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Title: Genotyping by sequencing enabled mapping and marker development for the By-2 potyvirus resistance allele in common bean

Author
item Hart, John
item GRIFFITHS, P. - Cornell University

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/25/2014
Publication Date: 3/13/2015
Citation: Hart, J.P., Griffiths, P.D. 2015. Genotyping by sequencing enabled mapping and marker development for the By-2 potyvirus resistance allele in common bean. The Plant Genome. 8. doi:10.3835/plantgenome2014.09.0058.

Interpretive Summary: Since 2001, crop yields of snap beans in the Great Lakes Region of the United States have been periodically damaged by a number of plant virus diseases that are transmitted by insect pests known as aphids. Because aphid populations increase and disperse quickly, and because the transmission of the plant viruses that they carry can occur within minutes of feeding, chemical pesticides are neither an effective, nor ecologically sensitive way to protect against crop damage. This situation requires the identification and development of snap beans with natural genetic resistance to the plant viruses. The objectives of this study were 1.) to investigate the inheritance of plant resistance to Bean yellow mosaic virus (BYMV) infection conferred by the natural resistance gene known as By-2 and 2.) to adapt and employ a cutting-edge next generation genome sequencing technology known as genotyping-by-sequencing to discover which region of the bean genome harbors this important resistance gene. To achieve this objective, we evaluated a collection of snap bean breeding lines for resistance or susceptibility to BYMV and then subsequently surveyed the genetic differences present in these lines through genotyping-by-sequencing. We discovered 7,530 single nucleotide polymorphisms (SNPs), or areas throughout the genome that were different amongst these breeding lines, and then sought to discover significant associations between some of these genetic differences and a plant’s resistance to BYMV by conducting a genome-wide association study. This resulted in the discovery of 44 SNPs present in a relatively narrow and specific region on chromosome 2 that were strongly associated with resistance to BYMV. The importance of this region for conferring resistance to BYMV was confirmed by tracking its inheritance with molecular markers in an additional population of 185 plants that were either resistant or susceptible. This research resulted in the development of a molecular marker that will allow for the precise selection of By-2 resistant plants and that ultimately could help to speed the development of multiple-virus resistant snap beans and reduce economic losses to U.S. snap bean production.

Technical Abstract: Since its emergence in 2001, an aphid-transmitted virus disease complex has caused substantial economic losses to snap bean (Phaseolus vulgaris L.) production and processing in the Great Lakes Region of the United States. The general ineffectiveness of chemical control measures for nonpersistently transmitted viruses established an urgent need for the development and deployment of cultivars with resistance to the component viruses. Our objectives were to further characterize the inheritance of resistance to Bean yellow mosaic virus (BYMV) that is conditioned by the By-2 allele, to adapt genotyping-by-sequencing (GBS) to common bean to discover and genotype genome-wide single nucleotide polymorphisms (SNPs) in a set of recombinant inbred lines (RILs) derived from an introgression program, and to enable and validate marker assisted selection for By-2. We optimized ApeKI for GBS and genotyped 7,530 high quality SNPs that segregated in our introgression RILs. A case-control genome-wide association study was employed to discover 44 GBS SNPs that were strongly associated with the resistance phenotype, and that delimited a 974 kb physical interval on the distal portion of chromosome 2. Seven of these SNPs were converted to single marker Kompetitive Allele-specific PCR (KASP) assays and were demonstrated to be tightly linked to BYMV resistance in an F2 population of 185 individuals. This research enables marker assisted selection of By-2, provides enhanced resolution for fine mapping, and demonstrates the potential of GBS as a highly efficient, high throughput genotyping platform for common bean breeding and genetics.