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Genome-Wide Association Study of Spot Form of Net Blotch Resistance in the Upper Midwest Barley Breeding Programs.
Phytopathology. 2017 01; 107(1):100-108.P

Abstract

Pyrenophora teres f. maculata, the causal agent of spot form of net blotch (SFNB), is an emerging pathogen of barley in the United States and Australia. Compared with net form of net blotch (NFNB), less is known in the U.S. Upper Midwest barley breeding programs about host resistance and quantitative trait loci (QTL) associated with SFNB in breeding lines. The main objective of this study was to identify QTL associated with SFNB resistance in the Upper Midwest two-rowed and six-rowed barley breeding programs using a genome-wide association study approach. A total of 376 breeding lines of barley were evaluated for SFNB resistance at the seedling stage in the greenhouse in Fargo in 2009. The lines were genotyped with 3,072 single nucleotide polymorphism (SNP) markers. Phenotypic evaluation showed a wide range of variability among populations from the four breeding programs and the two barley-row types. The two-rowed barley lines were more susceptible to SFNB than the six-rowed lines. Continuous distributions of SFNB severity indicate the quantitative nature of SFNB resistance. The mixed linear model (MLM) analysis, which included both population structure and kinship matrices, was used to identify significant SNP-SFNB associations. Principal component analysis was used to control false marker-trait association. The linkage disequilibrium (LD) estimates varied among chromosomes (10 to 20 cM). The MLM analysis identified 10 potential QTL in barley: SFNB-2H-8-10, SFNB-2H-38.03, SFNB-3H-58.64, SFNB-3H-78.53, SFNB-3H-91.88, SFNB-3H-117.1, SFNB-5H-155.3, SFNB-6H-5.4, SFNB-6H-33.74, and SFNB-7H-34.82. Among them, four QTL (SFNB-2H-8-10, SFNB-2H-38.03 SFNB-3H-78.53, and SFNB-3H-117.1) have not previously been published. Identification of SFNB resistant lines and QTL associated with SFNB resistance in this study will be useful in the development of barley genotypes with better SFNB resistance.

