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Martinez Boggio G, Monteiro HF, Lima FS, Figueiredo CC, Bisinotto RS, Santos JEP, Mion B, Schenkel FS, Ribeiro ES, Weigel KA, Peñagaricano F. Host and rumen microbiome contributions to feed efficiency traits in Holstein cows. J Dairy Sci 2024; 107:3090-3103. [PMID: 38135048 DOI: 10.3168/jds.2023-23869] [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: 06/14/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023]
Abstract
It is now widely accepted that dairy cow performance is influenced by both the host genome and rumen microbiome composition. The contributions of the genome and the microbiome to the phenotypes of interest are quantified by heritability (h2) and microbiability (m2), respectively. However, if the genome and microbiome are included in the model, then the h2 reflects only the contribution of the direct genetic effects quantified as direct heritability (hd2), and the holobiont effect reflects the joint action of the genome and the microbiome, quantified as the holobiability (ho2). The objectives of this study were to estimate h2, hd2,m2, and ho2 for dry matter intake, milk energy, and residual feed intake; and to evaluate the predictive ability of different models, including genome, microbiome, and their interaction. Data consisted of feed efficiency records, SNP genotype data, and 16S rRNA rumen microbial abundances from 448 mid-lactation Holstein cows from 2 research farms. Three kernel models were fit to each trait: one with only the genomic effect (model G), one with the genomic and microbiome effects (model GM), and one with the genomic, microbiome, and interaction effects (model GMO). The model GMO, or holobiont model, showed the best goodness-of-fit. The hd2 estimates were always 10% to 15% lower than h2 estimates for all traits, suggesting a mediated genetic effect through the rumen microbiome, and m2 estimates were moderate for all traits, and up to 26% for milk energy. The ho2 was greater than the sum of hd2 and m2, suggesting that the genome-by-microbiome interaction had a sizable effect on feed efficiency. Kernel models fitting the rumen microbiome (i.e., models GM and GMO) showed larger predictive correlations and smaller prediction bias than the model G. These findings reveal a moderate contribution of the rumen microbiome to feed efficiency traits in lactating Holstein cows and strongly suggest that the rumen microbiome mediates part of the host genetic effect.
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Affiliation(s)
| | - Hugo F Monteiro
- Department of Population Health and Reproduction, University of California, Davis, Davis, CA 95616
| | - Fabio S Lima
- Department of Population Health and Reproduction, University of California, Davis, Davis, CA 95616
| | - Caio C Figueiredo
- Department of Veterinary Clinical Sciences, Washington State University, Pullman, WA 99163
| | - Rafael S Bisinotto
- Department of Large Animal Clinical Sciences, University of Florida, Gainesville, FL 32610
| | - José E P Santos
- Department of Animal Sciences, University of Florida, Gainesville, FL 32611
| | - Bruna Mion
- Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada N1G-2W1
| | - Flavio S Schenkel
- Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada N1G-2W1
| | - Eduardo S Ribeiro
- Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada N1G-2W1
| | - Kent A Weigel
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI 53706
| | - Francisco Peñagaricano
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI 53706
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Peñagaricano F. Genomics and Dairy Bull Fertility. Vet Clin North Am Food Anim Pract 2024; 40:185-190. [PMID: 37669889 DOI: 10.1016/j.cvfa.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2023] Open
Abstract
Current evidence suggests that dairy bull fertility is influenced by genetic factors, and hence, it could be managed and improved by genetic means. There are major mutations that explain about 4% to 8% of the observed differences in conception rate between bulls segregating in most dairy breeds. Research has shown that genomic prediction of bull fertility is possible, and this could be used to make accurate genome-guided selection decisions, such as early culling of predicted subfertile bull calves. Inbreeding negatively influences bull fertility, and the increase in homozygosity seems an important risk factor for dairy bull subfertility.
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Ortega MS, Lockhart KN, Spencer TE. Impact of Sire on Embryo Development and Pregnancy. Vet Clin North Am Food Anim Pract 2024; 40:131-140. [PMID: 37704462 DOI: 10.1016/j.cvfa.2023.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2023] Open
Abstract
The use of in vitro embryo production (IVP) has increased globally, particularly in the United States. Although maternal factors influencing embryo development have been extensively studied, the influence of the sire is not well understood. Sperm plays a crucial role in embryo development providing DNA, triggering oocyte maturation, and aiding in mitosis. Current sire fertility measurements do not consistently align with embryo production outcomes. Low-fertility sires may perform well in IVP systems but produce fewer pregnancies. Testing sires in vitro could identify characteristics affecting embryo development and pregnancy loss risk in IVP and embryo transfer programs.
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Affiliation(s)
- M Sofia Ortega
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, 1675 Observatory Drive.
| | - Kelsey N Lockhart
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Thomas E Spencer
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
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Zhu L, Shen S, Pan C, Lan X, Li J. Bovine FRAS1: mRNA Expression Profile, Genetic Variations, and Significant Correlations with Ovarian Morphological Traits, Mature Follicle, and Corpus Luteum. Animals (Basel) 2024; 14:597. [PMID: 38396565 PMCID: PMC10886075 DOI: 10.3390/ani14040597] [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: 01/03/2024] [Revised: 01/29/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
The amelioration of bovine fertility caused by a multi-factorial problem has always been a hot topic, among which the detection of available target genes is the most crucial. It was hypothesized that the Fraser extracellular matrix complex subunit 1 (FRAS1) gene detected by GWAS is involved in physiological activities such as ovarian development. Herein, unilateral ovaries from 2111 cows were used to examine the mRNA expression profile and polymorphisms of bovine FRAS1 and their associations with fertility-related characteristics. Firstly, it was confirmed that FRAS1 gene transcripts are expressed in various bovine tissues. Then, among five potential insertion-deletion (indel) loci, the 20 bp (named P3-D20-bp) and 15 bp (P4-D15-bp) deletion mutations were confirmed to be polymorphic with linkage equilibrium. Secondly, the P3-D20-bp polymorphism was significantly associated with ovarian weight and corpus luteum diameter in the metaestrus phase and ovarian length in the dioestrum stage. Additionally, both ovarian length and mature follicle diameter in metaestrus are significantly correlated with different genotypes of P4-D15-bp. Thirdly, the transcriptional expression of the FRAS1 gene in groups with a minimum value of ovarian weight or volume was significantly higher than the expression in groups with a maximum value. Instead of that, the more corpus luteum and mature follicles there are, the higher the transcription expression of the FRAS1 gene is. Furthermore, FRAS1 expression in cows with a heterozygous genotype (ID) of P3-D20-bp was significantly higher than others. Eventually, P3-D20-bp deletion could disturb the binding efficiency of WT1-I and Sox2 to FRAS1 sequence according to binding prediction, indicating that mutation may affect gene expression and traits by influencing the binding of transcription factors. Overall, the polymorphisms of P3-D20-bp and P4-D15-bp of the bovine FRAS1 gene significantly correlated to follicle or ovarian traits that could be applied in optimizing female fertility in cow MAS breeding programs.
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Affiliation(s)
| | | | | | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (L.Z.); (S.S.); (C.P.)
| | - Jie Li
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (L.Z.); (S.S.); (C.P.)
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Ghoreishifar M, Vahedi SM, Salek Ardestani S, Khansefid M, Pryce JE. Genome-wide assessment and mapping of inbreeding depression identifies candidate genes associated with semen traits in Holstein bulls. BMC Genomics 2023; 24:230. [PMID: 37138201 PMCID: PMC10157977 DOI: 10.1186/s12864-023-09298-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 04/05/2023] [Indexed: 05/05/2023] Open
Abstract
BACKGROUND The reduction in phenotypic performance of a population due to mating between close relatives is called inbreeding depression. The genetic background of inbreeding depression for semen traits is poorly understood. Thus, the objectives were to estimate the effect of inbreeding and to identify genomic regions underlying inbreeding depression of semen traits including ejaculate volume (EV), sperm concentration (SC), and sperm motility (SM). The dataset comprised ~ 330 K semen records from ~ 1.5 K Holstein bulls genotyped with 50 K single nucleotide polymorphism (SNP) BeadChip. Genomic inbreeding coefficients were estimated using runs of homozygosity (i.e., FROH > 1 Mb) and excess of SNP homozygosity (FSNP). The effect of inbreeding was estimated by regressing phenotypes of semen traits on inbreeding coefficients. Associated variants with inbreeding depression were also detected by regressing phenotypes on ROH state of the variants. RESULTS Significant inbreeding depression was observed for SC and SM (p < 0.01). A 1% increase in FROH reduced SM and SC by 0.28% and 0.42% of the population mean, respectively. By splitting FROH into different lengths, we found significant reduction in SC and SM due to longer ROH, which is indicative of more recent inbreeding. A genome-wide association study revealed two signals positioned on BTA 8 associated with inbreeding depression of SC (p < 0.00001; FDR < 0.02). Three candidate genes of GALNTL6, HMGB2, and ADAM29, located in these regions, have established and conserved connections with reproduction and/or male fertility. Moreover, six genomic regions on BTA 3, 9, 21 and 28 were associated with SM (p < 0.0001; FDR < 0.08). These genomic regions contained genes including PRMT6, SCAPER, EDC3, and LIN28B with established connections to spermatogenesis or fertility. CONCLUSIONS Inbreeding depression adversely affects SC and SM, with evidence that longer ROH, or more recent inbreeding, being especially detrimental. There are genomic regions associated with semen traits that seems to be especially sensitive to homozygosity, and evidence to support some from other studies. Breeding companies may wish to consider avoiding homozygosity in these regions for potential artificial insemination sires.
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Affiliation(s)
- Mohammad Ghoreishifar
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria, 3083, Australia.
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, 3083, Australia.
| | - Seyed Milad Vahedi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, B2N5E3, Canada
| | | | - Majid Khansefid
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria, 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, 3083, Australia
| | - Jennie E Pryce
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria, 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, 3083, Australia
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Pausch H, Mapel XM. Review: Genetic mutations affecting bull fertility. Animal 2023; 17 Suppl 1:100742. [PMID: 37567657 DOI: 10.1016/j.animal.2023.100742] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 08/13/2023] Open
Abstract
Cattle are a well-suited "model organism" to study the genetic underpinnings of variation in male reproductive performance. The adoption of artificial insemination and genomic prediction in many cattle breeds provide access to microarray-derived genotypes and repeated measurements for semen quality and insemination success in several thousand bulls. Similar-sized mapping cohorts with phenotypes for male fertility are not available for most other species precluding powerful association testing. The repeated measurements of the artificial insemination bulls' semen quality enable the differentiation between transient and biologically relevant trait fluctuations, and thus, are an ideal source of phenotypes for variance components estimation and genome-wide association testing. Genome-wide case-control association testing involving bulls with either aberrant sperm quality or low insemination success revealed several causal recessive loss-of-function alleles underpinning monogenic reproductive disorders. These variants are routinely monitored with customised genotyping arrays in the male selection candidates to avoid the use of subfertile or infertile bulls for artificial insemination and natural service. Genome-wide association studies with quantitative measurements of semen quality and insemination success revealed quantitative trait loci for male fertility, but the underlying causal variants remain largely unknown. Moreover, these loci explain only a small part of the heritability of male fertility. Integrating genome-wide association studies with gene expression and other omics data from male reproductive tissues is required for the fine-mapping of candidate causal variants underlying variation in male reproductive performance in cattle.
