OsLG3 contributing to rice grain length and yield was mined by Ho-LAMap

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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12915-017-0365-7) contains supplementary material, which is available to authorized users.

Alternative splicing of OsLG3b controls grain length and yield in japonica rice

“…Plant BC 4 F 3 -78-11 was crossed with NIP and then selfed to produce a BC 5 F 2 population for fine mapping. All plant materials were grown under natural field conditions as described previously (Yu et al, 2017).…”

“…This approach utilized a mini-core collection (MCC) (Zhang et al, 2011) panel ( Figure S4 and Tables S5 and S6) of 266, as part of "The 3000 rice genomes project" (the rice 3k genome), which had been deeply sequenced (see URLs). High-density SNPs (one SNP per 40 bp on average) were obtained (Yu et al, 2017). We measured the grain length of each variety grown in five circumstances (Table S7) and observed substantial and highly significant variation in grain size, with high heritability values varying from 82% to 97% and an average of 89% ( Figure S5 and Table S8).…”

“…The primers used in vector construction are listed in Table S12. Two constructs were transformed to generate transgenic plants by Agrobacteriummediated transformation (Yu et al, 2017).…”

“…Therefore, it is important to study grain size for improving yield and quality as well as understanding the domestication process that has occurred in rice (Shomura et al, 2008). Although a number of quantitative trait loci (QTLs) conferring grain length (Huang et al, 2012a) have been isolated, only a few genes have been well studied, such as GS3, GW8, GL3.1, OsLG3, TGW6, qSW5 and GW2 (Ishimaru et al, 2013;Mao et al, 2010;Shomura et al, 2008;Song et al, 2007;Wang et al, 2012;Yu et al, 2017;Zhang et al, 2012b). Therefore, the genetic dissection and molecular characterization of more genes conferring grain length need to be conducted (Mao et al, 2010).…”

Natural alleles of GLA for grain length and awn development were differently domesticated in rice subspecies japonica and indica

“…To date, some domesticated genes are functionally characterized, such as seed shattering genes Sh4 (Li et al ., ) and qSH1 (Konishi et al ., ; Li et al ., ), prog1 controlling straight growth (Jin et al ., ; Tan et al ., ), OsLG1 regulating closed panicles (Ishii et al ., ; Zhu et al ., ), grain size genes GW5/GSE5 (Duan et al ., ; Liu et al ., ), GS3 (Mao et al ., ), OsLG3 (Yu et al ., ) and OsLG3b (Yu et al ., ), seed dormancy gene Sdr4 (Sugimoto et al ., ), seed hull colour genes Bh4 (Zhu et al ., ) and Rc (Sweeney et al ., ), NOG1 increasing grain production (Huo et al ., ) and awn development genes An‐1 (Luo et al ., ), An‐2/LABA1 (Gu et al ., ; Hua et al ., ) and GAD1/RAE2 (Bessho‐Uehara et al ., ; Jin et al ., ).…”