Analysis of genetic diversity among common bean germplasm by start codon targeted (SCoT) markers

Yeken, Mehmet Zahit; Emi̇rali̇oğlu, Orkun; Çi̇ftçi̇, Vahdettin; Bayraktar, Harun; Palacıoğlu, Gülsüm; Özer, Göksel

doi:10.1007/s11033-022-07229-z

Cited by 19 publications

(13 citation statements)

References 51 publications

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“…Detection of genetic diversity and higher genetic diversity provide extremely important information in selecting superior genotypes for plant breeding [ 19 ]. Many molecular methods, such as random amplified polymorphic DNA (RAPD) [ 20 ], inter-simple sequence repeat (ISSR) [ 21 ], amplified fragment length polymorphism (AFLP) [ 22 ], simple-sequence repeats (SSR) [ 4 ], inter-primer binding site (iPBS) retrotransposon [ 23 ], single-nucleotide polymorphisms (SNPs) [ 12 ], and start codon targeted markers (SCoT) [ 24 ], are used for the analysis of genetic diversity and population structure in beans. Among molecular markers, SSRs have special relevance in analyzing genetic diversity [ 25 ].…”

Section: Introductionmentioning

confidence: 99%

Determining Genetic Diversity and Population Structure of Common Bean (Phaseolus vulgaris L.) Landraces from Türkiye Using SSR Markers

Özkan

Haliloğlu

Türkoğlu

et al. 2022

Genes

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Assessment of genetic diversity among different varieties helps to improve desired characteristics of crops, including disease resistance, early maturity, high yield, and resistance to drought. Molecular markers are one of the most effective tools for discovering genetic diversity that can increase reproductive efficiency. Simple sequence repeats (SSRs), which are codominant markers, are preferred for the determination of genetic diversity because they are highly polymorphic, multi-allelic, highly reproducible, and have good genome coverage. This study aimed to determine the genetic diversity of 40 common bean (Phaseolus vulgaris L.) landraces collected from the Ispir district located in the Northeast Anatolia region of Türkiye and five commercial varieties using SSR markers. The Twenty-seven SSR markers produced a total of 142 polymorphic bands, ranging from 2 (GATS91 and PVTT001) to 12 (BM153) alleles per marker, with an average number of 5.26 alleles. The gene diversity per marker varied between 0.37 and 0.87 for BM053 and BM153 markers, respectively. When heterozygous individuals are calculated proportional to the population, the heterozygosity ranged from 0.00 to 1.00, with an average of 0.30. The expected heterozygosity of the SSR locus ranged from 0.37 (BM053) to 0.88 (BM153), with an average of 0.69. Nei’s gene diversity scored an average of 0.69. The polymorphic information content (PIC) values of SSR markers varied from 0.33 (BM053) to 0.86 (BM153), with an average of 0.63 per locus. The greatest genetic distance (0.83) was between lines 49, 50, 53, and cultivar Karacaşehir-90, while the shortest (0.08) was between lines 6 and 26. In cluster analysis using Nei’s genetic distance, 45 common bean genotypes were divided into three groups and very little relationship was found between the genotypes and the geographical distances. In genetic structure analysis, three subgroups were formed, including local landraces and commercial varieties. The result confirmed that the rich diversity existing in Ispir bean landraces could be used as a genetic resource in designing breeding programs and may also contribute to Türkiye bean breeding programs.

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Section: Introductionmentioning

confidence: 99%

Determining Genetic Diversity and Population Structure of Common Bean (Phaseolus vulgaris L.) Landraces from Türkiye Using SSR Markers

Özkan

Haliloğlu

Türkoğlu

et al. 2022

Genes

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“…Türkiye's historical position at the crossroads of the Palearctic region, both culturally and geographically, makes it potentially influential in the dissemination of common bean genotypes from Asia to Europe and Africa. Although Türkiye is not recognized as the primary origin or center of domestication for the common bean, the previous studies indicated a wide diversity in common bean germplasm from Türkiye (Nadeem et al, 2018;Haliloğlu et al, 2022;Özkan et al, 2022;Yeken et al, 2022). These studies revealed that the common landrace collection in Türkiye harbored a substantial amount of genetic diversity.…”

