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Mc Cartney AM, Scholz AH, Groussin M, Staunton C. Benefit-Sharing by Design: A Call to Action for Human Genomics Research. Annu Rev Genomics Hum Genet 2024; 25:369-395. [PMID: 38608642 DOI: 10.1146/annurev-genom-021623-104241] [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] [Indexed: 04/14/2024]
Abstract
The ethical standards for the responsible conduct of human research have come a long way; however, concerns surrounding equity remain in human genetics and genomics research. Addressing these concerns will help society realize the full potential of human genomics research. One outstanding concern is the fair and equitable sharing of benefits from research on human participants. Several international bodies have recognized that benefit-sharing can be an effective tool for ethical research conduct, but international laws, including the Convention on Biological Diversity and its Nagoya Protocol on Access and Benefit-Sharing, explicitly exclude human genetic and genomic resources. These agreements face significant challenges that must be considered and anticipated if similar principles are applied in human genomics research. We propose that benefit-sharing from human genomics research can be a bottom-up effort and embedded into the existing research process. We propose the development of a "benefit-sharing by design" framework to address concerns of fairness and equity in the use of human genomic resources and samples and to learn from the aspirations and decade of implementation of the Nagoya Protocol.
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Affiliation(s)
- Ann M Mc Cartney
- Genomics Institute, University of California, Santa Cruz, California, USA;
| | - Amber Hartman Scholz
- Department of Science Policy and Internationalisation, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany;
| | - Mathieu Groussin
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany;
| | - Ciara Staunton
- School of Law, University of KwaZulu-Natal, Durban, South Africa
- Institute for Biomedicine, Eurac Research, Bolzano, Italy;
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Bem RD, Benfica LF, Silva DA, Carrara ER, Brito LF, Mulim HA, Borges MS, Cyrillo JNSG, Canesin RC, Bonilha SFM, Mercadante MEZ. Assessing different metrics of pedigree and genomic inbreeding and inbreeding effect on growth, fertility, and feed efficiency traits in a closed-herd Nellore cattle population. BMC Genomics 2024; 25:738. [PMID: 39080557 PMCID: PMC11290228 DOI: 10.1186/s12864-024-10641-3] [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: 04/05/2024] [Accepted: 07/19/2024] [Indexed: 08/02/2024] Open
Abstract
BACKGROUND The selection of individuals based on their predicted breeding values and mating of related individuals can increase the proportion of identical-by-descent alleles. In this context, the objectives of this study were to estimate inbreeding coefficients based on alternative metrics and data sources such as pedigree (FPED), hybrid genomic relationship matrix H (FH), and ROH of different length (FROH); and calculate Pearson correlations between the different metrics in a closed Nellore cattle population selected for body weight adjusted to 378 days of age (W378). In addition to total FROH (all classes) coefficients were also estimated based on the size class of the ROH segments: FROH1 (1-2 Mb), FROH2 (2-4 Mb), FROH3 (4-8 Mb), FROH4 (8-16 Mb), and FROH5 (> 16 Mb), and for each chromosome (FROH_CHR). Furthermore, we assessed the effect of each inbreeding metric on birth weight (BW), body weights adjusted to 210 (W210) and W378, scrotal circumference (SC), and residual feed intake (RFI). We also evaluated the chromosome-specific effects of inbreeding on growth traits. RESULTS The correlation between FPED and FROH was 0.60 while between FH and FROH and FH and FPED were 0.69 and 0.61, respectively. The annual rate of inbreeding was 0.16% for FPED, 0.02% for FH, and 0.16% for FROH. A 1% increase in FROH5 resulted in a reduction of up to -1.327 ± 0.495 kg in W210 and W378. Four inbreeding coefficients (FPED, FH, FROH2, and FROH5) had a significant effect on W378, with reductions of up to -3.810 ± 1.753 kg per 1% increase in FROH2. There was an unfavorable effect of FPED on RFI (0.01 ± 0.0002 kg dry matter/day) and of FROH on SC (-0.056 ± 0.022 cm). The FROH_CHR coefficients calculated for BTA3, BTA5, and BTA8 significantly affected the growth traits. CONCLUSIONS Inbreeding depression was observed for all traits evaluated. However, these effects were greater for the criterion used for selection of the animals (i.e., W378). The increase in the genomic inbreeding was associated with a higher inbreeding depression on the traits evaluated when compared to pedigree-based inbreeding. Genomic information should be used as a tool during mating to optimize control of inbreeding and, consequently, minimize inbreeding depression in Nellore cattle.
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Affiliation(s)
- Ricardo D Bem
- Institute of Animal Science, Sertãozinho, SP, Brazil.
- Department of Animal Science, Faculty of Agricultural and Veterinary Sciences, Sao Paulo State University, Jaboticabal, SP, Brazil.
| | - Lorena F Benfica
- Department of Animal Sciences, Purdue University, 270 S. Russell Street, West Lafayette, IN, 47907, USA
| | - Delvan A Silva
- Department of Animal Sciences, Federal University of Viçosa, Viçosa, MG, Brazil
| | - Eula R Carrara
- Department of Animal Sciences, Federal University of Viçosa, Viçosa, MG, Brazil
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, 270 S. Russell Street, West Lafayette, IN, 47907, USA
| | - Henrique A Mulim
- Department of Animal Sciences, Purdue University, 270 S. Russell Street, West Lafayette, IN, 47907, USA
| | - Marcelo S Borges
- Department of Pathology, Reproduction and One Health, Faculty of Agricultural and Veterinary Sciences, Sao Paulo State University, Jaboticabal, SP, Brazil
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Akinsola OM, Musa AA, Muansangi L, Singh SP, Mukherjee S, Mukherjee A. Genomic insights into adaptation and inbreeding among Sub-Saharan African cattle from pastoral and agropastoral systems. Front Genet 2024; 15:1430291. [PMID: 39119582 PMCID: PMC11306176 DOI: 10.3389/fgene.2024.1430291] [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: 05/09/2024] [Accepted: 07/11/2024] [Indexed: 08/10/2024] Open
Abstract
Background In Sub-Saharan Africa (SSA), cattle are crucial for socioeconomic stability yet face numerous environmental stressors such as diseases, parasites, and extreme heat within pastoral and agropastoral systems. Despite their significance, gaps remain in understanding how genetic diversity and inbreeding influence traits essential for disease resistance and environmental adaptability. This study examines the genomic adaptations that enable SSA cattle to thrive under these conditions and assesses the impact of inbreeding on such adaptive traits. Methods We analyzed genomic data from 113 cattle across four breeds-Kuri, N'dama, Zebu-Fulani, and Zebu-Bororo-employing Runs of Homozygosity (ROH) and Integrated Haplotype Score (iHS) analyses to identify historical and recent genetic selections. Strict quality controls using PLINK software ensured accurate genomic pattern identification related to adaptation and inbreeding. Results ROH analysis revealed islands with genes such as RSAD2, CMPK2, and NOTCH1, which are involved in immune response and cellular stress management, highlighting regions of historical selection that have likely provided adaptive advantages in overcoming environmental and pathogenic stresses. In contrast, iHS analysis identified genes under recent selection like HIPK1, involved in stress response regulation, and EPHA5, which plays a crucial role in neural development and synaptic functions, potentially equipping these breeds with novel adaptations to ongoing and emergent environmental challenges. Conclusion This research confirms that selective pressures inherent in pastoral and agropastoral systems profoundly influence the genetic structure of SSA cattle. By delineating the genetic bases of key adaptive traits, our study offers crucial insights for targeted breeding programs to enhance cattle resilience and productivity. These findings provide a valuable framework for future genetic improvements and conservation strategies, crucial for sustainable livestock management and economic stability in SSA.
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Affiliation(s)
- Oludayo M. Akinsola
- Department of Theriogenology and Production, Faculty of Veterinary Medicine, University of Jos, Jos, Nigeria
| | | | - Lal Muansangi
- Animal Genetics and Breeding Division, Indian Council of Agricultural Research (ICAR)-National Dairy Research Institute (NDRI), Karnal, Haryana, India
| | - Sanchit P. Singh
- Animal Genetics and Breeding Division, Indian Council of Agricultural Research (ICAR)-National Dairy Research Institute (NDRI), Karnal, Haryana, India
| | - Sabyasachi Mukherjee
- Animal Genetics and Breeding Division, Indian Council of Agricultural Research (ICAR)-National Dairy Research Institute (NDRI), Karnal, Haryana, India
| | - Anupama Mukherjee
- Animal Genetics and Breeding Division, Indian Council of Agricultural Research (ICAR)-National Dairy Research Institute (NDRI), Karnal, Haryana, India
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Jighly A. Boosting genome-wide association power and genomic prediction accuracy for date palm fruit traits with advanced statistics. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 344:112110. [PMID: 38704095 DOI: 10.1016/j.plantsci.2024.112110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 03/05/2024] [Accepted: 04/30/2024] [Indexed: 05/06/2024]
Abstract
The date palm is economically vital in the Middle East and North Africa, providing essential fibres, vitamins, and carbohydrates. Understanding the genetic architecture of its traits remains complex due to the tree's perennial nature and long generation times. This study aims to address these complexities by employing advanced genome-wide association (GWAS) and genomic prediction models using previously published data involving fruit acid content, sugar content, dimension, and colour traits. The multivariate GWAS model identified seven QTL, including five novel associations, that shed light on the genetic control of these traits. Furthermore, the research evaluates different genomic prediction models that considered genotype by environment and genotype by trait interactions. While colour- traits demonstrate strong predictive power, other traits display moderate accuracies across different models and scenarios aligned with the expectations when using small reference populations. When designing the cross-validation to predict new individuals, the accuracy of the best multi-trait model was significantly higher than all single-trait models for dimension traits, but not for the remaining traits, which showed similar performances. However, the cross-validation strategy that masked random phenotypic records (i.e., mimicking the unbalanced phenotypic records) showed significantly higher accuracy for all traits except acid contents. The findings underscore the importance of understanding genetic architecture for informed breeding strategies. The research emphasises the need for larger population sizes and multivariate models to enhance gene tagging power and predictive accuracy to advance date palm breeding programs. These findings support more targeted breeding in date palm, improving productivity and resilience to various environments.
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Yang YC, Chu PY, Chen CC, Yang WC, Hsu TH, Gong HY, Liao IC, Huang CW. Transcriptomic Insights and the Development of Microsatellite Markers to Assess Genetic Diversity in the Broodstock Management of Litopenaeus stylirostris. Animals (Basel) 2024; 14:1685. [PMID: 38891732 PMCID: PMC11171113 DOI: 10.3390/ani14111685] [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: 04/28/2024] [Revised: 05/22/2024] [Accepted: 06/02/2024] [Indexed: 06/21/2024] Open
Abstract
The Pacific blue shrimp (Litopenaeus stylirostris) is a premium product in the international seafood market. However, intensified farming has increased disease incidence and reduced genetic diversity. In this study, we developed a transcriptome database for L. stylirostris and mined microsatellite markers to analyze their genetic diversity. Using the Illumina HiSeq 4000 platform, we identified 53,263 unigenes from muscle, hepatopancreas, the intestine, and lymphoid tissues. Microsatellite analysis identified 36,415 markers from 18,657 unigenes, predominantly dinucleotide repeats. Functional annotation highlighted key disease resistance pathways and enriched categories. The screening and PCR testing of 42 transcriptome-based and 58 literature-based markers identified 40 with successful amplification. The genotyping of 200 broodstock samples revealed that Na, Ho, He, PIC, and FIS values were 3, 0.54 ± 0.05, 0.43 ± 0.09, 0.41 ± 0.22, and 0.17 ± 0.27, respectively, indicating moderate genetic variability and significant inbreeding. Four universal microsatellite markers (CL1472.Contig13, CL517.Contig2, Unigene5692, and Unigene7147) were identified for precise diversity analysis in Pacific blue, Pacific white (Litopenaeus vannamei), and black tiger shrimps (Penaeus monodon). The transcriptome database supports the development of markers and functional gene analysis for selective breeding programs. Our findings underscore the need for an appropriate genetic management system to mitigate inbreeding depression, reduce disease susceptibility, and preserve genetic diversity in farmed shrimp populations.
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Affiliation(s)
- Ya-Chi Yang
- Department of Aquaculture, National Taiwan Ocean University, 2 Beining Road, Jhongjheng District, Keelung City 20224, Taiwan; (Y.-C.Y.); (P.-Y.C.); (C.-C.C.); (T.-H.H.); (H.-Y.G.)
| | - Pei-Yun Chu
- Department of Aquaculture, National Taiwan Ocean University, 2 Beining Road, Jhongjheng District, Keelung City 20224, Taiwan; (Y.-C.Y.); (P.-Y.C.); (C.-C.C.); (T.-H.H.); (H.-Y.G.)
| | - Che-Chun Chen
- Department of Aquaculture, National Taiwan Ocean University, 2 Beining Road, Jhongjheng District, Keelung City 20224, Taiwan; (Y.-C.Y.); (P.-Y.C.); (C.-C.C.); (T.-H.H.); (H.-Y.G.)
| | - Wen-Chin Yang
- Agricultural Biotechnology Research Center, Academia Sinica, No. 128, Academia Sinica Road, Sec. 2, Nankang, Taipei 11529, Taiwan;
| | - Te-Hua Hsu
- Department of Aquaculture, National Taiwan Ocean University, 2 Beining Road, Jhongjheng District, Keelung City 20224, Taiwan; (Y.-C.Y.); (P.-Y.C.); (C.-C.C.); (T.-H.H.); (H.-Y.G.)
- Center of Excellence for the Oceans, National Taiwan Ocean University, 2 Beining Road, Jhongjheng District, Keelung City 20224, Taiwan;
| | - Hong-Yi Gong
- Department of Aquaculture, National Taiwan Ocean University, 2 Beining Road, Jhongjheng District, Keelung City 20224, Taiwan; (Y.-C.Y.); (P.-Y.C.); (C.-C.C.); (T.-H.H.); (H.-Y.G.)
