Protein content is a key quality trait for the potato starch industry. The objective of this study was to identify allele-specific quantitative trait loci (QTLs) for tuber protein content in cultivated potato (Solanum tuberosum L.) at the tetraploid level. We analysed 496 full-sib F1 clones in a 3-year field trial to dissect the complex genetic architecture of soluble tuber protein content. Genotypic data from a 60K single nucleotide polymorphism (SNP) array was used for SNP dosage scoring, constructing homologue specific linkage maps and assembly of a dense integrated chromosomal linkage map. From the integrated map, probabilistic multi-locus identity-by-descent (IBD) haplotypes (alleles) were estimated and used to detect associations between the IBD haplotypes and the phenotypic trait values. Moderate levels of trait heritability were estimated between 40 and 74% that correspond with previous studies. Our contemporary naive analysis identified potential additive QTLs on chromosomes 2, 3, 5 (top arm) and 9 across the years. Moreover, cofactor QTL analysis identified two masked QTLs on chromosomes 1 and 5 (lower arm). The QTLs on chromosomes 2, 5 (lower arm) and 9 are reported here for the first time. The QTLs that we identified on chromosomes 1, 3 and 5 (top arm) show overlap with previous studies for protein content in potato. Collectively the naive QTLs explained 12 to 17% of the phenotypic variance. The underlying alleles of the QTLs provided both positive and negative effects on the phenotype. Our work uncovers the complex genetic architecture of this trait and describes potential breeding strategies for improvement. As protein has emerged as a high-value component from industrial potato starch production, the dissection of the genetic architecture and subsequent improvement of this trait by breeding has great economic and environmental relevance.

中文翻译：

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栽培四倍体马铃薯双亲群体蛋白质含量的多等位基因QTL分析

蛋白质含量是马铃薯淀粉行业的关键质量特性。本研究的目的是在四倍体水平上鉴定栽培马铃薯 (Solanum tuberosum L.) 块茎蛋白质含量的等位基因特异性数量性状位点 (QTL)。我们在为期 3 年的田间试验中分析了 496 个全同胞 F1 克隆，以剖析可溶性块茎蛋白质含量的复杂遗传结构。来自 60K 单核苷酸多态性 (SNP) 阵列的基因型数据用于 SNP 剂量评分、构建同源特异性连锁图和密集整合染色体连锁图的组装。从综合图谱中，估计了概率多基因座同一性（IBD）单倍型（等位基因）并用于检测 IBD 单倍型与表型性状值之间的关联。中等水平的性状遗传率估计在 40% 到 74% 之间，与之前的研究相符。我们当代的幼稚分析确定了多年来染色体 2、3、5（上臂）和 9 上的潜在附加 QTL。此外，辅因子 QTL 分析确定了染色体 1 和 5（下臂）上的两个掩蔽 QTL。2号、5号（下臂）和9号染色体上的QTL是首次报道。我们在 1、3 和 5 号染色体（上臂）上鉴定的 QTL 与之前对马铃薯蛋白质含量的研究有重叠。总的来说，初始 QTL 解释了 12% 到 17% 的表型变异。QTL 的潜在等位基因对表型产生积极和消极影响。我们的工作揭示了这种性状的复杂遗传结构，并描述了潜在的改良育种策略。