Fasulye (Phaseolus vulgaris L.)'de ekonomik öneme sahip bazı agronomik karakterleri kontrol eden DNA markırlarının ilişki haritalaması ile saptanması

Bağlantı dengesizliğine (Linkage Disequilibrum, LD) dayanan ilişki haritaları, kantitatif özellik lokusu (Quantitative Trait Locus, QTL) haritalarına alternatif ve önemli özellikleri kontrol eden genlerin belirlenmesinde etkili bir metotdur. Bu çalışmada 66 fasulye genotipi kullanılmış ve 233 Amplified Fragment Lenght Polymorphism (AFLP), 105 Single Nucleotide Polymorphism (SNP) ve 80 Simple Sequence Repeat (SSR) markırı analiz edilmiştir. Bu populasyonda LD ve populasyon yapısı belirlenmiştir. Tüm genomu kapsayacak şekilde yüksek LD değeri saptanmıştır (r2 ≥0.1, p<0.01). STRUCTURE programında populasyon yapısı belirlenmiştir ve 66 fasulye genotipi kendi arasında 7 (K=7) ana gruba ayrılmıştır. TASSEL (Trait Analysis by aSSociation, Evolutionand Linkage) programında Genel Lineer Model (General Linear Model, GLM) metodu kullanılarak markır ve 5 fenotipik özellik (liflilik özelliği, tohum taslağı sayısı, bitki tipi, bitki büyüme şekli ve çiçeklenme zamanı) arasında ilişki saptanmıştır. Beş fenotipik özellik ile ilişkili toplamda 62 markır önemli olarak belirlenmiştir (r 2 ≥0.1, p<0.01). Bu çalışma ile ilk kez 66 fasulye genotipi arasında ilişki haritası yapılmıştır. Fasulyede yapılan bu ilişki haritalama çalışması QTL haritalama metodlarına alternatif olacaktır

Determination of the population structure of common bean (Phaseolus vulgaris L.) accessions using lipoxygenase and resistance gene analog markers

WOS: 000353753500017The common bean (Phaseolus vulgaris L.) is an important food legume throughout the world. Because of the conservation across different plant species, it is possible to evaluate the degree of genetic diversity in the common bean using gene-based marker techniques. The lipoxygenase (LOX) and resistance gene analog (RGA) genes play an important role in the response to biotic and abiotic stresses. Eighty-six common bean accessions were genotyped using gene-based LOX and RGA markers. The total number of polymorphic bands ranged from 193 for LOX to 17 for RGA markers. We detected considerable diversity with a mean of 8.7 alleles per primer for the LOX analysis. For the RGA markers, the number of alleles per polymorphic locus varied from 1 to 4 with an average allele number of 2.8. The genetic similarity between the accessions based on the LOX and RGA markers ranged from 0.12 to 0.55. Using STRUCTURE, 3 groups were revealed among the accessions. The results of this study should provide valuable information for future studies on the genetic diversity of common bean accessions and for association mapping studies examining the relationships between the genotypic and phenotypic traits related to the stress response. (C) 2015 Elsevier Ltd. All rights reserved

Genetic diversity and population structure of common bean (Phaseolus vulgaris L.) accessions through retrotransposon-based interprimer binding sites (iPBSs) markers

WOS: 000363554800010The common bean (Phaseolus vulgaris L.) is an important crop throughout the world and is highly recommended for many developing countries due to its nutritional components. A retrotransposon-based DNA marker system, interprimer binding sites (iPBSs), developed from reverse transcriptase primer binding sites, was used to determine genetic diversity in common bean accessions. The genetic polymorphism and effectiveness of the marker system were evaluated. A total of 180 polymorphic bands were detected using 47 iPBS primers among 67 common bean accessions, with an average of 4 polymorphic fragments per primer. The genetic similarity between accessions was calculated using the software NTSYS-pc and ranged from 0.09 to 0.99. The average polymorphism information content value for the iPBS markers was 0.73. A model-based clustering method classified the common bean accessions into 4 populations using STRUCTURE software. The results indicated that the iPBS marker method can successfully determine the genetic diversity level in common bean accessions.Scientific and Technological Research Council of TurkeyTurkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [TUBITAK 114O555]We greatly appreciate our grant from the Scientific and Technological Research Council of Turkey for project "TUBITAK 114O555.