- Center of Excellence for the Oceans, National Taiwan Ocean University, 2 Beining Road, Jhongjheng District, Keelung City 20224, Taiwan;
| | - I Chiu Liao
- Center of Excellence for the Oceans, National Taiwan Ocean University, 2 Beining Road, Jhongjheng District, Keelung City 20224, Taiwan;
| | - Chang-Wen Huang
- Department of Aquaculture, National Taiwan Ocean University, 2 Beining Road, Jhongjheng District, Keelung City 20224, Taiwan; (Y.-C.Y.); (P.-Y.C.); (C.-C.C.); (T.-H.H.); (H.-Y.G.)
- Center of Excellence for the Oceans, National Taiwan Ocean University, 2 Beining Road, Jhongjheng District, Keelung City 20224, Taiwan;
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Niehoff TAM, Ten Napel J, Bijma P, Pook T, Wientjes YCJ, Hegedűs B, Calus MPL. Improving selection decisions with mating information by accounting for Mendelian sampling variances looking two generations ahead. Genet Sel Evol 2024; 56:41. [PMID: 38773363 PMCID: PMC11107025 DOI: 10.1186/s12711-024-00899-2] [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: 11/07/2023] [Accepted: 04/03/2024] [Indexed: 05/23/2024] Open
Abstract
BACKGROUND Breeding programs are judged by the genetic level of animals that are used to disseminate genetic progress. These animals are typically the best ones of the population. To maximise the genetic level of very good animals in the next generation, parents that are more likely to produce top performing offspring need to be selected. The ability of individuals to produce high-performing progeny differs because of differences in their breeding values and gametic variances. Differences in gametic variances among individuals are caused by differences in heterozygosity and linkage. The use of the gametic Mendelian sampling variance has been proposed before, for use in the usefulness criterion or Index5, and in this work, we extend existing approaches by not only considering the gametic Mendelian sampling variance of individuals, but also of their potential offspring. Thus, the criteria developed in this study plan one additional generation ahead. For simplicity, we assumed that the true quantitative trait loci (QTL) effects, genetic map and the haplotypes of all animals are known. RESULTS In this study, we propose a new selection criterion, ExpBVSelGrOff, which describes the genetic level of selected grand-offspring that are produced by selected offspring of a particular mating. We compare our criterion with other published criteria in a stochastic simulation of an ongoing breeding program for 21 generations for proof of concept. ExpBVSelGrOff performed better than all other tested criteria, like the usefulness criterion or Index5 which have been proposed in the literature, without compromising short-term gains. After only five generations, when selection is strong (1%), selection based on ExpBVSelGrOff achieved 5.8% more commercial genetic gain and retained 25% more genetic variance without compromising inbreeding rate compared to selection based only on breeding values. CONCLUSIONS Our proposed selection criterion offers a new tool to accelerate genetic progress for contemporary genomic breeding programs. It retains more genetic variance than previously published criteria that plan less far ahead. Considering future gametic Mendelian sampling variances in the selection process also seems promising for maintaining more genetic variance.
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Grants
- TKI Agri This study was financially supported by the Dutch Ministry of Economic Affairs (TKI Agri & Food Project LWV20054) and the Breed4Food partners Cobb Europe (Colchester, Essex, United Kingdom), CRV (Arnhem, the Netherlands), Hendrix Genetics (Boxmeer, the Net
- Food Project LWV20054 This study was financially supported by the Dutch Ministry of Economic Affairs (TKI Agri & Food Project LWV20054) and the Breed4Food partners Cobb Europe (Colchester, Essex, United Kingdom), CRV (Arnhem, the Netherlands), Hendrix Genetics (Boxmeer, the Net
- This study was financially supported by the Dutch Ministry of Economic Affairs (TKI Agri & Food Project LWV20054) and the Breed4Food partners Cobb Europe (Colchester, Essex, United Kingdom), CRV (Arnhem, the Netherlands), Hendrix Genetics (Boxmeer, the Net
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Affiliation(s)
- Tobias A M Niehoff
- Animal Breeding and Genomics, Wageningen University and Research, Droevendaalsesteeg 1, 6700AH, Wageningen, The Netherlands.
| | - Jan Ten Napel
- Animal Breeding and Genomics, Wageningen University and Research, Droevendaalsesteeg 1, 6700AH, Wageningen, The Netherlands
| | - Piter Bijma
- Animal Breeding and Genomics, Wageningen University and Research, Droevendaalsesteeg 1, 6700AH, Wageningen, The Netherlands
| | - Torsten Pook
- Animal Breeding and Genomics, Wageningen University and Research, Droevendaalsesteeg 1, 6700AH, Wageningen, The Netherlands
| | - Yvonne C J Wientjes
- Animal Breeding and Genomics, Wageningen University and Research, Droevendaalsesteeg 1, 6700AH, Wageningen, The Netherlands
| | - Bernadett Hegedűs
- Animal Breeding and Genomics, Wageningen University and Research, Droevendaalsesteeg 1, 6700AH, Wageningen, The Netherlands
| | - Mario P L Calus
- Animal Breeding and Genomics, Wageningen University and Research, Droevendaalsesteeg 1, 6700AH, Wageningen, The Netherlands
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Legarra A, Bermann M, Mei Q, Christensen OF. Redefining and interpreting genomic relationships of metafounders. Genet Sel Evol 2024; 56:34. [PMID: 38698373 DOI: 10.1186/s12711-024-00891-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 03/18/2024] [Indexed: 05/05/2024] Open
Abstract
Metafounders are a useful concept to characterize relationships within and across populations, and to help genetic evaluations because they help modelling the means and variances of unknown base population animals. Current definitions of metafounder relationships are sensitive to the choice of reference alleles and have not been compared to their counterparts in population genetics-namely, heterozygosities, FST coefficients, and genetic distances. We redefine the relationships across populations with an arbitrary base of a maximum heterozygosity population in Hardy-Weinberg equilibrium. Then, the relationship between or within populations is a cross-product of the formΓ b , b ' = 2 n 2 p b - 1 2 p b ' - 1 ' with p being vectors of allele frequencies at n markers in populations b and b ' . This is simply the genomic relationship of two pseudo-individuals whose genotypes are equal to twice the allele frequencies. We also show that this coding is invariant to the choice of reference alleles. In addition, standard population genetics metrics (inbreeding coefficients of various forms; FST differentiation coefficients; segregation variance; and Nei's genetic distance) can be obtained from elements of matrix Γ .
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Affiliation(s)
| | - Matias Bermann
- Animal and Dairy Science, University of Georgia, 425 River Rd, Athens, GA, 30602, USA
| | - Quanshun Mei
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Ole F Christensen
- Center for Quantitative Genetics and Genomics, Aarhus University, C. F. Møllers Allé 3, Bld. 1130, 8000, Aarhus C, Denmark
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Gomez Proto G, Mancin E, Sartori C, Mantovani R. Unraveling inbreeding patterns and selection signals in Alpine Grey cattle. Animal 2024; 18:101159. [PMID: 38718700 DOI: 10.1016/j.animal.2024.101159] [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: 11/14/2023] [Revised: 04/03/2024] [Accepted: 04/04/2024] [Indexed: 05/18/2024] Open
Abstract
Inbreeding plays a crucial role in livestock breeding, influencing genetic diversity and phenotypic traits. Genomic data have helped address limitations posed by incomplete pedigrees, providing deeper insights into breed genetic diversity. This study assesses inbreeding levels via pedigree and genomic approaches and analyzes old and recent inbreeding using runs of homozygosity (ROH), and selection signals in Alpine Grey cattle. Pedigree data from 165 575 individuals, analyzed with INBUPGF90 software, computed inbreeding coefficients. Genomic-based coefficients derived from PLINK v1.9. or DetectRUNS R package analyses of 1 180 individuals' genotypes. Common single nucleotide polymorphisms within ROH pinpointed genomic regions, aggregating into "ROH islands" indicative of selection pressure. Overlaps with USCS Genome Browser unveiled gene presence. Moderate correlations (0.20-0.54) existed between pedigree and genomic coefficients, with most genomic estimators having higher (>0.8) correlation values. Inbreeding averaged 0.04 in < 8 Mb ROH segments, and 0.03 in > 16 Mb segments; > 90% of ROHs were < 8 Mb, indicating ancient inbreeding prevalence. Recent inbreeding proved less detrimental than in cosmopolitan breeds. Two major ROH islands on chromosomes 6 and 7 harbored genes linked to immune response, disease resistance (PYURF, HERC3), and fertility (EIF4EBP3, SRA1). This study underscores the need for detailed inbreeding analyses to understand genetic characteristics and historical changes in local breeds like Alpine Grey cattle. Genomic insights, especially from ROH, facilitated overcoming pedigree limitations, illuminating breed genetic diversity. Our findings reveal ancient inbreeding's enduring genetic impact and ROH islands potential for selective sweeps, elucidating traits in Alpine Grey cattle.
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Affiliation(s)
- G Gomez Proto
- Department of Agronomy, Food, Natural Resources, Animals and Environmet, University of Padua, Viale dell'Università, 16, 35020 Legnaro, Italy.
| | - E Mancin
- Department of Agronomy, Food, Natural Resources, Animals and Environmet, University of Padua, Viale dell'Università, 16, 35020 Legnaro, Italy
| | - C Sartori
- Department of Agronomy, Food, Natural Resources, Animals and Environmet, University of Padua, Viale dell'Università, 16, 35020 Legnaro, Italy
| | - R Mantovani
- Department of Agronomy, Food, Natural Resources, Animals and Environmet, University of Padua, Viale dell'Università, 16, 35020 Legnaro, Italy
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Brandão MM, de Almeida Vieira F, Neves AGDS, dos Santos RM, de Carvalho D, Menezes EV, de Moreira PA, de Oliveira DA, Júnior AFDM, Royo VDA. Unraveling the genetic diversity of Ceiba pubiflora (Malvaceae) in isolated limestone outcrops: Conservation strategies. PLoS One 2024; 19:e0299361. [PMID: 38557644 PMCID: PMC10984428 DOI: 10.1371/journal.pone.0299361] [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: 08/13/2023] [Accepted: 02/09/2024] [Indexed: 04/04/2024] Open
Abstract
Seasonally Dry Tropical Forests (SDTFs) located on limestone outcrops are vulnerable to degradation caused by timber logging and limestone extraction for cement production. Some of these forests represent the last remnants of native vegetation cover, functioning as isolated islands. Ceiba pubiflora (Malvaceae) is a tree frequently found on limestone outcrops in the central region of Brazil. This study aimed to evaluate the genetic diversity and identify suitable populations for the establishment of Management Units (MUs) for conservation. Inter-simple sequence repeat markers were employed to assess the genetic diversity in ten populations sampled from the Caatinga, Cerrado, and Atlantic Forest biomes. The species exhibited substantial genetic diversity (HT = 0.345; PLP = 97.89%). Populations SAH, JAN, and MON demonstrated elevated rates of polymorphic loci (> 84.2%) along with notable genetic diversity (He > 0.325). Additionally, these populations were the primary contributors to gene flow. The analysis of molecular variance (AMOVA) indicated that most genetic variation occurs within populations (91.5%) than between them. In the Bayesian analysis, the ten populations were clustered into five groups, revealing the presence of at least three barriers to gene flow in the landscape: 1) the Central Plateau or Paranã River valley; 2) near the Espinhaço mountains or the São Francisco River valley; and 3) around the Mantiqueira mountain range, Chapada dos Veadeiros plateau, and disturbed areas. A positive and statistically significant correlation was observed between genetic (θB) and geographic distances (r = 0.425, p = 0.008). Based on these findings, we propose the establishment of Management Units in Minas Gerais state, encompassing the (1) southern region (MIN population), (2) central region (SAH population), and (3) north region (MON population), as well as in Goiás state, covering the (4) Central Plateau region. These units can significantly contribute to preserving the genetic diversity of these trees and protecting their habitat against ongoing threats.
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Affiliation(s)
- Murilo Malveira Brandão
- Department of Biological Sciences, State University of Montes Claros, Montes Claros, Minas Gerais, Brazil
| | - Fábio de Almeida Vieira
- Academic Unit Specialized in Agricultural Sciences, Federal University of Rio Grande do Norte, Macaíba, Rio Grande do Norte, Brazil
| | - Abidã Gênesis da Silva Neves
- Academic Unit Specialized in Agricultural Sciences, Federal University of Rio Grande do Norte, Macaíba, Rio Grande do Norte, Brazil
| | | | - Dulcineia de Carvalho
- Department of Forest Science, Federal University of Lavras, Lavras, Minas Gerais, Brazil
| | - Elytania Veiga Menezes
- Department of Biological Sciences, State University of Montes Claros, Montes Claros, Minas Gerais, Brazil
| | - Patrícia Abreu de Moreira
- Institute of Exact and Biological Sciences, Federal University of Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - Dario Alves de Oliveira
- Department of Biological Sciences, State University of Montes Claros, Montes Claros, Minas Gerais, Brazil
| | | | - Vanessa de Andrade Royo
- Department of Biological Sciences, State University of Montes Claros, Montes Claros, Minas Gerais, Brazil
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Tsheten G, Fuerst-Waltl B, Pfeiffer C, Sölkner J, Bovenhuis H, Mészáros G. Inbreeding depression and its effect on sperm quality traits in Pietrain pigs. J Anim Breed Genet 2023; 140:653-662. [PMID: 37409752 DOI: 10.1111/jbg.12816] [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: 07/13/2022] [Revised: 06/21/2023] [Accepted: 06/23/2023] [Indexed: 07/07/2023]
Abstract
In most cases, inbreeding is expected to have unfavourable effects on traits in livestock. The consequences of inbreeding depression could be substantial, primarily in reproductive and sperm quality traits, and thus lead to decreased fertility. Therefore, the objectives of this study were (i) to compute inbreeding coefficients using pedigree (FPED ) and genomic data based on runs of homozygosity (ROH) in the genome (FROH ) of Austrian Pietrain pigs, and (ii) to assess inbreeding depression on four sperm quality traits. In total, 74,734 ejaculate records from 1034 Pietrain boars were used for inbreeding depression analyses. Traits were regressed on inbreeding coefficients using repeatability animal models. Pedigree-based inbreeding coefficients were lower than ROH-based inbreeding values. The correlations between pedigree and ROH-based inbreeding coefficients ranged from 0.186 to 0.357. Pedigree-based inbreeding affected only sperm motility while ROH-based inbreeding affected semen volume, number of spermatozoa, and motility. For example, a 1% increase in pedigree inbreeding considering 10 ancestor generations (FPED10 ) was significantly (p < 0.05) associated with a 0.231% decrease in sperm motility. Almost all estimated effects of inbreeding on the traits studied were unfavourable. It is advisable to properly manage the level of inbreeding to avoid high inbreeding depression in the future. Further, analysis of effects of inbreeding depression for other traits, including growth and litter size for the Austrian Pietrain population is strongly advised.
