Abstract
Raphanus has undergone a lengthy evolutionary process and has rich diversity. However, the inter- and intraspecific phylogenetic relationships and genetic diversity of this genus are not well understood. Through SSR-sequencing and multi-analysis of 939 wild, semi-wild and cultivated accessions, we discovered that the European wild radish (EWR) population is separated from cultivated radishes and has a higher genetic diversity. Frequent intraspecific genetic exchanges occurred in the whole cultivated radish (WCR) population; there was considerable genetic differentiation within the European cultivated radish (ECR) population, which could drive radish diversity formation. Among the ECR subpopulations, European primitive cultivated radishes (EPCRs) with higher genetic diversity are most closely related to the EWR population and exhibit a gene flow with rat-tail radishes (RTRs) and black radishes (BRs)/oil radishes (ORs). Among Asian cultivated radishes (ACRs), Chinese big radishes (CBRs) with a relatively high diversity are furthest from the EWR population, and most Japanese/Korean big radishes (JKBRs) are close to CBR accessions, except for a few old Japanese landraces that are closer to the EPCR. The CBR and JKBR accessions are independent of RTR accessions; however, phylogenetic analysis indicates that the RTR is sister to the clade of CBR (including JWR), which suggests that the RTR may share the most recent common ancestry with CBRs and JWRs. In addition, Japanese wild radishes (JWRs), (namely, R. sativus forma raphanistroides) are mainly scattered between CBRs and EPCRs in PCoA analysis. Moreover, JWRs have a strong gene exchange with the JKBR, OR and RTR subpopulations. American wild radishes (AWRs) are closely related to European wild and cultivated radishes, and have a gene flow with European small radishes (ESRs), suggesting that the AWR developed from natural hybridization between the EWR and the ESR. Overall, this demonstrates that Europe was the origin center of the radish, and that Europe, South Asia and East Asia appear to have been three independent domestication centers. The EPCR, AWR and JWR, as semi-wild populations, might have played indispensable transitional roles in radish evolution. Our study provides new perspectives into the origin, evolution and genetic diversity of Raphanus and facilitates the conservation and exploitation of radish germplasm resources.
Highlights
Raphanus, a member of the Brassicaceae family, consists of two species: Raphanus sativus L.and R. raphanistrum L. [1]
The European primitive cultivated radishes (EPCRs) was composed of two parts: eighteen accessions were recorded as R. raphanistrum but had characteristics of taproots, flowers, and siliques that were similar to those of the cultivated radish; the other forty-two accessions with the Latin name of R. sativus L. convar. sativus had characteristics of non-enlarged taproots, white or purple flowers, and hard siliques that were between those of cultivated radishes and European wild radishes (EWR)
Our results essentially agreed with the viewpoint of Yamagishi [46] and Kim [21], that Japanese wild radishes (JWRs) accessions belong to cultivated radishes from the phylogenetic clustering tree; we suggest that they have a different variation from the East Asia cultivated radish (EACR) and South Asia cultivated radish (SACR) populations, because they carry more wild radish genetic background, according to the genetic structure analysis
Summary
A member of the Brassicaceae family, consists of two species: Raphanus sativus L.and R. raphanistrum L. [1]. A member of the Brassicaceae family, consists of two species: Raphanus sativus L. and R. raphanistrum L. R. raphanistrum L. is a wild relative species of R. sativus L., which is an important root vegetable crop species worldwide, comprising five different varieties; namely, R. sativus var. Radicular (European small radish) and R. sativus var. Some previous molecular studies have shown that the wild radish includes three species: R. raphanistrum, R. landra and R. maritimus [5,6]. Other researchers consider that these wild Raphanus species should be a single species with three subspecies: R. raphanistrum subsp. R. raphanistrum L. is generally considered to comprise two subspecies Compared with cultivated radish plants, the wild radish has distinct morphological traits, including non-fleshy roots, yellow or white flowers, nonshattering mature siliques containing 1~10 seeds, and strong growth habits influencing crop yields as weeds [9,10,11]
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