Agre Paterne A, Darkwa Kwabena, Kohtaro Iseki, Matsumoto Ryo, Asfaw Asrat
International Institute of Tropical Agriculture, Ibadan, 200001, Nigeria.
Savanah Agricultural Research Institute, CSIR-SARI, Tamale, Ghana.
Sci Rep. 2025 Jul 24;15(1):26929. doi: 10.1038/s41598-025-10344-z.
Yam (Dioscorea spp.) is a herbaceous vine crop valued for its starchy tubers, which are rich in essential nutrients. Its genome is highly heterozygous, contributing to considerable genetic diversity and adaptability. Understanding the polymorphism information content (PIC) of genetic markers is critical for enhancing key agronomic traits such as yield. In this study, we conducted a genome-wide association analysis that accounts for heterozygosity to investigate fresh tuber yield variation in white Guinea yam (Dioscorea rotundata Poir). A total of 173 genotypes including 86 elite breeding clones, 77 genebank accessions, and 10 farmer varieteies were genotyped through whole-genome resequencing, yielding approximately 1.6 million single nucleotide polymorphism (SNP) markers. Association analysis was performed using a multi-locus mixed linear model (MLM), incorporating kinship matrices derived from marker subsets grouped by PIC levels (≤ 0.1, 0.1-0.2, 0.2-0.4, and > 0.4), alongside population structure. The analysis revealed that high-PIC markers had greater influence on trait associations. Twelve stable SNPs were significantly associated with fresh tuber yield. Functional annotation of these markers revealed putative genes related to plant growth and cellular regulation. Notably, markers located in heterozygosity-rich genomic regions were linked to high-yielding genotypes, while those in homozygous regions were associated with lower yields. These findings underscore the potential of PIC-based marker selection and highlight the value of integrating heterozygosity metrics into genomic-assisted breeding strategies for improving fresh tuber yield in white Guinea yam.
山药（薯蓣属）是一种草本藤本作物，其富含淀粉的块茎具有重要价值，这些块茎富含必需营养素。它的基因组高度杂合，导致了相当大的遗传多样性和适应性。了解遗传标记的多态性信息含量（PIC）对于提高产量等关键农艺性状至关重要。在本研究中，我们进行了一项考虑杂合性的全基因组关联分析，以研究白几内亚山药（Dioscorea rotundata Poir）鲜块茎产量的变异。通过全基因组重测序对总共173个基因型进行了基因分型，其中包括86个优良育种克隆、77个基因库种质和10个农家品种，产生了约160万个单核苷酸多态性（SNP）标记。使用多基因座混合线性模型（MLM）进行关联分析，该模型纳入了根据PIC水平（≤0.1、0.1 - 0.2、0.2 - 0.4和>0.4）分组的标记子集得出的亲缘关系矩阵以及群体结构。分析表明，高PIC标记对性状关联的影响更大。十二个稳定的SNP与鲜块茎产量显著相关。对这些标记的功能注释揭示了与植物生长和细胞调控相关的推定基因。值得注意的是，位于富含杂合性的基因组区域的标记与高产基因型相关，而位于纯合区域的标记与较低产量相关。这些发现强调了基于PIC的标记选择的潜力，并突出了将杂合性指标纳入基因组辅助育种策略以提高白几内亚山药鲜块茎产量的价值。
