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Cao C, Zhou Q, Kang Y, Akhatayeva Z, Liu P, Bai Y, Li R, Jiang Y, Zhang Q, Lan X, Pan C. A repertoire of single nucleotide polymorphisms (SNPs) of major fecundity BMPR1B gene among 75 sheep breeds worldwide. Theriogenology 2024; 219:59-64. [PMID: 38401385 DOI: 10.1016/j.theriogenology.2024.02.019] [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: 09/09/2023] [Revised: 02/19/2024] [Accepted: 02/19/2024] [Indexed: 02/26/2024]
Abstract
The BMPR1B gene is a major determinant of sheep reproductive capacity. Previous studies revealed that Q249R (FecB) is a profound variant of BMPR1B that influences the ovulation rate and litter size in sheep. However, unlike Q249R locus, the full spectrum of single nucleotide polymorphisms (SNPs) within BMPR1B has not been extensively studied. A systematic screen of SNPs in BMPR1B would facilitate the discovery of novel variants that are associated with litter size. This study aimed to investigate SNPs in the BMPR1B gene via whole genome sequence (WGS) data from 2409 individuals of 75 sheep breeds worldwide. Herein, a total of 9688 variants were screened, among which 15 were coding variants and 8 were novel changes. Specifically, we presented the most comprehensive frequency distribution map of the well-known FecB mutation to date. Besides, among the above-mentioned SNPs, one synonymous mutation (g.30050773C > T) was found to be likely under selection and is potentially associated with fecundity in Duolang sheep. Thus, our study greatly expands the variation repertoire of the ovine BMPR1B gene and provides a valuable resource for exploring causative mutations and genetic markers associated with litter size.
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Affiliation(s)
- Chunna Cao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Qian Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Yuxin Kang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Zhanerke Akhatayeva
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Peiyao Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Yuheng Bai
- Sheep Industry Development Center of Yulin City, Yulin, 719053, China.
| | - Ran Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Qingfeng Zhang
- Tianjin Aoqun Sheep Industry Academy Company, Tianjin, 300000, China.
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Chuanying Pan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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Finzel JA, Brown AR, Busch RC, Doran MP, Harper JM, Macon DK, Ozeran RK, Stegemiller MR, Isaacs K, Van Eenennaam A. Field demonstration analyzing the implementation of individual animal electronic identification and genetic testing in western range sheep flocks. PLoS One 2023; 18:e0290281. [PMID: 37611008 PMCID: PMC10446171 DOI: 10.1371/journal.pone.0290281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 08/03/2023] [Indexed: 08/25/2023] Open
Abstract
Adoption of electronic identification ear tags (EID) and DNA testing by commercial range sheep producers in the Western United States has been low, despite the availability of these technologies for over a decade. Jointly, these technologies offer an approach to provide individual animal performance data to improve flock health, genetic and reproductive management. This project involved a collaboration with five California sheep producers representing a broad geographic range, varying levels of pre-project EID adoption, and diverse operational practices. Tissue samples were collected from, and ear EIDs were placed in, a total of 2,936 rams and their potential lambs. We partnered with a commercial packing company, Superior Farms, to genotype the animals. Superior Farms used a targeted genotyping panel to assign parentage, and link individual animal identification (ID) to camera-graded carcass measurements. This enabled the collection of individual progeny carcass data and provided insight into sire performance, providing for the within-flock identification of prolific sires that were producing lambs with significantly more saleable meat as compared to their flock mates. Overall, almost 91% of lambs were successfully matched to their sire, and prolificacy ranging from 0-135 lambs per ram. There was as much as an $80 difference in the average edible product from camera-graded carcasses derived from lamb groups sired by different rams. A partial budget analysis modeling investment in an EID system coupled with an autodrafter and scale to collect individual weights and improve labor efficiency during processing, and a sheep flip chute to improve worker safety during foot trimmings, yielded a greater than 7:1 return on investment over a five-year time frame. Ideally, the data collection enabled by EIDs and DNA testing would feed into data-driven genetic evaluation programs to enable selection for more productive and profitable animals, and allow the US sheep industry to accelerate the rate of genetic improvement.
