title: Genetic architecture of maize kernel row number and whole genome prediction.
abstract: Maize kernel row number might be dominated by a set of large additive or partially dominant loci and several small dominant loci and can be accurately predicted by fewer than 300 top KRN-associated SNPs. Kernel row number (KRN) is an important yield component in maize and directly affects grain yield. In this study, we combined linkage and association mapping to uncover the genetic architecture of maize KRN and to evaluate the phenotypic predictability using these detected loci. A genome-wide association study revealed 31 associated single nucleotide polymorphisms (SNPs) representing 17 genomic loci with an effect in at least one of five individual environments and the best linear unbiased prediction (BLUP) over all environments. Linkage mapping in three F2:3 populations identified 33 KRN quantitative trait loci (QTLs) representing 21 QTLs common to several population/environments. The majority of these common QTLs that displayed a large effect were additive or partially dominant. We found 70% KRN-associated genomic loci were mapped in KRN QTLs identified in this study, KRN-associated SNP hotspots detected in NAM population and/or previous identified KRN QTL hotspots. Furthermore, the KRN of inbred lines and hybrids could be predicted by the additive effect of the SNPs, which was estimated using inbred lines as a training set. The prediction accuracy using the top KRN-associated tag SNPs was obviously higher than that of the randomly selected SNPs, and approximately 300 top KRN-associated tag SNPs were sufficient for predicting the KRN of the inbred lines and hybrids. The results suggest that the KRN-associated loci and QTLs that were detected in this study show great potential for improving the KRN with genomic selection in maize breeding.
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China. leil@webmail.hzau.edu.cn.
authors.forename: Lei
authors.initials: L
authors.lastname: Liu
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China. yanfangdu@webmail.hzau.edu.cn.
authors.forename: Yanfang
authors.initials: Y
authors.lastname: Du
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China. dongaohuo@gmail.com.
authors.forename: Dongao
authors.initials: D
authors.lastname: Huo
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China. 15172538652@163.com.
authors.forename: Man
authors.initials: M
authors.lastname: Wang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China. 891114sxm@webmail.hzau.edu.cn.
authors.forename: Xiaomeng
authors.initials: X
authors.lastname: Shen
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China. yuebing@webmail.hzau.edu.cn.
authors.forename: Bing
authors.initials: B
authors.lastname: Yue
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China. qiufazhan@mail.hzau.edu.cn.
authors.forename: Fazhan
authors.initials: F
authors.lastname: Qiu
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China. zhyl@mail.hzau.edu.cn.
authors.forename: Yonglian
authors.initials: Y
authors.lastname: Zheng
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China. yjianbing@mail.hzau.edu.cn.
authors.forename: Jianbing
authors.initials: J
authors.lastname: Yan
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China. zuxinzhang@mail.hzau.edu.cn.
authors.forename: Zuxin
authors.initials: Z
authors.lastname: Zhang
mesh_terms: D002874:Chromosome Mapping; D005799:Genes, Dominant; D056726:Genetic Association Studies; D008040:Genetic Linkage; D005828:Genetics, Population; D018745:Genome, Plant; D008957:Models, Genetic; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D012639:Seeds; D003313:Zea mays / Q000235:genetics*