SNP Assay Development for Linkage Map Construction, Anchoring Whole-Genome Sequence, and Other Genetic and Genomic Applications in Common Bean

A total of 992,682 single-nucleotide polymorphisms (SNPs) was identified as ideal for Illumina Infinium II BeadChip design after sequencing a diverse set of 17 common bean (Phaseolus vulgaris L) varieties with the aid of next-generation sequencing technology. From these, two BeadChips each with >5000 SNPs were designed. The BARCBean6K_1 BeadChip was selected for the purpose of optimizing polymorphism among market classes and, when possible, SNPs were targeted to sequence scaffolds in the Phaseolus vulgaris 14× genome assembly with sequence lengths >10 kb. The BARCBean6K_2 BeadChip was designed with the objective of anchoring additional scaffolds and to facilitate orientation of large scaffolds. Analysis of 267 F2 plants from a cross of varieties Stampede × Red Hawk with the two BeadChips resulted in linkage maps with a total of 7040 markers including 7015 SNPs. With the linkage map, a total of 432.3 Mb of sequence from 2766 scaffolds was anchored to create the Phaseolus vulgaris v1.0 assembly, which accounted for approximately 89% of the 487 Mb of available sequence scaffolds of the Phaseolus vulgaris v0.9 assembly. A core set of 6000 SNPs (BARCBean6K_3 BeadChip) with high genotyping quality and polymorphism was selected based on the genotyping of 365 dry bean and 134 snap bean accessions with the BARCBean6K_1 and BARCBean6K_2 BeadChips. The BARCBean6K_3 BeadChip is a useful tool for genetics and genomics research and it is widely used by breeders and geneticists in the United States and abroad.

[1]  P. Cregan,et al.  Fingerprinting Soybean Germplasm and Its Utility in Genomic Research , 2015, G3: Genes, Genomes, Genetics.

[2]  Rod A Wing,et al.  A reference genome for common bean and genome-wide analysis of dual domestications , 2014, Nature Genetics.

[3]  J. Schmutz,et al.  Developing market class specific InDel markers from next generation sequence data in Phaseolus vulgaris L. , 2013, Front. Plant Sci..

[4]  M. Blair,et al.  A high-throughput SNP marker system for parental polymorphism screening, and diversity analysis in common bean (Phaseolus vulgaris L.) , 2013, Theoretical and Applied Genetics.

[5]  Randall L. Nelson,et al.  Development and Evaluation of SoySNP50K, a High-Density Genotyping Array for Soybean , 2013, PloS one.

[6]  Fernando J. Yuste-Lisbona,et al.  Marker-based linkage map of Andean common bean (Phaseolus vulgaris L.) and mapping of QTLs underlying popping ability traits , 2012, BMC Plant Biology.

[7]  M. Blair,et al.  New gene‐derived simple sequence repeat markers for common bean (Phaseolus vulgaris L.) , 2012, Molecular ecology resources.

[8]  R. Wing,et al.  Gene-based SSR markers for common bean (Phaseolus vulgaris L.) derived from root and leaf tissue ESTs: an integration of the BMc series , 2011, BMC Plant Biology.

[9]  I. Rao,et al.  Development of a Mesoamerican intra-genepool genetic map for quantitative trait loci detection in a drought tolerant × susceptible common bean (Phaseolus vulgaris L.) cross , 2010, Molecular Breeding.

[10]  Rex T. Nelson,et al.  Abundance of SSR Motifs and Development of Candidate Polymorphic SSR Markers (BARCSOYSSR_1.0) in Soybean , 2010 .

[11]  P. Cregan,et al.  High-throughput SNP discovery and assay development in common bean , 2010, BMC Genomics.

[12]  S. Jackson,et al.  Integration of physical and genetic maps of common bean through BAC-derived microsatellite markers , 2010, BMC Genomics.

[13]  R. Papa,et al.  Syntenic relationships among legumes revealed using a gene-based genetic linkage map of common bean (Phaseolus vulgaris L.) , 2010, Theoretical and Applied Genetics.

[14]  S. Linnarsson.  Recent advances in DNA sequencing methods - general principles of sample preparation. , 2010, Experimental cell research.

[15]  M. Santalla,et al.  Integration of genome and phenotypic scanning gives evidence of genetic structure in Mesoamerican common bean (Phaseolus vulgaris L.) landraces from the southwest of Europe , 2010, Theoretical and Applied Genetics.

[16]  M. Blair,et al.  Single strand conformation polymorphism based SNP and Indel markers for genetic mapping and synteny analysis of common bean (Phaseolus vulgaris L.) , 2009, BMC Genomics.

[17]  M. Blair,et al.  Development of microsatellite markers for common bean (Phaseolus vulgaris L.) based on screening of non-enriched, small-insert genomic libraries. , 2009, Genome.