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Affiliation(s)
- Hubert Pausch
- Animal Genomics, Department of Environmental Systems Science, ETH Zurich, Universitaetstrasse 2, 8092 Zurich, Switzerland.
| | - Xena Marie Mapel
- Animal Genomics, Department of Environmental Systems Science, ETH Zurich, Universitaetstrasse 2, 8092 Zurich, Switzerland
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Unravelling the genetics of non-random fertilization associated with gametic incompatibility. Sci Rep 2022; 12:22314. [PMID: 36566278 PMCID: PMC9789956 DOI: 10.1038/s41598-022-26910-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 12/21/2022] [Indexed: 12/25/2022] Open
Abstract
In the dairy industry, mate allocation is dependent on the producer's breeding goals and the parents' breeding values. The probability of pregnancy differs among sire-dam combinations, and the compatibility of a pair may vary due to the combination of gametic haplotypes. Under the hypothesis that incomplete incompatibility would reduce the odds of fertilization, and complete incompatibility would lead to a non-fertilizing or lethal combination, deviation from Mendelian inheritance expectations would be observed for incompatible pairs. By adding an interaction to a transmission ratio distortion (TRD) model, which detects departure from the Mendelian expectations, genomic regions linked to gametic incompatibility can be identified. This study aimed to determine the genetic background of gametic incompatibility in Holstein cattle. A total of 283,817 genotyped Holstein trios were used in a TRD analysis, resulting in 422 significant regions, which contained 2075 positional genes further investigated for network, overrepresentation, and guilt-by-association analyses. The identified biological pathways were associated with immunology and cellular communication and a total of 16 functional candidate genes were identified. Further investigation of gametic incompatibility will provide opportunities to improve mate allocation for the dairy cattle industry.
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Tahir MS, Porto-Neto LR, Reverter-Gomez T, Olasege BS, Sajid MR, Wockner KB, Tan AWL, Fortes MRS. Utility of multi-omics data to inform genomic prediction of heifer fertility traits. J Anim Sci 2022; 100:skac340. [PMID: 36239447 PMCID: PMC9733504 DOI: 10.1093/jas/skac340] [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: 06/18/2022] [Accepted: 10/12/2022] [Indexed: 12/15/2022] Open
Abstract
Biologically informed single nucleotide polymorphisms (SNPs) impact genomic prediction accuracy of the target traits. Our previous genomics, proteomics, and transcriptomics work identified candidate genes related to puberty and fertility in Brahman heifers. We aimed to test this biological information for capturing heritability and predicting heifer fertility traits in another breed i.e., Tropical Composite. The SNP from the identified genes including 10 kilobases (kb) region on either side were selected as biologically informed SNP set. The SNP from the rest of the Bos taurus genes including 10-kb region on either side were selected as biologically uninformed SNP set. Bovine high-density (HD) complete SNP set (628,323 SNP) was used as a control. Two populations-Tropical Composites (N = 1331) and Brahman (N = 2310)-had records for three traits: pregnancy after first mating season (PREG1, binary), first conception score (FCS, score 1 to 3), and rebreeding score (REB, score 1 to 3.5). Using the best linear unbiased prediction method, effectiveness of each SNP set to predict the traits was tested in two scenarios: a 5-fold cross-validation within Tropical Composites using biological information from Brahman studies, and application of prediction equations from one breed to the other. The accuracy of prediction was calculated as the correlation between genomic estimated breeding values and adjusted phenotypes. Results show that biologically informed SNP set estimated heritabilities not significantly better than the control HD complete SNP set in Tropical Composites; however, it captured all the observed genetic variance in PREG1 and FCS when modeled together with the biologically uninformed SNP set. In 5-fold cross-validation within Tropical Composites, the biologically informed SNP set performed marginally better (statistically insignificant) in terms of prediction accuracies (PREG1: 0.20, FCS: 0.13, and REB: 0.12) as compared to HD complete SNP set (PREG1: 0.17, FCS: 0.10, and REB: 0.11), and biologically uninformed SNP set (PREG1: 0.16, FCS: 0.10, and REB: 0.11). Across-breed use of prediction equations still remained a challenge: accuracies by all SNP sets dropped to around zero for all traits. The performance of biologically informed SNP was not significantly better than other sets in Tropical Composites. However, results indicate that biological information obtained from Brahman was successful to predict the fertility traits in Tropical Composite population.
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Affiliation(s)
- Muhammad S Tahir
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia Campus, Brisbane 4072, QLD, Australia
| | - Laercio R Porto-Neto
- Commonwealth Scientific and Industrial Research Organization, St. Lucia, Brisbane 4072, QLD, Australia
| | - Toni Reverter-Gomez
- Commonwealth Scientific and Industrial Research Organization, St. Lucia, Brisbane 4072, QLD, Australia
| | - Babatunde S Olasege
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia Campus, Brisbane 4072, QLD, Australia
| | - Mirza R Sajid
- Department of Statistics, University of Gujrat, 50700 Punjab, Pakistan
| | - Kimberley B Wockner
- Queensland Department of Agriculture and Fisheries, Brisbane 4072, QLD, Australia
| | - Andre W L Tan
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia Campus, Brisbane 4072, QLD, Australia
| | - Marina R S Fortes
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia Campus, Brisbane 4072, QLD, Australia
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Ma S, Li P, Liu H, Xi Y, Xu Q, Qi J, Wang J, Li L, Wang J, Hu J, He H, Han C, Bai L. Genome-wide association analysis of the primary feather growth traits of duck: identification of potential Loci for growth regulation. Poult Sci 2022; 102:102243. [PMID: 36334470 PMCID: PMC9636485 DOI: 10.1016/j.psj.2022.102243] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 10/05/2022] [Accepted: 10/05/2022] [Indexed: 11/28/2022] Open
Abstract
The feather is an important epidermal appendage, plays an important role in the life activities of avian specie, and has important economic value. Revealing the molecular regulation mechanism of feather growth has a significant meaning in studying adaptive evolution, physiology, and mating of avian species and also provides a theoretical reference for poultry breeding. In this study, the genome-wide association analysis (GWAS) of 358 ducks was based on primary feather length phenotypic data (28-60 d), length growth rates (LGRs), and maturity scores (60 d) to explore the genetic basis affecting feather growth and maturation. The results showed that, among the primary feather 1 to 5 in ducks, the mean LGR of primary feather 2 was the fastest, with the longest length. The primary feathers in males grew and matured slightly faster than in females. The mean maturity scores of primary feather 10∼7 were higher than primary feather 1 to 3 in ducks. GWAS further showed 116 SNPs associated with feather length traits. In addition, 2 candidate regions (Chr1: 127,407,230-127,524,879 bp and Chr21: 182,061,707-183,616,298 bp) were associated with LGR, which contain total 13 candidate genes (The extremely significant SNPs were mainly located in 2 genes: Chr1: REPS2 and Chr21: PTPRT). Four candidate regions (Chr1: 29,113,036-28,675,018 bp, Chr2: 18,253,612-149,111,290 bp, Chr15: 6,489,774 to 12,138,221 bp and Chr21: 6,578,021-8,472,904 bp) were associated with feather maturity, which contain total 24 candidate genes (The extremely significant SNPs were mainly located in 4 genes: Chr1: IMMP2L, DOCK4 and DDX10, Chr2: LDLRAD4). In conclusion, sex factors influence feather growth and maturity, and the genetic basis of the growth /maturity trait between different feathers is similar. REPS2, PTPRT genes, and IMMP2L, DOCK4, DDX10, and LDLRAD4 are important candidate genes that influence feather growth and maturity, respectively.
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Affiliation(s)
- Shengchao Ma
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, P. R. China,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. China,College of Animal Science, Xinjiang Agricultural University, P. R. China
| | - Pengcheng Li
- Berry Genomics Corporation, Beijing 100015, P. R. China
| | - Hehe Liu
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, P. R. China,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. China,Corresponding author:
| | - Yang Xi
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, P. R. China,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. China
| | - Qian Xu
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, P. R. China,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. China
| | - Jingjing Qi
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, P. R. China,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. China
| | - Jianmei Wang
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, P. R. China,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. China
| | - Liang Li
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, P. R. China,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. China
| | - Jiwen Wang
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, P. R. China,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. China
| | - Jiwei Hu
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, P. R. China,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. China
| | - Hua He
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, P. R. China,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. China
| | - Chunchun Han
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, P. R. China,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. China
| | - Lili Bai
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, P. R. China,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. China
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10
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van der Horst G, Maree L. Origin, Migration, and Reproduction of Indigenous Domestic Animals with Special Reference to Their Sperm Quality. Animals (Basel) 2022; 12:ani12050657. [PMID: 35268225 PMCID: PMC8909367 DOI: 10.3390/ani12050657] [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: 12/15/2021] [Revised: 02/17/2022] [Accepted: 02/20/2022] [Indexed: 01/25/2023] Open
Abstract
Simple Summary Indigenous domestic animals are derived from “wild” ancestors that have been domesticated as far back as 11,000 BP. In this investigation, we concentrate on indigenous domestic animals such as cattle, sheep, goats, pigs, and chickens and consider their fertility potential. In South Africa alone, more than 60 indigenous domestic breeds have been listed, and by and large, their sperm quality is similar to high fertility exotic breeds. Why are these indigenous breeds important? Particularly during the last 7000 years, different races migrated with their domestic animals, mainly from Northern to Southern Africa, and the animals were exposed to droughts, food scarcity, and many endo- and ecto-parasites. Accordingly, these animals are well-adapted to the harsh conditions of Southern Africa, and it is important to include them in breeding programs to exploit their favorable traits. Abstract Indigenous domestic animals such as cattle, sheep, goats, pigs, and chickens have a natural resistance to endo- and ecto-parasites and are tolerant in terms of harsh environmental conditions. These species orginated from the Fertile Cresent between 12,000 and 10,000 BP before migrating into surrounding continents. In view of limited information on the reproductive status of indigenous breeds, it is important to examine their semen characteristics in order to select males to improve livestock production. We have largely relied on existing literature but also our published and ongoing research on sperm quality assessment of several indigenous breeds. The sperm quality of these breeds is similar to current commercial breeds and has been quantified using cutting-edge methods. In this context, we have presented sperm functional tests which provide a better estimate of semen quality than just a standard semen analysis. Initial results suggest that the indigenous breeds have a high sperm quality and sperm functionality similar to currently farmed exotic or crossbreeds. In the long-term, the importance of preserving the favorable traits of these breeds is a priority in view of crossbreeding with existing good meat and milk producers.
