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An Operational SNP Panel Integrated to SSR Marker for the Assessment of Genetic Diversity and Population Structure of the Common Bean

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Abstract

The common bean, an important source of protein and minerals for humans, complements cereals both nutritionally and as a rotation crop, supplying nitrogen and reducing soil pathogens. The aim of this study was to develop an operational SNP-based panel for common bean in order to facilitate SSR employment in genetic diversity and population structure analyses, and its use in breeding programs. A set of 88 diverse and important common bean cultivars/lines (53), landraces (33) and wild accessions (2) were genotyped. Overall, the 58 SSRs performed better at evaluating genetic diversity (Ā = 7.38; He = 58.7 %; PI = 1.20E−45) than the 345 SNPs, of which the SSRs dinucleotides (SSR-di) were more informative (Ā = 9.92; He = 72.5 %; PI = 3.40E−26) and a selected set of 13 SSRs (Ā = 15.31/locus; He = 84.5 %; PI = 1.03E−19) allowed for the discrimination of all individuals. For the 345 high-quality scored SNPs a low combined PI (4.70E−119) and high PE (100 %) was obtained for the assessment of parentage and identity. The SNPs were very useful for linkage mapping in inter- (78.2 %) and intra-gene pool (17.7 %) crosses. Both markers afforded high resolution detection of inter-gene pool structure, with greater differentiation based on SNPs (K = 2, F ST = 0.759). The SSRs-di differentiated cultivars/lines and landraces (K = 3) of Mesoamerican origin. A set of 16 SSRs was selected to establish a routine and operational analysis of Genbank accessions allowing an efficient origin-based discrimination of common bean accessions. Operational genotyping panels based on SSRs and SNPs were derived, contributing to the growing integration of genomics with molecular breeding programs of the common bean.

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References

  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410

    Article  PubMed  CAS  Google Scholar 

  • Alzate-Marin AL, Cervigni GDL, Moreira MA, Barros EG (2005) Seleção assistida por marcadores moleculares visando ao desenvolvimento de plantas resistentes a doenças, com ênfase em feijoeiro e soja. Fitopatol Bras 30(4):333–342

    Article  Google Scholar 

  • Beebe SE, Rao IM, Blair MW, Acosta-Gallegos JA (2013) Phenotyping common beans for adaptation to drought. Front Physiol 4:35. doi:10.3389/fphys.2013.00035

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Bitocchi E, Bellucci E, Giardini A, Rau D, Rodriguez M, Biagetti E, Santilocchi R, Spagnoletti Zeuli P, Gioia T, Logozzo G, Attene G, Nanni L, Papa R (2013) Molecular analysis of the parallel domestication of the common bean (Phaseolus vulgaris) in Mesoamerica and the Andes. New Phytol 197(1):300–313. doi:10.1111/j.1469-8137.2012.04377.x

    Article  PubMed  CAS  Google Scholar 

  • Blair MW, Giraldo MC, Buendía HF, Tovar E, Duque MC, Beebe SE (2006) Microsatellite marker diversity in common bean (Phaseolus vulgaris L.). Theor Appl Genet 113:100–109. doi:10.1007/s00122-006-0276-4

    Article  PubMed  CAS  Google Scholar 

  • Blair MW, Astudillo C, Rengifo J, Beebe SE, Graham R (2011b) QTL analyses for seed iron and zinc concentrations in an intra-genepool population of Andean common beans (Phaseolus vulgaris L.). Theor Appl Genet 122:511–521. doi:10.1007/s00122-010-1465-8

    Article  PubMed  CAS  Google Scholar 

  • Blair MW, Soler A, Cortés AJ (2012) Diversification and population structure in common beans (Phaseolus vulgaris L.). PLoS One 7(11):e49488. doi:10.1371/journal.pone.0049488

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Blair MW, Cortés AJ, Penmetsa RV, Farmer A, Carrasquilla-Garcia N, Cook DR (2013a) 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. doi:10.1007/s00122-012-1999-z