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Affiliation(s)
- Julie A. Finzel
- University of California Cooperative Extension, Kern County, University of California Agriculture and Natural Resources, Bakersfield, California, United States of America
| | - Austin R. Brown
- Department of Animal Sciences, University of California, Davis, California, United States of America
| | - Roselle C. Busch
- Department of Animal Sciences, University of California, Davis, California, United States of America
| | - Morgan P. Doran
- University of California Cooperative Extension, Solano County, University of California Agriculture and Natural Resources, Woodland, California, United States of America
| | - John M. Harper
- University of California Cooperative Extension, Mendocino County, University of California Agriculture and Natural Resources, Ukiah, California, United States of America
| | - Daniel K. Macon
- University of California Cooperative Extension, Placer County, University of California Agriculture and Natural Resources, Auburn, California, United States of America
| | - Rebecca K. Ozeran
- University of California Cooperative Extension, Fresno County, University of California Agriculture and Natural Resources, Fresno, California, United States of America
| | - Morgan R. Stegemiller
- Department of Animal, Veterinary, and Food Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Karissa Isaacs
- Superior Farms, Denver, Colorado, United States of America
| | - Alison Van Eenennaam
- Department of Animal Sciences, University of California, Davis, California, United States of America
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Stegemiller MR, Redden RR, Notter DR, Taylor T, Taylor JB, Cockett NE, Heaton MP, Kalbfleisch TS, Murdoch BM. Using whole genome sequence to compare variant callers and breed differences of US sheep. Front Genet 2023; 13:1060882. [PMID: 36685812 PMCID: PMC9846548 DOI: 10.3389/fgene.2022.1060882] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/22/2022] [Indexed: 01/06/2023] Open
Abstract
As whole genome sequence (WGS) data sets have become abundant and widely available, so has the need for variant detection and scoring. The aim of this study was to compare the accuracy of commonly used variant calling programs, Freebayes and GATK HaplotypeCaller (GATK-HC), and to use U.S. sheep WGS data sets to identify novel breed-associated SNPs. Sequence data from 145 sheep consisting of 14 U.S. breeds were filtered and biallelic single nucleotide polymorphisms (SNPs) were retained for genotyping analyses. Genotypes from both programs were compared to each other and to genotypes from bead arrays. The SNPs from WGS were compared to the bead array data with breed heterozygosity, principal component analysis and identifying breed associated SNPs to analyze genetic diversity. The average sequence read depth was 2.78 reads greater with 6.11% more SNPs being identified in Freebayes compared to GATK-HC. The genotype concordance of the variant callers to bead array data was 96.0% and 95.5% for Freebayes and GATK-HC, respectively. Genotyping with WGS identified 10.5 million SNPs from all 145 sheep. This resulted in an 8% increase in measured heterozygosity and greater breed separation in the principal component analysis compared to the bead array analysis. There were 1,849 SNPs identified in only the Romanov sheep where all 10 rams were homozygous for one allele and the remaining 135 sheep from 13 breeds were homozygous for the opposite allele. Both variant calling programs had greater than 95% concordance of SNPs with bead array data, and either was suitably accurate for ovine WGS data sets. The use of WGS SNPs improved the resolution of PCA analysis and was critical for identifying Romanov breed-associated SNPs. Subsets of such SNPs could be used to estimate germplasm composition in animals without pedigree information.
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Affiliation(s)
- Morgan R. Stegemiller
- Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow, ID, United States
| | - Reid R. Redden
- Texas A&M AgriLife Research and Extension, Texas A&M University, San Angelo, TX, United States
| | - David R. Notter
- School of Animal Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Todd Taylor
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - J. Bret Taylor
- United States Sheep Experiment Station, United States Department of Agriculture, Agricultural Research Service, Dubois, ID, United States
| | - Noelle E. Cockett
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, United States
| | - Michael P. Heaton
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, United States
| | - Theodore S. Kalbfleisch
- Gluck Equine Research Center, College of Agriculture, Food, and Environment, University of Kentucky, Lexington, KY, United States,*Correspondence: Theodore S. Kalbfleisch, ; Brenda M. Murdoch,
| | - Brenda M. Murdoch
- Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow, ID, United States,*Correspondence: Theodore S. Kalbfleisch, ; Brenda M. Murdoch,
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Akhatayeva Z, Bi Y, He Y, Khan R, Li J, Li H, Pan C, Lan X. Survey of the relationship between polymorphisms within the BMPR1B gene and sheep reproductive traits. Anim Biotechnol 2021:1-10. [PMID: 34586970 DOI: 10.1080/10495398.2021.1979023] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The BMPRIB gene is one of the main genes that can be used as a molecular genetic marker for the early selection of highly productive ewes. It is well-documented that the p.Q249R (g.746A > G) is the first mutation in the kinase domain of the BMPR1B gene that is highly related to increased ovulation rate and litter size. It is likely that the presence of the p.Q249R mutation in the sheep population is one of the factors contributing to the outstanding productivity of the sheep. Moreover, in recent years, researchers have been explored other polymorphisms in the BMPR1B gene with respect to reproductive traits in sheep. Therefore, we carried out the current study to evaluate the association between polymorphisms in this gene and sheep litter size from all appropriate studies. As a result, among 41 polymorphisms in the ovine BMPRIB gene, eight variants, including p.Q249R (g.746A > G), g.29362047T > C, g.29427689G > A, BMPR1B-2 (ss:1960972599), g.29382337G > A, g.29382340G > A, rs1092293287 (10 bp insertion/deletion) and g.29380965A > G were found to be associated with litter size in sheep. This systematic analysis presents the most current data evidence for BMPRIB polymorphisms, highlighting the need for further large-scale studies to determine more important variants.
