Non-Mendelian Single-Nucleotide Polymorphism Inheritance and Atypical Meiotic Configurations are Prevalent in Hop
Hop ( 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 a...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Wiley
2017-11-01
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| Series: | The Plant Genome |
| Online Access: | https://dl.sciencesocieties.org/publications/tpg/articles/10/3/plantgenome2017.04.0032 |
| _version_ | 1818911294224334848 |
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| author | Dong Zhang Katherine A. Easterling Nicholi J. Pitra Mark C. Coles Edward S. Buckler Hank W. Bass Paul D. Matthews |
| author_facet | Dong Zhang Katherine A. Easterling Nicholi J. Pitra Mark C. Coles Edward S. Buckler Hank W. Bass Paul D. Matthews |
| author_sort | Dong Zhang |
| collection | DOAJ |
| description | Hop ( 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 F 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 (F) 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 . |
| first_indexed | 2024-12-19T22:56:25Z |
| format | Article |
| id | doaj.art-edb8c0a841744d5cbf106fc7f425a1f8 |
| institution | Directory Open Access Journal |
| issn | 1940-3372 |
| language | English |
| last_indexed | 2024-12-19T22:56:25Z |
| publishDate | 2017-11-01 |
| publisher | Wiley |
| record_format | Article |
| series | The Plant Genome |
| spelling | doaj.art-edb8c0a841744d5cbf106fc7f425a1f82022-12-21T20:02:38ZengWileyThe Plant Genome1940-33722017-11-0110310.3835/plantgenome2017.04.0032Non-Mendelian Single-Nucleotide Polymorphism Inheritance and Atypical Meiotic Configurations are Prevalent in HopDong ZhangKatherine A. EasterlingNicholi J. PitraMark C. ColesEdward S. BucklerHank W. BassPaul D. MatthewsHop ( 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 F 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 (F) 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 .https://dl.sciencesocieties.org/publications/tpg/articles/10/3/plantgenome2017.04.0032 |
| spellingShingle | Dong Zhang Katherine A. Easterling Nicholi J. Pitra Mark C. Coles Edward S. Buckler Hank W. Bass Paul D. Matthews Non-Mendelian Single-Nucleotide Polymorphism Inheritance and Atypical Meiotic Configurations are Prevalent in Hop The Plant Genome |
| title | Non-Mendelian Single-Nucleotide Polymorphism Inheritance and Atypical Meiotic Configurations are Prevalent in Hop |
| title_full | Non-Mendelian Single-Nucleotide Polymorphism Inheritance and Atypical Meiotic Configurations are Prevalent in Hop |
| title_fullStr | Non-Mendelian Single-Nucleotide Polymorphism Inheritance and Atypical Meiotic Configurations are Prevalent in Hop |
| title_full_unstemmed | Non-Mendelian Single-Nucleotide Polymorphism Inheritance and Atypical Meiotic Configurations are Prevalent in Hop |
| title_short | Non-Mendelian Single-Nucleotide Polymorphism Inheritance and Atypical Meiotic Configurations are Prevalent in Hop |
| title_sort | non mendelian single nucleotide polymorphism inheritance and atypical meiotic configurations are prevalent in hop |
| url | https://dl.sciencesocieties.org/publications/tpg/articles/10/3/plantgenome2017.04.0032 |
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