    Article  PubMed  Google Scholar 

  • Blair MW, Brondani RPV, Díaz LM, Del Pelosob MJ (2013b) Diversity and population structure of common bean from Brazil. Crop Sci 53:1983–1993. doi:10.2135/cropsci2012.09.0516

    Article  Google Scholar 

  • Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES (2007) TASSEL : software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633–2635. doi:10.1093/bioinformatics/btm308

    Article  PubMed  CAS  Google Scholar 

  • Broughton WJ, Hernández G, Blair M, Beebe S, Gepts P, Vanderleyden J (2003) Beans (Phaseolus spp.)—model food legumes. Plant Soil 252:55–128

    Article  CAS  Google Scholar 

  • Brown TA (2002) Genomes. Wiley-Liss, Oxford

    Google Scholar 

  • Brumfield RT, Beerli P, Nickerson DA, Edwards SV (2003) The utility of single nucleotide polymorphisms in inferences of population history. Trends Ecol Evol 18(5):249–256. doi:10.1016/S0169-5347(03)00018-1

    Article  Google Scholar 

  • 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. doi:10.1007/s00122-010-1350-5

    Article  PubMed  PubMed Central  Google Scholar 

  • Buso GSC, Amaral ZPS, Brondani RPV, Ferreira ME (2006) Microsatellite markers for the common bean Phaseolus vulgaris. Mol Ecol Notes 6:252–254. doi:10.1111/j.1471-8286.2006.01210.x

    Article  CAS  Google Scholar 

  • Cardoso PCB, Veiga MM, Menezes IPP, Valdisser PA, Borba TC, Melo LC, Del Peloso MJ, Brondani C, Vianello RP (2013) Molecular characterization of high performance inbred lines of Brazilian common beans. Genet Mol Res 12(4):5467–5484. doi:10.4238/2013.February.6.4

    Article  PubMed  CAS  Google Scholar 

  • Cardoso PC, Brondani C, Menezes IP, Valdisser PA, Borba TC, Del Peloso MJ, Vianello RP (2014) Discrimination of common bean cultivars using multiplexed microsatellite markers. Genet Mol Res 13(1):1964–1978. doi:10.4238/2014.March.24.1

    Article  PubMed  CAS  Google Scholar 

  • Chang S, Hartman GL, Singh RJ, Lambert KN, Hobbs HA, Domier LL (2013) Identification of high-quality single-nucleotide polymorphisms in Glycine latifolia using a heterologous reference genome sequence. Theor Appl Genet 126:1627–1638. doi:10.1007/s00122-013-2079-8

    Article  PubMed  CAS  Google Scholar 

  • Ching A, Caldwell KS, Jung M, Dolan M, Smith OS, Tingey S, Morgante M, Rafalski AJ (2002) SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genet 3:19. doi:10.1186/1471-2156-3-19

    Article  PubMed  PubMed Central  Google Scholar 

  • Cortés AJ, Chavarro MC, Blair MW (2011) SNP marker diversity in common bean (Phaseolus vulgaris L.). Theor Appl Genet 123:827–845. doi:10.1007/s00122-011-1630-8

    Article  PubMed  Google Scholar 

  • DeFaveri J, Viitaniemi H, Leder E, Merilä J (2013) Characterizing genic and nongenic molecular markers: comparison of microsatellites and SNPs. Mol Ecol Resour 13(3):377–392. doi:10.1111/1755-0998.12071

    Article  PubMed  CAS  Google Scholar 

  • Desiderio F, Bitocchi E, Bellucci E, Rau D, Rodriguez M, Attene G, Papa R, Nanni L (2013) Chloroplast microsatellite diversity in Phaseolus vulgaris. Front Plant Sci 22(3):312. doi:10.3389/fpls.2012.00312

    Google Scholar 

  • Earl DA, vonHoldt BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4(2):359–361. doi:10.1007/s12686-011-9548-7

