Abstract
BackgroundKernel row number (KRN) is an important trait for the domestication and improvement of maize. Exploring the genetic basis of KRN has great research significance and can provide valuable information for molecular assisted selection.ResultsIn this study, one single-locus method (MLM) and six multilocus methods (mrMLM, FASTmrMLM, FASTmrEMMA, pLARmEB, pKWmEB and ISIS EM-BLASSO) of genome-wide association studies (GWASs) were used to identify significant quantitative trait nucleotides (QTNs) for KRN in an association panel including 639 maize inbred lines that were genotyped by the MaizeSNP50 BeadChip. In three phenotyping environments and with best linear unbiased prediction (BLUP) values, the seven GWAS methods revealed different numbers of KRN-associated QTNs, ranging from 11 to 177. Based on these results, seven important regions for KRN located on chromosomes 1, 2, 3, 5, 9, and 10 were identified by at least three methods and in at least two environments. Moreover, 49 genes from the seven regions were expressed in different maize tissues. Among the 49 genes, ARF29 (Zm00001d026540, encoding auxin response factor 29) and CKO4 (Zm00001d043293, encoding cytokinin oxidase protein) were significantly related to KRN, based on expression analysis and candidate gene association mapping. Whole-genome prediction (WGP) of KRN was also performed, and we found that the KRN-associated tagSNPs achieved a high prediction accuracy. The best strategy was to integrate all of the KRN-associated tagSNPs identified by all GWAS models.ConclusionsThese results aid in our understanding of the genetic architecture of KRN and provide useful information for genomic selection for KRN in maize breeding.
Highlights
Kernel row number (KRN) is an important trait for the domestication and improvement of maize
Comparing KRN among the different environments, we found that it showed the smallest average (13.69), minimum (8.60) and maximum (20.60) values in XX, where all accessions were planted in summer (June)
Quantitative trait nucleotide (QTN) for KRN identified by different methods Single-locus analysis of KRN (MLM) Based on the MaizeSNP50 BeadChip, we obtained 42,667 high-quality single nucleotide polymorphism (SNP) distributed on 10 maize chromosomes
Summary
Kernel row number (KRN) is an important trait for the domestication and improvement of maize. Exploring the genetic basis of KRN has great research significance and can provide valuable information for molecular assisted selection. Its morphological characteristics, especially inflorescence architectures, differed profoundly [2, 3]. The shift from small ears in teosinte to larger ears in modern maize was accompanied by a dramatic increase in kernel row number (KRN) [4]. Constant efforts have been made to explore the genetic basis underlying the striking diversities in inflorescence architecture and KRN in maize. KRN is an important ear trait and is formed by multiple meristem types during female inflorescence development, including inflorescence meristems (IMs), spikelet pair meristems (SPMs), spikelet meristems (SMs) and floral meristems (FMs) [5].
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