A method to measure genetic distance between allogamous populations of alfalfa (Medicago sativa) using RAPD molecular markers

Ghérardi, M.; Mangin, Brigitte; Goffinet, Bruno; Bonnet, Delphine; Huguet, Thierry

doi:10.1007/s001220050756

Cited by 83 publications

(67 citation statements)

References 12 publications

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“…All the bands whether monomorphic or polymorphic were used for similarity calculation in order to avoid over estimation of distance (Gherardi et al 1998). Jaccard's coeffi cient of similarity (Jaccard 1908) was calculated and a dendrogram based on similarity coeffi cient was obtained through unweighted pair group method using arithmetic averages (UPGMA) (Sneath & Sokal 1973) and SHAN clustering.…”

Section: Discussionmentioning

confidence: 99%

Separation of the genera in the subtribe Cassiinae (Leguminosae: Caesalpinioidae) using molecular markers

2011

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Separation of the genera in the subtribe Cassiinae (Leguminosae: Caesalpinioidae) using molecular markers RESUMO (Separação dos gêneros na subtribo Cassiinae (Leguminosae: Caesalpinioidae) utilizando marcadores moleculares). Técnicas de Random amplified polymorphic DNA (RAPD), Inter simple sequence repeat (ISSR) e Amplified Fragment Length Polymorphism markers (AFLP) foram utilizadas para verificar a segregação do gênero Cassia L. senso lato em três diferentes gêneros, Chamaecrista Moench., Senna P. Mill. e Cassia L. senso stricto Dezoito representantes dos três táxons foram caracterizados com o uso de marcadores moleculares: 25 RAPD, seis iniciadores ("primers") ISSR e seis AFLP combinações de iniciadores, resultando na amplificação de 612, 115 e 622 bandas (loci), respectivamente. A maioria dos loci apresentou-se como polimórfico, mostrando um alto grau de diversidade genética entre os táxons estudados. O dendrograma construído com base nos dados de RAPD, ISSR e AFLP e agrupamento com procedimentos SHAN dividiu Cassia L. senso lato em três diferentes agrupamentos, chamados de Chamaecrista Moench., Senna P. Mill. e Cassia L. senso stricto Valores altos de bootstrap revelaram que todos os agrupamentos foram estáveis e robustos. Foi observado pela presente investigação que estes gêneros possuem identidade ao nível molecular, o que sustenta a elevação do genero Cassia L. senso lato para o nível de subtribo e a segregação dos três gêneros ao invés de formarem categorias infra-genéricas.Palavras-chave: AFLP, Cassia, fi logenia molecular, ISSR, RAPD Laxmikanta Acharya 1, 4 , Arup Kumar Mukherjee 2 and Pratap Chandra Panda 3 ABSTRACT(Separation of the genera in the subtribe Cassiinae (Leguminosae: Caesalpinioidae) using molecular markers). Random amplified polymorphic DNA (RAPD), Inter simple sequence repeat (ISSR) and Amplified fragment length polymorphism (AFLP) markers were used to verify the segregation of the genus Cassia L. senso lato into three distinct genera namely Chamaecrista Moench., Senna P. Mill. and Cassia L. sensostricto Eighteen representatives of the three taxa were characterized using the molecular markers. 25 RAPD, six ISSR primers and six AFLP primer combinations resulted in the amplification of 612, 115 and 622 bands (loci) respectively. Most of the loci are found to be polymorphic, showing high degrees of genetic diversity among the different taxa studied. The dendrogram constructed on the basis of the RAPD, ISSR and AFLP data using SHAN clustering, divided Cassia L. senso lato. into three different clusters as Chamaecrista Moench. Senna P. Mill. and Cassia L. senso stricto High bootstrap value revealed that all the clusters were stable and robust. It was observed from the present investigation that these genera have their identity at molecular level, which supports the elevation of the genus Cassia L. senso lato to the level of subtribe Cassiinae and segregation into three distinct genera instead of intrageneric categories. IntroductionCassia L. senso lato (Leguminosae: Caesalpinioideae) is on...

