Maize HapMap2 identifies extant variation from a genome in flux.
Whereas breeders have exploited diversity in maize for yield improvements, there has been limited progress in using beneficial alleles in undomesticated varieties. Characterizing standing variation in this complex genome has been challenging, with only a small fraction of it described to date. Using a population genetics scoring model, we identified 55 million SNPs in 103 lines across pre-domestication and domesticated Zea mays varieties, including a representative from the sister genus Tripsacum. We find that structural variations are pervasive in the Z. mays genome and are enriched at loci associated with important traits. By investigating the drivers of genome size variation, we find that the larger Tripsacum genome can be explained by transposable element abundance rather than an allopolyploid origin. In contrast, intraspecies genome size variation seems to be controlled by chromosomal knob content. There is tremendous overlap in key gene content in maize and Tripsacum, suggesting that adaptations from Tripsacum (for example, perennialism and frost and drought tolerance) can likely be integrated into maize.
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
Jer-Ming
JM
Chia
Chi
C
Song
Peter J
PJ
Bradbury
Denise
D
Costich
Natalia
N
de Leon
John
J
Doebley
Robert J
RJ
Elshire
Brandon
B
Gaut
Laura
L
Geller
Jeffrey C
JC
Glaubitz
Michael
M
Gore
Kate E
KE
Guill
Jim
J
Holland
Matthew B
MB
Hufford
Jinsheng
J
Lai
Meng
M
Li
Xin
X
Liu
Yanli
Y
Lu
Richard
R
McCombie
Rebecca
R
Nelson
Jesse
J
Poland
Boddupalli M
BM
Prasanna
Tanja
T
Pyhäjärvi
Tingzhao
T
Rong
Rajandeep S
RS
Sekhon
Qi
Q
Sun
Maud I
MI
Tenaillon
Feng
F
Tian
Jun
J
Wang
Xun
X
Xu
Zhiwu
Z
Zhang
Shawn M
SM
Kaeppler
Jeffrey
J
Ross-Ibarra
Michael D
MD
McMullen
Edward S
ES
Buckler
Gengyun
G
Zhang
Yunbi
Y
Xu
Doreen
D
Ware
D000483:Alleles; D004251:DNA Transposable Elements; D059646:Genome Size; D018745:Genome, Plant; D060148:HapMap Project; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic; D003313:Zea mays / Q000235:genetics*
D004251:DNA Transposable Elements