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Bilton TP, Alemu SW, Dodds KG, Henry H, Hess MK, Jordan R, Booker F, Hickey SM, Amyes N, Knowler K, Sandoval E, Peers-Adams J, van Stijn TC, Baird H, Watson T, Bain W, Veenvliet B, Pile G, Bryson B, Clarke SM, Johnson PL, McEwan JC, Rowe SJ. Rumen metagenome profiles are heritable and rank the New Zealand national sheep flock for enteric methane emissions. Genet Sel Evol 2025; 57:25. [PMID: 40426027 PMCID: PMC12117806 DOI: 10.1186/s12711-025-00973-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Accepted: 05/07/2025] [Indexed: 05/29/2025] Open
Abstract
BACKGROUND Global targets to reduce greenhouse gas emissions to meet international climate change commitments have driven the livestock industry to develop solutions to reduce methane emission in ruminants while maintaining production. Research has shown that selective breeding for low methane emitting ruminants using genomic selection is one viable solution to meet methane targets at a national level. However, this requires obtaining sufficient measures of methane on individual animals across the national herd. In sheep, one affordable method for measuring methane on-farm to rank animals on their methane emissions is portable accumulation chambers (PAC), although this method is not without its challenges. An alternative is to use a proxy trait that is genetically correlated with PAC methane measures. One such trait that has shown promise is rumen metagenome community (RMC) profiles. In this study, we investigate the potential of using RMC profiles as a proxy trait for methane emissions from PAC using a large sheep dataset consisting of 4585 mixed-sex lambs from several flocks and years across New Zealand. RESULTS RMC profiles were generated from rumen samples collected on the animals immediately after being measured through PAC using restriction enzyme-reduced representation sequencing. We predicted methane (CH4) and carbon dioxide (CO2) emissions (grams per day), as well as the ratio CH4/(CO2 + CH4) (CH4Ratio), from the RMC profiles and SNP-array genotype data. Heritability and microbiability estimates were similar to values found in the literature for all traits. The correlation of PAC methane with predicted methane was 1.9- to 2.3-fold (CH4) and 1.2- to 1.5-fold (CH4Ratio) greater for RMC profiles compared to host genomics only. The genetic correlation between methane predicted from RMC profiles and PAC methane was 0.75 ± 0.12 for CH4 and 0.64 ± 0.11 for CH4Ratio when using a validation set consisting of the animals with the most recent year of birth in the dataset. CONCLUSIONS RMC profiles are predictive of, and genetically correlated, with PAC methane measures. Therefore, RMC profiles are a suitable proxy trait for determining the genetic merit of an animal's methane emissions and could be incorporated into existing breeding programs to facilitate selective breeding for low methane emitting sheep.
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Affiliation(s)
- Timothy P Bilton
- AgResearch, Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand.
| | - Setegn W Alemu
- AgResearch, Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Ken G Dodds
- AgResearch, Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Hannah Henry
- AgResearch, Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Melanie K Hess
- AgResearch, Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Ronan Jordan
- AgResearch, Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Fern Booker
- AgResearch, Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Sharon M Hickey
- AgResearch, Ruakura Research Centre, Private Bag 3123, Hamilton, 3240, New Zealand
| | - Neville Amyes
- AgResearch, Ruakura Research Centre, Private Bag 3123, Hamilton, 3240, New Zealand
| | - Kevin Knowler
- AgResearch, Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Edgar Sandoval
- AgResearch, Grasslands Research Centre, Private Bag 11008, Palmerston North, 4442, New Zealand
| | | | - Tracey C van Stijn
- AgResearch, Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Hayley Baird
- AgResearch, Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Trevor Watson
- AgResearch, Ruakura Research Centre, Private Bag 3123, Hamilton, 3240, New Zealand
| | - Wendy Bain
- AgResearch, Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Barry Veenvliet
- AgResearch, Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Gerard Pile
- AgResearch, Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Brooke Bryson
- AgResearch, Woodlands Research Farm, RD1, Woodlands, Invercargill, 9871, New Zealand
| | - Shannon M Clarke
- AgResearch, Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Patricia L Johnson
- AgResearch, Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| | - John C McEwan
- AgResearch, Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Suzanne J Rowe
- AgResearch, Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
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Bilton TP, Hickey SM, Jonker A, McRae K, Hess MK, Perry BJ, Bryson B, Henry H, Bain W, Booker F, Veenvliet B, Peers-Adams J, Pile G, Waller E, Janssen PH, Tiplady KM, Reid P, Muetzel S, Agnew M, Dodds KG, McEwan JC, Rowe SJ. Milk fatty acids and rumen composition as proxy measures of enteric methane. J Dairy Sci 2025; 108:5125-5144. [PMID: 40139349 DOI: 10.3168/jds.2024-25876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2024] [Accepted: 02/12/2025] [Indexed: 03/29/2025]
Abstract
Genomic selection is a powerful tool to reduce methane emissions in ruminants. However, it requires large-scale on-farm phenotypic measures of methane. Current technologies to measure methane emissions have several limitations and may not be suitable for lactating animals. Because enteric methane is closely linked to the fermentation process in the rumen, which in turn affects milk composition, breeding for low-methane ruminants may change the rumen microbial and milk composition. Consequently, these compositions may provide proxy measures of methane for use in selective breeding of low-methane ruminants. We investigated the effect on rumen and milk composition in sheep bred for divergent methane yield and the potential for generating proxy measures of methane emissions from rumen or milk samples in lactating ewes. Four hundred genotyped lactating ewes from a sheep research flock bred specifically for high and low-methane emissions had methane measured and rumen and milk samples collected approximately 6 wk post-lambing across 4 lactation years. Rumen samples were processed to generate VFA and metagenomic profiles of the rumen microbial community, and fatty acid profiles and mid-infrared spectra were generated for the milk samples. Although no differences in total fat, protein, and lactose percentages in the milk were found, the milk fatty acid profiles differed between methane selection lines, with higher PUFA and branched-chain fatty acids levels, and lower total SFA contents in ewes from the low-methane line. Lower proportions of acetate relative to propionate were found in the rumen samples from the low-methane ewes. Predictions of methane were obtained from the rumen VFA and metagenomic profiles and the fatty acid profiles and mid-infrared spectra from milk. These predictions formed the proxy methane measures and were heritable (between 0.12 to 0.36) and correlated (between 0.29 and 0.42) with the measured methane values. The genetic correlation between proxies and measured methane was between 0.52 and 0.71. The estimated efficiency of indirect selection for methane was higher for the milk sample proxies (49%-75%) than the rumen metagenomic profiles (45%-47%) and rumen VFA profiles (12%-38%). These results suggest that milk fatty acid, MIR spectroscopic, and rumen microbial composition phenotypes have the potential to be used as proxy measures of methane in lactating ruminants, with the milk-based proxies showing greater promise. Results show that the number of animals with methane proxy measures could be increased substantially and will enable access to breeding technology in countries with limited methane measurement infrastructure.
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Affiliation(s)
- Timothy P Bilton
- Invermay Agricultural Centre, AgResearch, Mosgiel 9053, New Zealand.
| | - Sharon M Hickey
- Ruakura Agricultural Centre, AgResearch, Hamilton 3240, New Zealand
| | - Arjan Jonker
- Grasslands Research Centre, AgResearch, Palmerston North 4442, New Zealand
| | - Kathryn McRae
- Invermay Agricultural Centre, AgResearch, Mosgiel 9053, New Zealand
| | - Melanie K Hess
- Invermay Agricultural Centre, AgResearch, Mosgiel 9053, New Zealand
| | - Benjamin J Perry
- Invermay Agricultural Centre, AgResearch, Mosgiel 9053, New Zealand
| | - Brooke Bryson
- Woodlands Research Farm, AgResearch, Invercargill 9871, New Zealand
| | - Hannah Henry
- Invermay Agricultural Centre, AgResearch, Mosgiel 9053, New Zealand
| | - Wendy Bain
- Invermay Agricultural Centre, AgResearch, Mosgiel 9053, New Zealand
| | - Fern Booker
- Invermay Agricultural Centre, AgResearch, Mosgiel 9053, New Zealand
| | - Barry Veenvliet
- Invermay Agricultural Centre, AgResearch, Mosgiel 9053, New Zealand
| | | | - Gerrard Pile
- Invermay Agricultural Centre, AgResearch, Mosgiel 9053, New Zealand
| | - Erin Waller
- Invermay Agricultural Centre, AgResearch, Mosgiel 9053, New Zealand
| | - Peter H Janssen
- Grasslands Research Centre, AgResearch, Palmerston North 4442, New Zealand
| | - Kathryn M Tiplady
- Research & Development, Livestock Improvement Corporation, Hamilton 3240, New Zealand
| | - Peter Reid
- Grasslands Research Centre, AgResearch, Palmerston North 4442, New Zealand
| | - Stefan Muetzel
- Grasslands Research Centre, AgResearch, Palmerston North 4442, New Zealand
| | - Michael Agnew
- Grasslands Research Centre, AgResearch, Palmerston North 4442, New Zealand; Te Ohu Rangahau Kai, AgResearch, Palmerston North 4474, New Zealand
| | - Ken G Dodds
- Invermay Agricultural Centre, AgResearch, Mosgiel 9053, New Zealand
| | - John C McEwan
- Invermay Agricultural Centre, AgResearch, Mosgiel 9053, New Zealand
| | - Suzanne J Rowe
- Invermay Agricultural Centre, AgResearch, Mosgiel 9053, New Zealand
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Boocock J, Alexander N, Alamo Tapia L, Walter-McNeill L, Patel SP, Munugala C, Bloom JS, Kruglyak L. Single-cell eQTL mapping in yeast reveals a tradeoff between growth and reproduction. eLife 2025; 13:RP95566. [PMID: 40073070 PMCID: PMC11903034 DOI: 10.7554/elife.95566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2025] Open
Abstract
Expression quantitative trait loci (eQTLs) provide a key bridge between noncoding DNA sequence variants and organismal traits. The effects of eQTLs can differ among tissues, cell types, and cellular states, but these differences are obscured by gene expression measurements in bulk populations. We developed a one-pot approach to map eQTLs in Saccharomyces cerevisiae by single-cell RNA sequencing (scRNA-seq) and applied it to over 100,000 single cells from three crosses. We used scRNA-seq data to genotype each cell, measure gene expression, and classify the cells by cell-cycle stage. We mapped thousands of local and distant eQTLs and identified interactions between eQTL effects and cell-cycle stages. We took advantage of single-cell expression information to identify hundreds of genes with allele-specific effects on expression noise. We used cell-cycle stage classification to map 20 loci that influence cell-cycle progression. One of these loci influenced the expression of genes involved in the mating response. We showed that the effects of this locus arise from a common variant (W82R) in the gene GPA1, which encodes a signaling protein that negatively regulates the mating pathway. The 82R allele increases mating efficiency at the cost of slower cell-cycle progression and is associated with a higher rate of outcrossing in nature. Our results provide a more granular picture of the effects of genetic variants on gene expression and downstream traits.
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Affiliation(s)
- James Boocock
- Department of Human Genetics, University of California, Los AngelesLos AngelesUnited States
- Department of Biological Chemistry, University of California, Los AngelesLos AngelesUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
| | - Noah Alexander
- Department of Human Genetics, University of California, Los AngelesLos AngelesUnited States
- Department of Biological Chemistry, University of California, Los AngelesLos AngelesUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
| | - Leslie Alamo Tapia
- Department of Human Genetics, University of California, Los AngelesLos AngelesUnited States
- Department of Biological Chemistry, University of California, Los AngelesLos AngelesUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
| | - Laura Walter-McNeill
- Department of Human Genetics, University of California, Los AngelesLos AngelesUnited States
- Department of Biological Chemistry, University of California, Los AngelesLos AngelesUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
| | - Shivani Prashant Patel
- Department of Human Genetics, University of California, Los AngelesLos AngelesUnited States
- Department of Biological Chemistry, University of California, Los AngelesLos AngelesUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
| | - Chetan Munugala
- Department of Human Genetics, University of California, Los AngelesLos AngelesUnited States
- Department of Biological Chemistry, University of California, Los AngelesLos AngelesUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
| | - Joshua S Bloom
- Department of Human Genetics, University of California, Los AngelesLos AngelesUnited States
- Department of Biological Chemistry, University of California, Los AngelesLos AngelesUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
| | - Leonid Kruglyak
- Department of Human Genetics, University of California, Los AngelesLos AngelesUnited States
- Department of Biological Chemistry, University of California, Los AngelesLos AngelesUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
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Ehoche OG, Arojju SK, Jahufer MZZ, Jauregui R, Larking AC, Cousins G, Tate JA, Lockhart PJ, Griffiths AG. Genomic selection shows improved expected genetic gain over phenotypic selection of agronomic traits in allotetraploid white clover. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2025; 138:34. [PMID: 39847157 PMCID: PMC11757872 DOI: 10.1007/s00122-025-04819-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 01/06/2025] [Indexed: 01/24/2025]
Abstract
KEY MESSAGE Genomic selection using white clover multi-year-multi-site data showed predicted genetic gains through integrating among-half-sibling-family phenotypic selection and within-family genomic selection were up to 89% greater than half-sibling-family phenotypic selection alone. Genomic selection, an effective breeding tool used widely in plants and animals for improving low-heritability traits, has only recently been applied to forages. We explored the feasibility of implementing genomic selection in white clover (Trifolium repens L.), a key forage legume which has shown limited genetic improvement in dry matter yield (DMY) and persistence traits. We used data from a training population comprising 200 half-sibling (HS) families evaluated in a cattle-grazed field trial across three years and two locations. Combining phenotype and genotyping-by-sequencing (GBS) data, we assessed different two-stage genomic prediction models, including KGD-GBLUP developed for low-depth GBS data, on DMY, growth score, leaf size and stolon traits. Predictive abilities were similar among the models, ranging from -0.17 to 0.44 across traits, and remained stable for most traits when reducing model input to 100-120 HS families and 5500 markers, suggesting genomic selection is viable with fewer resources. Incorporating a correlated trait with a primary trait in multi-trait prediction models increased predictive ability by 28-124%. Deterministic modelling showed integrating among-HS-family phenotypic selection and within-family genomic selection at different selection pressures estimated up to 89% DMY genetic gain compared to phenotypic selection alone, despite a modest predictive ability of 0.3. This study demonstrates the potential benefits of combining genomic and phenotypic selection to boost genetic gains in white clover. Using cost-effective GBS paired with a prediction model optimized for low read-depth data, the approach can achieve prediction accuracies comparable to traditional models, providing a viable path for implementing genomic selection in white clover.
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Affiliation(s)
- O Grace Ehoche
- Grasslands Research Centre, AgResearch Ltd, Private Bag 11008, Palmerston North, 4442, New Zealand
- Massey University, Private Bag 11222, Palmerston North, 4442, New Zealand
- PGG-Wrightson Seeds , AgResearch Grasslands Research Centre, Palmerston North, New Zealand
| | - Sai Krishna Arojju
- Grasslands Research Centre, AgResearch Ltd, Private Bag 11008, Palmerston North, 4442, New Zealand
- Radiata Pine Breeding Company, University of Canterbury, Building EN27, Christchurch, 8041, New Zealand
| | - M Z Zulfi Jahufer
- Grasslands Research Centre, AgResearch Ltd, Private Bag 11008, Palmerston North, 4442, New Zealand
- School of Agriculture and Sustainable Food, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ruy Jauregui
- Grasslands Research Centre, AgResearch Ltd, Private Bag 11008, Palmerston North, 4442, New Zealand
- Animal Health Lab, Ministry for Primary Industries, Wallaceville, New Zealand
| | - Anna C Larking
- Grasslands Research Centre, AgResearch Ltd, Private Bag 11008, Palmerston North, 4442, New Zealand
| | - Greig Cousins
- PGG-Wrightson Seeds , AgResearch Grasslands Research Centre, Palmerston North, New Zealand
| | - Jennifer A Tate
- Massey University, Private Bag 11222, Palmerston North, 4442, New Zealand
| | - Peter J Lockhart
- Massey University, Private Bag 11222, Palmerston North, 4442, New Zealand
| | - Andrew G Griffiths
- Grasslands Research Centre, AgResearch Ltd, Private Bag 11008, Palmerston North, 4442, New Zealand.
