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.

多倍体化（polyploidization）是植物演化中古老且反复出现的过程，可影响自然种群的多样化与植物育种策略。多倍体化广泛存在于诸多重要作物中，但相较于二倍体物种，其对诸多农艺性状遗传的影响仍未得到充分解析。更高的等位基因剂量或等位基因间更复杂的互作，可能会影响表型表达。因此，本研究旨在解析同源四倍体（autotetraploid）蓝莓果实相关性状的遗传基础，并鉴定影响表型变异的候选基因。本研究开展了全基因组关联分析（genome-wide association study, GWAS），同时考虑二倍体与四倍体遗传模式，涵盖了多样化的基因作用模型，包括加性模型、通用模型、不同层级的等位基因互作模型以及对应的二倍体化模型。本研究采用序列捕获与下一代测序技术，对源自117个全同胞家系育种群体的1575份南高丛蓝莓（southern highbush blueberry）个体进行了基因分型，并对8项果实相关性状开展了表型鉴定。二倍体等位基因分型共检测到77496个单核苷酸多态性（single nucleotide polymorphism, SNP）位点，而四倍体等位基因分型则获得80591个SNP位点，二者重叠比例高达95%。本研究采用考量种群与家系结构的线性混合模型开展全基因组关联分析。通过对四倍体基因型进行建模，我们共检测到15个与5项果实相关性状显著关联的SNP位点。与之相比，采用二倍体模型时仅在2项性状中检测到7个显著SNP位点，其中2个位点与四倍体分析结果重合。本研究结果表明，四倍体模型的重要性因性状而异，而二倍体模型的使用阻碍了SNP-性状关联的检测，进而限制了同源四倍体物种中部分商业化重要性状的遗传结构解析。此外，14个SNP位点与候选基因存在共定位，其中5个位点导致了非同义氨基酸突变。本研究对这些SNP位点的潜在功能意义进行了讨论。