Yam (Dioscorea spp.) is a nutritional and medicinal staple tuber crop grown in the tropics and sub-tropics. Among the food yam species, water yam (Dioscorea alata L.) is the most widely distributed and cultivated species worldwide. Tuber dry matter content (DMC) and oxidative browning (OxB) are important quality attributes that determine cultivar acceptability in water yam. This study used a single nucleotide polymorphism (SNP) assay from a diversity arrays technology (DArT) platform for a genome-wide association study (GWAS) of the two quality traits in a panel of 100 water yam clones grown in three environments. The marker–trait association analysis identified significant SNPs associated with tuber DMC on chromosomes 6 and 19 and with OxB on chromosome 5. The significant SNPs cumulatively explained 45.87 and 12.74% of the total phenotypic variation for the tuber DMC and OxB, respectively. Gene annotation for the significant SNP loci identified important genes associated in the process of the proteolytic modification of carbohydrates in the dry matter accumulation pathway as well as fatty acid β-oxidation in peroxisome for enzymatic oxidation. Additional putative genes were also identified in the peak SNP sites for both tuber dry matter and enzymatic oxidation with unknown functions. The results of this study provide valuable insight for further dissection of the genetic architecture of tuber dry matter and enzymatic oxidation in water yam. They also highlight SNP variants and genes useful for genomics-informed selection decisions in the breeding process for improving food quality traits in water yam.

中文翻译：

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水山药（Dioscorea alata L.）块茎干物质和氧化褐变的全基因组关联分析。


山药（ Dioscorea spp.）是一种生长在热带和亚热带的营养和药用主要块茎作物。在食用山药品种中，水山药（ Dioscorea alata L. ）是世界范围内分布和栽培最广泛的品种。块茎干物质含量（DMC）和氧化褐变（OxB）是决定水山药品种可接受性的重要质量属性。本研究使用多样性阵列技术 (DArT) 平台的单核苷酸多态性 (SNP) 测定，对在三种环境中生长的 100 个水山药克隆的两个质量性状进行全基因组关联研究 (GWAS)。标记-性状关联分析确定了与 6 号和 19 号染色体上的块茎 DMC 以及 5 号染色体上的 OxB 相关的显着 SNP。这些显着 SNP 累计分别解释了块茎 DMC 和 OxB 总表型变异的 45.87% 和 12.74%。对重要 SNP 位点的基因注释鉴定了与干物质积累途径中碳水化合物的蛋白水解修饰过程以及过氧化物酶体中脂肪酸 β-氧化过程相关的重要基因。在块茎干物质和功能未知的酶氧化的峰值 SNP 位点中还鉴定了其他推定基因。这项研究的结果为进一步剖析块茎干物质的遗传结构和水山药中的酶氧化提供了宝贵的见解。他们还强调了 SNP 变异和基因，这些变异和基因对于育种过程中基于基因组学的选择决策有用，以改善水山药的食品质量性状。