Identification of Increased Grain Length 1 (IGL1), a novel gene encoded by a major QTL for modulating grain length in rice.

KEY MESSAGE: A novel quantitative trait locus qIGL1, which performed a positive function in regulating grain length in rice, was cloned by the map-based cloning approach; further studies revealed that it corresponded to LOC_Os03g30530, and the IGL1 appeared to contribute to lengthening and widening of the cells on the surface of grain hulls. Grain length is a prominent determinant for grain weight and appearance quality of rice. In this study, we conducted quantitative trait locus mapping to determine a genomic interval responsible for a long-grain phenotype observed in a japonica cultivar HD385. This led to the identification of a novel QTL for grain length on chromosome 3, named qIGL1 (for Increased Grain Length 1); the HD385 (Handao 385)-derived allele showed enhancement effects on grain length, and such an allele as well as NIP (Nipponbare)-derived allele was designated qigl1 HD385 and qIGL1NIP, respectively. Genetic analysis revealed that the qigl1HD385 allele displayed semidominant effects on grain length. Fine mapping further narrowed down the qIGL1 to an ~ 70.8-kb region containing 9 open reading frames (ORFs). A comprehensive analysis indicated that LOC_Os03g30530, which corresponded to ORF6 and carried base substitutions and deletions in HD385 relative to NIP, thereby causing changes or losses of amino-acid residues, was the true gene for qIGL1. Comparison of grain traits between a pair of near-isogenic lines (NILs), termed NIL-igl1HD385 and NIL-IGL1NIP, discovered that introduction of the igl1HD385 into the NIP background significantly resulted in the elevations of grain length and 1000-grain weight. Closer inspection of grain surfaces revealed that the cell length and width in the longitudinal direction were significantly longer and greater, respectively, in NIL-igl1HD385 line compared with in NIL-IGL1NIP line. Hence, our studies identified a new semidominant natural allele contributing to the increase of grain length and further shed light on the regulatory mechanisms of grain length.

Association analysis between constructed SNPLDBs and GCA effects of 9 quality-related traits in parents of hybrid rice (Oryza sativa L.).

BACKGROUND: The general combining ability (GCA) of parents in hybrid rice affects not only heterotic level of grain yield and other important agronomic traits, but also performance of grain quality traits of F2 bulk population which is the commodity consumed by humans. In order to make GCA improvement for quality traits in parents of hybrid rice by molecular marker assisted selection feasible, genome-wide GCA loci for quality traits in parents were detected through association analysis between the effects of GCA and constructed single nucleotide polymorphism linkage disequilibrium blocks (SNPLDBs), by using unhusked rice grains harvested from F1 plants of 48 crosses of Indica rice and 78 crosses of Japonica rice. GCA-SNPLDBs association analysis. RESULTS: Among the 8 CMS and 6 restorer lines of indica rice subspecies, CMS lines Zhenpin A, Zhenshan97 A, and 257A, and restorers Kanghui98, Minghui63 and Yanhui559 were recognized as good general combiners based on their GCA effect values for the 9 quality traits (brown rice rate, milled rice rate, head rice rate, percentage of chalky grains, chalky area size, chalkiness degree, gelatinization temperature, gel consistency and amylose content). Among the 13 CMS and 6 restorer lines of japonica rice subspecies, CMS 863A, 6427A and Xu 2A, and restorers C418, Ninghui8hao and Yunhui4hao showed elite GCA effect values for the 9 traits. GCA-SNPLDB association analysis revealed 39 significant SNPLDB loci associated with the GCA of the 9 quality-related traits, and the numbers of SNPLDB loci located on chromosome 1, 2, 3, 4, 5, 8, 9, 11 and 12 were 1, 4, 3, 9, 6, 5, 5, 4 and 2, respectively. Number of superior GCA alleles for the 9 traits among the 33 parents ranged from 1 to 26. CONCLUSIONS: Thirty-nine significant SNPLDBs loci were identified associated with the GCA of 9 quality-related traits, and the superior SNPLDB alleles could be used to improve the GCA of parents for the traits in the future by molecular marker assisted selection. The genetic basis of trait GCA in parents is different from that of trait itself.

Mining of favorable alleles for seed reserve utilization efficiency in Oryza sativa by means of association mapping.

BACKGROUND: Wet direct-seeded rice is a possible alternative to conventional puddled transplanted rice; the former uses less water and reduces labor requirements. Improving seed reserve utilization efficiency (SRUE) is a key factor in facilitating the application of this technology. However, the QTLs controlling this trait are poorly investigated. In this study, a genome-wide association study (GWAS) was conducted using a natural population composed of 542 accessions of rice (Oryza sativa L.) which were genotyped using 266 SSR markers. Large phenotypic variations in SRUE were found in the studied population. RESULTS: The average SRUE over 542 accessions across two years (2016 and 2017) was 0.52 mg.mg- 1, ranging from 0.22 mg.mg-1 to 0.93 mg.mg- 1, with a coefficient of variation of 22.66%. Overall, 2879 marker alleles were detected in the population by 266 pairs of SSR markers, indicating a large genetic variation existing in the population. Using general linear model method, 13 SSR marker loci associated with SRUE were detected and two (RM7309 and RM434) of the 13 loci, were also detected using mixed linear model analyses, with percentage of phenotypic variation explained (PVE) greater than 5% across two years. The 13 association loci (P < 0.01) were located on all chromosomes except chromosome 11, with PVE ranging from 5.05% (RM5158 on chromosome 5) to 12% (RM297 on chromosome 1). Association loci RM7309 on chromosome 6 and RM434 on chromosome 9 revealed by both models were detected in both years. Twenty-three favorable alleles were identified with phenotypic effect values (PEV) ranging from 0.10 mg.mg- 1 (RM7309-135 bp on chromosome 9) to 0.45 mg.mg- 1 (RM297-180 bp on chromosome 2). RM297-180 bp showed the largest phenotypic effect value (0.44 mg.mg- 1 in 2016 and 0.45 mg.mg- 1 in 2017) with 6.72% of the accessions carrying this allele and the typical carrier accession was Manyedao, followed by RM297-175 bp (0.43 mg.mg- 1 in 2016 and 0.44 mg.mg- 1 in 2017). CONCLUSION: Nine novel association loci for SRUE were identified, compared with previous studies. The optimal parental combinations for pyramiding more favorable alleles for SRUE were selected and could be used for breeding rice accessions suitable for wet direct seeding in the future.