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Haque MA, Lee YM, Ha JJ, Jin S, Park B, Kim NY, Won JI, Kim JJ. Genome-wide association study identifies genomic regions associated with key reproductive traits in Korean Hanwoo cows. BMC Genomics 2024; 25:496. [PMID: 38778305 PMCID: PMC11112828 DOI: 10.1186/s12864-024-10401-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 05/09/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Conducting genome-wide association studies (GWAS) for reproductive traits in Hanwoo cattle, including age at first calving (AFC), calving interval (CI), gestation length (GL), and number of artificial inseminations per conception (NAIPC), is of paramount significance. These analyses provided a thorough exploration of the genetic basis of these traits, facilitating the identification of key markers for targeted trait improvement. Breeders can optimize their selection strategies, leading to more efficient and sustainable breeding programs, by incorporating genetic insights. This impact extends beyond individual traits and contributes to the overall productivity and profitability of the Hanwoo beef cattle industry. Ultimately, GWAS is essential in ensuring the long-term genetic resilience and adaptability of Hanwoo cattle populations. The primary goal of this study was to identify significant single nucleotide polymorphisms (SNPs) or quantitative trait loci (QTLs) associated with the studied reproductive traits and subsequently map the underlying genes that hold promise for trait improvement. RESULTS A genome-wide association study of reproductive traits identified 68 significant single nucleotide polymorphisms (SNPs) distributed across 29 Bos taurus autosomes (BTA). Among them, BTA14 exhibited the highest number of identified SNPs (25), whereas BTA6, BTA7, BTA8, BTA10, BTA13, BTA17, and BTA20 exhibited 8, 5, 5, 3, 8, 2, and 12 significant SNPs, respectively. Annotation of candidate genes within a 500 kb region surrounding the significant SNPs led to the identification of ten candidate genes relevant to age at first calving. These genes were: FANCG, UNC13B, TESK1, TLN1, and CREB3 on BTA8; FAM110B, UBXN2B, SDCBP, and TOX on BTA14; and MAP3K1 on BTA20. Additionally, APBA3, TCF12, and ZFR2, located on BTA7 and BTA10, were associated with the calving interval; PAX1, SGCD, and HAND1, located on BTA7 and BTA13, were linked to gestation length; and RBM47, UBE2K, and GPX8, located on BTA6 and BTA20, were linked to the number of artificial inseminations per conception in Hanwoo cows. CONCLUSIONS The findings of this study enhance our knowledge of the genetic factors that influence reproductive traits in Hanwoo cattle populations and provide a foundation for future breeding strategies focused on improving desirable traits in beef cattle. This research offers new evidence and insights into the genetic variants and genome regions associated with reproductive traits and contributes valuable information to guide future efforts in cattle breeding.
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Affiliation(s)
- Md Azizul Haque
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, Korea
| | - Yun-Mi Lee
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, Korea
| | - Jae-Jung Ha
- Gyeongbuk Livestock Research Institute, Yeongju, 36052, Korea
| | - Shil Jin
- Hanwoo Research Institute, National Institute of Animal Science, Pyeongchang, 25340, Korea
| | - Byoungho Park
- Hanwoo Research Institute, National Institute of Animal Science, Pyeongchang, 25340, Korea
| | - Nam-Young Kim
- Hanwoo Research Institute, National Institute of Animal Science, Pyeongchang, 25340, Korea
| | - Jeong-Il Won
- Hanwoo Research Institute, National Institute of Animal Science, Pyeongchang, 25340, Korea.
| | - Jong-Joo Kim
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, Korea.
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Haque MA, Lee YM, Ha JJ, Jin S, Park B, Kim NY, Won JI, Kim JJ. Genomic Predictions in Korean Hanwoo Cows: A Comparative Analysis of Genomic BLUP and Bayesian Methods for Reproductive Traits. Animals (Basel) 2023; 14:27. [PMID: 38200758 PMCID: PMC10778388 DOI: 10.3390/ani14010027] [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: 11/03/2023] [Revised: 12/07/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
This study aimed to predict the accuracy of genomic estimated breeding values (GEBVs) for reproductive traits in Hanwoo cows using the GBLUP, BayesB, BayesLASSO, and BayesR methods. Accuracy estimates of GEBVs for reproductive traits were derived through fivefold cross-validation, analyzing a dataset comprising 11,348 animals and employing an Illumina Bovine 50K SNP chip. GBLUP showed an accuracy of 0.26 for AFC, while BayesB, BayesLASSO, and BayesR demonstrated values of 0.28, 0.29, and 0.29, respectively. For CI, GBLUP attained an accuracy of 0.19, whereas BayesB, BayesLASSO, and BayesR scored 0.21, 0.24, and 0.25, respectively. The accuracy for GL was uniform across GBLUP, BayesB, and BayesR at 0.31, whereas BayesLASSO showed a slightly higher accuracy of 0.33. For NAIPC, GBLUP showed an accuracy of 0.24, while BayesB, BayesLASSO, and BayesR recorded 0.22, 0.27, and 0.30, respectively. The variation in genomic prediction accuracy among methods indicated Bayesian approaches slightly outperformed GBLUP. The findings suggest that Bayesian methods, notably BayesLASSO and BayesR, offer improved predictive capabilities for reproductive traits. Future research may explore more advanced genomic approaches to enhance predictive accuracy and genetic gains in Hanwoo cattle breeding programs.
