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BackgroundMost agronomic traits in rice are complex and polygenic. The identification of quantitative trait loci (QTL) for grain length is an important objective of rice genetic research and breeding programs.ResultsHerein, we identified 99 QTL for grain length by GWAS based on approximately 10 million single nucleotide polymorphisms from 504 cultivated rice accessions (Oryza sativa L.), 13 of which were validated by four linkage populations and 92 were new loci for grain length. We scanned the Ho (observed heterozygosity per locus) index of coupled-parents of crosses mapping the same QTL, based on linkage and association mapping, and identified two new genes for grain length. We named this approach as Ho-LAMap. A simulation study of six known genes showed that Ho-LAMap could mine genes rapidly across a wide range of experimental variables using deep-sequencing data. We used Ho-LAMap to clone a new gene, OsLG3, as a positive regulator of grain length, which could improve rice yield without influencing grain quality. Sequencing of the promoter region in 283 rice accessions from a wide geographic range identified four haplotypes that seem to be associated with grain length. Further analysis showed that OsLG3 alleles in the indica and japonica evolved independently from distinct ancestors and low nucleotide diversity of OsLG3 in indica indicated artificial selection. Phylogenetic analysis showed that OsLG3 might have much potential value for improvement of grain length in japonica breeding.ConclusionsThe results demonstrated that Ho-LAMap is a potential approach for gene discovery and OsLG3 is a promising gene to be utilized in genomic assisted breeding for rice cultivar improvement.Electronic supplementary materialThe online version of this article (doi:10.1186/s12915-017-0365-7) contains supplementary material, which is available to authorized users.

SummaryGrain size, one of the important components determining grain yield in rice, is controlled by the multiple quantitative trait loci (QTLs). Intensive artificial selection for grain size during domestication is evidenced in modern cultivars compared to their wild relatives. Here, we report the molecular cloning and characterization of OsLG3b, a QTL for grain length in tropical japonica rice that encodes MADS‐box transcription factor 1 (OsMADS1). Six SNPs in the OsLG3b region led to alternative splicing, which were associated with grain length in an association analysis of candidate region. Quantitative PCR analysis indicated that OsLG3b expression was higher during the panicle and seed development stages. Analysis of haplotypes and introgression regions revealed that the long‐grain allele of OsLG3b might have arisen after domestication of tropical japonica and spread to subspecies indica or temperate japonica by natural crossing and artificial selection. OsLG3b is therefore a target of human selection for adaptation to tropical regions during domestication and/or improvement of rice. Phylogenetic analysis and pedigree records showed that OsLG3b had been employed by breeders, but the gene still has much breeding potential for increasing grain length in indica. These findings will not only aid efforts to elucidate the molecular basis of grain development and domestication, but also facilitate the genetic improvement of rice yield.

This study was conducted to determine the DE and ME content of 25 samples of corn distillers dried grains with solubles (DDGS) fed to growing pigs and to generate prediction equations for DE and ME based on chemical analysis. The 25 samples included 15 full-oil (no oil extracted; ether extract [EE] > 8%) DDGS and 10 reduced-oil (oil extracted; EE < 8%) DDGS collected from 17 ethanol plants in China. A corn–soybean meal diet constituted the basal diet and the other 25 diets replaced a portion of the corn, soybean meal, and lysine of the basal diet with 28.8% of 1 of the 25 corn DDGS sources. Seventy-eight barrows (initial BW = 42.6 ± 6.2 kg) were used in the experiment conducted over 2 consecutive periods (n = 6 per treatment) using a completely randomized design. For each period, pigs were placed in metabolism cages for a 5-d total collection of feces and urine following a 7-d adaptation to the diets. Among the 25 corn DDGS samples, EE, NDF, DE, and ME content (DM basis) ranged from 2.8 to 14.2%, 31.0 to 46.6%, 3,255 to 4,103 kcal/kg, and 2,955 to 3,899 kcal/kg, respectively. Using a stepwise regression analysis, a series of DE and ME prediction equations were developed not only among all 25 DDGS but also only within 15 full-oil DDGS and 10 reduced-oil DDGS samples. The best fit equations of DE (kcal/kg DM) for the complete set of 25 DDGS, 15 full-oil DDGS, and 10 reduced-oil DDGS were 2,064 – (38.51 × % NDF) + (0.64 × % GE) – (39.70 × % ash), –(87.53 × % ADF) + (1.02 × % GE) – (22.99 × % hemicellulose), and 3,491 – (40.25 × % NDF) + (46.95 × % CP), respectively. The best fit equations for ME (kcal/kg DM) for the complete set of 25 DDGS, 15 full-oil DDGS, and 10 reduced-oil DDGS were 1,554 – (44.11 × % NDF) + (0.77 × % GE) – (68.51 × % ash), 7,898 – (42.08 × % NDF) – (136.17 × % ash) + (101.19 × % EE) (103.83 × % CP), and 4,066 – (46.30 × % NDF) + (45.80 × % CP) – (106.19 × % ash), respectively. Using the sum of squared residuals to compare the accuracy of the 3 groups of prediction equations revealed that separate equations for full-oil DDGS and reduced-oil DDGS each provided a better fit than a single equation for the entire set of DDGS sources. These results indicated that the DE and ME values in corn DDGS are related to the chemical composition, primarily the EE and fiber concentrations. Specific prediction equations derived from full-oil and reduced-oil DDGS are better than equations derived from the entire set of DDGS.