Analysis of genetic diversity in the core collection of red clover (Trifolium pratense) with isozyme and RAPD markers

Dias, Paula Menna Barreto; Pretz, Viviane Falkembach; Dall'Agnol, Miguel; Schifino-Wittmann, María Teresa; Zuanazzi, José Ângelo Silveira

doi:10.12702/1984-7033.v08n03a04

Cited by 9 publications

(9 citation statements)

References 44 publications

(59 reference statements)

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“…The genetic variability of phenotypes ranged from 0.07 (T. glomeratum) to 0.61 (T. campestre) with an average of 0.30 based on the polymorphic information content (PIC). Levels of variability in this study were comparable to those of many enzymatic variation studies on Trifolium populations (Kongkiatngam et al 1995;Lange & Schifino-Wittmann 2000;Malaviya et al 2005Malaviya et al , 2008Dias et al 2008b).…”

Section: Discussionsupporting

confidence: 84%

“…Despite the use of DNA markers, isozyme polymorphism is also used effectively in species delimitation and conservation, genetic relationship between individual populations and closely related species. Sporadic reports within the genus Trifolium based on isozymic studies are available (Kongkiatngam et al 1995;Lange & Schifino-Wittmann 2000;Malaviya et al 2005Malaviya et al , 2008Dias et al 2008b).…”

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Evaluation of genetic variability in Algerian clover (Trifolium L.) based on morphological and isozyme markers

Medoukali¹,

Bellil²,

Khelifi³

2015

CZECH J GENET PLANT

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Medoukali I., Bellil I., Khelifi D. (2015): Evaluation of genetic variability in Algerian clover (Trifolium L.) based on morphological and isozyme markers. Czech J. Genet. Plant Breed., 51: 50-61.Genetic variation within and among fifteen Trifolium species represented by 157 accessions was assessed using morphological and isozyme markers. Most of morphometric characters contributed to the discrimination of the species. No significant relationship between the environment of the collection site and morphological features was detected. The two isozyme systems analysed, esterase (EST) and glutamate oxaloacetate transaminase (GOT), proved polymorphic. Phenotype diversity of isozyme markers ranged from 0.07 to 0.61 with an average of 0.31 based on the polymorphic information content. The pairwise Jaccard's similarity coefficient ranged between 0.10 and 0.60, indicating that the collection represents genetically diverse species. A considerable number of species-specific zymograms were detected which can be used for the species identification. The clustering pattern of isozyme markers was incongruent with the groupings based on quantitative traits. The rich isozyme variability present among the Algerian clover species indicates that they can provide good gene resources for breeding.

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Section: Discussionsupporting

confidence: 84%

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confidence: 99%

Evaluation of genetic variability in Algerian clover (Trifolium L.) based on morphological and isozyme markers

Medoukali¹,

Bellil²,

Khelifi³

2015

CZECH J GENET PLANT

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“…This data revealed no significant differences between the observed and expected levels of heterozygosity, as determined by the Goodness of Fit test ( Supplementary Table S2). However, each accession consists of a small number of plants (6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16), so these allele frequencies are not known with high accuracy.…”

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Population structure and genetic diversity in red clover (Trifolium pratense L.) germplasm

