Data from: Insights into the genetic basis of blueberry fruit-related traits using diploid and polyploid models in a GWAS context

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.