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Laseca N, Ziadi C, Perdomo-Gonzalez DI, Valera M, Demyda-Peyras S, Molina A. Reproductive traits in Pura Raza Española mares manifest inbreeding depression from low levels of homozygosity. J Anim Breed Genet 2024; 141:453-464. [PMID: 38299872 DOI: 10.1111/jbg.12856] [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: 06/27/2023] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/02/2024]
Abstract
Inbreeding depression is a genetic phenomenon associated with the loss of fitness and mean phenotypic performance due to mating between relatives. Historically, inbreeding coefficients have been estimated from pedigree information. However, the onset of genomic selection programs provides large datasets of individuals genotyped using SNP arrays, enabling more precise assessment of an individual's genomic-level inbreeding using genomic data. One of the traits most sensitive to issues stemming from increased inbreeding is reproduction. This is particularly important in equine, in which fertility is only moderate compared to other livestock species. To explore this further, we evaluated the effect of inbreeding on five reproductive traits (age at first foaling (AFF), average interval between foalings (AIF), total number of foalings (NF), productive life (PL) and reproductive efficiency (RE)) in Pura Raza Español mares using genomic data. Residual predicted phenotypes were obtained by purging these traits through the REML (wgResidual) and ssGREML (gResidual) approaches in reproductive data of 29,847 PRE mares using the BLUPF90+ program. Next, we used pedigree-based (Fped) and ROH-based genomic (FROH) inbreeding coefficients derived from 1018 animals genotyped with 61,271 SNPs to estimate the inbreeding depression (linear regression). Our results indicated significant levels of inbreeding depression for all reproductive traits, with the exception of the AIF trait when Fped was used. However, all traits were negatively affected by the increase in genomic inbreeding, and FROH was found to capture more inbreeding depression than Fped. Likewise, REML models (ssGREML) using genomic data for estimated predicted residual phenotypes resulted in higher variance explained by the model compared with the models not using genomics (REML). Finally, a segmented regression analysis was conducted to evaluate the effect of inbreeding depression, revealing that the levels of genealogical and genomic homozygosity do not manifest uniformly in reproductive traits. In contrast, the levels of inbreeding depression ranged from low to high as homozygosity increased. This analysis also showed that reproductive traits are very sensitive to inbreeding depression, even with relatively low levels of homozygosity.
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Affiliation(s)
- Nora Laseca
- Department of Genetics, University of Cordoba, Córdoba, Spain
| | - Chiraz Ziadi
- Department of Genetics, University of Cordoba, Córdoba, Spain
| | | | - Mercedes Valera
- Department of Agronomy, ETSIA, University of Seville, Seville, Spain
| | | | - Antonio Molina
- Department of Genetics, University of Cordoba, Córdoba, Spain
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2
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Mugambe J, Ahmed RH, Thaller G, Schmidtmann C. Impact of inbreeding on production, fertility, and health traits in German Holstein dairy cattle utilizing various inbreeding estimators. J Dairy Sci 2024; 107:4714-4725. [PMID: 38310961 DOI: 10.3168/jds.2023-23728] [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: 05/11/2023] [Accepted: 12/29/2023] [Indexed: 02/06/2024]
Abstract
In dairy cattle production, it is important to understand how inbreeding affects production, fertility, and health traits. However, there is still limited use of genomic information to estimate inbreeding, despite advancements in genotyping technologies. To address this gap, we investigated the effect of inbreeding on German Holstein dairy cattle using both pedigree-based and genomic-based inbreeding estimators. We employed one method based on pedigree information (Fped) together with 6 genomic-based methods, including 3 genome-wide complex trait analysis software estimators (Fhat1, Fhat2, Fhat3), VanRaden's first method (FVR1, with observed allele frequencies, and FVR0.5, when allele frequencies are set to 0.5), and one based on runs of homozygosity (Froh). Data from 24,489 cows with both phenotypes and genotypes were used, with a pedigree including 232,780 animals born between 1970 and 2018. We analyzed the effects of inbreeding depression on production, fertility, and health traits separately, using single-trait linear animal models as well as threshold models to account for the binary nature of the health traits. For the health traits, we transformed solutions from the liability scale to a probability scale for easier interpretation. Our results showed that the mean inbreeding coefficients from all estimators ranged from -0.003 to 0.243, with negative values observed for most genomic-based methods. We found out that a 1% increase in inbreeding caused a depression ranging from 25.94 kg (Fhat1) to 40.62 kg (Fhat3), 1.18 kg (Fhat2) to 1.70 kg (Fhat3), 0.90 kg (Fhat2) to 1.45 kg (Froh and Fhat3), 0.19 (Fped) to 0.34 d (Fhat3) for 305-d milk yield, fat, protein, and calving interval, respectively. The health traits showed very slight gradual changes when inbreeding was increased steadily from 0% to 50%, with digital dermatitis showing a rather contrasting trend to that of mastitis, which increased the more an animal was inbred. Overall, our study highlights the importance of considering both pedigree-based and genomic-based inbreeding estimators when assessing the impact on inbreeding, emphasizing that not all inbreeding is harmful.
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Affiliation(s)
- Julius Mugambe
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University Kiel, 24098 Kiel, Germany.
| | - Rana H Ahmed
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University Kiel, 24098 Kiel, Germany
| | - Georg Thaller
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University Kiel, 24098 Kiel, Germany
| | - Christin Schmidtmann
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University Kiel, 24098 Kiel, Germany; IT-Solutions for Animal Production (vit), 27283 Verden, Germany
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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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Värv S, Põlluäär T, Sild E, Viinalass H, Kaart T. Genetic Variation and Composition of Two Commercial Estonian Dairy Cattle Breeds Assessed by SNP Data. Animals (Basel) 2024; 14:1101. [PMID: 38612340 PMCID: PMC11010984 DOI: 10.3390/ani14071101] [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: 02/22/2024] [Revised: 03/29/2024] [Accepted: 04/02/2024] [Indexed: 04/14/2024] Open
Abstract
The aims of this study were to assess the genomic relatedness of Estonian and selected European dairy cattle breeds and to examine the within-breed diversity of two Estonian dairy breeds using genome-wide SNP data. This study was based on a genotyped heifer population of the Estonian Red (ER) and Estonian Holstein (EH) breeds, including about 10% of all female cattle born in 2017-2020 (sample sizes n = 215 and n = 2265, respectively). The within-breed variation study focused on the level of inbreeding using the ROH-based inbreeding coefficient. The genomic relatedness analyses were carried out among two Estonian and nine European breeds from the WIDDE database. Admixture analysis revealed the heterogeneity of ER cattle with a mixed pattern showing several ancestral populations containing a relatively low proportion (1.5-37.0%) of each of the reference populations used. There was a higher FROH in EH (FROH = 0.115) than in ER (FROH = 0.044). Compared to ER, the long ROHs of EH indicated more closely related parents. The paternal origin of the genetic material used in breeding had a low effect on the inbreeding level. However, among EH, the highest genomic inbreeding was estimated in daughters of USA-born sires.
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Affiliation(s)
- Sirje Värv
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Fr. R. Kreutzwaldi 1, 51006 Tartu, Estonia; (T.P.); (E.S.); (H.V.)
| | | | | | | | - Tanel Kaart
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Fr. R. Kreutzwaldi 1, 51006 Tartu, Estonia; (T.P.); (E.S.); (H.V.)
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Neustaeter A, Brito LF, Hanna WJB, Baird JD, Schenkel FS. Investigating the Genetic Background of Spastic Syndrome in North American Holstein Cattle Based on Heritability, Genome-Wide Association, and Functional Genomic Analyses. Genes (Basel) 2023; 14:1479. [PMID: 37510383 PMCID: PMC10378964 DOI: 10.3390/genes14071479] [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: 07/01/2023] [Revised: 07/12/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
Spastic syndrome is a chronic, progressive disorder of adult cattle characterized by episodes of sudden involuntary muscle contractions or spasms of the extensor and abductor muscles of one or both hind limbs. In this study, a case-control genome-wide association study (GWAS) was performed on an adult Holstein cattle cohort. Based on the 50 K and high-density (HD) SNP panel GWAS, we identified 98 and 522 SNPs, respectively. The most significant genomic regions identified are located on BTA9 at approximately 87 megabase pairs (Mb) and BTA7 between 1 and 20 Mb. Functional analyses of significant SNPs identified genes associated with muscle contraction, neuron growth or regulation, and calcium or sodium ion movement. Two candidate genes (FIG4 and FYN) were identified. FIG4 is ubiquitously expressed in skeletal muscle and FYN is involved with processes such as forebrain development, neurogenesis, locomotion, neurogenesis, synapse development, neuron migration, and the positive regulation of neuron projection development. The CACNA1A gene, which codes for a calcium channel subunit protein in the calcium signaling pathway, seems the most compelling candidate gene, as many calcium ion channel disorders are non-degenerative, and produce spastic phenotypes. These results suggest that spastic syndrome is of polygenic inheritance, with important genomic areas of interest on BTA7 and BTA9.
