Optimizing Sample Size to Assess the Genetic Diversity in Common Vetch (Vicia sativa L.) Populations Using Start Codon Targeted (SCoT) Markers

Chai, Xutian; Dong, Rui; Liu, Wenxian; Wang, Yanrong

doi:10.3390/molecules22040567

Cited by 28 publications

(18 citation statements)

References 39 publications

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“…Cluster analysis based on these traits grouped the genotypes into 8 separate clusters. CHAI et al (2017) investigate the optimal number of individuals that may represent the genetic diversity of a single population, using Start Codon Targeted (SCoT) markers. Two cultivated varieties and two wild accessions were evaluated using five SCoT primers, also testing different sampling sizes: 1, 2, 3, 5, 8, 10, 20, 30, 40, 50, and 60 individuals.…”

Section: Resultsmentioning

confidence: 99%

Start codon targeted polymorphism for evaluation of functional genetic variation and relationships in cultivated castor (Ricinus communis L.) genotypes

et al. 2019

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In the present study, 111 castor genotypes were differentiated by the DNA fingerprinting patterns using 37 SCoT primers. The selected primers amplified DNA fragments across the 111 genotypes studied with the number of amplified fragments varying from 3 (SCoT 14) to 10 (SCoT 30 and SCoT 44) and the amplicon size varied from 100 to 3000 bp. Of the 246 amplified bands, 186 were polymorphic with an average of 5.03 fragments per primer. The percentage of polymorphic bands ranged from 57.14 % (SCoT 34) to 100.00 % (SCoT 28 and SCoT 33) with an average of 77.50%. The polymorphic information content (PIC) values varied from 0.372 (SCoT 14) to 0.818 (SCoT 30) with an average of 0.677. A dendrogram was constructed from a genetic distance matrix based on profiles of the 37 SCoT primers using the unweighted pair-group method with the arithmetic average (UPGMA). According to analysis, the collection of 111 diverse accessions of castor was clustered into two main clusters (1 and 2). The first cluster were subdivided into two subclusters (1a and 1b). Subclaster 1a contained 11 genotypes of castor and subclaster 1b contained 6 genotypes of castor. Subclaster 2 were subdivided into two subclusters (2a and 2b). Subclaster 2a contained 44 castor genotypes and subclaster 2b contained 50 castor genotypes. Results showed the utility of SCoT markers for estimation of genetic diversity of castor genotypes leading to genotype identification.

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Section: Resultsmentioning

confidence: 99%

Start codon targeted polymorphism for evaluation of functional genetic variation and relationships in cultivated castor (Ricinus communis L.) genotypes

et al. 2019

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“…The hierarchical cluster analysis showed that the rye genotypes were divided into 2 main clusters. Chai et al (2017) investigate the optimal number of individuals that may represent the genetic diversity of a single population, using Start Codon Targeted (SCoT) markers. Two cultivated varieties and two wild accessions were evaluated using five SCoT primers, also testing different sampling sizes : 1, 2, 3, 5, 8, 10, 20, 30, 40, 50, and 60 individuals.…”

Section: Resultsmentioning

confidence: 99%

Identification of Tunisian Castor Genotypes (Ricinus Communis L.) Using SCoT Markers

Vivodík¹,

Saadaoui²,

Petrovičová³

et al. 2019

Agrobiodiversity for Improving of Nutrition, Health and Life Quality

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In the present investigation, 20 genotypes of Tunisian castor were analyzed using 5 start codon targeted (SCoT) markers. These primers produced total 33 fragments across 20 Tunisian castor genotypes, of which 26 (78.70%) were polymorphic with an average of 5.20 polymorphic fragments per primer and number of amplified fragments ranged from 4 (SCoT 66) to 9 (SCoT 65). The polymorphic information content (PIC) value ranged from 0.652 (ScoT 65) to 0.816 (SCoT 61) with an average of 0.738. The dendrogram based on hierarchical cluster analysis using UPGMA algorithm was prepared. The hierarchical cluster analysis showed that the Tunisian castor genotypes were divided into 3 main clusters. Cluster

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“…The non-uniform genetic distribution of cercariae among snails implies that sample size of snail hosts would affect the allele distribution of the cercaria suprapopulation (cercariae from all snails). Na, the basic index for indicating gene abundance of a population [45,46], was further evaluated for each locus in different cercariae subsets by selecting different numbers of snails randomly. Snails were selected randomly at each given number of snails, which was set from 1 to maximum in each group using the base function sample in R, with 100 replicates.…”

Section: Allele Distribution For Cercaria Subsets From the Different mentioning

confidence: 99%

The genetic variation of different developmental stages of Schistosoma japonicum: do the distribution in snails and pairing preference benefit the transmission?

Emery

et al. 2020

Parasites Vectors

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Background: Schistosoma japonicum is a waterborne parasite that causes schistosomiasis in humans and in more than 40 animal species. Schistosoma japonicum shows distinct genetic differentiation among geographical populations and multiple hosts, but the genetic diversity of different developmental stages of S. japonicum from is less studied. Such studies could elucidate ecological mechanisms in disease transmission by analysing feedbacks in individual physiology and population state. Methods: After infection using cercariae from a pool of snails shedding together (Method I) and infection using mixed equal numbers of cercariae from individually shed snails (Method II), different developmental stages of S. japonicum were genotyped with microsatellite loci, including 346 cercariae, 701 adult worms and 393 miracidia. Genetic diversity and molecular variation were calculated at different population levels. Kinships (I′) among cercariae at intra-snail and inter-snail levels were evaluated. Genetic distance (Dsw) was compared between paired and unpaired worms, and partner changing was investigated through paternity identification for miracidia. Results: The cercaria clones in individual snails varied from 1 to 8 and the kinship of cercariae within individual snails was significant higher (P < 0.001) than that among different snails after deleting near-identical multi-locus genotypes (niMLGs). The allelic diversity of worms in Method I was lower (P < 0.001) than that in Method II, and allele frequency among mice in Method I was also less consistent. The parents of some miracidia were worms that were not paired when collected. The Dsw between each female of paired and unpaired males was much larger (P < 0.001) than that between the female and male in each pair. Conclusions: Most of the infected snails contained multiple miracidia clones. The aggregation of genetically similar S. japonicum miracidia in individual snails and the unbalanced distribution of miracidia among snails suggests a nonuniform genetic distribution of cercariae among snails in the field. This further influenced the genetic structure of adult worms from infections with different cercariae sampling methods. Schistosoma japonicum in mice can change

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Optimizing Sample Size to Assess the Genetic Diversity in Common Vetch (Vicia sativa L.) Populations Using Start Codon Targeted (SCoT) Markers

Cited by 28 publications

References 39 publications

Start codon targeted polymorphism for evaluation of functional genetic variation and relationships in cultivated castor (Ricinus communis L.) genotypes

Start codon targeted polymorphism for evaluation of functional genetic variation and relationships in cultivated castor (Ricinus communis L.) genotypes

Identification of Tunisian Castor Genotypes (Ricinus Communis L.) Using SCoT Markers

The genetic variation of different developmental stages of Schistosoma japonicum: do the distribution in snails and pairing preference benefit the transmission?

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