Genetic Analysis of Turkey Common Bean (Phaseolus vulgaris L.) Genotypes by Simple Sequence Repeats Markers

Bilir, Özlem; Özmen, Canan Yüksel; Özcan, Sebahattin; Kibar, Umut

doi:10.1134/s1022795419010034

Cited by 6 publications

(8 citation statements)

References 29 publications

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“…Khaidizar et al (2012) reported 72 alleles at 30 SSR loci in bean genotypes sampled from North Anatolia. Bilir et al (2019), a total of 192 alleles were identified in 13 SSR markers, and the average number of alleles per locus was reported as 14.8. In the study of Ekbic and Hasancaoglu (2019), it was stated that 63 alleles (polymorphism rate 73%) belonging to 18 SSR loci in bean genotypes and the average number of alleles per locus was 2.55.…”

Section: Discussionmentioning

confidence: 99%

“…Since the genotypes used in this study belongs to commercial varieties and breeding materials, most of the samples have homozygous genotypes and therefore Ho was low. In Bilir et al (2019), the observed heterozygosity was calculated as 0.452 and the expected heterozygosity was 0.724. Valentini et al (2018) reported that genetic diversity (h) on 18 SSR loci in 109 bean genotypes sampled from Brazil was 0.44.…”

Section: Discussionmentioning

confidence: 99%

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Investigation of the Genetic Structure of Some Common Bean (Phaseolus vulgaris L.) Commercial Varieties and Genotypes Used as a Genitor with SSR and SNP markers

Bilgen¹

2021

Preprint

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Common bean is a species belonging to the Phaseolus genus of the Leguminosae family. It has economic importance due to being rich in protein, vitamin A and C, and minerals. Being one of the most cultivated species of legumes, the determination of genetic diversity in bean genotypes or populations has an important role in terms of our genetic resources. The objective of this study was to evaluate the genetic structure of 94 genotypes which were cultivated in different parts of the world and our country with SSR and SNP markers. 10 SSR loci and 73 SNP primers were used for the determination of genetic structure in commercial cultivars and breeding lines. All of the SSR and SNP loci used in the study were found to be polymorphic. A total of 89 alleles were identified for 10 SSR loci. Mean number of alleles per locus (Na=8.9), effective allele number (Ne=3.731), Shannon information index (I=1.468), observed heterozygosity (Ho=0.023), and expected heterozygosity (He=0.654) were calculated based on SSR analysis. According to the results of Bayesian-based STRUCTURE analysis using SSR and SNP data, 94 bean genotypes were genetically divided into three main clusters. According to genetic similarity based UPGMA dendrogram obtained from SSR and SNP analysis, 94 bean genotypes were divided into 2 main clusters. The obtained results provide important information about the genetic structures of the studied bean cultivars and breeding lines. With the obtained results, it will be possible to develop breeding programs to develop new cultivars by using our gene resources.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Investigation of the Genetic Structure of Some Common Bean (Phaseolus vulgaris L.) Commercial Varieties and Genotypes Used as a Genitor with SSR and SNP markers

Bilgen¹

2021

Preprint

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“…Molecular markers are used to reveal variations among the P. vulgaris landraces at the DNA level, providing a more reliable tool for germplasm (Bilir et al 2019). Simple Sequence Repeats (SSRs) also known as microsatellites are small stretches of repeated DNA, usually of one to six nucleotides (Mishra et al 2014).…”

Section: Introductionmentioning

confidence: 99%

“…Phaseolus vulgaris landraces from Turkey have high polymorphism, where the number of alleles ranges from 6 to 29 with a mean of 14.8 alleles per locus (Bilir et al 2019). The observed heterozygosity (H o ) ranges from 0.000 to 0.099 with the mean value of 0.006 across all markers for P. vulgaris landraces in Italy (Gioia et al 2019).…”

Section: Introductionmentioning

confidence: 99%

Morpho-agronomic and genetic variation among Phaseolus vulgaris landraces from selected provinces of South Africa