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Affiliation(s)
- Anna Neustaeter
- Centre for Genetic Improvement of Livestock (CGIL), Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Luiz F Brito
- Centre for Genetic Improvement of Livestock (CGIL), Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - W J Brad Hanna
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - John D Baird
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Flavio S Schenkel
- Centre for Genetic Improvement of Livestock (CGIL), Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
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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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Chen J, Wang Y, Qi X, Cheng H, Chen N, Ahmed Z, Chen Q, Lei C, Yang X. Genome-wide analysis emancipates genomic diversity and signature of selection in Altay white-headed cattle of Xinjiang, China. Front Genet 2023; 14:1144249. [PMID: 37065480 PMCID: PMC10098193 DOI: 10.3389/fgene.2023.1144249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 03/17/2023] [Indexed: 04/01/2023] Open
Abstract
Altay white-headed cattle have not received enough attention for several reasons. Due to irrational breeding and selection practices, the number of pure Altay white-headed cattle has decreased significantly and the breed is now on the eve of extinction. The genomic characterization will be a crucial step towards understanding the genetic basis of productivity and adaptability to survival under native Chinese agropastoral systems; nevertheless, no attempt has been made in Altay white-headed cattle. In the current study, we compared the genomes of 20 Altay white-headed cattle to the genomes of 144 individuals in representative breeds. Population genetic diversity revealed that the nucleotide diversity of Altay white-headed cattle was less than that of indicine breeds and comparable to that of Chinese taurus cattle. Using population structure analysis, we also found that Altay white-headed cattle carried the ancestry of the European and East Asian cattle lineage. In addition, we used three different methods (FST, θπ ratio and XP-EHH) to investigate the adaptability and white-headed phenotype of Altay white-headed cattle and compared it with Bohai black cattle. We found EPB41L5, SCG5 and KIT genes on the list of the top one percent genes, these genes might have an association with environmental adaptability and the white-headed phenotype for this breed. Our research reveals the distinctive genomic features of Altay white-headed cattle at the genome-wide level.
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Affiliation(s)
- Jialei Chen
- Life Science College, Luoyang Normal University, Luoyang, China
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yushu Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xingshan Qi
- Biyang Xianan Cattle Technology and Development Company Ltd., Biyang, China
| | - Haijian Cheng
- Shandong Key Lab of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Ningbo Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zulfiqar Ahmed
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, and Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
- Faculty of Veterinary and Animal Sciences, University of Poonch Rawalakot, Shabestar, Pakistan
| | - Qiuming Chen
- College of Animal Science, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
- *Correspondence: Chuzhao Lei, ; Xueyi Yang,
| | - Xueyi Yang
- Life Science College, Luoyang Normal University, Luoyang, China
- *Correspondence: Chuzhao Lei, ; Xueyi Yang,
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Ablondi M, Summer A, Stocco G, Finocchiaro R, van Kaam JT, Cassandro M, Dadousis C, Sabbioni A, Cipolat-Gotet C. The role of inbreeding depression on productive performance in the Italian Holstein breed. J Anim Sci 2023; 101:skad382. [PMID: 37983004 PMCID: PMC10693289 DOI: 10.1093/jas/skad382] [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: 05/31/2023] [Accepted: 11/18/2023] [Indexed: 11/21/2023] Open
Abstract
Inbreeding depression has become an urgent issue in cosmopolitan breeds where the massive genetic progress achieved in the latest generations is counterbalanced by a dramatic loss of genetic diversity causing increased health issues. Thus, the aim of this study was to estimate inbreeding depression on productive traits in Holstein dairy cattle. More precisely, we aimed to i) determine the level of inbreeding in 27,735 Italian Holstein dairy cows using pedigree and genotype data, ii) quantify the effect of inbreeding on 305-d in milk yield (MY; kg), fat yield (FY; kg), and protein yield (PY; kg) based on different statistical approaches, iii) determine if recent inbreeding has a more harmful impact than ancestral ones, and iv) quantify chromosomal homozygosity effect on productive traits. Quality control was performed on the autosomal chromosomes resulting in a final dataset of 84,443 single nucleotide polymorphisms. Four statistical models were used to evaluate the presence of inbreeding depression, which included linear regression analysis and division of FPED and FROH into percentile classes. Moreover, FROH was partitioned into i) length classes to assess the role of recent and ancestral inbreeding and ii) chromosome-specific contributions (FROH-CHR). Results evidenced that inbreeding negatively impacted the productive performance of Italian Holstein Friesian cows. However, differences between the estimated FPED and FROH coefficients resulted in different estimates of inbreeding depression. For instance, a 1% increase in FPED and FROH was associated with a decrease in MY of about 44 and 61 kg (P < 0.01). Further, when considering the extreme inbreeding percentile classes moving from the 5th lowest to the 95th highest, there was a reduction of -263 kg and -561 kg per lactation for FPED and FROH. Increased inbreeding, estimated by FPED and FROH, had also a negative effect on PY and FY, either fit as a regressor or percentile classes. When evaluating the impact of inbreeding based on runs of homozygosity (ROH) length classes, longer ROH (over 8 Mb) had a negative effect in all traits, indicating that recent inbreeding might be more harmful than the ancestral one. Finally, results within chromosome homozygosity highlighted specific chromosomes with a more deleterious effect on productive traits.
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Affiliation(s)
- Michela Ablondi
- Department of Veterinary Science, University of Parma, 43126 Parma, Italy
| | - Andrea Summer
- Department of Veterinary Science, University of Parma, 43126 Parma, Italy
| | - Giorgia Stocco
- Department of Veterinary Science, University of Parma, 43126 Parma, Italy
| | - Raffaella Finocchiaro
- Associazione Nazionale Allevatori della Razza Frisona Bruna e Jersey Italiana (ANAFIBJ), 26100 Cremona, Italy
| | - Jan-Thijs van Kaam
- Associazione Nazionale Allevatori della Razza Frisona Bruna e Jersey Italiana (ANAFIBJ), 26100 Cremona, Italy
| | - Martino Cassandro
- Associazione Nazionale Allevatori della Razza Frisona Bruna e Jersey Italiana (ANAFIBJ), 26100 Cremona, Italy
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, 35020 Legnaro, Italy
| | - Christos Dadousis
- Department of Veterinary Science, University of Parma, 43126 Parma, Italy
| | - Alberto Sabbioni
- Department of Veterinary Science, University of Parma, 43126 Parma, Italy
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Zhang M, Fu T, Huang Q, Xing Z, Yang J, Lu W, Hu M, Han LQ, Loor JJ, Gao TY. Size, number and phospholipid composition of milk fat globules are affected by dietary conjugated linoleic acid. J Anim Physiol Anim Nutr (Berl) 2022. [DOI: 10.1111/jpn.13788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 09/07/2022] [Accepted: 10/14/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Menglu Zhang
- Department of Animal Production and Husbandry, College of Animal Science and Technology Henan Agricultural University Zhengzhou P.R. China
| | - Tong Fu
- Department of Animal Production and Husbandry, College of Animal Science and Technology Henan Agricultural University Zhengzhou P.R. China
| | - Qixue Huang
- Department of Veterinary Biotechnology, College of Veterinary Medicine Henan Agricultural University Zhengzhou P.R. China
| | - Zhiyang Xing
- Department of Veterinary Biotechnology, College of Veterinary Medicine Henan Agricultural University Zhengzhou P.R. China
| | - Jingna Yang
- Department of Veterinary Biotechnology, College of Veterinary Medicine Henan Agricultural University Zhengzhou P.R. China
| | - Wenyan Lu
- Department of Veterinary Biotechnology, College of Veterinary Medicine Henan Agricultural University Zhengzhou P.R. China
| | - Mingyue Hu
- Department of Veterinary Biotechnology, College of Veterinary Medicine Henan Agricultural University Zhengzhou P.R. China
| | - Li Qiang Han
- Department of Veterinary Biotechnology, College of Veterinary Medicine Henan Agricultural University Zhengzhou P.R. China
| | - Juan J. Loor
- Department of Animal Science, Division of Nutritional Sciences University of Illinois Urbana Illinois USA
| | - Teng Yun Gao
- Department of Animal Production and Husbandry, College of Animal Science and Technology Henan Agricultural University Zhengzhou P.R. China
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Abstract
PRACTICAL RELEVANCE When compared with the number of individuals that make up a dog breed, the population within a given cat breed is very small. Therefore, to maintain a breed standard, a certain degree of inbreeding is necessary. However, when inbreeding reaches a certain threshold, it can lead to decreased fertility, which manifests as failure to conceive, smaller litter size, increased neonatal illness and neonatal mortality. Breeders should be encouraged to keep comprehensive records on breeding outcomes, including number of kittens born, neonatal vitality, daily kitten weights and kitten health at weaning. Commercially available DNA panels are available to inform and facilitate excellent breeding choices and can estimate the coefficient of inbreeding. Clinicians should include a review of the degree of inbreeding in the work-up for any cattery or cat colony experiencing decreased fertility. AIM The objective of this article is to provide clinicians, especially those working with cat breeders, with an easy-to-understand guide to genetics and to demonstrate how inbreeding influences fertility and neonatal survival. EQUIPMENT AND TECHNICAL SKILLS Medical records and the pedigree of the cats in question are required to investigate cases of infertility that may be related to inbreeding. A DNA analysis kit that measures genetic diversity and health parameters can also be helpful; those that have been developed by geneticists and veterinarians at universities are preferable, as they include access to highly skilled genetic counselors and researchers who are open to working up newly discovered genetic diseases. EVIDENCE BASE The material provided is based on current literature and the author's own studies examining outcomes in a closed cattery.