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Affiliation(s)
- Md Azizul Haque
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea; (M.A.H.); (Y.-M.L.)
| | - Yun-Mi Lee
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea; (M.A.H.); (Y.-M.L.)
| | - Jae-Jung Ha
- Gyeongbuk Livestock Research Institute, Yeongju 36052, Republic of Korea;
| | - Shil Jin
- Hanwoo Research Institute, National Institute of Animal Science, Pyeongchang 25340, Republic of Korea; (S.J.); (B.P.); (N.-Y.K.)
| | - Byoungho Park
- Hanwoo Research Institute, National Institute of Animal Science, Pyeongchang 25340, Republic of Korea; (S.J.); (B.P.); (N.-Y.K.)
| | - Nam-Young Kim
- Hanwoo Research Institute, National Institute of Animal Science, Pyeongchang 25340, Republic of Korea; (S.J.); (B.P.); (N.-Y.K.)
| | - Jeong-Il Won
- Hanwoo Research Institute, National Institute of Animal Science, Pyeongchang 25340, Republic of Korea; (S.J.); (B.P.); (N.-Y.K.)
| | - Jong-Joo Kim
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea; (M.A.H.); (Y.-M.L.)
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3
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Read CC, Edwards JL, Schrick FN, Rhinehart JD, Payton RR, Campagna SR, Castro HF, Klabnik JL, Moorey SE. Preovulatory serum estradiol concentration is positively associated with oocyte ATP and follicular fluid metabolite abundance in lactating beef cattle. J Anim Sci 2022; 100:6620784. [PMID: 35772749 PMCID: PMC9246671 DOI: 10.1093/jas/skac136] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/08/2022] [Indexed: 12/13/2022] Open
Abstract
Cattle induced to ovulate a small, physiologically immature preovulatory follicle had reduced oocyte developmental competence that resulted in decreased embryo cleavage and day 7 embryo quality compared with animals induced to ovulate a more advanced follicle. RNA-sequencing was performed on oocytes and their corresponding cumulus cells approximately 23 h after gonadotropin-releasing hormone (GnRH) administration to induce the preovulatory gonadotropin surge suggested reduced capacity for glucose metabolism and oxidative phosphorylation in the cumulus cells and oocytes from follicles ≤11.7 mm, respectively. We hypothesized that induced ovulation of a small, physiologically immature preovulatory follicle results in a suboptimal follicular microenvironment and reduced oocyte metabolic capacity. We performed a study with the objective to determine the impact of preovulatory follicle diameter and serum estradiol concentration at GnRH administration on oocyte metabolic competence and follicular fluid metabolome profiles. We synchronized the development of a preovulatory follicle and collected the follicle contents via transvaginal aspiration approximately 19 h after GnRH administration in lactating beef cows (n = 319). We determined ATP levels and mitochondrial DNA (mtDNA) copy number in 110 oocytes and performed ultra-high-performance liquid chromatography–high resolution mass spectrometry metabolomic studies on 45 follicular fluid samples. Intraoocyte ATP and the amount of ATP produced per mtDNA copy number were associated with serum estradiol concentration at GnRH and time from GnRH administration to follicle aspiration (P < 0.05). mtDNA copy number was not related to follicle diameter at GnRH, serum estradiol concentration at GnRH, or any potential covariates (P > 0.10). We detected 90 metabolites in the aspirated follicular fluid. We identified 22 metabolites associated with serum estradiol concentration at GnRH and 63 metabolites associated with follicular fluid progesterone concentration at the time of follicle aspiration (FDR < 0.10). Pathway enrichment analysis of significant metabolites suggested altered proteinogenesis, citric acid cycle, and pyrimidine metabolism in follicles of reduced estrogenic capacity pre-gonadotropin surge or reduced progesterone production by the time of follicle aspiration.