    Article  Google Scholar 

  • Ellwood SR, Phan HT, Jordan M, Hane J, Torres AM, Avila CM, Cruz-Izquierdo S, Oliver RP (2008) Construction of a comparative genetic map in faba bean (Vicia faba L.); conservation of genome structure with Lens culinaris. BMC Genomics 9:380. doi:10.1186/1471-2164-9-380

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 6(5):e19379. doi:10.1371/journal.pone.0019379

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • 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. doi:10.1111/j.1365-294X.2005.02553.x

    Article  PubMed  CAS  Google Scholar 

  • Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10:564–567. doi:10.1111/j.1755-0998.2010.02847.x

    Article  PubMed  Google Scholar 

  • Freyre R, Skroch PW, Geffroy V, Adam-Blondon AF et al (1998) Towards an integrated linkage map of common bean. 4. Development of a core linkage map and alignment of RFLP maps. Theor Appl Genet 97:847–856

    Article  CAS  Google Scholar 

  • 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 42:1228–1236

    Article  Google Scholar 

  • Galeano CH, Fernandez AC, Franco-Herrera N, Cichy KA, McClean PE, Vanderleyden J, Blair MW (2011) Saturation of an intra-gene pool linkage map: towards a unified consensus linkage map for fine mapping and synteny analysis in common bean. PLoS One 6:e28135. doi:10.1371/journal.pone.0028135

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Galeano CH, Cortés AJ, Fernández AC, Soler Á, Franco-Herrera N, Makunde G, Vanderleyden J, Blair MW (2012) Gene-based single nucleotide polymorphism markers for genetic and association mapping in common bean. BMC Genet 13:48. doi:10.1186/1471-2156-13-48

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Garcia RAV, Rangel PN, Brondani C, Martins WS, Melo LC, Carneiro MS, Borba TC, Brondani RP (2011) The characterization of a new set of EST-derived simple sequence repeat (SSR) markers as a resource for the genetic analysis of Phaseolus vulgaris. BMC Genet 12:41. doi:10.1186/1471-2156-12-41

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Garcia RAV, Rangel PN, Bassinello PZ, Brondani C, Melo LC, Sibov ST, Vianello-Brondani RP (2012) QTL mapping for the cooking time of common beans. Euphytica 186:779–792. doi:10.1007/s10681-011-0587-7

    Article  Google Scholar 

  • Grattapaglia D, Sederoff R (1994) Genetic linkage maps of Eucalyptus grandis and E. urophylla using a pseudo-testcross strategy and RAPD markers. Genetics 137(4):1121–1137

    PubMed  PubMed Central  CAS  Google Scholar 

  • Grattapaglia D, Silva-Junior OB, Kirst M, de Lima BM, Faria DA, Pappas GJ Jr (2011) High-throughput SNP genotyping in the highly heterozygous genome of Eucalyptus: assay success, polymorphism and transferability across species. BMC Plant Biol 11:65. doi:10.1186/1471-2229-11-65

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Grisi MCM, Blair MW, Gepts P, Brondani C (2007) Genetic mapping of a new set of microsatellite markers in a reference common bean (Phaseolus vulgaris) population BAT 93 x Jalo EEP 558. Genet Mol Res 6(3):691–706

    PubMed  CAS  Google Scholar 

  • Hammer Ø, Harper DAT, Ryan PD (2001) Past: paleontological statistics software package for education and data analysis. Palaeontol Electron 4(1):1–9

    Google Scholar 

  • Hanai LR, De Campos T, Eduardo L et al (2007) Development, characterization, and comparative analysis of polymorphism at common bean SSR loci isolated from genic and genomic sources. Genome 50:266–277. doi:10.1139/G07-007

    Article  PubMed  CAS  Google Scholar 

  • Hougaard BK, Madsen LH, Sandal N, Moretzsohn MD, Fredslund J, Schauser L, Nielsen AM, Rohde T, Sato S, Tabata S, Bertioli DJ, Stougaard J (2008) Legume anchor markers link syntenic regions between Phaseolus vulgaris, Lotus japonicus, Medicago truncatula and Arachis. Genetics 179(4):2299–2312. doi:10.1534/genetics.108.090084

