Isolation and characterisation of microsatellite loci in Calystegia soldanella (Convolvulaceae), an endangered coastal plant isolated in Lake Biwa, Japan

Noda, Asuka; Nomura, Naofumi; Mitsui, Yuki; Setoguchi, Hiroaki

doi:10.1007/s10592-008-9695-x

Cited by 5 publications

(5 citation statements)

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“…Genotypes of 478 individuals were determined using eight nSSR markers developed for this study (AC2, AC5, AC24, AC30, AC41, TC4, TC10, and TC11) (Noda et al ., 2009b). The primers used are listed in Table 3.…”

Section: Methodsmentioning

confidence: 99%

Long-term isolation of the coastal plant Calystegia soldanella (Convolvulaceae) in ancient freshwater Lake Biwa, Japan

Noda

Mitsui

Ikeda

et al. 2010

Biological Journal of the Linnean Society

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Lake Biwa is an ancient freshwater lake that was formed approximately 4 Mya and harbours many coastal plants that commonly inhabit the seashore. We used chloroplast DNA haplotype analysis using two spacer sequences and simple sequence repeat (SSR) analysis using eight nuclear microsatellite markers to detect genomic signatures indicating long-term isolation of inland populations of Calystegia soldanella in Lake Biwa from coastal populations. We used 348 samples from 63 populations for haplotype analysis and 478 samples from 27 populations for SSR analysis covering the inland and coastal distribution of the species. We detected seven haplotypes, and the distribution pattern of these haplotypes was geographically highly structured between Lake Biwa and the coast. Nuclear SSR analysis also supported genetic differentiation between Lake Biwa and coastal populations (analyses of molecular variance, 43%), and the grouping of Lake Biwa and coastal populations by a Neighbour-joining tree. In addition, genetic diversity of the inland populations (mean HE = 0.153) was significantly lower than that of coastal populations (mean HE = 0.328). These results suggested that inland populations at Lake Biwa have been isolated from coastal populations for a very long time. The inland populations most likely experienced a bottleneck effect, resulting in sufficient in situ genetic divergence to clearly distinguish them from coastal populations.

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Section: Methodsmentioning

confidence: 99%

Long-term isolation of the coastal plant Calystegia soldanella (Convolvulaceae) in ancient freshwater Lake Biwa, Japan

Noda

Mitsui

Ikeda

et al. 2010

Biological Journal of the Linnean Society

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“…The SSR technique has been used to start conserving endangered species, such as Calystegia soldanella [51], Tricyrtis ishiiana [52], Galium catalinense subspecies acrispum [53], and Primula reinni [54]. In another example, the genetic diversity of Pennisetum glaucum hybrids and their parental line was studied using 55 microsatellite markers.…”

Section: Microsatellitesmentioning

confidence: 99%

Assessment of plant genetic variations using molecular markers: A review

Hussain¹,

Nisar²

2020

J Appl Biol Biotech

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Climatic changes affect various organisms, including plant species, becoming unfavorable for the environment and socioeconomic value, prompting an increase in activities related to plant resources conservation. The successful conservation of plant genetic resources depends on the proper identification and characterization of plant material. One of the notable developments in genetic conservation is the use of molecular markers for assessing the conservation and use of plant genetic resources. This review is devoted to the use of molecular marker techniques for genetic assessment of plant genetic variations. Development in these techniques provides smooth, reliable, and effortless ways for assessing known and unknown taxa, between and within species. These techniques provide a revelation to researchers on taxonomical and evolutionary questions which were not possible earlier. The polymerase chain reaction-based molecular markers give rise to various novel techniques due to the simplicity and high reproducibility of the methods. Examples including a combination of earlier techniques, such as restriction fragment length polymorphism, random amplification of polymorphic DNA, simple sequence repeat, intersimple sequence repeats, single nucleotide polymorphism, and amplified fragment length polymorphism, have been used for plant genetic variations and polymorphism studies. Progress in the advanced high-throughput sequencing techniques or next-generation sequencing technologies has been rapidly utilized to study genetic diversity broadly and to identify suitable genes and alleles rapidly. These techniques offer a practical resolution to the challenges in crop genomics. This review explains the recent advances in the molecular marker techniques, along with the advantages, uses, and limitations. Each technique differs in resolving the genetic variations and polymorphism in plant species.

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“…Microsatellites developed for particular species can often be applied to closely related species, but the percentage of loci that successfully amplify may decrease with increasing genetic distance [ 62 ]. Microsatellite technique has recently been used to establish conservation strategy of endangered plants like Calystegia soldanella [ 63 ], Tricyrtis ishiiana [ 64 ] and Galium catalinense subspecies acrispum [ 65 ].…”

Section: Microsatellitesmentioning

confidence: 99%

A Brief Review of Molecular Techniques to Assess Plant Diversity

Arif

Bakir

Khan

et al. 2010

IJMS

142

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Massive loss of valuable plant species in the past centuries and its adverse impact on environmental and socioeconomic values has triggered the conservation of plant resources. Appropriate identification and characterization of plant materials is essential for the successful conservation of plant resources and to ensure their sustainable use. Molecular tools developed in the past few years provide easy, less laborious means for assigning known and unknown plant taxa. These techniques answer many new evolutionary and taxonomic questions, which were not previously possible with only phenotypic methods. Molecular techniques such as DNA barcoding, random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), microsatellites and single nucleotide polymorphisms (SNP) have recently been used for plant diversity studies. Each technique has its own advantages and limitations. These techniques differ in their resolving power to detect genetic differences, type of data they generate and their applicability to particular taxonomic levels. This review presents a basic description of different molecular techniques that can be utilized for DNA fingerprinting and molecular diversity analysis of plant species.

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Isolation and characterisation of microsatellite loci in Calystegia soldanella (Convolvulaceae), an endangered coastal plant isolated in Lake Biwa, Japan

Cited by 5 publications

References 5 publications

Long-term isolation of the coastal plant Calystegia soldanella (Convolvulaceae) in ancient freshwater Lake Biwa, Japan

Long-term isolation of the coastal plant Calystegia soldanella (Convolvulaceae) in ancient freshwater Lake Biwa, Japan

Assessment of plant genetic variations using molecular markers: A review

A Brief Review of Molecular Techniques to Assess Plant Diversity

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