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Boocock J, Alexander N, Tapia LA, Walter-McNeill L, Patel SP, Munugala C, Bloom JS, Kruglyak L. Single-cell eQTL mapping in yeast reveals a tradeoff between growth and reproduction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.07.570640. [PMID: 38106186 PMCID: PMC10723400 DOI: 10.1101/2023.12.07.570640] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Expression quantitative trait loci (eQTLs) provide a key bridge between noncoding DNA sequence variants and organismal traits. The effects of eQTLs can differ among tissues, cell types, and cellular states, but these differences are obscured by gene expression measurements in bulk populations. We developed a one-pot approach to map eQTLs in Saccharomyces cerevisiae by single-cell RNA sequencing (scRNA-seq) and applied it to over 100,000 single cells from three crosses. We used scRNA-seq data to genotype each cell, measure gene expression, and classify the cells by cell-cycle stage. We mapped thousands of local and distant eQTLs and identified interactions between eQTL effects and cell-cycle stages. We took advantage of single-cell expression information to identify hundreds of genes with allele-specific effects on expression noise. We used cell-cycle stage classification to map 20 loci that influence cell-cycle progression. One of these loci influenced the expression of genes involved in the mating response. We showed that the effects of this locus arise from a common variant (W82R) in the gene GPA1, which encodes a signaling protein that negatively regulates the mating pathway. The 82R allele increases mating efficiency at the cost of slower cell-cycle progression and is associated with a higher rate of outcrossing in nature. Our results provide a more granular picture of the effects of genetic variants on gene expression and downstream traits.
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Affiliation(s)
- James Boocock
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Noah Alexander
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Leslie Alamo Tapia
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Laura Walter-McNeill
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Shivani Prashant Patel
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Chetan Munugala
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Joshua S Bloom
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Leonid Kruglyak
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
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Prescott LA, Scholtens MR, Walker SP, Clarke SM, Dodds KG, Miller MR, Semmens JM, Carter CG, Symonds JE. Genetic parameters and genotype-by-environment interaction estimates for growth and feed efficiency related traits in Chinook salmon, Oncorhynchus tshawytscha, reared under low and moderate flow regimes. Genet Sel Evol 2024; 56:63. [PMID: 39266967 PMCID: PMC11396914 DOI: 10.1186/s12711-024-00929-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 08/23/2024] [Indexed: 09/14/2024] Open
Abstract
BACKGROUND A genotype-by-environment (G × E) interaction is defined as genotypes responding differently to different environments. In salmonids, G × E interactions can occur in different rearing conditions, including changes in salinity or temperature. However, water flow, an important variable that can influence metabolism, has yet to be considered for potential G × E interactions, although water flows differ across production stages. The salmonid industry is now manipulating flow in tanks to improve welfare and production performance, and expanding sea pen farming offshore, where flow dynamics are substantially greater. Therefore, there is a need to test whether G × E interactions occur under low and higher flow regimes to determine if industry should consider modifying their performance evaluation and selection criteria to account for different flow environments. Here, we used genotype-by-sequencing to create a genomic-relationship matrix of 37 Chinook salmon, Oncorhynchus tshawytscha, families to assess possible G × E interactions for production performance under two flow environments: a low flow regime (0.3 body lengths per second; bl s-1) and a moderate flow regime (0.8 bl s-1). RESULTS Genetic correlations for the same production performance trait between flow regimes suggest there is minimal evidence of a G × E interaction between the low and moderate flow regimes tested in this study, for Chinook salmon reared from 82.9 ± 16.8 g ( x ¯ ± s.d.) to 583.2 ± 117.1 g ( x ¯ ± s.d.). Estimates of genetic and phenotypic correlations between traits did not reveal any unfavorable trait correlations for size- (weight and condition factor) and growth-related traits, regardless of the flow regime, but did suggest measuring feed intake would be the preferred approach to improve feed efficiency because of the strong correlations between feed intake and feed efficiency, consistent with previous studies. CONCLUSION This new information suggests that Chinook salmon families do not need to be selected separately for performance across different flow regimes. However, further studies are needed to confirm this across a wider range of fish sizes and flows. This information is key for breeding programs to determine if separate evaluation groups are required for different flow regimes that are used for production (e.g., hatchery, post smolt recirculating aquaculture system, or offshore).
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Affiliation(s)
- Leteisha A Prescott
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, 7001, Australia.
- Blue Economy Cooperative Research Centre, PO Box 897, Launceston, TAS, 7250, Australia.
- Cawthron Institute, Nelson, 7010, New Zealand.
| | | | | | - Shannon M Clarke
- AgResearch, Invermay Agricultural Centre, Puddle Alley, Mosgiel, 9053, New Zealand
| | - Ken G Dodds
- AgResearch, Invermay Agricultural Centre, Puddle Alley, Mosgiel, 9053, New Zealand
| | - Matthew R Miller
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, 7001, Australia
- Cawthron Institute, Nelson, 7010, New Zealand
| | - Jayson M Semmens
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, 7001, Australia
| | - Chris G Carter
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, 7001, Australia
- Blue Economy Cooperative Research Centre, PO Box 897, Launceston, TAS, 7250, Australia
| | - Jane E Symonds
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, 7001, Australia
- Cawthron Institute, Nelson, 7010, New Zealand
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Croft L, Matheson P, Butterworth NJ, McGaughran A. Fitness consequences of population bottlenecks in an invasive blowfly. Mol Ecol 2024; 33:e17492. [PMID: 39136044 DOI: 10.1111/mec.17492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 07/14/2024] [Accepted: 08/02/2024] [Indexed: 08/28/2024]
Abstract
Invasive species often undergo demographic bottlenecks that cause a decrease in genetic diversity and associated reductions in population fitness. Despite this, they manage to thrive in novel environments. Investigating the effects of inbreeding and genetic bottlenecks on population fitness for invasive species is, therefore, key to understanding how they may survive in new environments. We used the blowfly Calliphora vicina (Sciences, Mathématiques et Physique, 1830, 2, 1), which is native to Europe and was introduced to Australia and New Zealand, to examine the effects of genetic diversity on population fitness. We first collected 59 samples from 15 populations across New Zealand and one in Australia, and used 20,501 biallelic SNPs to investigate population genomic diversity, structure and admixture. We then explored the impacts of repeated experimental bottlenecks on population fitness by creating inbred and outbred lines of C. vicina and measuring a variety of fitness traits. In wild-caught samples, we found low overall genetic diversity, signals of genetic admixture and limited (<3%) genetic differentiation between North and South Island populations, with genetic links between the South Island and Australia. Following experimental bottlenecks, we found significant reductions in fitness for inbred lines. However, fitness effects were not felt equally across all phenotypic traits. Moreover, they were not enough to cause population collapse in any experimental line, suggesting that C. vicina (when under relaxed selection, as in laboratory settings) may be able to compensate for population bottlenecks even when highly inbred. Our results demonstrate the value of a tractable experimental system for investigating processes that may facilitate or hamper biological invasion.
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Affiliation(s)
- Lilly Croft
- Te Aka Mātuatua - School of Science, University of Waikato, Hamilton, New Zealand
| | - Paige Matheson
- Te Aka Mātuatua - School of Science, University of Waikato, Hamilton, New Zealand
| | | | - Angela McGaughran
- Te Aka Mātuatua - School of Science, University of Waikato, Hamilton, New Zealand
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Wang X, Stein L, Black M, Kubenka K, Randall J, Ding C. Phenotypic diversity and population structure of Pecan (Carya illinoinensis) collections reveals geographic patterns. Sci Rep 2024; 14:18592. [PMID: 39127859 PMCID: PMC11316781 DOI: 10.1038/s41598-024-69521-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 08/06/2024] [Indexed: 08/12/2024] Open
Abstract
Pecan (Carya illinoinensis) is an economically important nut crop known for its genetic diversity and adaptability to various climates. Understanding the growth variability, phenological traits, and population structure of pecan populations is crucial for breeding programs and conservation. In this study, plant growth and phenological traits were evaluated over three consecutive seasons (2015-2017) for 550 genotypes from 26 provenances. Significant variations in plant height, stem diameter, and budbreak were observed among provenances, with Southern provenances exhibiting faster growth and earlier budbreak compared to Northern provenances. Population structure analysis using SNP markers revealed eight distinct subpopulations, reflecting genetic differentiation among provenances. Notably, Southern Mexico collections formed two separate clusters, while Western collections, such as 'Allen 3', 'Allen 4', and 'Riverside', were distinguished from others. 'Burkett' and 'Apache' were grouped together due to their shared maternal parentage. Principal component analysis and phylogenetic tree analysis further supported subpopulation differentiation. Genetic differentiation among the 26 populations was evident, with six clusters highly in agreement with the subpopulations identified by STRUCTURE and fastSTRUCTURE. Principal components analysis (PCA) revealed distinct groups, corresponding to subpopulations identified by genetic analysis. Discriminant analysis of PCA (DAPC) based on provenance origin further supported the genetic structure, with clear separation of provenances into distinct clusters. These findings provide valuable insights into the genetic diversity and growth patterns of pecan populations. Understanding the genetic basis of phenological traits and population structure is essential for selecting superior cultivars adapted to diverse environments. The identified subpopulations can guide breeding efforts to develop resilient rootstocks and contribute to the sustainable management of pecan genetic resources. Overall, this study enhances our understanding of pecan genetic diversity and informs conservation and breeding strategies for the long-term viability of pecan cultivation.
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Affiliation(s)
- Xinwang Wang
- USDA ARS Pecan Breeding & Genetics, College Station, TX, 77845, USA.
| | - Larry Stein
- Texas A&M University AgriLife Research and Extension Center, Uvalde, TX, 78802, USA
| | - Mark Black
- Texas A&M University AgriLife Research and Extension Center, Uvalde, TX, 78802, USA
| | - Keith Kubenka
- USDA ARS Pecan Breeding & Genetics, College Station, TX, 77845, USA
| | - Jennifer Randall
- Entomology, Plant Pathology, and Weed Science, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Chen Ding
- College of Forestry, Wildlife and Environment, Auburn University, Auburn, AL, 36849, USA
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9
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Bond DM, Veale A, Alexander A, Hore TA. Coat colour in marsupials: genetic variants at the ASIP locus determine grey and black fur of the brushtail possum. ROYAL SOCIETY OPEN SCIENCE 2024; 11:240806. [PMID: 39086822 PMCID: PMC11288674 DOI: 10.1098/rsos.240806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 07/05/2024] [Accepted: 07/05/2024] [Indexed: 08/02/2024]
Abstract
The possession of fur or hair is a defining characteristic of mammals and can occur in a variety of colours and patterns. While genetic determinants of coat colour are well described in eutherian 'placental' mammals, the other major mammalian infraclass, marsupials, is grossly understudied. The fur of the common brushtail possum (Trichosurus vulpecula), an iconic native mammal found throughout Australia and introduced into Aotearoa New Zealand, possesses two main colour morphs: grey and black. To identify genetic variants associated with coat colour, we performed a genome-wide association study (GWAS) with genotype by sequencing (GBS) data. Single nucleotide variants (SNVs) on chromosome 3, close to the agouti signalling protein (ASIP) gene that controls the temporal and spatial distribution of pigments in eutherian mammals, were identified. Fine-mapping identified a C>T variant at chr3:100483705 that results in a ASIP:p.Arg115Cys missense substitution, and animals homozygous for this variant have black fur. In addition to uncovering the first genetic determinant of coat colour in a natural marsupial population, comparative analysis of ASIP in divergent marsupial species identified the dasyurids as having accelerated evolution, reflecting their well described diversity of coat colour and pattern.
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Affiliation(s)
- Donna M. Bond
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Andrew Veale
- Manaaki Whenua—Landcare Research, Lincoln, New Zealand
| | - Alana Alexander
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Timothy A. Hore
- Department of Anatomy, University of Otago, Dunedin, New Zealand
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10
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Kardos M, Waples RS. Low-coverage sequencing and Wahlund effect severely bias estimates of inbreeding, heterozygosity and effective population size in North American wolves. Mol Ecol 2024:e17415. [PMID: 38785346 DOI: 10.1111/mec.17415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 05/03/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024]
Abstract
vonHoldt et al. ((2024), Molecular Ecology, 33, e17231) (vH24) used low-coverage (average ~ 7X read depth) restriction site-associated DNA sequence data to estimate individual inbreeding and heterozygosity, and recent effective population size (Ne), in Great Lakes (GL) and Northern Rocky Mountain (RM) wolves. They concluded that RM heterozygosity rapidly declined between 1991 and 2020, and that Ne declined substantially in GL and RM over the last 50 generations. Here, we evaluate the effects of low sequence coverage and sampling strategy on vH24's findings and provide general recommendations for using sequence data to evaluate inbreeding, heterozygosity and Ne. Low-coverage sequencing resulted in downwardly biased estimates of individual inbreeding and heterozygosity, and an erroneous large temporal decline in RM heterozygosity due to declining read depth through time. Additionally, vH24's sampling strategy-which combined individuals from several genetically differentiated populations and across at least eight wolf generations-is expected to have resulted in severe downward bias in estimates of recent Ne for RM. We recommend using high-coverage sequence data (≥ $$ \ge $$ 15-20X) to estimate inbreeding and heterozygosity. Carefully filtering individuals, loci and genotypes, and using genotype imputation or likelihoods can help to minimise bias when low-coverage sequence data must be used. For estimation of contemporary Ne, the marginal benefits of using more than 103-104 loci are small, so aggressive filtering of loci with low average read depth potentially can retain most individuals without sacrificing much precision. Individuals are relatively more valuable than loci because analyses of contemporary Ne should focus on roughly single-generation samples from local breeding populations.
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Affiliation(s)
- Marty Kardos
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, USA
| | - Robin S Waples
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, USA
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11
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Moran IG, Loo YY, Louca S, Young NBA, Whibley A, Withers SJ, Salloum PM, Hall ML, Stanley MC, Cain KE. Vocal convergence and social proximity shape the calls of the most basal Passeriformes, New Zealand Wrens. Commun Biol 2024; 7:575. [PMID: 38750083 PMCID: PMC11096322 DOI: 10.1038/s42003-024-06253-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 04/26/2024] [Indexed: 05/18/2024] Open
Abstract
Despite extensive research on avian vocal learning, we still lack a general understanding of how and when this ability evolved in birds. As the closest living relatives of the earliest Passeriformes, the New Zealand wrens (Acanthisitti) hold a key phylogenetic position for furthering our understanding of the evolution of vocal learning because they share a common ancestor with two vocal learners: oscines and parrots. However, the vocal learning abilities of New Zealand wrens remain unexplored. Here, we test for the presence of prerequisite behaviors for vocal learning in one of the two extant species of New Zealand wrens, the rifleman (Acanthisitta chloris). We detect the presence of unique individual vocal signatures and show how these signatures are shaped by social proximity, as demonstrated by group vocal signatures and strong acoustic similarities among distantly related individuals in close social proximity. Further, we reveal that rifleman calls share similar phenotypic variance ratios to those previously reported in the learned vocalizations of the zebra finch, Taeniopygia guttata. Together these findings provide strong evidence that riflemen vocally converge, and though the mechanism still remains to be determined, they may also suggest that this vocal convergence is the result of rudimentary vocal learning abilities.
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Affiliation(s)
- Ines G Moran
- School of Biological Sciences, University of Auckland, Auckland, 1142, Aotearoa New Zealand.
- Centre for Biodiversity and Biosecurity, University of Auckland, Auckland, 1142, Aotearoa New Zealand.
| | - Yen Yi Loo
- School of Biological Sciences, University of Auckland, Auckland, 1142, Aotearoa New Zealand
- Centre for Biodiversity and Biosecurity, University of Auckland, Auckland, 1142, Aotearoa New Zealand
| | - Stilianos Louca
- Department of Biology, University of Oregon, Eugene, 97403-1210, OR, USA
| | - Nick B A Young
- Centre for eResearch, University of Auckland, Auckland, 1142, Aotearoa New Zealand
| | - Annabel Whibley
- School of Biological Sciences, University of Auckland, Auckland, 1142, Aotearoa New Zealand
| | - Sarah J Withers
- School of Biological Sciences, University of Auckland, Auckland, 1142, Aotearoa New Zealand
| | - Priscila M Salloum
- Department of Zoology, University of Otago, Dunedin, 9016, Aotearoa New Zealand
| | - Michelle L Hall
- School of BioSciences, University of Melbourne, Melbourne, VIC, 3010, Australia
- Bush Heritage Australia, Melbourne, VIC, 3000, Australia
- School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia
| | - Margaret C Stanley
- School of Biological Sciences, University of Auckland, Auckland, 1142, Aotearoa New Zealand
- Centre for Biodiversity and Biosecurity, University of Auckland, Auckland, 1142, Aotearoa New Zealand
| | - Kristal E Cain
- School of Biological Sciences, University of Auckland, Auckland, 1142, Aotearoa New Zealand
- Centre for Biodiversity and Biosecurity, University of Auckland, Auckland, 1142, Aotearoa New Zealand
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12
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Bilton TP, Sharma SK, Schofield MR, Black MA, Jacobs JME, Bryan GJ, Dodds KG. Construction of relatedness matrices in autopolyploid populations using low-depth high-throughput sequencing data. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:64. [PMID: 38430392 PMCID: PMC10908621 DOI: 10.1007/s00122-024-04568-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 01/30/2024] [Indexed: 03/03/2024]
Abstract
KEY MESSAGE An improved estimator of genomic relatedness using low-depth high-throughput sequencing data for autopolyploids is developed. Its outputs strongly correlate with SNP array-based estimates and are available in the package GUSrelate. High-throughput sequencing (HTS) methods have reduced sequencing costs and resources compared to array-based tools, facilitating the investigation of many non-model polyploid species. One important quantity that can be computed from HTS data is the genetic relatedness between all individuals in a population. However, HTS data are often messy, with multiple sources of errors (i.e. sequencing errors or missing parental alleles) which, if not accounted for, can lead to bias in genomic relatedness estimates. We derive a new estimator for constructing a genomic relationship matrix (GRM) from HTS data for autopolyploid species that accounts for errors associated with low sequencing depths, implemented in the R package GUSrelate. Simulations revealed that GUSrelate performed similarly to existing GRM methods at high depth but reduced bias in self-relatedness estimates when the sequencing depth was low. Using a panel consisting of 351 tetraploid potato genotypes, we found that GUSrelate produced GRMs from genotyping-by-sequencing (GBS) data that were highly correlated with a GRM computed from SNP array data, and less biased than existing methods when benchmarking against the array-based GRM estimates. GUSrelate provides researchers with a tool to reliably construct GRMs from low-depth HTS data.