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Affiliation(s)
- Margret L Casal
- University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA, USA
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11
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Raz R, Roth Z, Gershoni M. ExAgBov: A public database of annotated variations from hundreds of bovine whole-exome sequencing samples. Sci Data 2022; 9:469. [PMID: 35918364 PMCID: PMC9345876 DOI: 10.1038/s41597-022-01597-8] [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: 12/24/2021] [Accepted: 07/26/2022] [Indexed: 11/09/2022] Open
Abstract
Large reference datasets of annotated genetic variations from genome-scale sequencing are essential for interpreting identified variants, their functional impact, and their possible contribution to diseases and traits. However, to date, no such database of annotated variation from broad cattle populations is publicly available. To overcome this gap and advance bovine NGS-driven variant discovery and interpretation, we obtained and analyzed raw data deposited in the SRA public repository. Short reads from 262 whole-exome sequencing samples of Bos Taurus were mapped to the Bos Taurus ARS-UCD1.2 reference genome. The GATK best practice workflow was applied for variant calling. Comprehensive annotation of all recorded variants was done using the Ensembl Variant Effect Predictor (VEP). An in-depth analysis of the population structure revealed the breeds comprising the database. The Exomes Aggregate of Bovine- ExAgBov is a comprehensively annotated dataset of more than 20 million short variants, of which ~2% are located within open reading frames, splice regions, and UTRs, and more than 60,000 variants are predicted to be deleterious.
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Affiliation(s)
- Rotem Raz
- Department of Ruminant Science, Institute of Animal Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion, 7505101, Israel.,Department of Animal Sciences, Robert H. Smith Faculty of Agriculture, Food and Environment, the Hebrew University, Rehovot, 76100, Israel
| | - Zvi Roth
- Department of Ruminant Science, Institute of Animal Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion, 7505101, Israel
| | - Moran Gershoni
- Department of Ruminant Science, Institute of Animal Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion, 7505101, Israel.
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Nagai R, Kinukawa M, Watanabe T, Ogino A, Kurogi K, Adachi K, Satoh M, Uemoto Y. Genomic dissection of repeatability considering additive and non-additive genetic effects for semen production traits in beef and dairy bulls. J Anim Sci 2022; 100:6647626. [PMID: 35860946 DOI: 10.1093/jas/skac241] [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: 04/12/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
The low heritability and moderate repeatability of semen production traits in beef and dairy bulls suggest that non-additive genetic effects, such as dominance and epistatic effects, play an important role in semen production and should therefore be considered in genetic improvement programs. In this study, the repeatability of semen production traits in Japanese Black bulls (JB) as beef bulls and Holstein bulls (HOL) as dairy bulls was evaluated by considering additive and non-additive genetic effects using the Illumina BovineSNP50 BeadChip. We also evaluated the advantage of using more complete models that include non-additive genetic effects by comparing the rank of genotyped animals and the phenotype prediction ability of each model. In total, 65,463 records for 615 genotyped JB and 48,653 records for 845 genotyped HOL were used to estimate additive and non-additive (dominance and epistatic) variance components for semen volume (VOL), sperm concentration (CON), sperm motility (MOT), MOT after freeze-thawing (aMOT), and sperm number (NUM). In the model including both additive and non-additive genetic effects, the broad-sense heritability (0.17-0.43) was more than twice as high as the narrow-sense heritability (0.04-0.11) for all traits and breeds, and the differences between the broad-sense heritability and repeatability were very small for VOL, NUM, and CON in both breeds. A large proportion of permanent environmental variance was explained by epistatic variance. The epistatic variance as a proportion of total phenotypic variance was 0.07-0.33 for all traits and breeds. In addition, heterozygosity showed significant positive relationships with NUM, MOT, and aMOT in JB and NUM in HOL, when the heterozygosity rate was included as a covariate. In a comparison of models, the inclusion of non-additive genetic effects resulted in a re-ranking of the top genotyped bulls for the additive effects. Adjusting for non-additive genetic effects could be expected to produce a more accurate breeding value, even if the models have similar fitting. However, including non-additive genetic effects did not improve the ability of any model to predict phenotypic values for any trait or breed compared with the predictive ability of a model that includes only additive effects. Consequently, although non-additive genetic effects, especially epistatic effects, play an important role in semen production traits, they do not improve prediction accuracy in beef and dairy bulls.
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Affiliation(s)
- Rintaro Nagai
- Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi 980-8572, Japan
| | - Masashi Kinukawa
- Maebashi Institute of Animal Science, Livestock Improvement Association of Japan, Inc., Maebashi 371-0121, Japan
| | - Toshio Watanabe
- Maebashi Institute of Animal Science, Livestock Improvement Association of Japan, Inc., Maebashi 371-0121, Japan
| | - Atsushi Ogino
- Maebashi Institute of Animal Science, Livestock Improvement Association of Japan, Inc., Maebashi 371-0121, Japan
| | - Kazuhito Kurogi
- Cattle Breeding Department, Livestock Improvement Association of Japan, Inc., Tokyo 135-0041, Japan
| | - Kazunori Adachi
- Cattle Breeding Department, Livestock Improvement Association of Japan, Inc., Tokyo 135-0041, Japan
| | - Masahiro Satoh
- Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi 980-8572, Japan
| | - Yoshinobu Uemoto
- Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi 980-8572, Japan
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13
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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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14
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Wang S, Yang J, Li G, Ding R, Zhuang Z, Ruan D, Wu J, Yang H, Zheng E, Cai G, Wang X, Wu Z. Identification of Homozygous Regions With Adverse Effects on the Five Economic Traits of Duroc Pigs. Front Vet Sci 2022; 9:855933. [PMID: 35573406 PMCID: PMC9096619 DOI: 10.3389/fvets.2022.855933] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
Runs of homozygosity (ROH) are widely used to estimate genomic inbreeding, which is linked to inbreeding depression on phenotypes. However, the adverse effects of specific homozygous regions on phenotypic characteristics are rarely studied in livestock. In this study, the 50 K SNP data of 3,770 S21 Duroc (American origin) and 2,096 S22 Duroc (Canadian origin) pigs were used to investigate the harmful ROH regions on five economic traits. The results showed that the two Duroc lines had different numbers and distributions of unfavorable ROHs, which may be related to the different selection directions and intensities between the two lines. A total of 114 and 58 ROH segments were found with significant adverse effects on the economic traits of S21 and S22 pigs, respectively. Serval pleiotropic ROHs were detected to reduce two or multiple phenotypic performances in two Duroc populations. Candidate genes in these shared regions were mainly related to growth, fertility, immunity, and fat deposition. We also observed that some ROH genotypes may cause opposite effects on different traits. This study not only enhances our understanding of the adverse effects of ROH on phenotypes, but also indicates that ROH information could be incorporated into breeding programs to estimate and control the detrimental effects of homozygous regions.
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Affiliation(s)
- Shiyuan Wang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Jie Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, China
| | - Guixin Li
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Rongrong Ding
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Zhanwei Zhuang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Donglin Ruan
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Jie Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Huaqiang Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Enqin Zheng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Gengyuan Cai
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Xiaopeng Wang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
- *Correspondence: Xiaopeng Wang
| | - Zhenfang Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, China
- Zhenfang Wu
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15
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Genomic Prediction of Complex Traits in Perennial Plants: A Case for Forest Trees. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2467:493-520. [PMID: 35451788 DOI: 10.1007/978-1-0716-2205-6_18] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
This chapter provides an overview of the genomic selection progress in long-lived forest tree species. Factors affecting the prediction accuracy in genomic prediction are assessed with examples from empirical studies. Infrastructure and resources required for the implementation of genomic selection are evaluated. Some general guidelines are provided for the successful application of genomic selection in forest tree breeding programs.
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16
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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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17
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Gutiérrez-Reinoso MA, Aponte PM, García-Herreros M. A review of inbreeding depression in dairy cattle: current status, emerging control strategies, and future prospects. J DAIRY RES 2022; 89:1-10. [PMID: 35225176 DOI: 10.1017/s0022029922000188] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Dairy cattle breeding has historically focused on relatively small numbers of elite bulls as sires of sons. In recent years, even if generation intervals were reduced and more diverse sires of sons could have been selected, genomic selection has not fundamentally changed the fact that a large number of individuals are being analyzed. However, a relatively small number of elite bulls are still siring those animals. Therefore inbreeding-derived negative consequences in the gene pool have brought concern. The detrimental effects of non-additive genetic changes such as inbreeding depression and dominance have been widely disseminated while seriously affecting bioeconomically important parameters because of an antagonistic relationship between dairy production and reproductive traits. Therefore, the estimation of benefits and limitations of inbreeding and variance of the selection response deserves to be evaluated and discussed to preserve genetic variability, a significant concern in the selection of individuals for reproduction and production. Short-term strategies for genetic merit improvement through modern breeding programs have severely lowered high-producing dairy cattle fertility potential. Since the current selection programs potentially increase long-term costs, genetic diversity has decreased globally as a consequence. Therefore, a greater understanding of the potential that selection programs have for supporting long-term genetic sustainability and genetic diversity among dairy cattle populations should be prioritized in managing farm profitability. The present review provides a broad approach to current inbreeding-derived problems, identifying critical points to be solved and possible alternative strategies to control selection against homozygous haplotypes while maintaining sustained selection pressure. Moreover, this manuscript explores future perspectives, emphasizing theoretical applications and critical points, and strategies to avoid the adverse effects of inbreeding in dairy cattle. Finally, this review provides an overview of challenges that will soon require multidisciplinary approaches to managing dairy cattle populations, intending to combine increases in productive trait phenotypes with improvements in reproductive, health, welfare, linear conformation, and adaptability traits into the foreseeable future.