    Article  PubMed  PubMed Central  Google Scholar 

  • Hyten DL, Choi I-Y, Song Q, Shoemaker RC, Nelson RL, Costa JM, Specht JE, Cregan PB (2007) Highly variable patterns of linkage disequilibrium in multiple soybean populations. Genetics 175(4):1937–1944. doi:10.1534/genetics.106.069740

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • 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. doi:10.1186/1471-2164-11-475

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Jakobsson M, Rosenberg NA (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23:1801–1806. doi:10.1093/bioinformatics/btm233

    Article  PubMed  CAS  Google Scholar 

  • Kaczorowski KA, Kim KS, Diers BW, Hudson ME (2008) Microarray-based genetic mapping using soybean near-isogenic lines and generation of SNP markers in the Rag1 aphid resistance interval. Plant Genome 1:89–98

    Article  CAS  Google Scholar 

  • Kim S, Misra A (2007) SNP genotyping: technologies and biomedical applications. Annu Rev Biomed Eng 9:289–320

    Article  PubMed  CAS  Google Scholar 

  • Krzywinski M, Schein J, Birol İ, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA (2009) Circos: an information aesthetic for comparative genomics. Genome Res 19:1639–1645. doi:10.1101/gr.092759.109

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • 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. doi:10.1007/s00122-008-0955-4

    Article  PubMed  CAS  Google Scholar 

  • Li Y-H, Li W, Zhang C, Yang L, Chang RZ, Gaut BS, Qiu LJ (2010) Genetic diversity in domesticated soybean (Glycine max) and its wild progenitor (Glycine soja) for simple sequence repeat and single-nucleotide polymorphism loci. New Phytol 188(1):242–253. doi:10.1111/j.1469-8137.2010.03344.x

    Article  PubMed  CAS  Google Scholar 

  • Loridon K, Burgarella C, Chantret N, Martins F, Gouzy J, Prospéri JM, Ronfort J (2012) Single-nucleotide polymorphism discovery and diversity in the model legume Medicago truncatula. Mol Ecol Resour 13:84–95. doi:10.1111/1755-0998.12021

    Article  PubMed  CAS  Google Scholar 

  • Mamidi S, Rossi M, Annam D, Moghaddam S, Lee R, Papa R, McClean P (2011) Investigation of the domestication of common bean (Phaseolus vulgaris) using multilocus sequence data. Funct Plant Biol 38:953–967

    Article  CAS  Google Scholar 

  • 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(3):267–276. doi:10.1038/hdy.2012.82

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Mammadov J, Aggarwal R, Buyyarapu R, Kumpatla S (2012) SNP markers and their impact on plant breeding. Int J Plant Genomics 2012:728398. doi:10.1155/2012/728398

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Maughan PJ, Yourstone SM, Byers RL, Smith SM, Udall JA (2010) Single-nucleotide polymorphism genotyping in mapping populations via genomic reduction and next-generation sequencing: proof of concept. Plant Genome J 3:166. doi:10.3835/plantgenome2010.07.0016

    Article  CAS  Google Scholar 

  • Moragues M, Comadran J, Waugh R, Milne I, Flavell AJ, Russell JR (2010) Effects of ascertainment bias and marker number on estimations of barley diversity from high-throughput SNP genotype data. Theor Appl Genet 120(8):1525–1534. doi:10.1007/s00122-010-1273-1

    Article  PubMed  CAS  Google Scholar 

  • Müller BSF, Sakamoto T, Menezes IPP, Prado GS, Martins WS, Brondani C, Barros EG, Vianello RP (2014) Analysis of BAC-end sequences in common bean (Phaseolus vulgaris L.) towards the development and characterization of long motifs SSRs. Plant Mol Biol 86(4–5):455–470. doi:10.1007/s11103-014-0240-7