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Affiliation(s)
- Timothy P Bilton
- AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand.
- Department of Mathematics and Statistics, University of Otago, Dunedin, New Zealand.
| | - Sanjeev Kumar Sharma
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, UK
| | - Matthew R Schofield
- Department of Mathematics and Statistics, University of Otago, Dunedin, New Zealand
| | - Michael A Black
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | | | - Glenn J Bryan
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, UK
| | - Ken G Dodds
- AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
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13
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Volkova NA, Romanov MN, Abdelmanova AS, Larionova PV, German NY, Vetokh AN, Shakhin AV, Volkova LA, Sermyagin AA, Anshakov DV, Fisinin VI, Griffin DK, Sölkner J, Brem G, McEwan JC, Brauning R, Zinovieva NA. Genome-Wide Association Study Revealed Putative SNPs and Candidate Genes Associated with Growth and Meat Traits in Japanese Quail. Genes (Basel) 2024; 15:294. [PMID: 38540354 PMCID: PMC10970133 DOI: 10.3390/genes15030294] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/08/2024] [Accepted: 02/23/2024] [Indexed: 06/14/2024] Open
Abstract
The search for SNPs and candidate genes that determine the manifestation of major selected traits is one crucial objective for genomic selection aimed at increasing poultry production efficiency. Here, we report a genome-wide association study (GWAS) for traits characterizing meat performance in the domestic quail. A total of 146 males from an F2 reference population resulting from crossing a fast (Japanese) and a slow (Texas White) growing breed were examined. Using the genotyping-by-sequencing technique, genomic data were obtained for 115,743 SNPs (92,618 SNPs after quality control) that were employed in this GWAS. The results identified significant SNPs associated with the following traits at 8 weeks of age: body weight (nine SNPs), daily body weight gain (eight SNPs), dressed weight (33 SNPs), and weights of breast (18 SNPs), thigh (eight SNPs), and drumstick (three SNPs). Also, 12 SNPs and five candidate genes (GNAL, DNAJC6, LEPR, SPAG9, and SLC27A4) shared associations with three or more traits. These findings are consistent with the understanding of the genetic complexity of body weight-related traits in quail. The identified SNPs and genes can be used in effective quail breeding as molecular genetic markers for growth and meat characteristics for the purpose of genetic improvement.
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Affiliation(s)
- Natalia A. Volkova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.); (A.A.S.)
| | - Michael N. Romanov
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.); (A.A.S.)
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, Kent, UK;
| | - Alexandra S. Abdelmanova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.); (A.A.S.)
| | - Polina V. Larionova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.); (A.A.S.)
| | - Nadezhda Yu. German
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.); (A.A.S.)
| | - Anastasia N. Vetokh
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.); (A.A.S.)
| | - Alexey V. Shakhin
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.); (A.A.S.)
| | - Ludmila A. Volkova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.); (A.A.S.)
| | - Alexander A. Sermyagin
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.); (A.A.S.)
| | - Dmitry V. Anshakov
- Breeding and Genetic Center “Zagorsk Experimental Breeding Farm”—Branch of the Federal Research Center “All-Russian Poultry Research and Technological Institute”, Russian Academy of Sciences, Sergiev Posad 141311, Moscow Oblast, Russia;
| | - Vladimir I. Fisinin
- Federal Research Center “All-Russian Poultry Research and Technological Institute” of the Russian Academy of Sciences, Sergiev Posad 141311, Moscow Oblast, Russia;
| | - Darren K. Griffin
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, Kent, UK;
| | - Johann Sölkner
- Institute of Livestock Sciences (NUWI), University of Natural Resources and Life Sciences Vienna, 1180 Vienna, Austria;
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, 1210 Vienna, Austria;
| | - John C. McEwan
- AgResearch, Invermay Agricultural Centre, Mosgiel 9053, New Zealand; (J.C.M.); (R.B.)
| | - Rudiger Brauning
- AgResearch, Invermay Agricultural Centre, Mosgiel 9053, New Zealand; (J.C.M.); (R.B.)
| | - Natalia A. Zinovieva
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.); (A.A.S.)
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14
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Croft L, Matheson P, Flemming C, Butterworth NJ, McGaughran A. Population structure and interspecific hybridisation of two invasive blowflies (Diptera: Calliphoridae) following replicated incursions into New Zealand. Ecol Evol 2024; 14:e10832. [PMID: 38192906 PMCID: PMC10772223 DOI: 10.1002/ece3.10832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 01/10/2024] Open
Abstract
Rates of biological invasion are increasing globally, with associated negative effects on native biodiversity and ecosystem services. Among other genetic processes, hybridisation can facilitate invasion by producing new combinations of genetic variation that increase adaptive potential and associated population fitness. Yet the role of hybridisation (and resulting gene flow) in biological invasion in invertebrate species is under-studied. Calliphora hilli and Calliphora stygia are blowflies proposed to have invaded New Zealand separately from Australia between 1779 and 1841, and are now widespread throughout the country. Here, we analysed genome-wide single nucleotide polymorphisms (SNPs), generating genotyping-by-sequencing data for 154 individuals collected from 24 populations across New Zealand and Australia to assess the extent of gene flow and hybridisation occurring within and between these blowflies and to better understand their overall population structure. We found that New Zealand populations of both species had weak genetic structure, suggesting high gene flow and an absence of dispersal limitations across the country. We also found evidence that interspecific hybridisation is occurring in the wild between C. hilli and C. stygia in both the native and invasive ranges, and that intraspecific admixture is occurring among populations at appreciable rates. Collectively, these findings provide new insights into the population structure of these two invasive invertebrates and highlight the potential importance of hybridisation and gene flow in biological invasion.
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Affiliation(s)
- Lilly Croft
- Te Aka Mātuatua – School of ScienceUniversity of WaikatoHamiltonNew Zealand
| | - Paige Matheson
- Te Aka Mātuatua – School of ScienceUniversity of WaikatoHamiltonNew Zealand
| | - Chloe Flemming
- Te Aka Mātuatua – School of ScienceUniversity of WaikatoHamiltonNew Zealand
| | | | - Angela McGaughran
- Te Aka Mātuatua – School of ScienceUniversity of WaikatoHamiltonNew Zealand
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15
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McGuinness CF, Black MA, Dunbier AK. Restriction site associated DNA sequencing for tumour mutation burden estimation and mutation signature analysis. Cancer Med 2023; 12:21545-21560. [PMID: 37974533 PMCID: PMC10726921 DOI: 10.1002/cam4.6711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 11/05/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND Genome-wide measures of genetic disruption such as tumour mutation burden (TMB) and mutation signatures are emerging as useful biomarkers to stratify patients for treatment. Clinicians commonly use cancer gene panels for tumour mutation burden estimation, and whole genome sequencing is the gold standard for mutation signature analysis. However, the accuracy and cost associated with these assays limits their utility at scale. METHODS WGS data from 560 breast cancer patients was used for in silico library simulations to evaluate the accuracy of an FDA approved cancer gene panel as well as restriction enzyme associated DNA sequencing (RADseq) libraries for TMB estimation and mutation signature analysis. We also transfected a mouse mammary cell line with APOBEC enzymes and sequenced resulting clones to evaluate the efficacy of RADseq in an experimental setting. RESULTS RADseq had improved accuracy of TMB estimation and derivation of mutation profiles when compared to the FDA approved cancer panel. Using simulated immune checkpoint blockade (ICB) trials, we show that inaccurate TMB estimation leads to a reduction in power for deriving an optimal TMB cutoff to stratify patients for immune checkpoint blockade treatment. Additionally, prioritisation of APOBEC hypermutated tumours in these trials optimises TMB cutoff determination for breast cancer. The utility of RADseq in an experimental setting was also demonstrated, based on characterisation of an APOBEC mutation signature in an APOBEC3A transfected mouse cell line. CONCLUSION In conclusion, our work demonstrates that RADseq has the potential to be used as a cost-effective, accurate solution for TMB estimation and mutation signature analysis by both clinicians and basic researchers.
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Affiliation(s)
- Conor F. McGuinness
- Department of BiochemistryUniversity of OtagoDunedinNew Zealand
- Peter MacCallum Cancer CentreMelbourneVictoriaAustralia
- Sir Peter MacCallum Department of OncologyThe University of MelbourneMelbourneVictoriaAustralia
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16
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Volkova NA, Romanov MN, Abdelmanova AS, Larionova PV, German NY, Vetokh AN, Shakhin AV, Volkova LA, Anshakov DV, Fisinin VI, Narushin VG, Griffin DK, Sölkner J, Brem G, McEwan JC, Brauning R, Zinovieva NA. Genotyping-by-Sequencing Strategy for Integrating Genomic Structure, Diversity and Performance of Various Japanese Quail ( Coturnix japonica) Breeds. Animals (Basel) 2023; 13:3439. [PMID: 38003057 PMCID: PMC10668688 DOI: 10.3390/ani13223439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/23/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
Traces of long-term artificial selection can be detected in genomes of domesticated birds via whole-genome screening using single-nucleotide polymorphism (SNP) markers. This study thus examined putative genomic regions under selection that are relevant to the development history, divergence and phylogeny among Japanese quails of various breeds and utility types. We sampled 99 birds from eight breeds (11% of the global gene pool) of egg (Japanese, English White, English Black, Tuxedo and Manchurian Golden), meat (Texas White and Pharaoh) and dual-purpose (Estonian) types. The genotyping-by-sequencing analysis was performed for the first time in domestic quails, providing 62,935 SNPs. Using principal component analysis, Neighbor-Net and Admixture algorithms, the studied breeds were characterized according to their genomic architecture, ancestry and direction of selective breeding. Japanese and Pharaoh breeds had the smallest number and length of homozygous segments indicating a lower selective pressure. Tuxedo and Texas White breeds showed the highest values of these indicators and genomic inbreeding suggesting a greater homozygosity. We revealed evidence for the integration of genomic and performance data, and our findings are applicable for elucidating the history of creation and genomic variability in quail breeds that, in turn, will be useful for future breeding improvement strategies.
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Affiliation(s)
- Natalia A. Volkova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
| | - Michael N. Romanov
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK;
| | - Alexandra S. Abdelmanova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
| | - Polina V. Larionova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
| | - Nadezhda Yu. German
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
| | - Anastasia N. Vetokh
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
| | - Alexey V. Shakhin
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
| | - Ludmila A. Volkova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
| | - Dmitry V. Anshakov
- Breeding and Genetic Center Zagorsk Experimental Breeding Farm—Branch of the Federal Research Centre, All-Russian Poultry Research and Technological Institute, Russian Academy of Sciences, Sergiev Posad 141311, Moscow Oblast, Russia;
| | - Vladimir I. Fisinin
- Federal Research Center “All-Russian Poultry Research and Technological Institute” of the Russian Academy of Sciences, Sergiev Posad 141311, Moscow Oblast, Russia;
| | - Valeriy G. Narushin
- Research Institute for Environment Treatment, 69032 Zaporizhya, Ukraine;
- Vita-Market Co., Ltd., 69032 Zaporizhya, Ukraine
| | - Darren K. Griffin
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK;
| | - Johann Sölkner
- Institute of Livestock Sciences (NUWI), University of Natural Resources and Life Sciences Vienna, 1180 Vienna, Austria;
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, 1210 Vienna, Austria;
| | - John C. McEwan
- AgResearch, Invermay Agricultural Centre, Mosgiel 9053, New Zealand; (J.C.M.); (R.B.)
| | - Rudiger Brauning
- AgResearch, Invermay Agricultural Centre, Mosgiel 9053, New Zealand; (J.C.M.); (R.B.)
| | - Natalia A. Zinovieva
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
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17
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Guhlin J, Le Lec MF, Wold J, Koot E, Winter D, Biggs PJ, Galla SJ, Urban L, Foster Y, Cox MP, Digby A, Uddstrom LR, Eason D, Vercoe D, Davis T, Howard JT, Jarvis ED, Robertson FE, Robertson BC, Gemmell NJ, Steeves TE, Santure AW, Dearden PK. Species-wide genomics of kākāpō provides tools to accelerate recovery. Nat Ecol Evol 2023; 7:1693-1705. [PMID: 37640765 DOI: 10.1038/s41559-023-02165-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 07/11/2023] [Indexed: 08/31/2023]
Abstract
The kākāpō is a critically endangered, intensively managed, long-lived nocturnal parrot endemic to Aotearoa New Zealand. We generated and analysed whole-genome sequence data for nearly all individuals living in early 2018 (169 individuals) to generate a high-quality species-wide genetic variant callset. We leverage extensive long-term metadata to quantify genome-wide diversity of the species over time and present new approaches using probabilistic programming, combined with a phenotype dataset spanning five decades, to disentangle phenotypic variance into environmental and genetic effects while quantifying uncertainty in small populations. We find associations for growth, disease susceptibility, clutch size and egg fertility within genic regions previously shown to influence these traits in other species. Finally, we generate breeding values to predict phenotype and illustrate that active management over the past 45 years has maintained both genome-wide diversity and diversity in breeding values and, hence, evolutionary potential. We provide new pathways for informing future conservation management decisions for kākāpō, including prioritizing individuals for translocation and monitoring individuals with poor growth or high disease risk. Overall, by explicitly addressing the challenge of the small sample size, we provide a template for the inclusion of genomic data that will be transformational for species recovery efforts around the globe.
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Affiliation(s)
- Joseph Guhlin
- Genomics Aotearoa, Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, Aotearoa New Zealand
| | - Marissa F Le Lec
- Genomics Aotearoa, Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, Aotearoa New Zealand
| | - Jana Wold
- School of Biological Sciences, University of Canterbury, Christchurch, Aotearoa New Zealand
| | - Emily Koot
- The New Zealand Institute for Plant and Food Research Ltd, Palmerston North, Aotearoa New Zealand
| | - David Winter
- School of Natural Sciences, Massey University, Palmerston North, Aotearoa New Zealand
| | - Patrick J Biggs
- School of Natural Sciences, Massey University, Palmerston North, Aotearoa New Zealand
- School of Veterinary Science, Massey University, Palmerston North, Aotearoa New Zealand
| | - Stephanie J Galla
- School of Biological Sciences, University of Canterbury, Christchurch, Aotearoa New Zealand
- Department of Biological Sciences, Boise State University, Boise, ID, USA
| | - Lara Urban
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, Aotearoa New Zealand
- Helmholtz Pioneer Campus, Helmholtz Zentrum Muenchen, Neuherberg, Germany
- Helmholtz AI, Helmholtz Zentrum Muenchen, Neuherberg, Germany
- School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Yasmin Foster
- Department of Zoology, University of Otago, Dunedin, Aotearoa New Zealand
| | - Murray P Cox
- School of Natural Sciences, Massey University, Palmerston North, Aotearoa New Zealand
- Department of Statistics, University of Auckland, Auckland, Aotearoa New Zealand
| | - Andrew Digby
- Kākāpō Recovery Programme, Department of Conservation, Invercargill, Aotearoa New Zealand
| | - Lydia R Uddstrom
- Kākāpō Recovery Programme, Department of Conservation, Invercargill, Aotearoa New Zealand
| | - Daryl Eason
- Kākāpō Recovery Programme, Department of Conservation, Invercargill, Aotearoa New Zealand
| | - Deidre Vercoe
- Kākāpō Recovery Programme, Department of Conservation, Invercargill, Aotearoa New Zealand
| | - Tāne Davis
- Rakiura Tītī Islands Administering Body, Invercargill, Aotearoa New Zealand
| | - Jason T Howard
- Neurogenetics of Language Lab, The Rockefeller University, New York, NY, USA
- Mirxes, Cambridge, MA, USA
| | - Erich D Jarvis
- The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Fiona E Robertson
- Department of Zoology, University of Otago, Dunedin, Aotearoa New Zealand
| | - Bruce C Robertson
- Department of Zoology, University of Otago, Dunedin, Aotearoa New Zealand
| | - Neil J Gemmell
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, Aotearoa New Zealand
| | - Tammy E Steeves
- School of Biological Sciences, University of Canterbury, Christchurch, Aotearoa New Zealand
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, Aotearoa New Zealand
| | - Peter K Dearden
- Genomics Aotearoa, Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, Aotearoa New Zealand.