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Affiliation(s)
- Zhanerke Akhatayeva
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yi Bi
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yiwen He
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.,Library of Northwest A&F University, Northwest A&F University, Yangling, Shaanxi, China
| | - Rajwali Khan
- Department of Livestock Management, Breeding and Genetics, The University of Agriculture, Peshawar, Pakistan
| | - Jie Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Haixia Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Chuanying Pan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
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Çelikeloğlu K, Tekerli M, Erdoğan M, Koçak S, Hacan Ö, Bozkurt Z. An investigation of the effects of BMPR1B, BMP15, and GDF9 genes on litter size in Ramlıç and Dağlıç sheep. Arch Anim Breed 2021; 64:223-230. [PMID: 34159253 PMCID: PMC8209503 DOI: 10.5194/aab-64-223-2021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 04/27/2021] [Indexed: 11/11/2022] Open
Abstract
This study was carried out to determine the presence of polymorphisms in genes affecting litter size. The SNPs in bone morphogenetic protein receptor type 1B (BMPR1B), bone morphogenetic protein 15 (BMP15), and growth differentiation factor 9 (GDF9) genes were detected in 60 uniparous and 60 multiparous ewes from Ramlıç and Dağlıç breeds. The ewes are maintained in nine public herds at the breeding station of the Afyonkarahisar Sheep and Goats Breeders' Association and lambed in two consecutive breeding seasons. PCR and DNA sequencing analyses were conducted, and 36, 4, and 11 SNPs in Ramlıç and 40, 3, and 11 SNPs in Dağlıç were detected in BMPR1B, BMP15, and GDF9 genes, respectively. A total of 16 SNPs in Ramlıç and 10 SNPs in Dağlıç breeds for three genes were found to be significant (P<0.05). The resulting analyses showed that four SNPs (g.49496G>A, c.1658A>C, c.2037C>T, c.2053C>T) of the BMPR1B gene and one deletion mutation (c.28_30delCTT) in the BMP15 gene of the Ramlıç breed as well as five SNPs (c.1487C>A, c.2492C>T, c.2523G>A, c.2880A>G, and c.2763G>A) of the BMPR1B gene of the Dağlıç breed have significant positive regression coefficients in the desired direction of the rare allele. The observed mutations have potential to be used as genetic markers in the selection of prolific animals for both breeds.
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Affiliation(s)
- Koray Çelikeloğlu
- Department of Animal Science, Faculty of Veterinary Medicine, Afyonkarahisar, Turkey
| | - Mustafa Tekerli
- Department of Animal Science, Faculty of Veterinary Medicine, Afyonkarahisar, Turkey
| | - Metin Erdoğan
- Department of Veterinary Biology and Genetics, Faculty of Veterinary Medicine, Afyonkarahisar, Turkey
| | - Serdar Koçak
- Department of Animal Science, Faculty of Veterinary Medicine, Afyonkarahisar, Turkey
| | - Özlem Hacan
- Department of Animal Science, Faculty of Veterinary Medicine, Afyonkarahisar, Turkey
| | - Zehra Bozkurt
- Department of Animal Science, Faculty of Veterinary Medicine, Afyonkarahisar, Turkey
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Yaman Y, Aymaz R, Keleş M, Bay V, Ün C, Heaton MP. Association of TLR2 haplotypes encoding Q650 with reduced susceptibility to ovine Johne's disease in Turkish sheep. Sci Rep 2021; 11:7088. [PMID: 33782507 PMCID: PMC8007707 DOI: 10.1038/s41598-021-86605-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 03/18/2021] [Indexed: 02/06/2023] Open
Abstract
Ovine Johne’s disease (OJD) is caused by Mycobacterium avium subsp. paratuberculosis (MAP) and carries a potential zoonotic risk for humans. Selective breeding strategies for reduced OJD susceptibility would be welcome tools in disease eradication efforts, if available. The Toll-like receptor 2 gene (TLR2) plays an important signaling role in immune response to MAP, and missense variants are associated with mycobacterial infections in mammals. Our aim was to identify and evaluate ovine TLR2 missense variants for association with OJD in Turkish sheep. Eleven TLR2 missense variants and 17 haplotype configurations were identified in genomic sequences of 221 sheep from 61 globally-distributed breeds. The five most frequent haplotypes were tested for OJD association in 102 matched pairs of infected and uninfected ewes identified in 2257 Turkish sheep. Ewes with one or two copies of TLR2 haplotypes encoding glutamine (Q) at position 650 (Q650) in the Tir domain were 6.6-fold more likely to be uninfected compared to ewes with arginine (R650) at that position (CI95 = 2.6 to 16.9, p-value = 3.7 × 10–6). The protective TLR2 Q650 allele was present in at least 25% of breeds tested and thus may facilitate selective breeding for sheep with reduced susceptibility to OJD.