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Affiliation(s)
- Casey C Read
- Department of Animal Science, University of Tennessee, Knoxville, TN 37996, USA
| | - J Lannett Edwards
- Department of Animal Science, University of Tennessee, Knoxville, TN 37996, USA
| | - F Neal Schrick
- Department of Animal Science, University of Tennessee, Knoxville, TN 37996, USA
| | - Justin D Rhinehart
- Department of Animal Science, University of Tennessee, Knoxville, TN 37996, USA
| | - Rebecca R Payton
- Department of Animal Science, University of Tennessee, Knoxville, TN 37996, USA
| | - Shawn R Campagna
- Department of Chemistry, University of Tennessee, Knoxville, TN 37996, USA
| | - Hector F Castro
- Department of Chemistry, University of Tennessee, Knoxville, TN 37996, USA
| | - Jessica L Klabnik
- Department of Animal Science, University of Tennessee, Knoxville, TN 37996, USA
| | - Sarah E Moorey
- Department of Animal Science, University of Tennessee, Knoxville, TN 37996, USA
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Correlation between Pre-Ovulatory Follicle Diameter and Follicular Fluid Metabolome Profiles in Lactating Beef Cows. Metabolites 2021; 11:metabo11090623. [PMID: 34564438 PMCID: PMC8471867 DOI: 10.3390/metabo11090623] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/10/2021] [Accepted: 09/11/2021] [Indexed: 01/01/2023] Open
Abstract
Induced ovulation of small pre-ovulatory follicles reduced pregnancy rates, embryo survival, day seven embryo quality, and successful embryo cleavage in beef cows undergoing fixed-time artificial insemination. RNA-sequencing of oocytes and associated cumulus cells collected from pre-ovulatory follicles 23 h after gonadotropin-releasing hormone (GnRH) administration to induce the pre-ovulatory gonadotropin surge suggested reduced capacity for glucose metabolism in cumulus cells of follicles ≤11.7 mm. We hypothesized that the follicular fluid metabolome influences metabolic capacity of the cumulus-oocyte complex and contributes to reduced embryo cleavage and quality grade observed following induced ovulation of small follicles. Therefore, we performed a study to determine the correlation between pre-ovulatory follicle diameter and follicular fluid metabolome profiles in lactating beef cows (Angus, n = 130). We synchronized the development of a pre-ovulatory follicle and collected the follicular contents approximately 20 h after GnRH administration. We then performed ultra-high performance liquid chromatography-high resolution mass spectrometry (UHPLC-HRMS) metabolomic studies on 43 follicular fluid samples and identified 38 metabolites within pre-ovulatory follicles of increasing size. We detected 18 metabolites with a significant, positive correlation to follicle diameter. Individual and pathway enrichment analysis of significantly correlated metabolites suggest that altered glucose and amino acid metabolism likely contribute to reduced developmental competence of oocytes when small pre-ovulatory follicles undergo induced ovulation.
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5
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Devani K, Valente TS, Crowley JJ, Orsel K. Development of optimal genetic evaluations for teat and udder structure in Canadian Angus cattle. J Anim Sci 2019; 97:4445-4452. [PMID: 31598680 PMCID: PMC6827401 DOI: 10.1093/jas/skz314] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 10/03/2019] [Indexed: 11/30/2022] Open
Abstract
Despite their heritability and influence on female productivity, there are currently no genetic evaluations for teat and udder structure in Canadian Angus cattle. The objective of this study was to develop optimal genetic evaluations for these traits in the Canadian Angus population. Guidelines recommended by Beef Improvement Federation (BIF) were used to score teat and udder structure in 1,735 Canadian Angus cows from 10 representative herds. Cows scored ranged in parity from 1 to 13; however, >70% of cows were parity ≤4. Scores ranged from 1 (large, bottle shaped) to 9 (very small) for teats and from 1 (very pendulous) to 9 (very tight) for udders. Consistent with parity distribution, >70% of teat and udder scores were ≥6. Teat and udder scores (TS9 and US9, respectively) were modeled using a multiple trait animal model with random effects of contemporary group (herd-year-season) and additive genetic effect, and fixed effects of breed, parity group, and days between calving and scoring. To test good versus poor structure, a binary classification of 1 or 2 (TS2, US2) [comprised of scores 1 to 5 = 1 (poor structure) and scores 6 to 9 = 2 (good structure)] was created. Further, to assess the impact of grouping less frequently observed poor scores, a 1 to 7 scale (TS7, US7) was created by combining teat and udder scores 1 to 3. Analyses for teat and udder scores on scales TS9, US9, TS7, US7, and TS2, US2 were compared. In addition, both threshold and linear animal models were used to estimate variance components for the traits. Data treatment and models were evaluated based on correlation of resulting estimated breeding value (EBV) with corrected phenotypes, Spearman's rank correlation coefficient, average EBV accuracies (r), and deviance information criteria (DIC). TS9, US9 scales for teat and udder scores and linear models performed best. Estimates of heritability (SE) for teat and udder score were 0.32 (0.06) and 0.15 (0.04), respectively, indicating these traits were moderately heritable and that genetic improvement for teat and udder scores was possible. Estimates of phenotypic and genotypic correlations for teat and udder score were 0.46 (0.02) and 0.71 (0.09), respectively. Estimates of genotypic correlations with birth weight (BW), weaning weight (WW), and yearling weight (YW), ranged from -0.04 (0.10) to -0.20 (0.12), verifying the importance of selecting for improved teat and udder score as individual traits, alongside performance traits.