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Affiliation(s)
- Gyembo Tsheten
- Department of Livestock, Ministry of Agriculture and Livestock, Thimphu, Bhutan
| | - Birgit Fuerst-Waltl
- University of Natural Resources and Life Sciences, Division of Livestock Sciences, Vienna, Austria
| | | | - Johann Sölkner
- University of Natural Resources and Life Sciences, Division of Livestock Sciences, Vienna, Austria
| | - Henk Bovenhuis
- Wageningen University and Research, Animal Breeding and Genomics, Wageningen, The Netherlands
| | - Gábor Mészáros
- University of Natural Resources and Life Sciences, Division of Livestock Sciences, Vienna, Austria
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11
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Arias KD, Gutiérrez JP, Fernández I, Álvarez I, Goyache F. Approaching autozygosity in a small pedigree of Gochu Asturcelta pigs. Genet Sel Evol 2023; 55:74. [PMID: 37880572 PMCID: PMC10601182 DOI: 10.1186/s12711-023-00846-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 10/03/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND In spite of the availability of single nucleotide polymorphism (SNP) array data, differentiation between observed homozygosity and that caused by mating between relatives (autozygosity) introduces major difficulties. Homozygosity estimators show large variation due to different causes, namely, Mendelian sampling, population structure, and differences among chromosomes. Therefore, the ascertainment of how inbreeding is reflected in the genome is still an issue. The aim of this research was to study the usefulness of genomic information for the assessment of genetic diversity in the highly endangered Gochu Asturcelta pig breed. Pedigree depth varied from 0 (founders) to 4 equivalent discrete generations (t). Four homozygosity parameters (runs of homozygosity, FROH; heterozygosity-rich regions, FHRR; Li and Horvitz's, FLH; and Yang and colleague's FYAN) were computed for each individual, adjusted for the variability in the base population (BP; six individuals) and further jackknifed over autosomes. Individual increases in homozygosity (depending on t) and increases in pairwise homozygosity (i.e., increase in the parents' mean) were computed for each individual in the pedigree, and effective population size (Ne) was computed for five subpopulations (cohorts). Genealogical parameters (individual inbreeding, individual increase in inbreeding, and Ne) were used for comparisons. RESULTS The mean F was 0.120 ± 0.074 and the mean BP-adjusted homozygosity ranged from 0.099 ± 0.081 (FLH) to 0.152 ± 0.075 (FYAN). After jackknifing, the mean values were slightly lower. The increase in pairwise homozygosity tended to be twofold higher than the corresponding individual increase in homozygosity values. When compared with genealogical estimates, estimates of Ne obtained using FYAN tended to have low root-mean-squared errors. However, Ne estimates based on increases in pairwise homozygosity using both FROH and FHRR estimates of genomic inbreeding had lower root-mean-squared errors. CONCLUSIONS Parameters characterizing homozygosity may not accurately depict losses of variability in small populations in which breeding policy prohibits matings between close relatives. After BP adjustment, the performance of FROH and FHRR was highly consistent. Assuming that an increase in homozygosity depends only on pedigree depth can lead to underestimating it in populations with shallow pedigrees. An increase in pairwise homozygosity computed from either FROH or FHRR is a promising approach for characterizing autozygosity.
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Affiliation(s)
- Katherine D Arias
- Área de Genética y Reproducción Animal, SERIDA-Deva, Camino de Rioseco 1225, 33394, Gijón, Spain
| | - Juan Pablo Gutiérrez
- Departamento de Producción Animal, Universidad Complutense de Madrid, Avda. Puerta de Hierro S/N, 28040, Madrid, Spain
| | - Iván Fernández
- Área de Genética y Reproducción Animal, SERIDA-Deva, Camino de Rioseco 1225, 33394, Gijón, Spain
| | - Isabel Álvarez
- Área de Genética y Reproducción Animal, SERIDA-Deva, Camino de Rioseco 1225, 33394, Gijón, Spain
| | - Félix Goyache
- Área de Genética y Reproducción Animal, SERIDA-Deva, Camino de Rioseco 1225, 33394, Gijón, Spain.
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12
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Kinghorn B, Kinghorn A. Management of diversity and inbreeding when importing new stock into an inbred population. J Hered 2023; 114:492-503. [PMID: 37119054 PMCID: PMC10445517 DOI: 10.1093/jhered/esad027] [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: 12/20/2022] [Accepted: 04/27/2023] [Indexed: 04/30/2023] Open
Abstract
This article relates to breeding programs that seek to manage genetic diversity. The method maximizes a multicomponent objective function, applicable across breeding scenarios. However, this paper focuses on breeding decisions following immigration of 10 unrelated individuals into a highly inbred simulated population (F ≈ 0.34). We use Optimal Contribution Selection to maximize retention of genetic diversity. However, some treatments add Coancestry Assortative Mating (CAM). This helps to avoid early dilution of immigrant genetic material, maximizing its ability to contribute to genetic diversity in the longer term. After 20 generations, this resulted in considerably increased genetic diversity, with mean coancestries 59% of what random pairing gave. To manage progeny inbreeding, common practice is to reject matings above an upper limit. As a suboptimal rules-based approach, this resulted in 26% decreased genetic diversity and 8% increased inbreeding in the long term, compared with random pairing. In contrast, including mean progeny inbreeding as a continuous variable in the overall objective function decreased final inbreeding by 37% compared with random pairing. Adding some emphasis on selection for a single trait resulted in a similar pattern of effects on coancestry and inbreeding, with 12% higher trait response under CAM. Results indicate the properties of alternative methods, but we encourage users to do their own investigations of particular scenarios, such as including inbreeding depression. Practical implementation of these methods is discussed: they have been widely adopted in domestic animal breeding and are highly flexible to accommodate a wide range of technical and logistical objectives and constraints.
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Affiliation(s)
- Brian Kinghorn
- School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
| | - Alexander Kinghorn
- School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
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13
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Gautason E, Sahana G, Guldbrandtsen B, Berg P. Impact of kinship matrices on genetic gain and inbreeding with optimum contribution selection in a genomic dairy cattle breeding program. Genet Sel Evol 2023; 55:48. [PMID: 37460999 DOI: 10.1186/s12711-023-00826-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 07/07/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND Genomic selection has increased genetic gain in dairy cattle, but in some cases it has resulted in higher inbreeding rates. Therefore, there is need for research on efficient management of inbreeding in genomically-selected dairy cattle populations, especially for local breeds with a small population size. Optimum contribution selection (OCS) minimizes the increase in average kinship while it maximizes genetic gain. However, there is no consensus on how to construct the kinship matrix used for OCS and whether it should be based on pedigree or genomic information. VanRaden's method 1 (VR1) is a genomic relationship matrix in which centered genotype scores are scaled with the sum of 2p(1-p) where p is the reference allele frequency at each locus, and VanRaden's method 2 (VR2) scales each locus with 2p(1-p), thereby giving greater weight to loci with a low minor allele frequency. We compared the effects of nine kinship matrices on genetic gain, kinship, inbreeding, genetic diversity, and minor allele frequency when applying OCS in a simulated small dairy cattle population. We used VR1 and VR2, each using base animals, all genotyped animals, and the current generation of animals to compute reference allele frequencies. We also set the reference allele frequencies to 0.5 for VR1 and the pedigree-based relationship matrix. We constrained OCS to select a fixed number of sires per generation for all scenarios. Efficiency of the different matrices were compared by calculating the rate of genetic gain for a given rate of increase in average kinship. RESULTS We found that: (i) genomic relationships were more efficient than pedigree-based relationships at managing inbreeding, (ii) reference allele frequencies computed from base animals were more efficient compared to reference allele frequencies computed from recent animals, and (iii) VR1 was slightly more efficient than VR2, but the difference was not statistically significant. CONCLUSIONS Using genomic relationships for OCS realizes more genetic gain for a given amount of kinship and inbreeding than using pedigree relationships when the number of sires is fixed. For a small genomic dairy cattle breeding program, we recommend that the implementation of OCS uses VR1 with reference allele frequencies estimated either from base animals or old genotyped animals.
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Affiliation(s)
- Egill Gautason
- Center for Quantitative Genetics and Genomics, Aarhus University, 8000, Aarhus, Denmark.
- Faculty of Agricultural Sciences, Agricultural University of Iceland, 311, Borgarbyggð, Iceland.
| | - Goutam Sahana
- Center for Quantitative Genetics and Genomics, Aarhus University, 8000, Aarhus, Denmark
| | - Bernt Guldbrandtsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870, Frederiksberg C, Denmark
| | - Peer Berg
- Center for Quantitative Genetics and Genomics, Aarhus University, 8000, Aarhus, Denmark
- Faculty of Life Sciences, Norwegian University of Life Sciences, 1430, Ås, Norway
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Pocrnic I, Obšteter J, Gaynor RC, Wolc A, Gorjanc G. Assessment of long-term trends in genetic mean and variance after the introduction of genomic selection in layers: a simulation study. Front Genet 2023; 14:1168212. [PMID: 37234871 PMCID: PMC10206274 DOI: 10.3389/fgene.2023.1168212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/02/2023] [Indexed: 05/28/2023] Open
Abstract
Nucleus-based breeding programs are characterized by intense selection that results in high genetic gain, which inevitably means reduction of genetic variation in the breeding population. Therefore, genetic variation in such breeding systems is typically managed systematically, for example, by avoiding mating the closest relatives to limit progeny inbreeding. However, intense selection requires maximum effort to make such breeding programs sustainable in the long-term. The objective of this study was to use simulation to evaluate the long-term impact of genomic selection on genetic mean and variance in an intense layer chicken breeding program. We developed a large-scale stochastic simulation of an intense layer chicken breeding program to compare conventional truncation selection to genomic truncation selection optimized with either minimization of progeny inbreeding or full-scale optimal contribution selection. We compared the programs in terms of genetic mean, genic variance, conversion efficiency, rate of inbreeding, effective population size, and accuracy of selection. Our results confirmed that genomic truncation selection has immediate benefits compared to conventional truncation selection in all specified metrics. A simple minimization of progeny inbreeding after genomic truncation selection did not provide any significant improvements. Optimal contribution selection was successful in having better conversion efficiency and effective population size compared to genomic truncation selection, but it must be fine-tuned for balance between loss of genetic variance and genetic gain. In our simulation, we measured this balance using trigonometric penalty degrees between truncation selection and a balanced solution and concluded that the best results were between 45° and 65°. This balance is specific to the breeding program and depends on how much immediate genetic gain a breeding program may risk vs. save for the future. Furthermore, our results show that the persistence of accuracy is better with optimal contribution selection compared to truncation selection. In general, our results show that optimal contribution selection can ensure long-term success in intensive breeding programs using genomic selection.
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Affiliation(s)
- Ivan Pocrnic
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh, United Kingdom
| | - Jana Obšteter
- Agricultural Institute of Slovenia, Ljubljana, Slovenia
| | - R. Chris Gaynor
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh, United Kingdom
| | - Anna Wolc
- Department of Animal Science, Iowa State University, Ames, IA, United States
- Hy-Line International, Dallas Center, IA, United States
| | - Gregor Gorjanc
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh, United Kingdom
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15
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Pappas F, Kurta K, Vanhala T, Jeuthe H, Hagen Ø, Beirão J, Palaiokostas C. Whole-genome re-sequencing provides key genomic insights in farmed Arctic charr ( Salvelinus alpinus) populations of anadromous and landlocked origin from Scandinavia. Evol Appl 2023; 16:797-813. [PMID: 37124091 PMCID: PMC10130564 DOI: 10.1111/eva.13537] [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: 07/19/2022] [Revised: 12/05/2022] [Accepted: 02/12/2023] [Indexed: 03/03/2023] Open
Abstract
Arctic charr (Salvelinus alpinus) is a niche-market high-value species for Nordic aquaculture. Similar to other salmonids, both anadromous and landlocked populations are encountered. Whole-genome re-sequencing (22X coverage) was performed on two farmed populations of anadromous (Sigerfjord; n = 24) and landlocked (Arctic Superior; n = 24) origin from Norway and Sweden respectively. More than 5 million SNPs were used to study their genetic diversity and to scan for selection signatures. The two populations were clearly distinguished through principal component analysis, with the mean fixation index being ~0.12. Furthermore, the levels of genomic inbreeding estimated from runs of homozygosity were 6.23% and 8.66% for the Norwegian and the Swedish population respectively. Biological processes that could be linked to selection pressure associated primarily with the anadromous background and/or secondarily with domestication were suggested. Overall, our study provided insights regarding the genetic composition of two main strains of farmed Arctic charr from Scandinavia. At the same time, ample genomic resources were produced in the magnitude of millions of SNPs that could assist the transition of Nordic Arctic charr farming in the genomics era.