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Affiliation(s)
- Yalçın Yaman
- Department of Biometry and Genetics, Sheep Breeding and Research Institute, 10200, Bandırma, Balıkesir, Turkey.
| | - Ramazan Aymaz
- Department of Biometry and Genetics, Sheep Breeding and Research Institute, 10200, Bandırma, Balıkesir, Turkey
| | - Murat Keleş
- Department of Biometry and Genetics, Sheep Breeding and Research Institute, 10200, Bandırma, Balıkesir, Turkey
| | - Veysel Bay
- Department of Biometry and Genetics, Sheep Breeding and Research Institute, 10200, Bandırma, Balıkesir, Turkey
| | - Cemal Ün
- Department of Biology, Faculty of Science, Ege University, 35000, İzmir, Turkey
| | - Michael P Heaton
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA
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Polymorphism Detection of GDF9 Gene and Its Association with Litter Size in Luzhong Mutton Sheep ( Ovis aries). Animals (Basel) 2021; 11:ani11020571. [PMID: 33671790 PMCID: PMC7926531 DOI: 10.3390/ani11020571] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/09/2021] [Accepted: 02/18/2021] [Indexed: 12/24/2022] Open
Abstract
Simple Summary GDF9 and BMPR1B are two important reproduction genes. In this study, the whole coding region of GDF9 was sequenced, of which the mutations were detected in Luzhong mutton sheep. The results suggested that two single nucleotide polymorphisms (SNPs), g.41768501A > G and g.41768485 G > A in GDF9 gene were associated with litter size. The g.41768485 G > A is a missense mutation which is predicted to affect the tertiary structure of the protein. Thus, these two mutations may be potential effective genetic markers to improve the litter size in sheep. Abstract Litter size is one of the most important economic traits in sheep. GDF9 and BMPR1B are major genes affecting the litter size of sheep. In this study, the whole coding region of GDF9 was sequenced and all the SNPs (single nucleotide polymorphisms) were determined in Luzhong mutton ewes. The FecB mutation was genotyped using the Sequenom MassARRAY®SNP assay technology. Then, the association analyses between polymorphic loci of GDF9 gene, FecB, and litter size were performed using a general linear model procedure. The results showed that eight SNPs were detected in GDF9 of Luzhong mutton sheep, including one novel mutation (g.41769606 T > G). The g.41768501A > G, g.41768485 G > A in GDF9 and FecB were significantly associated with litter size in Luzhong mutton ewes. The g.41768485 G > A is a missense mutation in the mature GDF9 protein region and is predicted to affect the tertiary structure of the protein. The results preliminarily demonstrated that GDF9 was a major gene affecting the fecundity of Luzhong mutton sheep and the two loci g.41768501A > G and g.41768485 G > A may be potential genetic markers for improving litter size.
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Murphy TW, Freking BA. Comparison of performance of F1 Romanov crossbred ewes with wool and hair breeds during fall lambing and body weight and longevity through six production years. J Anim Sci 2021; 99:skaa400. [PMID: 33340044 PMCID: PMC7799584 DOI: 10.1093/jas/skaa400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 12/15/2020] [Indexed: 11/12/2022] Open
Abstract
The objective of this study was to evaluate wool (Dorset and Rambouillet) and hair (Dorper, Katahdin, and White Dorper) breeds for their ability to complement Romanov germplasm in an annual fall lambing system by estimating direct maternal grandsire and sire breed effects on economically important lamb and ewe traits. After 3 yr of evaluation under spring lambing, ewes of the five F1 types were transitioned to spring mating, exposed to composite terminal sires, and evaluated under a barn lambing system at 4, 5, and 6 yr of age. A total of 527 first generation crossbred (F1) ewes produced 1,151 litters and 2,248 lambs from 1,378 May exposures. After accounting for differences in dam age, birth type, and sex, lamb survival to weaning was unaffected by maternal grandsire breed (P = 0.30). However, lambs born to 50% Dorset (16.8 ± 0.21 kg) or 50% White Dorper ewes (16.8 ± 0.28 kg) were heavier at weaning than those born to 50% Katahdin dams (13.8 ± 0.32 kg; P < 0.001). Additionally, lambs born to 50% Dorset ewes were heavier than those born to 50% Rambouillet (16.0 ± 0.22 kg) and 50% Dorper ewes (15.7 ± 0.33; P ≤ 0.03), but no other pairwise maternal grandsire breed differences were observed (P ≥ 0.06). Ewe body weight (n = 3,629) was recorded prior to each of six possible mating seasons and, across ages, was greatest for Dorset- and Rambouillet-sired ewes (56.7 ± 0.44 and 56.5 ± 0.45 kg, respectively), intermediate for Dorper- and White Dorper-sired ewes (54.7 ± 0.78 and 54.1 ± 0.64 kg, respectively), and least for Katahdin-sired ewes (51.5 ± 0.45 kg). Fertility after spring mating (0.80 ± 0.03 to 0.87 ± 0.02), litter size at birth (1.46 ± 0.09 to 1.71 ± 0.07), and litter size at weaning (1.25 ± 0.06 to 1.46 ± 0.06) were not impacted by sire breed (P ≥ 0.16). Ewe longevity, assessed as the probability of being present after 6 production years, was also not affected by sire breed (0.39 ± 0.03 to 0.47 ± 0.03; P = 0.44). Rambouillet-sired ewes weaned more total weight of lamb (21.5 ± 0.94 kg) than Katahdin-sired ewes (17.8 ± 0.94 kg; P = 0.05), but no other sire breed differences were detected (P ≥ 0.07). Results demonstrated that incorporating the Romanov into a crossbreeding system is a practical means of improving out-of-season ewe productivity.
