title: Analysis of the genetic architecture of maize ear and grain morphological traits by combined linkage and association mapping.
abstract: Using combined linkage and association mapping, 26 stable QTL and six stable SNPs were detected across multiple environments for eight ear and grain morphological traits in maize. One QTL, PKS2, might play an important role in maize yield improvement. In the present study, one bi-parental population and an association panel were used to identify quantitative trait loci (QTL) for eight ear and grain morphological traits. A total of 108 QTL related to these traits were detected across four environments using an ultra-high density bin map constructed using recombinant inbred lines (RILs) derived from a cross between Ye478 and Qi319, and 26 QTL were identified in more than two environments. Furthermore, 64 single nucleotide polymorphisms (SNPs) were found to be significantly associated with the eight ear and grain morphological traits (-log10(P) > 4) in an association panel of 240 maize inbred lines. Combining the two mapping populations, a total of 17 pleiotropic QTL/SNPs (pQTL/SNPs) were associated with various traits across multiple environments. PKS2, a stable locus influencing kernel shape identified on chromosome 2 in a genome-wide association study (GWAS), was within the QTL confidence interval defined by the RILs. The candidate region harbored a short 13-Kb LD block encompassing four SNPs (SYN11386, PHM14783.16, SYN11392, and SYN11378). In the association panel, 13 lines derived from the hybrid PI78599 possessed the same allele as Qi319 at the PHM14783.16 (GG) locus, with an average value of 0.21 for KS, significantly lower than that of the 34 lines derived from Ye478 that carried a different allele (0.25, P < 0.05). Therefore, further fine mapping of PKS2 will provide valuable information for understanding the genetic components of grain yield and improving molecular marker-assisted selection (MAS) in maize.
authors.affiliation: College of Agronomy, Northeast Agricultural University, Mucai Street, XiangFang District, Harbin, 150030, Heilongjiang, China.|Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China.
authors.forename: Chaoshu
authors.initials: C
authors.lastname: Zhang
authors.affiliation: Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China.
authors.forename: Zhiqiang
authors.initials: Z
authors.lastname: Zhou
authors.affiliation: Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China.
authors.forename: Hongjun
authors.initials: H
authors.lastname: Yong
authors.affiliation: College of Agronomy, Northeast Agricultural University, Mucai Street, XiangFang District, Harbin, 150030, Heilongjiang, China.|Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China.
authors.forename: Xiaochong
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China.
authors.forename: Zhuanfang
authors.initials: Z
authors.lastname: Hao
authors.affiliation: College of Agronomy, Northeast Agricultural University, Mucai Street, XiangFang District, Harbin, 150030, Heilongjiang, China.|Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China.
authors.forename: Fangjun
authors.initials: F
authors.lastname: Zhang
authors.affiliation: Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China.
authors.forename: Mingshun
authors.initials: M
authors.lastname: Li
authors.affiliation: Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China.
authors.forename: Degui
authors.initials: D
authors.lastname: Zhang
authors.affiliation: Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China.
authors.forename: Xinhai
authors.initials: X
authors.lastname: Li
authors.affiliation: College of Agronomy, Northeast Agricultural University, Mucai Street, XiangFang District, Harbin, 150030, Heilongjiang, China. zhenhuawang_2006@163.com.
authors.forename: Zhenhua
authors.initials: Z
authors.lastname: Wang
authors.affiliation: Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China. wengjianfeng@caas.cn.
authors.forename: Jianfeng
authors.initials: J
authors.lastname: Weng
mesh_terms: D002874:Chromosome Mapping; D002523:Edible Grain / Q000235:genetics; D004777:Environment; D056726:Genetic Association Studies; D008040:Genetic Linkage; D058685:Genetic Pleiotropy; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D012639:Seeds / Q000033:anatomy & histology / Q000235:genetics; D003313:Zea mays / Q000235:genetics*