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18
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Hess MK, Hodgkinson HE, Hess AS, Zetouni L, Budel JCC, Henry H, Donaldson A, Bilton TP, van Stijn TC, Kirk MR, Dodds KG, Brauning R, McCulloch AF, Hickey SM, Johnson PL, Jonker A, Morton N, Hendy S, Oddy VH, Janssen PH, McEwan JC, Rowe SJ. Large-scale analysis of sheep rumen metagenome profiles captured by reduced representation sequencing reveals individual profiles are influenced by the environment and genetics of the host. BMC Genomics 2023; 24:551. [PMID: 37723422 PMCID: PMC10506323 DOI: 10.1186/s12864-023-09660-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 09/07/2023] [Indexed: 09/20/2023] Open
Abstract
BACKGROUND Producing animal protein while reducing the animal's impact on the environment, e.g., through improved feed efficiency and lowered methane emissions, has gained interest in recent years. Genetic selection is one possible path to reduce the environmental impact of livestock production, but these traits are difficult and expensive to measure on many animals. The rumen microbiome may serve as a proxy for these traits due to its role in feed digestion. Restriction enzyme-reduced representation sequencing (RE-RRS) is a high-throughput and cost-effective approach to rumen metagenome profiling, but the systematic (e.g., sequencing) and biological factors influencing the resulting reference based (RB) and reference free (RF) profiles need to be explored before widespread industry adoption is possible. RESULTS Metagenome profiles were generated by RE-RRS of 4,479 rumen samples collected from 1,708 sheep, and assigned to eight groups based on diet, age, time off feed, and country (New Zealand or Australia) at the time of sample collection. Systematic effects were found to have minimal influence on metagenome profiles. Diet was a major driver of differences between samples, followed by time off feed, then age of the sheep. The RF approach resulted in more reads being assigned per sample and afforded greater resolution when distinguishing between groups than the RB approach. Normalizing relative abundances within the sampling Cohort abolished structures related to age, diet, and time off feed, allowing a clear signal based on methane emissions to be elucidated. Genus-level abundances of rumen microbes showed low-to-moderate heritability and repeatability and were consistent between diets. CONCLUSIONS Variation in rumen metagenomic profiles was influenced by diet, age, time off feed and genetics. Not accounting for environmental factors may limit the ability to associate the profile with traits of interest. However, these differences can be accounted for by adjusting for Cohort effects, revealing robust biological signals. The abundances of some genera were consistently heritable and repeatable across different environments, suggesting that metagenomic profiles could be used to predict an individual's future performance, or performance of its offspring, in a range of environments. These results highlight the potential of using rumen metagenomic profiles for selection purposes in a practical, agricultural setting.
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Affiliation(s)
- Melanie K Hess
- AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand.
| | - Hannah E Hodgkinson
- AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Andrew S Hess
- AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
- Agriculture, Veterinary & Rangeland Sciences, University of Nevada-Reno, 1664 N. Virginia St. Mail stop 202, Reno, NV, 89557, USA
| | - Larissa Zetouni
- AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
- Wageningen University & Research, P.O. Box 338, 6700, AH, Wageningen, The Netherlands
| | - Juliana C C Budel
- AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
- Graduate Program in Animal Science, Universidade Federal do Pará (UFPa), Castanhal, Brazil
| | - Hannah Henry
- AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Alistair Donaldson
- NSW Department of Primary Industries, University of New England, Armidale, 2351, Australia
| | - Timothy P Bilton
- AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Tracey C van Stijn
- AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Michelle R Kirk
- AgResearch Ltd., Grasslands Research Centre, Private Bag 11,008, Palmerston North, 4410, New Zealand
| | - Ken G Dodds
- AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Rudiger Brauning
- AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Alan F McCulloch
- AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Sharon M Hickey
- AgResearch Ltd., Ruakura Research Centre, Private Bag 3115, Hamilton, 3214, New Zealand
| | - Patricia L Johnson
- AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Arjan Jonker
- AgResearch Ltd., Grasslands Research Centre, Private Bag 11,008, Palmerston North, 4410, New Zealand
| | - Nickolas Morton
- Te Pūnaha Matatini, University of Auckland, Auckland, 1010, New Zealand
| | - Shaun Hendy
- Te Pūnaha Matatini, University of Auckland, Auckland, 1010, New Zealand
| | - V Hutton Oddy
- NSW Department of Primary Industries, University of New England, Armidale, 2351, Australia
| | - Peter H Janssen
- AgResearch Ltd., Grasslands Research Centre, Private Bag 11,008, Palmerston North, 4410, New Zealand
| | - John C McEwan
- AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Suzanne J Rowe
- AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
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19
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Moravčíková N, Kasarda R, Židek R, McEwan JC, Brauning R, Landete-Castillejos T, Chonco L, Ciberej J, Pokorádi J. Traces of Human-Mediated Selection in the Gene Pool of Red Deer Populations. Animals (Basel) 2023; 13:2525. [PMID: 37570333 PMCID: PMC10417186 DOI: 10.3390/ani13152525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 07/27/2023] [Accepted: 07/30/2023] [Indexed: 08/13/2023] Open
Abstract
In this study, we analysed the effect of human-mediated selection on the gene pool of wild and farmed red deer populations based on genotyping-by-sequencing data. The farmed red deer sample covered populations spread across seven countries and two continents (France, Germany, Hungary, Latvia, New Zealand, Poland, and Slovakia). The Slovak and Spain wild red deer populations (the latter one in a large game estate) were used as control outgroups. The gene flow intensity, relationship and admixture among populations were tested by the Bayesian approach and discriminant analysis of principal components (DAPC). The highest gene diversity (He = 0.19) and the lowest genomic inbreeding (FHOM = 0.04) found in Slovak wild population confirmed our hypothesis that artificial selection accompanied by bottlenecks has led to the increase in overall genomic homozygosity. The Bayesian approach and DAPC consistently identified three separate genetic groups. As expected, the farmed populations were clustered together, while the Slovak and Spanish populations formed two separate clusters. Identified traces of genetic admixture in the gene pool of farmed populations reflected a strong contemporary migration rate between them. This study suggests that even if the history of deer farming has been shorter than traditional livestock species, it may leave significant traces in the genome structure.
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Affiliation(s)
- Nina Moravčíková
- Faculty of Agrobiology and Food Resources, Slovak University of Agriculture, 949 76 Nitra, Slovakia;
| | - Radovan Kasarda
- Faculty of Agrobiology and Food Resources, Slovak University of Agriculture, 949 76 Nitra, Slovakia;
| | - Radoslav Židek
- Faculty of Agrobiology and Food Resources, Slovak University of Agriculture, 949 76 Nitra, Slovakia;
| | - John Colin McEwan
- AgResearch, Invermay Agricultural Research Centre, Mosgiel 9024, New Zealand; (J.C.M.); (R.B.)
| | - Rudiger Brauning
- AgResearch, Invermay Agricultural Research Centre, Mosgiel 9024, New Zealand; (J.C.M.); (R.B.)
| | - Tomás Landete-Castillejos
- Instituto de Recursos Cinegéticos-Instituto de Desarrollo Regional, University of Castilla-La Mancha, 02071 Albacete, Spain; (T.L.-C.); (L.C.)
| | - Louis Chonco
- Instituto de Recursos Cinegéticos-Instituto de Desarrollo Regional, University of Castilla-La Mancha, 02071 Albacete, Spain; (T.L.-C.); (L.C.)
| | - Juraj Ciberej
- Department of Breeding and Diseases of Game, Fish and Bees, Ecology and Cynology, University of Veterinary Medicine and Pharmacy, 041 81 Košice, Slovakia
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20
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Herry F, Hérault F, Lecerf F, Lagoutte L, Doublet M, Picard-Druet D, Bardou P, Varenne A, Burlot T, Le Roy P, Allais S. Restriction site-associated DNA sequencing technologies as an alternative to low-density SNP chips for genomic selection: a simulation study in layer chickens. BMC Genomics 2023; 24:271. [PMID: 37208589 DOI: 10.1186/s12864-023-09321-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 04/18/2023] [Indexed: 05/21/2023] Open
Abstract
BACKGROUND To reduce the cost of genomic selection, a low-density (LD) single nucleotide polymorphism (SNP) chip can be used in combination with imputation for genotyping selection candidates instead of using a high-density (HD) SNP chip. Next-generation sequencing (NGS) techniques have been increasingly used in livestock species but remain expensive for routine use for genomic selection. An alternative and cost-efficient solution is to use restriction site-associated DNA sequencing (RADseq) techniques to sequence only a fraction of the genome using restriction enzymes. From this perspective, use of RADseq techniques followed by an imputation step on HD chip as alternatives to LD chips for genomic selection was studied in a pure layer line. RESULTS Genome reduction and sequencing fragments were identified on reference genome using four restriction enzymes (EcoRI, TaqI, AvaII and PstI) and a double-digest RADseq (ddRADseq) method (TaqI-PstI). The SNPs contained in these fragments were detected from the 20X sequence data of the individuals in our population. Imputation accuracy on HD chip with these genotypes was assessed as the mean correlation between true and imputed genotypes. Several production traits were evaluated using single-step GBLUP methodology. The impact of imputation errors on the ranking of the selection candidates was assessed by comparing a genomic evaluation based on ancestry using true HD or imputed HD genotyping. The relative accuracy of genomic estimated breeding values (GEBVs) was investigated by considering the GEBVs estimated on offspring as a reference. With AvaII or PstI and ddRADseq with TaqI and PstI, more than 10 K SNPs were detected in common with the HD SNP chip, resulting in an imputation accuracy greater than 0.97. The impact of imputation errors on genomic evaluation of the breeders was reduced, with a Spearman correlation greater than 0.99. Finally, the relative accuracy of GEBVs was equivalent. CONCLUSIONS RADseq approaches can be interesting alternatives to low-density SNP chips for genomic selection. With more than 10 K SNPs in common with the SNPs of the HD SNP chip, good imputation and genomic evaluation results can be obtained. However, with real data, heterogeneity between individuals with missing data must be considered.
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Affiliation(s)
- Florian Herry
- NOVOGEN, 5 rue des Compagnons, Secteur du Vau Ballier, Plédran, 22960, France
- PEGASE, INRAE, Institut Agro, Saint-Gilles, 35590, France
| | | | | | | | | | | | - Philippe Bardou
- SIGENAE, GenPhySE, Université de Toulouse, INRA, ENVT, 24 chemin de Borde-Rouge - Auzeville Tolosane, Castanet Tolosan, 31326, France
| | - Amandine Varenne
- NOVOGEN, 5 rue des Compagnons, Secteur du Vau Ballier, Plédran, 22960, France
| | - Thierry Burlot
- NOVOGEN, 5 rue des Compagnons, Secteur du Vau Ballier, Plédran, 22960, France
| | - Pascale Le Roy
- PEGASE, INRAE, Institut Agro, Saint-Gilles, 35590, France
| | - Sophie Allais
- PEGASE, INRAE, Institut Agro, Saint-Gilles, 35590, France.
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21
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Digby A, Eason D, Catalina A, Lierz M, Galla S, Urban L, Le Lec MF, Guhlin J, Steeves TE, Dearden PK, Joustra T, Lees C, Davis T, Vercoe D, Kākāpō Recovery Team. Hidden impacts of conservation management on fertility of the critically endangered kākāpō. PeerJ 2023; 11:e14675. [PMID: 36755872 PMCID: PMC9901309 DOI: 10.7717/peerj.14675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 12/11/2022] [Indexed: 02/05/2023] Open
Abstract
Background Animal conservation often requires intensive management actions to improve reproductive output, yet any adverse effects of these may not be immediately apparent, particularly in threatened species with small populations and long lifespans. Hand-rearing is an example of a conservation management strategy which, while boosting populations, can cause long-term demographic and behavioural problems. It is used in the recovery of the critically endangered kākāpō (Strigops habroptilus), a flightless parrot endemic to New Zealand, to improve the slow population growth that is due to infrequent breeding, low fertility and low hatching success. Methods We applied Bayesian mixed models to examine whether hand-rearing and other factors were associated with clutch fertility in kākāpō. We used projection predictive variable selection to compare the relative contributions to fertility from the parents' rearing environment, their age and previous copulation experience, the parental kinship, and the number of mates and copulations for each clutch. We also explored how the incidence of repeated copulations and multiple mates varied with kākāpō density. Results The rearing status of the clutch father and the number of mates and copulations of the clutch mother were the dominant factors in predicting fertility. Clutches were less likely to be fertile if the father was hand-reared compared to wild-reared, but there was no similar effect for mothers. Clutches produced by females copulating with different males were more likely to be fertile than those from repeated copulations with one male, which in turn had a higher probability of fertility than those from a single copulation. The likelihood of multiple copulations and mates increased with female:male adult sex ratio, perhaps as a result of mate guarding by females. Parental kinship, copulation experience and age all had negligible associations with clutch fertility. Conclusions These results provide a rare assessment of factors affecting fertility in a wild threatened bird species, with implications for conservation management. The increased fertility due to multiple mates and copulations, combined with the evidence for mate guarding and previous results of kākāpō sperm morphology, suggests that an evolutionary mechanism exists to optimise fertility through sperm competition in kākāpō. The high frequency of clutches produced from single copulations in the contemporary population may therefore represent an unnatural state, perhaps due to too few females. This suggests that opportunity for sperm competition should be maximised by increasing population densities, optimising sex ratios, and using artificial insemination. The lower fertility of hand-reared males may result from behavioural defects due to lack of exposure to conspecifics at critical development stages, as seen in other taxa. This potential negative impact of hand-rearing must be balanced against the short-term benefits it provides.
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Affiliation(s)
- Andrew Digby
- Kākāpō Recovery Programme, Department of Conservation, Invercargill, New Zealand
| | - Daryl Eason
- Kākāpō Recovery Programme, Department of Conservation, Invercargill, New Zealand
| | | | - Michael Lierz
- Clinic for Birds, Reptiles, Amphibians and Fish, Justus-Liebig University Giessen, Giessen, Germany
| | - Stephanie Galla
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Department of Biological Sciences, Boise State University, Boise, ID, United States of America
| | - Lara Urban
- Genomics Aotearoa, Dunedin, New Zealand
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Marissa F. Le Lec
- Genomics Aotearoa, Dunedin, New Zealand
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Joseph Guhlin
- Genomics Aotearoa, Dunedin, New Zealand
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Tammy E. Steeves
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Genomics Aotearoa, Christchurch, New Zealand
| | - Peter K. Dearden
- Genomics Aotearoa, Dunedin, New Zealand
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | | | - Caroline Lees
- IUCN SSC Conservation Planning Specialist Group, Auckland, New Zealand
| | - Tane Davis
- Te Rūnanga o Ngāi Tahu, Christchurch, New Zealand
| | - Deidre Vercoe
- Kākāpō Recovery Programme, Department of Conservation, Invercargill, New Zealand
| | - Kākāpō Recovery Team
- Kākāpō Recovery Programme, Department of Conservation, Invercargill, New Zealand
- Department of Computer Science, Aalto University, Espoo, Finland
- Clinic for Birds, Reptiles, Amphibians and Fish, Justus-Liebig University Giessen, Giessen, Germany
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Department of Biological Sciences, Boise State University, Boise, ID, United States of America
- Genomics Aotearoa, Dunedin, New Zealand
- Department of Anatomy, University of Otago, Dunedin, New Zealand
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
- Genomics Aotearoa, Christchurch, New Zealand
- Unaffiliated, Auckland, New Zealand
- IUCN SSC Conservation Planning Specialist Group, Auckland, New Zealand
- Te Rūnanga o Ngāi Tahu, Christchurch, New Zealand
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22
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Bedhiaf-Romdhani S, Baazaoui I, Dodds KG, Brauning R, Anderson RM, Van Stijn TC, McCulloch AF, McEwan JC. Efficiency of genotyping by sequencing in inferring genomic relatedness and molecular insights into fat tail selection in Tunisian sheep. Anim Genet 2023; 54:389-397. [PMID: 36727208 DOI: 10.1111/age.13296] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 12/14/2022] [Accepted: 01/12/2023] [Indexed: 02/03/2023]
Abstract
In developing countries, the use of simple and cost-efficient molecular technology is crucial for genetic characterization of local animal resources and better development of conservation strategies. The genotyping by sequencing (GBS) technique, also called restriction enzyme- reduced representational sequencing, is an efficient, cost-effective method for simultaneous discovery and genotyping of many markers. In the present study, we applied a two-enzyme GBS protocol (PstI/MspI) to discover and genotype SNP markers among 197 Tunisian sheep samples. A total of 100 333 bi-allelic SNPs were discovered and genotyped with an SNP call rate of 0.69 and mean sample depth 3.33. The genomic relatedness between 183 samples grouped the samples perfectly to their populations and pointed out a high genetic relatedness of inbred subpopulation reflecting the current adopted reproductive strategies. The genome-wide association study contrasting fat vs. thin-tailed breeds detected 41 significant variants including a peak positioned on OAR20. We identified FOXC1, GMDS, VEGFA, OXCT1, VRTN and BMP2 as the most promising for sheep tail-type trait. The GBS data have been useful to assess the population structure and improve our understanding of the genomic architecture of distinctive characteristics shaped by selection pressure in local sheep breeds. This study successfully investigates a cost-efficient method to discover genotypes, assign populations and understand insights into sheep adaptation to arid area. GBS could be of potential utility in livestock species in developing/emerging countries.