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Affiliation(s)
- Thomas W Murphy
- U.S. Meat Animal Research Center, USDA, ARS, Clay Center, NE, USA
| | - Brad A Freking
- U.S. Meat Animal Research Center, USDA, ARS, Clay Center, NE, USA
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Freking BA, Murphy TW. Comparison of performance of F1 Romanov crossbred ewes with wool and hair breeds during spring lambing under intensive and extensive production systems. J Anim Sci 2021; 99:skaa397. [PMID: 33313796 PMCID: PMC7787146 DOI: 10.1093/jas/skaa397] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 12/10/2020] [Indexed: 11/14/2022] Open
Abstract
The objective was to evaluate wool (Dorset and Rambouillet) and hair (Dorper, Katahdin, and White Dorper) breeds for their ability to complement Romanov germplasm in two distinct production systems by estimating direct sire and grandsire effects on lamb growth, survival, and ewe productivity traits. Rams of the five breeds (n = 75) were mated to Romanov ewes (n = 459) over a 3-yr period to produce five types of crossbred lambs (n = 2,739). Sire breed (P > 0.06) did not impact body weight or survival traits of the first-generation crossbred (F1) lambs. The productivity of retained crossbred ewes (n = 830) mated to Suffolk and Texel terminal sires was evaluated at 1, 2, and 3 yr of age in each production system. In the intensive production system, labor and harvested feed were provided for sheep that lambed in March in barns, and ewes were limited to rearing two lambs with additional lambs reared artificially. Ewes in the extensive production system lambed in May on pasture and were responsible for rearing all lambs born with no labor or supplemental feed provided before weaning. A total of 1,962 litters and 4,171 lambs from 2,229 exposures to two terminal sire breeds (Suffolk and Texel) were produced in the experiment. Crossbred ewes in the intensive production system were mated in October, resulting in larger litter sizes than crossbred ewes mated in December for the extensive production system. However, single- and twin-born lamb mortality was similar between the two systems that differed greatly in labor, feed, and facilities. Lambs produced in the intensive system received concentrate feed from an early age and were heavier at 24 wk of age than lambs produced in the extensive system. These outcomes resulted in greater 24-wk litter weight in the intensive than in the extensive system (P < 0.0001). Unexpectedly, the relative performance of crossbred types did not differ importantly between production systems. White Dorper × Romanov crossbred ewes had numerical advantages in productivity in each system; however, differences between ewe types were not significant. In the extensive system, without labor and shelter at lambing or supplemental feed until weaning, 3-yr-old crossbred ewes of all types averaged 1.78 lambs marketed per ewe lambing, and 40% of the ewes that gave birth to triplets weaned their entire litters. These results document that prolific sheep and extensive systems can be successfully combined if appropriate crossbred types are used.