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Affiliation(s)
- Miguel A Gutiérrez-Reinoso
- Universidad Técnica de Cotopaxi, Facultad de Ciencias Agropecuarias y Recursos Naturales, Carrera de Medicina Veterinaria (UTC), Latacunga, Ecuador
- Laboratorio de Biotecnología Animal, Departamento de Ciencia Animal, Facultad de Ciencias Veterinarias, Universidad de Concepción, Chillán (UdeC), Chile
| | - Pedro M Aponte
- Universidad San Francisco de Quito (USFQ), Colegio de Ciencias Biológicas y Ambientales (COCIBA), Campus Cumbayá, Quito, Ecuador
- Instituto de Investigaciones en Biomedicina, iBioMed, Universidad San Francisco de Quito (USFQ), Campus Cumbayá, Quito, Ecuador
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18
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Ablondi M, Sabbioni A, Stocco G, Cipolat-Gotet C, Dadousis C, van Kaam JT, Finocchiaro R, Summer A. Genetic Diversity in the Italian Holstein Dairy Cattle Based on Pedigree and SNP Data Prior and After Genomic Selection. Front Vet Sci 2022; 8:773985. [PMID: 35097040 PMCID: PMC8792952 DOI: 10.3389/fvets.2021.773985] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/30/2021] [Indexed: 01/09/2023] Open
Abstract
Genetic diversity has become an urgent matter not only in small local breeds but also in more specialized ones. While the use of genomic data in livestock breeding programs increased genetic gain, there is increasing evidence that this benefit may be counterbalanced by the potential loss of genetic variability. Thus, in this study, we aimed to investigate the genetic diversity in the Italian Holstein dairy cattle using pedigree and genomic data from cows born between 2002 and 2020. We estimated variation in inbreeding, effective population size, and generation interval and compared those aspects prior to and after the introduction of genomic selection in the breed. The dataset contained 84,443 single-nucleotide polymorphisms (SNPs), and 74,485 cows were analyzed. Pedigree depth based on complete generation equivalent was equal to 10.67. A run of homozygosity (ROH) analysis was adopted to estimate SNP-based inbreeding (FROH). The average pedigree inbreeding was 0.07, while the average FROH was more than double, being equal to 0.17. The pattern of the effective population size based on pedigree and SNP data was similar although different in scale, with a constant decrease within the last five generations. The overall inbreeding rate (ΔF) per year was equal to +0.27% and +0.44% for Fped and FROH throughout the studied period, which corresponded to about +1.35% and +2.2% per generation, respectively. A significant increase in the ΔF was found since the introduction of genomic selection in the breed. This study in the Italian Holstein dairy cattle showed the importance of controlling the loss of genetic diversity to ensure the long-term sustainability of this breed, as well as to guarantee future market demands.
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Affiliation(s)
- Michela Ablondi
- Dipartimento di Scienze Medico-Veterinarie, University of Parma, Parma, Italy
| | - Alberto Sabbioni
- Dipartimento di Scienze Medico-Veterinarie, University of Parma, Parma, Italy
| | - Giorgia Stocco
- Dipartimento di Scienze Medico-Veterinarie, University of Parma, Parma, Italy
| | - Claudio Cipolat-Gotet
- Dipartimento di Scienze Medico-Veterinarie, University of Parma, Parma, Italy
- *Correspondence: Claudio Cipolat-Gotet
| | - Christos Dadousis
- Dipartimento di Scienze Medico-Veterinarie, University of Parma, Parma, Italy
| | - Jan-Thijs van Kaam
- Associazione Nazionale Allevatori della Razza Frisona Bruna e Jersey Italiana, Cremona, Italy
| | - Raffaella Finocchiaro
- Associazione Nazionale Allevatori della Razza Frisona Bruna e Jersey Italiana, Cremona, Italy
| | - Andrea Summer
- Dipartimento di Scienze Medico-Veterinarie, University of Parma, Parma, Italy
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19
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The effect of inbreeding, body size and morphology on health in dog breeds. Canine Med Genet 2021; 8:12. [PMID: 34852838 PMCID: PMC8638537 DOI: 10.1186/s40575-021-00111-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 11/02/2021] [Indexed: 11/10/2022] Open
Abstract
Background Dog breeds are known for their distinctive body shape, size, coat color, head type and behaviors, features that are relatively similar across members of a breed. Unfortunately, dog breeds are also characterized by distinct predispositions to disease. We explored the relationships between inbreeding, morphology and health using genotype based inbreeding estimates, body weight and insurance data for morbidity. Results The average inbreeding based on genotype across 227 breeds was Fadj = 0.249 (95% CI 0.235–0.263). There were significant differences in morbidity between breeds with low and high inbreeding (H = 16.49, P = 0.0004). There was also a significant difference in morbidity between brachycephalic breeds and non-brachycephalic breeds (P = 0.0048) and between functionally distinct groups of breeds (H = 14.95 P < 0.0001). Morbidity was modeled using robust regression analysis and both body weight (P < 0.0001) and inbreeding (P = 0.013) were significant (r2 = 0.77). Smaller less inbred breeds were healthier than larger more inbred breeds. Conclusions In this study, body size and inbreeding along with deleterious morphologies contributed to increases in necessary health care in dogs. Supplementary Information The online version contains supplementary material available at 10.1186/s40575-021-00111-4.
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Forneris NS, Garcia-Baccino CA, Cantet RJC, Vitezica ZG. Estimating inbreeding depression for growth and reproductive traits using pedigree and genomic methods in Argentinean Brangus cattle. J Anim Sci 2021; 99:6396951. [PMID: 34648628 DOI: 10.1093/jas/skab289] [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: 05/03/2021] [Accepted: 10/13/2021] [Indexed: 12/20/2022] Open
Abstract
Inbreeding depression reduces the mean phenotypic value of important traits in livestock populations. The goal of this work was to estimate the level of inbreeding and inbreeding depression for growth and reproductive traits in Argentinean Brangus cattle, in order to obtain a diagnosis and monitor breed management. Data comprised 359,257 (from which 1,990 were genotyped for 40,678 single nucleotide polymorphisms [SNPs]) animals with phenotypic records for at least one of three growth traits: birth weight (BW), weaning weight (WW), and finishing weight (FW). For scrotal circumference (SC), 52,399 phenotypic records (of which 256 had genotype) were available. There were 530,938 animals in pedigree. Three methods to estimate inbreeding coefficients were used. Pedigree-based inbreeding coefficients were estimated accounting for missing parents. Inbreeding coefficients combining genotyped and nongenotyped animal information were also computed from matrix H of the single-step approach. Genomic inbreeding coefficients were estimated using homozygous segments obtained from a Hidden Markov model (HMM) approach. Inbreeding depression was estimated from the regression of the phenotype on inbreeding coefficients in a multiple-trait mixed model framework, either for the whole dataset or for the dataset of genotyped animals. All traits were unfavorably affected by inbreeding depression. A 10% increase in pedigree-based or combined inbreeding would result in a reduction of 0.34 to 0.39 kg in BW, 2.77 to 3.28 kg in WW, and 0.23 cm in SC. For FW, a 10% increase in pedigree-based, genomic, or combined inbreeding would result in a decrease of 8.05 to 11.57 kg. Genomic inbreeding based on the HMM was able to capture inbreeding depression, even in such a compressed genotyped dataset.
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Affiliation(s)
- Natalia S Forneris
- Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, C1417DSQ Buenos Aires, Argentina.,CONICET-Universidad de Buenos Aires, Instituto de Investigaciones en Producción Animal (INPA), C1427CWO Buenos Aires, Argentina
| | - Carolina A Garcia-Baccino
- Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, C1417DSQ Buenos Aires, Argentina
| | - Rodolfo J C Cantet
- Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, C1417DSQ Buenos Aires, Argentina.,CONICET-Universidad de Buenos Aires, Instituto de Investigaciones en Producción Animal (INPA), C1427CWO Buenos Aires, Argentina
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21
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Pilon B, Hinterneder K, Hay EHA, Fragomeni B. Inbreeding Calculated with Runs of Homozygosity Suggests Chromosome-Specific Inbreeding Depression Regions in Line 1 Hereford. Animals (Basel) 2021; 11:ani11113105. [PMID: 34827837 PMCID: PMC8614356 DOI: 10.3390/ani11113105] [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: 09/30/2021] [Revised: 10/19/2021] [Accepted: 10/25/2021] [Indexed: 01/12/2023] Open
Abstract
The goal of this study was to evaluate inbreeding in a closed beef cattle population and assess phenotype prediction accuracy using inbreeding information. Effects of inbreeding on average daily gain phenotype in the Line 1 Hereford cattle population were assessed in this study. Genomic data were used to calculate inbreeding based on runs of homozygosity (ROH), and pedigree information was used to calculate the probability of an allele being identical by descent. Prediction ability of phenotypes using inbreeding coefficients calculated based on pedigree information and runs of homozygosity over the whole genome was close to 0, even in the case of significant inbreeding coefficient effects. On the other hand, inbreeding calculated per individual chromosomes' ROH yielded higher accuracies of prediction. Additionally, including only ROH from chromosomes with higher predicting ability further increased prediction accuracy. Phenotype prediction accuracy, inbreeding depression, and the effects of chromosome-specific ROHs varied widely across the genome. The results of this study suggest that inbreeding should be evaluated per individual regions of the genome. Moreover, mating schemes to avoid inbreeding depression should focus more on specific ROH with negative effects. Finally, using ROH as added information may increase prediction of the genetic merit of animals in a genomic selection program.
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Affiliation(s)
- Bethany Pilon
- Department of Animal Science, University of Connecticut, Storrs, CT 06269, USA; (B.P.); (K.H.)
- College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Kelly Hinterneder
- Department of Animal Science, University of Connecticut, Storrs, CT 06269, USA; (B.P.); (K.H.)
- College of Veterinary Medicine, Lincoln Memorial University, Harrogate, TN 37752, USA
| | - El Hamidi A. Hay
- Fort Keogh Livestock and Range Research Laboratory, ARS, USDA, Miles City, MT 59301, USA;
| | - Breno Fragomeni
- Department of Animal Science, University of Connecticut, Storrs, CT 06269, USA; (B.P.); (K.H.)