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Affiliation(s)
- Sonia Bedhiaf-Romdhani
- Laboratoire des Productions Animales et Fourragères, INRA-Tunisie, Université de Carthage, Tunis, Tunisia
| | - Imen Baazaoui
- Faculty of Sciences of Bizerte, University of Carthage, Bizerte, Tunisia
| | - Ken G Dodds
- AgResearch Limited, Invermay Agricultural Centre, Mosgiel, New Zealand
| | - Rudiger Brauning
- AgResearch Limited, Invermay Agricultural Centre, Mosgiel, New Zealand
| | - Rayna M Anderson
- AgResearch Limited, Invermay Agricultural Centre, Mosgiel, New Zealand
| | | | - Alan F McCulloch
- AgResearch Limited, Invermay Agricultural Centre, Mosgiel, New Zealand
| | - John Colin McEwan
- AgResearch Limited, Invermay Agricultural Centre, Mosgiel, New Zealand
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23
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Pearson SM, Griffiths AG, Maclean P, Larking AC, Hong SW, Jauregui R, Miller P, McKenzie CM, Lockhart PJ, Tate JA, Ford JL, Faville MJ. Outlier analyses and genome-wide association study identify glgC and ERD6-like 4 as candidate genes for foliar water-soluble carbohydrate accumulation in Trifolium repens. FRONTIERS IN PLANT SCIENCE 2023; 13:1095359. [PMID: 36699852 PMCID: PMC9868827 DOI: 10.3389/fpls.2022.1095359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Increasing water-soluble carbohydrate (WSC) content in white clover is important for improving nutritional quality and reducing environmental impacts from pastoral agriculture. Elucidation of genes responsible for foliar WSC variation would enhance genetic improvement by enabling molecular breeding approaches. The aim of the present study was to identify single nucleotide polymorphisms (SNPs) associated with variation in foliar WSC in white clover. A set of 935 white clover individuals, randomly sampled from five breeding pools selectively bred for divergent (low or high) WSC content, were assessed with 14,743 genotyping-by-sequencing SNPs, using three outlier detection methods: PCAdapt, BayeScan and KGD-FST. These analyses identified 33 SNPs as discriminating between high and low WSC populations and putatively under selection. One SNP was located in the intron of ERD6-like 4, a gene coding for a sugar transporter located on the vacuole membrane. A genome-wide association study using a subset of 605 white clover individuals and 5,757 SNPs, identified a further 12 SNPs, one of which was associated with a starch biosynthesis gene, glucose-1-phosphate adenylyltransferase, glgC. Our results provide insight into genomic regions underlying WSC accumulation in white clover, identify candidate genomic regions for further functional validation studies, and reveal valuable information for marker-assisted or genomic selection in white clover.
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Affiliation(s)
- Sofie M. Pearson
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
- Resilient Agriculture, AgResearch Grasslands, Palmerston North, New Zealand
| | | | - Paul Maclean
- Resilient Agriculture, AgResearch Grasslands, Palmerston North, New Zealand
| | - Anna C. Larking
- Resilient Agriculture, AgResearch Grasslands, Palmerston North, New Zealand
| | - S. Won Hong
- Resilient Agriculture, AgResearch Grasslands, Palmerston North, New Zealand
| | - Ruy Jauregui
- Resilient Agriculture, AgResearch Grasslands, Palmerston North, New Zealand
| | - Poppy Miller
- Resilient Agriculture, AgResearch Grasslands, Palmerston North, New Zealand
| | | | - Peter J. Lockhart
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Jennifer A. Tate
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - John L. Ford
- Grasslands, PGG Wrightson Seeds Limited, Palmerston North, New Zealand
| | - Marty J. Faville
- Resilient Agriculture, AgResearch Grasslands, Palmerston North, New Zealand
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Genetic diversity and population structure of wild and cultivated Crotalaria species based on genotyping-by-sequencing. PLoS One 2022; 17:e0272955. [PMID: 36048841 PMCID: PMC9436042 DOI: 10.1371/journal.pone.0272955] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 07/28/2022] [Indexed: 11/19/2022] Open
Abstract
Crotalaria is a plant genus that is found all over the world, with over 700 species of herbs and shrubs. The species are potential alternative food and industrial crops due to their adaptability to different environments. Currently, information on the genetic diversity and population structure of these species is scanty. Genotyping-by-sequencing (GBS) is a cost-effective high-throughput technique in diversity evaluation of plant species that have not been fully sequenced. In the current study, de novo GBS was used to characterize 80 Crotalaria accessions from five geographical regions in Kenya. A total of 9820 single nucleotide polymorphism (SNP) markers were obtained after thinning and filtering, which were then used for the analysis of genetic diversity and population structure in Crotalaria. The proportion of SNPs with a minor allele frequency (maf) > = 0.05 was 45.08%, while the Guanine-Cytosine (GC) content was 0.45, from an average sequence depth of 455,909 reads per base. The transition vs transversion ratio was 1.81 and Heterozygosity (He) ranged between 0.01–0.07 in all the sites and 0.04 to 0.52 in the segregating sites. The mean Tajima’s D value for the population was -0.094, suggesting an excess of rare alleles. The fixation index (Fst) between the different populations based on the Wright Fst (1943) ranged from 0.0119 to 0.066 for the Eastern-Western and Nairobi-Western populations. Model based techniques of population structure analysis including structure, k-means and cross-entropy depicted eight clusters in the study accessions. Non-model based techniques especially DAPC depicted poor population stratification. Correspondence Analysis (CA), Principal coordinate analyses (PCoA) and phylogenetic analysis identified a moderate level of population stratification. Results from this study will help conservationists and breeders understand the genetic diversity of Crotalaria. The study also provides valuable information for genetic improvement of domesticated species.
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Liu Q, Johnson LJ, Applegate ER, Arfmann K, Jauregui R, Larking A, Mace WJ, Maclean P, Walker T, Johnson RD. Identification of Genetic Diversity, Pyrrocidine-Producing Strains and Transmission Modes of Endophytic Sarocladium zeae Fungi from Zea Crops. Microorganisms 2022; 10:microorganisms10071415. [PMID: 35889134 PMCID: PMC9316807 DOI: 10.3390/microorganisms10071415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/12/2022] [Accepted: 07/12/2022] [Indexed: 12/10/2022] Open
Abstract
Genotyping by sequencing (GBS) was used to reveal the inherent genetic variation within the haploid fungi Sarocladium zeae isolated from diverse Zea germplasm, including modern Zea mays and its wild progenitors—the teosintes. In accordance with broad host relationship parameters, GBS analysis revealed significant host lineages of S. zeae genetic diversity, indicating that S. zeae genetic variation may associate with different evolutionary histories of host species or varieties. Based on a recently identified PKS-NRPS gene responsible for pyrrocidine biosynthesis in S. zeae fungi, a novel PCR assay was developed to discriminate pyrrocidine-producing S. zeae strains. This molecular method for screening bioactive strains of S. zeae is complementary to other approaches, such as chemical analyses. An eGFP-labelled S. zeae strain was also developed to investigate the endophytic transmission of S. zeae in Z. mays seedlings, which has further improved our understanding of the transmission modes of S. zeae endophytes in maize tissues.
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26
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Heuchel A, Hall D, Zhao W, Gao J, Wennström U, Wang XR. Genetic diversity and background pollen contamination in Norway spruce and Scots pine seed orchard crops. FORESTRY RESEARCH 2022; 2:8. [PMID: 39525423 PMCID: PMC11524256 DOI: 10.48130/fr-2022-0008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/10/2022] [Indexed: 11/16/2024]
Abstract
Seed orchards are the key link between tree breeding and production forest for conifer trees. In Sweden, Scots pine and Norway spruce seed orchards currently supply ca. 85% of seedlings used in annual reforestation. The functionality of these seed orchards is thus crucial for supporting long-term production gain and sustainable diversity. We conducted a large-scale genetic investigation of pine and spruce orchards across Sweden using genotyping-by-sequencing. We genotyped 3,300 seedlings/trees from six orchards and 10 natural stands to gain an overview of mating structure and genetic diversity in orchard crops. We found clear differences in observed heterozygosity (H O) and background pollen contamination (BPC) rates between species, with pine orchard crops showing higher H O and BPC than spruce. BPC in pine crops varied from 87% at young orchard age to 12% at mature age, wherease this rate ranged between 27%-4% in spruce crops. Substantial variance in parental contribution was observed in all orchards with 30%-50% parents contibuting to 80% of the progeny. Selfing was low (2%-6%) in all seed crops. Compared to natural stands, orchard crops had slightly lower H O but no strong signal of inbreeding. Our results provide valuable references for orchard management.
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Affiliation(s)
- Alisa Heuchel
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, Umeå SE-90187, Sweden
| | - David Hall
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, Umeå SE-90187, Sweden
| | - Wei Zhao
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, Umeå SE-90187, Sweden
| | - Jie Gao
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun 666303, Yunnan, China
| | - Ulfstand Wennström
- The Forestry Research Institute of Sweden (Skogforsk), Sävar SE-918 21, Sweden
| | - Xiao-Ru Wang
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, Umeå SE-90187, Sweden
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Miller AK, Timoshevskaya N, Smith JJ, Gillum J, Sharif S, Clarke S, Baker C, Kitson J, Gemmell NJ, Alexander A. Population genomics of New Zealand pouched lamprey (kanakana; piharau; Geotria australis). J Hered 2022; 113:380-397. [PMID: 35439308 PMCID: PMC9308044 DOI: 10.1093/jhered/esac014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 03/23/2022] [Indexed: 11/12/2022] Open
Abstract
Pouched lamprey (Geotria australis) or kanakana/piharau is a culturally and ecologically significant jawless fish that is distributed throughout Aotearoa New Zealand. Despite its importance, much remains unknown about historical relationships and gene flow between populations of this enigmatic species within New Zealand. To help inform management, we assembled a draft G. australis genome and completed the first comprehensive population genomics analysis of pouched lamprey within New Zealand using targeted gene sequencing (Cyt-b and COI) and restriction site-associated DNA sequencing (RADSeq) methods. Employing 16 000 genome-wide single nucleotide polymorphisms (SNPs) derived from RADSeq (n = 186) and sequence data from Cyt-b (766 bp, n = 94) and COI (589 bp, n = 20), we reveal low levels of structure across 10 sampling locations spanning the species range within New Zealand. F-statistics, outlier analyses, and STRUCTURE suggest a single panmictic population, and Mantel and EEMS tests reveal no significant isolation by distance. This implies either ongoing gene flow among populations or recent shared ancestry among New Zealand pouched lamprey. We can now use the information gained from these genetic tools to assist managers with monitoring effective population size, managing potential diseases, and conservation measures such as artificial propagation programs. We further demonstrate the general utility of these genetic tools for acquiring information about elusive species.
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Affiliation(s)
- Allison K Miller
- Anatomy Department, School of Biomedical Sciences, University of Otago, 270 Great King Street, Dunedin, 9016, New Zealand
| | - Nataliya Timoshevskaya
- Department of Biology, University of Kentucky, 101 Morgan Building, Lexington, Kentucky, 40506-0225 USA
| | - Jeramiah J Smith
- Department of Biology, University of Kentucky, 101 Morgan Building, Lexington, Kentucky, 40506-0225 USA
| | - Joanne Gillum
- Anatomy Department, School of Biomedical Sciences, University of Otago, 270 Great King Street, Dunedin, 9016, New Zealand
| | - Saeed Sharif
- Anatomy Department, School of Biomedical Sciences, University of Otago, 270 Great King Street, Dunedin, 9016, New Zealand
| | - Shannon Clarke
- AgResearch, Invermay Agricultural Centre, Mosgiel 9053, New Zealand
| | - Cindy Baker
- National Institute of Water and Atmospheric Research Limited, PO Box 11 115, Hamilton 3251 New Zealand
| | - Jane Kitson
- Ngāi Tahu, Kitson Consulting Ltd, Invercargill/Waihopai, 9879, New Zealand
| | - Neil J Gemmell
- Anatomy Department, School of Biomedical Sciences, University of Otago, 270 Great King Street, Dunedin, 9016, New Zealand
| | - Alana Alexander
- Anatomy Department, School of Biomedical Sciences, University of Otago, 270 Great King Street, Dunedin, 9016, New Zealand
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28
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Barre P, Asp T, Byrne S, Casler M, Faville M, Rognli OA, Roldan-Ruiz I, Skøt L, Ghesquière M. Genomic Prediction of Complex Traits in Forage Plants Species: Perennial Grasses Case. Methods Mol Biol 2022; 2467:521-541. [PMID: 35451789 DOI: 10.1007/978-1-0716-2205-6_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The majority of forage grass species are obligate outbreeders. Their breeding classically consists of an initial selection on spaced plants for highly heritable traits such as disease resistances and heading date, followed by familial selection on swards for forage yield and quality traits. The high level of diversity and heterozygosity, and associated decay of linkage disequilibrium (LD) over very short genomic distances, has hampered the implementation of genomic selection (GS) in these species. However, next generation sequencing technologies in combination with the development of genomic resources have recently facilitated implementation of GS in forage grass species such as perennial ryegrass (Lolium perenne L.), switchgrass (Panicum virgatum L.), and timothy (Phleum pratense L.). Experimental work and simulations have shown that GS can increase significantly the genetic gain per unit of time for traits with different levels of heritability. The main reasons are (1) the possibility to select single plants based on their genomic estimated breeding values (GEBV) for traits measured at sward level, (2) a reduction in the duration of selection cycles, and less importantly (3) an increase in the selection intensity associated with an increase in the genetic variance used for selection. Nevertheless, several factors should be taken into account for the successful implementation of GS in forage grasses. For example, it has been shown that the level of relatedness between the training and the selection population is particularly critical when working with highly structured meta-populations consisting of several genetic groups. A sufficient number of markers should be used to estimate properly the kinship between individuals and to reflect the variability of major QTLs. It is also important that the prediction models are trained for relevant environments when dealing with traits with high genotype × environment interaction (G × E). Finally, in these outbreeding species, measures to reduce inbreeding should be used to counterbalance the high selection intensity that can be achieved in GS.
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Affiliation(s)
| | - Torben Asp
- Center for Quantitative Genetics and Genomics, Aarhus University, Slagelse, Denmark
| | - Stephen Byrne
- Teagasc, Crop Science Department, Oak Park, Carlow, Ireland
| | - Michael Casler
- U.S. Dairy Forage Research Center, USDA-ARS, Madison, WI, USA
| | - Marty Faville
- AgResearch Ltd , Grasslands Research Centre, Palmerston North, New Zealand
| | - Odd Arne Rognli
- Department of Plant Sciences, Faculty of Biosciences, Norwegian, University of Life Sciences (NMBU), Ås, Norway
| | - Isabel Roldan-Ruiz
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO)-Plant Sciences Unit, Melle, Belgium
| | - Leif Skøt
- IBERS, Aberystwyth University, Ceredigion, UK
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Caulton A, Dodds KG, McRae KM, Couldrey C, Horvath S, Clarke SM. Development of Epigenetic Clocks for Key Ruminant Species. Genes (Basel) 2021; 13:96. [PMID: 35052436 PMCID: PMC8775075 DOI: 10.3390/genes13010096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 12/20/2021] [Accepted: 12/22/2021] [Indexed: 01/08/2023] Open
Abstract
Robust biomarkers of chronological age have been developed in humans and model mammalian species such as rats and mice using DNA methylation data. The concept of these so-called "epigenetic clocks" has emerged from a large body of literature describing the relationship between genome-wide methylation levels and age. Epigenetic clocks exploit this phenomenon and use small panels of differentially methylated cytosine (CpG) sites to make robust predictions of chronological age, independent of tissue type. Here, we present highly accurate livestock epigenetic clocks for which we have used the custom mammalian methylation array "HorvathMammalMethyl40" to construct the first epigenetic clock for domesticated goat (Capra hircus), cattle (Bos taurus), Red (Cervus elaphus) and Wapiti deer (Cervus canadensis) and composite-breed sheep (Ovis aries). Additionally, we have constructed a 'farm animal clock' for all species included in the study, which will allow for robust predictions to be extended to various breeds/strains. The farm animal clock shows similarly high accuracy to the individual species' clocks (r > 0.97), utilizing only 217 CpG sites to estimate age (relative to the maximum lifespan of the species) with a single mathematical model. We hypothesise that the applications of this livestock clock could extend well beyond the scope of chronological age estimates. Many independent studies have demonstrated that a deviation between true age and clock derived molecular age is indicative of past and/or present health (including stress) status. There is, therefore, untapped potential to utilize livestock clocks in breeding programs as a predictor for age-related production traits.