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Ugur MR, Guerreiro DD, Moura AA, Memili E. Identification of biomarkers for bull fertility using functional genomics. Anim Reprod 2022; 19:e20220004. [PMID: 35573862 PMCID: PMC9083437 DOI: 10.1590/1984-3143-ar2022-0004] [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: 02/07/2022] [Accepted: 03/28/2022] [Indexed: 09/21/2023] Open
Abstract
Prediction of bull fertility is critical for the sustainability of both dairy and beef cattle production. Even though bulls produce ample amounts of sperm with normal parameters, some bulls may still suffer from subpar fertility. This causes major economic losses in the cattle industry because using artificial insemination, semen from one single bull can be used to inseminate hundreds of thousands of cows. Although there are several traditional methods to estimate bull fertility, such methods are not sufficient to explain and accurately predict the subfertility of individual bulls. Since fertility is a complex trait influenced by a number of factors including genetics, epigenetics, and environment, there is an urgent need for a comprehensive methodological approach to clarify uncertainty in male subfertility. The present review focuses on molecular and functional signatures of bull sperm associated with fertility. Potential roles of functional genomics (proteome, small noncoding RNAs, lipidome, metabolome) on determining male fertility and its potential as a fertility biomarker are discussed. This review provides a better understanding of the molecular signatures of viable and fertile sperm cells and their potential to be used as fertility biomarkers. This information will help uncover the underlying reasons for idiopathic subfertility.
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Affiliation(s)
| | | | - Arlindo A. Moura
- Universidade Federal do Ceará, Brasil; Universidade Federal do Ceará, Brasil
| | - Erdogan Memili
- Mississippi State University, USA; Prairie View A&M University, USA
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12
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Cavani L, Poindexter MB, Nelson CD, Santos JEP, Peñagaricano F. Gene mapping, gene-set analysis, and genomic prediction of postpartum blood calcium in Holstein cows. J Dairy Sci 2021; 105:525-534. [PMID: 34756434 DOI: 10.3168/jds.2021-20872] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/11/2021] [Indexed: 12/15/2022]
Abstract
The onset of lactation results in a sudden irreversible loss of Ca for colostrum and milk synthesis. Some cows are unable to quickly adapt to this demand and succumb to clinical hypocalcemia, whereas a larger proportion of cows develop subclinical hypocalcemia that predisposes them to other peripartum diseases. The objective of this study was to perform a comprehensive genomic analysis of blood total Ca concentration in periparturient Holstein cows. We first performed a genomic scan and a subsequent gene-set analysis to identify candidate genes, biological pathways, and molecular mechanisms affecting postpartum Ca concentration. Then, we assessed the prediction of postpartum Ca concentration using genomic information. Data consisted of 7,691 records of plasma or serum concentrations of Ca measured in the first, second, and third day after parturition of 959 primiparous and 1,615 multiparous cows that calved between December 2015 and June 2020 in 2 dairy herds. All cows were genotyped with 80k SNPs. The statistical model included lactation (1 to 5+), calf category (male, females, twins), and day as fixed effects, and season-treatment-experiment, animal, and permanent environmental as random effects. Model predictive ability was evaluated using 10-fold cross-validation. Heritability and repeatability estimates were 0.083 (standard error = 0.017) and 0.444 (standard error = 0.028). The association mapping identified 2 major regions located on Bos taurus autosome (BTA)6 and BTA16 that explained 1.2% and 0.7% of additive genetic variance of Ca concentration, respectively. Interestingly, the region on BTA6 harbors the GC gene, which encodes the vitamin D binding protein, and the region on BTA16 harbors LRRC38, which is actively involved in K transport. Other sizable peaks were identified on BTA5, BTA2, BTA7, BTA14, and BTA9. These regions harbor genes associated with Ca channels (CACNA1S, CRACR2A), K channels (KCNK9), bone remodeling (LRP6), and milk production (SOCS2). The gene-set analysis revealed terms related to vitamin transport, calcium ion transport, calcium ion binding, and calcium signaling. Genomic predictions of phenotypic and genomic estimated breeding values of Ca concentration yielded predictive correlations up to 0.50 and 0.15, respectively. Overall, the present study contributes to a better understanding of the genetic basis of postpartum blood Ca concentration in Holstein cows. In addition, the findings may contribute to the development of novel selection and management strategies for reducing periparturient hypocalcemia in dairy cattle.
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Affiliation(s)
- Ligia Cavani
- Department of Animal and Dairy Sciences, University of Wisconsin, Madison 53706
| | | | - Corwin D Nelson
- Department of Animal Sciences, University of Florida, Gainesville 32608
| | - José E P Santos
- Department of Animal Sciences, University of Florida, Gainesville 32608
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13
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Vu NT, Phuc TH, Oanh KTP, Sang NV, Trang TT, Nguyen NH. Accuracies of genomic predictions for disease resistance of striped catfish to Edwardsiella ictaluri using artificial intelligence algorithms. G3-GENES GENOMES GENETICS 2021; 12:6408442. [PMID: 34788431 PMCID: PMC8727988 DOI: 10.1093/g3journal/jkab361] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 10/10/2021] [Indexed: 02/04/2023]
Abstract
Assessments of genomic prediction accuracies using artificial intelligent (AI) algorithms (i.e., machine and deep learning methods) are currently not available or very limited in aquaculture species. The principal aim of this study was to examine the predictive performance of these new methods for disease resistance to Edwardsiella ictaluri in a population of striped catfish Pangasianodon hypophthalmus and to make comparisons with four common methods, i.e., pedigree-based best linear unbiased prediction (PBLUP), genomic-based best linear unbiased prediction (GBLUP), single-step GBLUP (ssGBLUP) and a nonlinear Bayesian approach (notably BayesR). Our analyses using machine learning (i.e., ML-KAML) and deep learning (i.e., DL-MLP and DL-CNN) together with the four common methods (PBLUP, GBLUP, ssGBLUP, and BayesR) were conducted for two main disease resistance traits (i.e., survival status coded as 0 and 1 and survival time, i.e., days that the animals were still alive after the challenge test) in a pedigree consisting of 560 individual animals (490 offspring and 70 parents) genotyped for 14,154 single nucleotide polymorphism (SNPs). The results using 6,470 SNPs after quality control showed that machine learning methods outperformed PBLUP, GBLUP, and ssGBLUP, with the increases in the prediction accuracies for both traits by 9.1–15.4%. However, the prediction accuracies obtained from machine learning methods were comparable to those estimated using BayesR. Imputation of missing genotypes using AlphaFamImpute increased the prediction accuracies by 5.3–19.2% in all the methods and data used. On the other hand, there were insignificant decreases (0.3–5.6%) in the prediction accuracies for both survival status and survival time when multivariate models were used in comparison to univariate analyses. Interestingly, the genomic prediction accuracies based on only highly significant SNPs (P < 0.00001, 318–400 SNPs for survival status and 1,362–1,589 SNPs for survival time) were somewhat lower (0.3–15.6%) than those obtained from the whole set of 6,470 SNPs. In most of our analyses, the accuracies of genomic prediction were somewhat higher for survival time than survival status (0/1 data). It is concluded that although there are prospects for the application of genomic selection to increase disease resistance to E. ictaluri in striped catfish breeding programs, further evaluation of these methods should be made in independent families/populations when more data are accumulated in future generations to avoid possible biases in the genetic parameters estimates and prediction accuracies for the disease-resistant traits studied in this population of striped catfish P. hypophthalmus.
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Affiliation(s)
- Nguyen Thanh Vu
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia.,Genecology Research Center, University of the Sunshine Coast, Sippy Downs, QLD, Australia.,Research Institute for Aquaculture No.2, Ho Chi Minh 710000, Vietnam
| | - Tran Huu Phuc
- Research Institute for Aquaculture No.2, Ho Chi Minh 710000, Vietnam
| | - Kim Thi Phuong Oanh
- Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Nguyen Van Sang
- Research Institute for Aquaculture No.2, Ho Chi Minh 710000, Vietnam
| | - Trinh Thi Trang
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia.,Genecology Research Center, University of the Sunshine Coast, Sippy Downs, QLD, Australia.,Vietnam National University of Agriculture, Gia Lam 131000, Vietnam
| | - Nguyen Hong Nguyen
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia.,Genecology Research Center, University of the Sunshine Coast, Sippy Downs, QLD, Australia
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14
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Haile-Mariam M, Pryce JE. Use of insemination data for joint evaluation of male and female fertility in predominantly seasonal-calving dairy herds. J Dairy Sci 2021; 104:11807-11819. [PMID: 34419266 DOI: 10.3168/jds.2020-20006] [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: 12/07/2020] [Accepted: 06/30/2021] [Indexed: 11/19/2022]
Abstract
Conception in dairy cattle is influenced by the fertility of the cow and the bull and their interaction. Despite genetic selection for female fertility in many countries, selection for male fertility is largely not practiced. The primary objective of this study was to quantify variation in male and female fertility using insemination data from predominantly seasonal-calving herds. Nonreturn rate (NRR) was derived by coding each insemination as successful (1) or failed (0) based on a minimum of at least 25 d. The NRR was treated as a trait of the bull with semen (male fertility) and the cow that is mated (female fertility). The data (805,463 cows that mated to 5,776 bulls) were used to estimate parameters using either models that only included bulls with mating data or models that fitted the genetic and permanent environmental (PE) effects of bulls and cows simultaneously. We also evaluated whether fitting genetic and PE effects of bulls as one term is better for ranking bulls based on NRR compared with a model that ignored genetic effect. The age of cows that were mated, age of the bulls with semen data, season of mating, breed of cow that mated, inbreeding of cows and bulls, and days from calving to mating date were found to have a significant effect on NRR. Only about 3% of the total variance was explained by the random effects in the model, despite fitting the genetic and PE effects of the bull and cow. The 2 components of fertility (male and fertility) were not correlated. The heritability of male fertility was low (0.001 to 0.008), and that of female fertility was also low (~0.016). The highest heritability estimate for male fertility was obtained from the model that fitted the additive genetic relationship matrix and PE component of the bull as one term. When this model was used to calculate bull solutions, the difference between bulls with at least 100 inseminations was up to 19.2% units (-9.6 to 9.6%). Bull solutions from this model were compared with bull solutions that were predicted fitting bull effects ignoring pedigree. Bull solutions that were obtained considering pedigree had (1) the highest accuracy of prediction when early insemination was used to predict yet-to-be observed insemination data of bulls, and (2) improved model stability (i.e., a higher correlation between bull solutions from 2 randomly split herds) compared with the model which fitted bull with no pedigree. For practical purposes, the model that fitted genetic and PE effect as one term can provide more accurate semen fertility values for bulls than the model without genetic effect. To conclude, insemination data from predominantly seasonal-calving herds can be used to quantify variability between bulls for male fertility, which makes their ranking on NRR feasible. Potentially this information can be used for monitoring bulls and can supplement efforts to improve herd fertility by avoiding or minimizing the use of semen from subfertile bulls.
