Abstract
The extensive genetic variation present in maize (Zea mays) germplasm makes it possible to detect signatures of positive artificial selection that occurred during temperate and tropical maize improvement. Here we report an analysis of 532,815 polymorphisms from a maize association panel consisting of 368 diverse temperate and tropical inbred lines. We developed a gene-oriented approach adapting exonic polymorphisms to identify recently selected alleles by comparing haplotypes across the maize genome. This analysis revealed evidence of selection for more than 1100 genomic regions during recent improvement, and included regulatory genes and key genes with visible mutant phenotypes. We find that selected candidate target genes in temperate maize are enriched in biosynthetic processes, and further examination of these candidates highlights two cases, sucrose flux and oil storage, in which multiple genes in a common pathway can be cooperatively selected. Finally, based on available parallel gene expression data, we hypothesize that some genes were selected for regulatory variations, resulting in altered gene expression.
Highlights
To identify specific regions of the maize genome affected by selection during temperate or tropical maize improvement, we used a haplotype-base approach (XP-Extended Haplotype Heterozygosity (EHH) test) to scan for selection signals based on population comparisons of the diverse maize inbred lines
We focused our analyses on the regions that include the Single Nucleotide Polymorphisms (SNPs) at the top 1% cutoff of XP-EHH scores
The average value of Tajima’s D
Summary
We use 532,815 common Single Nucleotide Polymorphisms (SNPs) from our previous RNA sequencing study of 368 diverse maize lines to detect genomic regions affected by recent improvement by comparing diverse temperate and tropical inbred lines. We performed a genome scan using the XP-EHH test between temperate and tropical maize lines.
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