- Institute for System Genomics, University of Connecticut, Storrs, CT 06269, USA
- Correspondence:
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22
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Investigating inbreeding in the turkey (Meleagris gallopavo) genome. Poult Sci 2021; 100:101366. [PMID: 34525446 PMCID: PMC8445901 DOI: 10.1016/j.psj.2021.101366] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 06/02/2021] [Accepted: 06/24/2021] [Indexed: 02/06/2023] Open
Abstract
The detrimental effects of increased homozygosity due to inbreeding have prompted the development of methods to reduce inbreeding. The detection of runs of homozygosity (ROH), or contiguous stretches of homozygous marker genotypes, can be used to describe and quantify the level of inbreeding in an individual. The estimation of inbreeding coefficients can be calculated based on pedigree information, ROH, or the genomic relationship matrix. The aim of this study was to detect and describe ROH in the turkey genome and compare estimates of pedigree-based inbreeding coefficients (FPED) with genomic-based inbreeding coefficients estimated from ROH (FROH) and the genomic relationship matrix (FGRM). A total of 2,616,890 pedigree records were available. Of these records, 6,371 genotyped animals from three purebred turkey (Meleagris gallopavo) lines between 2013 and 2019 were available, and these were obtained using a dense single nucleotide polymorphism array (56,452 SNPs). The overall mean length of detected ROH was 2.87 ± 0.29 Mb with a mean number of 84.87 ± 8.79 ROH per animal. Short ROH with lengths of 1 to 2 Mb long were the most abundant throughout the genome. Mean ROH coverage differed greatly between chromosomes and lines. Considering inbreeding coefficient means across all lines, genomic derived inbreeding coefficients (FROH = 0.27; FGRM = 0.32) were higher than coefficients estimated from pedigree records (FPED = 0.14). Correlations between FROH and FPED, FROH and FGRM, and FPED and FGRM ranged between 0.19 to 0.31, 0.68 to 0.73, and 0.17 to 0.30, respectively. Additionally, correlations between FROH from different lengths and FPED substantially increased with ROH length from -0.06 to 0.33. Results of the current research, including the distribution of ROH throughout the genome and ROH-derived inbreeding estimates, can provide a more comprehensive description of inbreeding in the turkey genome. This knowledge can be used to evaluate genetic diversity, a requirement for genetic improvement, and develop methods to minimize inbreeding in turkey breeding programs.
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Makanjuola BO, Maltecca C, Miglior F, Marras G, Abdalla EA, Schenkel FS, Baes CF. Identification of unique ROH regions with unfavorable effects on production and fertility traits in Canadian Holsteins. Genet Sel Evol 2021; 53:68. [PMID: 34461820 PMCID: PMC8406729 DOI: 10.1186/s12711-021-00660-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 08/19/2021] [Indexed: 12/02/2022] Open
Abstract
Background The advent of genomic information and the reduction in the cost of genotyping have led to the use of genomic information to estimate genomic inbreeding as an alternative to pedigree inbreeding. Using genomic measures, effects of genomic inbreeding on production and fertility traits have been observed. However, there have been limited studies on the specific genomic regions causing the observed negative association with the trait of interest. Our aim was to identify unique run of homozygosity (ROH) genotypes present within a given genomic window that display negative associations with production and fertility traits and to quantify the effects of these identified ROH genotypes. Methods In total, 50,575 genotypes based on a 50K single nucleotide polymorphism (SNP) array and 259,871 pedigree records were available. Of these 50,575 genotypes, 46,430 cows with phenotypic records for production and fertility traits and having a first calving date between 2008 and 2018 were available. Unique ROH genotypes identified using a sliding-window approach were fitted into an animal mixed model as fixed effects to determine their effect on production and fertility traits. Results In total, 133 and 34 unique ROH genotypes with unfavorable effects were identified for production and fertility traits, respectively, at a 1% genome-wise false discovery rate. Most of these ROH regions were located on bovine chromosomes 8, 13, 14 and 19 for both production and fertility traits. For production traits, the average of all the unfavorably identified unique ROH genotypes effects were estimated to decrease milk yield by 247.30 kg, fat yield by 11.46 kg and protein yield by 8.11 kg. Similarly, for fertility traits, an average 4.81-day extension in first service to conception, a 0.16 increase in number of services, and a − 0.07 incidence in 56-day non-return rate were observed. Furthermore, a ROH region located on bovine chromosome 19 was identified that, when homozygous, had a negative effect on production traits. Signatures of selection proximate to this region have implicated GH1 as a potential candidate gene, which encodes the growth hormone that binds the growth hormone receptor. This observed negative effect could be a consequence of unfavorable alleles in linkage disequilibrium with favorable alleles. Conclusions ROH genotypes with unfavorable effects on production and fertility traits were identified within and across multiple traits on most chromosomes. These identified ROH genotypes could be included in mate selection programs to minimize their frequency in future generations. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00660-z.
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Affiliation(s)
- Bayode O Makanjuola
- Centre for Genomic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada.
| | - Christian Maltecca
- Centre for Genomic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada.,Department of Animal Science and Genetics Program, North Carolina State University, Raleigh, NC, 27607, USA
| | - Filippo Miglior
- Centre for Genomic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | | | - Emhimad A Abdalla
- Centre for Genomic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Flavio S Schenkel
- Centre for Genomic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Christine F Baes
- Centre for Genomic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada.,Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
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Genetic Diversity and Identification of Homozygosity-Rich Genomic Regions in Seven Italian Heritage Turkey ( Meleagris gallopavo) Breeds. Genes (Basel) 2021; 12:genes12091342. [PMID: 34573324 PMCID: PMC8470100 DOI: 10.3390/genes12091342] [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: 07/26/2021] [Revised: 08/24/2021] [Accepted: 08/26/2021] [Indexed: 01/10/2023] Open
Abstract
Italian autochthonous turkey breeds are an important reservoir of genetic biodiversity that should be maintained with an in vivo approach. The aim of this study, part of the TuBAvI national project on biodiversity, was to use run of homozygosity (ROH), together with others statistical approaches (e.g., Wright's F-statistics, principal component analysis, ADMIXTURE analysis), to investigate the genomic diversity in several heritage turkey breeds. We performed a genome-wide characterization of ROH-rich regions in seven autochthonous turkey breeds, i.e., Brianzolo (Brzl), Bronzato Comune Italiano (BrCI), Bronzato dei Colli Euganei (CoEu), Parma e Piacenza (PrPc), Nero d'Italia (NeIt), Ermellinato di Rovigo (ErRo) and Romagnolo (Roma). ROHs were detected based on a 650K SNP genotyping. ROH_islands were identified as homozygous ROH regions shared by at least 75% of birds (within breed). Annotation of genes was performed with DAVID. The admixture analyses revealed that six breeds are unique populations while the Roma breed consists in an admixture of founder populations. Effective population size estimated on genomic data shows a numeric contraction. ROH_islands harbour genes that may be interesting for target selection in commercial populations also. Among them the PTGS2 and PLA2G4A genes on chr10 were related to reproduction efficiency. This is the first study mapping genetic variation in autochthonous turkey populations. Breeds were genetically different among them, with the Roma breed proving to be a mixture of the other breeds. The ROH_islands identified harboured genes peculiar to the selection that occurred in heritage breeds. Finally, this study releases previously undisclosed information on existing genetic variation in the turkey species.
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How Depressing Is Inbreeding? A Meta-Analysis of 30 Years of Research on the Effects of Inbreeding in Livestock. Genes (Basel) 2021; 12:genes12060926. [PMID: 34207101 PMCID: PMC8234567 DOI: 10.3390/genes12060926] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/12/2021] [Accepted: 06/15/2021] [Indexed: 11/17/2022] Open
Abstract
Inbreeding depression has been widely documented for livestock and other animal and plant populations. Inbreeding is generally expected to have a stronger unfavorable effect on fitness traits than on other traits. Traditionally, the degree of inbreeding depression in livestock has been estimated as the slope of the linear regression of phenotypic values on pedigree-based inbreeding coefficients. With the increasing availability of SNP-data, pedigree inbreeding can now be replaced by SNP-based measures. We performed a meta-analysis of 154 studies, published from 1990 to 2020 on seven livestock species, and compared the degree of inbreeding depression (1) across different trait groups, and (2) across different pedigree-based and SNP-based measures of inbreeding. Across all studies and traits, a 1% increase in pedigree inbreeding was associated with a median decrease in phenotypic value of 0.13% of a trait’s mean, or 0.59% of a trait’s standard deviation. Inbreeding had an unfavorable effect on all sorts of traits and there was no evidence for a stronger effect on primary fitness traits (e.g., reproduction/survival traits) than on other traits (e.g., production traits or morphological traits). p-values of inbreeding depression estimates were smaller for SNP-based inbreeding measures than for pedigree inbreeding, suggesting more power for SNP-based measures. There were no consistent differences in p-values for percentage of homozygous SNPs, inbreeding based on runs of homozygosity (ROH) or inbreeding based on a genomic relationship matrix. The number of studies that directly compares these different measures, however, is limited and comparisons are furthermore complicated by differences in scale and arbitrary definitions of particularly ROH-based inbreeding. To facilitate comparisons across studies in future, we provide the dataset with inbreeding depression estimates of 154 studies and stress the importance of always reporting detailed information (on traits, inbreeding coefficients, and models used) along with inbreeding depression estimates.
