Spatial structure of microsatellite variability within and among populations of wild radish Raphanus sativus L. var. hortensis Backer f. raphanistroides Makino (Brassicaceae) in Japan

Ohsako, Takanori; Hirai, Masashi; Yamabuki, Makoto

doi:10.1270/jsbbs.60.195

Cited by 10 publications

(10 citation statements)

References 39 publications

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“…In addition, the numerous multidirectional tributaries of sea currents surrounding the Japanese archipelago are also responsible for the expansion of wild radish populations. Our results are consistent with the positive correlation of IBD in wild radish reported by Ohsako et al [ 27 ] using microsatellite loci, as well as in other coastal plants such as Cakile maritima , Salsola kali , and Halimione portulacoides in the Atlantic clusters [ 1 ].…”

Section: Discussionsupporting

confidence: 92%

“…The presence of null alleles increases the numbers of homozygotes. Similar degrees of heterozygotic deficiency were evident in Japanese and Korean wild radish populations subjected to analysis of microsatellite [ 27 ] and allozyme variations [ 21 ]. As the wild radish is self-incompatible, any excess of homozygotes is attributable to the genetic substructure of a local population, in which either the Wahlund effect and/or biparental inbreeding may be in play.…”

Section: Resultsmentioning

confidence: 77%

“…Nine microsatellite markers were selected based on their clarity and reproducibility [ 27 – 29 ] ( S1 Table ). PCR amplification was performed in a final volume of 5 μL (containing 40–60 ng genomic DNA) following the standard protocol of the Qiagen Multiplex PCR kit (Qiagen, Hilden, Germany).…”

Section: Methodsmentioning

confidence: 99%

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Distinct Phylogeographic Structures of Wild Radish (Raphanus sativus L. var. raphanistroides Makino) in Japan

et al. 2015

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Coastal plants with simple linear distribution ranges along coastlines provide a suitable system for improving our understanding of patterns of intra-specific distributional history and genetic variation. Due to the combination of high seed longevity and high dispersibility of seeds via seawater, we hypothesized that wild radish would poorly represent phylogeographic structure at the local scale. On the other hand, we also hypothesized that wild radish populations might be geographically differentiated, as has been exhibited by their considerable phenotypic variations along the islands of Japan. We conducted nuclear DNA microsatellite loci and chloroplast DNA haplotype analyses for 486 samples and 144 samples, respectively, from 18 populations to investigate the phylogeographic structure of wild radish in Japan. Cluster analysis supported the existence of differential genetic structures between the Ryukyu Islands and mainland Japan populations. A significant strong pattern of isolation by distance and significant evidence of a recent bottleneck were detected. The chloroplast marker analysis resulted in the generation of eight haplotypes, of which two haplotypes (A and B) were broadly distributed in most wild radish populations. High levels of variation in microsatellite loci were identified, whereas cpDNA displayed low levels of genetic diversity within populations. Our results indicate that the Kuroshio Current would have contributed to the sculpting of the phylogeographic structure by shaping genetic gaps between isolated populations. In addition, the Tokara Strait would have created a geographic barrier between the Ryukyu Islands and mainland Japan. Finally, extant habitat disturbances (coastal erosion), migration patterns (linear expansion), and geographic characteristics (small islands and sea currents) have influenced the expansion and historical population dynamics of wild radish. Our study is the first to record the robust phylogeographic structure in wild radish between the Ryukyu Islands and mainland Japan, and might provide new insight into the genetic differentiation of coastal plants across islands.

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Section: Discussionsupporting

confidence: 92%

Section: Resultsmentioning

confidence: 77%

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Distinct Phylogeographic Structures of Wild Radish (Raphanus sativus L. var. raphanistroides Makino) in Japan

et al. 2015

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“…Also, SSRs are abundantly applied in molecular mapping, genetic diversity research, cultivar fingerprinting due to multiple advantages including co-dominant inheritance nature, high variability, high feasibility of detection, and good transferability (Li et al, 2004 ). Next-generation sequencing technology for SSR mining has been used in various plant species such as rubber tree (Li et al, 2012 ), castor bean (Qiu et al, 2010 ), sesame (Zhang et al, 2012a ), and some Brassicaceae plants (Wang et al, 2007 ; Yamane et al, 2009 ; Kamei et al, 2010 ; Ohsako et al, 2010 ). However, so far, little has been reported about the TF and SSR profiles due to limited genome information in R. sativus .…”

Section: Introductionmentioning

confidence: 99%

Sequencing, de novo assembly and comparative analysis of Raphanus sativus transcriptome

Zhang

Yin

et al. 2015

Front. Plant Sci.