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Affiliation(s)
- Mekonnen Haile-Mariam
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria, 3083, Australia.
| | - J E Pryce
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria, 3083, Australia; School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, 3083 Australia
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15
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Zheng J, Deng T, Jiang E, Li J, Wijayanti D, Wang Y, Ding X, Lan X. Genetic variations of bovine PCOS-related DENND1A gene identified in GWAS significantly affect female reproductive traits. Gene 2021; 802:145867. [PMID: 34352299 DOI: 10.1016/j.gene.2021.145867] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 07/13/2021] [Accepted: 07/30/2021] [Indexed: 12/20/2022]
Abstract
Genome-wide association studies (GWAS) have identified DENND1A as a potential candidate gene linked to the fertility-related phenotypes in dairy cows. However, to date, no studies have examined the association of the DENND1A insertion/deletions (indels) to bovine fertility on a large scale. Herein, two indel sites, including P4-del-26-bp and P8-ins-15-bp were identified in 1064 Holstein cows. The values of the minor allelic frequency (MAF) ranged between 0.471 (deletion) and 0.230 (deletion), respectively, and combined four different haplotypes by analyzing the haplotype combination. It is noteworthy that P4-del-26-bp is associated with the ovarian width (P = 0.0004) and corpus luteum diameter (P = 0.004). Meanwhile, P8-ins-15-bp was found to have a significant association with the ovarian width (P = 0.020), ovarian weight (P = 0.004), the number of mature follicles (P = 0.020), and diameter of the mature follicles (P = 0.016). Furthermore, the combinatorial analysis showed that the two indel combined-genotypes were significantly related to several reproductive traits (ovarian width, ovarian weight, etc.). Collectively, our findings indicated that these two novel indels and their combinations are correlated with the reproductive traits, and hence, they can serve in the marker-assisted selection (MAS) in cattle breeding. Nevertheless, further functional experiments are needed for understanding the mechanisms of these indels in cattle reproduction in a better way.
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Affiliation(s)
- Juanshan Zheng
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Laboratory of Animal Genome and Gene Function, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Tianyu Deng
- Laboratory of Animal Genome and Gene Function, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Enhui Jiang
- Laboratory of Animal Genome and Gene Function, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jie Li
- Laboratory of Animal Genome and Gene Function, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Dwi Wijayanti
- Laboratory of Animal Genome and Gene Function, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yongsheng Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xuezhi Ding
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China.
| | - Xianyong Lan
- Laboratory of Animal Genome and Gene Function, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
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16
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Pacheco HA, Battagin M, Rossoni A, Cecchinato A, Peñagaricano F. Evaluation of bull fertility in Italian Brown Swiss dairy cattle using cow field data. J Dairy Sci 2021; 104:10896-10904. [PMID: 34304869 DOI: 10.3168/jds.2021-20332] [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: 02/19/2021] [Accepted: 06/10/2021] [Indexed: 11/19/2022]
Abstract
Dairy bull fertility is traditionally evaluated using semen production and quality traits; however, these attributes explain only part of the differences observed in fertility among bulls. Alternatively, bull fertility can be directly evaluated using cow field data. The main objective of this study was to investigate bull fertility in the Italian Brown Swiss dairy cattle population using confirmed pregnancy records. The data set included a total of 397,926 breeding records from 1,228 bulls and 129,858 lactating cows between first and fifth lactation from 2000 to 2019. We first evaluated cow pregnancy success, including factors related to the bull under evaluation, such as bull age, bull inbreeding, and AI organization, and factors associated with the cow that receives the dose of semen, including herd-year-season, cow age, parity, and milk yield. We then estimated sire conception rate using only factors related to the bull. Model predictive ability was evaluated using 10-fold cross-validation with 10 replicates. Interestingly, our analyses revealed that there is a substantial variation in conception rate among Brown Swiss bulls, with more than 20% conception rate difference between high-fertility and low-fertility bulls. We also showed that the prediction of bull fertility is feasible as our cross-validation analyses achieved predictive correlations equal to 0.30 for sire conception rate. Improving reproduction performance is one of the major challenges of the dairy industry worldwide, and for this, it is essential to have accurate predictions of service sire fertility. This study represents the foundation for the development of novel tools that will allow dairy producers, breeders, and artificial insemination companies to make enhanced management and selection decisions on Brown Swiss male fertility.
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Affiliation(s)
- Hendyel A Pacheco
- Department of Animal and Dairy Sciences, University of Wisconsin, Madison 53706
| | - Mara Battagin
- Italian Brown Breeders Association, Bussolengo, Verona 37012, Italy
| | - Attilio Rossoni
- Italian Brown Breeders Association, Bussolengo, Verona 37012, Italy
| | - Alessio Cecchinato
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Legnaro, Padua 35020, Italy
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17
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Hussain S, Alex R, Alyethodi RR, Sharma S, Verma N, Sirohi AS, Singh U, Kumar S, Chand N, Sengar GS, Sharma A, Tyagi R, Arya S, Tyagi S. Development of a RAPD marker-based classification criterion for quality semen production in Holstein crossbred bulls. Reprod Domest Anim 2021; 56:736-743. [PMID: 33559234 DOI: 10.1111/rda.13912] [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: 08/19/2020] [Revised: 11/19/2020] [Accepted: 02/04/2021] [Indexed: 11/30/2022]
Abstract
In cattle production systems, an intense selection pressure for production traits has resulted in the decline of fertility traits. To optimize an efficient reproduction system, the inclusion of both male and female fertility traits in the selection process is very much essential. RAPD (Random Amplified Polymorphic DNA) was developed as a molecular biology tool and has been extensively used, to study intra- and interspecific genetic diversity. The present study was undertaken to utilize RAPD primers to investigate the association between DNA markers and semen quality traits viz. Sperm concentration, total sperm count ejaculate and initial sperm motility and thereby to identify good/poor semen producers. DNA isolated from the blood samples of healthy bulls was subjected to RAPD-PCR. The multiple regression analysis followed by independent t test was carried out to identify suitable markers. Based on the results, only 12 bands were identified as marker suitable for any of the quality trait. This includes, OPA2 ~ 760, OPA2 ~ 700, OPA6 ~ 1,200, OPA9 ~ 400, OPA9 ~ 380, OPA12 ~ 970, OPA14 ~ 715, OPA14 ~ 605, OPA16 ~ 485, OPA17 ~ 860 and OPA18 ~ 480. Multiple regression analysis selected, OPA2 ~ 760 and OPA2 ~ 1,750 for sperm concentration and OPA2 ~ 760, OPA2 ~ 700, OPA9 ~ 620, OPA4 ~ 670 and OPA18 ~ 1,015 for total sperm count/ejaculate. But the t test revealed a significant association between OPA2 ~ 760 and total sperm count. Further, discriminant function analysis also identified this marker in the first step itself. The results of the present study can be exploited as a low-cost alternative strategy for identification of good /poor semen producers in crossbred bulls at an early age.
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Affiliation(s)
- Shaziya Hussain
- Department of Biotechnology and Microbiology, MIET, Meerut, India
| | - Rani Alex
- ICAR-National Dairy Research Institute, Karnal, India
| | | | - Shalini Sharma
- Department of Biotechnology and Microbiology, MIET, Meerut, India
| | - Nitika Verma
- Department of Biotechnology and Microbiology, MIET, Meerut, India
| | | | - Umesh Singh
- ICAR-Central Institute for Research on Cattle, Meerut, India
| | - Sushil Kumar
- ICAR-Central Institute for Research on Cattle, Meerut, India
| | - Naimi Chand
- ICAR-Central Institute for Research on Cattle, Meerut, India
| | | | - Ankur Sharma
- ICAR-Central Institute for Research on Cattle, Meerut, India
| | - Rachna Tyagi
- ICAR-Central Institute for Research on Cattle, Meerut, India
| | - Sarmesh Arya
- ICAR-Central Institute for Research on Cattle, Meerut, India
| | - Srikant Tyagi
- ICAR-Central Institute for Research on Cattle, Meerut, India
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18
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Morgante F, Huang W, Sørensen P, Maltecca C, Mackay TFC. Leveraging Multiple Layers of Data To Predict Drosophila Complex Traits. G3 (BETHESDA, MD.) 2020; 10:4599-4613. [PMID: 33106232 PMCID: PMC7718734 DOI: 10.1534/g3.120.401847] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/12/2020] [Indexed: 02/07/2023]
Abstract
The ability to accurately predict complex trait phenotypes from genetic and genomic data are critical for the implementation of personalized medicine and precision agriculture; however, prediction accuracy for most complex traits is currently low. Here, we used data on whole genome sequences, deep RNA sequencing, and high quality phenotypes for three quantitative traits in the ∼200 inbred lines of the Drosophila melanogaster Genetic Reference Panel (DGRP) to compare the prediction accuracies of gene expression and genotypes for three complex traits. We found that expression levels (r = 0.28 and 0.38, for females and males, respectively) provided higher prediction accuracy than genotypes (r = 0.07 and 0.15, for females and males, respectively) for starvation resistance, similar prediction accuracy for chill coma recovery (null for both models and sexes), and lower prediction accuracy for startle response (r = 0.15 and 0.14 for female and male genotypes, respectively; and r = 0.12 and 0.11, for females and male transcripts, respectively). Models including both genotype and expression levels did not outperform the best single component model. However, accuracy increased considerably for all the three traits when we included gene ontology (GO) category as an additional layer of information for both genomic variants and transcripts. We found strongly predictive GO terms for each of the three traits, some of which had a clear plausible biological interpretation. For example, for starvation resistance in females, GO:0033500 (r = 0.39 for transcripts) and GO:0032870 (r = 0.40 for transcripts), have been implicated in carbohydrate homeostasis and cellular response to hormone stimulus (including the insulin receptor signaling pathway), respectively. In summary, this study shows that integrating different sources of information improved prediction accuracy and helped elucidate the genetic architecture of three Drosophila complex phenotypes.