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Affiliation(s)
- Fotis Pappas
- Department of Animal Breeding and GeneticsSwedish University of Agricultural SciencesUppsalaSweden
| | - Khrystyna Kurta
- Department of Animal Breeding and GeneticsSwedish University of Agricultural SciencesUppsalaSweden
| | - Tytti Vanhala
- Department of Animal Breeding and GeneticsSwedish University of Agricultural SciencesUppsalaSweden
| | - Henrik Jeuthe
- Department of Animal Breeding and GeneticsSwedish University of Agricultural SciencesUppsalaSweden
- Aquaculture Center NorthKälarneSweden
| | - Ørjan Hagen
- Faculty of Bioscience and AquacultureNord UniversityBodøNorway
| | - José Beirão
- Faculty of Bioscience and AquacultureNord UniversityBodøNorway
| | - Christos Palaiokostas
- Department of Animal Breeding and GeneticsSwedish University of Agricultural SciencesUppsalaSweden
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16
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Arguello-Blanco MN, Sneller CH. The effect of cycles of genomic selection on the wheat (T. aestivum) genome. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:70. [PMID: 36952091 DOI: 10.1007/s00122-023-04279-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 12/07/2022] [Indexed: 06/18/2023]
Abstract
We documented changes in the wheat genome attributed to genomic selection including loss of diversity, and changes in population structure and linkage disequilibrium patterns. We conclude that training and prediction populations need to co-evolve instead of the use of a static training population. Genomic selection (GS) is widely used in plant breeding to shorten breeding cycles. Our objective was to assess the impact of rapid cycling GS on the wheat genome. We used 3927 markers to genotype a training population (YTP) and individuals from five cycles (YC1-YC5) of GS for grain yield. We assessed changes of allele frequency, genetic distance, population structure, and linkage disequilibrium (LD). We found 27.3% of all markers had a significant allele frequency change by YC5, 18% experienced a significant change attributed to selection, and 9.3% had a significant change due to either drift or selection. A total of 725 of 3927 markers were fixed by YC5 with selection fixing 7.3% of the 725 markers. The genetic distance between cycles increased over time. The Fst value of 0.224 between YTP and YC5 indicates their relationship was low. The number LD blocks decreased over time and the correlation between LD matrices also decreased over time. Overall, we found a reduction in genetic diversity, increased genetic differentiation of cycles from the training population, and restructuring of the LD patterns over cycles. The accuracy of GS depends on the genomic similarity of the training population and the prediction populations. Our results show that the similarity can decline rapidly over cycles of GS and compromise the predictive ability of the YTP-based model. Our results support implementing a GS scheme where the training and prediction populations co-evolve instead of the use of a static training population.
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Affiliation(s)
- M N Arguello-Blanco
- Department of Horticulture and Crop Science, The Ohio State University, 1680 Madison Av, Wooster, OH, 446591, USA
| | - Clay H Sneller
- Department of Horticulture and Crop Science, The Ohio State University, 1680 Madison Av, Wooster, OH, 446591, USA.
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17
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Morales-González E, Villanueva B, Toro MÁ, Fernández J. Maintenance of genetic diversity in subdivided populations using genomic coancestry matrices. Mol Ecol Resour 2023. [PMID: 36906916 DOI: 10.1111/1755-0998.13781] [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: 07/11/2022] [Revised: 01/16/2023] [Accepted: 02/01/2023] [Indexed: 03/13/2023]
Abstract
For both undivided and subdivided populations, the consensus method to maintain genetic diversity is the Optimal Contribution (OC) method. For subdivided populations, this method determines the optimal contribution of each candidate to each subpopulation to maximize global genetic diversity (which implicitly optimizes migration between subpopulations) while balancing the relative levels of coancestry between and within subpopulations. Inbreeding can be controlled by increasing the weight given to within-subpopulation coancestry (λ). Here we extend the original OC method for subdivided populations that used pedigree-based coancestry matrices, to the use of more accurate genomic matrices. Global levels of genetic diversity, measured as expected heterozygosity and allelic diversity, their distributions within and between subpopulations, and the migration pattern between subpopulations, were evaluated via stochastic simulations. The temporal trajectory of allele frequencies was also investigated. The genomic matrices investigated were (i) the matrix based on deviations of the observed number of alleles shared by two individuals from the expected number under Hardy-Weinberg equilibrium; and (ii) a matrix based on a genomic relationship matrix. The matrix based on deviations led to higher global and within-subpopulation expected heterozygosities, lower inbreeding and similar allelic diversity than the second genomic and pedigree-based matrices when a relatively high weight was given to the within-subpopulation coancestries (λ ≥ 5). Under this scenario, allele frequencies moved only slightly away from the initial frequencies. Therefore, the recommended strategy is to use the former matrix in the OC methodology giving a high weight to the within-subpopulation coancestry.
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Affiliation(s)
| | - Beatriz Villanueva
- Departamento de Mejora Genética Animal, INIA-CSIC, Ctra. de La Coruña, km 7.5, 28040, Madrid, Spain
| | - Miguel Á Toro
- Departamento de Producción Agraria, ETSI Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28040, Madrid, Spain
| | - Jesús Fernández
- Departamento de Mejora Genética Animal, INIA-CSIC, Ctra. de La Coruña, km 7.5, 28040, Madrid, Spain
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18
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Steyn Y, Lawlor T, Masuda Y, Tsuruta S, Legarra A, Lourenco D, Misztal I. Nonparallel genome changes within subpopulations over time contributed to genetic diversity within the US Holstein population. J Dairy Sci 2023; 106:2551-2572. [PMID: 36797192 DOI: 10.3168/jds.2022-21914] [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: 02/01/2022] [Accepted: 10/03/2022] [Indexed: 02/16/2023]
Abstract
Maintaining genetic variation in a population is important for long-term genetic gain. The existence of subpopulations within a breed helps maintain genetic variation and diversity. The 20,990 genotyped animals, representing the breeding animals in the year 2014, were identified as the sires of animals born after 2010 with at least 25 progenies, and females measured for type traits within the last 2 yr of data. K-means clustering with 5 clusters (C1, C2, C3, C4, and C5) was applied to the genomic relationship matrix based on 58,990 SNP markers to stratify the selected candidates into subpopulations. The general higher inbreeding resulting from within-cluster mating than across-cluster mating suggests the successful stratification into genetically different groups. The largest cluster (C4) contained animals that were less related to each animal within and across clusters. The average fixation index was 0.03, indicating that the populations were differentiated, and allele differences across the subpopulations were not due to drift alone. Starting with the selected candidates within each cluster, a family unit was identified by tracing back through the pedigree, identifying the genotyped ancestors, and assigning them to a pseudogeneration. Each of the 5 families (F1, F2, F3, F4, and F5) was traced back for 10 generations, allowing for changes in frequency of individual SNPs over time to be observed, which we call allele frequencies change. Alternative procedures were used to identify SNPs changing in a parallel or nonparallel way across families. For example, markers that have changed the most in the whole population, markers that have changed differently across families, and genes previously identified as those that have changed in allele frequency. The genomic trajectory taken by each family involves selective sweeps, polygenic changes, hitchhiking, and epistasis. The replicate frequency spectrum was used to measure the similarity of change across families and showed that populations have changed differently. The proportion of markers that reversed direction in allele frequency change varied from 0.00 to 0.02 if the rate of change was greater than 0.02 per generation, or from 0.14 to 0.24 if the rate of change was greater than 0.005 per generation within each family. Cluster-specific SNP effects for stature were estimated using only females and applied to obtain indirect genomic predictions for males. Reranking occurs depending on SNP effects used. Additive genetic correlations between clusters show possible differences in populations. Further research is required to determine how this knowledge can be applied to maintain diversity and optimize selection decisions in the future.
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Affiliation(s)
- Y Steyn
- Department of Animal and Dairy Science, University of Georgia, 425 River Road, Athens 30602.
| | - T Lawlor
- Holstein Association USA Inc., Brattleboro, VT 05302
| | - Y Masuda
- Department of Animal and Dairy Science, University of Georgia, 425 River Road, Athens 30602
| | - S Tsuruta
- Department of Animal and Dairy Science, University of Georgia, 425 River Road, Athens 30602
| | - A Legarra
- GenPhySE, INRA, INPT, ENVT, Université de Toulouse, Castanet-Tolosan 31520, France
| | - D Lourenco
- Department of Animal and Dairy Science, University of Georgia, 425 River Road, Athens 30602
| | - I Misztal
- Department of Animal and Dairy Science, University of Georgia, 425 River Road, Athens 30602
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19
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Ogawa S, Zoda A, Kagawa R, Obinata R. Comparing Methods to Select Candidates for Re-Genotyping to Impute Higher-Density Genotype Data in a Japanese Black Cattle Population: A Case Study. Animals (Basel) 2023; 13:ani13040638. [PMID: 36830425 PMCID: PMC9951718 DOI: 10.3390/ani13040638] [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: 12/19/2022] [Revised: 02/04/2023] [Accepted: 02/10/2023] [Indexed: 02/15/2023] Open
Abstract
As optimization methods to identify the best animals for dense genotyping to construct a reference population for genotype imputation, the MCA and MCG methods, which use the pedigree-based additive genetic relationship matrix (A matrix) and the genomic relationship matrix (G matrix), respectively, have been proposed. We assessed the performance of MCA and MCG methods using 575 Japanese Black cows. Pedigree data were provided to trace back up to five generations to construct the A matrix with changing the pedigree depth from 1 to 5 (five MCA methods). Genotype information on 36,426 single-nucleotide polymorphisms was used to calculate the G matrix based on VanRaden's methods 1 and 2 (two MCG methods). The MCG always selected one cow per iteration, while MCA sometimes selected multiple cows. The number of commonly selected cows between the MCA and MCG methods was generally lower than that between different MCA methods or between different MCG methods. For the studied population, MCG appeared to be more reasonable than MCA in selecting cows as a reference population for higher-density genotype imputation to perform genomic prediction and a genome-wide association study.
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Affiliation(s)
- Shinichiro Ogawa
- Division of Meat Animal and Poultry Research, Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization (NARO), Tsukuba 305-0901, Japan
- Correspondence: ; Tel.: +81-29-838-8627
| | - Atsushi Zoda
- Research and Development Group, Zen-Noh Embryo Transfer Center, Kamishihoro 080-1407, Japan
| | - Rino Kagawa
- Research and Development Group, Zen-Noh Embryo Transfer Center, Kamishihoro 080-1407, Japan
| | - Rui Obinata
- Research and Development Group, Zen-Noh Embryo Transfer Center, Kamishihoro 080-1407, Japan
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20
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Hu X, Carver BF, El-Kassaby YA, Zhu L, Chen C. Weighted kernels improve multi-environment genomic prediction. Heredity (Edinb) 2023; 130:82-91. [PMID: 36522412 PMCID: PMC9905581 DOI: 10.1038/s41437-022-00582-6] [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: 08/25/2021] [Revised: 11/27/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
Crucial to variety improvement programs is the reliable and accurate prediction of genotype's performance across environments. However, due to the impactful presence of genotype by environment (G×E) interaction that dictates how changes in expression and function of genes influence target traits in different environments, prediction performance of genomic selection (GS) using single-environment models often falls short. Furthermore, despite the successes of genome-wide association studies (GWAS), the genetic insights derived from genome-to-phenome mapping have not yet been incorporated in predictive analytics, making GS models that use Gaussian kernel primarily an estimator of genomic similarity, instead of the underlying genetics characteristics of the populations. Here, we developed a GS framework that, in addition to capturing the overall genomic relationship, can capitalize on the signal of genetic associations of the phenotypic variation as well as the genetic characteristics of the populations. The capacity of predicting the performance of populations across environments was demonstrated by an overall gain in predictability up to 31% for the winter wheat DH population. Compared to Gaussian kernels, we showed that our multi-environment weighted kernels could better leverage the significance of genetic associations and yielded a marked improvement of 4-33% in prediction accuracy for half-sib families. Furthermore, the flexibility incorporated in our Bayesian implementation provides the generalizable capacity required for predicting multiple highly genetic heterogeneous populations across environments, allowing reliable GS for genetic improvement programs that have no access to genetically uniform material.
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Affiliation(s)
- Xiaowei Hu
- grid.65519.3e0000 0001 0721 7331Department of Statistics, Oklahoma State University, Stillwater, OK USA ,grid.27755.320000 0000 9136 933XPresent Address: Center for Public Health Genomics, University of Virginia, Charlottesville, VA USA
| | - Brett F. Carver
- grid.65519.3e0000 0001 0721 7331Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK USA
| | - Yousry A. El-Kassaby
- grid.17091.3e0000 0001 2288 9830Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC Canada
| | - Lan Zhu
- grid.65519.3e0000 0001 0721 7331Department of Statistics, Oklahoma State University, Stillwater, OK USA
| | - Charles Chen
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, USA.
