Yıl: 2017 Cilt: 41 Sayı: 5 Sayfa Aralığı: 389 - 404 Metin Dili: İngilizce İndeks Tarihi: 10-04-2019

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

Öz:
The common bean (Phaseolus vulgaris L.) is the most consumed food legume in the world and is a major source of dietaryprotein, 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 generatingthousands of genotyped single nucleotide polymorphisms (SNPs) for a genome-wide analysis of genetic diversity. In this study, weaimed to characterize common bean accessions using SNPs detected by a DArTseq approach. A total of 43,018 SNPs were identifiedfrom 173 common bean accessions, including Andean and Mesoamerican genotypes. After filtering raw and redundant data, a totalof 16,366 SNPs were considered for further analyses. According to population structure analysis, the genotypes were roughly dividedinto 2 gene pools of Andean and Mesoamerican types. Pairwise fixation index (Fst) values were calculated to resolve the differentiationbetween populations. This study demonstrated that discovering SNPs from the whole genome is a potential resource for identifyingnaturally diverse accessions and also the information could be used in breeding programs to develop new common bean varieties.
Anahtar Kelime:

Konular: Ziraat Mühendisliği
Belge Türü: Makale Makale Türü: Araştırma Makalesi Erişim Türü: Erişime Açık
  • Bajaj D, Das S, Badoni S, Kumar V, Singh M, Bansal KC, Tyagi AK, Parida SK (2014). Genome-wide high-throughput SNP discovery and genotyping for understanding natural (functional) allelic diversity and domestication patterns in wild chickpea. Sci Rep 5: 12468.
  • Bastien M, Sonah H, Belzile F (2014). Genome wide association mapping of Sclerotinia sclerotiorum resistance in soybean with a genotyping-by-sequencing approach. Plant Genome 7: 1-13.
  • Becerra VV, Paredes MC, Debouck D (2011). Genetic relationships of common bean (Phaseolus vulgaris L.) race Chile with wild Andean and Mesoamerican germplasm. Chil J Ag Res 71: 3-15.
  • Benjak A, Ercisli S, Vokurka A, Maletic E, Pejic I (2005). Genetic relationships among grapevine cultivars native to Croatia, Greece and Turkey. Vitis 44: 73-77.
  • Bitocchi E, Nanni L, Bellucci E, Rossi M, Giardini A, Zeuli PS, Logozzo G, Stougaard J, McClean P, Attene G et al. (2012). Mesoamerican origin of the common bean (Phaseolus vulgaris L.) is revealed by sequence data. P Natl Acad Sci USA 109: 788- 796.
  • Blair M, Diaz LM, Buendia HF, Duque MC (2009). Genetic diversity, seed size associations and population structure of a core collection of common beans (Phaseolus vulgaris L.). Theor Appl Genet 119: 955-972.
  • Blair MW, Cortés AJ, Penmetsa RV, Farmer A, Carrasquilla-Garcia N, Cook DR (2013). A high-throughput SNP marker system for parental polymorphism screening, and diversity analysis in common bean (Phaseolus vulgaris L.). Theor Appl Genet 126: 535-548.
  • Blair MW, Soler A, Cortés AJ (2012). Diversification and population structure in common beans (Phaseolus vulgaris L.). PLoS One 7: e49488.
  • Bolibok-Brągoszewska H, Heller-Uszyńska K, Wenzl P, Uszyński G, Kilian A, Rakoczy-Trojanowska M (2009). DArT markers for the rye genome - genetic diversity and mapping. BMC Genomics 10: 578.
  • Burle ML, Fonseca JR, Kami JA, Gepts P (2010). Microsatellite diversity and genetic structure among common bean (Phaseolus vulgaris L.) landraces in Brazil, a secondary center of diversity. Theor Appl Genet 121: 801-813.