    Article  PubMed  CAS  Google Scholar 

  • Nagasaki H, Ebana K, Shibaya T, Yonemaru J, Yano M (2010) Core single-nucleotide polymorphisms—a tool for genetic analysis of the Japanese rice population. Breeding Sci 60(5):648–655

    Article  Google Scholar 

  • Oliveira LK, Melo LC, Brondani C, Peloso MJD, Brondani RPV (2008) Backcross assisted by microsatellite markers in common bean. Genet Mol Res 7(4):1000–1010

    Article  PubMed  CAS  Google Scholar 

  • Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research–an update. Bioinformatics 28:2537–2539. doi:10.1093/bioinformatics/bts460

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Perrier X, Jacquemoud-Collet JP (2006) DARwin software. Available at. http://darwin.cirad.fr/. Accessed on Feb 23, 2013

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    PubMed  PubMed Central  CAS  Google Scholar 

  • Rosenberg NA (2004) Distruct: a program for the graphical display of population structure. Mol Ecol Notes 4:137–138. doi:10.1046/j.1471-8286.2003.00566.x

    Article  Google Scholar 

  • 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. doi:10.1111/j.1752-4571.2009.00082.x

    Article  PubMed  PubMed Central  Google Scholar 

  • Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Bio Evol 4:406–425

    CAS  Google Scholar 

  • Saxena RK, Penmetsa RV, Upadhyaya HD, Kumar A, Carrasquilla-Garcia N, Schlueter JA, Farmer A, Whaley AM, Sarma BK, May GD, Cook DR, Varshney RK (2012) Large-scale development of cost-effective single-nucleotide polymorphism marker assays for genetic mapping in pigeonpea and comparative mapping in legumes. DNA Res 19:449–461. doi:10.1093/dnares/dss025

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Schmutz J, Cannon SB, Schlueter J et al (2010) Genome sequence of the palaeopolyploid soybean. Nature 463(7278):178–183. doi:10.1038/nature08670

    Article  PubMed  CAS  Google Scholar 

  • Schmutz J, McClean PE, Mamidi S et al (2014) A reference genome for common bean and genome-wide analysis of dual domestications. Nat Genet 46(7):707–713. doi:10.1038/ng.3008

    Article  PubMed  CAS  Google Scholar 

  • Sefc KM, Steinkellner H, Wagner HW, Glössl J, Regner F (1997) Application of microsatellite markers to parentage studies in grapevine. Vitis 36(4):179–183

    Google Scholar 

  • Silva OF, Wander AE (2013) O feijão-comum no Brasil passado, presente e futuro. Santo Antônio de Goiás, Embrapa Arroz e Feijão. Documentos 287, ISSN 1678–9644; 287, 63 p

  • Song Q, Hyten DL, Jia G, Quigley CV, Fickus EW, Nelson RL, Cregan PB (2013) Development and evaluation of SoySNP50K, a high-density genotyping array for soybean. PLoS One 8:e54985. doi:10.1371/journal.pone.0054985

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Souza TLPO, Barros EG, Bellato CM, Hwang EY, Cregan PB, Pastor-Corrales MA (2012) Single nucleotide polymorphism discovery in common bean. Mol Breeding 30(1):419–428. doi:10.1007/s11032-011-9632-4

    Article  CAS  Google Scholar 

  • Thomson MJ, Zhao K, Wright M et al (2012) High-throughput single nucleotide polymorphism genotyping for breeding applications in rice using the BeadXpress platform. Mol Breeding 29:875–886. doi:10.1007/s11032-011-9663-x

    Article  CAS  Google Scholar 

  • Van K, Hwang EY, Kim MY, Park HJ, Lee SH, Cregan PB (2005) Discovery of SNPs in soybean genotypes frequently used as the parents of mapping populations in the United States and Korea. J Hered 96:529–535