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Affiliation(s)
- Kajal Devani
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, Canada
| | - Tiago S Valente
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
| | - John J Crowley
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
- AbacusBio International Ltd, Roslin Innovation Centre, East Bush, Midlothian, Edinburgh, UK
| | - Karin Orsel
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, Canada
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6
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Dickinson SE, Elmore MF, Kriese-Anderson L, Elmore JB, Walker BN, Dyce PW, Rodning SP, Biase FH. Evaluation of age, weaning weight, body condition score, and reproductive tract score in pre-selected beef heifers relative to reproductive potential. J Anim Sci Biotechnol 2019; 10:18. [PMID: 30891236 PMCID: PMC6390375 DOI: 10.1186/s40104-019-0329-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 01/28/2019] [Indexed: 12/24/2022] Open
Abstract
Background Artificial insemination is a preferred breeding method for beef heifers as it advances the genetic background, produces a predictive and profitable calving season, and extends the heifer's reproductive life span. As reproductive efficiency in heifers is key for the success of beef cattle production systems, following artificial insemination, heifers are exposed to a bull for the remainder of the breeding season. Altogether, up to 95% of heifers might become pregnant in their first breeding season. Heifers that do not become pregnant at the end of the breeding season represent an irreparable economical loss. Additionally, heifers conceiving late in the breeding season to natural service, although acceptable, poses serious losses to producers. To minimize losses due to reproductive failure, different phenotypic parameters can be assessed and utilized as selection tools. Here, we tested the hypothesis that in a group of pre-selected heifers, records of weaning weight, age at weaning, age at artificial insemination, and age of dam differ among heifers of varied reproductive outcomes during the first breeding season. Results None of the parameters tested presented predictive ability to discriminate the heifers based on the response variable ('pregnant to artificial insemination', 'pregnant to natural service', 'not pregnant'). Heifers categorized with body condition score = 6 and reproductive tract score ≥ 4 had the greatest proportion of pregnancy to artificial insemination (49% and 44%, respectively). Furthermore, it was notable that heifers presenting body condition score = 6 and reproductive tract score = 5 presented the greatest pregnancy rate at end of the breeding season (89%). Heifers younger than 368 d at the start of the breeding season did not become pregnant to artificial insemination. Those young heifers had 12.5% chance to become pregnant in their first breeding season, compared to 87.5% if the heifers were older than 368 days. Conclusion Our results suggest that beef heifers with body condition score = 6 and reproductive tract score ≥ 4 are more likely to become pregnant to artificial insemination. Careful assessment should be undertaken when developing replacement heifers that will not reach 12 months of age by the beginning of the breeding season.
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Affiliation(s)
- Sarah E Dickinson
- 1Department of Animal Sciences, Auburn University, 559 Devall Dr, Auburn, AL 36839 USA
| | - Michelle F Elmore
- 1Department of Animal Sciences, Auburn University, 559 Devall Dr, Auburn, AL 36839 USA.,Alabama Cooperative Extension System, Auburn, AL USA
| | - Lisa Kriese-Anderson
- 1Department of Animal Sciences, Auburn University, 559 Devall Dr, Auburn, AL 36839 USA
| | | | - Bailey N Walker
- 1Department of Animal Sciences, Auburn University, 559 Devall Dr, Auburn, AL 36839 USA
| | - Paul W Dyce
- 1Department of Animal Sciences, Auburn University, 559 Devall Dr, Auburn, AL 36839 USA
| | - Soren P Rodning
- 1Department of Animal Sciences, Auburn University, 559 Devall Dr, Auburn, AL 36839 USA
| | - Fernando H Biase
- 1Department of Animal Sciences, Auburn University, 559 Devall Dr, Auburn, AL 36839 USA
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7
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Toghiani S, Hay E, Sumreddee P, Geary TW, Rekaya R, Roberts AJ. Genomic prediction of continuous and binary fertility traits of females in a composite beef cattle breed. J Anim Sci 2018; 95:4787-4795. [PMID: 29293708 DOI: 10.2527/jas2017.1944] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Reproduction efficiency is a major factor in the profitability of the beef cattle industry. Genomic selection (GS) is a promising tool that may improve the predictive accuracy and genetic gain of fertility traits. There is a wide range of traits used to measure fertility in dairy and beef cattle including continuous (days open), discrete (pregnancy status), and count (number of inseminations) responses. In this study, a joint analysis of age of puberty (AOP), age at first calving (AOC), and the heifer pregnancy status (HPS) was performed. Data used in this study consisted of records from 1,365 Composite Gene Combination (CGC; 50% Red Angus, 25% Charolais, 25% Tarentaise) first parity females born between 2002 and 2011. The pedigree file included 5,374 animals. A total of 3,902 animals were genotyped with different density SNP chips (3K to 50K SNP). Animals genotyped with low-density arrays were imputed to higher density (BovineSNP50 BeadChip) using FImpute. Data were analyzed using univariate and multivariate classical quantitative models (pedigree based) and univariate genomic approaches. For the latter, 3 different Bayesian methods (BayesA, BayesB, and BayesCπ) were implemented and compared. Estimates of heritabilities using univariate and multivariate analyses based on pedigree relationships ranged between 0.03 (for AOC) to 0.2 (AOP). Heritability of pregnancy status was 0.15 and 0.09 using the univariate and multivariate analyses, respectively. Genetic correlation between pregnancy status and the other 2 traits was low being 0.08 with age at puberty and -0.10 with age at first calving. Heritability estimates were slightly higher using genomic rather than average additive relationships. The accuracy of genomic prediction was similar across the 3 Bayesian methods with higher accuracies for age of puberty than the age at first calving likely due to the higher heritability of the former. The prediction of the binary pregnancy status measured using the area under the curve increased by 27% to 29% compared to a random classifier. Due to the small size of the data, all estimates have large posterior standard deviations and results should be interpreted with caution.