Authors+Show Affiliations

First and second authors: Department of Plant Pathology, North Dakota State University, NDSU Dept. 7660, P.O. Box 6050, Fargo 58108-6050; third author: U.S. Department of Agriculture-Agricultural Research Service Cereal Crops Research Unit, 1605 Albrecht Blvd., Biosciences Research Laboratory, Fargo, ND 58105-5674; fourth and seventh authors: Department of Agronomy and Plant Genetics, University of Minnesota, 411 Borlaug Hall, 1991 Upper Buford Circle, St. Paul 55108-6026; fifth author: Department of Plant Sciences, North Dakota State University, NDSU Dept. 7670, P.O. Box 6050, Fargo 58108-6050; sixth author: Busch Agricultural Resources Inc. (BARI), 3515 E. Richards Lake Rd., Ft. Collins, CO 80524; and eighth author: Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD 4350, Australia.First and second authors: Department of Plant Pathology, North Dakota State University, NDSU Dept. 7660, P.O. Box 6050, Fargo 58108-6050; third author: U.S. Department of Agriculture-Agricultural Research Service Cereal Crops Research Unit, 1605 Albrecht Blvd., Biosciences Research Laboratory, Fargo, ND 58105-5674; fourth and seventh authors: Department of Agronomy and Plant Genetics, University of Minnesota, 411 Borlaug Hall, 1991 Upper Buford Circle, St. Paul 55108-6026; fifth author: Department of Plant Sciences, North Dakota State University, NDSU Dept. 7670, P.O. Box 6050, Fargo 58108-6050; sixth author: Busch Agricultural Resources Inc. (BARI), 3515 E. Richards Lake Rd., Ft. Collins, CO 80524; and eighth author: Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD 4350, Australia.First and second authors: Department of Plant Pathology, North Dakota State University, NDSU Dept. 7660, P.O. Box 6050, Fargo 58108-6050; third author: U.S. Department of Agriculture-Agricultural Research Service Cereal Crops Research Unit, 1605 Albrecht Blvd., Biosciences Research Laboratory, Fargo, ND 58105-5674; fourth and seventh authors: Department of Agronomy and Plant Genetics, University of Minnesota, 411 Borlaug Hall, 1991 Upper Buford Circle, St. Paul 55108-6026; fifth author: Department of Plant Sciences, North Dakota State University, NDSU Dept. 7670, P.O. Box 6050, Fargo 58108-6050; sixth author: Busch Agricultural Resources Inc. (BARI), 3515 E. Richards Lake Rd., Ft. Collins, CO 80524; and eighth author: Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD 4350, Australia.First and second authors: Department of Plant Pathology, North Dakota State University, NDSU Dept. 7660, P.O. Box 6050, Fargo 58108-6050; third author: U.S. Department of Agriculture-Agricultural Research Service Cereal Crops Research Unit, 1605 Albrecht Blvd., Biosciences Research Laboratory, Fargo, ND 58105-5674; fourth and seventh authors: Department of Agronomy and Plant Genetics, University of Minnesota, 411 Borlaug Hall, 1991 Upper Buford Circle, St. Paul 55108-6026; fifth author: Department of Plant Sciences, North Dakota State University, NDSU Dept. 7670, P.O. Box 6050, Fargo 58108-6050; sixth author: Busch Agricultural Resources Inc. (BARI), 3515 E. Richards Lake Rd., Ft. Collins, CO 80524; and eighth author: Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD 4350, Australia.First and second authors: Department of Plant Pathology, North Dakota State University, NDSU Dept. 7660, P.O. Box 6050, Fargo 58108-6050; third author: U.S. Department of Agriculture-Agricultural Research Service Cereal Crops Research Unit, 1605 Albrecht Blvd., Biosciences Research Laboratory, Fargo, ND 58105-5674; fourth and seventh authors: Department of Agronomy and Plant Genetics, University of Minnesota, 411 Borlaug Hall, 1991 Upper Buford Circle, St. Paul 55108-6026; fifth author: Department of Plant Sciences, North Dakota State University, NDSU Dept. 7670, P.O. Box 6050, Fargo 58108-6050; sixth author: Busch Agricultural Resources Inc. (BARI), 3515 E. Richards Lake Rd., Ft. Collins, CO 80524; and eighth author: Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD 4350, Australia.First and second authors: Department of Plant Pathology, North Dakota State University, NDSU Dept. 7660, P.O. Box 6050, Fargo 58108-6050; third author: U.S. Department of Agriculture-Agricultural Research Service Cereal Crops Research Unit, 1605 Albrecht Blvd., Biosciences Research Laboratory, Fargo, ND 58105-5674; fourth and seventh authors: Department of Agronomy and Plant Genetics, University of Minnesota, 411 Borlaug Hall, 1991 Upper Buford Circle, St. Paul 55108-6026; fifth author: Department of Plant Sciences, North Dakota State University, NDSU Dept. 7670, P.O. Box 6050, Fargo 58108-6050; sixth author: Busch Agricultural Resources Inc. (BARI), 3515 E. Richards Lake Rd., Ft. Collins, CO 80524; and eighth author: Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD 4350, Australia.First and second authors: Department of Plant Pathology, North Dakota State University, NDSU Dept. 7660, P.O. Box 6050, Fargo 58108-6050; third author: U.S. Department of Agriculture-Agricultural Research Service Cereal Crops Research Unit, 1605 Albrecht Blvd., Biosciences Research Laboratory, Fargo, ND 58105-5674; fourth and seventh authors: Department of Agronomy and Plant Genetics, University of Minnesota, 411 Borlaug Hall, 1991 Upper Buford Circle, St. Paul 55108-6026; fifth author: Department of Plant Sciences, North Dakota State University, NDSU Dept. 7670, P.O. Box 6050, Fargo 58108-6050; sixth author: Busch Agricultural Resources Inc. (BARI), 3515 E. Richards Lake Rd., Ft. Collins, CO 80524; and eighth author: Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD 4350, Australia.First and second authors: Department of Plant Pathology, North Dakota State University, NDSU Dept. 7660, P.O. Box 6050, Fargo 58108-6050; third author: U.S. Department of Agriculture-Agricultural Research Service Cereal Crops Research Unit, 1605 Albrecht Blvd., Biosciences Research Laboratory, Fargo, ND 58105-5674; fourth and seventh authors: Department of Agronomy and Plant Genetics, University of Minnesota, 411 Borlaug Hall, 1991 Upper Buford Circle, St. Paul 55108-6026; fifth author: Department of Plant Sciences, North Dakota State University, NDSU Dept. 7670, P.O. Box 6050, Fargo 58108-6050; sixth author: Busch Agricultural Resources Inc. (BARI), 3515 E. Richards Lake Rd., Ft. Collins, CO 80524; and eighth author: Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD 4350, Australia.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