  • Cabral PDS, Soares TCB, Lima ABP, de Miranda FD, Souza FB, Gonçalves LSA (2011). Genetic diversity in local and commercial dry bean (Phaseolus vulgaris) accessions based on microsatellite markers. Genet Mol Res 10: 140-149.
  • Corrado G, Piffanelli P, Caramante M, Coppola M, Rao R (2013). SNP genotyping reveals genetic diversity between cultivated landraces and contemporary varieties of tomato. BMC Genomics 14: 835.
  • Cortés AJ, Chavarro MC, Blair MW (2011). SNP marker diversity in common bean (Phaseolus vulgaris L.). Theor Appl Genet 123: 827-845.
  • Courtois B, Audebert A, Dardou A, Roques S, Ghneim-Herrera T, Droc G, Frouin J, Rouan L, Goze E, Kilian A et al. (2013). Genome-wide association mapping of root traits in a japonica rice panel. PLoS One 8: e78037.
  • Cruz VMV, Kilian A, Dierig DA (2013). Development of DArT marker platforms and genetic diversity assessment of the U.S. collection of the new oilseed crop Lesquerella and related species. PLoS One 8: e64062.
  • Degner JC (2014). Using a genotyping-by-sequencing (GBS) approach to elucidate population structure in Garry oak (Quercus garryana). PhD, University of British Columbia, Vancouver, Canada.
  • De La Fuente M, González AM, De Ron AM, Santalla M (2013). Patterns of genetic diversity in the Andean gene pool of common bean reveal a candidate domestication gene. Mol Breed 31: 501-516.
  • Doyle JJ, Doyle JL (1987). A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19: 11-15.
  • Earl D, VonHoldt B (2011). Structure Harvester: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4: 359-361.
  • Evanno G, Regnaut S, Goudet J (2005). Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14: 2611-2620.
  • Farah Fazwa MA, Siti Salwana H, Maideen H, Mohamad O (2013). An assessment of genetic relationship among superior accessions of Labisia pumila analized by amplified fragment length polymorphism (AFLP) markers. Open Science Repository Agriculture Online 2013: e70081945.
  • Gaitán-Solís E, Duque MC, Edwards KJ, Tohme J (2002). Microsatellite repeats in common bean (Phaseolus vulgaris): isolation, characterization, and cross-species amplification in Phaseolus ssp. Crop Sci 42: 2128-2136.
  • Galeano CH, Gomez M, Rodriguez LM, Blair MW (2009). CEL I nuclease digestion for SNP discovery and marker development in common bean (Phaseolus vulgaris L.). Crop Sci 49: 381-394.
  • Ganal MW, Altmann T, Röder MS (2009). SNP identification in crop plants. Curr Opin Plant Biol 12: 211-217.
  • Gepts P, Debouck D (1991). Origin, domestication, and evolution of the common bean (Phaseolus vulgaris L.). In: Van Schoonhoven A, Voysest O, editors. Common Beans: Research for Crop Improvement. Wallingford, UK: CAB International, pp. 7-53.
  • Gepts P, Francisco JL, Aragão F, de Barros E, Blair MW, Brondani R, Broughton W, Galasso I, Hernandez G, Kami J et al. (2008). Genomics of Phaseolus beans, a major source of dietary protein and micronutrients in the tropics. In: Moore P, Ming R, editors. Genomics of Tropical Crop Plants. Berlin, Germany: Springer. pp. 113-143.
  • Gepts P, Osborn TC, Rashka K, Bliss FA (1986). Phaseolin-protein variability in wild forms and landraces of the common bean (Phaseolus vulgaris)-evidence for multiple centers of domestication. Econ Bot 40: 451-468.
  • Gill-Langarica HR, Muruaga-Martínez JS, Vargas-Vázquez MLP, Rosales-Serna R, Mayek-Pérez N (2011). Genetic diversity analysis of common beans based on molecular markers. Genet Molec Biol 34: 595-605.
  • Graham P, Vance C (2003). Legumes: importance and constraints to greater use. Plant Physiol 131: 872-877.
