The Genetic Basis of Plant Architecture in 10 Maize Recombinant Inbred Line Populations

Abstract

Plant architecture is a key factor affecting planting density and grain yield in maize (Zea mays). However, the genetic mechanisms underlying plant architecture in diverse genetic backgrounds have not been fully addressed. Here, we performed a large-scale phenotyping of 10 plant architecture-related traits and dissected the genetic loci controlling these traits in 10 recombinant inbred line populations derived from 14 diverse genetic backgrounds. Nearly 800 quantitative trait loci (QTLs) with major and minor effects were identified as contributing to the phenotypic variation of plant architecture-related traits. Ninety-two percent of these QTLs were detected in only one population, confirming the diverse genetic backgrounds of the mapping populations and the prevalence of rare alleles in maize. The numbers and effects of QTLs are positively associated with the phenotypic variation in the population, which, in turn, correlates positively with parental phenotypic and genetic variations. A large proportion (38.5%) of QTLs was associated with at least two traits, suggestive of the frequent occurrence of pleiotropic loci or closely linked loci. Key developmental genes, which previously were shown to affect plant architecture in mutant studies, were found to colocalize with many QTLs. Five QTLs were further validated using the segregating populations developed from residual heterozygous lines present in the recombinant inbred line populations. Additionally, one new plant height QTL, qPH3, has been fine-mapped to a 600-kb genomic region where three candidate genes are located. These results provide insights into the genetic mechanisms controlling plant architecture and will benefit the selection of ideal plant architecture in maize breeding.

Beyond pathways: genetic dissection of tocopherol content in maize kernels by combining linkage and association analyses

“…Our study sheds light on the genetic architecture of tocopherols in maize kernels. Tocopherol content is controlled by a few loci with major effects and a number of loci with minor effects, in contrast to the patterns for several other complex quantitative traits in the same genetic background (Liu et al, 2017;Pan et al, 2017;Xiao et al, 2016). Epistasis only plays a minor role, as reported by others (Liu et al, 2017;Pan et al, 2017;Xiao et al, 2016).…”

“…Tocopherol content is controlled by a few loci with major effects and a number of loci with minor effects, in contrast to the patterns for several other complex quantitative traits in the same genetic background (Liu et al ., ; Pan et al ., ; Xiao et al ., ). Epistasis only plays a minor role, as reported by others (Liu et al ., ; Pan et al ., ; Xiao et al ., ). In terms of the allele frequency of the identified loci, minor alleles with a frequency of <0.1 were the favourable alleles for most of the significant loci identified.…”

Genetic mapping of folate QTLs using a segregated population in maize

“…Those traits have a highly polygenic genetic architecture that is mainly controlled by many small effect QTLs (Mickelson et al ; Peiffer et al ; Raihan et al ; Xu et al ). Parental phenotypic and genetic distances are positively associated with the effects and numbers of QTLs yielded (Pan et al ), and major‐effect QTLs can be more easily mapped to a higher resolution (Wang et al ). In our case, the phenotypic variation contribution rates were 26.7% ( q5‐F‐THFa ) and 14.9% ( q5‐F‐THFb ), respectively, reflecting that both are major‐effect QTLs.…”

Dynamic plant height QTL revealed in maize through remote sensing phenotyping using a high-throughput unmanned aerial vehicle (UAV)

“…To verify the accuracy of the QTL, we compared the previously reported QTLs and genes related to plant height and found that 45% of the QTLs overlapped with previous research (Peiffer et al, 2014; Yang et al, 2014; Dell’Acqua et al, 2015; Zhou et al, 2016; Pan et al, 2017). In addition, genes involving the GA and auxin pathway were also detected to be associated with plant height, such as ARFTF4 , D3 , GA2OX8 , KS3 , PIN1 and PIN11 , indicating that the QTL results of this study were highly reliable (Tudroszen et al, 1977; Winkler and Helentjaris,1995; Lo et al,2008; Yamaguchi, 2008; Li et al, 2016; Weijers et al, 2018).…”

“…Plant height was so important that people have made unremitting efforts to exploring its genetic mechanism. So far, there were plenty of quantitative trait loci (QTLs) identified for maize plant height using a diversity of genetic populations (Peiffer et al, 2014; Yang et al, 2014; Dell’Acqua et al, 2015; Zhou et al, 2016; Pan et al, 2017). Some of these genes were cloned, such as an1 , dwarf3 , dwarf8 , dwarf9 and br2 , which were mainly involved in the synthesis and transportation of gibberellin and auxin (Winkler and Freeling, 1994; Bensen et al, 1995; Winkler et al, 1995; Fujioka et al, 1988; Xing et al, 2012).…”