Abstract
Abstract Polyploidization is an ancient and recurrent process in plant evolution, impacting the diversification of natural populations and plant breeding strategies. Polyploidization occurs in many important crops; however, its effects on inheritance of many agronomic traits are still poorly understood compared with diploid species. Higher levels of allelic dosage or more complex interactions between alleles could affect the phenotype expression. Hence, the present study aimed to dissect the genetic basis of fruit-related traits in autotetraploid blueberries and identify candidate genes affecting phenotypic variation. We performed a genome-wide association study (GWAS) assuming diploid and tetraploid inheritance, encompassing distinct models of gene action (additive, general, different orders of allelic interaction and the corresponding diploidized models). A total of 1,575 southern highbush blueberry individuals from a breeding population of 117 full-sib families were genotyped using sequence capture and next-generation sequencing, and evaluated for eight fruit-related traits. For the diploid allele calling, 77,496 SNPs were detected; while 80,591 SNPs were obtained in tetraploid, with a high degree of overlap (95%) between them. A linear mixed model that accounted for population and family structure was used for the GWAS analyses. By modeling tetraploid genotypes, we detected 15 SNPs significantly associated with five fruit-related traits. Alternatively, seven significant SNPs were detected for only two traits using diploid genotypes, with two SNPs overlapping with the tetraploid scenario. Our results showed that the importance of tetraploid models varied by trait and that the use of diploid models has hindered the detection of SNP-trait associations and, consequently, the genetic architecture of some commercially important traits in autotetraploid species. Furthermore, 14 SNPs co-localized with candidate genes, five of which lead to non-synonymous amino acid changes. The potential functional significance of these SNPs is discussed.
Highlights
Polyploidy is a widespread phenomenon among the flowering plants
A total of 1,575 blueberry plants from 117 crosses were phenotyped for eight fruit-related traits
single nucleotide polymorphism (SNP) were sampled throughout the genome, not evenly distributed, which was expected due to the target design strategy used in this study (Figure 2)
Summary
Rounds of ancient and recent polyploidization events have been shaping the genomes and the evolutionary trajectories of plant lineages, driving phenotypic diversification (Adams and Wendel, 2005; Paterson, 2005; Jiao et al, 2011; Blischak et al, 2016). The molecular mechanisms contributing to phenotypic variation shortly after polyploidization are not well-understood, but probably involve more complex genetic and epigenetic effects of higher allelic dosage and heterosis (Osborn et al, 2003; Jackson and Chen, 2010; Renny-Byfield and Wendel, 2014; Fort et al, 2016). Genome-wide gene expression studies in resynthesized polyploid plants and yeasts have shown ploidydependent gene expression alterations, which likely affect the phenotype (Guo et al, 1996; Galitski et al, 1999; Osborn et al, 2003; Pumphrey et al, 2009; Jackson and Chen, 2010)
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