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Affiliation(s)
- Fabio Morgante
- Department of Biological Sciences and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC 27695
- Program in Genetics, North Carolina State University, Raleigh, NC 27695
| | - Wen Huang
- Department of Biological Sciences and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC 27695
- Program in Genetics, North Carolina State University, Raleigh, NC 27695
| | - Peter Sørensen
- Center of Quantitative Genetics and Genomics and Department of Molecular Biology and Genetics, Aarhus University, Tjele 8830, Denmark
| | - Christian Maltecca
- Program in Genetics, North Carolina State University, Raleigh, NC 27695
- Department of Animal Science, North Carolina State University, Raleigh, NC 27695
| | - Trudy F C Mackay
- Department of Biological Sciences and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC 27695
- Program in Genetics, North Carolina State University, Raleigh, NC 27695
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Ye S, Li J, Zhang Z. Multi-omics-data-assisted genomic feature markers preselection improves the accuracy of genomic prediction. J Anim Sci Biotechnol 2020; 11:109. [PMID: 33292577 PMCID: PMC7708144 DOI: 10.1186/s40104-020-00515-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 09/22/2020] [Indexed: 12/02/2022] Open
Abstract
Background Presently, multi-omics data (e.g., genomics, transcriptomics, proteomics, and metabolomics) are available to improve genomic predictors. Omics data not only offers new data layers for genomic prediction but also provides a bridge between organismal phenotypes and genome variation that cannot be readily captured at the genome sequence level. Therefore, using multi-omics data to select feature markers is a feasible strategy to improve the accuracy of genomic prediction. In this study, simultaneously using whole-genome sequencing (WGS) and gene expression level data, four strategies for single-nucleotide polymorphism (SNP) preselection were investigated for genomic predictions in the Drosophila Genetic Reference Panel. Results Using genomic best linear unbiased prediction (GBLUP) with complete WGS data, the prediction accuracies were 0.208 ± 0.020 (0.181 ± 0.022) for the startle response and 0.272 ± 0.017 (0.307 ± 0.015) for starvation resistance in the female (male) lines. Compared with GBLUP using complete WGS data, both GBLUP and the genomic feature BLUP (GFBLUP) did not improve the prediction accuracy using SNPs preselected from complete WGS data based on the results of genome-wide association studies (GWASs) or transcriptome-wide association studies (TWASs). Furthermore, by using SNPs preselected from the WGS data based on the results of the expression quantitative trait locus (eQTL) mapping of all genes, only the startle response had greater accuracy than GBLUP with the complete WGS data. The best accuracy values in the female and male lines were 0.243 ± 0.020 and 0.220 ± 0.022, respectively. Importantly, by using SNPs preselected based on the results of the eQTL mapping of significant genes from TWAS, both GBLUP and GFBLUP resulted in great accuracy and small bias of genomic prediction. Compared with the GBLUP using complete WGS data, the best accuracy values represented increases of 60.66% and 39.09% for the starvation resistance and 27.40% and 35.36% for startle response in the female and male lines, respectively. Conclusions Overall, multi-omics data can assist genomic feature preselection and improve the performance of genomic prediction. The new knowledge gained from this study will enrich the use of multi-omics in genomic prediction.
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Affiliation(s)
- Shaopan Ye
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Centre for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Jiaqi Li
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Centre for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Zhe Zhang
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Centre for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China.
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20
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Gross N, Taylor T, Crenshaw T, Khatib H. The Intergenerational Impacts of Paternal Diet on DNA Methylation and Offspring Phenotypes in Sheep. Front Genet 2020; 11:597943. [PMID: 33250925 PMCID: PMC7674940 DOI: 10.3389/fgene.2020.597943] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 10/14/2020] [Indexed: 11/13/2022] Open
Abstract
Knowledge of non-genomic inheritance of traits is currently limited. Although it is well established that maternal diet influences offspring inheritance of traits through DNA methylation, studies on the impact of prepubertal paternal diet on DNA methylation are rare. This study aimed to evaluate the impact of prepubertal diet in Polypay rams on complex traits, DNA methylation, and transmission of traits to offspring. A total of 10 littermate pairs of F0 rams were divided so that one ram was fed a control diet, and the other was fed the control diet with supplemental methionine. Diet was associated with earlier age at puberty in treatment vs. control F0 rams. F0 treatment rams tended to show decreased pubertal weight compared to control rams; however, no differences were detected in overall growth. A total of ten F0 rams were bred, and the entire F1 generation was fed a control diet. Diet of F0 rams had a significant association with scrotal circumference (SC) and weight at puberty of F1 offspring. The paternal diet was not significantly associated with F1 ram growth or age at puberty. The DNA methylation of F0 ram sperm was assessed, and genes related to both sexual development (e.g., DAZAP1, CHD7, TAB1, MTMR2, CELSR1, MGAT1) and body weight (e.g., DUOX2, DUOXA2) were prevalent in the data. These results provide novel information about the mechanisms through which the prepubertal paternal diet may alter body weight at puberty and sexual development.
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Affiliation(s)
- Nicole Gross
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Todd Taylor
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Thomas Crenshaw
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Hasan Khatib
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States
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21
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Marker-assisted selection vis-à-vis bull fertility: coming full circle-a review. Mol Biol Rep 2020; 47:9123-9133. [PMID: 33099757 DOI: 10.1007/s11033-020-05919-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 10/13/2020] [Indexed: 10/23/2022]
Abstract
Bull fertility is considered an indispensable trait, as far as farm economics is concerned since it is the successful conception in a cow that provides calf crop, along with the ensuing lactation. This ensures sustainability of a dairy farm. Traditionally, bull fertility did not receive much attention by the farm managers and breeding animals were solely evaluated based on phenotypic predictors, namely, sire conception rate and seminal parameters in bull. With the advent of the molecular era in animal breeding, attempts were made to unravel the genetic complexity of bull fertility by the identification of genetic markers related to the trait. Marker-Assisted Selection (MAS) is a methodology that aims at utilizing the genetic information at markers and selecting improved populations for important traits. Traditionally, MAS was pursued using a candidate gene approach for identifying markers related to genes that are already known to have a physiological function related to the trait but this approach had certain shortcomings like stringent criteria for significance testing. Now, with the availability of genome-wide data, the number of markers identified and variance explained in relation to bull fertility has gone up. So, this presents a unique opportunity to revisit MAS by selection based on the information of a large number of genome-wide markers and thus, improving the accuracy of selection.
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Rezende FM, Haile-Mariam M, Pryce JE, Peñagaricano F. Across-country genomic prediction of bull fertility in Jersey dairy cattle. J Dairy Sci 2020; 103:11618-11627. [PMID: 32981736 DOI: 10.3168/jds.2020-18910] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 07/15/2020] [Indexed: 12/11/2022]
Abstract
The use of information across populations is an attractive approach to increase the accuracy of genomic predictions for numerically small breeds and traits that are time-consuming and difficult to measure, such as male fertility in cattle. This study was conducted to evaluate genomic prediction of Jersey bull fertility using an across-country reference population combining records from the United States and Australia. The data set consisted of 1,570 US Jersey bulls with sire conception rate (SCR) records, 603 Australian Jersey bulls with semen fertility value (SFV) records and SNP genotypes for roughly 90,000 loci. Both SCR and SFV are evaluations of service sire fertility based on cow field data, and both are intended as phenotypic evaluations because the estimates include genetic and nongenetic effects. Within- and across-country genomic predictions were evaluated using univariate and bivariate genomic best linear unbiased prediction models. Predictive ability was assessed in 5-fold cross-validation using the correlation between observed and predicted fertility values and mean squared error of prediction. Within-country genomic predictions exhibited predictive correlations of around 0.28 and 0.02 for the United States and Australia, respectively. The Australian Jersey population is genetically diverse and small in size, so careful selection of the reference population by including only closely related animals (e.g., excluding New Zealand bulls, which is a less-related population) increased the predictive correlations up to 0.20. Notably, the use of bivariate models fitting all US Jersey records and the optimized Australian population resulted in predictive correlations around of 0.24 for SFV values, which is a relative increase in predictive ability of 20%. Conversely, for predicting SCR values, the use of an across-country reference population did not outperform the standard approach using pure US Jersey reference data set. Our findings indicate that genomic prediction of male fertility in dairy cattle is feasible, and the use of an across-country reference population would be beneficial when local populations are small and genetically diverse.
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Affiliation(s)
- Fernanda M Rezende
- Department of Animal Sciences, University of Florida, Gainesville 32611; Faculdade de Medicina Veterinária, Universidade Federal de Uberlândia, Uberlândia MG 38410-337, Brazil
| | - Mekonnen Haile-Mariam
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, Victoria 3083, Australia
| | - Jennie E Pryce
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, Victoria 3083, Australia; School of Applied Systems Biology, La Trobe University, Bundoora, Victoria 3083, Australia
| | - Francisco Peñagaricano
- Department of Animal Sciences, University of Florida, Gainesville 32611; Department of Animal and Dairy Sciences, University of Wisconsin-Madison, 53706.
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23
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Gross N, Peñagaricano F, Khatib H. Integration of whole-genome DNA methylation data with RNA sequencing data to identify markers for bull fertility. Anim Genet 2020; 51:502-510. [PMID: 32323873 DOI: 10.1111/age.12941] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2020] [Indexed: 02/06/2023]
Abstract
Predicting bull fertility prior to breeding is a current challenge for the dairy industry. The use of molecular biomarkers has been previously assessed. However, the integration of this information has not been performed to extract biologically relevant markers. The goal of this study was to integrate DNA methylation data with previously published RNA-sequencing results in order to identify candidate markers for sire fertility. A total of 1765 differentially methylated cytosines were found between high- and low-fertility sires. Ten genes associated with 11 differentially methylated cytosines were found in a previous study of gene expression between high- and low-fertility sires. Additionally, two of these genes code for proteins found exclusively in bull seminal plasma. Collectively, our results reveal 10 genes that could be used in the future as a panel for predicting bull fertility.
