Abstract
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.
Highlights
Most agronomic traits in rice are complex and polygenic
Ninety-nine quantitative trait loci (QTL) for grain length were detected by Genome-wide association analysis (GWAS) based on high-density single nucleotide polymorphism (SNP) We investigated grain length in a diverse panel of 504 cultivated rice varieties from worldwide sources (Additional file 1: Figure S1 and Additional file 32: Table S1, Additional file 33: Table S2) grown in five environments at two different latitudes (Additional file 33: Table S3)
After aligning the reads against the rice reference genome of the temperate japonica variety, Nipponbare, we identified a total of 10 million SNPs (1 SNP per 40 bp on average) from these accessions and 3,585,229 SNPs with missing rates of less than 30% and a
Summary
Most 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. Rice (O. sativa L.) is a staple food and the world’s most important cereal crop. Grain yield is determined by three component traits, namely grain weight, number of grains per panicle, and number of panicles per plant. Grain size is a prime breeding target, as it affects both yield and quality. The study of grain size is highly important for the improvement of rice yield and quality as well as for the understanding of the rice domestication process [1]. For fine mapping, very large sample sizes are required; typically, thousands of individuals are needed and the fieldwork involved is extremely laborious, usually involving
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