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Section: Discussionmentioning

confidence: 99%

Separation of the genera in the subtribe Cassiinae (Leguminosae: Caesalpinioidae) using molecular markers

2011

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“…Compared to other forage material, the breeding of orchardgrass is hampered by its strong self-incompatibility system and severe inbreeding depression, which makes it difficult to produce inbred lines and construct fingerprinting (Xie et al, 2011). A series of molecule studies indicate that the conventional method of bulking could be effectively used for evaluating the diversity of cross-pollinated forage grass species (Marshall and Brown, 1975;Morell et al, 1995;Ghérardi et al, 1998;Forster et al, 2001;Bolaric et al, 2005), which requires a suitable sample size per population (Marshall and Brown, 1975). Moreover, more than 15 plants per population should be used for allogamous species (Morell et al, 1995).…”

Section: Samplesizeselectionandfingerprintingconstructionmentioning

confidence: 99%

“…Furthermore, for each species and specific marker system, a certain sample size should be tested before conducting a diversity study (Bolaric et al, 2005). For example, a minimum sample size of 40 individuals per populations is required for the characterization of the allogamous tetraploid crop alfalfa (Medicago sativa L.) (Ghérardi et al, 1998), while 20 individuals are required for perennial ryegrass (Lolium perenne L.) cultivars (Bolaric et al, 2005). In this report, a sample size of 25 individuals per population was used for orchardgrass, with an average of 0.848, 7.9, and 92.1% for PIC, TB, and P, respectively.…”

Section: Samplesizeselectionandfingerprintingconstructionmentioning

confidence: 99%

Identification of orchardgrass (Dactylis glomerata L.) cultivars by using simple sequence repeat markers

Jiang¹,

Zhang²,

Ma³

et al. 2013

Genet. Mol. Res.

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ABSTRACT. The accurate identification of orchardgrass (Dactylis glomerata L.) cultivars is necessary to ensure purity for consumers, the effective utilization of cultivars, and to protect the intellectual property for breeders. Therefore, this study aimed to use SSR to construct DNA fingerprinting of orchardgrass cultivars. The genetic diversity of 32 orchardgrass cultivars originated from 21 countries, but grown in China, was assessed using a set of 29 SSR markers distributed across 9 linkage groups of the orchardgrass genome. A total of 229 bands were detected, with an average of 7.9 bands per marker. The average polymorphic rate for the species was 92.1%. The polymorphism information content ranged from 0.771 to 0.893. The genetic similarity ranged from 0.55 to 0.84, which confirmed a high level of genetic diversity among orchardgrass cultivars. The unweighted pair-group method, in combination with the arithmetic mean algorithm (UPGMA) dendrogram and principal coordinate analysis, showed a separation of 6 major clusters among 32 cultivars. The number of distinguishable cultivars ranged from 3 to 23, with an average of 12.1 per primer. Moreover, 11 bands that showed stable and repeatable SSR patterns were amplified by A01E14, A01K14, and D02K13. These bands were used to develop the DNA fingerprints for 32 orchardgrass cultivars. In the DNA fingerprints constructed, each cultivar had a unique fingerprinting pattern that was easily distinguished from the others. These results indicate that the SSR marker was polymorphic, and reliable for use in potential large-scale DNA fingerprinting of orchardgrass cultivars.

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“…All the alleles were scored to avoid over/under estimate the diversity [31]. Diffused alleles or alleles revealing ambiguity in scoring were considered as missing data and designated as '9'.…”

Section: Data Scoring and Statistical Analysismentioning

confidence: 99%

Assessment of genetic diversity in Shorea robusta: an economically important tropical tree species

2017

J App Biol Biotech

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The present investigation reports an elucidation of genetic diversity among four-populations of most economically and ecologically important tree species, sal (Shorea robusta Gaertn.) for the first time in India, using ISSR markers. A total of one-hundred individual S. robusta trees were sampled from four different populations, considering twenty-five individuals from each population. In total, twenty-ISSR primers were screened with S. robusta DNA, and out of twenty, sixteen-primer produced reproducible amplicons. Sixteen selected ISSR markers were amplified a total of 118 alleles and the total number of amplicons for individual primers ranged from 5 to 12, with a mean of 7.37 alleles per primer, of which 74 were polymorphic with an average of 4.62 alleles per primer. The ISSR primer (GA)8YG yielded highest number of alleles (12) A dendrogram based on UPGMA analysis grouped the four populations into two major clusters, having Keonjhar population into first cluster and rest three populations into second cluster. It was notable that the second major cluster was further divided into three-separate sub-clusters, representing population from each three locations. Analysis of molecular variance (AMOVA) revealed that the majority of genetic variation exists within populations, compared to the variation that exists among the populations. The present study is a clear-cut indication that inter-and intra-population genetic variation exists in S. robusta and ISSRs appears to be an efficient marker system in quantifying genetic variability in different populations of S. robusta.

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A method to measure genetic distance between allogamous populations of alfalfa (Medicago sativa) using RAPD molecular markers

Cited by 83 publications

References 12 publications

Separation of the genera in the subtribe Cassiinae (Leguminosae: Caesalpinioidae) using molecular markers

Separation of the genera in the subtribe Cassiinae (Leguminosae: Caesalpinioidae) using molecular markers

Identification of orchardgrass (Dactylis glomerata L.) cultivars by using simple sequence repeat markers

Assessment of genetic diversity in Shorea robusta: an economically important tropical tree species

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