title: OsLG3 contributing to rice grain length and yield was mined by Ho-LAMap.
abstract: 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.
  
  
  
  Herein, 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.
  
  
  
  The 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.
authors.affiliation: Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
authors.forename: Jianping
authors.initials: J
authors.lastname: Yu
authors.affiliation: Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
authors.forename: Haiyan
authors.initials: H
authors.lastname: Xiong
authors.affiliation: Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
authors.forename: Xiaoyang
authors.initials: X
authors.lastname: Zhu
authors.affiliation: Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
authors.forename: Hongliang
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Huihui
authors.initials: H
authors.lastname: Li
authors.affiliation: Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
authors.forename: Jinli
authors.initials: J
authors.lastname: Miao
authors.affiliation: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Wensheng
authors.initials: W
authors.lastname: Wang
authors.affiliation: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
authors.forename: Zuoshun
authors.initials: Z
authors.lastname: Tang
authors.affiliation: Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
authors.forename: Zhanying
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
authors.forename: Guoxin
authors.initials: G
authors.lastname: Yao
authors.affiliation: Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.|Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China.
authors.forename: Yinghua
authors.initials: Y
authors.lastname: Pan
authors.affiliation: Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Wang
authors.affiliation: Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
authors.forename: M A R
authors.initials: MAR
authors.lastname: Rashid
authors.affiliation: Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
authors.forename: Jinjie
authors.initials: J
authors.lastname: Li
authors.affiliation: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Yongming
authors.initials: Y
authors.lastname: Gao
authors.affiliation: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Zhikang
authors.initials: Z
authors.lastname: Li
authors.affiliation: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
authors.forename: Weicai
authors.initials: W
authors.lastname: Yang
authors.affiliation: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
authors.forename: Xiangdong
authors.initials: X
authors.lastname: Fu
authors.affiliation: Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China. lizichao@cau.edu.cn.
authors.forename: Zichao
authors.identifier: 0000-0002-3186-1132
authors.initials: Z
authors.lastname: Li
mesh_terms: D001483:Base Sequence; D001947:Breeding; D002452:Cell Count; D002467:Cell Nucleus / Q000378:metabolism; D002874:Chromosome Mapping / Q000379:methods*; D003198:Computer Simulation; D004843:Epistasis, Genetic; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D008040:Genetic Linkage; D055106:Genome-Wide Association Study; D006239:Haplotypes / Q000235:genetics; D006579:Heterozygote; D012275:Oryza / Q000033:anatomy & histology* / Q000235:genetics*; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D011401:Promoter Regions, Genetic / Q000235:genetics; D040641:Quantitative Trait Loci / Q000235:genetics; D015203:Reproducibility of Results; D012639:Seeds / Q000033:anatomy & histology* / Q000166:cytology; D015533:Transcriptional Activation / Q000235:genetics
keywords: Artificial selection; GWAS; Genetic interaction; Grain length; Ho-LAMap; Linkage mapping; Observed heterozygosity; OsLG3; Rice domestication