2009, Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, 25, 1754, 10.1093/bioinformatics/btp324 Li, 2012, Evaluating the effective numbers of independent tests and significant p-value thresholds in commercial genotyping arrays and public imputation reference datasets, Hum. Genet., 131, 747, 10.1007/s00439-011-1118-2 Li, 2008, Identification and fine mapping of S-d, a new locus conferring the partial pollen sterility of intersubspecific F1 hybrids in rice (Oryza sativa L.), Theor. Appl. Genet., 116, 915, 10.1007/s00122-008-0723-5 Li, 2020, Analysis of genetic architecture and favorable allele usage of agronomic traits in a large collection of Chinese rice accessions, Sci. China Life Sci., 63, 1688, 10.1007/s11427-019-1682-6 Liang, 2015, Partial dominance, overdominance and epistasis as the genetic basis of heterosis in upland cotton (Gossypium hirsutum L.), PLoS ONE, 10, 10.1371/journal.pone.0143548 Lin, 2020, Heterosis-associated genes confer high yield in super hybrid rice, Theor. Appl. Genet., 133, 3287, 10.1007/s00122-020-03669-y Lin, 2020, Divergent selection and genetic introgression shape the genome landscape of heterosis in hybrid rice, Proc. Natl. Acad. Sci. U. S. A., 117, 4623, 10.1073/pnas.1919086117 Lv, 2016, Theory and practice on breeding of two-line hybrid rice, Liangyoupeijiu, Sci. Agric. Sin., 49, 1635 Lv, 2020, Resequencing of 1,143 indica rice accessions reveals important genetic variations and different heterosis patterns, Nat. Commun., 11, 4778, 10.1038/s41467-020-18608-0 Ma, 2010, Breeding and application of late japonica CMS line Yongjing 2A and its late indica-japonica hybrid rice Combinations, Za Jiao Shui Dao, 25, 185 McKenna, 2010, The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data, Genome Res., 20, 1297, 10.1101/gr.107524.110 Meng, 2015, QTL IciMapping: integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations, Crop J., 3, 269, 10.1016/j.cj.2015.01.001 Mi, 2016, Stacking S5-n and f5-n to overcome sterility in indica-japonica hybrid rice, Theor. Appl. Genet., 129, 563, 10.1007/s00122-015-2648-0 Mi, 2019, An effective strategy for fertility improvement of indica-japonica hybrid rice by pyramiding S5-n, f5-n, and pf12-j, Mol. Breed., 39, 138, 10.1007/s11032-019-1044-x Minvielle, 1987, Dominance is not necessary for heterosis: a two-locus model, Genet. Res., 49, 245, 10.1017/S0016672300027142 Moll, 1962, Heterosis and genetic diversity in variety crosses of maize, Crop Sci., 2, 197, 10.2135/cropsci1962.0011183X000200030005x Ouyang, 2016, Progress of indica-japonica hybrid sterility and wide-compatibility in rice, Chin. Sci. Bull., 61, 3833, 10.1360/N972016-01012 Ouyang, 2016, Origination and establishment of a trigenic reproductive isolation system in rice, Mol. Plant, 9, 1542, 10.1016/j.molp.2016.07.008 Schliep, 2011, phangorn: phylogenetic analysis in R, Bioinformatics, 27, 592, 10.1093/bioinformatics/btq706 Schnell, 1992, Multiplicative vs. arbitrary gene action in heterosis, Genetics, 131, 461, 10.1093/genetics/131.2.461 Shen, 2017, Genomic structural variation-mediated allelic suppression causes hybrid male sterility in rice, Nat. Commun., 8, 1310, 10.1038/s41467-017-01400-y Shen, 2008, Construction of genetic linkage map based on a RIL population derived from super hybrid rice, XY9308, Mol. Plant Breed., 6, 861 Shull, 1908, The composition of a field of maize, J. Hered., 296, 10.1093/jhered/os-4.1.296 Song, 2016, Review and prospect on utilization of heterosis between indica-japonica rice subspecies, Chin. Sci. Bull., 61, 3778, 10.1360/N972016-01039 Song, 2007, A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase, Nat. Genet., 39, 623, 10.1038/ng2014 Stuber, 1992, Identification of genetic factors contributing to heterosis in a hybrid from two elite maize inbred lines using molecular markers, Genetics, 132, 823, 10.1093/genetics/132.3.823 Tan, 2004, Identification of the Rf gene conferring fertility restoration of the CMS Dian-type 1 in rice by using simple sequence repeat markers and advanced inbred lines of restorer and maintainer, Plant Breed, 123, 338, 10.1111/j.1439-0523.2004.01004.x Taylor, 2017, R package