Ndlangamandla

Ntuli

2021

J. Crop Sci. Biotechnol.

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Key message The morpho-agronomic and genetic studies recorded variations in vegetative and reproductive traits, and in molecular information through population structure and clustering approaches among South African Phaseolus vulgaris landraces. Abstract Phaseolus vulgaris L., commonly known as common beans, is widely used for its edible leaves, immature pods, and dry seeds. Studies on variation in morphology and genetics among P. vulgaris landraces are limited in South Africa. Therefore, the current study aimed to determine the morpho-agronomic and genetic variations among P. vulgaris landraces. Thirty-eight landraces from different agro-ecological origins, planted in a randomized complete block design, had their variation in vegetative and reproductive traits determined. These landraces were studied for their genetic diversity using simple sequence repeat (SSR) markers. The landraces were clustered in a biplot and dendrogram based on their seed coats, shape, similar morpho-agronomic traits, and their areas of origin. A total of 57 alleles were produced with a mean of 3.64 per SSR locus. The polymorphism information content ranged from 0.00 to 0.58. The population structure had the highest delta value K = 2, thus the 38 landraces were divided into two subpopulations based on the Bayesian approach. The population structure showed an overlap among the landraces as several from the Mesoamerican carried some seed traits or genes from the Andean gene pool, and showed a high level of admixtures. The principal coordinate analysis and the dendrogram had a similar clustering pattern as the population structure. This study revealed the potential markers with high diversity that can be used to determine genetically homogenous/heterogeneous landraces. Therefore, the use of PV-ctt001, PV-ag001, and PV-at003 could be beneficial in future breeding, conservation, and marker-assisted selection studies.

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“…Genetic assessments through screening plant genetic sources with the molecular markers and identification of genetic relationships and similarities among the genotypes will construct the bases for further breeding studies (Sarıkamış, 2014). Various methods have used molecular markers including Amplified Fragment Length Polymorphisms (AFLP) (Sustar-Vozlic et al, 2006), Random Amplified Polymorphic DNA (RAPD) (Erdinc et al, 2017), Sequence Characterized Amplified Region (SCAR) (Madakbaş et al, 2016), Inter Simple Sequence Repeat (ISSR) (Dagnew et al, 2014), Simple Sequence Repeats (SSR) (Sarıkamış et al, 2009;Bilir et al, 2019), Sequence-Related Amplified Polymorphism (SRAP) (Ceylan et al, 2014), and Expressed Sequence Tag (EST) (Garcia et al, 2011), all to assess genetic diversity and relationships among several Phaseolus vulgaris species. Inter-primer binding site (iPBS) is a universal method for DNA fingerprinting and retrotransposon isolation.…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity of pinto and fresh bean (Phaseolusvulgaris L.) germplasm collected from Erzincan province of Turkey by inter-primer binding site (iPBS) retrotransposon markers

Öztürk¹,

Dursun²,

Türkoğlu³

et al. 2020

Turk J Agric For

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In this study, genetic diversity among 71 bean genotypes (41 pinto beans and 30 fresh bean genotypes) and 4 commercial cultivars (Aleyna, Gina, Perolar, and Serra) commonly grown at Erzincan province in Turkey were investigated. The iPBS (inter-primer binding site) markers were used to investigate the genetic diversity of the genotypes. Polymorphism ratio was identified as 100% in all primers. Twenty-seven primers were studied and number of alleles in primers varied between 13-69 (with an average value of 37.14). According to cluster analysis based on iPBS data, genotypes were divided into 2 groups. Polymorphic information content (PIC) values varied between 0.19 (iPBS 2077) and 0.42 (iPBS 2381, iPBS 2385, and iPBS 2389) with an average PIC value of 0.33. According to genetic structure analysis, genotypes were divided into 2 subpopulations. Majority of the genotypes of the regions from where beans were collected were placed in the same groups.

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Genetic Analysis of Turkey Common Bean (Phaseolus vulgaris L.) Genotypes by Simple Sequence Repeats Markers

Cited by 6 publications

References 29 publications

Investigation of the Genetic Structure of Some Common Bean (Phaseolus vulgaris L.) Commercial Varieties and Genotypes Used as a Genitor with SSR and SNP markers

Investigation of the Genetic Structure of Some Common Bean (Phaseolus vulgaris L.) Commercial Varieties and Genotypes Used as a Genitor with SSR and SNP markers

Morpho-agronomic and genetic variation among Phaseolus vulgaris landraces from selected provinces of South Africa

Genetic diversity of pinto and fresh bean (Phaseolusvulgaris L.) germplasm collected from Erzincan province of Turkey by inter-primer binding site (iPBS) retrotransposon markers

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