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Title: SNP marker development for linkage map construction, anchoring of the common bean whole genome sequence and genetic research

Author
item Song, Qijian
item JIA, GAOFENG - Nanjing Agricultural University
item HYTEN, DAVID - Dupont Pioneer Hi-Bred
item JENKINS, JERRY - Hudsonalpha Institute For Biotechnology
item HWANG, EUN-YOUNG - University Of Maryland
item Schroeder, Steven - Steve
item SCHMUTZ, JEREMY - Hudsonalpha Institute For Biotechnology
item JACKSON, SCOTT - University Of Georgia
item MCCLEAN, PHILLIP - North Dakota State University
item CREGAN, PERRY - Retired ARS Employee

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/27/2015
Publication Date: 8/28/2015
Citation: Song, Q., Jia, G., Hyten, D.L., Jenkins, J., Hwang, E., Schroeder, S.G., Schmutz, J., Jackson, S.A., Mcclean, P., Cregan, P. 2015. SNP marker development for linkage map construction, anchoring of the common bean whole genome sequence and genetic research. G3, Genes/Genomes/Genetics. doi: 10.1534/g3.115.020594.

Interpretive Summary: Genetic linkage maps are the basic tool to determine the position of quantitative trait loci or genes on the chromosomes of an organism. Single nucleotide polymorphisms (SNPs) are the most abundant form of DNA marker and are suitable for the development of high-throughput, easy-to-automate genotyping methods. Before the common bean whole genome sequence v1.0 was released, the Joint Genome Institute, Department of Energy generated two assemblies of the common bean whole genome sequence. Both assemblies contained more than 10,000 short DNA sequences (scaffolds). Anchoring these scaffolds to create 11 chromosome sequences required the development of a large number of DNA markers and the creation of a dense molecular genetic map. With the aid of next-generation DNA sequencing technology, we identified large numbers of SNPs in the common bean genome and designed two SNP analysis assays (BARCBean6K_1 and BARCBean6K_2 BeadChips), each with >5,000 SNP DNA markers. Analysis of lines from a mapping population developed from a cross of the common bean cultivars “Stampede” x “Red Hawk” with the two assays resulted in linkage maps with a total of 7,040 markers. With these maps, the short sequences were anchored to create the 11 chromosome sequences of the common bean v1.0 genome assembly which was recently published in Nature Genetics. In addition, a core set of 6,000 SNPs (BARCBean6K_3 BeadChip) with high quality was selected based on the analysis of a large number of common 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 U.S. and abroad.

Technical Abstract: Our objectives were to identify SNP DNA markers based on a diverse set of common bean cultivars via next generation sequencing technologies; to develop Illumina Infinium BeadChip assays containing SNPs with high polymorphism within and between common bean market classes, to create high density genetic linkage maps, to anchor and orient large common bean sequence scaffolds generated by the Joint Genome Institute, Department of Energy (JGI) and to select a core set of highly informative SNP markers for use by common bean breeders and geneticists. We identified 992,682 SNPs ideal for Illumina Infinium II BeadChip design after sequencing a diverse set of 17 common bean cultivars with the aid of next-generation sequencing technology. From these, two BeadChips each with >5,000 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 14x genome assembly with sequence lengths >10kb. The BARCBean6K_2 BeadChip was designed with the objective of anchoring additional scaffolds and to facilitate orientation of large scaffolds. Analysis of 267 F2 lines from a cross of cultivars Stampede x Red Hawk with the two BeadChips resulted in linkage maps with a total of 7,040 markers including 7,015 SNPs. With the linkage map, a total of 432.3Mb of sequence from 2,766 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 6,000 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 U.S. and abroad.