[18]  L. Camargo,et al.  Extension of the core map of common bean with EST-SSR, RGA, AFLP, and putative functional markers , 2009, Molecular Breeding.

[19]  P. Gepts,et al.  Structure of genetic diversity in the two major gene pools of common bean (Phaseolus vulgaris L., Fabaceae) , 2009, Theoretical and Applied Genetics.

[20]  P. Cregan,et al.  Single Nucleotide Polymorphisms in Common Bean: Their Discovery and Genotyping Using a Multiplex Detection System , 2008 .

[21]  R. Nelson,et al.  SSR marker diversity of soybean aphid resistance sources in North America. , 2007, Genome.

[22]  M. Blair,et al.  Genetic mapping of a new set of microsatellite markers in a reference common bean (Phaseolus vulgaris) population BAT93 x Jalo EEP558. , 2007, Genetics and molecular research : GMR.

[23]  P. McClean,et al.  Genetic architecture of chalcone isomerase non-coding regions in common bean (Phaseolus vulgaris L.). , 2007, Genome.

[24]  B. Méndez-Vigo,et al.  A genetic linkage map of Phaseolus vulgaris L. and localization of genes for specific resistance to six races of anthracnose (Colletotrichum lindemuthianum) , 2007, Theoretical and Applied Genetics.

[25]  P. Cregan,et al.  BARCSoySNP23: a panel of 23 selected SNPs for soybean cultivar identification , 2007, Theoretical and Applied Genetics.

[26]  Tianzhen Zhang,et al.  QTL mapping for plant architecture traits in upland cotton using RILs and SSR markers. , 2006, Yi chuan xue bao = Acta genetica Sinica.

[27]  P. Cregan,et al.  Development and mapping of microsatellite (SSR) markers in wheat , 2005, Theoretical and Applied Genetics.

[28]  J. E. Specht,et al.  A new integrated genetic linkage map of the soybean , 2004, Theoretical and Applied Genetics.

[29]  E. Cober,et al.  Simple sequence repeat (SSR) markers linked to E1, E3, E4, and E7 maturity genes in soybean. , 2003, Genome.

[30]  M. Blair,et al.  Development of a genome-wide anchored microsatellite map for common bean (Phaseolus vulgaris L.) , 2003, Theoretical and Applied Genetics.

[31]  M. Karaca,et al.  Simple sequence repeat (SSR) markers linked to the Ligon lintless (Li(1)) mutant in cotton. , 2002, The Journal of heredity.

[32]  M. Ferreira,et al.  QTL mapping and introgression of yield-related traits from Oryza glumaepatula to cultivated rice (Oryza sativa) using microsatellite markers , 2002, Theoretical and Applied Genetics.

[33]  Steven G. Schroeder,et al.  Development and mapping of SSR markers for maize , 2002, Plant Molecular Biology.

[34]  P. McClean,et al.  Molecular and phenotypic mapping of genes controlling seed coat pattern and color in common bean (Phaseolus vulgaris L.). , 2002, The Journal of heredity.

[35]  J. P. Yang,et al.  [Construction of a genetic map and location of quantitative trait loci for yield component traits in maize by SSR markers]. , 2001, Yi chuan xue bao = Acta genetica Sinica.

[36]  P. Cregan,et al.  DNA markers for Fusarium head blight resistance QTLs in two wheat populations , 2001, Theoretical and Applied Genetics.

[37]  P. Gepts,et al.  Integration of simple sequence repeat (SSR) markers into a molecular linkage map of common bean (Phaseolus vulgaris L.). , 2000, The Journal of heredity.

[38]  A. Brookes.  The essence of SNPs. , 1999, Gene.

[39]  A. Adam-Blondon,et al.  Towards an integrated linkage map of common bean. 4. Development of a core linkage map and alignment of RFLP maps , 1998, Theoretical and Applied Genetics.

[40]  M. Ganal,et al.  A microsatellite map of wheat. , 1998, Genetics.

[41]  M. Blair,et al.  Microsatellite marker development, mapping and applications in rice genetics and breeding , 1997, Plant Molecular Biology.

[42]  M. Sandmeier.  Selfing rates of pearl millet (Pennisetum typhoides Stapf and Hubb.) under natural conditions , 1993, Theoretical and Applied Genetics.

[43]  E. D. Earle,et al.  Nuclear DNA content of some important plant species , 1991, Plant Molecular Biology Reporter.

[44]  Shengnan Jin,et al.  High-throughput methods for SNP genotyping. , 2009, Methods in molecular biology.

[45]  J. Ooijen,et al.  JoinMap® 4, Software for the calculation of genetic linkage maps in experimental populations , 2006 .

[46]  R. Gilbertson,et al.  Towards an integrated linkage map of common bean 2. Development of an RFLP-based linkage map , 2004, Theoretical and Applied Genetics.