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Terán E, Azcona F, Ramón M, Molina A, Dorado J, Hidalgo M, Ross P, Goszczynski D, Demyda-Peyrás S. Sperm morphometry is affected by increased inbreeding in the Retinta cattle breed: A molecular approach. Mol Reprod Dev 2021; 88:416-426. [PMID: 34009693 DOI: 10.1002/mrd.23475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 03/02/2021] [Accepted: 04/14/2021] [Indexed: 12/11/2022]
Abstract
The effect of inbreeding depression on sperm motility is well documented, but its influence on sperm morphometry has been scarcely examined to date. Here, we combined the use of computer-assisted sperm morphometry analysis (CASMA) with a SNP-based genomic approach to determine and characterize the effect of inbreeding on the sperm shape of a highly inbred cattle population. We determined seven morphometric parameters on frozen-thawed sperm samples of 57 Retinta bulls: length (L, µm), width (W, µm), area (A, µm2 ), perimeter (P, µm), ellipticity (ELI; L/W), elongation (L-W)/(L + W) and perimeter-to-area shape factor (p2a; P2 /4 × π × A). The comparison of highly inbred (HI) and lowly inbreed (LI) individuals based on runs of homozygosity (ROH) inbreeding values (F ROH ) showed no differences between groups. An additional two-step unsupervised sperm subpopulation analysis based on morphometric parameters showed significant differences in the abundance of different sperm subpopulations between groups (p < 0.05). This analysis revealed that HI bulls harbored a higher percentage of narrow-head sperm as opposed to the higher percentage of large- and round-headed sperm detected in LI. A further genomic characterization revealed 23 regions differentially affected by inbreeding in both groups, detecting six genes (SPAG6, ARMC3, PARK7, VAMP3, DYNLRB2, and PHF7) previously related to different spermatogenesis-associated processes.
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Affiliation(s)
- Ester Terán
- IGEVET - Instituto de Genética Veterinaria, UNLP - CONICET, Facultad de Ciencias Veterinarias Universidad Nacional de la Plata, La Plata, Buenos Aires, Argentina.,Departamento de Producción Animal, Facultad de Ciencias Veterinarias, UNLP - CONICET, Facultad de Ciencias Veterinarias Universidad Nacional de la Plata, La Plata, Buenos Aires, Argentina
| | - Florencia Azcona
- IGEVET - Instituto de Genética Veterinaria, UNLP - CONICET, Facultad de Ciencias Veterinarias Universidad Nacional de la Plata, La Plata, Buenos Aires, Argentina
| | - Manuel Ramón
- CERSYRA-Centro Regional de Selección y Reproducción Animal de Castilla-La Mancha, Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal (IRIAF), Valdepeñas, España
| | - Antonio Molina
- Departamento de Genética, Universidad de Córdoba, Córdoba, España
| | - Jesús Dorado
- Grupo de Reproducción Veterinaria, Departamento de Medicina y Cirugía animal, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, España
| | - Manuel Hidalgo
- Grupo de Reproducción Veterinaria, Departamento de Medicina y Cirugía animal, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, España
| | - Pablo Ross
- Department of Animal Science, University of California at Davis, Davis, California, USA
| | - Daniel Goszczynski
- Department of Animal Science, University of California at Davis, Davis, California, USA
| | - Sebastián Demyda-Peyrás
- Departamento de Producción Animal, Facultad de Ciencias Veterinarias, UNLP - CONICET, Facultad de Ciencias Veterinarias Universidad Nacional de la Plata, La Plata, Buenos Aires, Argentina
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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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Tao L, He X, Wang X, Di R, Chu M. Litter Size of Sheep ( Ovis aries): Inbreeding Depression and Homozygous Regions. Genes (Basel) 2021; 12:109. [PMID: 33477586 PMCID: PMC7831309 DOI: 10.3390/genes12010109] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 02/07/2023] Open
Abstract
Ovine litter size (LS) is an important trait showing variability within breeds. It remains largely unknown whether inbreeding depression on LS exists based on genomic homozygous regions, and whether the homozygous regions resulted from inbreeding are significantly associated with LS in sheep. We here reanalyze a set of single nucleotide polymorphism (SNP) chip of six breeds to characterize the patterns of runs of homozygosity (ROH), to evaluate inbreeding levels and inbreeding depressions on LS, and to identify candidate homozygous regions responsible for LS. Consequently, unique ROH patterns were observed among six sheep populations. Inbreeding depression on LS was only found in Hu sheep, where a significant reduction of 0.016, 0.02, and 0.02 per 1% elevated inbreeding FROH4-8, FROH>8 and the total inbreeding measure was observed, respectively. Nine significantly homozygous regions were found for LS in Hu sheep, where some promising genes for LS possibly via regulation of the development of oocytes (NGF, AKT1, and SYCP1), fertilization (SPAG17, MORC1, TDRD9, ZFYVE21, ADGRB3, and CKB), embryo implantation (PPP1R13B, INF2, and VANGL1) and development (DPPA2, DPPA4, CDCA4, CSDE1, and ADSSL1), and reproductive health (NRG3, BAG5, CKB, and XRCC3) were identified. These results from the present study would provide insights into the genetic management and complementary understandings of LS in sheep.
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Affiliation(s)
| | | | | | | | - Mingxing Chu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (L.T.); (X.H.); (X.W.); (R.D.)
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Antonios S, Rodríguez-Ramilo ST, Aguilar I, Astruc JM, Legarra A, Vitezica ZG. Genomic and pedigree estimation of inbreeding depression for semen traits in the Basco-Béarnaise dairy sheep breed. J Dairy Sci 2020; 104:3221-3230. [PMID: 33358787 DOI: 10.3168/jds.2020-18761] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 10/05/2020] [Indexed: 01/09/2023]
Abstract
Inbreeding depression is associated with a decrease in performance and fitness of the animals. The goal of this study was to evaluate pedigree-based and genomic methods to estimate the level of inbreeding and inbreeding depression for 3 semen traits (volume, concentration, and motility score) in the Basco-Béarnaise sheep breed. Data comprised 16,196 (or 15,071) phenotypic records from 620 rams (of which 533 rams had genotypes of 36,464 SNPs). The pedigree included 8,266 animals, composed of the 620 rams and their ancestors. The number of equivalent complete generations for the 620 rams was 7.04. Inbreeding coefficients were estimated using genomic and pedigree-based information. Genomic inbreeding coefficients were estimated from individual SNP and using segments of homozygous SNP (runs of homozygosity, ROH). Short ROH are of old origin, whereas long ROH are due to recent inbreeding. Considering that the equivalent number of generations in Basco-Béarnaise was 6, inbreeding coefficients for ROH with a length >4 Mb refer to all (recent + old) inbreeding, those with a length >17 Mb correspond to recent inbreeding, and the difference between them indicates old inbreeding. Pedigree-based inbreeding coefficients were also estimated classically, or accounting for nonzero relationships for unknown parents, or including metafounder relationships (estimated using markers) to account for missing pedigree information. Finally, inbreeding coefficients combining genotyped and nongenotyped animal information were computed from matrix H of the single-step approach, also including metafounders. Inbreeding depression was estimated differently depending on the approach used to compute inbreeding coefficients. These 8 estimators of inbreeding coefficients were included as covariates in different animal models. No inbreeding depression was detected for sperm volume or sperm concentration. Inbreeding depression was significant for the motility of spermatozoa. The effect of old and recent inbreeding on motility was null and negative, respectively, demonstrating the existence of purging by selection of deleterious recessive alleles affecting motility. A 10% increase in inbreeding would result in a reduction in mean motility ranging between 0.09 and 0.22 points in the score (from 0 to 5). Motility is unfavorably affected by increasing recent inbreeding but the impact is very small. Runs of homozygosity and metafounders allow us to accurately estimate inbreeding depression and detect recent inbreeding.
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Affiliation(s)
- S Antonios
- GenPhySE, INPT, INRAE, ENVT, F-31326, Castanet Tolosan, France
| | | | - I Aguilar
- Instituto Nacional de Investigación Agropecuaria (INIA), 11100, Montevideo, Uruguay
| | - J M Astruc
- Institut de l'Elevage, 149 rue de Bercy, F-75595 Paris, France
| | - A Legarra
- GenPhySE, INPT, INRAE, ENVT, F-31326, Castanet Tolosan, France
| | - Z G Vitezica
- GenPhySE, INPT, INRAE, ENVT, F-31326, Castanet Tolosan, France.
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Bérodier M, Berg P, Meuwissen T, Boichard D, Brochard M, Ducrocq V. Improved dairy cattle mating plans at herd level using genomic information. Animal 2020; 15:100016. [PMID: 33516018 DOI: 10.1016/j.animal.2020.100016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 07/17/2020] [Accepted: 07/28/2020] [Indexed: 11/19/2022] Open
Abstract
From 2012 to 2018, 223 180 Montbéliarde females were genotyped in France and the number of newly genotyped females increased at a rate of about 33% each year. With female genotyping information, farmers have access to the genomic estimated breeding values of the females in their herd and to their carrier status for genetic defects or major genes segregating in the breed. This information, combined with genomic coancestry, can be used when planning matings in order to maximize the expected on-farm profit of future female offspring. We compared different mating allocation approaches for their capacity to maximize the expected genetic gain while limiting expected progeny inbreeding and the probability to conceive an offspring homozygous for a lethal recessive allele. Three mate allocation strategies (random mating (RAND), sequential mating (gSEQ€) and linear programing mating (gLP€)) were compared on 160 actual Montbéliarde herds using male and female genomic information. Then, we assessed the benefit of using female genomic information by comparing matings planned using only female pedigree information with the equivalent strategy using genomic information. We measured the benefit of adding genomic expected inbreeding and risk of conception of an offspring homozygous for a lethal recessive allele to Net merit in mating plans. The influence of three constraints was tested: by relaxing the constraint on availability of a particular semen type (sexed or conventional) for bulls, by adding an upper limit of 8.5% coancestry between mate pairs or by using a more stringent maximum use of a bull in a herd (5% vs 10%). The use of genomic information instead of pedigree information improved the mate allocation method in terms of progeny expected genetic merit, genetic diversity and risk to conceive an offspring homozygous for a lethal recessive allele. Optimizing mate allocation using linear programming and constraining coancestry to a maximum of 8.5% per mate pair reduced the average coancestry with a small impact on expected Net Merit. In summary, for male and female selection pathways, using genomic information is more efficient than using pedigree information to maximize genetic gain while constraining the expected inbreeding of the progeny and the risk to conceive an offspring homozygous for a lethal recessive allele. This study also underlines the key role of semen type (sexed vs conventional) and the associated constraints on the mate allocation algorithm to maximize genetic gain while maintaining genetic diversity and limiting the risk to conceive an offspring homozygous for a lethal recessive allele.