27552325

Citation

Burlakoti, R R., et al. "Genome-Wide Association Study of Spot Form of Net Blotch Resistance in the Upper Midwest Barley Breeding Programs." Phytopathology, vol. 107, no. 1, 2017, pp. 100-108.
Burlakoti RR, Gyawali S, Chao S, et al. Genome-Wide Association Study of Spot Form of Net Blotch Resistance in the Upper Midwest Barley Breeding Programs. Phytopathology. 2017;107(1):100-108.
Burlakoti, R. R., Gyawali, S., Chao, S., Smith, K. P., Horsley, R. D., Cooper, B., Muehlbauer, G. J., & Neate, S. M. (2017). Genome-Wide Association Study of Spot Form of Net Blotch Resistance in the Upper Midwest Barley Breeding Programs. Phytopathology, 107(1), 100-108.
Burlakoti RR, et al. Genome-Wide Association Study of Spot Form of Net Blotch Resistance in the Upper Midwest Barley Breeding Programs. Phytopathology. 2017;107(1):100-108. PubMed PMID: 27552325.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Genome-Wide Association Study of Spot Form of Net Blotch Resistance in the Upper Midwest Barley Breeding Programs. AU - Burlakoti,R R, AU - Gyawali,S, AU - Chao,S, AU - Smith,K P, AU - Horsley,R D, AU - Cooper,B, AU - Muehlbauer,G J, AU - Neate,S M, Y1 - 2016/10/11/ PY - 2016/8/24/pubmed PY - 2017/7/1/medline PY - 2016/8/24/entrez KW - Hordeum vulgare KW - association mapping SP - 100 EP - 108 JF - Phytopathology JO - Phytopathology VL - 107 IS - 1 N2 - Pyrenophora teres f. maculata, the causal agent of spot form of net blotch (SFNB), is an emerging pathogen of barley in the United States and Australia. Compared with net form of net blotch (NFNB), less is known in the U.S. Upper Midwest barley breeding programs about host resistance and quantitative trait loci (QTL) associated with SFNB in breeding lines. The main objective of this study was to identify QTL associated with SFNB resistance in the Upper Midwest two-rowed and six-rowed barley breeding programs using a genome-wide association study approach. A total of 376 breeding lines of barley were evaluated for SFNB resistance at the seedling stage in the greenhouse in Fargo in 2009. The lines were genotyped with 3,072 single nucleotide polymorphism (SNP) markers. Phenotypic evaluation showed a wide range of variability among populations from the four breeding programs and the two barley-row types. The two-rowed barley lines were more susceptible to SFNB than the six-rowed lines. Continuous distributions of SFNB severity indicate the quantitative nature of SFNB resistance. The mixed linear model (MLM) analysis, which included both population structure and kinship matrices, was used to identify significant SNP-SFNB associations. Principal component analysis was used to control false marker-trait association. The linkage disequilibrium (LD) estimates varied among chromosomes (10 to 20 cM). The MLM analysis identified 10 potential QTL in barley: SFNB-2H-8-10, SFNB-2H-38.03, SFNB-3H-58.64, SFNB-3H-78.53, SFNB-3H-91.88, SFNB-3H-117.1, SFNB-5H-155.3, SFNB-6H-5.4, SFNB-6H-33.74, and SFNB-7H-34.82. Among them, four QTL (SFNB-2H-8-10, SFNB-2H-38.03 SFNB-3H-78.53, and SFNB-3H-117.1) have not previously been published. Identification of SFNB resistant lines and QTL associated with SFNB resistance in this study will be useful in the development of barley genotypes with better SFNB resistance. SN - 0031-949X UR - https://www.unboundmedicine.com/medline/citation/27552325/Genome_Wide_Association_Study_of_Spot_Form_of_Net_Blotch_Resistance_in_the_Upper_Midwest_Barley_Breeding_Programs_ DB - PRIME DP - Unbound Medicine ER -