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8
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de Tarso SGS, Gastal GDA, Bashir ST, Gastal MO, Apgar GA, Gastal EL. Follicle vascularity coordinates corpus luteum blood flow and progesterone production. Reprod Fertil Dev 2018; 29:448-457. [PMID: 28442057 DOI: 10.1071/rd15223] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 07/24/2015] [Indexed: 11/23/2022] Open
Abstract
Colour Doppler ultrasonography was used to compare the ability of preovulatory follicle (POF) blood flow and its dimensions to predict the size, blood flow and progesterone production capability of the subsequent corpus luteum (CL). Cows (n=30) were submitted to a synchronisation protocol. Follicles ≥7mm were measured and follicular wall blood flow evaluated every 12h for approximately 3.5 days until ovulation. After ovulation, cows were scanned daily for 8 days and similar parameters were evaluated for the CL. Blood samples were collected and plasma progesterone concentrations quantified. All parameters were positively correlated. Correlation values ranged from 0.26 to 0.74 on data normalised to ovulation and from 0.31 to 0.74 on data normalised to maximum values. Correlations between calculated ratios of both POF and CL in data normalised to ovulation and to maximum values ranged from moderate (0.57) to strong (0.87). Significant (P<0.0001) linear regression analyses were seen in all comparisons. In conclusion, higher correlations were observed between the dimensions of POF and/or CL and blood flow of both structures, as well as POF and/or CL blood flow with plasma progesterone concentrations of the resultant CL. These findings indicate that follicle vascularity coordinates CL blood flow and progesterone production in synchronised beef cows.
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Affiliation(s)
- S G S de Tarso
- Department of Animal Science, Food and Nutrition, Southern Illinois University, 1205 Lincoln Drive, MC 4417, Carbondale, IL 62901, USA
| | - G D A Gastal
- Department of Animal Science, Food and Nutrition, Southern Illinois University, 1205 Lincoln Drive, MC 4417, Carbondale, IL 62901, USA
| | - S T Bashir
- Department of Animal Science, Food and Nutrition, Southern Illinois University, 1205 Lincoln Drive, MC 4417, Carbondale, IL 62901, USA
| | - M O Gastal
- Department of Animal Science, Food and Nutrition, Southern Illinois University, 1205 Lincoln Drive, MC 4417, Carbondale, IL 62901, USA
| | - G A Apgar
- Department of Animal Science, Food and Nutrition, Southern Illinois University, 1205 Lincoln Drive, MC 4417, Carbondale, IL 62901, USA
| | - E L Gastal
- Department of Animal Science, Food and Nutrition, Southern Illinois University, 1205 Lincoln Drive, MC 4417, Carbondale, IL 62901, USA
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9
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Dickinson SE, Griffin BA, Elmore MF, Kriese-Anderson L, Elmore JB, Dyce PW, Rodning SP, Biase FH. Transcriptome profiles in peripheral white blood cells at the time of artificial insemination discriminate beef heifers with different fertility potential. BMC Genomics 2018; 19:129. [PMID: 29426285 PMCID: PMC5807776 DOI: 10.1186/s12864-018-4505-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 01/29/2018] [Indexed: 11/21/2022] Open
Abstract
Background Infertility is a longstanding limitation in livestock production with important economic impact for the cattle industry. Female reproductive traits are polygenic and lowly heritable in nature, thus selection for fertility is challenging. Beef cattle operations leverage estrous synchronization in combination with artificial insemination (AI) to breed heifers and benefit from an early and uniform calving season. A couple of weeks following AI, heifers are exposed to bulls for an opportunity to become pregnant by natural breeding (NB), but they may also not become pregnant during this time period. Focusing on beef heifers, in their first breeding season, we hypothesized that: a- at the time of AI, the transcriptome of peripheral white blood cells (PWBC) differs between heifers that become pregnant to AI and heifers that become pregnant late in the breeding season by NB or do not become pregnant during the breeding season; and b- the ratio of transcript abundance between genes in PWBC classifies heifers according to pregnancy by AI, NB, or failure to become pregnant. Results We generated RNA-sequencing data from 23 heifers from two locations (A: six AI-pregnant and five NB-pregnant; and B: six AI-pregnant and six non-pregnant). After filtering out lowly expressed genes, we quantified transcript abundance for 12,538 genes. The comparison of gene expression levels between AI-pregnant and NB-pregnant heifers yielded 18 differentially expressed genes (DEGs) (ADAM20, ALDH5A1, ANG, BOLA-DQB, DMBT1, FCER1A, GSTM3, KIR3DL1, LOC107131247, LOC618633, LYZ, MNS1, P2RY12, PPP1R1B, SIGLEC14, TPPP, TTLL1, UGT8, eFDR≤0.02). The comparison of gene expression levels between AI-pregnant and non-pregnant heifers yielded six DEGs (ALAS2, CNKSR3, LOC522763, SAXO2, TAC3, TFF2, eFDR≤0.05). We calculated the ratio of expression levels between all gene pairs and assessed their potential to classify samples according to experimental groups. Considering all samples, relative expression from two gene pairs correctly classified 10 out of 12 AI-pregnant heifers (P = 0.0028) separately from the other 11 heifers (NB-pregnant, or non-pregnant). Conclusion The transcriptome profile in PWBC, at the time of AI, is associated with the fertility potential of beef heifers. Transcript levels of specific genes may be further explored as potential classifiers, and thus selection tools, of heifer fertility. Electronic supplementary material The online version of this article (10.1186/s12864-018-4505-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sarah E Dickinson