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21
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Eriksson S, Strandberg E, Johansson AM. Changes in genomic inbreeding and diversity over half a century in Swedish Red and Swedish Holstein dairy cattle. J Anim Breed Genet 2023; 140:295-303. [PMID: 36645266 DOI: 10.1111/jbg.12758] [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: 07/02/2022] [Accepted: 01/03/2023] [Indexed: 01/17/2023]
Abstract
Swedish Red (SR) and Swedish Holstein (SH) are the dominating commercial dairy cattle breeds in Sweden. Both breeds have undergone substantial changes during the last half century due to intensive selection for breeding goal traits, but also resulting from increased international exchange of breeding animals and genetic drift. The aim of this study was to learn more about changes in genomic diversity and inbreeding in these two breeds over time. Therefore, semen samples from old bulls were genotyped using the 150K Genomic Profiler SNP array and combined with 50K SNP array genotype data, obtained for more recent bulls from the Nordic Cattle Genetic Evaluation. Different measures of level of homozygosity, genomic inbreeding, relatedness and changes in allele frequency were estimated for bulls born during different time periods from the 1950s until 2020. In total, more than 33,000 SNPs for 9737 SR and 5041 SH bulls were included in the analysis using PLINK v1.9. The results showed higher average homozygosity for SR than for SH bulls up to around 2000, but the difference was very small after that. The average inbreeding coefficients based on deviation from expected homozygosity as well as on runs of homozygosity decreased until the early 1980s in both breeds, whereafter they started to increase again for SH, but stayed more stable for SR. From the 1990s onwards, SH displayed higher average inbreeding coefficients than SR. In the last studied birth year group (2015-2020), the mean inbreeding coefficient based on runs of homozygosity was 5.9% for SH and 3.7% for SR. A principal component analysis showed a pattern of genetic relationships related to the birth year period of the bulls, illustrating the gradual change of the genetic material within each breed. The change in allele frequency over time was generally larger for SH than for SR. The results show that the inbreeding level was higher half a century ago than at present, and the inbreeding levels were lower than in some other studied populations. Still, the increase seen for inbreeding coefficients and homozygosity, especially in SH during recent years, should be considered in future breeding strategies.
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Affiliation(s)
- Susanne Eriksson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Erling Strandberg
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anna M Johansson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
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22
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Cowling WA, Castro-Urrea FA, Stefanova KT, Li L, Banks RG, Saradadevi R, Sass O, Kinghorn BP, Siddique KHM. Optimal Contribution Selection Improves the Rate of Genetic Gain in Grain Yield and Yield Stability in Spring Canola in Australia and Canada. PLANTS (BASEL, SWITZERLAND) 2023; 12:383. [PMID: 36679096 PMCID: PMC9863350 DOI: 10.3390/plants12020383] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 12/14/2022] [Accepted: 01/07/2023] [Indexed: 06/17/2023]
Abstract
Crop breeding must achieve higher rates of genetic gain in grain yield (GY) and yield stability to meet future food demands in a changing climate. Optimal contributions selection (OCS) based on an index of key economic traits should increase the rate of genetic gain while minimising population inbreeding. Here we apply OCS in a global spring oilseed rape (canola) breeding program during three cycles of S0,1 family selection in 2016, 2018, and 2020, with several field trials per cycle in Australia and Canada. Economic weights in the index promoted high GY, seed oil, protein in meal, and Phoma stem canker (blackleg) disease resistance while maintaining plant height, flowering time, oleic acid, and seed size and decreasing glucosinolate content. After factor analytic modelling of the genotype-by-environment interaction for the additive effects, the linear rate of genetic gain in GY across cycles was 0.059 or 0.087 t ha-1 y-1 (2.9% or 4.3% y-1) based on genotype scores for the first factor (f1) expressed in trait units or average predicted breeding values across environments, respectively. Both GY and yield stability, defined as the root-mean-square deviation from the regression line associated with f1, were predicted to improve in the next cycle with a low achieved mean parental coancestry (0.087). These methods achieved rapid genetic gain in GY and other traits and are predicted to improve yield stability across global spring canola environments.
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Affiliation(s)
- Wallace A. Cowling
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
| | - Felipe A. Castro-Urrea
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
| | - Katia T. Stefanova
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia
| | - Li Li
- Animal Genetics and Breeding Unit, University of New England, Armidale, NSW 2351, Australia
| | - Robert G. Banks
- Animal Genetics and Breeding Unit, University of New England, Armidale, NSW 2351, Australia
| | - Renu Saradadevi
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
| | - Olaf Sass
- Norddeutsche Pflanzenzucht Hans-Georg Lembke KG, Hohenlieth, 24363 Holtsee, Germany
| | - Brian P. Kinghorn
- School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia
| | - Kadambot H. M. Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
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Steyn Y, Masuda Y, Tsuruta S, Lourenco D, Misztal I, Lawlor T. Identifying influential sires and distinct clusters of selection candidates based on genomic relationships to reduce inbreeding in the US Holstein. J Dairy Sci 2022; 105:9810-9821. [DOI: 10.3168/jds.2022-22143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 07/19/2022] [Indexed: 11/05/2022]
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Li Y, Kaur S, Pembleton LW, Valipour-Kahrood H, Rosewarne GM, Daetwyler HD. Strategies of preserving genetic diversity while maximizing genetic response from implementing genomic selection in pulse breeding programs. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1813-1828. [PMID: 35316351 PMCID: PMC9205836 DOI: 10.1007/s00122-022-04071-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 02/26/2022] [Indexed: 06/14/2023]
Abstract
KEY MESSAGE Genomic selection maximizes genetic gain by recycling parents to germplasm pool earlier and preserves genetic diversity by restricting the number of fixed alleles and the relationship in pulse breeding programs. Using a stochastic computer simulation, we investigated the benefit of optimization strategies in the context of genomic selection (GS) for pulse breeding programs. We simulated GS for moderately complex to highly complex traits such as disease resistance, grain weight and grain yield in multiple environments with a high level of genotype-by-environment interaction for grain yield. GS led to higher genetic gain per unit of time and higher genetic diversity loss than phenotypic selection by shortening the breeding cycle time. The genetic gain obtained from selecting the segregating parents early in the breeding cycle (at F1 or F2 stages) was substantially higher than selecting at later stages even though prediction accuracy was moderate. Increasing the number of F1 intercross (F1i) families and keeping the total number of progeny of F1i families constant, we observed a decrease in genetic gain and increase in genetic diversity, whereas increasing the number of progeny per F1i family while keeping a constant number of F1i families increased the rate of genetic gain and had higher genetic diversity loss per unit of time. Adding 50 F2 family phenotypes to the training population increased the accuracy of genomic breeding values (GEBVs) and genetic gain per year and decreased the rate of genetic diversity loss. Genetic diversity could be preserved by applying a strategy that restricted both the percentage of alleles fixed and the average relationship of the group of selected parents to preserve long-term genetic improvement in the pulse breeding program.
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Affiliation(s)
- Yongjun Li
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC, 3083, Australia.
| | - Sukhjiwan Kaur
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC, 3083, Australia
| | - Luke W Pembleton
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC, 3083, Australia
| | | | - Garry M Rosewarne
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, 3400, Australia
| | - Hans D Daetwyler
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC, 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
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Heidaritabar M, Carney V, Groenen MAM, Plastow G. Assessing the genomic diversity and relatedness in 10 Canadian heritage chicken lines using whole-genome sequence data. J Anim Breed Genet 2022; 139:556-573. [PMID: 35579203 DOI: 10.1111/jbg.12720] [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: 03/24/2021] [Accepted: 05/01/2022] [Indexed: 11/29/2022]
Abstract
In the past 50 years, there has been a steep increase in the demand for poultry products, met by increasing production along with genetic selection for improved growth, efficiency, health and reproduction. The selection tends to reduce the number and type of genetic resources contributing to the majority of production. The University of Alberta maintains 10 heritage chicken lines (Brown Leghorn (BL), Light Sussex (LS), New Hampshire (NH), Saskatchewan Barred Rock (SaskBR), Shaver Barred Rock (ShaverBR), Shaver Rhode Island Red (RIR), White Leghorn (WL) and three commercial crosses called Alberta Meat Control strains 1957 (AMC-1957), 1978 sire line (AMC-1978-20S) and 1978 dam line (AMC-1978-30D), that played a large role in the evolution of the poultry industry in Canada. Since these lines have not been subjected to the same intensive selection pressures as commercial counterparts, they may contain unique genetic variants lost in commercial lines. Thus, for conservation management of these lines, the first step is to assess their genetic diversity. 71 male samples from across 10 lines were analysed using whole-genome sequencing and patterns of genetic diversity and relatedness among these lines were explored. AMC-1978-30D showed the highest genetic diversity as reflected in observed and expected heterozygosity (0.327 and 0.250), percentage of polymorphic markers (~ 65%) and average recent inbreeding coefficient (-0.039), followed by AMC-1978-20S and AMC-1957. BL showed the lowest genetic diversity as reflected in observed and expected heterozygosity (0.130 and 0.116), percentage of polymorphic markers (~31%) and average recent inbreeding coefficient (0.577), followed by LS, WL and NH. Our findings highlight the need for special attention for the populations of BL, WL, LS and NH, with the largest levels of inbreeding. Our results can be used to develop a breeding strategy to optimize and conserve the genetic variation present in heritage lines.
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Affiliation(s)
- Marzieh Heidaritabar
- Department of Agricultural, Food and Nutritional Science, Livestock Gentec, University of Alberta, Edmonton, Alberta, Canada
| | - Valerie Carney
- Poultry Innovation Partnership, University of Alberta, Edmonton, Alberta, Canada
| | - Martien A M Groenen
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, the Netherlands
| | - Graham Plastow
- Department of Agricultural, Food and Nutritional Science, Livestock Gentec, University of Alberta, Edmonton, Alberta, Canada
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Dadousis C, Ablondi M, Cipolat-Gotet C, van Kaam JT, Marusi M, Cassandro M, Sabbioni A, Summer A. Genomic inbreeding coefficients using imputed genotypes: Assessing different estimators in Holstein-Friesian dairy cows. J Dairy Sci 2022; 105:5926-5945. [DOI: 10.3168/jds.2021-21125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 03/08/2022] [Indexed: 11/19/2022]
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27
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Wu RS, Wang HC, Su CL, Wang PH, Lin EC. Pedigree-based analyses of changes in genetic variability in three major swine breeds in Taiwan after a disease outbreak. Transl Anim Sci 2022; 6:txac043. [PMID: 35592093 PMCID: PMC9113419 DOI: 10.1093/tas/txac043] [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: 11/10/2021] [Accepted: 03/31/2022] [Indexed: 11/14/2022] Open
Abstract
Pedigree analysis was performed in three major Taiwanese swine breeds to evaluate the genetic variability in the current population and determine the main reason for genetic diversity (GD) loss after the occurrence of foot-and-mouth disease (FMD) in Taiwan. The pedigree files of the Duroc, Landrace, and Yorkshire breeds, containing 60,237, 87,177, and 34,373 records, respectively, were analyzed. We divided the population into two subpopulations (pre-1998 and post-1998) to determine the role of FMD in GD loss. Pedigree completeness and related indicators were analyzed to evaluate the pedigree quality, and several parameters were used to measure the levels of GD and further used to determine the major cause of GD loss. The pedigree completeness indexes for the different breeds were higher than 0.60, and the trend was enhanced after the FMD outbreak. The estimated proportion of random genetic drift in GD loss increased in all breeds over time (from 62.64% to 78.44% in Duroc; from 26.26% to 57.99% in Landrace; and from 47.97% to 55.00% in Yorkshire, respectively). The effective population size of Duroc and Landrace were increased by the time (Duroc: from 61.73 to 84.75; Landrace: from 108.70 to 113.64); however, it shows opposite trend in Yorkshire population (decline from 86.21 to 50.00). In summary, the occurrence of FMD led to the major loss of GD loss by random genetic drift. Therefore, for the recovery of GD, breeders in Taiwan should increase the effective population size with newly imported genetic materials and adjust the breeding strategy to reduce the inbreeding rate.
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Affiliation(s)
- Ruei-Syuan Wu
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan
| | | | | | - Pei-Hwa Wang
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan
| | - En-Chung Lin
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan
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28
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Hjortø L, Andersen T, Kargo M, Sørensen AC. Breeding schemes with optimum-contribution selection or truncation selection for beef cattle destined for use on dairy females. J Dairy Sci 2022; 105:4314-4323. [PMID: 35307183 DOI: 10.3168/jds.2021-21258] [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: 09/07/2021] [Accepted: 01/26/2022] [Indexed: 11/19/2022]
Abstract
We tested the hypothesis that the size of a beef cattle population destined for use on dairy females is smaller under optimum-contribution selection (OCS) than under truncation selection (TRS) at the same genetic gain (ΔG) and the same rate of inbreeding (ΔF). We used stochastic simulation to estimate true ΔG realized at a 0.005 ΔF in breeding schemes with OCS or TRS. The schemes for the beef cattle population also differed in the number of purebred offspring per dam and the total number of purebred offspring per generation. Dams of the next generation were exclusively selected among the one-year-old heifers. All dams were donors for embryo transfer and produced a maximum of 5 or 10 offspring. The total number of purebred offspring per generation was: 400, 800, 1,600 or 4,000 calves, and it was used as a measure of population size. Rate of inbreeding was predicted and controlled using pedigree relationships. Each OCS (TRS) scheme was simulated for 10 discrete generations and replicated 100 (200) times. The OCS scheme and the TRS scheme with a maximum of 10 offspring per dam required approximately 783 and 1,257 purebred offspring per generation to realize a true ΔG of €14 and a ΔF of 0.005 per generation. Schemes with a maximum of 5 offspring per dam required more purebred offspring per generation to realize a similar true ΔG and a similar ΔF. Our results show that OCS and multiple ovulation and embryo transfer act on selection intensity through different mechanisms to achieve fewer selection candidates and fewer selected sires and dams than under TRS at the same ΔG and a fixed ΔF. Therefore, we advocate the use of a breeding scheme with OCS and multiple ovulation and embryo transfer for beef cattle destined for use on dairy females because it is favorable both from an economic perspective and a carbon footprint perspective.