  • Halasz J, Pedryc A, Ercişli S, Yılmaz KU, Hegedus A (2010). S-genotyping supports the genetic relationships between Turkish and Hungarian apricot germplasm. J Am Soc Hortic Sci 135: 410-417.
  • Huang YF, Poland JA, Wight CP, Jackson EW, Tinker NA (2014). Using genotyping-by-sequencing (GBS) for genomic discovery in cultivated oat. PLoS One 9: e102448.
  • Hyten DL, Song Q, Fickus EW, Quigley CV, Lim JS, Choi IY, Hwang EY, Pastor-Corrales M, Cregan PB (2010). High throughput SNP discovery and assay development in common bean. BMC Genomics 11: 475.
  • İpek A, Türkmen O, Fidan S, İpek M, Karcı H (2016). Genetic variation within the purple carrot population grown in Ereğli District in Turkey. Turk J Agric For 40: 570-576.
  • Iqbal MJ, Mamidi S, Ahsan R, Kianian SF, Coyne CJ, Hamama AA, Narina SS, Bhardwaj HL (2012). Population structure and linkage disequilibrium in Lupinus albus L. germplasm and its implication for association mapping. Theor Appl Genet 125: 517-530.
  • Jaccoud D, Peng K, Feinstein D, Kilian A (2001). Diversity arrays: a solid state technology for sequence independent genotyping. Nucleic Acids Res 29: e25.
  • Jarquín D, Koçak K, Posadas L, Hyma K, Jedlicka Jo, Graef G, Lorenz A (2014). Genotyping by sequencing for genomic prediction in a soybean breeding population. BMC Genomics 15: 740.
  • Jombart T (2008). Adegenet: A R package for the multivariate analysis of genetic markers. Bioinformatics 24: 1403-1405.
  • Kaur S, Cogan NOI, Forster JW, Paull JG (2014). Assessment of genetic diversity in faba bean based on single nucleotide polymorphism. Diversity 6: 88-101.
  • Kilian A, Sanewski G, Ko L (2016). The application of DArTseq technology to pineapple. Acta Hortic 1111: 181-188.
  • Kumar V, Sharma S, Kero S, Sharma S, Sharma K, Kumar M, Bhat KV (2008a). Assessment of genetic diversity in common bean (Phaseolus vulgaris L.) germplasm using amplified fragment length polymorphism (AFLP). Scientia Hort 116: 138-143.
  • Kumar V, Sharma S, Sharma AK, Kumar M, Sharma S, Malik S, Singh KP, Sanger RS, Bha KV (2008b). Genetic diversity in Indian common bean (Phaseolus vulgaris L.) using random amplified polymorphic DNA markers. Physiol Mol Biol Plants 14: 383- 387.
  • Kwak M, Gepts P (2009). Structure of genetic diversity in the two major gene pools of common bean (Phaseolus vulgaris L., Fabaceae). Theor Appl Genet 118: 979-992.
  • Kwak M, Kami J, Gepts P (2009). The putative Mesoamerican domestication center of Phaseolus vulgaris is located in the Lerma-Santiago Basin of Mexico. Crop Sci 49: 554-563.
  • Langridge P, Barr AR (2003). Preface. Aust J Agric Res 54: 1-4. Liu K, Muse SV (2005). Power Marker: integrated analysis environment for genetic marker data. Bioinformatics 21: 2128- 2129.
  • Lombardi M, Materne M, Cogan NOI, Rodda M, Daetwyler HD, Slater AT, Forster JW, Kaur S (2014). Assessment of genetic variation within a global collection of lentil (Lens culinaris Medik.) cultivars and landraces using SNP markers. BMC Genet 15: 150.
  • Mace ES, Xia L, Jordan DR, Halloran K, Parh DK, Huttner E, Wenzl PM, Kilian A (2008). DArT markers: diversity analyses and mapping in Sorghum bicolor. BMC Genomics 9: 26.
