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Identification of quantitative trait loci for net form net blotch resistance in contemporary barley breeding germplasm from the USA using genome-wide association mapping

Abstract

Key message

Association mapping study conducted in a population of 3490 elite barley breeding lines from ten barley breeding programs of the USA identified 12 QTLs for resistance/susceptibility to net form of net blotch.

Abstract

Breeding resistant varieties is the best management strategy for net form of net blotch (NFNB) in barley (Hordeum vulgare L.) caused by Pyrenophora teres f. teres (Ptt). Several resistance QTL have been previously identified in barley via linkage mapping and genome-wide association studies (GWAS). A GWAS conducted in a collection of advanced breeding lines (n = 3490) representing elite germplasm from ten barley breeding programs of the USA identified 42 unique marker-trait associations (MTA) for NFNB resistance. The lines were genotyped with 3072 SNP markers and phenotyped with four Ptt isolates in controlled environment. The lines were used to construct 13 different GWAS panels. Efficient mixed model association method with principal components and kinship was used for GWAS. Significance threshold for MTA was set at a false discovery rate of 0.05. Two, eight, six, one and 25 MTA were identified in chromosomes 1H, 3H, 4H, 5H and 6H, respectively. Based on genetic positions and linkage disequilibrium, these MTA’s correspond to two, three, two, one and four QTLs in chromosome 1H, 3H, 4H, 5H and 6H, respectively. A comparison with previous linkage and GWAS studies revealed several previously identified and novel QTLs. Moreover, different genomic regions were found to be responsible for NFNB resistance in two-row versus six-row germplasm. The germplasm-specific SNP markers with additive effects and allelic distribution is reported to facilitate breeders in selection of markers for MAS to introgress novel net blotch resistance.

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Acknowledgements

The authors would like to acknowledge the funding from American Malting Barley Association. The authors would also like to acknowledge help from Amar Elakkad, and Beheshteh Zargaran during phenotyping and Dr. Ahmad Sallam and Dr. Austin Case during data analysis.

Author information

RDM, KPS and BJS planned the experiments. RDM conducted the phenotyping. AA conducted the analysis and drafted the manuscript. KPS and RDM guided the analysis and manuscript writing. All authors reviewed the manuscript.

Correspondence to Anil Adhikari or Ruth Dill-Macky.

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Adhikari, A., Steffenson, B.J., Smith, K.P. et al. Identification of quantitative trait loci for net form net blotch resistance in contemporary barley breeding germplasm from the USA using genome-wide association mapping. Theor Appl Genet 133, 1019–1037 (2020). https://doi.org/10.1007/s00122-019-03528-5

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