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Makanjuola BO, Maltecca C, Miglior F, Schenkel FS, Baes CF. Effect of recent and ancient inbreeding on production and fertility traits in Canadian Holsteins. BMC Genomics 2020; 21:605. [PMID: 32873253 PMCID: PMC7466804 DOI: 10.1186/s12864-020-07031-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 08/27/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Phenotypic performances of livestock animals decline with increasing levels of inbreeding, however, the noticeable decline known as inbreeding depression, may not be due only to the total level of inbreeding, but rather could be distinctly associated with more recent or more ancient inbreeding. Therefore, splitting inbreeding into different age classes could help in assessing detrimental effects of different ages of inbreeding. Hence, this study sought to investigate the effect of recent and ancient inbreeding on production and fertility traits in Canadian Holstein cattle with both pedigree and genomic records. Furthermore, inbreeding coefficients were estimated using traditional pedigree measure (FPED) and genomic measures using segment based (FROH) and marker-by-marker (FGRM) based approaches. RESULTS Inbreeding depression was found for all production and most fertility traits, for example, every 1% increase in FPED, FROH and FGRM was observed to cause a - 44.71, - 40.48 and - 48.72 kg reduction in 305-day milk yield (MY), respectively. Similarly, an extension in first service to conception (FSTC) of 0.29, 0.24 and 0.31 day in heifers was found for every 1% increase in FPED, FROH and FGRM, respectively. Fertility traits that did not show significant depression were observed to move in an unfavorable direction over time. Splitting both pedigree and genomic inbreeding into age classes resulted in recent age classes showing more detrimental inbreeding effects, while more distant age classes caused more favorable effects. For example, a - 1.56 kg loss in 305-day protein yield (PY) was observed for every 1% increase in the most recent pedigree age class, whereas a 1.33 kg gain was found per 1% increase in the most distant pedigree age class. CONCLUSIONS Inbreeding depression was observed for production and fertility traits. In general, recent inbreeding had unfavorable effects, while ancestral inbreeding had favorable effects. Given that more negative effects were estimated from recent inbreeding when compared to ancient inbreeding suggests that recent inbreeding should be the primary focus of selection programs. Also, further work to identify specific recent homozygous regions negatively associated with phenotypic traits could be investigated.
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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
| | - 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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Nani JP, Peñagaricano F. Whole-genome homozygosity mapping reveals candidate regions affecting bull fertility in US Holstein cattle. BMC Genomics 2020; 21:338. [PMID: 32366228 PMCID: PMC7199307 DOI: 10.1186/s12864-020-6758-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 04/27/2020] [Indexed: 01/10/2023] Open
Abstract
Background Achieving rapid genetic progress while maintaining adequate genetic diversity is one of the main challenges facing the dairy industry. The increase in inbreeding can be used to monitor the loss of genetic diversity. Inbreeding tends to increase the proportion of homozygous loci, some of which cause homozygosity of recessive alleles that results in reduced performance. This phenomenon is known as inbreeding depression and tends to be most prominent on fitness-related traits, such as male fertility. Traditionally, inbreeding has been monitored using pedigree information, or more recently, genomic data. Alternatively, it can be quantified using runs of homozygosity (ROH), i.e., contiguous lengths of homozygous genotypes observed in an individual’s chromosome. Results The objective of this study was to evaluate the association between ROH and sire conception rate. ROH were evaluated using 268 k genetic markers in 11,790 US Holstein bulls. Interestingly, either the sum, mean, or maximum length of ROH were negatively associated with bull fertility. The association analysis between ROH and sire fertility was performed comparing 300 high-fertility vs. 300 low-fertility bulls. Both the average and sum of ROH length were higher in the low-fertility group. The enrichment of ROH regions in bulls with low fertility was assessed using a Fisher’s exact test. Nine regions were significantly enriched in low-fertility compared to high-fertility bulls. Notably, these regions harbor genes that are closely related to sperm biology and male fertility, including genes exclusively or highly expressed in testis. Conclusions The results of this study can help not only to manage inbreeding in genomic selection programs by designing custom mating schemes, but also to better understand the mechanisms underlying male fertility in dairy cattle.
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Affiliation(s)
- Juan Pablo Nani
- Department of Animal Sciences, University of Florida, 2250 Shealy Drive, Gainesville, FL, 32611, USA.,Estación Experimental Agropecuaria Rafaela, Instituto Nacional de Tecnología Agropecuaria, 22-2300, Rafaela, SF, Argentina
| | - Francisco Peñagaricano
- Department of Animal Sciences, University of Florida, 2250 Shealy Drive, Gainesville, FL, 32611, USA. .,University of Florida Genetics Institute, University of Florida, Gainesville, FL, 32610, USA.