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Affiliation(s)
- M Bérodier
- UMR GABI, AgroParisTech, INRAE, Université Paris-Saclay, 78350 Jouy-en-Josas, France; MO3, 01250, Ceyzériat, France.
| | - P Berg
- Norwegian University of Life Sciences, PB 5002, N-1432 Ås, Norway
| | - T Meuwissen
- Norwegian University of Life Sciences, PB 5002, N-1432 Ås, Norway
| | - D Boichard
- UMR GABI, AgroParisTech, INRAE, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - M Brochard
- MO3, 01250, Ceyzériat, France; Umotest, 01250, Ceyzériat, France
| | - V Ducrocq
- UMR GABI, AgroParisTech, INRAE, Université Paris-Saclay, 78350 Jouy-en-Josas, France
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31
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Gutiérrez-Reinoso MA, Aponte PM, Cabezas J, Rodriguez-Alvarez L, Garcia-Herreros M. Genomic Evaluation of Primiparous High-Producing Dairy Cows: Inbreeding Effects on Genotypic and Phenotypic Production-Reproductive Traits. Animals (Basel) 2020; 10:ani10091704. [PMID: 32967074 PMCID: PMC7552765 DOI: 10.3390/ani10091704] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Improving the genomic prediction methodologies in high-producing dairy cattle is a key factor for the selection of suitable individuals to ensure better productivity. However, the most advanced prediction tools based on genotyping show ~75% reliability. Nowadays, the incorporation of new indices to genomic prediction methods, such as the Inbreeding Index (II), can significantly facilitate the selection of reliable production and reproductive traits for progeny selection. Thus, the objective of this study was to determine the impact of II (low: LI and high: HI), based on genomic analysis, and its effect on production and reproductive phenotypic traits in high-producing primiparous dairy cows. Individuals with II between ≥2.5 and ≤5.0 have shown up to a two-fold increase in negative correlations comparing LI versus HI genomic production and reproductive parameters, severely affecting important traits such as Milk Production at 305 d, Protein Production at 305 d, Fertility Index, and Daughter Pregnancy Rate. Therefore, high-producing dairy cows face an increased risk of negative II-derived effects in their selection programs, particularly at II ≥ 2.5. Abstract The main objective of this study was to analyze the effects of the inbreeding degree in high-producing primiparous dairy cows genotypically and phenotypically evaluated and its impacts on production and reproductive parameters. Eighty Holstein–Friesian primiparous cows (age: ~26 months; ~450 kg body weight) were previously genomically analyzed to determine the Inbreeding Index (II) and were divided into two groups: low inbreeding group (LI: <2.5; n = 40) and high inbreeding group (HI: ≥2.5 and ≤5.0; n = 40). Genomic determinations of production and reproductive parameters (14 in total), together with analyses of production (12) and reproductive (11) phenotypic parameters (23 in total) were carried out. Statistically significant differences were obtained between groups concerning the genomic parameters of Milk Production at 305 d and Protein Production at 305 d and the reproductive parameter Daughter Calving Ease, the first two being higher in cows of the HI group and the third lower in the LI group (p < 0.05). For the production phenotypic parameters, statistically significant differences were observed between both groups in the Total Fat, Total Protein, and Urea parameters, the first two being higher in the LI group (p < 0.05). Also, significant differences were observed in several reproductive phenotypic parameters, such as Number of Services per Conception, Calving to Conception Interval, Days Open Post Service, and Current Inter-Partum Period, all of which negatively influenced the HI group (p < 0.05). In addition, correlation analyses were performed between production and reproductive genomic parameters separately and in each consanguinity group. The results showed multiple positive and negative correlations between the production and reproductive parameters independently of the group analyzed, being these correlations more remarkable for the reproductive parameters in the LI group and the production parameters in the HI group (p < 0.05). In conclusion, the degree of inbreeding significantly influenced the results, affecting different genomic and phenotypic production and reproductive parameters in high-producing primiparous cows. The determination of the II in first-calf heifers is crucial to evaluate the negative effects associated with homozygosity avoiding an increase in inbreeding depression on production and reproductive traits.
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Affiliation(s)
- Miguel A. Gutiérrez-Reinoso
- Departamento de Ciencia Animal, Laboratorio de Biotecnología Animal, Facultad de Ciencias Veterinarias, Universidad de Concepción (UdeC), Chillán 3780000, Chile; (M.A.G.-R.); (J.C.)
- Facultad de Ciencias Agropecuarias y Recursos Naturales, Carrera de Medicina Veterinaria, Universidad Técnica de Cotopaxi (UTC), Latacunga 050150, Ecuador
| | - Pedro Manuel Aponte
- Colegio de Ciencias Biológicas y Ambientales (COCIBA), Universidad San Francisco de Quito (USFQ), Quito 170157, Ecuador;
- Instituto de Investigaciones en Biomedicina “One-health”, Universidad San Francisco de Quito (USFQ), Campus Cumbayá, Quito 170157, Ecuador
| | - Joel Cabezas
- Departamento de Ciencia Animal, Laboratorio de Biotecnología Animal, Facultad de Ciencias Veterinarias, Universidad de Concepción (UdeC), Chillán 3780000, Chile; (M.A.G.-R.); (J.C.)
| | - Lleretny Rodriguez-Alvarez
- Departamento de Ciencia Animal, Laboratorio de Biotecnología Animal, Facultad de Ciencias Veterinarias, Universidad de Concepción (UdeC), Chillán 3780000, Chile; (M.A.G.-R.); (J.C.)
- Correspondence: (L.R.-A.); (M.G.-H.); Tel.: +56-42-220-8835 (L.R.-A.); Fax: +351-24-3767 (ext. 330) (M.G.-H.)
| | - Manuel Garcia-Herreros
- Instituto Nacional de Investigação Agrária e Veterinária (INIAV), 2005-048 Santarém, Portugal
- Correspondence: (L.R.-A.); (M.G.-H.); Tel.: +56-42-220-8835 (L.R.-A.); Fax: +351-24-3767 (ext. 330) (M.G.-H.)
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Cesarani A, Gaspa G, Pauciullo A, Degano L, Vicario D, Macciotta NPP. Genome-wide analysis of homozygosity regions in european simmental bulls. J Anim Breed Genet 2020; 138:69-79. [PMID: 33263211 DOI: 10.1111/jbg.12502] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 07/08/2020] [Accepted: 07/18/2020] [Indexed: 01/15/2023]
Abstract
The study of Runs of Homozygosity (ROH) is a useful approach for the characterization of the genome of livestock populations. Due to their high relationship with autozygosity, ROH allow to make inference about population genetic history, to estimate the level of inbreeding, to assess within breed heterogeneity and to detect the footprints of selection on livestock genomes. Aim of this study was to investigate the distribution of runs of homozygosity in bulls belonging to five European Simmental populations and to assess the relationship between three production traits (milk yield, fat and protein contents) and autozygosity. ROH count, distribution and ROH-based coefficient of inbreeding (FROH ) were calculated for 3,845 Simmental bulls of five different European countries: Austria (AT), Switzerland (CH), Czech Republic (CZ), Germany (DE) and Italy (IT). Average values of ROH number per animal, and total genome length covered by ROH were 77.8 ± 20.7 and 205 ± 74.4 Mb, respectively. Bulls from AT, DE and IT exhibited similar ROH characteristics. Swiss animals showed the highest (12.6%), while CZ the lowest (4.6%) FROH coefficient. The relationship between ROH occurrence and milk production traits was investigated through a genome-wide ROH-traits association analysis (GWRA). A total of 34 regions previously associated with milk traits (yield and/or composition) were identified by GWRA. Results of the present research highlight a mixed genetic background in the 5 European Simmental populations, with the possible presence of three subgroups. Moreover, a strong relationship between autozygosity and production traits has been detected.