ASMap: efficient genetic linkage map construction and diagnosis, J. Stat. Software, 79, 1 Ting, 1949, Origination of the rice cultivation in China, J. College Agric. Sun Yat-Sen Univ., 7, 11 Wang, 2006, Fine mapping of f5-Du, a gene conferring wide-compatibility for pollen fertility in inter-subspecific hybrids of rice (Oryza sativa L.), Theor. Appl. Genet., 112, 382, 10.1007/s00122-005-0141-x Wang, 2018, Genomic variation in 3,010 diverse accessions of Asian cultivated rice, Nature, 557, 43, 10.1038/s41586-018-0063-9 Wang, 2015, Copy number variation at the GL7 locus contributes to grain size diversity in rice, Nat. Genet., 47, 944, 10.1038/ng.3346 Wei, 2013, Characteristics of super-high yield population in Yongyou series of hybrid rice, Acta Agron. Sin., 39, 2201, 10.3724/SP.J.1006.2013.02201 Wu, 2013, Association of functional nucleotide polymorphisms at DTH2 with the northward expansion of rice cultivation in Asia, Proc. Natl. Acad. Sci. U. S. A., 110, 2775, 10.1073/pnas.1213962110 Xiao, 1995, Dominance is the major genetic-basis of heterosis in rice as revealed by Qtl analysis using molecular markers, Genetics, 140, 745, 10.1093/genetics/140.2.745 Xie, 2015, Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc. Natl. Acad. Sci. U. S. A., 112, E5411, 10.1073/pnas.1515919112 Xie, 2019, Molecular mechanisms of hybrid sterility in rice, Sci. China Life Sci., 62, 737, 10.1007/s11427-019-9531-7 Yan, 2011, A major QTL, Ghd8, plays pleiotropic roles in regulating grain productivity, plant height, and heading date in rice, Mol. Plant, 4, 319, 10.1093/mp/ssq070 Yang, 2012, A killer-protector system regulates both hybrid sterility and segregation distortion in rice, Science, 337, 1336, 10.1126/science.1223702 Yano, 2019, GWAS with principal component analysis identifies a gene comprehensively controlling rice architecture, Proc. Natl. Acad. Sci. U. S. A., 116, 21262, 10.1073/pnas.1904964116 Yano, 2015, Isolation of a novel lodging resistance QTL gene involved in strigolactone signaling and its pyramiding with a QTL gene involved in another mechanism, Mol. Plant, 8, 303, 10.1016/j.molp.2014.10.009 Yu, 2007, TAC1, a major quantitative trait locus controlling tiller angle in rice, Plant J., 52, 891, 10.1111/j.1365-313X.2007.03284.x Yu, 2017, GGTREE: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data, Methods Ecol. Evol., 8, 28, 10.1111/2041-210X.12628 Yu, 1997, Importance of epistasis as the genetic basis of heterosis in an elite rice hybrid, Proc. Natl. Acad. Sci. U. S. A., 94, 9226, 10.1073/pnas.94.17.9226 Yu, 2020, Re-evaluation of the rice ‘Green Revolution’ gene: the weak allele SD1-EQ from japonica rice may be beneficial for super indica rice breeding in the post-Green Revolution era, Mol. Breed., 40, 84, 10.1007/s11032-020-01164-2 Zhang, 2019, Genetic interactions among Ghd7, Ghd8, OsPRR37 and Hd1 contribute to large variation in heading date in rice, Rice, 12, 1, 10.1186/s12284-019-0314-x Zhang, 2014, LSCHL4 from Japonica Cultivar, which is allelic to NAL1, increases yield of indica super rice 93-11, Mol. Plant, 7, 1350, 10.1093/mp/ssu055 Zhang, 2011, A major locus qS12, located in a duplicated segment of chromosome 12, causes spikelet sterility in an indica-japonica rice hybrid, Theor. Appl. Genet., 123, 1247, 10.1007/s00122-011-1663-z Zhang, 2015, Combinations of the Ghd7, Ghd8 and Hd1 genes largely define the ecogeographical adaptation and yield potential of cultivated rice, New Phytol., 208, 1056, 10.1111/nph.13538 Zhang, 2022, Dissection of heterotic loci for grain yield using interconnected chromosome segment substitution lines in rice, Crop J., 10, 323, 10.1016/j.cj.2021.07.002 Zhang, 2017, A natural tandem array alleviates epigenetic repression of IPA1 and leads to superior yielding rice, Nat. Commun., 8, 14789, 10.1038/ncomms14789 Zhou, 2012, Genetic composition of yield heterosis in an elite rice hybrid, Proc. Natl. Acad. Sci. U. S. A., 109, 15847, 10.1073/pnas.1214141109 Zhou, 2021, Combinations of Ghd7, Ghd8, and Hd1 determine strong heterosis of commercial rice hybrids in diverse ecological regions, J. Exp. Bot., 72, 6963, 10.1093/jxb/erab344