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Affiliation(s)
- Nicole Gross
- Department of Animal Sciences, University of Wisconsin, Madison, WI, 53706, USA
| | | | - Hasan Khatib
- Department of Animal Sciences, University of Wisconsin, Madison, WI, 53706, USA
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24
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Abdollahi-Arpanahi R, Gianola D, Peñagaricano F. Deep learning versus parametric and ensemble methods for genomic prediction of complex phenotypes. Genet Sel Evol 2020; 52:12. [PMID: 32093611 PMCID: PMC7038529 DOI: 10.1186/s12711-020-00531-z] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 02/13/2020] [Indexed: 12/19/2022] Open
Abstract
Background Transforming large amounts of genomic data into valuable knowledge for predicting complex traits has been an important challenge for animal and plant breeders. Prediction of complex traits has not escaped the current excitement on machine-learning, including interest in deep learning algorithms such as multilayer perceptrons (MLP) and convolutional neural networks (CNN). The aim of this study was to compare the predictive performance of two deep learning methods (MLP and CNN), two ensemble learning methods [random forests (RF) and gradient boosting (GB)], and two parametric methods [genomic best linear unbiased prediction (GBLUP) and Bayes B] using real and simulated datasets. Methods The real dataset consisted of 11,790 Holstein bulls with sire conception rate (SCR) records and genotyped for 58k single nucleotide polymorphisms (SNPs). To support the evaluation of deep learning methods, various simulation studies were conducted using the observed genotype data as template, assuming a heritability of 0.30 with either additive or non-additive gene effects, and two different numbers of quantitative trait nucleotides (100 and 1000). Results In the bull dataset, the best predictive correlation was obtained with GB (0.36), followed by Bayes B (0.34), GBLUP (0.33), RF (0.32), CNN (0.29) and MLP (0.26). The same trend was observed when using mean squared error of prediction. The simulation indicated that when gene action was purely additive, parametric methods outperformed other methods. When the gene action was a combination of additive, dominance and of two-locus epistasis, the best predictive ability was obtained with gradient boosting, and the superiority of deep learning over the parametric methods depended on the number of loci controlling the trait and on sample size. In fact, with a large dataset including 80k individuals, the predictive performance of deep learning methods was similar or slightly better than that of parametric methods for traits with non-additive gene action. Conclusions For prediction of traits with non-additive gene action, gradient boosting was a robust method. Deep learning approaches were not better for genomic prediction unless non-additive variance was sizable.
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Affiliation(s)
| | - Daniel Gianola
- Departments of Animal Sciences and Dairy Science, University of Wisconsin-Madison, Madison, WI, USA
| | - Francisco Peñagaricano
- Department of Animal Sciences, University of Florida, Gainesville, FL, USA. .,University of Florida Genetics Institute, University of Florida, Gainesville, FL, USA.
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Pacheco HA, Rezende FM, Peñagaricano F. Gene mapping and genomic prediction of bull fertility using sex chromosome markers. J Dairy Sci 2020; 103:3304-3311. [PMID: 32063375 DOI: 10.3168/jds.2019-17767] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 12/09/2019] [Indexed: 12/29/2022]
Abstract
Service sire has been recognized as an important factor affecting dairy herd fertility. Our group has reported promising results on gene mapping and genomic prediction of dairy bull fertility using autosomal SNP markers. Little is known, however, about the genetic contribution of sex chromosomes, which are enriched in genes related to sexual development and reproduction. As such, the main goal of this study was to investigate the effect of SNP markers on X and Y chromosomes (BTAX and BTAY, respectively) on sire conception rate (SCR) in US Holstein bulls. The analysis included a total of 5,014 bulls with SCR records and genotypes for roughly 291k SNP located on the autosomes, 1.5k SNP located on the pseudoautosomal region (PAR), 13.7k BTAX-specific SNP, and 24 BTAY-specific SNP. We first performed genomic scans of the sex chromosomes, and then we evaluated the genomic prediction of SCR including BTAX SNP markers in the predictive models. Two markers located on PAR and 3 markers located on the X-specific region showed significant associations with sire fertility. Interestingly, these regions harbor genes, such as FAM9B, TBL1X, and PIH1D3, that are directly implicated in testosterone concentration, spermatogenesis, and sperm motility. On the other hand, BTAY showed very low genetic variability, and none of the segregating markers were associated with SCR. Notably, model predictive ability was largely improved by including BTAX markers. Indeed, the combination of autosomal with BTAX SNP delivered predictive correlations around 0.343, representing an increase in accuracy of about 7.5% compared with the standard whole autosomal genome approach. Overall, this study provides evidence of the importance of both PAR and X-specific regions in male fertility in dairy cattle. These findings may help to improve conception rates in dairy herds through accurate genome-guided decisions on bull fertility.
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Affiliation(s)
- Hendyel A Pacheco
- Department of Animal Sciences, University of Florida, Gainesville 32611
| | - Fernanda M Rezende
- Department of Animal Sciences, University of Florida, Gainesville 32611; Faculdade de Medicina Veterinária, Universidade Federal de Uberlândia, Uberlândia MG 38400-902, Brazil
| | - Francisco Peñagaricano
- Department of Animal Sciences, University of Florida, Gainesville 32611; University of Florida Genetics Institute, University of Florida, Gainesville 32610.
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26
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Shan S, Xu F, Bleyer M, Becker S, Melbaum T, Wemheuer W, Hirschfeld M, Wacker C, Zhao S, Schütz E, Brenig B. Association of α/β-Hydrolase D16B with Bovine Conception Rate and Sperm Plasma Membrane Lipid Composition. Int J Mol Sci 2020; 21:E627. [PMID: 31963602 PMCID: PMC7014312 DOI: 10.3390/ijms21020627] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 01/14/2020] [Accepted: 01/15/2020] [Indexed: 02/01/2023] Open
Abstract
We have identified a Holstein sire named Tarantino who had been approved for artificial insemination that is based on normal semen characteristics (i.e., morphology, thermoresistance, motility, sperm concentration), but had no progeny after 412 first inseminations, resulting in a non-return rate (NRdev) of -29. Using whole genome association analysis and next generation sequencing, an associated nonsense variant in the α/β-hydrolase domain-containing 16B gene (ABHD16B) on bovine chromosome 13 was identified. The frequency of the mutant allele in the German Holstein population was determined to be 0.0018 in 222,645 investigated cattle specimens. The mutant allele was traced back to Whirlhill Kingpin (bornFeb. 13th, 1959) as potential founder. The expression of ABHD16B was detected by Western blotting and immunohistochemistry in testis and epididymis of control bulls. A lipidome comparison of the plasma membrane of fresh semen from carriers and controls showed significant differences in the concentration of phosphatidylcholine (PC), diacylglycerol (DAG), ceramide (Cer), sphingomyelin (SM), and phosphatidylcholine (-ether) (PC O-), indicating that ABHD16B plays a role in lipid biosynthesis. The altered lipid contents may explain the reduced fertilization ability of mutated sperms.
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Affiliation(s)
- Shuwen Shan
- Institute of Veterinary Medicine, University of Goettingen, 37077 Goettingen, Germany
| | - Fangzheng Xu
- Institute of Veterinary Medicine, University of Goettingen, 37077 Goettingen, Germany
| | - Martina Bleyer
- Pathology Unit, German Primate Center, Leibniz-Institute for Primate Research Goettingen, 37077 Goettingen, Germany
| | - Svenja Becker
- Institute of Veterinary Medicine, University of Goettingen, 37077 Goettingen, Germany
| | - Torben Melbaum
- Institute of Veterinary Medicine, University of Goettingen, 37077 Goettingen, Germany
| | - Wilhelm Wemheuer
- Institute of Veterinary Medicine, University of Goettingen, 37077 Goettingen, Germany
| | - Marc Hirschfeld
- Institute of Veterinary Medicine, University of Goettingen, 37077 Goettingen, Germany
- Department of Obstetrics and Gynecology, University Medical Center Freiburg, 79106 Freiburg, Germany
| | - Christin Wacker
- Institute of Veterinary Medicine, University of Goettingen, 37077 Goettingen, Germany
| | - Shuhong Zhao
- Key Lab of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ekkehard Schütz
- Institute of Veterinary Medicine, University of Goettingen, 37077 Goettingen, Germany
| | - Bertram Brenig
- Institute of Veterinary Medicine, University of Goettingen, 37077 Goettingen, Germany
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27
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28
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Butler ML, Bormann JM, Weaber RL, Grieger DM, Rolf MM. Selection for bull fertility: a review. Transl Anim Sci 2019; 4:423-441. [PMID: 32705001 PMCID: PMC6994025 DOI: 10.1093/tas/txz174] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 11/28/2019] [Indexed: 11/20/2022] Open
Abstract
Fertility is a critically important factor in cattle production because it directly relates to the ability to produce the offspring necessary to offset costs in production systems. Female fertility has received much attention and has been enhanced through assisted reproductive technologies, as well as genetic selection; however, improving bull fertility has been largely ignored. Improvements in bull reproductive performance are necessary to optimize the efficiency of cattle production. Selection and management to improve bull fertility not only have the potential to increase conception rates but also have the capacity to improve other economically relevant production traits. Bull fertility has reportedly been genetically correlated with traits such as average daily gain, heifer pregnancy, and calving interval. Published studies show that bull fertility traits are low to moderately heritable, indicating that improvements in bull fertility can be realized through selection. Although female fertility has continued to progress according to increasing conception rates, the reported correlation between male and female fertility is low, indicating that male fertility cannot be improved by selection for female fertility. Correlations between several bull fertility traits, such as concentration, number of spermatozoa, motility, and number of spermatozoa abnormalities, vary among studies. Using male fertility traits in selection indices would provide producers with more advanced selection tools. The objective of this review was to discuss current beef bull fertility measurements and to discuss the future of genetic evaluation of beef bull fertility and potential genetic improvement strategies.