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Affiliation(s)
- Line Hjortø
- SEGES Innovation P/S, Agro Food Park 15, 8200 Aarhus N, Denmark.
| | - Trine Andersen
- SEGES Innovation P/S, Agro Food Park 15, 8200 Aarhus N, Denmark
| | - Morten Kargo
- Center for Quantitative Genetics and Genomics, Aarhus University, Blichers Allé 20, 8830 Tjele, Denmark
| | - Anders Christian Sørensen
- Center for Quantitative Genetics and Genomics, Aarhus University, Blichers Allé 20, 8830 Tjele, Denmark; Danish Pig Research Centre, Danish Agriculture & Food Council, Axeltorv 3, 1609 Copenhagen V, Denmark
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29
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Mulim HA, Brito LF, Pinto LFB, Ferraz JBS, Grigoletto L, Silva MR, Pedrosa VB. Characterization of runs of homozygosity, heterozygosity-enriched regions, and population structure in cattle populations selected for different breeding goals. BMC Genomics 2022; 23:209. [PMID: 35291953 PMCID: PMC8925140 DOI: 10.1186/s12864-022-08384-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 02/10/2022] [Indexed: 01/12/2023] Open
Abstract
Background A decline in the level of genetic diversity in livestock can result in reduced response to selection, greater incidence of genetic defects, and inbreeding depression. In this context, various metrics have been proposed to assess the level of genetic diversity in selected populations. Therefore, the main goals of this study were to: 1) investigate the population structure of 16 cattle populations from 15 different pure breeds or composite populations, which have been selected for different breeds goals; and, 2) identify and compare runs of homozygosity (ROH) and heterozygosity-enriched regions (HER) based on different single nucleotide polymorphism (SNP) panels and whole-genome sequence data (WGS), followed by functional genomic analyses. Results A total of 24,187 ROH were found across all cattle populations, with 55% classified in the 2-4 Mb size group. Fourteen homozygosity islands were found in five populations, where four ROH islands located on BTA1, BTA5, BTA16, and BTA19 overlapped between the Brahman (BRM) and Gyr (GIR) breeds. A functional analysis of the genes found in these islands revealed candidate genes known to play a role in the melanogenesis, prolactin signaling, and calcium signaling pathways. The correlations between inbreeding metrics ranged from 0.02 to 0.95, where the methods based on homozygous genotypes (FHOM), uniting of gametes (FUNI), and genotype additive variance (FGRM) showed strong correlations among them. All methods yielded low to moderate correlations with the inbreeding coefficients based on runs of homozygosity (FROH). For the HER, 3576 runs and 26 islands, distributed across all autosomal chromosomes, were found in regions containing genes mainly related to the immune system, indicating potential balancing selection. Although the analyses with WGS did not enable detection of the same island patterns, it unraveled novel regions not captured when using SNP panel data. Conclusions The cattle populations that showed the largest amount of ROH and HER were Senepol (SEN) and Montana (MON), respectively. Overlapping ROH islands were identified between GIR and BRM breeds, indicating a possible historical connection between the populations. The distribution and pattern of ROH and HER are population specific, indicating that different breeds have experienced divergent selection processes or different genetic processes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08384-0.
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Affiliation(s)
| | - Luiz F Brito
- Department of Animal Science, Purdue University, West Lafayette, Indiana, USA
| | | | - José Bento Sterman Ferraz
- Department of Animal Sciences, College of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Lais Grigoletto
- Department of Animal Science, Purdue University, West Lafayette, Indiana, USA.,Department of Animal Sciences, College of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | | | - Victor Breno Pedrosa
- Department of Animal Science, Federal University of Bahia, Salvador, Bahia, Brazil. .,Department of Animal Science, State University of Ponta Grossa, Av. General Carlos Cavalcanti, 4748 - Uvaranas, Ponta Grossa, PR, 84030-900, Brazil.
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Špehar M, Ramljak J, Kasap A. Estimation of genetic parameters and the effect of inbreeding on dairy traits in Istrian sheep. ITALIAN JOURNAL OF ANIMAL SCIENCE 2022. [DOI: 10.1080/1828051x.2022.2031320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Marija Špehar
- Croatian Agency for Agriculture and Food, Zagreb, Croatia
| | - Jelena Ramljak
- Zavod za specijalno stočarstvo, University of Zagreb Faculty of Agriculture, Zagreb, Croatia
| | - Ante Kasap
- Zavod za specijalno stočarstvo, University of Zagreb Faculty of Agriculture, Zagreb, Croatia
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Abstract
Traditional tree improvement is cumbersome and costly. Our main objective was to assess the extent to which genomic data can currently accelerate and improve decision making in this field. We used diameter at breast height (DBH) and wood density (WD) data for 4430 tree genotypes and single-nucleotide polymorphism (SNP) data for 2446 tree genotypes. Pedigree reconstruction was performed using a combination of maximum likelihood parentage assignment and matching based on identity-by-state (IBS) similarity. In addition, we used best linear unbiased prediction (BLUP) methods to predict phenotypes using SNP markers (GBLUP), recorded pedigree information (ABLUP), and single-step “blended” BLUP (HBLUP) combining SNP and pedigree information. We substantially improved the accuracy of pedigree records, resolving the inconsistent parental information of 506 tree genotypes. This led to substantially increased predictive ability (i.e., by up to 87%) in HBLUP analyses compared to a baseline from ABLUP. Genomic prediction was possible across populations and within previously untested families with moderately large training populations (N = 800–1200 tree genotypes) and using as few as 2000–5000 SNP markers. HBLUP was generally more effective than traditional ABLUP approaches, particularly after dealing appropriately with pedigree uncertainties. Our study provides evidence that genome-wide marker data can significantly enhance tree improvement. The operational implementation of genomic selection has started in radiata pine breeding in New Zealand, but further reductions in DNA extraction and genotyping costs may be required to realise the full potential of this approach.
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Development and Validation of a 36K SNP Array for Radiata Pine (Pinus radiata D.Don). FORESTS 2022. [DOI: 10.3390/f13020176] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Radiata pine (Pinus radiata D.Don) is one of the world’s most domesticated pines and a key economic species in New Zealand. Thus, the development of genomic resources for radiata pine has been a high priority for both research and commercial breeding. Leveraging off a previously developed exome capture panel, we tested the performance of 438,744 single nucleotide polymorphisms (SNPs) on a screening array (NZPRAD01) and then selected 36,285 SNPs for a final genotyping array (NZPRAD02). These SNPs aligned to 15,372 scaffolds from the Pinus taeda L. v. 1.01e assembly, and 20,039 contigs from the radiata pine transcriptome assembly. The genotyping array was tested on more than 8000 samples, including material from archival progenitors, current breeding trials, nursery material, clonal lines, and material from Australia. Our analyses indicate that the array is performing well, with sample call rates greater than 98% and a sample reproducibility of 99.9%. Genotyping in two linkage mapping families indicated that the SNPs are well distributed across the 12 linkage groups. Using genotypic data from this array, we were also able to differentiate representatives of the five recognized provenances of radiata pine, Año Nuevo, Monterey, Cambria, Cedros and Guadalupe. Furthermore, principal component analysis of genotyped trees revealed clear patterns of population structure, with the primary axis of variation driven by provenance ancestry and the secondary axis reflecting breeding activities. This represents the first commercial use of genomics in a radiata pine breeding program.
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Cortellari M, Bionda A, Negro A, Frattini S, Mastrangelo S, Somenzi E, Lasagna E, Sarti FM, Ciani E, Ciampolini R, Marletta D, Liotta L, Ajmone Marsan P, Pilla F, Colli L, Talenti A, Crepaldi P. Runs of homozygosity in the Italian goat breeds: impact of management practices in low-input systems. Genet Sel Evol 2021; 53:92. [PMID: 34895134 PMCID: PMC8666052 DOI: 10.1186/s12711-021-00685-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 11/23/2021] [Indexed: 11/16/2022] Open
Abstract
Background Climate and farming systems, several of which are considered as low-input agricultural systems, vary between goat populations from Northern and Southern Italy and have led to different management practices. These processes have impacted genome shaping in terms of inbreeding and regions under selection and resulted in differences between the northern and southern populations. Both inbreeding and signatures of selection can be pinpointed by the analysis of runs of homozygosity (ROH), which provides useful information to assist the management of this species in different rural areas. Results We analyzed the ROH distribution and inbreeding (FROH) in 902 goats from the Italian Goat Consortium2 dataset. We evaluated the differences in individual ROH number and length between goat breeds from Northern (NRD) and Central-southern (CSD) Italy. Then, we identified the signatures of selection that differentiate these two groups using three methods: ROH, ΔROH, and averaged FST. ROH analyses showed that some Italian goat breeds have a lower inbreeding coefficient, which is attributable to their management and history. ROH are longer in breeds that are undergoing non-optimal management or with small population size. In several small breeds, the ROH length classes are balanced, reflecting more accurate mating planning. The differences in climate and management between the NRD and CSD groups have resulted in different ROH lengths and numbers: the NRD populations bred in isolated valleys present more and shorter ROH segments, while the CSD populations have fewer and longer ROH, which is likely due to the fact that they have undergone more admixture events during the horizontal transhumance practice followed by a more recent standardization. We identified four genes within signatures of selection on chromosome 11 related to fertility in the NRD group, and 23 genes on chromosomes 5 and 6 related to growth in the CSD group. Finally, we identified 17 genes on chromosome 12 related to environmental adaptation and body size with high homozygosity in both groups. Conclusions These results show how different management practices have impacted the level of genomic inbreeding in two Italian goat groups and could be useful to assist management in a low-input system while safeguarding the diversity of small populations. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00685-4.
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Affiliation(s)
- Matteo Cortellari
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Milan, Italy
| | - Arianna Bionda
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Milan, Italy.
| | - Alessio Negro
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Milan, Italy
| | - Stefano Frattini
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Milan, Italy
| | - Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | - Elisa Somenzi
- Dipartimento di Scienze Animali, Della Nutrizione e Degli Alimenti and BioDNA Centro di Ricerca Sulla Biodiversità e Sul DNA Antico, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Emiliano Lasagna
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Francesca M Sarti
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Elena Ciani
- Dipartimento di Bioscienze Biotecnologie e Biofarmaceutica, Università degli Studi di Bari, Bari, Italy
| | | | - Donata Marletta
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università degli Studi di Catania, Catania, Italy
| | - Luigi Liotta
- Dipartimento di Scienze Veterinarie, Università degli Studi di Messina, Messina, Italy
| | - Paolo Ajmone Marsan
- Dipartimento di Scienze Animali, Della Nutrizione e Degli Alimenti and BioDNA Centro di Ricerca Sulla Biodiversità e Sul DNA Antico, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Fabio Pilla
- Dipartimento Agricoltura, Ambiente e Alimenti, Università degli Studi del Molise, Campobasso, Italy
| | - Licia Colli
- Dipartimento di Scienze Animali, Della Nutrizione e Degli Alimenti and BioDNA Centro di Ricerca Sulla Biodiversità e Sul DNA Antico, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Andrea Talenti
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Paola Crepaldi
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Milan, Italy
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Zhao Q, Liu H, Qadri QR, Wang Q, Pan Y, Su G. Long-term impact of conventional and optimal contribution conservation methods on genetic diversity and genetic gain in local pig breeds. Heredity (Edinb) 2021; 127:546-553. [PMID: 34750534 PMCID: PMC8626428 DOI: 10.1038/s41437-021-00484-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 10/25/2021] [Accepted: 10/25/2021] [Indexed: 11/09/2022] Open
Abstract
There are rich and vast genetic resources of indigenous pig breeds in the world. Currently, great attention is paid to either crossbreeding or conservation of these indigenous pig breeds, and insufficient attention is paid to the combination of conservation and breeding along with their long-term effects on genetic diversity. Therefore, the objective of this study is to compare the long-term effects of using conventional conservation and optimal contribution selection methods on genetic diversity and genetic gain. A total of 11 different methods including conventional conservation and optimal contribution selection methods were investigated using stochastic simulations. The long-term effects of using these methods were evaluated in terms of genetic diversity metrices such as expected heterozygosity (He) and the rate of genetic gain. The results indicated that the rates of true inbreeding in these conventional conservation methods were maintained at around 0.01. The optimal contribution selection methods based either on the pedigree (POCS) or genome (GOCS) information showed more genetic gain than conventional methods, and POCS achieved the largest genetic gain. Furthermore, the effect of using GOCS methods on most of the genetic diversity metrics was slightly better than the conventional conservation methods when the rate of true inbreeding was the same, but this also required more sires used in OCS methods. According to the rate of true inbreeding, there was no significant difference among these conventional methods. In conclusion, there is no significant difference in different ways of selecting sows on inbreeding when we use different conventional conservation methods. Compared with conventional methods, POCS method could achieve the most genetic gain. However, GOCS methods can not only achieve higher genetic gain, but also maintain a relatively high level of genetic diversity. Therefore, GOCS is a better choice if we want to combine conservation and breeding in actual production in the conservation farms.
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Affiliation(s)
- Qingbo Zhao
- grid.16821.3c0000 0004 0368 8293School of Agriculture and Biology, Department of Animal Science, Shanghai Jiao Tong University, Shanghai, 200240 PR China ,grid.7048.b0000 0001 1956 2722Center for Quantitative Genetics and Genomics, Faculty of Science and Technology, Aarhus University, Tjele, 8830 Denmark
| | - Huiming Liu
- grid.7048.b0000 0001 1956 2722Center for Quantitative Genetics and Genomics, Faculty of Science and Technology, Aarhus University, Tjele, 8830 Denmark
| | - Qamar Raza Qadri
- grid.16821.3c0000 0004 0368 8293School of Agriculture and Biology, Department of Animal Science, Shanghai Jiao Tong University, Shanghai, 200240 PR China
| | - Qishan Wang
- grid.13402.340000 0004 1759 700XDepartment of Animal Breeding and Reproduction, College of Animal Science, Zhejiang University, Hangzhou, 310030 PR China
| | - Yuchun Pan
- Department of Animal Breeding and Reproduction, College of Animal Science, Zhejiang University, Hangzhou, 310030, PR China.
| | - Guosheng Su
- Center for Quantitative Genetics and Genomics, Faculty of Science and Technology, Aarhus University, Tjele, 8830, Denmark.