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Raphanus sativus is an important Brassicaceae plant and also an edible vegetable with great economic value. However, currently there is not enough transcriptome information of R. sativus tissues, which impedes further functional genomics research on R. sativus. In this study, RNA-seq technology was employed to characterize the transcriptome of leaf tissues. Approximately 70 million clean pair-end reads were obtained and used for de novo assembly by Trinity program, which generated 68,086 unigenes with an average length of 576 bp. All the unigenes were annotated against GO and KEGG databases. In the meanwhile, we merged leaf sequencing data with existing root sequencing data and obtained better de novo assembly of R. sativus using Oases program. Accordingly, potential simple sequence repeats (SSRs), transcription factors (TFs) and enzyme codes were identified in R. sativus. Additionally, we detected a total of 3563 significantly differentially expressed genes (DEGs, P = 0.05) and tissue-specific biological processes between leaf and root tissues. Furthermore, a TFs-based regulation network was constructed using Cytoscape software. Taken together, these results not only provide a comprehensive genomic resource of R. sativus but also shed light on functional genomic and proteomic research on R. sativus in the future.

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“…마커를 이용하여 분석한 결과를 보고하였고 (Huh and Ohnishi, 2002;Ohsako et al, 2010), 미토콘드리아의 염기서열을 이 용하여 야생종 무와 재배종의 근연관계 분석을 통해 유럽 과 아시아의 재배종 무의 기원에 대한 연구 (Yamagishi and Terachi, 2003;Yamane, 2004)와 엽록체 염기서열을 이용한 분석 결과 (Lü et al, 2008;Yamane et al, 2005)를 보고하였 다. 한국에서는 RAPD 마커를 이용하여 한국 재래종과 야생 종과의 근연관계 분석을 보고하였으며 (Choi et al, 2008), AFLP 마커를 이용하여 품종구분에 관하여 보고하였다 (Kwon et al, 2003).…”

Section: 일본에서 동아시아에 분포하는 야생종 무간에 Aflp Ssrunclassified

Analysis of the Genetic Diversity of Radish Germplasm through SSR Markers Derived from Chinese Cabbage

Park¹,

Choi²,

Lee³

et al. 2013

Korean Journal of Horticultural Science and Technology

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Abstract. Since the early 1980s, the National Institute of Horticultural & Herbal Sciences has been breeding and collecting diverse radish breeds to select those samples with better horticultural characteristics, to ultimately expand and develop as good radish produce. Genetic diversity is a crucial factor in crop improvement and therefore it is very important to obtain various variations through sample collection. The collected samples were compared with one another in order to assess the level of diversity among the collections, and this procedure allowed for increased application of the gathered resources and aided in determining the direction to secure further samples. Towards this end, this experiment was conducted in order to examine whether the SSR markers derived from Chinese cabbage samples could be transferred to the radish samples. Among the radish breeding lines and introduced resources, 44 lines were used as materials to analyze the genotype using 22 SSR markers selected. As a result, the analysis showed that among all the selected markers, 'cnu_m139' and 'cnu_m289' were the most useful markers for diversity evaluation. The genetic relationship of the radish genetic resources showed that the geographic origins affected the diversity. Furthermore, the different types of radish groups were also determined by the year they were bred. This result demonstrated that there are differences between the older radish breeds and the more recently developed radish breeds. Even though a relatively small number of markers were used in the analysis, it was possible to distinguish whether the radish was bred 30 years ago or in the 2000s, and that the similar physical shapes comprised a particular group, showed that the SSR markers can indeed be successfully applied to to study the diversity within radish breeding lines. Through the results of this study, it can be concluded that the SSR marker developed for the Chinese cabbage can be applied to examine the genetic diversity and analyze the relationship (genetic resource determination) of radish.

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Spatial structure of microsatellite variability within and among populations of wild radish Raphanus sativus L. var. hortensis Backer f. raphanistroides Makino (Brassicaceae) in Japan

Cited by 10 publications

References 39 publications

Distinct Phylogeographic Structures of Wild Radish (Raphanus sativus L. var. raphanistroides Makino) in Japan

Distinct Phylogeographic Structures of Wild Radish (Raphanus sativus L. var. raphanistroides Makino) in Japan

Sequencing, de novo assembly and comparative analysis of Raphanus sativus transcriptome

Analysis of the Genetic Diversity of Radish Germplasm through SSR Markers Derived from Chinese Cabbage

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