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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #358259

Research Project: Improving Crop Efficiency Using Genomic Diversity and Computational Modeling

Location: Plant, Soil and Nutrition Research

Title: Non-mendelian single-nucleotide polymorphism inheritance and atypical meiotic configurations are prevalent in hop

Author
item Zhang, Dong - Ss Steiner, Inc
item Easterling, Katherine - Ss Steiner, Inc
item Pitra, Nicholi - Ss Steiner, Inc
item Coles, Mark - Ss Steiner, Inc
item Buckler, Edward - Ed
item Bass, Hank - Florida State University
item Matthews, Paul - Ss Steiner, Inc

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/31/2017
Publication Date: 11/28/2017
Citation: Zhang, D., Easterling, K., Pitra, N., Coles, M., Buckler IV, E.S., Bass, H., Matthews, P. 2017. Non-mendelian single-nucleotide polymorphism inheritance and atypical meiotic configurations are prevalent in hop. The Plant Genome. 10(3). doi: 10.3835/plantgenome2017.04.0032
DOI: https://doi.org/10.3835/plantgenome2017.04.0032

Interpretive Summary: Hops are used to brew beer across the globe. However, the tremendous genetic diversity available across the species and varieties is not being fully used to provide new flavors, aroma, or disease resistance. The general approach for tapping this diversity is by making crosses between different types of hops from around the world. However, these crosses and their offspring were not exhibiting the level of natural genetic mixing that is normally seen in breeding. This study identified that natural chromosomal rearrangements are likely preventing the efficient mixing of this diversity. There are a number of genetic and breeding approaches for dealing with these rearrangements, which would need to be deployed in order to make more effective use of hop diversity in the regular breeding process.

Technical Abstract: Hop (Humulus lupulus L.) breeding programs seek to exploit genetic resources for bitter flavor, aroma, and disease resistance. However, these efforts have been thwarted by segregation distortion including female-biased sex ratios. To better understand the transmission genetics of hop, we genotyped 4512 worldwide accessions of hop, including cultivars, landraces, and over 100 wild accessions using a genotyping-by-sequencing (GBS) approach. From the resulting ~1.2 million single-nucleotide polymorphisms (SNPs), prequalified GBS markers were validated by inferences in population structures and phylogeny. Analysis of pseudo-testcross (Pt) mapping data from F1 families revealed mixed patterns of Mendelian and non-Mendelian segregation. Three-dimensional (3D) cytogenetic analysis of late meiotic prophase nuclei from two wild and two cultivated hop revealed conspicuous and prevalent occurrences of multiple, atypical, nondisomic chromosome complexes including autosomes. We used genome-wide association studies (GWAS) and fixation index (Fst) analysis to demonstrate selection mapping of genetic loci for key traits including sex, bitter acids, and drought tolerance. Among the possible mechanisms underlying the observed segregation distortion from the genomic data analysis, the cytogenetic analysis points to meiotic chromosome behavior as one of the contributing factors. The findings shed light on long-standing questions on the unusual transmission genetics and phenotypic variation in hop, with major implications for breeding, cultivation, and the natural history of Humulus.