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Bengtsson C, Stålhammar H, Thomasen JR, Eriksson S, Fikse WF, Strandberg E. Mating allocations in Nordic Red Dairy Cattle using genomic information. J Dairy Sci 2021; 105:1281-1297. [PMID: 34799119 DOI: 10.3168/jds.2021-20849] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 09/08/2021] [Indexed: 11/19/2022]
Abstract
In this study, we compared mating allocations in Nordic Red Dairy Cattle using genomic information. We used linear programming to optimize different economic scores within each herd, considering genetic level, semen cost, the economic impact of recessive genetic defects, and genetic relationships. We selected 9,841 genotyped females born in Denmark, Finland, or Sweden in 2019 for mating allocations. We used 2 different pedigree relationship coefficients, the first tracing the pedigree 3 generations back from the parents of the potential mating and the second based on all available pedigree information. We used 3 different genomic relationship coefficients, 1 SNP-by-SNP genomic relationship and 2 based on shared genomic segments. We found high correlations (≥0.83) between the pedigree and genomic relationship measures. The mating results showed that it was possible to reduce the different genetic relationships between parents with minimal effect on genetic level. Including the cost of known recessive genetic defects eliminated expression of genetic defects. It was possible to reduce genomic relationships between parents with pedigree measures, but it was best done with genomic measures. Linear programming maximized the economic score for all herds studied within seconds, which means that it is suitable for implementation in mating software to be used by advisors and farmers.
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Affiliation(s)
- C Bengtsson
- VikingGenetics, VikingGenetics Sweden AB, 53294 Skara, Sweden; Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, 75007 Uppsala, Sweden.
| | - H Stålhammar
- VikingGenetics, VikingGenetics Sweden AB, 53294 Skara, Sweden
| | - J R Thomasen
- VikingGenetics, VikingGenetics Sweden AB, 53294 Skara, Sweden
| | - S Eriksson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, 75007 Uppsala, Sweden
| | - W F Fikse
- Växa Sverige, Växa Sverige, Box 288, 75105 Uppsala, Sweden
| | - E Strandberg
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, 75007 Uppsala, Sweden
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Correlation of Genomic and Pedigree Inbreeding Coefficients in Small Cattle Populations. Animals (Basel) 2021; 11:ani11113234. [PMID: 34827966 PMCID: PMC8614534 DOI: 10.3390/ani11113234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary This study aimed to evaluate the consistency of different methodologies and sources of information used to estimate inbreeding coefficients in small populations by analyzing the correlation between them in the Holstein population of Mexico and to choose the best option in order to aid breeding programs to improve the productive traits of Holstein cattle in small-specialized populations. Abstract This study aimed to identify inbreeding coefficient (F) estimators useful for improvement programs in a small Holstein population through the evaluation of different methodologies in the Mexican Holstein population. F was estimated as follows: (a) from pedigree information (Fped); (b) through runs of homozygosity (Froh); (c) from the number of observed and expected homozygotic SNP in the individuals (Fgeno); (d) through the genomic relationship matrix (Fmg). The study included information from 4277 animals with pedigree records and 100,806 SNP. The average and standard deviation values of F were 3.11 ± 2.30 for Fped, −0.02 ± 3.55 for Fgeno, 2.77 ± 0.71 for Froh and 3.03 ± 3.05 for Fmg. The correlations between coefficients varied from 0.30 between Fped and Froh, to 0.96 between Fgeno and Fmg. Differences in the level of inbreeding among the parent’s country of origin were found regardless of the method used. The correlations among genomic inbreeding coefficients were high; however, they were low with Fped, so further research on this topic is required.
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Tiret M, Pégard M, Sánchez L. How to achieve a higher selection plateau in forest tree breeding? Fostering heterozygote × homozygote relationships in optimal contribution selection in the case study of Populus nigra. Evol Appl 2021; 14:2635-2646. [PMID: 34815744 PMCID: PMC8591327 DOI: 10.1111/eva.13300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 09/07/2021] [Indexed: 12/27/2022] Open
Abstract
In breeding, optimal contribution selection (OCS) is one of the most effective strategies to balance short- and long-term genetic responses, by maximizing genetic gain and minimizing global coancestry. Considering genetic diversity in the selection dynamic-through coancestry-is undoubtedly the reason for the success of OCS, as it avoids preliminary loss of favorable alleles. Originally formulated with the pedigree relationship matrix, global coancestry can nowadays be assessed with one of the possible formulations of the realized genomic relationship matrix. Most formulations were optimized for genomic evaluation, but few for the management of coancestry. We introduce here an alternative formulation specifically developed for genomic OCS (GOCS), intended to better control heterozygous loci, and thus better account for Mendelian sampling. We simulated a multigeneration breeding program with mate allocation and under GOCS for twenty generations, solved with quadratic programming. With the case study of Populus nigra, we have shown that, although the dynamic was mainly determined by the trade-off between genetic gain and genetic diversity, better formulations of the genomic relationship matrix, especially those fostering individuals carrying multiple heterozygous loci, can lead to better short-term genetic gain and a higher selection plateau.
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Affiliation(s)
- Mathieu Tiret
- BioForA, INRAE, ONFOrléansFrance
- Department of Ecology and GeneticsEvolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Marie Pégard
- BioForA, INRAE, ONFOrléansFrance
- INRAE, BIOGECOUniv. BordeauxCestasFrance
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da Silva ÉDB, Xavier A, Faria MV. Impact of Genomic Prediction Model, Selection Intensity, and Breeding Strategy on the Long-Term Genetic Gain and Genetic Erosion in Soybean Breeding. Front Genet 2021; 12:637133. [PMID: 34539725 PMCID: PMC8440908 DOI: 10.3389/fgene.2021.637133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 08/05/2021] [Indexed: 11/21/2022] Open
Abstract
Genomic-assisted breeding has become an important tool in soybean breeding. However, the impact of different genomic selection (GS) approaches on short- and long-term gains is not well understood. Such gains are conditional on the breeding design and may vary with a combination of the prediction model, family size, selection strategies, and selection intensity. To address these open questions, we evaluated various scenarios through a simulated closed soybean breeding program over 200 breeding cycles. Genomic prediction was performed using genomic best linear unbiased prediction (GBLUP), Bayesian methods, and random forest, benchmarked against selection on phenotypic values, true breeding values (TBV), and random selection. Breeding strategies included selections within family (WF), across family (AF), and within pre-selected families (WPSF), with selection intensities of 2.5, 5.0, 7.5, and 10.0%. Selections were performed at the F4 generation, where individuals were phenotyped and genotyped with a 6K single nucleotide polymorphism (SNP) array. Initial genetic parameters for the simulation were estimated from the SoyNAM population. WF selections provided the most significant long-term genetic gains. GBLUP and Bayesian methods outperformed random forest and provided most of the genetic gains within the first 100 generations, being outperformed by phenotypic selection after generation 100. All methods provided similar performances under WPSF selections. A faster decay in genetic variance was observed when individuals were selected AF and WPSF, as 80% of the genetic variance was depleted within 28-58 cycles, whereas WF selections preserved the variance up to cycle 184. Surprisingly, the selection intensity had less impact on long-term gains than did the breeding strategies. The study supports that genetic gains can be optimized in the long term with specific combinations of prediction models, family size, selection strategies, and selection intensity. A combination of strategies may be necessary for balancing the short-, medium-, and long-term genetic gains in breeding programs while preserving the genetic variance.
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Affiliation(s)
| | - Alencar Xavier
- Department of Biostatistics, Corteva Agriscience, Johnston, IA, United States
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
| | - Marcos Ventura Faria
- Department of Agronomy, Universidade Estadual do Centro-Oeste, Guarapuava, Brazil
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Brito LF, Bedere N, Douhard F, Oliveira HR, Arnal M, Peñagaricano F, Schinckel AP, Baes CF, Miglior F. Review: Genetic selection of high-yielding dairy cattle toward sustainable farming systems in a rapidly changing world. Animal 2021; 15 Suppl 1:100292. [PMID: 34294547 DOI: 10.1016/j.animal.2021.100292] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 11/28/2022] Open
Abstract
The massive improvement in food production, as a result of effective genetic selection combined with advancements in farming practices, has been one of the greatest achievements of modern agriculture. For instance, the dairy cattle industry has more than doubled milk production over the past five decades, while the total number of cows has been reduced dramatically. This was achieved mainly through the intensification of production systems, direct genetic selection for milk yield and a limited number of related traits, and the use of modern technologies (e.g., artificial insemination and genomic selection). Despite the great betterment in production efficiency, strong drawbacks have occurred along the way. First, across-breed genetic diversity reduced dramatically, with the worldwide use of few common dairy breeds, as well as a substantial reduction in within-breed genetic diversity. Intensive selection for milk yield has also resulted in unfavorable genetic responses for traits related to fertility, health, longevity, and environmental sensitivity. Moving forward, the dairy industry needs to continue refining the current selection indexes and breeding goals to put greater emphasis on traits related to animal welfare, health, longevity, environmental efficiency (e.g., methane emission and feed efficiency), and overall resilience. This needs to be done through the definition of criteria (traits) that (a) represent well the biological mechanisms underlying the respective phenotypes, (b) are heritable, and (c) can be cost-effectively measured in a large number of animals and as early in life as possible. The long-term sustainability of the dairy cattle industry will also require diversification of production systems, with greater investments in the development of genetic resources that are resilient to perturbations occurring in specific farming systems with lesser control over the environment (e.g., organic, agroecological, and pasture-based, mountain-grazing farming systems). The conservation, genetic improvement, and use of local breeds should be integrated into the modern dairy cattle industry and greater care should be taken to avoid further genetic diversity losses in dairy cattle populations. In this review, we acknowledge the genetic progress achieved in high-yielding dairy cattle, closely related to dairy farm intensification, that reaches its limits. We discuss key points that need to be addressed toward the development of a robust and long-term sustainable dairy industry that maximize animal welfare (fundamental needs of individual animals and positive welfare) and productive efficiency, while also minimizing the environmental footprint, inputs required, and sensitivity to external factors.
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Affiliation(s)
- L F Brito
- Department of Animal Sciences, Purdue University, 270 S. Russell Street, West Lafayette, IN 47 907, USA.
| | - N Bedere
- INRAE, Institut Agro, PEGASE, 35 590 Saint-Gilles, France
| | - F Douhard
- GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326 Castanet Tolosan, France
| | - H R Oliveira
- Department of Animal Sciences, Purdue University, 270 S. Russell Street, West Lafayette, IN 47 907, USA; Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - M Arnal
- GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326 Castanet Tolosan, France; Institut de l'Elevage, Chemin de Borde Rouge, 31 326 Castanet-Tolosan cedex, France
| | - F Peñagaricano
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI 53 706, USA
| | - A P Schinckel
- Department of Animal Sciences, Purdue University, 270 S. Russell Street, West Lafayette, IN 47 907, USA
| | - C F Baes
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada; Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern 3 000, Switzerland
| | - F Miglior
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
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Fugeray-Scarbel A, Bastien C, Dupont-Nivet M, Lemarié S. Why and How to Switch to Genomic Selection: Lessons From Plant and Animal Breeding Experience. Front Genet 2021; 12:629737. [PMID: 34305998 PMCID: PMC8301370 DOI: 10.3389/fgene.2021.629737] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 06/11/2021] [Indexed: 11/25/2022] Open
Abstract
The present study is a transversal analysis of the interest in genomic selection for plant and animal species. It focuses on the arguments that may convince breeders to switch to genomic selection. The arguments are classified into three different “bricks.” The first brick considers the addition of genotyping to improve the accuracy of the prediction of breeding values. The second consists of saving costs and/or shortening the breeding cycle by replacing all or a portion of the phenotyping effort with genotyping. The third concerns population management to improve the choice of parents to either optimize crossbreeding or maintain genetic diversity. We analyse the relevance of these different bricks for a wide range of animal and plant species and sought to explain the differences between species according to their biological specificities and the organization of breeding programs.
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Affiliation(s)
| | | | | | | | - Stéphane Lemarié
- Université Grenoble Alpes, INRAE, CNRS, Grenoble INP, GAEL, Grenoble, France
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Palaiokostas C, Anjum A, Jeuthe H, Kurta K, Lopes Pinto F, Koning DJ. A genomic‐based vision on the genetic diversity and key performance traits in selectively bred Arctic charr (
Salvelinus alpinus
). Evol Appl 2021; 15:565-577. [PMID: 35505879 PMCID: PMC9046918 DOI: 10.1111/eva.13261] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/19/2021] [Accepted: 05/29/2021] [Indexed: 12/25/2022] Open
Abstract
Routine implementation of genomic information for guiding selection decisions is not yet common in the majority of aquaculture species. Reduced representation sequencing approaches offer a cost‐effective solution for obtaining genome‐wide information in species with a limited availability of genomic resources. In the current study, we implemented double‐digest restriction site‐associated DNA sequencing (ddRAD‐seq) on an Arctic charr strain with the longest known history of selection (approximately 40 years) aiming to improve selection decisions. In total, 1730 animals reared at four different farms in Sweden and spanning from year classes 2013–2017 were genotyped using ddRAD‐seq. Approximately 5000 single nucleotide polymorphisms (SNPs) were identified, genetic diversity‐related metrics were estimated, and genome‐wide association studies (GWAS) for body length at different time points and age of sexual maturation were conducted. Low genetic differentiation amongst animals from the different farms was observed based on both the results from pairwise Fst values and principal component analysis (PCA). The existence of associations was investigated between the mean genome‐wide heterozygosity of each full‐sib family (year class 2017) and the corresponding inbreeding coefficient or survival to the eyed stage. A moderate correlation (−0.33) was estimated between the mean observed heterozygosity of each full‐sib family and the corresponding inbreeding coefficient, while no linear association was obtained with the survival to the eyed stage. GWAS did not detect loci with major effect for any of the studied traits. However, genomic regions explaining more than 1% of the additive genetic variance for either studied traits were suggested across 14 different chromosomes. Overall, key insights valuable for future selection decisions of Arctic charr have been obtained, suggesting ddRAD as an attractive genotyping platform for obtaining genome‐wide information in a cost‐effective manner.