Jones

Vega

Lloyd

et al. 2020

Sci Rep

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Red clover (Trifolium pratense L.) is a highly adaptable forage crop for temperate livestock agriculture. Genetic variation can be identified, via molecular techniques, and used to assess diversity among populations that may otherwise be indistinguishable. Here we have used genotyping by sequencing (GBS) to determine the genetic variation and population structure in red clover natural populations from Europe and Asia, and varieties or synthetic populations. Cluster analysis differentiated the collection into four large regional groups: Asia, Iberia, UK, and Central Europe. The five varieties clustered with the geographical area from which they were derived. two methods (BayeScan and Samβada) were used to search for outlier loci indicating signatures of selection. A total of 60 loci were identified by both methods, but no specific genomic region was highlighted. The rate of decay in linkage disequilibrium was fast, and no significant evidence of any bottlenecks was found. Phenotypic analysis showed that a more prostrate and spreading growth habit was predominantly found among populations from Iberia and the UK. A genome wide association study identified a single nucleotide polymorphism (SNP) located in a homologue of the VEG2 gene from pea, associated with flowering time. The identification of genetic variation within the natural populations is likely to be useful for enhancing the breeding of red clover in the future. Red clover is a forage legume, which is used primarily in temperate livestock agriculture. It declined in importance when industrially produced nitrogen fertiliser became available in the early to mid-20th century; but before that, it and other forage legumes were key to maintaining soil fertility, and providing high protein forage for ruminant livestock 1. However, as we move towards a more sustainable agriculture policy, increased legume use is being encouraged, due to the recognition of their utility 2. This includes increased production potential, especially in mixtures with grasses; environmentally friendly N input into grassland by virtue of their symbiotic N 2 fixation; high protein content, and higher voluntary intake and thus better livestock performance 2. Red clover is a relatively newly domesticated species, and it was not until around 1000 years ago, that it was first intentionally grown in Southern Spain 1. Many of the varieties currently on the market in Europe originate from a Mattenklee type of plant, with their growth habit characterised by tall upright stems. However, some natural populations show varied growth habits, characteristically with less dependency on the central crown and a more prostrate nature to stem growth. Under certain temperature and moisture conditions, stems of these prostrate plants are able to produce nodal root growth 3. The genetics underlying the prostrate growth habit of such red clover ecotypes, as well as the latent disease resistance often associated with natural populations, is of considerable interest for breeding programmes, in terms of furthering t...

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“…The bulked samples approach is based on mixing equal quantities of genomic DNA, and can reduce the experimental effort, as the large size of a collection makes its management and use difficult (Michelmore et al 1991, Kongkiatngam et al 1996, Taški-Ajduković et al 2014. Hence, this approach has been widely used for estimating genetic variation and relationships among species, cultivars, and populations, such as alfalfa (Yu and Pauls 1993, Segovia-Lerma et al 2003, Taški-Ajduković et al 2014, red clover (Kölliker et al 2001, Dias et al 2008, Brumus catharticus (Puecher et al 2001), radish (Muminović et al 2005, Wang et al 2008, B. napus (Dulson et al 1998), and B. oleracea (Lázaro andAguinagalde 1998, Divaret et al 1999), and the efficacy of this strategy has been examined. The bulked samples approach simplifies the marker profile of an individual cultivar or population because it favors the detection of consensus fragments (i.e., common alleles) in each population (Michelmore et al 1991, Yu andPauls 1993).…”

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Comparison of Individual- and Bulked-Samples-Based Approaches Using RAPD and ISSR Markers for Identifying Genetic Relationships in <i>Brassica</i> Cultivars

et al. 2019

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Random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) variation among 24 cultivars of four Brassica species (B. rapa, B. juncea, B. napus, and B. oleracea) was examined using individual-and bulked-samples-based approaches. In both the approaches, eight plants were sampled for each cultivar, and were amplified individually and as bulked DNA, respectively. In total, 305 and 422 bands were scored in the individual-and bulked-samples-based approaches, respectively, and almost all the bands (99.8-100%) were polymorphic. Based on the individual-samples dataset, the within cultivar variation was smaller than the among cultivars variation, leading to a distribution reflecting genome compositions of each cultivar with principal coordinates analysis (PCoA) and unweighted pair-group method with arithmetic average (UPGMA) analysis. Although PCoA and UPGMA analysis based on bulked-samples data clustered the cultivars into groups with more emphasized variance among species than the results obtained by the individual-based approach, both PCoA plots and dendrograms of the individual-and bulked-samples-based approaches, respectively, were highly correlated with each other. These findings indicate that the number of individuals used to profile each cultivar can be reduced to eight per cultivar for analysis of the genetic variability in Brassica using RAPD and ISSR polymorphism, and the bulked-samples-based approach can be used to describe the genetic relationship among Brassica cultivars.

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Analysis of genetic diversity in the core collection of red clover (Trifolium pratense) with isozyme and RAPD markers

Cited by 9 publications

References 44 publications

Evaluation of genetic variability in Algerian clover (Trifolium L.) based on morphological and isozyme markers

Evaluation of genetic variability in Algerian clover (Trifolium L.) based on morphological and isozyme markers

Population structure and genetic diversity in red clover (Trifolium pratense L.) germplasm

Comparison of Individual- and Bulked-Samples-Based Approaches Using RAPD and ISSR Markers for Identifying Genetic Relationships in <i>Brassica</i> Cultivars

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