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Affiliation(s)
- Brad A Freking
- U.S. Meat Animal Research Center, USDA, ARS, Clay Center, NE
| | - Tom W Murphy
- U.S. Meat Animal Research Center, USDA, ARS, Clay Center, NE
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Ibrahim A, Budisatria IGS, Widayanti R, Artama WT. The genetic profiles and maternal origin of local sheep breeds on Java Island (Indonesia) based on complete mitochondrial DNA D-loop sequences. Vet World 2020; 13:2625-2634. [PMID: 33487980 PMCID: PMC7811546 DOI: 10.14202/vetworld.2020.2625-2634] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/21/2020] [Indexed: 11/16/2022] Open
Abstract
Background and Aim: Java Island is one of the islands in Indonesia which has local sheep breeds with specific characteristics and native development geography in certain regions. This study aimed to determine the genetic profiles and maternal origin of six local sheep breeds on Java Island. Materials and Methods: This study was conducted by identifying the profiles of complete mitochondrial DNA (mtDNA) displacement loop (D-loop) region sequences on a total of 22 individual in six local sheep breeds on Java Island, including Javanese thin-tailed (JTT), Javanese Fat-Tailed (JFT), Batur (BTR), Wonosobo (WSB), Garut (GRT), and Priangan (PRG) sheep. The D-loop region was amplified using specific primers, and the polymerase chain reaction (PCR) was performed. The PCR products were purified and sequenced. Results: The mtDNA D-loop analysis identified 21 haplotypes in the analyzed 22 animals with 123 polymorphic sites (V) consisting of 60 singleton variable sites (S) and 63 parsimony informative sites (P). Within all breeds tested, the haplotype diversity, the average number of pairwise differences (K), and nucleotide diversity (Pi) were 0.99567, 25.36364, and 0.02153, respectively. The genetic distance (D) within groups and between groups was 0.001-0.006 and 0.004-0.036, respectively. The phylogeny resulted in the presence of two haplogroups (Hap), which are 5 Hap A and 16 Hap B. All JTT, JFT, BTR, and WSB breeds were in the same cluster in Hap B, whereas GRT and PRG breeds were in clusters in both Hap A and Hap B. Conclusion: The high genetic diversity in six local sheep breeds on Java Island suggests that they originated from different genetic sources. JTT sheep have closer genetic relationships to JFT, BTR, and WSB sheep, and they are close to European sheep, whereas GRT sheep have closer genetic relationships to PRG sheep. Both are closer to Asian sheep than to European sheep.
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Affiliation(s)
- Alek Ibrahim
- Veterinary Science Postgraduate Study Program, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - I Gede Suparta Budisatria
- Department of Animal Production, Faculty of Animal Science, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Rini Widayanti
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Wayan Tunas Artama
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
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Li H, Xu H, Akhatayeva Z, Liu H, Lin C, Han X, Lu X, Lan X, Zhang Q, Pan C. Novel indel variations of the sheep FecB gene and their effects on litter size. Gene 2020; 767:145176. [PMID: 33002573 DOI: 10.1016/j.gene.2020.145176] [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: 05/28/2020] [Revised: 09/02/2020] [Accepted: 09/23/2020] [Indexed: 12/14/2022]
Abstract
Various studies had shown that the FecB gene (also known as BMPRIB, BMPR1B or ALK-6) was the major gene influencing sheep litter size, for which its SNPs' variations were reportedly linked. Yet, surprisingly, there was no published information on the insertion/deletion (indel) variation of this gene. Herein, using a population of Chinese Australian White sheep (n = 932), we identified five novel indels in the different introns of the FecB gene. Among them, the 12-bp indel was distinguished as a splicing region variation that was completely linked to the 17-bp indel. Analysis of variance revealed that only the 10-bp indel was significantly associated with sheep litter size (P = 0.010), for which the deletion/deletion (DD) genotype was the harmful one for fecundity. Nevertheless, the combined genotypes of these five indels were significantly (P = 0.033) correlated with the litter size. These findings would provide fresh insight into developing a sounder basis to accelerate molecular breeding in sheep via DNA markers in a marker-assisted selection strategy.
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Affiliation(s)
- Haixia Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hongwei Xu
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu 730030, China
| | - Zhanerke Akhatayeva
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hongfei Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chunjian Lin
- Tianjin Aoqun Sheep Industry Academy Company, Tianjin 300000, China
| | - Xufei Han
- Tianjin Aoqun Sheep Industry Academy Company, Tianjin 300000, China
| | - Xiaofang Lu
- Tianjin Aoqun Sheep Industry Academy Company, Tianjin 300000, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qingfeng Zhang
- Tianjin Aoqun Sheep Industry Academy Company, Tianjin 300000, China.
| | - Chuanying Pan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
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12
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13
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Rice ES, Koren S, Rhie A, Heaton MP, Kalbfleisch TS, Hardy T, Hackett PH, Bickhart DM, Rosen BD, Ley BV, Maurer NW, Green RE, Phillippy AM, Petersen JL, Smith TPL. Continuous chromosome-scale haplotypes assembled from a single interspecies F1 hybrid of yak and cattle. Gigascience 2020; 9:giaa029. [PMID: 32242610 PMCID: PMC7118895 DOI: 10.1093/gigascience/giaa029] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 01/08/2020] [Accepted: 03/10/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The development of trio binning as an approach for assembling diploid genomes has enabled the creation of fully haplotype-resolved reference genomes. Unlike other methods of assembly for diploid genomes, this approach is enhanced, rather than hindered, by the heterozygosity of the individual sequenced. To maximize heterozygosity and simultaneously assemble reference genomes for 2 species, we applied trio binning to an interspecies F1 hybrid of yak (Bos grunniens) and cattle (Bos taurus), 2 species that diverged nearly 5 million years ago. The genomes of both of these species are composed of acrocentric autosomes. RESULTS We produced the most continuous haplotype-resolved assemblies for a diploid animal yet reported. Both the maternal (yak) and paternal (cattle) assemblies have the largest 2 chromosomes in single haplotigs, and more than one-third of the autosomes similarly lack gaps. The maximum length haplotig produced was 153 Mb without any scaffolding or gap-filling steps and represents the longest haplotig reported for any species. The assemblies are also more complete and accurate than those reported for most other vertebrates, with 97% of mammalian universal single-copy orthologs present. CONCLUSIONS The high heterozygosity inherent to interspecies crosses maximizes the effectiveness of the trio binning method. The interspecies trio binning approach we describe is likely to provide the highest-quality assemblies for any pair of species that can interbreed to produce hybrid offspring that develop to sufficient cell numbers for DNA extraction.