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Affiliation(s)
- Christos Palaiokostas
- Department of Animal Breeding and Genetics Swedish University of Agricultural Sciences Uppsala Sweden
| | - Anam Anjum
- Department of Animal Breeding and Genetics Swedish University of Agricultural Sciences Uppsala Sweden
| | - Henrik Jeuthe
- Department of Animal Breeding and Genetics Swedish University of Agricultural Sciences Uppsala Sweden
- Aquaculture Center North Kälarne Sweden
| | - Khrystyna Kurta
- Department of Animal Breeding and Genetics Swedish University of Agricultural Sciences Uppsala Sweden
| | - Fernando Lopes Pinto
- Department of Animal Breeding and Genetics Swedish University of Agricultural Sciences Uppsala Sweden
| | - Dirk Jan Koning
- Department of Animal Breeding and Genetics Swedish University of Agricultural Sciences Uppsala Sweden
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Lozada-Soto EA, Maltecca C, Lu D, Miller S, Cole JB, Tiezzi F. Trends in genetic diversity and the effect of inbreeding in American Angus cattle under genomic selection. Genet Sel Evol 2021; 53:50. [PMID: 34134619 PMCID: PMC8207663 DOI: 10.1186/s12711-021-00644-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 06/07/2021] [Indexed: 11/10/2022] Open
Abstract
Background While the adoption of genomic evaluations in livestock has increased genetic gain rates, its effects on genetic diversity and accumulation of inbreeding have raised concerns in cattle populations. Increased inbreeding may affect fitness and decrease the mean performance for economically important traits, such as fertility and growth in beef cattle, with the age of inbreeding having a possible effect on the magnitude of inbreeding depression. The purpose of this study was to determine changes in genetic diversity as a result of the implementation of genomic selection in Angus cattle and quantify potential inbreeding depression effects of total pedigree and genomic inbreeding, and also to investigate the impact of recent and ancient inbreeding. Results We found that the yearly rate of inbreeding accumulation remained similar in sires and decreased significantly in dams since the implementation of genomic selection. Other measures such as effective population size and the effective number of chromosome segments show little evidence of a detrimental effect of using genomic selection strategies on the genetic diversity of beef cattle. We also quantified pedigree and genomic inbreeding depression for fertility and growth. While inbreeding did not affect fertility, an increase in pedigree or genomic inbreeding was associated with decreased birth weight, weaning weight, and post-weaning gain in both sexes. We also measured the impact of the age of inbreeding and found that recent inbreeding had a larger depressive effect on growth than ancient inbreeding. Conclusions In this study, we sought to quantify and understand the possible consequences of genomic selection on the genetic diversity of American Angus cattle. In both sires and dams, we found that, generally, genomic selection resulted in decreased rates of pedigree and genomic inbreeding accumulation and increased or sustained effective population sizes and number of independently segregating chromosome segments. We also found significant depressive effects of inbreeding accumulation on economically important growth traits, particularly with genomic and recent inbreeding. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00644-z.
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Affiliation(s)
| | - Christian Maltecca
- Department of Animal Science, North Carolina State University, Raleigh, NC, 27607, USA
| | - Duc Lu
- Angus Genetics Inc, St. Joseph, MO, 64506, USA
| | | | - John B Cole
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Service, USDA, Beltsville, MD, 20705, USA
| | - Francesco Tiezzi
- Department of Animal Science, North Carolina State University, Raleigh, NC, 27607, USA
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Cortés AJ, López-Hernández F. Harnessing Crop Wild Diversity for Climate Change Adaptation. Genes (Basel) 2021; 12:783. [PMID: 34065368 PMCID: PMC8161384 DOI: 10.3390/genes12050783] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/28/2021] [Accepted: 05/19/2021] [Indexed: 12/20/2022] Open
Abstract
Warming and drought are reducing global crop production with a potential to substantially worsen global malnutrition. As with the green revolution in the last century, plant genetics may offer concrete opportunities to increase yield and crop adaptability. However, the rate at which the threat is happening requires powering new strategies in order to meet the global food demand. In this review, we highlight major recent 'big data' developments from both empirical and theoretical genomics that may speed up the identification, conservation, and breeding of exotic and elite crop varieties with the potential to feed humans. We first emphasize the major bottlenecks to capture and utilize novel sources of variation in abiotic stress (i.e., heat and drought) tolerance. We argue that adaptation of crop wild relatives to dry environments could be informative on how plant phenotypes may react to a drier climate because natural selection has already tested more options than humans ever will. Because isolated pockets of cryptic diversity may still persist in remote semi-arid regions, we encourage new habitat-based population-guided collections for genebanks. We continue discussing how to systematically study abiotic stress tolerance in these crop collections of wild and landraces using geo-referencing and extensive environmental data. By uncovering the genes that underlie the tolerance adaptive trait, natural variation has the potential to be introgressed into elite cultivars. However, unlocking adaptive genetic variation hidden in related wild species and early landraces remains a major challenge for complex traits that, as abiotic stress tolerance, are polygenic (i.e., regulated by many low-effect genes). Therefore, we finish prospecting modern analytical approaches that will serve to overcome this issue. Concretely, genomic prediction, machine learning, and multi-trait gene editing, all offer innovative alternatives to speed up more accurate pre- and breeding efforts toward the increase in crop adaptability and yield, while matching future global food demands in the face of increased heat and drought. In order for these 'big data' approaches to succeed, we advocate for a trans-disciplinary approach with open-source data and long-term funding. The recent developments and perspectives discussed throughout this review ultimately aim to contribute to increased crop adaptability and yield in the face of heat waves and drought events.
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Affiliation(s)
- Andrés J. Cortés
- Corporación Colombiana de Investigación Agropecuaria AGROSAVIA, C.I. La Selva, Km 7 Vía Rionegro, Las Palmas, Rionegro 054048, Colombia;
- Departamento de Ciencias Forestales, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Sede Medellín, Medellín 050034, Colombia
| | - Felipe López-Hernández
- Corporación Colombiana de Investigación Agropecuaria AGROSAVIA, C.I. La Selva, Km 7 Vía Rionegro, Las Palmas, Rionegro 054048, Colombia;
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Villanueva B, Fernández A, Saura M, Caballero A, Fernández J, Morales-González E, Toro MA, Pong-Wong R. The value of genomic relationship matrices to estimate levels of inbreeding. Genet Sel Evol 2021; 53:42. [PMID: 33933002 PMCID: PMC8088726 DOI: 10.1186/s12711-021-00635-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 04/19/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Genomic relationship matrices are used to obtain genomic inbreeding coefficients. However, there are several methodologies to compute these matrices and there is still an unresolved debate on which one provides the best estimate of inbreeding. In this study, we investigated measures of inbreeding obtained from five genomic matrices, including the Nejati-Javaremi allelic relationship matrix (FNEJ), the Li and Horvitz matrix based on excess of homozygosity (FL&H), and the VanRaden (methods 1, FVR1, and 2, FVR2) and Yang (FYAN) genomic relationship matrices. We derived expectations for each inbreeding coefficient, assuming a single locus model, and used these expectations to explain the patterns of the coefficients that were computed from thousands of single nucleotide polymorphism genotypes in a population of Iberian pigs. RESULTS Except for FNEJ, the evaluated measures of inbreeding do not match with the original definitions of inbreeding coefficient of Wright (correlation) or Malécot (probability). When inbreeding coefficients are interpreted as indicators of variability (heterozygosity) that was gained or lost relative to a base population, both FNEJ and FL&H led to sensible results but this was not the case for FVR1, FVR2 and FYAN. When variability has increased relative to the base, FVR1, FVR2 and FYAN can indicate that it decreased. In fact, based on FYAN, variability is not expected to increase. When variability has decreased, FVR1 and FVR2 can indicate that it has increased. Finally, these three coefficients can indicate that more variability than that present in the base population can be lost, which is also unreasonable. The patterns for these coefficients observed in the pig population were very different, following the derived expectations. As a consequence, the rate of inbreeding depression estimated based on these inbreeding coefficients differed not only in magnitude but also in sign. CONCLUSIONS Genomic inbreeding coefficients obtained from the diagonal elements of genomic matrices can lead to inconsistent results in terms of gain and loss of genetic variability and inbreeding depression estimates, and thus to misleading interpretations. Although these matrices have proven to be very efficient in increasing the accuracy of genomic predictions, they do not always provide a useful measure of inbreeding.
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Affiliation(s)
- Beatriz Villanueva
- Departamento de Mejora Genética Animal, INIA, Ctra. de La Coruña, km 7.5, 28040 Madrid, Spain
| | - Almudena Fernández
- Departamento de Mejora Genética Animal, INIA, Ctra. de La Coruña, km 7.5, 28040 Madrid, Spain
| | - María Saura
- Departamento de Mejora Genética Animal, INIA, Ctra. de La Coruña, km 7.5, 28040 Madrid, Spain
| | - Armando Caballero
- Centro de Investigación Mariña, Universidade de Vigo, Departamento de Bioquímica, Genética E Inmunología, Campus de Vigo, 36310 Vigo, Spain
| | - Jesús Fernández
- Departamento de Mejora Genética Animal, INIA, Ctra. de La Coruña, km 7.5, 28040 Madrid, Spain
| | | | - Miguel A. Toro
- Departamento de Producción Agraria, ETSI Agrónomos, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Ricardo Pong-Wong
- Genetics and Genomics, The Roslin Institute and the R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG UK
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Changes in Allele Frequencies When Different Genomic Coancestry Matrices Are Used for Maintaining Genetic Diversity. Genes (Basel) 2021; 12:genes12050673. [PMID: 33947136 PMCID: PMC8146037 DOI: 10.3390/genes12050673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/21/2021] [Accepted: 04/29/2021] [Indexed: 11/16/2022] Open
Abstract
A main objective in conservation programs is to maintain genetic variability. This can be achieved using the Optimal Contributions (OC) method that optimizes the contributions of candidates to the next generation by minimizing the global coancestry. However, it has been argued that maintaining allele frequencies is also important. Different genomic coancestry matrices can be used on OC and the choice of the matrix will have an impact not only on the genetic variability maintained, but also on the change in allele frequencies. The objective of this study was to evaluate, through stochastic simulations, the genetic variability maintained and the trajectory of allele frequencies when using two different genomic coancestry matrices in OC to minimize the loss of diversity: (i) the matrix based on deviations of the observed number of alleles shared between two individuals from the expected numbers under Hardy–Weinberg equilibrium (θLH); and (ii) the matrix based on VanRaden’s genomic relationship matrix (θVR). The results indicate that the use of θLH resulted in a higher genetic variability than the use of θVR. However, the use of θVR maintained allele frequencies closer to those in the base population than the use of θLH.
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Freitas PHF, Wang Y, Yan P, Oliveira HR, Schenkel FS, Zhang Y, Xu Q, Brito LF. Genetic Diversity and Signatures of Selection for Thermal Stress in Cattle and Other Two Bos Species Adapted to Divergent Climatic Conditions. Front Genet 2021; 12:604823. [PMID: 33613634 PMCID: PMC7887320 DOI: 10.3389/fgene.2021.604823] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 01/15/2021] [Indexed: 12/21/2022] Open
Abstract
Understanding the biological mechanisms of climatic adaptation is of paramount importance for the optimization of breeding programs and conservation of genetic resources. The aim of this study was to investigate genetic diversity and unravel genomic regions potentially under selection for heat and/or cold tolerance in thirty-two worldwide cattle breeds, with a focus on Chinese local cattle breeds adapted to divergent climatic conditions, Datong yak (Bos grunniens; YAK), and Bali (Bos javanicus) based on dense SNP data. In general, moderate genetic diversity levels were observed in most cattle populations. The proportion of polymorphic SNP ranged from 0.197 (YAK) to 0.992 (Mongolian cattle). Observed and expected heterozygosity ranged from 0.023 (YAK) to 0.366 (Sanhe cattle; SH), and from 0.021 (YAK) to 0.358 (SH), respectively. The overall average inbreeding (±SD) was: 0.118 ± 0.028, 0.228 ± 0.059, 0.194 ± 0.041, and 0.021 ± 0.004 based on the observed versus expected number of homozygous genotypes, excess of homozygosity, correlation between uniting gametes, and runs of homozygosity (ROH), respectively. Signatures of selection based on multiple scenarios and methods (F ST, HapFLK, and ROH) revealed important genomic regions and candidate genes. The candidate genes identified are related to various biological processes and pathways such as heat-shock proteins, oxygen transport, anatomical traits, mitochondrial DNA maintenance, metabolic activity, feed intake, carcass conformation, fertility, and reproduction. This highlights the large number of biological processes involved in thermal tolerance and thus, the polygenic nature of climatic resilience. A comprehensive description of genetic diversity measures in Chinese cattle and YAK was carried out and compared to 24 worldwide cattle breeds to avoid potential biases. Numerous genomic regions under positive selection were detected using three signature of selection methods and candidate genes potentially under positive selection were identified. Enriched function analyses pinpointed important biological pathways, molecular function and cellular components, which contribute to a better understanding of the biological mechanisms underlying thermal tolerance in cattle. Based on the large number of genomic regions identified, thermal tolerance has a complex polygenic inheritance nature, which was expected considering the various mechanisms involved in thermal stress response.
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Affiliation(s)
- Pedro H. F. Freitas
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - Yachun Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA – National Engineering Laboratory for Animal Breeding – College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ping Yan
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Hinayah R. Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Flavio S. Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Yi Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA – National Engineering Laboratory for Animal Breeding – College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qing Xu
- College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing, China
| | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
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