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Affiliation(s)
- Madison L Butler
- Department of Animal Science, Kansas State University, Manhattan, KS
| | | | - Robert L Weaber
- Department of Animal Science, Kansas State University, Manhattan, KS
| | - David M Grieger
- Department of Animal Science, Kansas State University, Manhattan, KS
| | - Megan M Rolf
- Department of Animal Science, Kansas State University, Manhattan, KS
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Grigoletto L, Brito LF, Mattos EC, Eler JP, Bussiman FO, Silva BDCA, da Silva RP, Carvalho FE, Berton MP, Baldi F, Ferraz JBS. Genome-wide associations and detection of candidate genes for direct and maternal genetic effects influencing growth traits in the Montana Tropical® Composite population. Livest Sci 2019. [DOI: 10.1016/j.livsci.2019.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Ortega MS, Moraes JGN, Patterson DJ, Smith MF, Behura SK, Poock S, Spencer TE. Influences of sire conception rate on pregnancy establishment in dairy cattle. Biol Reprod 2019; 99:1244-1254. [PMID: 29931362 DOI: 10.1093/biolre/ioy141] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 06/15/2018] [Indexed: 12/15/2022] Open
Abstract
Establishment of pregnancy in cattle is complex and encompasses ovulation, fertilization, blastocyst formation and growth into an elongated conceptus, pregnancy recognition signaling, and development of the embryo and placenta. The objective here was to investigate sire influences on pregnancy establishment in cattle. First, 10 Holstein bulls were classified as high or low fertility based on their sire conception rate (SCR) value. In a field trial, pregnancy at first timed insemination was not different between high and low SCR bulls. Next, 5 of the 10 sires were phenotyped using in vitro and in vivo embryo production. There was no effect of SCR classification on in vitro embryo cleavage rate, but low SCR sires produced fewer day 8 blastocysts. In superovulated heifers, high SCR bulls produced a lower percentage of unfertilized oocytes and fewer degenerated embryos compared to low SCR bulls. Recipient heifers received three to five in vivo produced embryos from either high or low SCR sires on day 7 postestrus. Day 16 conceptus recovery and length were not different between SCR groups, and the conceptus transcriptome was not appreciably different between high and low SCR sires. The reduced ability of embryos from low SCR bulls to establish pregnancy is multifactorial and encompasses sperm fertilizing ability, preimplantation embryonic development, and development of the embryo and placenta after conceptus elongation and pregnancy recognition. These studies highlight the importance of understanding genetic contributions of the sire to pregnancy establishment that is crucial to increase reproductive efficiency in dairy cattle.
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Affiliation(s)
- M Sofia Ortega
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, USA
| | - João G N Moraes
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, USA
| | - David J Patterson
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, USA
| | - Michael F Smith
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, USA
| | - Susanta K Behura
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, USA
| | - Scott Poock
- College of Veterinary Medicine, University of Missouri, Columbia, Missouri, USA
| | - Thomas E Spencer
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, USA
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31
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Nani JP, Rezende FM, Peñagaricano F. Predicting male fertility in dairy cattle using markers with large effect and functional annotation data. BMC Genomics 2019; 20:258. [PMID: 30940077 PMCID: PMC6444482 DOI: 10.1186/s12864-019-5644-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 03/25/2019] [Indexed: 11/22/2022] Open
Abstract
Background Fertility is among the most important economic traits in dairy cattle. Genomic prediction for cow fertility has received much attention in the last decade, while bull fertility has been largely overlooked. The goal of this study was to assess genomic prediction of dairy bull fertility using markers with large effect and functional annotation data. Sire conception rate (SCR) was used as a measure of service sire fertility. Dataset consisted of 11.5 k U.S. Holstein bulls with SCR records and about 300 k single nucleotide polymorphism (SNP) markers. The analyses included the use of both single-kernel and multi-kernel predictive models fitting either all SNPs, markers with large effect, or markers with presumed functional roles, such as non-synonymous, synonymous, or non-coding regulatory variants. Results The entire set of SNPs yielded predictive correlations of 0.340. Five markers located on chromosomes BTA8, BTA9, BTA13, BTA17, and BTA27 showed marked dominance effects. Interestingly, the inclusion of these five major markers as fixed effects in the predictive models increased predictive correlations to 0.403, representing an increase in accuracy of about 19% compared with the standard model. Single-kernel models fitting functional SNP classes outperformed their counterparts using random sets of SNPs, suggesting that the predictive power of these functional variants is driven in part by their biological roles. Multi-kernel models fitting all the functional SNP classes together with the five major markers exhibited predictive correlations around 0.405. Conclusions The inclusion of markers with large effect markedly improved the prediction of dairy sire fertility. Functional variants exhibited higher predictive ability than random variants, but did not outperform the standard whole-genome approach. This research is the foundation for the development of novel strategies that could help the dairy industry make accurate genome-guided selection decisions on service sire fertility.
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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
| | - Fernanda M Rezende
- Department of Animal Sciences, University of Florida, 2250 Shealy Drive, Gainesville, FL, 32611, USA.,Faculdade de Medicina Veterinária, Universidade Federal de Uberlândia, Uberlândia, MG, 38410-337, Brazil
| | - 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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Díaz-Miranda EA, Maitan PP, Machado TP, Camilo BS, Lima DA, Okano DS, Penitente-Filho JM, Machado-Neves M, de Oliveira LL, Guimarães SEF, da Costa EP, Guimarães JD. Disruption of bovine sperm functions in the presence of aplastic midpiece defect. Andrology 2019; 8:201-210. [PMID: 30908900 DOI: 10.1111/andr.12618] [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: 07/20/2018] [Revised: 02/14/2019] [Accepted: 03/04/2019] [Indexed: 11/26/2022]
Abstract
BACKGROUND Bulls are of great importance in the productive chain and for this reason they should have a good semen quality. There is no doubt that sperm morphology is very important to bull fertility, although little is known about how exactly the abnormal morphologies may affect sperm functions. OBJECTIVES To detail the morphological description of the aplastic midpiece defect (AMD), as well as to understand its consequences for male fertility based on membrane and acrosome status, mitochondrial membrane potential and DNA integrity parameters. MATERIALS AND METHODS The bulls were divided into two groups: control, consisting of satisfactory potential breeders (n = 3); and AMD, consisting of unsatisfactory potential breeders with a high percentage of AMD (n = 3). Bulls were evaluated by the breeding soundness evaluation; five ejaculates were collected from each animal and analyzed by flow cytometry. RESULTS Spermatozoa from AMD group exhibited lower sperm motility and vigor (p < 0.05). In addition, it also exhibited lower mitochondrial membrane potential (p < 0.05), a higher percentage of spermatozoa with DNA fragmentation (p < 0.05), lower acrosome and plasma membrane integrity (p < 0.05), and higher lipid bilayer sperm membrane disorganization (p < 0.05) in comparison with control bulls. DISCUSSION These findings may be due to oxidative stress and a reduction of the energy production capacity in addition to an alteration in the structural composition of the sperm cell. Moreover, semen with a high percentage of AMD may also be undergoing apoptosis. CONCLUSION Bulls with a high percentage of AMD in their semen are not suitable for reproduction. Furthermore, it suggests there is a putative genetic basis for this sperm defect.
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Affiliation(s)
- E A Díaz-Miranda
- Department of Veterinary, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - P P Maitan
- Department of Veterinary, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - T P Machado
- Department of Veterinary, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - B S Camilo
- Department of Veterinary, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - D A Lima
- Department of Veterinary, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - D S Okano
- Department of Veterinary, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - J M Penitente-Filho
- Department of Veterinary, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - M Machado-Neves
- Department of General Biology, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - L L de Oliveira
- Department of General Biology, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - S E F Guimarães
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - E P da Costa
- Department of Veterinary, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - J D Guimarães
- Department of Veterinary, Universidade Federal de Viçosa, Viçosa, MG, Brazil
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33
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Rezende FM, Nani JP, Peñagaricano F. Genomic prediction of bull fertility in US Jersey dairy cattle. J Dairy Sci 2019; 102:3230-3240. [PMID: 30712930 DOI: 10.3168/jds.2018-15810] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 11/29/2018] [Indexed: 01/02/2023]
Abstract
Service sire has a major effect on reproductive success in dairy cattle. Recent studies have reported accurate predictions for Holstein bull fertility using genomic data. The objective of this study was to assess the feasibility of genomic prediction of sire conception rate (SCR) in US Jersey cattle using alternative predictive models. Data set consisted of 1.5k Jersey bulls with SCR records and 95k SNP covering the entire genome. The analyses included the use of linear and Gaussian kernel-based models fitting either all the SNP or subsets of markers with presumed functional roles, such as SNP significantly associated with SCR or SNP located within or close to annotated genes. Model predictive ability was evaluated using 5-fold cross-validation with 10 replicates. The entire SNP set exhibited predictive correlations around 0.30. Interestingly, either SNP marginally associated with SCR or genic SNP achieved higher predictive abilities than their counterparts using random sets of SNP. Among alternative SNP subsets, Gaussian kernel models fitting significant SNP achieved the best performance with increases in predictive correlation up to 7% compared with the standard whole-genome approach. Notably, the use of a multi-breed reference population including the entire US Holstein SCR data set (11.5k bulls) allowed us to achieve predictive correlations up to 0.315, gaining 8% in accuracy compared with the standard model fitting a pure Jersey reference set. Overall, our findings indicate that genomic prediction of Jersey bull fertility is feasible. The use of Gaussian kernels fitting markers with relevant roles and the inclusion of Holstein records in the training set seem to be promising alternatives to the standard whole-genome approach. These results have the potential to help the dairy industry improve US Jersey sire fertility through accurate genome-guided decisions.
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Affiliation(s)
- Fernanda M Rezende
- Department of Animal Sciences, University of Florida, Gainesville 32611; Faculdade de Medicina Veterinária, Universidade Federal de Uberlândia, Uberlândia MG 38410-337, Brazil
| | - Juan Pablo Nani
- Department of Animal Sciences, University of Florida, Gainesville 32611; Estación Experimental Agropecuaria Rafaela, Instituto Nacional de Tecnología Agropecuaria, Rafaela SF 22-2300, Argentina
| | - Francisco Peñagaricano
- Department of Animal Sciences, University of Florida, Gainesville 32611; University of Florida Genetics Institute, University of Florida, Gainesville 32610.
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34
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Bach À. Effects of nutrition and genetics on fertility in dairy cows. Reprod Fertil Dev 2019; 31:40-54. [DOI: 10.1071/rd18364] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Optimal reproductive function in dairy cattle is mandatory to maximise profits. Dairy production has progressively improved milk yields, but, until recently, the trend in reproductive performance has been the opposite. Nutrition, genetics, and epigenetics are important aspects affecting the reproductive performance of dairy cows. In terms of nutrition, the field has commonly fed high-energy diets to dairy cows during the 3 weeks before calving in an attempt to minimise postpartum metabolic upsets. However, in the recent years it has become clear that feeding high-energy diets during the dry period, especially as calving approaches, may be detrimental to cow health, or at least unnecessary because cows, at that time, have low energy requirements and sufficient intake capacity. After calving, dairy cows commonly experience a period of negative energy balance (NEB) characterised by low blood glucose and high non-esterified fatty acid (NEFA) concentrations. This has both direct and indirect effects on oocyte quality and survival. When oocytes are forced to depend highly on the use of energy resources derived from body reserves, mainly NEFA, their development is compromised due to a modification in mitochondrial β-oxidation. Furthermore, the indirect effect of NEB on reproduction is mediated by a hormonal (both metabolic and reproductive) environment. Some authors have attempted to overcome the NEB by providing the oocyte with external sources of energy via dietary fat. Conversely, fertility is affected by a large number of genes, each with small individual effects, and thus it is unlikely that the decline in reproductive function has been directly caused by genetic selection for milk yield per se. It is more likely that the decline is the consequence of a combination of homeorhetic mechanisms (giving priority to milk over other functions) and increased metabolic pressure (due to a shortage of nutrients) with increasing milk yields. Nevertheless, genetics is an important component of reproductive efficiency, and the incorporation of genomic information is allowing the detection of genetic defects, degree of inbreeding and specific single nucleotide polymorphisms directly associated with reproduction, providing pivotal information for genetic selection programs. Furthermore, focusing on improving bull fertility in gene selection programs may represent an interesting opportunity. Conversely, the reproductive function of a given cow depends on the interaction between her genetic background and her environment, which ultimately modulates gene expression. Among the mechanisms modulating gene expression, microRNAs (miRNAs) and epigenetics seem to be most relevant. Several miRNAs have been described to play active roles in both ovarian and testicular function, and epigenetic effects have been described as a consequence of the nutrient supply and hormonal signals to which the offspring was exposed at specific stages during development. For example, there are differences in the epigenome of cows born to heifers and those born to cows, and this epigenome seems to be sensitive to the availability of methyl donor compounds of the dam. Lastly, recent studies in other species have shown the relevance of paternal epigenetic marks, but this aspect has been, until now, largely overlooked in dairy cattle.