    Article  PubMed  CAS  Google Scholar 

  • Vieira RF, Mendes IC, Reis-Junior FB, Hungria M (2010) Symbiotic nitrogen fixation in tropical food grain legumes: Current Status. In: Khan MS, Musarrat J, Zaidi A (eds) Microbes for legume improvement, 1st edn. Springer, Vienna, pp 427–472. doi:10.1007/978-3-211-99753-6_18

    Chapter  Google Scholar 

  • Wortmann CS, Kirkby RA, Elude CA, Allen DJ (1998) Atlas of common bean (Phaseolus vulgaris L.) production in Africa. CIAT. http://ciat-library.ciat.cgiar.org/Articulos_CIAT/Atlas_common_bean_Africa.pdf. Accessed 10 August 2014

  • Würschum T, Maurer HP, Kraft T, Janssen G, Nilsson C, Reif JC (2011) Genome-wide association mapping of agronomic traits in sugar beet. Theor Appl Genet 123:1121–1131. doi:10.1007/s00122-011-1653-1

    Article  PubMed  Google Scholar 

  • Yang X, Xu Y, Shah T, Li H, Han Z, Li J, Yan J (2011) Comparison of SSRs and SNPs in assessment of genetic relatedness in maize. Genetica 139:1045–1054. doi:10.1007/s10709-011-9606-9

    Article  PubMed  CAS  Google Scholar 

  • Yu K, Park SJ, Poysa V, Gepts P (2000) Integration of simple sequence repeat (SSR) markers into a molecular linkage map of common bean (Phaseolus vulgaris L.). J Hered 91(6):429–434

    Article  PubMed  CAS  Google Scholar 

  • Yu H, Xie W, Wang J, Xing Y, Xu C, Li X, Xiao J, Zhang Q (2011) Gains in QTL detection using an ultra-high density SNP map based on population sequencing relative to traditional RFLP/SSR markers. PLoS One 6:e17595. doi:10.1371/journal.pone.0017595

    Article  PubMed  PubMed Central  CAS  Google Scholar 

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Acknowledgments

We would like to thank the National Council for Scientific and Technological Development (CNPq) for the grants to CB, EGB and RPV; the Coordination for the Improvement of Higher Education Personnel/Ministry of Education (CAPES/MEC) for the grants to BSFM, the Minas Gerais State Research Foundation (FAPEMIG) for the grant to TS; and the Brazilian Agricultural Research Corporation (EMBRAPA) for financial support for this research.

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The authors declare that they have no conflict of interest.

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Authors and Affiliations

  1. Laboratory of Plant Molecular Genetics, Institute of Applied Biotechnology to Agriculture (BIOAGRO), Federal University of Viçosa, Viçosa, MG, Brazil

    Bárbara S. F. Müller & Everaldo G. Barros

  2. Department of Cellular Biology, University of Brasilia, Brasilia, DF, Brazil

    Georgios J. Pappas Jr

  3. Laboratory of Biotechnology, EMBRAPA Rice and Beans, Santo Antonio de Goias, GO, Brazil

    Bárbara S. F. Müller, Paula A. M. R. Valdisser, Gesimária R. C. Coelho, Aluana G. Abreu, Tereza C. O. Borba, Claudio Brondani & Rosana P. Vianello

  4. Laboratory of Genetics and Molecular Biology, Department of Biology, Federal Institute Goiano, Urutai, GO, Brazil

    Ivandilson P. P. de Menezes

  5. Laboratory of BioData, Institute of Biological Science, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil

    Tetsu Sakamoto

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  1. Bárbara S. F. Müller
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  2. Georgios J. Pappas Jr
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  3. Paula A. M. R. Valdisser
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Correspondence to Rosana P. Vianello.

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Müller, B.S.F., Pappas, G.J., Valdisser, P.A.M.R. et al. An Operational SNP Panel Integrated to SSR Marker for the Assessment of Genetic Diversity and Population Structure of the Common Bean. Plant Mol Biol Rep 33, 1697–1711 (2015). https://doi.org/10.1007/s11105-015-0866-x

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