DYNAMIC QUANTITATIVE TRAIT LOCI AND COPY NUMBER VARIATION: THE MISSING HERITABILITY OF COMPLEX AGRONOMIC TRAITS

Abstract

There is a great need for improved crop varieties to feed the growing population under the changing climate. To achieve this, a central goal is to map genotype to phenotype. Genetic studies have identified thousands of loci controlling various agronomic traits, revealing important biological pathways and providing valuable insights into genetic basis of many traits variation. However, genome-wide association studies (GWAs) have explained relatively a small heritability of most complex trait. This has led to an important question of where is this ‘missing’ heritability. This study examined the potential sources of the ‘missing’ heritability and provides some experimental data that offer ideas on the underlying genetic architecture of complex trait such as biomass accumulation in maize. The study used 12 main effect and 6-pair of epistasis quantitative trait loci (QTL) displaying different patterns of expression at different developmental time point in 261 maize genotypes. Genotyping of the 261 genotypes was carried out using MaizeSNP50 chip. In addition, copy number variation (CNV) and presence absence variation (PAV) was used to study the genetic architecture of maize genome in 34 maize genotypes. The identified dynamic QTL and CNV were mapped on maize B73 as reference genome. A total of 182 genes were found to be harboured in the detected QTL regions. A complex CNV architecture, such as smaller CNV nested within larger CNV or overlapping CNV regions was detected throughout the maize genome, which may explain the extraordinary traits variation observed in maize. The complex CNV genomic architecture, differential gene expression and their interactions at different developmental time points, which are missing in many GWAs, may explain the missing heritability. Consequently, the genetic model from final trait values cannot reflect the real gene action during the entire growth and development of the plant. Therefore, it is necessary to understand the CNV and the dynamics of gene expression for complex trait at different developmental stages as a basis for quantitative trait manipulation.