  • Mamidi S, Rossi M, Moghaddam SM, Annam D, Lee R, Papa R, McClean PE (2013). Demographic factors shaped diversity in the two gene pools of wild common bean Phaseolus vulgaris L. Heredity 110: 267-276.
  • Maras M, Sustar-Vozlic J, Javornik B, Meglic V (2008). The efficiency of AFLP and SSR markers in genetic diversity estimation and gene pool classification of common bean (Phaseolus vulgaris L.). Acta Agric Sloven 91: 87-96.
  • McClean PE, Lee RK, Miklas PN (2004). Sequence diversity analysis of dihydroflavonol 4-reductase intron 1 in common bean. Genome 47: 266-280.
  • Nemli S, Kutlu B, Tanyolaç B (2015). Determination of the population structure of common bean (Phaseolus vulgaris L.) accessions using lipoxygenase and resistance gene analog markers. Biochem Sys Ecol 59: 107-115.
  • Nimmakayala P, Levi A, Abburi L, Abburi VL, Tomason YR, Saminathan T, Vajja VG (2014). Single nucleotide polymorphisms generated by genotyping by sequencing to characterize genome-wide diversity, linkage disequilibrium, and selective sweeps in cultivated watermelon. BMC Genomics 15: 767.
  • Okii D, Tukamuhabwa P, Kami J, Namayanja A, Paparu P, Ugen M, Gepts P (2014). The genetic diversity and population structure of common bean (Phaseolus vulgaris L.) germplasm in Uganda. Afr J Biotechnol 13: 2935-2949.
  • Oliveira EC, Amaral Junior AT, Goncalves LS, Pena GF, Freitas JSP, Ribeiro RM, Pereira MG (2010). Optimizing the efficiency of the touchdown technique for detecting inter-simple sequence repeat markers in corn (Zea mays). Genet Mol Res 9: 835-842.
  • Palmer JD (1992). Mitochondrial DNA in plant systematics: applications and limitations. In: Soltis P, Doley J, editors. Molecular Systematics of Plants. New York, NY, USA: Chapman and Hall, pp. 36-49.
  • Paradis E, Claude J, Strimmer K (2004). APE: Analyses of Phylogenetics and Evolution in R language. Bioinformatics 20: 289-290.
  • Perseguini JMKC, Silva GMB, Rosa JRBF, Gazaffi R, Marçal JF, Carbonell SAM, Chiorato AF (2015). Developing a common bean core collection suitable for association mapping studies. Genet Mol Biol 38: 67-78.
  • Phuong Phung NT, Mai CD, Mournet P, Frouin J, Droc G, Kim Ta N, Jouannic S, Thi Lê L, Do VN, Gantet P et al. (2014). Characterization of a panel of Vietnamese rice varieties using DArT and SNP markers for association mapping purposes. BMC Plant Biology 14: 1.
  • Poland JA, Rife TW (2012). Genotyping-by-sequencing for plant breeding and genetics. Plant Genome 5: 92-102.
  • Pritchard J, Stephens M, Donnelly (2000). Inference of population structure using multilocus genotype data. Genetics 155: 945- 959.
  • Raman H, Raman R, Kilian A, Detering F, Carling J, Coombes N, Diffey S, Kadkol G, Edwards D, McCully M et al. (2014). Genome-wide delineation of natural variation for pod shatter resistance in Brassica napus. PLoS One 9: e101673.
  • Ren R, Ray R, Li P, Xu J, Zhang M, Liu G, Yao X, Kilian A, Yang X (2015). Construction of a high-density DArTseq SNPbased genetic map and identification of genomic regions with segregation distortion in a genetic population derived from a cross between feral and cultivated-type watermelon. Mol Genet Genomics 290: 1457-1470.
  • Rodriguez M, Rau D, Bitocchi E, Bellucci E, Biagetti E, Carboni A, Gepts P, Nanni L, Papa R, Attene G (2015). Landscape genetics, adaptive diversity and population structure in Phaseolus vulgaris. New Phytol 209: 1781-1794.
