Genic and nongenic contributions to natural variation of quantitative traits in maize.
The complex genomes of many economically important crops present tremendous challenges to understand the genetic control of many quantitative traits with great importance in crop production, adaptation, and evolution. Advances in genomic technology need to be integrated with strategic genetic design and novel perspectives to break new ground. Complementary to individual-gene-targeted research, which remains challenging, a global assessment of the genomic distribution of trait-associated SNPs (TASs) discovered from genome scans of quantitative traits can provide insights into the genetic architecture and contribute to the design of future studies. Here we report the first systematic tabulation of the relative contribution of different genomic regions to quantitative trait variation in maize. We found that TASs were enriched in the nongenic regions, particularly within a 5-kb window upstream of genes, which highlights the importance of polymorphisms regulating gene expression in shaping the natural variation. Consistent with these findings, TASs collectively explained 44%-59% of the total phenotypic variation across maize quantitative traits, and on average, 79% of the explained variation could be attributed to TASs located in genes or within 5 kb upstream of genes, which together comprise only 13% of the genome. Our findings suggest that efficient, cost-effective genome-wide association studies (GWAS) in species with complex genomes can focus on genic and promoter regions.
Department of Agronomy, Kansas State University, Manhattan, Kansas 66506, USA.
Xianran
X
Li
Chengsong
C
Zhu
Cheng-Ting
CT
Yeh
Wei
W
Wu
Elizabeth M
EM
Takacs
Katherine A
KA
Petsch
Feng
F
Tian
Guihua
G
Bai
Edward S
ES
Buckler
Gary J
GJ
Muehlbauer
Marja C P
MC
Timmermans
Michael J
MJ
Scanlon
Patrick S
PS
Schnable
Jianming
J
Yu
D002874:Chromosome Mapping; D017343:Genes, Plant; D014644:Genetic Variation; D015810:Linkage Disequilibrium; D009154:Mutation; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D018749:RNA, Plant / Q000235:genetics; D017423:Sequence Analysis, RNA; D024363:Transcription Initiation Site; D059467:Transcriptome; D003313:Zea mays / Q000235:genetics*
D018749:RNA, Plant