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Abeyratne CR, Macaya-Sanz D, Zhou R, Barry KW, Daum C, Haiby K, Lipzen A, Stanton B, Yoshinaga Y, Zane M, Tuskan GA, DiFazio SP. High-resolution mapping reveals hotspots and sex-biased recombination in Populus trichocarpa. G3 (Bethesda) 2022; 13:6762080. [PMID: 36250890 PMCID: PMC9836356 DOI: 10.1093/g3journal/jkac269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 09/28/2022] [Indexed: 12/14/2022]
Abstract
Fine-scale meiotic recombination is fundamental to the outcome of natural and artificial selection. Here, dense genetic mapping and haplotype reconstruction were used to estimate recombination for a full factorial Populus trichocarpa cross of 7 males and 7 females. Genomes of the resulting 49 full-sib families (N = 829 offspring) were resequenced, and high-fidelity biallelic SNP/INDELs and pedigree information were used to ascertain allelic phase and impute progeny genotypes to recover gametic haplotypes. The 14 parental genetic maps contained 1,820 SNP/INDELs on average that covered 376.7 Mb of physical length across 19 chromosomes. Comparison of parental and progeny haplotypes allowed fine-scale demarcation of cross-over regions, where 38,846 cross-over events in 1,658 gametes were observed. Cross-over events were positively associated with gene density and negatively associated with GC content and long-terminal repeats. One of the most striking findings was higher rates of cross-overs in males in 8 out of 19 chromosomes. Regions with elevated male cross-over rates had lower gene density and GC content than windows showing no sex bias. High-resolution analysis identified 67 candidate cross-over hotspots spread throughout the genome. DNA sequence motifs enriched in these regions showed striking similarity to those of maize, Arabidopsis, and wheat. These findings, and recombination estimates, will be useful for ongoing efforts to accelerate domestication of this and other biomass feedstocks, as well as future studies investigating broader questions related to evolutionary history, perennial development, phenology, wood formation, vegetative propagation, and dioecy that cannot be studied using annual plant model systems.
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Affiliation(s)
| | - David Macaya-Sanz
- Department of Forest Ecology & Genetics, CIFOR-INIA, CSIC, Madrid 28040, Spain
| | - Ran Zhou
- Warnell School of Forestry and Natural Resources, Department of Genetics, and Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Kerrie W Barry
- Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | - Christopher Daum
- Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | | | - Anna Lipzen
- Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | | | - Yuko Yoshinaga
- Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | - Matthew Zane
- Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | - Gerald A Tuskan
- Biosciences Division, Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Stephen P DiFazio
- Corresponding author: Department of Biology, West Virginia University, Morgantown, WV 26506, USA.
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