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Affiliation(s)
- Alex Caulton
- AgResearch Limited, Invermay Agricultural Centre, Puddle Alley, Mosgiel 9092, New Zealand; (K.G.D.); (K.M.M.); (S.M.C.)
- Department of Biochemistry, University of Otago, Dunedin 9016, New Zealand
| | - Ken G. Dodds
- AgResearch Limited, Invermay Agricultural Centre, Puddle Alley, Mosgiel 9092, New Zealand; (K.G.D.); (K.M.M.); (S.M.C.)
| | - Kathryn M. McRae
- AgResearch Limited, Invermay Agricultural Centre, Puddle Alley, Mosgiel 9092, New Zealand; (K.G.D.); (K.M.M.); (S.M.C.)
| | | | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA;
| | - Shannon M. Clarke
- AgResearch Limited, Invermay Agricultural Centre, Puddle Alley, Mosgiel 9092, New Zealand; (K.G.D.); (K.M.M.); (S.M.C.)
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Semagn K, Iqbal M, Alachiotis N, N'Diaye A, Pozniak C, Spaner D. Genetic diversity and selective sweeps in historical and modern Canadian spring wheat cultivars using the 90K SNP array. Sci Rep 2021; 11:23773. [PMID: 34893626 PMCID: PMC8664822 DOI: 10.1038/s41598-021-02666-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 11/22/2021] [Indexed: 12/14/2022] Open
Abstract
Previous molecular characterization studies conducted in Canadian wheat cultivars shed some light on the impact of plant breeding on genetic diversity, but the number of varieties and markers used was small. Here, we used 28,798 markers of the wheat 90K single nucleotide polymorphisms to (a) assess the extent of genetic diversity, relationship, population structure, and divergence among 174 historical and modern Canadian spring wheat varieties registered from 1905 to 2018 and 22 unregistered lines (hereinafter referred to as cultivars), and (b) identify genomic regions that had undergone selection. About 91% of the pairs of cultivars differed by 20-40% of the scored alleles, but only 7% of the pairs had kinship coefficients of < 0.250, suggesting the presence of a high proportion of redundancy in allelic composition. Although the 196 cultivars represented eight wheat classes, our results from phylogenetic, principal component, and the model-based population structure analyses revealed three groups, with no clear structure among most wheat classes, breeding programs, and breeding periods. FST statistics computed among different categorical variables showed little genetic differentiation (< 0.05) among breeding periods and breeding programs, but a diverse level of genetic differentiation among wheat classes and predicted groups. Diversity indices were the highest and lowest among cultivars registered from 1970 to 1980 and from 2011 to 2018, respectively. Using two outlier detection methods, we identified from 524 to 2314 SNPs and 41 selective sweeps of which some are close to genes with known phenotype, including plant height, photoperiodism, vernalization, gluten strength, and disease resistance.
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Affiliation(s)
- Kassa Semagn
- Department of Agricultural, Food, and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
| | - Muhammad Iqbal
- Department of Agricultural, Food, and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Nikolaos Alachiotis
- Faculty of Electrical Engineering, Mathematics and Computer Science, University of Twente, 3230, Enschede, OV, The Netherlands
| | - Amidou N'Diaye
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Curtis Pozniak
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Dean Spaner
- Department of Agricultural, Food, and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
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Possamai T, Wiedemann-Merdinoglu S, Merdinoglu D, Migliaro D, De Mori G, Cipriani G, Velasco R, Testolin R. Construction of a high-density genetic map and detection of a major QTL of resistance to powdery mildew (Erysiphe necator Sch.) in Caucasian grapes (Vitis vinifera L.). BMC PLANT BIOLOGY 2021; 21:528. [PMID: 34763660 PMCID: PMC8582213 DOI: 10.1186/s12870-021-03174-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 08/09/2021] [Indexed: 05/30/2023]
Abstract
BACKGROUND Vitis vinifera L. is the most cultivated grapevine species worldwide. Erysiphe necator Sch., the causal agent of grape powdery mildew, is one of the main pathogens affecting viticulture. V. vinifera has little or no genetic resistances against E. necator and the grape industry is highly dependent on agrochemicals. Some Caucasian V. vinifera accessions have been reported to be resistant to E. necator and to have no genetic relationships to known sources of resistance to powdery mildew. The main purpose of this work was the study and mapping of the resistance to E. necator in the Caucasian grapes 'Shavtsitska' and 'Tskhvedianis tetra'. RESULTS The Caucasian varieties 'Shavtsitska' and 'Tskhvedianis tetra' showed a strong partial resistance to E. necator which segregated in two cross populations: the resistant genotypes delayed and limited the pathogen mycelium growth, sporulation intensity and number of conidia generated. A total of 184 seedlings of 'Shavtsitska' x 'Glera' population were genotyped through the Genotyping by Sequencing (GBS) technology and two high-density linkage maps were developed for the cross parents. The QTL analysis revealed a major resistance locus, explaining up to 80.15% of the phenotypic variance, on 'Shavtsitska' linkage group 13, which was associated with a reduced pathogen infection as well as an enhanced plant necrotic response. The genotyping of 105 Caucasian accessions with SSR markers flanking the QTL revealed that the resistant haplotype of 'Shavtsitska' was shared by 'Tskhvedianis tetra' and a total of 25 Caucasian grape varieties, suggesting a widespread presence of this resistance in the surveyed germplasm. The uncovered QTL was mapped in the region where the Ren1 locus of resistance to E. necator, identified in the V. vinifera 'Kishmish vatkana' and related grapes of Central Asia, is located. The genetic analysis conducted revealed that the Caucasian grapes in this study exhibit a resistant haplotype different from that of Central Asian grape accessions. CONCLUSIONS The QTL isolated in 'Shavtsitska' and present in the Caucasian V. vinifera varieties could be a new candidate gene of resistance to E. necator to use in breeding programmes. It co-localizes with the Ren1 locus but shows a different haplotype from that of grapevines of Central Asia. We therefore consider that the Caucasian resistance locus, named Ren1.2, contains a member of a cluster of R-genes, of which the region is rich, and to be linked with, or possibly allelic, to Ren1.
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Affiliation(s)
- Tyrone Possamai
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, via delle Scienze 206, 33100, Udine, Italy.
- CREA - Research Centre for Viticulture and Enology, viale XXVIII Aprile 26, 31015, Conegliano, TV, Italy.
| | | | - Didier Merdinoglu
- INRAE, Université de Strasbourg, SVQV UMR-A 1131, 28 rue de Herrlisheim, 68000, Colmar, France
| | - Daniele Migliaro
- CREA - Research Centre for Viticulture and Enology, viale XXVIII Aprile 26, 31015, Conegliano, TV, Italy
| | - Gloria De Mori
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, via delle Scienze 206, 33100, Udine, Italy
| | - Guido Cipriani
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, via delle Scienze 206, 33100, Udine, Italy
| | - Riccardo Velasco
- CREA - Research Centre for Viticulture and Enology, viale XXVIII Aprile 26, 31015, Conegliano, TV, Italy
| | - Raffaele Testolin
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, via delle Scienze 206, 33100, Udine, Italy
- Institute of Applied Genomics, Science & Technology Park "Luigi Danieli", via Jacopo Linussio 51, 33100, Udine, Italy
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32
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Foster Y, Dutoit L, Grosser S, Dussex N, Foster BJ, Dodds KG, Brauning R, Van Stijn T, Robertson F, McEwan JC, Jacobs JME, Robertson BC. Genomic signatures of inbreeding in a critically endangered parrot, the kākāpō. G3 (BETHESDA, MD.) 2021; 11:jkab307. [PMID: 34542587 PMCID: PMC8527487 DOI: 10.1093/g3journal/jkab307] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 08/23/2021] [Indexed: 02/06/2023]
Abstract
Events of inbreeding are inevitable in critically endangered species. Reduced population sizes and unique life-history traits can increase the severity of inbreeding, leading to declines in fitness and increased risk of extinction. Here, we investigate levels of inbreeding in a critically endangered flightless parrot, the kākāpō (Strigops habroptilus), wherein a highly inbred island population and one individual from the mainland of New Zealand founded the entire extant population. Genotyping-by-sequencing (GBS), and a genotype calling approach using a chromosome-level genome assembly, identified a filtered set of 12,241 single-nucleotide polymorphisms (SNPs) among 161 kākāpō, which together encompass the total genetic potential of the extant population. Multiple molecular-based estimates of inbreeding were compared, including genome-wide estimates of heterozygosity (FH), the diagonal elements of a genomic-relatedness matrix (FGRM), and runs of homozygosity (RoH, FRoH). In addition, we compared levels of inbreeding in chicks from a recent breeding season to examine if inbreeding is associated with offspring survival. The density of SNPs generated with GBS was sufficient to identify chromosomes that were largely homozygous with RoH distributed in similar patterns to other inbred species. Measures of inbreeding were largely correlated and differed significantly between descendants of the two founding populations. However, neither inbreeding nor ancestry was found to be associated with reduced survivorship in chicks, owing to unexpected mortality in chicks exhibiting low levels of inbreeding. Our study highlights important considerations for estimating inbreeding in critically endangered species, such as the impacts of small population sizes and admixture between diverse lineages.
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Affiliation(s)
- Yasmin Foster
- Department of Zoology, University of Otago, Dunedin 9054, New Zealand
| | - Ludovic Dutoit
- Department of Zoology, University of Otago, Dunedin 9054, New Zealand
| | - Stefanie Grosser
- Department of Zoology, University of Otago, Dunedin 9054, New Zealand
| | - Nicolas Dussex
- Centre for Palaeogenetics, SE-106 91 Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-104 05 Stockholm, Sweden
- Department of Zoology, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Brodie J Foster
- Department of Zoology, University of Otago, Dunedin 9054, New Zealand
| | - Ken G Dodds
- AgResearch Invermay Agricultural Centre, Mosgiel 9053, New Zealand
| | - Rudiger Brauning
- AgResearch Invermay Agricultural Centre, Mosgiel 9053, New Zealand
| | - Tracey Van Stijn
- AgResearch Invermay Agricultural Centre, Mosgiel 9053, New Zealand
| | - Fiona Robertson
- Department of Zoology, University of Otago, Dunedin 9054, New Zealand
| | - John C McEwan
- AgResearch Invermay Agricultural Centre, Mosgiel 9053, New Zealand
| | | | - Bruce C Robertson
- Department of Zoology, University of Otago, Dunedin 9054, New Zealand
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Undin M, Lockhart PJ, Hills SFK, Armstrong DP, Castro I. Mixed Mating in a Multi-Origin Population Suggests High Potential for Genetic Rescue in North Island Brown Kiwi, Apteryx mantelli. FRONTIERS IN CONSERVATION SCIENCE 2021. [DOI: 10.3389/fcosc.2021.702128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Reinforcement translocations are increasingly utilised in conservation with the goal of achieving genetic rescue. However, concerns regarding undesirable results, such as genetic homogenisation or replacement, are widespread. One factor influencing translocation outcomes is the rate at which the resident and the introduced individuals interbreed. Consequently, post-release mate choice is a key behaviour to consider in conservation planning. Here we studied mating, and its consequences for genomic admixture, in the North Island brown kiwi Apteryx mantelli population on Ponui Island which was founded by two translocation events over 50 years ago. The two source populations used are now recognised as belonging to two separate management units between which birds differ in size and are genetically differentiated. We examined the correlation between male and female morphometrics for 17 known pairs and quantified the relatedness of 20 pairs from this admixed population. In addition, we compared the genetic similarity and makeup of 106 Ponui Island birds, including 23 known pairs, to birds representing the source populations for the original translocations. We found no evidence for size-assortative mating. On the contrary, genomic SNP data suggested that kiwi of one feather did not flock together, meaning that mate choice resulted in pairing between individuals that were less related than expected by random chance. Furthermore, the birds in the current Ponui Island population were found to fall along a gradient of genomic composition consistent with non-clustered representation of the two parental genomes. These findings indicate potential for successful genetic rescue in future Apteryx reinforcement translocations, a potential that is currently under utilised due to restrictive translocation policies. In light of our findings, we suggest that reconsideration of these policies could render great benefits for the future diversity of this iconic genus in New Zealand.
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Macnee N, Hilario E, Tahir J, Currie A, Warren B, Rebstock R, Hallett IC, Chagné D, Schaffer RJ, Bulley SM. Peridermal fruit skin formation in Actinidia sp. (kiwifruit) is associated with genetic loci controlling russeting and cuticle formation. BMC PLANT BIOLOGY 2021; 21:334. [PMID: 34261431 PMCID: PMC8278711 DOI: 10.1186/s12870-021-03025-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 05/10/2021] [Indexed: 05/10/2023]
Abstract
BACKGROUND The skin (exocarp) of fleshy fruit is hugely diverse across species. Most fruit types have a live epidermal skin covered by a layer of cuticle made up of cutin while a few create an outermost layer of dead cells (peridermal layer). RESULTS In this study we undertook crosses between epidermal and peridermal skinned kiwifruit, and showed that epidermal skin is a semi-dominant trait. Furthermore, backcrossing these epidermal skinned hybrids to a peridermal skinned fruit created a diverse range of phenotypes ranging from epidermal skinned fruit, through fruit with varying degrees of patches of periderm (russeting), to fruit with a complete periderm. Quantitative trait locus (QTL) analysis of this population suggested that periderm formation was associated with four loci. These QTLs were aligned either to ones associated with russet formation on chromosome 19 and 24, or cuticle integrity and coverage located on chromosomes 3, 11 and 24. CONCLUSION From the segregation of skin type and QTL analysis, it appears that skin development in kiwifruit is controlled by two competing factors, cuticle strength and propensity to russet. A strong cuticle will inhibit russeting while a strong propensity to russet can create a continuous dead skinned periderm.
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Affiliation(s)
- Nikolai Macnee
- The New Zealand Institute for Plant and Food Research Ltd. (PFR), Private Bag 92169, Auckland, 1142, New Zealand
- School of Biological Science, The University of Auckland, Auckland, 1146, New Zealand
| | - Elena Hilario
- The New Zealand Institute for Plant and Food Research Ltd. (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Jibran Tahir
- PFR, Private Bag 11600, Palmerston North, 4442, New Zealand
| | | | - Ben Warren
- The New Zealand Institute for Plant and Food Research Ltd. (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Ria Rebstock
- The New Zealand Institute for Plant and Food Research Ltd. (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Ian C Hallett
- The New Zealand Institute for Plant and Food Research Ltd. (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - David Chagné
- PFR, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Robert J Schaffer
- School of Biological Science, The University of Auckland, Auckland, 1146, New Zealand
- PFR, 55 Old Mill Road, RD3, Motueka, 7198, New Zealand
| | - Sean M Bulley
- PFR, 412 No 1 Road RD 2, Te Puke, 3182, New Zealand.
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Genetic basis and identification of candidate genes for wooden breast and white striping in commercial broiler chickens. Sci Rep 2021; 11:6785. [PMID: 33762630 PMCID: PMC7990949 DOI: 10.1038/s41598-021-86176-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 03/08/2021] [Indexed: 02/07/2023] Open
Abstract
Wooden breast (WB) and white striping (WS) are highly prevalent and economically damaging muscle disorders of modern commercial broiler chickens characterized respectively by palpable firmness and fatty white striations running parallel to the muscle fiber. High feed efficiency and rapid growth, especially of the breast muscle, are believed to contribute to development of such muscle defects; however, their etiology remains poorly understood. To gain insight into the genetic basis of these myopathies, a genome-wide association study was conducted using a commercial crossbred broiler population (n = 1193). Heritability was estimated at 0.5 for WB and WS with high genetic correlation between them (0.88). GWAS revealed 28 quantitative trait loci (QTL) on five chromosomes for WB and 6 QTL on one chromosome for WS, with the majority of QTL for both myopathies located in a ~ 8 Mb region of chromosome 5. This region has highly conserved synteny with a portion of human chromosome 11 containing a cluster of imprinted genes associated with growth and metabolic disorders such as type 2 diabetes and Beckwith-Wiedemann syndrome. Candidate genes include potassium voltage-gated channel subfamily Q member 1 (KCNQ1), involved in insulin secretion and cardiac electrical activity, lymphocyte-specific protein 1 (LSP1), involved in inflammation and immune response.
