Comparative population genomics of maize domestication and improvement.
Domestication and plant breeding are ongoing 10,000-year-old evolutionary experiments that have radically altered wild species to meet human needs. Maize has undergone a particularly striking transformation. Researchers have sought for decades to identify the genes underlying maize evolution, but these efforts have been limited in scope. Here, we report a comprehensive assessment of the evolution of modern maize based on the genome-wide resequencing of 75 wild, landrace and improved maize lines. We find evidence of recovery of diversity after domestication, likely introgression from wild relatives, and evidence for stronger selection during domestication than improvement. We identify a number of genes with stronger signals of selection than those previously shown to underlie major morphological changes. Finally, through transcriptome-wide analysis of gene expression, we find evidence both consistent with removal of cis-acting variation during maize domestication and improvement and suggestive of modern breeding having increased dominance in expression while targeting highly expressed genes.
Department of Plant Sciences, University of California, Davis, California, USA.
Matthew B
MB
Hufford
Xun
X
Xu
Joost
J
van Heerwaarden
Tanja
T
Pyhäjärvi
Jer-Ming
JM
Chia
Reed A
RA
Cartwright
Robert J
RJ
Elshire
Jeffrey C
JC
Glaubitz
Kate E
KE
Guill
Shawn M
SM
Kaeppler
Jinsheng
J
Lai
Peter L
PL
Morrell
Laura M
LM
Shannon
Chi
C
Song
Nathan M
NM
Springer
Ruth A
RA
Swanson-Wagner
Peter
P
Tiffin
Jun
J
Wang
Gengyun
G
Zhang
John
J
Doebley
Michael D
MD
McMullen
Doreen
D
Ware
Edward S
ES
Buckler
Shuang
S
Yang
Jeffrey
J
Ross-Ibarra
D001947:Breeding / Q000379:methods; D018556:Crops, Agricultural / Q000235:genetics*; D019143:Evolution, Molecular; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D056186:Metagenomics / Q000379:methods; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic; D059467:Transcriptome / Q000235:genetics; D003313:Zea mays / Q000235:genetics*