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Baes CF, Makanjuola BO, Miglior F, Marras G, Howard JT, Fleming A, Maltecca C. Symposium review: The genomic architecture of inbreeding: How homozygosity affects health and performance. J Dairy Sci 2019; 102:2807-2817. [DOI: 10.3168/jds.2018-15520] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 11/21/2018] [Indexed: 11/19/2022]
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Goszczynski D, Molina A, Terán E, Morales-Durand H, Ross P, Cheng H, Giovambattista G, Demyda-Peyrás S. Runs of homozygosity in a selected cattle population with extremely inbred bulls: Descriptive and functional analyses revealed highly variable patterns. PLoS One 2018; 13:e0200069. [PMID: 29985951 PMCID: PMC6037354 DOI: 10.1371/journal.pone.0200069] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 06/19/2018] [Indexed: 01/05/2023] Open
Abstract
The analysis of runs of homozygosity (ROH), using high throughput genomic data, has become a valuable and frequently used methodology to characterize the genomic and inbreeding variation of livestock and wildlife animal populations. However, this methodology has been scarcely used in highly inbred domestic animals. Here, we analyzed and characterized the occurrence of ROH fragments in highly inbred (HI; average pedigree-based inbreeding coefficient FPED = 0.164; 0.103 to 0.306) and outbred Retinta bulls (LI; average FPED = 0.008; 0 to 0.025). We studied the length of the fragments, their abundance, and genome distribution using high-density microarray data. The number of ROH was significantly higher in the HI group, especially for long fragments (>8Mb). In the LI group, the number of ROH continuously decreased with fragment length. Genome-wide distribution of ROH was highly variable between samples. Some chromosomes presented a larger number of fragments (BTA1, BTA19, BTA29), others had longer fragments (BTA4, BTA12, BTA17), while other ones showed an increased ROH accumulation over specific loci (BTA2, BTA7, BTA23, BTA29). Similar differences were observed in the analysis of 12 individuals produced by a similar inbred event (FPED3 = 0.125). The correlation between the fraction of the genome covered by ROH (FROH) and FPED was high (0.79), suggesting that ROH-based estimations are indicative of inbreeding levels. On the other hand, the correlation between FPED and the microsatellite-based inbreeding coefficient (FMIC) was only moderate (r = 0.44), suggesting that STR-based inbreeding estimations should be avoided. Similarly, we found a very low correlation (r = -0.0132) between recombination rate and ROH abundance across the genome. Finally, we performed functional annotation analyses of genome regions with significantly enriched ROH abundance. Results revealed gene clusters related to pregnancy-associated proteins and immune reaction. The same analysis performed for regions enriched with recently formed ROH (> 8 Mb) showed gene clusters related to flagellum assembly. In both cases, the processes were related to male and female reproductive functions, which may partially explain the reduced fertility associated with inbred populations.
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Affiliation(s)
- Daniel Goszczynski
- IGEVET–Instituto de Genética Veterinaria "Ing. Fernando N. Dulout” (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias UNLP, La Plata, Argentina
| | - Antonio Molina
- Departamento de Genética, Universidad de Córdoba, Córdoba, España
| | - Ester Terán
- IGEVET–Instituto de Genética Veterinaria "Ing. Fernando N. Dulout” (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias UNLP, La Plata, Argentina
| | - Hernán Morales-Durand
- IGEVET–Instituto de Genética Veterinaria "Ing. Fernando N. Dulout” (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias UNLP, La Plata, Argentina
| | - Pablo Ross
- Department of Animal Science, University of California, Davis, Davis, California, United States of America
| | - Hao Cheng
- Department of Animal Science, University of California, Davis, Davis, California, United States of America
| | - Guillermo Giovambattista
- IGEVET–Instituto de Genética Veterinaria "Ing. Fernando N. Dulout” (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias UNLP, La Plata, Argentina
- Departamento de Genética, Universidad de Córdoba, Córdoba, España
- Department of Animal Science, University of California, Davis, Davis, California, United States of America
- Departamento de Producción Animal, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Sebastián Demyda-Peyrás
- IGEVET–Instituto de Genética Veterinaria "Ing. Fernando N. Dulout” (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias UNLP, La Plata, Argentina
- Departamento de Genética, Universidad de Córdoba, Córdoba, España
- Department of Animal Science, University of California, Davis, Davis, California, United States of America
- Departamento de Producción Animal, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
- * E-mail:
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Hoff JL, Decker JE, Schnabel RD, Taylor JF. Candidate lethal haplotypes and causal mutations in Angus cattle. BMC Genomics 2017; 18:799. [PMID: 29047335 PMCID: PMC5648474 DOI: 10.1186/s12864-017-4196-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 10/08/2017] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND If unmanaged, high rates of inbreeding in livestock populations adversely impact their reproductive fitness. In beef cattle, historical selection strategies have increased the frequency of several segregating fatal autosomal recessive polymorphisms. Selective breeding has also decreased the extent of haplotypic diversity genome-wide. By identifying haplotypes for which homozygotes are not observed but would be expected based on their frequency, candidates for developmentally lethal recessive loci can be localized. This analysis comes without the need for observation of the loss-associated phenotype (e.g., failure to implant, first trimester abortion, deformity at birth). In this study, haplotypes were estimated for 3961 registered Angus individuals using 52,545 SNP loci using findhap v2, which exploited the complex pedigree among the individuals in this population. RESULTS Seven loci were detected to possess haplotypes that were not observed in homozygous form despite a sufficiently high frequency and pedigree-based expectation of homozygote occurrence. These haplotypes were identified as candidates for harboring autosomal recessive lethal alleles. Of the genotyped individuals, 109 were resequenced to an average 27X depth of coverage to identify putative loss-of-function alleles genome-wide and had variants called using a custom in-house developed pipeline. For the candidate lethal-harboring haplotypes present in these bulls, sequence-called genotypes were used to identify concordant variants. In addition, whole-genome sequence imputation of variants was performed into the set of 3961 genotyped animals using the 109 resequenced animals to identify candidate lethal recessive variants at the seven loci. Following the imputation, no variants were identified that were fully concordant with the marker-based diplotypes. CONCLUSIONS Selective breeding programs could utilize the predicted lethal haplotypes associated with SNP genotypes. Sequencing and other methods for identifying the causal variants underlying these haplotypes can allow for more efficient methods of management such as gene editing. These two methods in total will reduce the negative impacts of inbreeding on fertility and maximize overall genetic gains.
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Affiliation(s)
- Jesse L Hoff
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Jared E Decker
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.,Informatics Institute, University of Missouri, Columbia, MO, 65211, USA
| | - Robert D Schnabel
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.,Informatics Institute, University of Missouri, Columbia, MO, 65211, USA
| | - Jeremy F Taylor
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.
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