HIGH LEVELS OF GENETIC VARIATION AS DETECTED BY AFLP IN Sideritis tmolea FROM WESTERN TURKEY

ABSTRAC

HIGH LEVELS OF GENETIC VARIATION AS DETECTED BY AFLP IN Sideritis tmolea FROM WESTERN TURKEY

ABSTRAC

HIGH LEVELS OF GENETIC VARIATION AS DETECTED BY AFLP IN Sideritis tmolea FROM WESTERN TURKEY

ABSTRAC

Diversity and genetic analysis through DArTseq in common bean (Phaseolus vulgaris L.) germplasm from Turkey

WOS: 000414902800008The common bean (Phaseolus vulgaris L.) is the most consumed food legume in the world and is a major source of dietary protein, carbohydrates, and valuable micronutrients, especially in developing countries. Diversity Arrays Technology (DArTseq), based on genome reduction with restriction enzymes, provides a rapid, high-throughput, and cost-effective tool capable of generating thousands of genotyped single nucleotide polymorphisms (SNPs) for a genome-wide analysis of genetic diversity. In this study, we aimed to characterize common bean accessions using SNPs detected by a DArTseq approach. A total of 43,018 SNPs were identified from 173 common bean accessions, including Andean and Mesoamerican genotypes. After filtering raw and redundant data, a total of 16,366 SNPs were considered for further analyses. According to population structure analysis, the genotypes were roughly divided into 2 gene pools of Andean and Mesoamerican types. Pairwise fixation index (Fst) values were calculated to resolve the differentiation between populations. This study demonstrated that discovering SNPs from the whole genome is a potential resource for identifying naturally diverse accessions and also the information could be used in breeding programs to develop new common bean varieties.Scientific and Technological Research Council of Turkey (TUBITAK)Turkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [TUBITAK-114O555]The study was supported by the Scientific and Technological Research Council of Turkey (TUBITAK) with Project No. TUBITAK-114O555. We would like to thank Paul Gepts from the University of California-Davis (USA) for kindly sharing his control group of common bean accessions (Mesoamerican and Andean gene pools)

HIGH LEVELS OF GENETIC VARIATION AS DETECTED BY AFLP IN Sideritis tmolea FROM WESTERN TURKEY

WOS: 000346626200013The objective of this study was to evaluate the level of genetic diversity among 29 S. tmolea genotypes collected from Bozdag, Turkey, using the Amplified Fragment Length Polymorphism (AFLP) technique. A total of 392 AFLP markers were detected using 14 primer combinations. The number of polymorphic bands per AFLP primer combination ranged from 16 to 42, with an average of 28. The Polymorphism Information Content (PIC) values varied from 0.25 (M-CTC/E-AGC) to 0.72 (M-CAC/E-AAG) among 14 selective primers. The genetic dissimilarity that was detected using the NTSYS-PC software ranged from 0.09 to 0.82. According to the dissimilarity results, a high level of genetic diversity existed among the studied genotypes. A model-based structural analysis revealed the presence of 2 populations. The defined population structure was helpful when studying the S. tmolea genotypes for diversity and classification.Scientific and Technological Research Council of Turkey (TUBITAK)Turkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [108T851]; Ege University Science and Technology Centre (EBILTEM)Ege University [2010BIL03]The authors would like to thank the Scientific and Technological Research Council of Turkey (TUBITAK Project No: 108T851) and the Ege University Science and Technology Centre (EBILTEM) for supporting this study (Project No: 2010BIL03)