摘要
Maize(Zea mays) is an essential crop and a great model for plant research. However,the great genetic diversity and complex genome structure makes it ever challenging in variant calling and following genomic studies. In present study,we provided an integrated strategy in variant calling and imputation for large maize population(1404 individuals) at such low sequencing coverage(~1x). Over 53 M SNPs,2.8M In Dels,660 K SVs,600 M novel sequences were finally obtained,which constituted the highest density and the most diverse maize variant map to date. The SNP set was found >99% consistency compared with genotypes derived from array-and assembly-based methods,while the percent of validated large structural variants was considered as ~60%. This variant map was further shown to be excellent in association mapping,taking plant height as an example,some known genes and potentially novel loci have been identified simultaneously. In brief,the variant map,together with the methodological practices,would be a great valuable resource for the plant community.
Maize(Zea mays) is an essential crop and a great model for plant research. However,the great genetic diversity and complex genome structure makes it ever challenging in variant calling and following genomic studies. In present study,we provided an integrated strategy in variant calling and imputation for large maize population(1404 individuals) at such low sequencing coverage(~1x). Over 53 M SNPs,2.8M In Dels,660 K SVs,600 M novel sequences were finally obtained,which constituted the highest density and the most diverse maize variant map to date. The SNP set was found >99% consistency compared with genotypes derived from array-and assembly-based methods,while the percent of validated large structural variants was considered as ~60%. This variant map was further shown to be excellent in association mapping,taking plant height as an example,some known genes and potentially novel loci have been identified simultaneously. In brief,the variant map,together with the methodological practices,would be a great valuable resource for the plant community.
引文
