title: Genotyping-by-sequencing-based genome-wide association studies on Verticillium wilt resistance in autotetraploid alfalfa (Medicago sativa L.).
abstract: Verticillium wilt (VW) is a fungal disease that causes severe yield losses in alfalfa. The most effective method to control the disease is through the development and use of resistant varieties. The identification of marker loci linked to VW resistance can facilitate breeding for disease-resistant alfalfa. In the present investigation, we applied an integrated framework of genome-wide association with genotyping-by-sequencing (GBS) to identify VW resistance loci in a panel of elite alfalfa breeding lines. Phenotyping was performed by manual inoculation of the pathogen to healthy seedlings, and scoring for disease resistance was carried out according to the standard test of the North America Alfalfa Improvement Conference (NAAIC). Marker-trait association by linkage disequilibrium identified 10 single nucleotide polymorphism (SNP) markers significantly associated with VW resistance. Alignment of the SNP marker sequences to the M. truncatula genome revealed multiple quantitative trait loci (QTLs). Three, two, one and five markers were located on chromosomes 5, 6, 7 and 8, respectively. Resistance loci found on chromosomes 7 and 8 in the present study co-localized with the QTLs reported previously. A pairwise alignment (blastn) using the flanking sequences of the resistance loci against the M. truncatula genome identified potential candidate genes with putative disease resistance function. With further investigation, these markers may be implemented into breeding programmes using marker-assisted selection, ultimately leading to improved VW resistance in alfalfa.
authors.affiliation: United States Department of Agriculture-Agricultural Research Service, Plant Germplasm Introduction and Testing Research, 24106 N Bunn Road, Prosser, WA, 99350 USA.
authors.forename: Long-Xi
authors.initials: LX
authors.lastname: Yu
authors.affiliation: Department of Horticulture, Washington State University, Pullman, WA, 99164 USA.
authors.forename: Ping
authors.initials: P
authors.lastname: Zheng
authors.affiliation: United States Department of Agriculture-Agricultural Research Service, Plant Germplasm Introduction and Testing Research, 24106 N Bunn Road, Prosser, WA, 99350 USA.
authors.forename: Tiejun
authors.initials: T
authors.lastname: Zhang
authors.affiliation: Forage Genetics International, Inc., 7661 Becker Road, Davis, CA, 95618 USA.
authors.forename: Jonas
authors.initials: J
authors.lastname: Rodringuez
authors.affiliation: Department of Horticulture, Washington State University, Pullman, WA, 99164 USA.
authors.forename: Dorrie
authors.initials: D
authors.lastname: Main
mesh_terms: D060467:Disease Resistance / Q000235:genetics*; D005787:Gene Frequency / Q000235:genetics; D017343:Genes, Plant; D056426:Genetic Loci; D005819:Genetic Markers; D055106:Genome-Wide Association Study; D060005:Genotyping Techniques / Q000379:methods*; D006579:Heterozygote; D000455:Medicago sativa / Q000235:genetics* / Q000382:microbiology*; D010641:Phenotype; D010935:Plant Diseases / Q000235:genetics / Q000382:microbiology; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D011123:Polyploidy; D025341:Principal Component Analysis; D019655:Quantitative Trait, Heritable; D017422:Sequence Analysis, DNA / Q000379:methods*; D020172:Verticillium / Q000502:physiology*
chemical_list: D005819:Genetic Markers
keywords: fungal disease; genotyping-by-sequencing; linkage disequilibrium; marker-assisted selection; quantitative trait loci