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Affiliation(s)
- Alberto Cesarani
- Department of Agricultural Sciences, University of Sassari, Sassari, Italy.,Associazione Nazionale Allevatori Pezzata Rossa Italiana (ANAPRI), Udine, Italy
| | - Giustino Gaspa
- Department of Agricultural, Forestry and Alimentary Sciences, University of Torino, Grugliasco, Italy
| | - Alfredo Pauciullo
- Department of Agricultural, Forestry and Alimentary Sciences, University of Torino, Grugliasco, Italy
| | - Lorenzo Degano
- Associazione Nazionale Allevatori Pezzata Rossa Italiana (ANAPRI), Udine, Italy
| | - Daniele Vicario
- Associazione Nazionale Allevatori Pezzata Rossa Italiana (ANAPRI), Udine, Italy
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Maltecca C, Tiezzi F, Cole JB, Baes C. Symposium review: Exploiting homozygosity in the era of genomics-Selection, inbreeding, and mating programs. J Dairy Sci 2020; 103:5302-5313. [PMID: 32331889 DOI: 10.3168/jds.2019-17846] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 02/25/2020] [Indexed: 01/06/2023]
Abstract
The advent of genomic selection paved the way for an unprecedented acceleration in genetic progress. The increased ability to select superior individuals has been coupled with a drastic reduction in the generation interval for most dairy populations, representing both an opportunity and a challenge. Homozygosity is now rapidly accumulating in dairy populations. Currently, inbreeding depression is managed mostly by culling at the farm level and by controlling the overall accumulation of homozygosity at the population level. A better understanding of how homozygosity and recessive load are related will guarantee continued genetic improvement while curtailing the accumulation of harmful recessives and maintaining enough genetic variability to ensure the possibility of selection in the face of changing environmental conditions. In this review, we present a snapshot of the current dairy selection structure as it relates to response to selection and accumulation of homozygosity, briefly outline the main approaches currently used to manage inbreeding and overall variability, and present some approaches that can be used in the short term to control accumulation of harmful recessives while maintaining sustained selection pressure.
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Affiliation(s)
- C Maltecca
- Animal Science Department, North Carolina State University, Raleigh 27695.
| | - F Tiezzi
- Animal Science Department, North Carolina State University, Raleigh 27695
| | - J B Cole
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705
| | - C Baes
- Centre for Genomic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, N1G 2W1 Guelph, Ontario, Canada; Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
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Makanjuola BO, Miglior F, Abdalla EA, Maltecca C, Schenkel FS, Baes CF. Effect of genomic selection on rate of inbreeding and coancestry and effective population size of Holstein and Jersey cattle populations. J Dairy Sci 2020; 103:5183-5199. [PMID: 32278553 DOI: 10.3168/jds.2019-18013] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 02/13/2020] [Indexed: 12/22/2022]
Abstract
Genetic diversity in livestock populations is a significant contributor to the sustainability of animal production. Also, genetic diversity allows animal production to become more responsive to environmental changes and market demands. The loss of genetic diversity can result in a plateau in production and may also result in loss of fitness or viability in animal production. In this study, we investigated the rate of inbreeding (ΔF), rate of coancestry (Δf), and effective population size (Ne) as important quantitative indicators of genetic diversity and evaluated the effect of the recent implementation of genomic selection on the loss of genetic diversity in North American Holstein and Jersey dairy cattle. To estimate the rate of inbreeding and coancestry, inbreeding and coancestry coefficients were calculated using the traditional pedigree method and genomic methods estimated from segment- and marker-based approaches. Furthermore, we estimated Ne from the rate of inbreeding and coancestry and extent of linkage disequilibrium. A total of 205,755 and 89,238 pedigreed and genotyped animals born between 1990 and 2018 inclusively were available for Holsteins and Jerseys, respectively. The estimated average pedigree inbreeding coefficients were 7.74 and 7.20% for Holsteins and Jerseys, respectively. The corresponding values for the segment and marker-by-marker genomic inbreeding coefficients were 13.61, 15.64, and 31.40% for Holsteins and 21.16, 22.54, and 42.62% for Jerseys, respectively. The average coancestry coefficients were 8.33 and 15.84% for Holsteins and 9.23 and 23.46% for Jerseys with pedigree and genomic measures, respectively. Generation interval for the whole 29-yr time period averaged approximately 5 yr for all selection pathways combined. The ΔF per generation based on pedigree, segment, and marker-by-marker genomic measures for the entire 29-yr period was estimated to be 0.75, 1.10, 1.16, and 1.02% for Holstein animals and 0.67, 0.62, 0.63, and 0.59% for Jersey animals, respectively. The Δf was estimated to be 0.98 and 0.98% for Holsteins and 0.73 and 0.78% for Jerseys with pedigree and genomic measures, respectively. These ΔF and Δf translated to an Ne that ranged from 43 to 66 animals for Holsteins and 64 to 85 animals for Jerseys. In addition, the Ne based on linkage disequilibrium was 58 and 120 for Holsteins and Jerseys, respectively. The 10-yr period that involved the application of genomic selection resulted in an increased ΔF per generation with ranges from 1.19 to 2.06% for pedigree and genomic measures in Holsteins. Given the rate at which inbreeding is increasing after the implementation of genomic selection, there is a need to implement measures and means for controlling the rate of inbreeding per year, which will help to manage and maintain farm animal genetic resources.
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Affiliation(s)
- Bayode O Makanjuola
- Centre for Genomic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1 Canada
| | - Filippo Miglior
- Centre for Genomic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1 Canada; Ontario Genomics, ON, M5G 1M1 Canada
| | - Emhimad A Abdalla
- Centre for Genomic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1 Canada
| | - Christian Maltecca
- Centre for Genomic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1 Canada; Department of Animal Science and Genetics Program, North Carolina State University, Raleigh 27607
| | - Flavio S Schenkel
- Centre for Genomic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1 Canada
| | - Christine F Baes
- Centre for Genomic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1 Canada; Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern 3001, Switzerland.
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Martikainen K, Koivula M, Uimari P. Identification of runs of homozygosity affecting female fertility and milk production traits in Finnish Ayrshire cattle. Sci Rep 2020; 10:3804. [PMID: 32123255 PMCID: PMC7052207 DOI: 10.1038/s41598-020-60830-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 02/17/2020] [Indexed: 11/09/2022] Open
Abstract
Inbreeding gives rise to continuous lengths of homozygous genotypes called runs of homozygosity (ROH) that occur when identical haplotypes are inherited from both parents. ROHs are enriched for deleterious recessive alleles and can therefore be linked to inbreeding depression, defined as decreased phenotypic performance of the animals. However, not all ROHs within a region are expected to have harmful effects on the trait of interest. We aimed to identify ROHs that unfavourably affect female fertility and milk production traits in the Finnish Ayrshire population. The estimated effect of ROHs with the highest statistical significance varied between parities from 9 to 17 days longer intervals from calving to first insemination, from 13 to 38 days longer intervals from first to last insemination and from 0.3 to 1.0 more insemination per conception. Similarly, for milk production traits ROHs were associated with a reduction of 208 kg for milk yield, 7 kg for protein yield and 16 kg for fat yield. We also found regions where ROHs displayed unfavourable effects across multiple traits. Our findings can be exploited for more efficient control of inbreeding depression, for example by minimizing the occurrence of unfavourable haplotypes as homozygous state in breeding programmes.
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Affiliation(s)
- K Martikainen
- Department of Agricultural Sciences, University of Helsinki, P.O. Box 28, FI-00014, Helsinki, Finland.
| | - M Koivula
- Natural Resources Institute Finland (Luke), Green Technology, FI-31600, Jokioinen, Finland
| | - P Uimari
- Department of Agricultural Sciences, University of Helsinki, P.O. Box 28, FI-00014, Helsinki, Finland
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Nguyen NH, Phuthaworn C, Knibb W. Genomic prediction for disease resistance to Hepatopancreatic parvovirus and growth, carcass and quality traits in Banana shrimp Fenneropenaeus merguiensis. Genomics 2019; 112:2021-2027. [PMID: 31765824 DOI: 10.1016/j.ygeno.2019.11.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 11/12/2019] [Accepted: 11/19/2019] [Indexed: 01/12/2023]
Abstract
Conventional genetic improvement of disease resistance in aquatic animal species involves challenge tests or using qPCR to quantify viral load that is costly, time-consuming and causing biosecurity concerns. Recent developments in high throughput next generation genome sequencing platforms such as genotyping by sequencing (GBS) have opened new possibilities for improving disease traits based on DNA information. The principal aim of this study was thus to examine potential application of genomic selection to improve resistance to hepatopancreatic parvovirus (HPV) in banana shrimp Fenneropenaeus merguiensis. Specifically, we used a total of 9472 single nucleotide polymorphisms (SNPs) developed de novo from GBS platforms to assess accuracy of genomic prediction for HPV resistance and growth, carcass and quality-related traits in this white shrimp species. Our multi-locus mixed model analysis showed moderate heritabilities for HPV resistance (h2 = 0.46) and other traits studied (0.10 to 0.55). Genetic correlations of HPV titre with growth and carcass traits, estimated using SNPs markers, were negative (i.e., favourable), suggesting that selection for improved growth and carcass traits may have increased HPV resistance (i.e., reduced HPV titre). More importantly, our gBLUP model demonstrated that the accuracy of gBLUP prediction was moderate for HPV disease resistance (0.46). The genomic prediction accuracy was somewhat greater for growth and carcass related traits especially for body weight (0.76) and meat or tail weight (0.77). On the other hand, the prediction accuracy was from 0.25 to 0.41 for quality traits (raw and cooked colour and flesh streaks). Collectively, it is concluded that there are prospects to apply genomic selection in the genetic improvement for increased disease resistance, carcass and quality-related traits in this population of banana shrimp F. merguiensis.
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Affiliation(s)
- Nguyen Hong Nguyen
- Genecology Research Centre, School of Science and Engineering, University of the Sunshine Coast, Locked Bag 4, Maroochydore DC, Queensland 4558, Australia.
| | - Chontida Phuthaworn
- Genecology Research Centre, School of Science and Engineering, University of the Sunshine Coast, Locked Bag 4, Maroochydore DC, Queensland 4558, Australia
| | - Wayne Knibb
- Genecology Research Centre, School of Science and Engineering, University of the Sunshine Coast, Locked Bag 4, Maroochydore DC, Queensland 4558, Australia
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