  • Rohlf FJ (2000). NTSYS-pc: Numerical Taxonomy and Multivariate Analysis System, Version 2.1. Setauket, NY, USA: Exeter Software.
  • Romay MC, Millard MJ, Glaubitz JC, Peiffer JA, Swarts KL, Casstevens TM, Elshire RJ (2013). Comprehensive genotyping of the USA national maize inbred seed bank. Genome Biology 14: R55.
  • Rossi M, Bitocchi E, Bellucci E, Nanni L, Rau D, Attene G, Papa R (2009). Linkage disequilibrium and population structure in wild and domesticated populations of Phaseolus vulgaris L. Evol Appl 2: 504-522.
  • Sakar E, Ünver H (2016). Molecular characterization of ancient olive genotypes from Hatay province in Turkey. Turk J Agric For 40: 795-801.
  • Schmutz J, McClean PE, Mamidi S, We GA, Cannon SB, Grimwood J, Jenkins J, Shu S, Song Q, Chavarro C (2014). A reference genome for common bean and genome-wide analysis of dual domestications. Nat Genet 46: 707-713.
  • Schröder S, Mamidi S, Lee R, McKain MR, McClean PE, Osorno JM (2016). Optimization of genotyping by sequencing (GBS) data in common bean (Phaseolus vulgaris L.). Mol Breeding 36: 6.
  • Silva J, Scheffler B, Sanabria Y, De Guzman C, Galam D, Farmer A, Woodward J, May G, Oard J (2012). Identification of candidate genes in rice for resistance to sheath blight disease by whole genome sequencing. Theor Appl Genet 124: 63-74.
  • Sonah H, Bastien M, Iquira E, Tardivel A, Légaree G, Boyle B, Normandeau É, Laroche J, Larose S, Jean M et al. (2013). An improved genotyping by sequencing (GBS) approach offering increased versatility and efficiency of SNP discovery and genotyping. PLoS One 8: e54603.
  • Sorkheh K, Khaleghi E (2016). Molecular characterization of genetic variability and structure of olive (Olea europaea L.) germplasm collection analyzed by agromorphological traits and microsatellite markers. Turk J Agric For 40: 583-596.
  • Svetleva D, Pereira G, Carlier J, Cabrita L, Leitão J, Genchev D (2006). Molecular characterization of Phaseolus vulgaris L. genotypes included in Bulgarian collection by ISSR and AFLP analyses. Sci Hortic 109: 198-206.
  • Valdisser PAMR, Pappas GJ, de Menezes IPP, Müller BSF, Pereira WJ, Narciso MG, Brondani C, Souza TLP, Borba TCO, Vianello RP (2016). SNP discovery in common bean by restrictionassociated DNA (RAD) sequencing for genetic diversity and population structure analysis. Mol Genet Genomics 291: 1277- 1291.
  • Wright S (1978). Evolution and the Genetics of Populations, Volume 4: Variability Within and Among Natural Populations. Chicago, IL, USA: University of Chicago Press.
  • Zhao K, Wright M, Kimball J, Eizenga G, McClung A, Kovach M, Tyagi W, Ali ML, Tung CW, Reynolds A et al. (2010). Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome. PLoS One 5: e10780.
APA NEMLİ S, KAYGISIZ AŞÇIOĞUL T, ATEŞ D, ESIYOK D, TANYOLAÇ M (2017). Diversity and genetic analysis through DArTseq in common bean (Phaseolus vulgaris L.) germplasm from Turkey. , 389 - 404.
Chicago NEMLİ Seda,KAYGISIZ AŞÇIOĞUL TANSEL,ATEŞ Duygu,ESIYOK DURSUN,TANYOLAÇ Muhammed Bahattin Diversity and genetic analysis through DArTseq in common bean (Phaseolus vulgaris L.) germplasm from Turkey. (2017): 389 - 404.