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Affiliation(s)
- Edward S Rice
- Department of Animal Science, University of Nebraska–Lincoln, C203 ANSC, Lincoln, NE 68583, USA
- Bond Life Sciences Center, University of Missouri, 1201 Rollins Street, Columbia, MO 65201, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Michael P Heaton
- US Meat Animal Research Center, US Department of Agriculture, State Spur 18D, Clay Center, NE 68933, USA
| | - Theodore S Kalbfleisch
- Gluck Equine Research Center, University of Kentucky, 1400 Nicholasville Rd., Lexington, KY 40546, USA
| | | | | | - Derek M Bickhart
- Dairy Forage Research Center, 1925 Linden Drive, ARS USDA, Madison, WI 53706, USA
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, 10300 Baltimore Ave., ARS USDA, Beltsville, MD 20705, USA
| | - Brian Vander Ley
- Great Plains Veterinary Educational Center, School of Veterinary Medicine and Biomedical Sciences, University of Nebraska–Lincoln, 820 Road 313, Clay Center, NE 68933, USA
| | - Nicholas W Maurer
- Department of Biomolecular Engineering, University of California, 1156 High St., Santa Cruz, CA 95064, USA
| | - Richard E Green
- Department of Biomolecular Engineering, University of California, 1156 High St., Santa Cruz, CA 95064, USA
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Jessica L Petersen
- Department of Animal Science, University of Nebraska–Lincoln, C203 ANSC, Lincoln, NE 68583, USA
| | - Timothy P L Smith
- US Meat Animal Research Center, US Department of Agriculture, State Spur 18D, Clay Center, NE 68933, USA
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Freking BA, Bennett GL. Rambouillet and Romanov reciprocal breed effects on survival and growth traits of F1 lambs and on reproductive traits of F1 ewes. J Anim Sci 2019; 97:578-586. [PMID: 30561683 DOI: 10.1093/jas/sky474] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/12/2018] [Indexed: 12/22/2022] Open
Abstract
Objectives were to estimate reciprocal effects of Romanov and Rambouillet breeds on survival, growth, and reproductive traits of F1 progeny and direct breed effects (Suffolk and Composite - ½ Columbia, ¼ Hampshire, and ¼ Suffolk) on survival and growth traits of the subsequent terminally sired lambs. Mature Rambouillet ewes (n = 243) were exposed to 20 Romanov rams over two seasons producing 621 lambs for evaluation of growth and survival traits with 274 F1 ewes being evaluated for reproduction traits through 4 yr of age. Similarly, mature Romanov ewes (n = 116) were exposed to 20 Rambouillet rams producing 601 lambs for evaluation of growth and survival traits with 176 F1 ewes being evaluated for reproduction traits through 4 yr of age. A total of 433 of those F1 ewes produced 3,431 lambs (1,552 litters) from 1,634 exposures to terminal sires over 4 yr. Terminal sires consisted of 38 Suffolk and 44 Composite rams. Reciprocal crossbred ewe lambs were produced from dramatically different uterine and neonatal environments, with litter size at birth from Romanov dams exceeding those from Rambouillet dams by 1.52 lambs (P < 0.001) and birth weight of lambs from Romanov dams averaged 3.41 kg compared with 4.26 kg from Rambouillet dams. Differences in BW were still evident at 140 d (P < 0.001) for dam-reared lambs. However, reciprocal ewe first breeding BW of both types were similar (P = 0.38). Minimal differences were observed in performance of reciprocal cross ewes through 4 yr for productivity, longevity, or progeny growth and survival. One exception was BW at 140 d where an interaction of dam breed with terminal sire breed reached significance for both dam-reared (P = 0.05) and nursery-reared (P = 0.02) lambs. This interaction was due to the lower weight of Composite-sired lambs out of reciprocal cross ewes born from Rambouillet dams. Composite rams increased number born (P < 0.01) and number weaned (P < 0.05) of the reciprocal cross ewes. Suffolk rams increased (P < 0.001) BW and growth rates from birth to 140 d of terminal progeny. Thus, there were little cumulative differences accrued over the 4 yr and no differences were detected for cumulative kilogram of lamb generated at 140 d per ewe exposed. The practical outcome of this evaluation was that performance levels of both types of Romanov crossbred ewes was similar allowing the industry to produce the desired crossbred ewes without needing large purebred ewe flocks of the less numerous Romanov breed.