- Department of Animal Sciences, Auburn University, 559 Devall Dr, Auburn, AL, 36839, USA.,Alabama Cooperative Extension System, Auburn, AL, USA
| | - Brock A Griffin
- Department of Animal Sciences, Auburn University, 559 Devall Dr, Auburn, AL, 36839, USA
| | - Michelle F Elmore
- Department of Animal Sciences, Auburn University, 559 Devall Dr, Auburn, AL, 36839, USA.,Alabama Cooperative Extension System, Auburn, AL, USA
| | - Lisa Kriese-Anderson
- Department of Animal Sciences, Auburn University, 559 Devall Dr, Auburn, AL, 36839, USA
| | | | - Paul W Dyce
- Department of Animal Sciences, Auburn University, 559 Devall Dr, Auburn, AL, 36839, USA
| | - Soren P Rodning
- Department of Animal Sciences, Auburn University, 559 Devall Dr, Auburn, AL, 36839, USA
| | - Fernando H Biase
- Department of Animal Sciences, Auburn University, 559 Devall Dr, Auburn, AL, 36839, USA.
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10
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Barbero M, Santos D, Takada L, de Camargo G, Freitas A, Diaz I, de Souza F, Tonhati H, Albuquerque L, Oliveira H. Prospecting polymorphisms in the PPP3CA and FABP4 genes and their association with early pregnancy probability in Nellore heifers. Livest Sci 2017. [DOI: 10.1016/j.livsci.2017.07.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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11
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Richardson BN, Hill SL, Stevenson JS, Djira GD, Perry GA. Expression of estrus before fixed-time AI affects conception rates and factors that impact expression of estrus and the repeatability of expression of estrus in sequential breeding seasons. Anim Reprod Sci 2016; 166:133-40. [DOI: 10.1016/j.anireprosci.2016.01.013] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 01/06/2016] [Accepted: 01/08/2016] [Indexed: 10/22/2022]
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Shorten PR, Morris CA, Cullen NG. The effects of age, weight, and sire on pregnancy rate in cattle. J Anim Sci 2016; 93:1535-45. [PMID: 26020175 DOI: 10.2527/jas.2014-8490] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The goal was to estimate the heritabilities and genetic variances for pregnancy rate (PR) and calving date (CD) in Angus cattle along with the effect of weight, age, and sire on PR and CD. The data consisted of 4,999 records on PR and CD. Statistical models included year as a fixed effect; premating/postmating weight and age as covariates; and sire of embryo, maternal grandsire (MGS), and permanent maternal environmental effects as random effects. The models also included the interactions between herd and weight (weight change). Direct and maternal effects on PR and CD were estimated using sire MGS and animal models in REML. Pregnancy rate increased from age 2 to 6 and decreased from age 7 to 11 (P < 0.01) and this effect was independent of the culling strategy. There was a quadratic effect of premating cow weight independent of age on PR, with lower PR for low weights (P < 0.01). Overall, cows with a premating weight of 550 kg had the greatest PR. Cows that lost weight during mating had lower PR (P < 0.01). The maternal additive heritability for PR was 0.001 ± 0.012 and the direct additive heritability was 0.024 ± 0.020. The ratio of permanent maternal environmental variance to phenotypic variance was significant (0.048 ± 0.017; P < 0.01). This demonstrates that permanent maternal environmental effects play a major role in the repeatability of PR (0.049 ± 0.015; P < 0.01). The maternal additive heritability for CD was 0.040 ± 0.022, and the direct additive heritability was 0.076 ± 0.045. The ratio of permanent maternal environmental variance to phenotypic variance was low (0.014 ± 0.017) and the repeatability for CD was significant (0.0544 ± 0.0180; P < 0.01). This suggests that maternal genetic effects are as important as direct genetic effects on CD. There was a positive quadratic relationship between premating cow weight and CD with delayed calving for low/high weights (P < 0.01). Cows that lost weight over mating also had a later CD (P < 0.01). Comparisons of a weight-selected herd to the control herd showed differences (P < 0.05) in the optimal premating weight for early calving (control, 480 kg, and weight selected, 615 kg). Calving date was also more sensitive to changes in weight over mating in the weight selection herd (P < 0.05). Therefore, the set point in the weight-fertility axis and the sensitivity of fertility to changes in weight both changed in the weight selection herd.
