Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China.
Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China.
Int J Mol Sci. 2023 Feb 7;24(4):3341. doi: 10.3390/ijms24043341.
L. (Dioscoreaceae), commonly known as greater yam, water yam, or winged yam, is a popular tuber vegetable/food crop worldwide, with nutritional, health, and economical importance. China is an important domestication center of , and hundreds of cultivars (accessions) have been established. However, genetic variations among Chinese accessions remain ambiguous, and genomic resources currently available for the molecular breeding of this species in China are very scarce. In this study, we generated the first pan-plastome of based on 44 Chinese accessions and 8 African accessions, and investigated the genetic variations, plastome evolution, and phylogenetic relationships within and among members of the section . The pan-plastome encoded 113 unique genes and ranged in size from 153,114 to 153,161 bp. A total of four whole-plastome haplotypes (Haps I-IV) were identified in the Chinese accessions, showing no geographical differentiation, while all eight African accessions shared the same whole-plastome haplotype (Hap I). Comparative genomic analyses revealed that all four whole plastome haplotypes harbored identical GC content, gene content, gene order, and IR/SC boundary structures, which were also highly congruent with other species of . In addition, four highly divergent regions, i.e., -, -, -, and exon 3 of were identified as potential DNA barcodes. Phylogenetic analyses clearly separated all the accessions into four distinct clades corresponding to the four haplotypes, and strongly supported that was more closely related to and than , and . Overall, these results not only revealed the genetic variations among Chinese accessions, but also provided the necessary groundwork for molecular-assisted breeding and industrial utilization of this species.
盾叶薯蓣（Dioscoreaceae），俗称大薯、山药或翼薯，是一种在全球范围内广受欢迎的根茎蔬菜/粮食作物，具有营养价值、健康益处和经济重要性。中国是盾叶薯蓣的重要驯化中心，已建立了数百个品种（品系）。然而，中国品种之间的遗传变异仍不清楚，目前可用于该物种分子育种的基因组资源非常稀缺。在这项研究中，我们基于 44 个中国品种和 8 个非洲品种生成了第一个盾叶薯蓣泛基因组，并研究了中国品种内和品种间的遗传变异、质体进化和系统发育关系。盾叶薯蓣的泛基因组编码 113 个独特的基因，大小在 153114 到 153161bp 之间。在中国品种中总共鉴定出四个全质体单倍型（Haps I-IV），没有地理分化，而所有 8 个非洲品种都共享相同的全质体单倍型（Hap I）。比较基因组分析表明，所有四个全质体单倍型都具有相同的 GC 含量、基因组成、基因顺序和 IR/SC 边界结构，与其他薯蓣属物种也高度一致。此外，还鉴定出了四个高度分化的区域，即 -、-、- 和 的外显子 3，可作为潜在的 DNA 条形码。系统发育分析清楚地将所有 44 个盾叶薯蓣品种分为四个不同的分支，与四个单倍型相对应，并强烈支持盾叶薯蓣与 、 比 、 、 更密切相关。总的来说，这些结果不仅揭示了中国盾叶薯蓣品种之间的遗传变异，也为该物种的分子辅助育种和工业利用提供了必要的基础。