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Affiliation(s)
- Brad A Freking
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE
| | - Gary L Bennett
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE
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15
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Structure-Guided Identification of a Nonhuman Morbillivirus with Zoonotic Potential. J Virol 2018; 92:JVI.01248-18. [PMID: 30232185 PMCID: PMC6232486 DOI: 10.1128/jvi.01248-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 09/10/2018] [Indexed: 02/07/2023] Open
Abstract
Morbilliviruses infect a broad range of mammalian hosts, including ruminants, carnivores, and humans. The recent eradication of rinderpest virus (RPV) and the active campaigns for eradication of the human-specific measles virus (MeV) have raised significant concerns that the remaining morbilliviruses may emerge in so-called vacated ecological niches. Seeking to assess the zoonotic potential of nonhuman morbilliviruses within human populations, we found that peste des petits ruminants virus (PPRV)-the small-ruminant morbillivirus-is restricted at the point of entry into human cells due to deficient interactions with human SLAMF1-the immune cell receptor for morbilliviruses. Using a structure-guided approach, we characterized a single amino acid change, mapping to the receptor-binding domain in the PPRV hemagglutinin (H) protein, which overcomes this restriction. The same mutation allowed escape from some cross-protective, human patient, anti-MeV antibodies, raising concerns that PPRV is a pathogen with zoonotic potential. Analysis of natural variation within human and ovine SLAMF1 also identified polymorphisms that could correlate with disease resistance. Finally, the mechanistic nature of the PPRV restriction was also investigated, identifying charge incompatibility and steric hindrance between PPRV H and human SLAMF1 proteins. Importantly, this research was performed entirely using surrogate virus entry assays, negating the requirement for in situ derivation of a human-tropic PPRV and illustrating alternative strategies for identifying gain-of-function mutations in viral pathogens.IMPORTANCE A significant proportion of viral pandemics occur following zoonotic transmission events, where animal-associated viruses jump species into human populations. In order to provide forewarnings of the emergence of these viruses, it is necessary to develop a better understanding of what determines virus host range, often at the genetic and structural levels. In this study, we demonstrated that the small-ruminant morbillivirus, a close relative of measles, is unable to use human receptors to enter cells; however, a change of a single amino acid in the virus is sufficient to overcome this restriction. This information will be important for monitoring this virus's evolution in the field. Of note, this study was undertaken in vitro, without generation of a fully infectious virus with this phenotype.
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Kalbfleisch TS, Murdoch BM, Smith TPL, Murdoch JD, Heaton MP, McKay SD. A SNP resource for studying North American moose. F1000Res 2018; 7:40. [PMID: 29479424 PMCID: PMC5801567 DOI: 10.12688/f1000research.13501.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/04/2018] [Indexed: 11/20/2022] Open
Abstract
Background: Moose ( Alces alces) colonized the North American continent from Asia less than 15,000 years ago, and spread across the boreal forest regions of Canada and the northern United States (US). Contemporary populations have low genetic diversity, due either to low number of individuals in the original migration (founder effect), and/or subsequent population bottlenecks in North America. Genetic tests based on informative single nucleotide polymorphism (SNP) markers are helpful in forensic and wildlife conservation activities, but have been difficult to develop for moose, due to the lack of a reference genome assembly and whole genome sequence (WGS) data. Methods: WGS data were generated for four individual moose from the US states of Alaska, Idaho, Wyoming, and Vermont with minimum and average genome coverage depths of 14- and 19-fold, respectively. Cattle and sheep reference genomes were used for aligning sequence reads and identifying moose SNPs. Results: Approximately 11% and 9% of moose WGS reads aligned to cattle and sheep genomes, respectively. The reads clustered at genomic segments, where sequence identity between these species was greater than 95%. In these segments, average mapped read depth was approximately 19-fold. Sets of 46,005 and 36,934 high-confidence SNPs were identified from cattle and sheep comparisons, respectively, with 773 and 552 of those having minor allele frequency of 0.5 and conserved flanking sequences in all three species. Among the four moose, heterozygosity and allele sharing of SNP genotypes were consistent with decreasing levels of moose genetic diversity from west to east. A minimum set of 317 SNPs, informative across all four moose, was selected as a resource for future SNP assay design. Conclusions: All SNPs and associated information are available, without restriction, to support development of SNP-based tests for animal identification, parentage determination, and estimating relatedness in North American moose.
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Affiliation(s)
- Theodore S Kalbfleisch
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Louisville, Louisville, Kentucky, USA
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