Section: Introductionmentioning

confidence: 93%

Exploring I, bc-12 and bc-3 Gene Locus in Promising Common Bean Lines

Emi̇rali̇oğlu

Yeken

Çeli̇k

et al. 2023

Black Sea Journal of Agriculture

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Common beans (Phaseolus vulgaris L.), known as the "poor man's meat", is an internationally important legume crop that appeals to farmers as well as consumers. Many biotic stressors such as bean common mosaic virus (BCMV), bean common mosaic necrosis virus (BCMNV) cause significant yield and quality losses in common bean. The most efficient and cost-effective way to lessen the of these factors is to develop resistant cultivars. Local genotypes have been cultivated in many areas for years and have varied distinguishing characteristics as a result of spontaneous mutations. Identifying bean germplasm harboring gene sources is critical for developing resistant cultivars against BCMV and BCMNV. For this purpose, a total of 43 promising common bean lines selected from local genotypes cultivated across various regions of Türkiye were subjected to screening using diverse molecular markers (ROC11, SBD-5 and SW-13) to investigate gene sources associated with BCMV and BCMNV. The findings revealed that 21 lines had both the I and bc-12 gene locus. In addition, the bc-12+bc-3 gene loci were discovered to be present in the 8 common bean lines. The combination of I+bc-3 resistance genes, which guarantees immune reaction to BCMV and BCMNV, was found in only one line; YLV-32. These gene sources can be evaluated in marker-assisted breeding to develop modern cultivars resistant to BCMV and BCMNV by breeders.

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“…In the different marker systems, numerous Polymerase Chain Reaction (PCR)-based markers were proven to be efficient for the investigation of genetic variability in collections of plant species [18], including the common bean. Many molecular markers, including RAPD [19][20][21], AFLP [22][23][24], ISSR [25,26], SSR [27][28][29], and SCoT [30,31], were successfully applied in the molecular variability analyses of the common bean. Random Amplified Polymorphic DNA (RAPD) markers are one of the types of arbitrarily amplified dominant markers.…”

Section: Introductionmentioning

confidence: 99%

Efficiency of RAPD and SCoT Markers in the Genetic Diversity Assessment of the Common Bean

Hromadová

Gálová

Mikolášová

et al. 2023

Plants

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Knowledge about the genetic diversity of the available common bean germplasm can help breeders properly direct the choice of genetic material in the breeding process. The aim of the present work was to estimate the usefulness of 10 RAPD and 10 SCoT markers in genetic diversity detection among 33 common bean genotypes. Both molecular marker systems were able to generate high levels of polymorphism in the genetic material, which was supported by the relatively high polymorphic information content (PIC) values observed for the used markers. The Diversity Detection Index (DDI) and Marker Index (MI) were used to compare the effectiveness of RAPD and SCoT markers. For both techniques, high values of MI and DDI were calculated, representing their effectivity. The SCoT markers showed higher values of the parameters used (MI = 7.474, DI = 2.265) than the RAPD markers (MI = 5.323, DDI = 1.612), indicating their higher efficiency in the detection of molecular variability. Three constructed dendrograms and PCoA plots were created using RAPD and SCoT, and both methods combined confirmed sufficient separation of the bean genotypes from each other. At the same time, a higher efficiency of SCoT markers compared to RAPD markers in the detection of the genetic diversity of beans was also proven. The results may be of future interest in the choice of genetically distant material for breeding purposes.

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Analysis of genetic diversity among common bean germplasm by start codon targeted (SCoT) markers

Cited by 19 publications

References 51 publications

Determining Genetic Diversity and Population Structure of Common Bean (Phaseolus vulgaris L.) Landraces from Türkiye Using SSR Markers

Determining Genetic Diversity and Population Structure of Common Bean (Phaseolus vulgaris L.) Landraces from Türkiye Using SSR Markers

Exploring I, bc-12 and bc-3 Gene Locus in Promising Common Bean Lines

Efficiency of RAPD and SCoT Markers in the Genetic Diversity Assessment of the Common Bean

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