MLA NEMLİ Seda,KAYGISIZ AŞÇIOĞUL TANSEL,ATEŞ Duygu,ESIYOK DURSUN,TANYOLAÇ Muhammed Bahattin Diversity and genetic analysis through DArTseq in common bean (Phaseolus vulgaris L.) germplasm from Turkey. , 2017, ss.389 - 404.
AMA NEMLİ S,KAYGISIZ AŞÇIOĞUL T,ATEŞ D,ESIYOK D,TANYOLAÇ M Diversity and genetic analysis through DArTseq in common bean (Phaseolus vulgaris L.) germplasm from Turkey. . 2017; 389 - 404.
Vancouver NEMLİ S,KAYGISIZ AŞÇIOĞUL T,ATEŞ D,ESIYOK D,TANYOLAÇ M Diversity and genetic analysis through DArTseq in common bean (Phaseolus vulgaris L.) germplasm from Turkey. . 2017; 389 - 404.
IEEE NEMLİ S,KAYGISIZ AŞÇIOĞUL T,ATEŞ D,ESIYOK D,TANYOLAÇ M "Diversity and genetic analysis through DArTseq in common bean (Phaseolus vulgaris L.) germplasm from Turkey." , ss.389 - 404, 2017.
ISNAD NEMLİ, Seda vd. "Diversity and genetic analysis through DArTseq in common bean (Phaseolus vulgaris L.) germplasm from Turkey". (2017), 389-404.
APA NEMLİ S, KAYGISIZ AŞÇIOĞUL T, ATEŞ D, ESIYOK D, TANYOLAÇ M (2017). Diversity and genetic analysis through DArTseq in common bean (Phaseolus vulgaris L.) germplasm from Turkey. Turkish Journal of Agriculture and Forestry, 41(5), 389 - 404.
Chicago NEMLİ Seda,KAYGISIZ AŞÇIOĞUL TANSEL,ATEŞ Duygu,ESIYOK DURSUN,TANYOLAÇ Muhammed Bahattin Diversity and genetic analysis through DArTseq in common bean (Phaseolus vulgaris L.) germplasm from Turkey. Turkish Journal of Agriculture and Forestry 41, no.5 (2017): 389 - 404.
MLA NEMLİ Seda,KAYGISIZ AŞÇIOĞUL TANSEL,ATEŞ Duygu,ESIYOK DURSUN,TANYOLAÇ Muhammed Bahattin Diversity and genetic analysis through DArTseq in common bean (Phaseolus vulgaris L.) germplasm from Turkey. Turkish Journal of Agriculture and Forestry, vol.41, no.5, 2017, ss.389 - 404.
AMA NEMLİ S,KAYGISIZ AŞÇIOĞUL T,ATEŞ D,ESIYOK D,TANYOLAÇ M Diversity and genetic analysis through DArTseq in common bean (Phaseolus vulgaris L.) germplasm from Turkey. Turkish Journal of Agriculture and Forestry. 2017; 41(5): 389 - 404.
Vancouver NEMLİ S,KAYGISIZ AŞÇIOĞUL T,ATEŞ D,ESIYOK D,TANYOLAÇ M Diversity and genetic analysis through DArTseq in common bean (Phaseolus vulgaris L.) germplasm from Turkey. Turkish Journal of Agriculture and Forestry. 2017; 41(5): 389 - 404.
IEEE NEMLİ S,KAYGISIZ AŞÇIOĞUL T,ATEŞ D,ESIYOK D,TANYOLAÇ M "Diversity and genetic analysis through DArTseq in common bean (Phaseolus vulgaris L.) germplasm from Turkey." Turkish Journal of Agriculture and Forestry, 41, ss.389 - 404, 2017.
ISNAD NEMLİ, Seda vd. "Diversity and genetic analysis through DArTseq in common bean (Phaseolus vulgaris L.) germplasm from Turkey". Turkish Journal of Agriculture and Forestry 41/5 (2017), 389-404.