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Gao N, Teng J, Ye S, Yuan X, Huang S, Zhang H, Zhang X, Li J, Zhang Z. Genomic Prediction of Complex Phenotypes Using Genic Similarity Based Relatedness Matrix. Front Genet 2018; 9:364. [PMID: 30233646 PMCID: PMC6127733 DOI: 10.3389/fgene.2018.00364] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 08/21/2018] [Indexed: 11/13/2022] Open
Abstract
In the last years, a series of methods for genomic prediction (GP) have been established, and the advantages of GP over pedigree best linear unbiased prediction (BLUP) have been reported. However, the majority of previously proposed GP models are purely based on mathematical considerations while seldom take the abundant biological knowledge into account. Prediction ability of those models largely depends on the consistency between the statistical assumptions and the underlying genetic architectures of traits of interest. In this study, gene annotation information was incorporated into GP models by constructing haplotypes with SNPs mapped to genic regions. Haplotype allele similarity between pairs of individuals was measured through different approaches at single gene level and then converted into whole genome level, which was then treated as a special kernel and used in kernel based GP models. Results shown that the gene annotation guided methods gave higher or at least comparable predictive ability in some traits, especially in the Arabidopsis dataset and the rice breeding population. Compared to SNP models and haplotype models without gene annotation, the gene annotation based models improved the predictive ability by 0.56~26.67% in the Arabidopsis and 1.62~16.53% in the rice breeding population, respectively. However, incorporating gene annotation slightly improved the predictive ability for several traits but did not show any extra gain for the rest traits in a chicken population. In conclusion, integrating gene annotation into GP models could be beneficial for some traits, species, and populations compared to SNP models and haplotype models without gene annotation. However, more studies are yet to be conducted to implicitly investigate the characteristics of these gene annotation guided models.
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Affiliation(s)
- Ning Gao
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Jinyan Teng
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Shaopan Ye
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Xiaolong Yuan
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Shuwen Huang
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Hao Zhang
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Xiquan Zhang
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Jiaqi Li
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Zhe Zhang
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
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Rezende FM, Dietsch GO, Peñagaricano F. Genetic dissection of bull fertility in US Jersey dairy cattle. Anim Genet 2018; 49:393-402. [PMID: 30109710 PMCID: PMC6175157 DOI: 10.1111/age.12710] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2018] [Indexed: 02/06/2023]
Abstract
The service sire has been recognized as an important factor affecting herd fertility in dairy cattle. Recent studies suggest that genetic factors explain part of the difference in fertility among Holstein sires. The main objective of this study was to dissect the genetic architecture of sire fertility in US Jersey cattle. The dataset included 1.5 K Jersey bulls with sire conception rate (SCR) records and 96 K single nucleotide polymorphism (SNP) markers spanning the whole genome. The analysis included whole‐genome scans for both additive and non‐additive effects and subsequent functional enrichment analyses using KEGG Pathway, Gene Ontology (GO) and Medical Subject Headings (MeSH) databases. Ten genomic regions located on eight different chromosomes explained more than 0.5% of the additive genetic variance for SCR. These regions harbor genes, such as PKDREJ,EPB41L2,PDGFD,STX2,SLC25A20 and IP6K1, that are directly implicated in testis development and spermatogenesis, sperm motility and the acrosome reaction. In addition, the genomic scan for non‐additive effects identified two regions on BTA11 and BTA25 with marked recessive effects. These regions harbor three genes—FER1L5,CNNM4 and DNAH3—with known roles in sperm biology. Moreover, the gene‐set analysis revealed terms associated with calcium regulation and signaling, membrane fusion, sperm cell energy metabolism, GTPase activity and MAPK signaling. These gene sets are directly implicated in sperm physiology and male fertility. Overall, this integrative genomic study unravels genetic variants and pathways affecting Jersey bull fertility. These findings may contribute to the development of novel genomic strategies for improving sire fertility in Jersey cattle.
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Affiliation(s)
- F M Rezende
- Department of Animal Sciences, University of Florida, Gainesville, FL, 32611, USA.,Faculdade de Medicina Veterinária, Universidade Federal de Uberlândia, Uberlândia, MG, 38400-902, Brazil
| | - G O Dietsch
- Department of Animal Sciences, University of Florida, Gainesville, FL, 32611, USA
| | - F Peñagaricano
- Department of Animal Sciences, University of Florida, Gainesville, FL, 32611, USA.,University of Florida Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
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Abstract
The ability to predict the fertility of bulls before semen is released into the field has been a long-term objective of the animal breeding industry. However, the recent shift in the dairy industry towards the intensive use of young genomically selected bulls has increased its urgency. Such bulls, which are often in the highest demand, are frequently only used intensively for one season and consequently there is limited time to track their field fertility. A more pressing issue is that they produce fewer sperm per ejaculate than mature bulls and therefore there is a need to reduce the sperm number per straw to the minimum required without a concomitant reduction in fertility. However, as individual bulls vary in the minimum number of sperm required to achieve their maximum fertility, this cannot be currently achieved without extensive field-testing. Although an in vitro semen quality test, or combination of tests, which can accurately and consistently determine a bull's fertility and the optimum sperm number required represent the 'holy grail' in terms of semen assessment, this has not been achieved to date. Understanding the underlying causes of variation in bull fertility is a key prerequisite to achieving this goal. In this review, we consider the reliability of sire conception rate estimates and then consider where along the pregnancy establishment axis the variation in reproductive loss between bulls occurs. We discuss the aetiology of these deficiencies in sperm function and propose avenues for future investigation.
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Abstract
Fertility is one of the most economically important traits in both beef and dairy cattle production; however, only female fertility is typically subjected to selection. Male and female fertility have only a small positive genetic correlation which is likely due to the existence of a relatively small number of genetic variants within each breed that cause embryonic and developmental losses. Genomic tools have been developed that allow the identification of lethal recessive loci based upon marker haplotypes. Selection against haplotypes harbouring lethal alleles in conjunction with selection to improve female fertility will result in an improvement in male fertility. Genomic selection has resulted in a two to fourfold increase in the rate of genetic improvement of most dairy traits in US Holstein cattle, including female fertility. Considering the rapidly increasing rate of adoption of high-throughput single nucleotide polymorphism genotyping in both the US dairy and beef industries, genomic selection should be the most effective of all currently available approaches to improve male fertility. However, male fertility phenotypes are not routinely recorded in natural service mating systems and when artificial insemination is used, semen doses may be titrated to lower post-thaw progressively motile sperm numbers for high-merit and high-demand bulls. Standardization of sperm dosages across bull studs for semen distributed from young bulls would allow the capture of sire conception rate phenotypes for young bulls that could be used to generate predictions of genetic merit for male fertility in both males and females. These data would allow genomic selection to be implemented for male fertility in addition to female fertility within the US dairy industry. While the rate of use of artificial insemination is much lower within the US beef industry, the adoption of sexed semen in the dairy industry has allowed dairy herds to select cows from which heifer replacements are produced and cows that are used to produce terminal crossbred bull calves sired by beef breed bulls. Capture of sire conception rate phenotypes in dairy herds utilizing sexed semen will contribute data enabling genomic selection for male fertility in beef cattle breeds. As the commercial sector of the beef industry increasingly adopts fixed-time artificial insemination, sire conception rate phenotypes can be captured to facilitate the development of estimates of genetic merit for male fertility within US beef breeds.
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Nicolini P, Amorín R, Han Y, Peñagaricano F. Whole-genome scan reveals significant non-additive effects for sire conception rate in Holstein cattle. BMC Genet 2018; 19:14. [PMID: 29486732 PMCID: PMC5830072 DOI: 10.1186/s12863-018-0600-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 02/21/2018] [Indexed: 01/04/2023] Open
Abstract
Background Service sire has a considerable impact on reproductive success in dairy cattle. Most gene mapping studies for bull fertility have focused on additive effects, while non-additive effects have been largely ignored. The main goal of this study was to assess the relevance of non-additive effects on Sire Conception Rate (SCR) in Holstein dairy cattle. The analysis included 7.5 k Holstein bulls with both SCR records and 57.8 k single nucleotide polymorphism (SNP) markers spanning the entire genome. Results The importance of non-additive effects was evaluated using an efficient two-step mixed model-based approach. Four genomic regions located on chromosomes BTA8, BTA9, BTA13 and BTA17 showed marked dominance and/or recessive effects. Most of these regions harbor genes, such as ADAM28, DNAJA1, TBC1D20, SPO11, PIWIL3 and TMEM119, that are directly implicated in testis development, male germ line maintenance, and sperm maturation. Conclusions This study provides further evidence for the relevance of non-additive effects in fitness-related traits, such as male fertility. In addition, these findings may point out new strategies for improving service sire fertility in dairy cattle via marker-assisted selection.
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Affiliation(s)
- Paula Nicolini
- Department of Animal Sciences, University of Florida, 2250 Shealy Drive, Gainesville, FL, 32611, USA.,Polo de Desarrollo Universitario, Universidad de la República, Tacuarembó, Uruguay
| | - Rocío Amorín
- Department of Animal Sciences, University of Florida, 2250 Shealy Drive, Gainesville, FL, 32611, USA
| | - Yi Han
- Department of Animal Sciences, University of Florida, 2250 Shealy Drive, Gainesville, FL, 32611, USA
| | - 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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