A fast-linear mixed model for genome-wide haplotype association analysis: application to agronomic traits in maize
文献类型： 外文期刊
作者： Chen, Heli 1 ; Hao, Zhiyu 2 ; Zhao, Yunfeng 1 ; Yang, Runqing 1 ;
作者机构： 1.Chinese Acad Fishery Sci, Res Ctr Aquat Biotechnol, Beijing 100141, Peoples R China
2.Northeast Agr Univ, Coll Anim Sci & Technol, Harbin 150030, Peoples R China
关键词： GWAS; Linear mixed model; R/fastLmPure; Genomic heritability; Haplotype; Maize
期刊名称：BMC GENOMICS （ 影响因子：3.969； 五年影响因子：4.478 ）
ISSN： 1471-2164
年卷期： 2020 年 21 卷 1 期
页码：
收录情况： SCI
摘要： Background Haplotypes combine the effects of several single nucleotide polymorphisms (SNPs) with high linkage disequilibrium, which benefit the genome-wide association analysis (GWAS). In the haplotype association analysis, both haplotype alleles and blocks are tested. Haplotype alleles can be inferred with the same statistics as SNPs in the linear mixed model, while blocks require the formulation of unified statistics to fit different genetic units, such as SNPs, haplotypes, and copy number variations. Results Based on the FaST-LMM, the fastLmPure function in the R/RcppArmadillo package has been introduced to speed up genome-wide regression scans by a re-weighted least square estimation. When large or highly significant blocks are tested based on EMMAX, the genome-wide haplotype association analysis takes only one to two rounds of genome-wide regression scans. With a genomic dataset of 541,595 SNPs from 513 maize inbred lines, 90,770 haplotype blocks were constructed across the whole genome, and three types of markers (SNPs, haplotype alleles, and haplotype blocks) were genome-widely associated with 17 agronomic traits in maize using the software developed here. Conclusions Two SNPs were identified for LNAE, four haplotype alleles for TMAL, LNAE, CD, and DTH, and only three blocks reached the significant level for TMAL, CD, and KNPR. Compared to the R/lm function, the computational time was reduced by similar to 10-15 times.
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