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Pappas F, Palaiokostas C. Genotyping Strategies Using ddRAD Sequencing in Farmed Arctic Charr ( Salvelinus alpinus). Animals (Basel) 2021; 11:899. [PMID: 33801139 PMCID: PMC8004150 DOI: 10.3390/ani11030899] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/13/2021] [Accepted: 03/16/2021] [Indexed: 12/17/2022] Open
Abstract
Incorporation of genomic technologies into fish breeding programs is a modern reality, promising substantial advances regarding the accuracy of selection, monitoring the genetic diversity and pedigree record verification. Single nucleotide polymorphism (SNP) arrays are the most commonly used genomic tool, but the investments required make them unsustainable for emerging species, such as Arctic charr (Salvelinus alpinus), where production volume is low. The requirement to genotype a large number of animals for breeding practices necessitates cost effective genotyping approaches. In the current study, we used double digest restriction site-associated DNA (ddRAD) sequencing of either high or low coverage to genotype Arctic charr from the Swedish national breeding program and performed analytical procedures to assess their utility in a range of tasks. SNPs were identified and used for deciphering the genetic structure of the studied population, estimating genomic relationships and implementing an association study for growth-related traits. Missing information and underestimation of heterozygosity in the low coverage set were limiting factors in genetic diversity and genomic relationship analyses, where high coverage performed notably better. On the other hand, the high coverage dataset proved to be valuable when it comes to identifying loci that are associated with phenotypic traits of interest. In general, both genotyping strategies offer sustainable alternatives to hybridization-based genotyping platforms and show potential for applications in aquaculture selective breeding.
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Affiliation(s)
| | - Christos Palaiokostas
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, P.O. Box 7090, 750 07 Uppsala, Sweden;
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Ben-David E, Boocock J, Guo L, Zdraljevic S, Bloom JS, Kruglyak L. Whole-organism eQTL mapping at cellular resolution with single-cell sequencing. eLife 2021; 10:e65857. [PMID: 33734084 PMCID: PMC8062134 DOI: 10.7554/elife.65857] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/17/2021] [Indexed: 12/11/2022] Open
Abstract
Genetic regulation of gene expression underlies variation in disease risk and other complex traits. The effect of expression quantitative trait loci (eQTLs) varies across cell types; however, the complexity of mammalian tissues makes studying cell-type eQTLs highly challenging. We developed a novel approach in the model nematode Caenorhabditis elegans that uses single-cell RNA sequencing to map eQTLs at cellular resolution in a single one-pot experiment. We mapped eQTLs across cell types in an extremely large population of genetically distinct C. elegans individuals. We found cell-type-specific trans eQTL hotspots that affect the expression of core pathways in the relevant cell types. Finally, we found single-cell-specific eQTL effects in the nervous system, including an eQTL with opposite effects in two individual neurons. Our results show that eQTL effects can be specific down to the level of single cells.
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Affiliation(s)
- Eyal Ben-David
- Department of Human Genetics, Department of Biological Chemistry, and Howard Hughes Medical Institute, University of California, Los AngelesLos AngelesUnited States
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, The Hebrew University School of MedicineJerusalemIsrael
| | - James Boocock
- Department of Human Genetics, Department of Biological Chemistry, and Howard Hughes Medical Institute, University of California, Los AngelesLos AngelesUnited States
| | - Longhua Guo
- Department of Human Genetics, Department of Biological Chemistry, and Howard Hughes Medical Institute, University of California, Los AngelesLos AngelesUnited States
| | - Stefan Zdraljevic
- Department of Human Genetics, Department of Biological Chemistry, and Howard Hughes Medical Institute, University of California, Los AngelesLos AngelesUnited States
| | - Joshua S Bloom
- Department of Human Genetics, Department of Biological Chemistry, and Howard Hughes Medical Institute, University of California, Los AngelesLos AngelesUnited States
| | - Leonid Kruglyak
- Department of Human Genetics, Department of Biological Chemistry, and Howard Hughes Medical Institute, University of California, Los AngelesLos AngelesUnited States
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Zhao H, Li Y, Petkowski J, Kant S, Hayden MJ, Daetwyler HD. Genomic prediction and genomic heritability of grain yield and its related traits in a safflower genebank collection. THE PLANT GENOME 2021; 14:e20064. [PMID: 33140563 DOI: 10.1002/tpg2.20064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 09/11/2020] [Accepted: 09/13/2020] [Indexed: 05/28/2023]
Abstract
Safflower, a minor oilseed crop, is gaining increased attention for food and industrial uses. Safflower genebank collections are an important genetic resource for crop enhancement and future breeding programs. In this study, we investigated the population structure of a safflower collection sourced from the Australian Grain Genebank and assessed the potential of genomic prediction (GP) to evaluate grain yield and related traits using single and multi-site models. Prediction accuracies (PA) of genomic best linear unbiased prediction (GBLUP) from single site models ranged from 0.21 to 0.86 for all traits examined and were consistent with estimated genomic heritability (h2 ), which varied from low to moderate across traits. We generally observed a low level of genome × environment interactions (g × E). Multi-site g × E GBLUP models only improved PA for accessions with at least some phenotypes in the training set. We observed that relaxing quality filtering parameters for genotype-by-sequencing (GBS), such as missing genotype call rate, did not affect PA but upwardly biased h2 estimation. Our results indicate that GP is feasible in safflower evaluation and is potentially a cost-effective tool to facilitate fast introgression of desired safflower trait variation from genebank germplasm into breeding lines.
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Affiliation(s)
- Huanhuan Zhao
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, 3400, Australia
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Yongjun Li
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Joanna Petkowski
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Surya Kant
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, 3400, Australia
- Centre for Agricultural Innovation, The University of Melbourne, Melbourne, VIC, Australia
| | - Matthew J Hayden
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Hans D Daetwyler
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
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Petersen GEL, Fennessy PF, Dearden PK. Management tools for genetic diversity in an isolated population of the honeybee (Apis mellifera) in New Zealand. ANIMAL PRODUCTION SCIENCE 2021. [DOI: 10.1071/an21102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Context
Beekeepers and honeybee queen breeders alike currently have few tools at their disposal for the management of genetic diversity inside their populations. Pedigree information is often absent, beekeepers cannot afford to genotype selection candidates due to costs, and acquisition of material for genotyping without risk to individual queen bees is difficult. However, in New World honeybee populations where import of additional genetic material to refresh the population is restricted (e.g. Australia) or impossible (e.g. New Zealand), management of genetic diversity is important for population sustainability. While the role of individual beekeepers in maintaining genetic resources becomes crucial under these circumstances, a more holistic approach to the management of genetic diversity is needed to allow for maximum impact of their contribution.
Aims
The establishment of affordable genotyping methodologies for successful strategies in managing honeybee genetic diversity, as well as the necessary delivery systems for the results to support the beekeeping community by providing interpretation in the context of the wider population.
Methods
Genotyping-by-sequencing of honeybee samples collected as part of a national survey were used as the basis for assessment of New Zealand’s honeybee genetic diversity and development of a tool with largely self-explanatory outputs that can be used directly by beekeepers.
Key results
It would appear that New Zealand’s honeybee population is sufficiently diverse to maintain population viability. However, both within regions and within companies, genetic diversity is significantly reduced, especially in the case of specialised queen breeders, indicating that active management will be necessary to achieve long-term sustainability.
Conclusions
Interactive tools are needed to help beekeepers understand their role in maintaining overall genetic diversity in the honeybee population as well as the potential impact of planned bee movement and queen acquisitions. Regular rounds of voluntary bee sampling can be used as the basis for management decisions without concentrating genotyping load on specific operators and restricting diversity assessments to subpopulations.
Implications
The described strategy is expected to both improve the outlook of New Zealand’s honeybee population as a whole and facilitate stringent genetic improvement programs by enabling queen breeders to make informed selection decisions and giving beekeepers confidence in the viability of their population.
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Lamb HJ, Hayes BJ, Nguyen LT, Ross EM. The Future of Livestock Management: A Review of Real-Time Portable Sequencing Applied to Livestock. Genes (Basel) 2020; 11:E1478. [PMID: 33317066 PMCID: PMC7763041 DOI: 10.3390/genes11121478] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/10/2020] [Accepted: 12/01/2020] [Indexed: 12/12/2022] Open
Abstract
Oxford Nanopore Technologies' MinION has proven to be a valuable tool within human and microbial genetics. Its capacity to produce long reads in real time has opened up unique applications for portable sequencing. Examples include tracking the recent African swine fever outbreak in China and providing a diagnostic tool for disease in the cassava plant in Eastern Africa. Here we review the current applications of Oxford Nanopore sequencing in livestock, then focus on proposed applications in livestock agriculture for rapid diagnostics, base modification detection, reference genome assembly and genomic prediction. In particular, we propose a future application: 'crush-side genotyping' for real-time on-farm genotyping for extensive industries such as northern Australian beef production. An initial in silico experiment to assess the feasibility of crush-side genotyping demonstrated promising results. SNPs were called from simulated Nanopore data, that included the relatively high base call error rate that is characteristic of the data, and calling parameters were varied to understand the feasibility of SNP calling at low coverages in a heterozygous population. With optimised genotype calling parameters, over 85% of the 10,000 simulated SNPs were able to be correctly called with coverages as low as 6×. These results provide preliminary evidence that Oxford Nanopore sequencing has potential to be used for real-time SNP genotyping in extensive livestock operations.
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Affiliation(s)
- Harrison J. Lamb
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4067, Australia; (B.J.H.); (L.T.N.); (E.M.R.)
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de Bem Oliveira I, Amadeu RR, Ferrão LFV, Muñoz PR. Optimizing whole-genomic prediction for autotetraploid blueberry breeding. Heredity (Edinb) 2020; 125:437-448. [PMID: 33077896 PMCID: PMC7784927 DOI: 10.1038/s41437-020-00357-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 08/11/2020] [Accepted: 08/11/2020] [Indexed: 11/19/2022] Open
Abstract
Blueberry (Vaccinium spp.) is an important autopolyploid crop with significant benefits for human health. Apart from its genetic complexity, the feasibility of genomic prediction has been proven for blueberry, enabling a reduction in the breeding cycle time and increasing genetic gain. However, as for other polyploid crops, sequencing costs still hinder the implementation of genome-based breeding methods for blueberry. This motivated us to evaluate the effect of training population sizes and composition, as well as the impact of marker density and sequencing depth on phenotype prediction for the species. For this, data from a large real breeding population of 1804 individuals were used. Genotypic data from 86,930 markers and three traits with different genetic architecture (fruit firmness, fruit weight, and total yield) were evaluated. Herein, we suggested that marker density, sequencing depth, and training population size can be substantially reduced with no significant impact on model accuracy. Our results can help guide decisions toward resource allocation (e.g., genotyping and phenotyping) in order to maximize prediction accuracy. These findings have the potential to allow for a faster and more accurate release of varieties with a substantial reduction of resources for the application of genomic prediction in blueberry. We anticipate that the benefits and pipeline described in our study can be applied to optimize genomic prediction for other diploid and polyploid species.
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Affiliation(s)
- Ivone de Bem Oliveira
- Blueberry Breeding and Genomics Lab, Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Rodrigo Rampazo Amadeu
- Blueberry Breeding and Genomics Lab, Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Luis Felipe Ventorim Ferrão
- Blueberry Breeding and Genomics Lab, Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Patricio R Muñoz
- Blueberry Breeding and Genomics Lab, Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA.
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Tahir J, Brendolise C, Hoyte S, Lucas M, Thomson S, Hoeata K, McKenzie C, Wotton A, Funnell K, Morgan E, Hedderley D, Chagné D, Bourke PM, McCallum J, Gardiner SE, Gea L. QTL Mapping for Resistance to Cankers Induced by Pseudomonas syringae pv. actinidiae (Psa) in a Tetraploid Actinidia chinensis Kiwifruit Population. Pathogens 2020; 9:E967. [PMID: 33233616 PMCID: PMC7709049 DOI: 10.3390/pathogens9110967] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/11/2020] [Accepted: 11/16/2020] [Indexed: 11/30/2022] Open
Abstract
Polyploidy is a key driver of significant evolutionary changes in plant species. The genus Actinidia (kiwifruit) exhibits multiple ploidy levels, which contribute to novel fruit traits, high yields and resistance to the canker-causing dieback disease incited by Pseudomonas syringae pv. actinidiae (Psa) biovar 3. However, the genetic mechanism for resistance to Psa observed in polyploid kiwifruit is not yet known. In this study we performed detailed genetic analysis of a tetraploid Actinidia chinensis var. chinensis population derived from a cross between a female parent that exhibits weak tolerance to Psa and a highly Psa-resistant male parent. We used the capture-sequencing approach across the whole kiwifruit genome and generated the first ultra-dense maps in a tetraploid kiwifruit population. We located quantitative trait loci (QTLs) for Psa resistance on these maps. Our approach to QTL mapping is based on the use of identity-by-descent trait mapping, which allowed us to relate the contribution of specific alleles from their respective homologues in the male and female parent, to the control of Psa resistance in the progeny. We identified genes in the diploid reference genome whose function is suggested to be involved in plant defense, which underly the QTLs, including receptor-like kinases. Our study is the first to cast light on the genetics of a polyploid kiwifruit and suggest a plausible mechanism for Psa resistance in this species.
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Affiliation(s)
- Jibran Tahir
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92-169, Auckland 1025, New Zealand; (J.T.); (C.B.)
| | - Cyril Brendolise
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92-169, Auckland 1025, New Zealand; (J.T.); (C.B.)
| | - Stephen Hoyte
- The New Zealand Institute for Plant and Food Research Limited, Hamilton 3214, New Zealand;
| | - Marielle Lucas
- Breeding Department, Enza Zaden, 1602 DB Enkhuizen, The Netherlands;
| | - Susan Thomson
- The New Zealand Institute for Plant and Food Research Limited, Lincoln 7608, New Zealand;
| | - Kirsten Hoeata
- The New Zealand Institute for Plant and Food Research Limited, 412 No 1 Road, RD2, Te Puke 3182, New Zealand; (K.H.); (C.M.)
| | - Catherine McKenzie
- The New Zealand Institute for Plant and Food Research Limited, 412 No 1 Road, RD2, Te Puke 3182, New Zealand; (K.H.); (C.M.)
| | - Andrew Wotton
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11030, Manawatu Mail Centre, Palmerston North 4442, New Zealand; (A.W.); (K.F.); (E.M.); (D.H.); (D.C.)
| | - Keith Funnell
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11030, Manawatu Mail Centre, Palmerston North 4442, New Zealand; (A.W.); (K.F.); (E.M.); (D.H.); (D.C.)
| | - Ed Morgan
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11030, Manawatu Mail Centre, Palmerston North 4442, New Zealand; (A.W.); (K.F.); (E.M.); (D.H.); (D.C.)
| | - Duncan Hedderley
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11030, Manawatu Mail Centre, Palmerston North 4442, New Zealand; (A.W.); (K.F.); (E.M.); (D.H.); (D.C.)
| | - David Chagné
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11030, Manawatu Mail Centre, Palmerston North 4442, New Zealand; (A.W.); (K.F.); (E.M.); (D.H.); (D.C.)
| | - Peter M. Bourke
- Plant Sciences Group, Department of Plant Sciences, Wageningen University and Research, Droevendaalsesteeg 1, P.O. Box 386, 6700 AJ Wageningen, The Netherlands;
| | - John McCallum
- The New Zealand Institute for Plant and Food Research Limited, Lincoln 7608, New Zealand;
| | - Susan E. Gardiner
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11030, Manawatu Mail Centre, Palmerston North 4442, New Zealand; (A.W.); (K.F.); (E.M.); (D.H.); (D.C.)
| | - Luis Gea
- The New Zealand Institute for Plant and Food Research Limited, 412 No 1 Road, RD2, Te Puke 3182, New Zealand; (K.H.); (C.M.)
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Calleja-Rodriguez A, Pan J, Funda T, Chen Z, Baison J, Isik F, Abrahamsson S, Wu HX. Evaluation of the efficiency of genomic versus pedigree predictions for growth and wood quality traits in Scots pine. BMC Genomics 2020; 21:796. [PMID: 33198692 PMCID: PMC7667760 DOI: 10.1186/s12864-020-07188-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 10/26/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Genomic selection (GS) or genomic prediction is a promising approach for tree breeding to obtain higher genetic gains by shortening time of progeny testing in breeding programs. As proof-of-concept for Scots pine (Pinus sylvestris L.), a genomic prediction study was conducted with 694 individuals representing 183 full-sib families that were genotyped with genotyping-by-sequencing (GBS) and phenotyped for growth and wood quality traits. 8719 SNPs were used to compare different genomic with pedigree prediction models. Additionally, four prediction efficiency methods were used to evaluate the impact of genomic breeding value estimations by assigning diverse ratios of training and validation sets, as well as several subsets of SNP markers. RESULTS Genomic Best Linear Unbiased Prediction (GBLUP) and Bayesian Ridge Regression (BRR) combined with expectation maximization (EM) imputation algorithm showed slightly higher prediction efficiencies than Pedigree Best Linear Unbiased Prediction (PBLUP) and Bayesian LASSO, with some exceptions. A subset of approximately 6000 SNP markers, was enough to provide similar prediction efficiencies as the full set of 8719 markers. Additionally, prediction efficiencies of genomic models were enough to achieve a higher selection response, that varied between 50-143% higher than the traditional pedigree-based selection. CONCLUSIONS Although prediction efficiencies were similar for genomic and pedigree models, the relative selection response was doubled for genomic models by assuming that earlier selections can be done at the seedling stage, reducing the progeny testing time, thus shortening the breeding cycle length roughly by 50%.
