Accurate Determination of Genotypic Variance of Cell Wall Characteristics of a Populus trichocarpa Pedigree Using High-Throughput Pyrolysis-Molecular Beam Mass Spectrometry

Harman‐Ware, Anne E.; Macaya‐Sanz, David; Abeyratne, Chanaka Roshan; Doeppke, Crissa; Haiby, Kathleen; Tuskan, Gerald A.; Stanton, Brian J.; DiFazio, Stephen P.; Davis, Mark F.

doi:10.21203/rs.3.rs-23478/v2

Cited by 2 publications

(2 citation statements)

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“…The P. trichocarpa mapping population used in the study consists of a total of 829 progeny from 49 full-sib families derived from a full-factorial cross between 7 males and 7 females ( Harman-Ware et al 2021 ) ( Supplementary Table 1 ). The parents were originally collected as part of a population of 448 genotypes from natural riparian stands in WA and OR, USA ( Supplementary Fig.…”

Section: Methodsmentioning

confidence: 99%

High-resolution mapping reveals hotspots and sex-biased recombination inPopulus trichocarpa

Abeyratne

Macaya‐Sanz

Zhou

et al. 2022

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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 seven males and seven females. Genomes of the resulting 49 full-sib families (N = 829 offspring) were re-sequenced, and high-fidelity biallelic SNP/INDELs and pedigree information were used to ascertain allelic phase and impute progeny genotypes to recover gametic haplotypes. The fourteen parental genetic maps contained 1820 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 (CO) regions, where 38,846 CO events in 1,658 gametes were observed. CO 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 COs in males in 8 out of 19 chromosomes. Regions with elevated male CO rates had lower gene density and GC content than windows showing no sex bias. High-resolution analysis identified 67 candidate CO 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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Section: Methodsmentioning

confidence: 99%

High-resolution mapping reveals hotspots and sex-biased recombination inPopulus trichocarpa

Abeyratne

Macaya‐Sanz

Zhou

et al. 2022

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show abstract

“…The P. trichocarpa mapping population used in the study consists of a total of 829 progeny from 49 full-sib families derived from a full-factorial cross between seven males and seven females (H arman -W are et al . 2021) (Table S1).…”

Section: Methodsmentioning

confidence: 99%

High resolution mapping reveals hotspots and sex-biased recombination inPopulus trichocarpa

Abeyratne

Macaya‐Sanz²,

Zhou

et al. 2022

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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 seven males and seven females. Genomes of the resulting 49 full-sib families (N=829 offspring) were re-sequenced, and high-fidelity biallelic SNP/INDELs and pedigree information were used to ascertain allelic phase and impute progeny genotypes to recover gametic haplotypes. The fourteen parental genetic maps contained 1820 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 (CO) regions, where 38,846 CO events in 1,658 gametes were observed. CO 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 COs in males in 8 out of 19 chromosomes. Regions with elevated male CO rates had lower gene density and GC content than windows showing no sex bias. High-resolution analysis identified 67 candidate CO 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.

show abstract

Accurate Determination of Genotypic Variance of Cell Wall Characteristics of a Populus trichocarpa Pedigree Using High-Throughput Pyrolysis-Molecular Beam Mass Spectrometry

Cited by 2 publications

References 52 publications

High-resolution mapping reveals hotspots and sex-biased recombination inPopulus trichocarpa

High-resolution mapping reveals hotspots and sex-biased recombination inPopulus trichocarpa

High resolution mapping reveals hotspots and sex-biased recombination inPopulus trichocarpa

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