3.2.3. Population structure analysis
According to the result output from STRUCTURE HARVESTER, when ΔK was at a maximum, the optimal K value was 2 (Fig. 4-A). At K = 2, 112 accessions were divided into two subgroups, with red representing the first subgroup (63 accessions) and green representing the second subgroup (49 accessions). The first subgroup was a collection of D. alata ,D. persimilis , D. fordii , and D. esculenta , the second subgroup was mainly derived from D. opposita , which accounted for 43.75%. At K = 3, the accessions of D. oppositaand D. persimilis were gathered separately, whereas the remaining species were gathered together. At K = 4, the accessions of D. fordii and D. esculenta were mixed together, whereas those of the other three species were gathered separately (Fig. 4-B).
4. Discussion
4.1 Genetic differences of local Yam Varieties in China were discovered by the combining analyses of phenotypic traits investigation and molecular marker identification
Phenotypic diversity is the external manifestation of genetic diversity, and it is the most basic method for germplasm selection and genetic background research (Mignouna et al., 2002; Sartie et al., 2012; Zhang et al, 2019). In this study, the phenotype diversity of 112 local varieties of yam was high, and the I s of leaf shape, petiole color, and stem color of yam were all greater than 1, the local resources of Chinese yam were clustered into 6 groups based on phenotypic traits variations, which was consistent generally with the classification of classical biology (Pei and Ding, 1985). In addition, the typical phenotypic traits were screened for identifying special yam resources. For instance, the stem wings can be effectively used for identification of D. alata (Bressan et al., 2011), and the leaf morphology is the most notable feature of D. opposite (Pei and Ding, 1985;), Additionally, the typical characteristic of D. esculenta is the stem spines and the stem rotates to the left. (Chaïr et al. 2005).
Additionally, flowering is a very important breeding requirement in any crop, but the entire genus Dioscorea is characterized by dioecy, and most important yam varieties are cultivated for their edible tubers and do not bloom (Renner, 2014; Girma, 2017). In the present study, only 43 accessions (38.39%) were bloomed, 26 of which produced female flowers, and the accessions of D. esculenta , D. alata andD. persimilis did not bloom. In recent years, Tamiru et al., (2017) identified a genomic region and W locus related to sex determination by whole-genome resequencing of white Guinea yam, and a diagnostic marker for sex identification could be developed for yam breeding. The bud bursting stage of yam is generally just at the early stage of expansion of underground tuber. Moreover, the flowering period of the male plants is relatively short (50 days), the flowers are prone to self-withering, and the impact on the underground tubers is also small. Its yield and quality are higher than the female plants (et al., 2011).
Molecular markers have been widely used in species genetic diversity analysis (Yan et al., 2019; Saini et al.,2019; Nicholas et al., 2019). In order to clarify the genetic differences of local Chinese yam varieties at the molecular level, In this study, SSR and SRAP and markers were used to the genetic differences of all accessions, The results of phenotypic and molecular analyses showed good consistency, and the difference was that molecular markers could successfully identify the accessions of D. opposita and D. persimilis , while the accessions of D. fordii and D. alata could be identified by phenotypic trait. Moreover, the combination analysis can also identify local varieties (Siqueira et al., 2014; Nicholas et al., 2019). For instance, CY-3 (ZhuGaoShu) is a local variety cultivated for 500 years, in Jiangxi Province, its leaves looks like D. persimilis , but the tuber grows just like D. opposita , so it is not clear for its species,” Zhugaoshu” yam now is identified as D. persimilis based on our results. Furthermore, we collected CY-76, CY-79, CY-80, CY-81 and CY-194 in Ruichang County, Jiangxi Province, which have been considered as D. opposita before, but their phenotypic characteristics are different from this species. Combining with current study and chloroplast genome sequencing analysis (data not shown), we preliminarily speculated that it may be a new species or a new variant of D. opposita .