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Affiliation(s)
- Ainhoa Calleja-Rodriguez
- Skogforsk (The Forestry Research Institute of Sweden), Box 3, Sävar, SE 918 21 Sweden
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, SE - 901 83 Sweden
| | - Jin Pan
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, SE - 901 83 Sweden
| | - Tomas Funda
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, SE - 901 83 Sweden
- Department of Genetics and Breeding, Faculty of Agrobiology and Natural Resources, Czech University of Life Sciences Prague, Prague, 165 00 Czech Republic
- Key Laboratory of Forest Genetics and Biotechnology, Nanjing Forestry University, Nanjing, 210037 China
| | - Zhiqiang Chen
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, SE - 901 83 Sweden
| | - John Baison
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, SE - 901 83 Sweden
- RAGT Seeds, Essex, CB 101TA United Kingdom
| | - Fikret Isik
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695 USA
| | - Sara Abrahamsson
- Skogforsk (The Forestry Research Institute of Sweden), Box 3, Sävar, SE 918 21 Sweden
| | - Harry X. Wu
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, SE - 901 83 Sweden
- Beijing Advanced Innovation Centre for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083 China
- National Research Collection Australia, CSIRO, Canberra, ACT 2601 Australia
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44
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Development and validation of a RAD-Seq target-capture based genotyping assay for routine application in advanced black tiger shrimp (Penaeus monodon) breeding programs. BMC Genomics 2020; 21:541. [PMID: 32758142 PMCID: PMC7430818 DOI: 10.1186/s12864-020-06960-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 07/29/2020] [Indexed: 11/26/2022] Open
Abstract
Background The development of genome-wide genotyping resources has provided terrestrial livestock and crop industries with the unique ability to accurately assess genomic relationships between individuals, uncover the genetic architecture of commercial traits, as well as identify superior individuals for selection based on their specific genetic profile. Utilising recent advancements in de-novo genome-wide genotyping technologies, it is now possible to provide aquaculture industries with these same important genotyping resources, even in the absence of existing genome assemblies. Here, we present the development of a genome-wide SNP assay for the Black Tiger shrimp (Penaeus monodon) through utilisation of a reduced-representation whole-genome genotyping approach (DArTseq). Results Based on a single reduced-representation library, 31,262 polymorphic SNPs were identified across 650 individuals obtained from Australian wild stocks and commercial aquaculture populations. After filtering to remove SNPs with low read depth, low MAF, low call rate, deviation from HWE, and non-Mendelian inheritance, 7542 high-quality SNPs were retained. From these, 4236 high-quality genome-wide loci were selected for baits-probe development and 4194 SNPs were included within a finalized target-capture genotype-by-sequence assay (DArTcap). This assay was designed for routine and cost effective commercial application in large scale breeding programs, and demonstrates higher confidence in genotype calls through increased call rate (from 80.2 ± 14.7 to 93.0% ± 3.5%), increased read depth (from 20.4 ± 15.6 to 80.0 ± 88.7), as well as a 3-fold reduction in cost over traditional genotype-by-sequencing approaches. Conclusion Importantly, this assay equips the P. monodon industry with the ability to simultaneously assign parentage of communally reared animals, undertake genomic relationship analysis, manage mate pairings between cryptic family lines, as well as undertake advance studies of genome and trait architecture. Critically this assay can be cost effectively applied as P. monodon breeding programs transition to undertaking genomic selection.
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45
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Robust genome-wide ancestry inference for heterogeneous datasets: illustrated using the 1,000 genome project with 3D facial images. Sci Rep 2020; 10:11850. [PMID: 32678112 PMCID: PMC7367291 DOI: 10.1038/s41598-020-68259-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 06/19/2020] [Indexed: 11/17/2022] Open
Abstract
Estimates of individual-level genomic ancestry are routinely used in human genetics, and related fields. The analysis of population structure and genomic ancestry can yield insights in terms of modern and ancient populations, allowing us to address questions regarding admixture, and the numbers and identities of the parental source populations. Unrecognized population structure is also an important confounder to correct for in genome-wide association studies. However, it remains challenging to work with heterogeneous datasets from multiple studies collected by different laboratories with diverse genotyping and imputation protocols. This work presents a new approach and an accompanying open-source toolbox that facilitates a robust integrative analysis for population structure and genomic ancestry estimates for heterogeneous datasets. We show robustness against individual outliers and different protocols for the projection of new samples into a reference ancestry space, and the ability to reveal and adjust for population structure in a simulated case–control admixed population. Given that visually evident and easily recognizable patterns of human facial characteristics co-vary with genomic ancestry, and based on the integration of three different sources of genome data, we generate average 3D faces to illustrate genomic ancestry variations within the 1,000 Genome project and for eight ancient-DNA profiles, respectively.
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46
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Genetic Diversity in Invasive Populations of Argentine Stem Weevil Associated with Adaptation to Biocontrol. INSECTS 2020; 11:insects11070441. [PMID: 32674400 PMCID: PMC7411575 DOI: 10.3390/insects11070441] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 06/21/2020] [Accepted: 07/04/2020] [Indexed: 12/19/2022]
Abstract
Modified, agricultural landscapes are susceptible to damage by insect pests. Biological control of pests is typically successful once a control agent has established, but this depends on the agent’s capacity to co-evolve with the host. Theoretical studies have shown that different levels of genetic variation between the host and the control agent will lead to rapid evolution of resistance in the host. Although this has been reported in one instance, the underlying genetics have not been studied. To address this, we measured the genetic variation in New Zealand populations of the pasture pest, Argentine stem weevil (Listronotus bonariensis), which is controlled with declining effectiveness by a parasitoid wasp, Microctonus hyperodae. We constructed a draft reference genome of the weevil, collected samples from a geographical survey of 10 sites around New Zealand, and genotyped them using a modified genotyping-by-sequencing approach. New Zealand populations of Argentine stem weevil have high levels of heterozygosity and low population structure, consistent with a large effective population size and frequent gene flow. This implies that Argentine stem weevils were able to evolve more rapidly than their biocontrol agent, which reproduces asexually. These findings show that monitoring genetic diversity in biocontrol agents and their targets is critical for long-term success of biological control.
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47
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Palaiokostas C, Clarke SM, Jeuthe H, Brauning R, Bilton TP, Dodds KG, McEwan JC, De Koning DJ. Application of Low Coverage Genotyping by Sequencing in Selectively Bred Arctic Charr ( Salvelinus alpinus). G3 (BETHESDA, MD.) 2020; 10:2069-2078. [PMID: 32312839 PMCID: PMC7263669 DOI: 10.1534/g3.120.401295] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 04/16/2020] [Indexed: 12/12/2022]
Abstract
Arctic charr (Salvelinus alpinus) is a species of high economic value for the aquaculture industry, and of high ecological value due to its Holarctic distribution in both marine and freshwater environments. Novel genome sequencing approaches enable the study of population and quantitative genetic parameters even on species with limited or no prior genomic resources. Low coverage genotyping by sequencing (GBS) was applied in a selected strain of Arctic charr in Sweden originating from a landlocked freshwater population. For the needs of the current study, animals from year classes 2013 (171 animals, parental population) and 2017 (759 animals; 13 full sib families) were used as a template for identifying genome wide single nucleotide polymorphisms (SNPs). GBS libraries were constructed using the PstI and MspI restriction enzymes. Approximately 14.5K SNPs passed quality control and were used for estimating a genomic relationship matrix. Thereafter a wide range of analyses were conducted in order to gain insights regarding genetic diversity and investigate the efficiency of the genomic information for parentage assignment and breeding value estimation. Heterozygosity estimates for both year classes suggested a slight excess of heterozygotes. Furthermore, FST estimates among the families of year class 2017 ranged between 0.009 - 0.066. Principal components analysis (PCA) and discriminant analysis of principal components (DAPC) were applied aiming to identify the existence of genetic clusters among the studied population. Results obtained were in accordance with pedigree records allowing the identification of individual families. Additionally, DNA parentage verification was performed, with results in accordance with the pedigree records with the exception of a putative dam where full sib genotypes suggested a potential recording error. Breeding value estimation for juvenile growth through the usage of the estimated genomic relationship matrix clearly outperformed the pedigree equivalent in terms of prediction accuracy (0.51 opposed to 0.31). Overall, low coverage GBS has proven to be a cost-effective genotyping platform that is expected to boost the selection efficiency of the Arctic charr breeding program.
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Affiliation(s)
- Christos Palaiokostas
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7090, 750 07 Uppsala, Sweden,
| | - Shannon M Clarke
- Invermay Agricultural Centre, AgResearch, Private Bag 50034, Mosgiel 9053, New Zealand
| | - Henrik Jeuthe
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7090, 750 07 Uppsala, Sweden
- Aquaculture Center North, Åvägen 17, 844 61 Kälarne, Sweden, and
| | - Rudiger Brauning
- Invermay Agricultural Centre, AgResearch, Private Bag 50034, Mosgiel 9053, New Zealand
| | - Timothy P Bilton
- Invermay Agricultural Centre, AgResearch, Private Bag 50034, Mosgiel 9053, New Zealand
- Department of Mathematics and Statistics, University of Otago, Dunedin 9054, New Zealand
| | - Ken G Dodds
- Invermay Agricultural Centre, AgResearch, Private Bag 50034, Mosgiel 9053, New Zealand
| | - John C McEwan
- Invermay Agricultural Centre, AgResearch, Private Bag 50034, Mosgiel 9053, New Zealand
| | - Dirk-Jan De Koning
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7090, 750 07 Uppsala, Sweden
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48
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Sabahat S, Brauning R, Clarke SM, Nadeem A, Thomson PC, Khatkar MS. SNP discovery and population structure analysis in Lassi and Marecha camel breeds using a genotyping by sequencing method. Anim Genet 2020; 51:620-623. [PMID: 32421863 DOI: 10.1111/age.12953] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 04/24/2020] [Accepted: 04/24/2020] [Indexed: 11/27/2022]
Abstract
Pakistani camels have been classified socio-geographically into 20 breeds, but they have not yet been subjected to substantial selective pressures and the genetic basis for these breeds is not understood. However, it should be possible to distinguish them by use of molecular data. This study investigated the genetic diversity and population structure within and between two major Pakistani camel breeds, Marecha and Lassi. As no SNP array is currently available, we first identified 63 619 SNPs using a genotyping by sequencing approach. After quality control, a panel of 36 926 SNPs was used in the analysis. Population structure was investigated with a principal coordinate analysis as well as a cluster analysis using NetView, and multilocus heterozygosity analysis to explore between- and within-breed genetic variation. In addition, between-breed variation was explored using the fixation index, FST . We also compared relationship matrices computed using the VanRaden SNP-based method and a method developed specifically for genotyping by sequencing data. Among the two camel breeds, Lassi showed a lower level of genetic diversity whereas Marecha showed a higher level. As a genotyping platform has not yet been developed for the camel, the SNPs discovered in this study will be useful in future genetic studies in camels.
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Affiliation(s)
- S Sabahat
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Shaykh Abdul Qadir Jilani Road, Lahore, 54000, Pakistan.,Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, 425 Werombi Road, Camden, NSW, 2570, Australia
| | - R Brauning
- Invermay Agricultural Centre, AgResearch, 176 Puddle Alley, Mosgiel, 9092, New Zealand
| | - S M Clarke
- Invermay Agricultural Centre, AgResearch, 176 Puddle Alley, Mosgiel, 9092, New Zealand
| | - A Nadeem
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Shaykh Abdul Qadir Jilani Road, Lahore, 54000, Pakistan
| | - P C Thomson
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Shaykh Abdul Qadir Jilani Road, Lahore, 54000, Pakistan.,Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, 425 Werombi Road, Camden, NSW, 2570, Australia
| | - M S Khatkar
- Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, 425 Werombi Road, Camden, NSW, 2570, Australia
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49
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Galla SJ, Moraga R, Brown L, Cleland S, Hoeppner MP, Maloney RF, Richardson A, Slater L, Santure AW, Steeves TE. A comparison of pedigree, genetic and genomic estimates of relatedness for informing pairing decisions in two critically endangered birds: Implications for conservation breeding programmes worldwide. Evol Appl 2020; 13:991-1008. [PMID: 32431748 PMCID: PMC7232769 DOI: 10.1111/eva.12916] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 12/27/2019] [Accepted: 01/02/2020] [Indexed: 12/18/2022] Open
Abstract
Conservation management strategies for many highly threatened species include conservation breeding to prevent extinction and enhance recovery. Pairing decisions for these conservation breeding programmes can be informed by pedigree data to minimize relatedness between individuals in an effort to avoid inbreeding, maximize diversity and maintain evolutionary potential. However, conservation breeding programmes struggle to use this approach when pedigrees are shallow or incomplete. While genetic data (i.e., microsatellites) can be used to estimate relatedness to inform pairing decisions, emerging evidence indicates this approach may lack precision in genetically depauperate species, and more effective estimates will likely be obtained from genomic data (i.e., thousands of genome-wide single nucleotide polymorphisms, or SNPs). Here, we compare relatedness estimates and subsequent pairing decisions using pedigrees, microsatellites and SNPs from whole-genome resequencing approaches in two critically endangered birds endemic to New Zealand: kakī/black stilt (Himantopus novaezelandiae) and kākāriki karaka/orange-fronted parakeet (Cyanoramphus malherbi). Our findings indicate that SNPs provide more precise estimates of relatedness than microsatellites when assessing empirical parent-offspring and full sibling relationships. Further, our results show that relatedness estimates and subsequent pairing recommendations using PMx are most similar between pedigree- and SNP-based approaches. These combined results indicate that in lieu of robust pedigrees, SNPs are an effective tool for informing pairing decisions, which has important implications for many poorly pedigreed conservation breeding programmes worldwide.
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Affiliation(s)
- Stephanie J. Galla
- School of Biological SciencesUniversity of CanterburyChristchurchNew Zealand
| | - Roger Moraga
- Tea Break Bioinformatics, LtdPalmerston NorthNew Zealand
| | - Liz Brown
- New Zealand Department of ConservationTwizelNew Zealand
| | | | - Marc P. Hoeppner
- Institute for Clinical Molecular BiologyChristian‐Albrechts‐University KielKielGermany
| | | | - Anne Richardson
- The Isaac Conservation and Wildlife TrustChristchurchNew Zealand
| | - Lyndon Slater
- New Zealand Department of ConservationRangioraNew Zealand
| | - Anna W. Santure
- School of Biological SciencesUniversity of AucklandAucklandNew Zealand
| | - Tammy E. Steeves
- School of Biological SciencesUniversity of CanterburyChristchurchNew Zealand
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50
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Dierickx EG, Sin SYW, van Veelen HPJ, Brooke MDL, Liu Y, Edwards SV, Martin SH. Genetic diversity, demographic history and neo-sex chromosomes in the Critically Endangered Raso lark. Proc Biol Sci 2020; 287:20192613. [PMID: 32126957 PMCID: PMC7126062 DOI: 10.1098/rspb.2019.2613] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Small effective population sizes could expose island species to inbreeding and loss of genetic variation. Here, we investigate factors shaping genetic diversity in the Raso lark, which has been restricted to a single islet for approximately 500 years, with a population size of a few hundred. We assembled a reference genome for the related Eurasian skylark and then assessed diversity and demographic history using RAD-seq data (75 samples from Raso larks and two related mainland species). We first identify broad tracts of suppressed recombination in females, indicating enlarged neo-sex chromosomes. We then show that genetic diversity across autosomes in the Raso lark is lower than in its mainland relatives, but inconsistent with long-term persistence at its current population size. Finally, we find that genetic signatures of the recent population contraction are overshadowed by an ancient expansion and persistence of a very large population until the human settlement of Cape Verde. Our findings show how genome-wide approaches to study endangered species can help avoid confounding effects of genome architecture on diversity estimates, and how present-day diversity can be shaped by ancient demographic events.
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Affiliation(s)
- Elisa G Dierickx
- Department of Zoology, University of Cambridge, Cambridge, UK.,Fauna and Flora International, Cambridge, UK
| | - Simon Yung Wa Sin
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA.,School of Biological Sciences, University of Hong Kong, Hong Kong, People's Republic of China
| | - H Pieter J van Veelen
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, The Netherlands.,Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - M de L Brooke
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Yang Liu
- Department of Ecology, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Simon H Martin
- Department of Zoology, University of Cambridge, Cambridge, UK.,Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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