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Akanno EC, Plastow G, Fitzsimmons C, Miller SP, Baron V, Ominski K, Basarab JA. Genome-wide association for heifer reproduction and calf performance traits in beef cattle. Genome 2015; 58:549-57. [PMID: 26484575 DOI: 10.1139/gen-2015-0031] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The aim of this study was to identify SNP markers that associate with variation in beef heifer reproduction and performance of their calves. A genome-wide association study was performed by means of the generalized quasi-likelihood score (GQLS) method using heifer genotypes from the BovineSNP50 BeadChip and estimated breeding values for pre-breeding body weight (PBW), pregnancy rate (PR), calving difficulty (CD), age at first calving (AFC), calf birth weight (BWT), calf weaning weight (WWT), and calf pre-weaning average daily gain (ADG). Data consisted of 785 replacement heifers from three Canadian research herds, namely Brandon Research Centre, Brandon, Manitoba, University of Alberta Roy Berg Kinsella Ranch, Kinsella, Alberta, and Lacombe Research Centre, Lacombe, Alberta. After applying a false discovery rate correction at a 5% significance level, a total of 4, 3, 3, 9, 6, 2, and 1 SNPs were significantly associated with PBW, PR, CD, AFC, BWT, WWT, and ADG, respectively. These SNPs were located on chromosomes 1, 5-7, 9, 13-16, 19-21, 24, 25, and 27-29. Chromosomes 1, 5, and 24 had SNPs with pleiotropic effects. New significant SNPs that impact functional traits were detected, many of which have not been previously reported. The results of this study support quantitative genetic studies related to the inheritance of these traits, and provides new knowledge regarding beef cattle quantitative trait loci effects. The identification of these SNPs provides a starting point to identify genes affecting heifer reproduction traits and performance of their calves (BWT, WWT, and ADG). They also contribute to a better understanding of the biology underlying these traits and will be potentially useful in marker- and genome-assisted selection and management.
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Affiliation(s)
- Everestus C Akanno
- a Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Graham Plastow
- a Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Carolyn Fitzsimmons
- a Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.,b Lacombe Research Centre, Agriculture and Agri-Food Canada, 6000 C & E Trail, Lacombe, AB, Canada
| | - Stephen P Miller
- a Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.,e AgResearch Limited, Invermay Agricultural Centre, Mosgiel, New Zealand
| | - Vern Baron
- b Lacombe Research Centre, Agriculture and Agri-Food Canada, 6000 C & E Trail, Lacombe, AB, Canada
| | - Kimberly Ominski
- d Department of Animal Science, University of Manitoba, Winnipeg, MB, Canada
| | - John A Basarab
- a Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.,c Lacombe Research Centre, Alberta Agriculture and Rural Development, 6000 C & E Trail, Lacombe, AB, Canada
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Santana ML, Eler JP, Bignardi AB, Ferraz JBS. Two-trait random regression model to estimate the genetic association of scrotal circumference with female reproductive performance in Nelore cattle. Theriogenology 2015; 83:1534-40. [PMID: 25747195 DOI: 10.1016/j.theriogenology.2015.02.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 01/31/2015] [Accepted: 02/01/2015] [Indexed: 10/24/2022]
Abstract
In an attempt to determine when scrotal circumference (SC) could be a reasonable indicator of female reproductive performance, a series of two-trait random regression model (regression for SC on age at measurement) using Gibbs sampling was applied to field data of Nelore cattle raised in a tropical environment. The female traits evaluated were age at first calving (AFC), first calving interval (FCI), heifer pregnancy (HP), and stayability (STAY). The posterior means of heritability of female traits ranged from 0.15 for AFC to 0.46 for HP and were about 0.50 for SC. The posterior means of genetic correlations between SC and AFC, FCI, HP, STAY were up to -0.70, -0.25, 0.48, and 0.29, respectively. Genetically, SC could be a reasonable indicator of female puberty (e.g., HP) as long as it is measured at a young age (400-440 days). However, for female reproductive traits measured at an older age (e.g., STAY), SC is merely a modest or even poor indicator. The use of sire expected progeny differences for female reproductive traits will be more effective than the use of expected progeny differences for SC to improve the reproductive performance of female cattle.
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Affiliation(s)
- M L Santana
- Grupo de Melhoramento Animal de Mato Grosso (GMAT), Instituto de Ciências Agrárias e Tecnológicas, Campus Universitário de Rondonópolis, Universidade Federal de Mato Grosso, Rondonópolis, Mato Grosso, Brazil.
| | - J P Eler
- Grupo de Melhoramento Animal e Biotecnologia (GMAB), Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Medicina Veterinária, Universidade de São Paulo, Pirassununga, São Paulo, Brazil
| | - A B Bignardi
- Grupo de Melhoramento Animal de Mato Grosso (GMAT), Instituto de Ciências Agrárias e Tecnológicas, Campus Universitário de Rondonópolis, Universidade Federal de Mato Grosso, Rondonópolis, Mato Grosso, Brazil
| | - J B S Ferraz
- Grupo de Melhoramento Animal e Biotecnologia (GMAB), Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Medicina Veterinária, Universidade de São Paulo, Pirassununga, São Paulo, Brazil
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Incorporation of genetic technologies associated with applied reproductive technologies to enhance world food production. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 752:77-96. [PMID: 24170355 DOI: 10.1007/978-1-4614-8887-3_4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
Animal breeding and reproductive physiology have been closely related throughout the history of animal production science. Artificial insemination provides the best method of increasing the influence of sires with superior genetics to improve production traits. Multiple ovulation embryo transfer (MOET) provides some ability to increase the genetic influence of the maternal line as well. The addition of genetic technologies to this paradigm allows for improved methods of selecting sires and dams carrying the best genes for production and yield of edible products and resistance to diseases and parasites. However, decreasing the number of influential parents within a population also increases the risk of propagating a recessive gene that could negatively impact the species (Reprod Domest Anim 44:792-796, 2009; BMC Genomics 11:337, 2010). Furthermore, antagonistic genotypic relationships between production traits and fertility (Anim Prod Sci 49:399-412, 2009; Anim Genet 43:442-446, 2012) suggest that care must be taken to ensure that increasing the frequency of genes with a positive influence on production does not negatively impact the fertility of the replacement females entering the herd.
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Cushman RA, Allan MF, Thallman RM, Cundiff LV. Characterization of biological types of cattle (Cycle VII): Influence of postpartum interval and estrous cycle length on fertility12. J Anim Sci 2007; 85:2156-62. [PMID: 17504970 DOI: 10.2527/jas.2007-0136] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Genetic improvement in reproductive efficiency through selection is difficult because many reproductive traits are binomial and have low heritabilities. Before genetic markers can be generated for fertility in cows, greater characterization of reproductive phenotypes is needed to understand the components of the trait. The current study tested the hypotheses that: 1) breeds vary in postpartum interval to estrus (PPIE) and estrous cycle length, 2) a longer estrous cycle immediately before breeding increased pregnancy rates, and 3) a greater number of cycles before breeding increased conception rates. The postpartum interval to estrus, estrous cycle length, and number of cycles before breeding were examined in F1 cows (n = 519) obtained from mating Hereford, Angus, and MARC III cows to Hereford, Angus, Simmental, Limousin, Charolais, Gelbvieh, and Red Angus sires. Cows were classified as having 0, 1, 2, or 3 observed estrous cycles before breeding. All traits analyzed were adjusted to constant BCS. Sire breed of the cow influenced length of the PPIE and number of cycles before the start of breeding (P <0.001). Simmental-sired cows had the shortest PPIE and greatest number of cycles before breeding, whereas Limousin-sired cows had the longest PPIE and least number of cycles before breeding. Cows with a greater number of cycles before breeding did not have greater conception rates than cows that had not exhibited standing estrus before breeding (P = 0.87). In cows that cycled before breeding, the length of the estrous cycle immediately before breeding was influenced by dam breed and BCS (P <0.01). Cows out of Hereford dams had shorter estrous cycles than cows out of MARC III or Angus dams, and estrous cycle length increased as BCS increased. Conception rate decreased as length of the estrous cycle immediately before breeding increased (P = 0.05, -2.2% per d of cycle length). Therefore, previously anestrous cows were just as likely to conceive as cows that had cycled before breeding, and an increased number of observed estrous cycles before breeding did not increase conception rates. There may be an influence of the length of estrous cycle immediately before breeding on conception rates, possibly because a longer estrous cycle results in a persistent follicle with greater potential for a lower quality oocyte. Breed differences in PPIE and estrous cycle length suggest that there are genetic components to these traits.
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Affiliation(s)
- R A Cushman
- USDA, ARS, Roman L. Hruska US Meat Animal Research Center, Clay Center, NE 68933-0166, USA.
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