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Zhao J, Mu Y, Gong P, Liu B, Zhang F, Zhu L, Shi C, Lv X, Luo J. Whole-genome resequencing of native and imported dairy goat identifies genes associated with productivity and immunity. Front Vet Sci 2024; 11:1409282. [PMID: 39040818 PMCID: PMC11260678 DOI: 10.3389/fvets.2024.1409282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 05/23/2024] [Indexed: 07/24/2024] Open
Abstract
Understanding the differences in genetic variation between local Chinese dairy goat breeds and imported breeds can help germplasm innovation and molecular breeding. However, the research is limited in this area. In this study, whole-genome resequencing data from 134 individuals of both local and imported dairy goat breeds were analyzed, and their differences in genomic genetic variation, genetic diversity, and population structure were subsequently identified. We also screened candidate genes associated with important traits of dairy goats such as milk production (STK3, GHR, PRELID3B), reproduction (ATP5E), growth and development (CTSZ, GHR), and immune function (CTSZ, NELFCD). Furthermore, we examined allele frequency distributions for the genes of interest and found significant differences between the two populations. This study provides valuable resources for the study of genetic diversity in dairy goats and lays the foundation for the selective breeding of dairy goats in the future.
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Affiliation(s)
- Jianqing Zhao
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Yuanpan Mu
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Ping Gong
- Institute of Animal Husbandry Quality Standards, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Baolong Liu
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Fuhong Zhang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Lu Zhu
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Chenbo Shi
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Xuefeng Lv
- Institute of Animal Husbandry Quality Standards, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Jun Luo
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
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Qin Q, Zhang CY, Liu ZC, Wang YC, Kong DQ, Zhao D, Zhang JW, Lan MX, Wang ZX, Alatan SH, Batu I, Qi XD, Zhao RQ, Li JQ, Wang BY, Liu ZH. Estimation of the genetic parameters of sheep growth traits based on machine vision acquisition. Animal 2024; 18:101196. [PMID: 38917726 DOI: 10.1016/j.animal.2024.101196] [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: 01/04/2024] [Revised: 05/08/2024] [Accepted: 05/14/2024] [Indexed: 06/27/2024] Open
Abstract
In the realm of animal phenotyping, manual measurements are frequently utilised. While machine-generated data show potential for enhancing high-throughput breeding, additional research and validation are imperative before incorporating them into genetic evaluation processes. This research presents a method for managing meat sheep and collecting data, utilising the Sheep Data Recorder system for data input and the Sheep Body Size Collector system for image capture. The study aimed to investigate the genetic parameter changes of growth traits in Ujumqin sheep by comparing machine-generated measurements with manual measurements. The dataset consisted of 552 data points from the offspring of 75 breeding rams and 399 breeding ewes. Six distinct random regression models were assessed to pinpoint the most suitable model for estimating genetic parameters linked to growth traits. These models were distinguished based on the inclusion or exclusion of maternal genetic effects, maternal permanent environmental effects, and covariance between maternal and direct genetic effects. Fixed factors such as individual age, individual sex, and ewe age were taken into account in the analysis. The genetic parameters for the yearling growth traits of Ujumqin sheep were calculated using ASReml software. The Akaike information criterion, the Bayesian information criterion, and fivefold cross-validation were employed to identify the optimal model. Research findings indicate that the most accurate models for manually measured data revealed heritability estimates of 0.12 ± 0.15 for BW, 0.05 ± 0.07 for body slanting length, 0.03 ± 0.07 for withers height, 0.15 ± 0.12 for hip height, 0.11 ± 0.11 for chest depth, 0.13 ± 0.13 for shoulder width, and 0.53 ± 0.15 for chest circumference. The optimal models for machine-predicted data showed heritability estimates of 0.1 ± 0.09 for body slanting length, 0.14 ± 0.12 for withers height, 0.55 ± 0.15 for hip height, 0.34 ± 0.15 for chest depth, 0.26 ± 0.15 for shoulder width, and 0.47 ± 0.16 for chest circumference. In manually measured data, genetic correlations ranged from 0.35 to 0.99, while phenotypic correlations ranged from 0.07 to 0.90. In machine data, genetic correlations ranged from -0.05 to 0.99, while phenotypic correlations ranged from 0.03 to 0.84. The results suggest that machine-based estimations may lead to an overestimation of heritability, but this discrepancy does not impact the selection of breeding models.
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Affiliation(s)
- Q Qin
- Inner Mongolia Agricultural University Animal Science Department, Inner Mongolia Agricultural University, Zhaowuda Road, No.8 Teaching and Research Building, 010018 Hohhot City, Inner Mongolia Autonomous Region, China; Key Laboratory Of Mutton Sheep and Goat Genetics And Breeding, Ministry Of Agriculture And Rural Affairs, Zhaowuda Road, No.8 Teaching and Research Building, 010018, Hohhot City, Inner Mongolia Autonomous Region, China
| | - C Y Zhang
- Inner Mongolia Agricultural University Animal Science Department, Inner Mongolia Agricultural University, Zhaowuda Road, No.8 Teaching and Research Building, 010018 Hohhot City, Inner Mongolia Autonomous Region, China; Key Laboratory of Animal Genetics, Breeding and Reproduction in Inner Mongolia Autonomous Region, Zhaowuda Road, No.8 Teaching and Research Building, 010018, Hohhot City, Inner Mongolia Autonomous Region, China
| | - Z C Liu
- Inner Mongolia Agricultural University Animal Science Department, Inner Mongolia Agricultural University, Zhaowuda Road, No.8 Teaching and Research Building, 010018 Hohhot City, Inner Mongolia Autonomous Region, China; Key Laboratory of Animal Genetics, Breeding and Reproduction in Inner Mongolia Autonomous Region, Zhaowuda Road, No.8 Teaching and Research Building, 010018, Hohhot City, Inner Mongolia Autonomous Region, China
| | - Y C Wang
- Inner Mongolia Agricultural University Animal Science Department, Inner Mongolia Agricultural University, Zhaowuda Road, No.8 Teaching and Research Building, 010018 Hohhot City, Inner Mongolia Autonomous Region, China; Key Laboratory of Animal Genetics, Breeding and Reproduction in Inner Mongolia Autonomous Region, Zhaowuda Road, No.8 Teaching and Research Building, 010018, Hohhot City, Inner Mongolia Autonomous Region, China
| | - D Q Kong
- Inner Mongolia Agricultural University Animal Science Department, Inner Mongolia Agricultural University, Zhaowuda Road, No.8 Teaching and Research Building, 010018 Hohhot City, Inner Mongolia Autonomous Region, China; Key Laboratory Of Mutton Sheep and Goat Genetics And Breeding, Ministry Of Agriculture And Rural Affairs, Zhaowuda Road, No.8 Teaching and Research Building, 010018, Hohhot City, Inner Mongolia Autonomous Region, China
| | - D Zhao
- Inner Mongolia Agricultural University Animal Science Department, Inner Mongolia Agricultural University, Zhaowuda Road, No.8 Teaching and Research Building, 010018 Hohhot City, Inner Mongolia Autonomous Region, China; Key Laboratory Of Mutton Sheep and Goat Genetics And Breeding, Ministry Of Agriculture And Rural Affairs, Zhaowuda Road, No.8 Teaching and Research Building, 010018, Hohhot City, Inner Mongolia Autonomous Region, China
| | - J W Zhang
- Inner Mongolia Agricultural University Animal Science Department, Inner Mongolia Agricultural University, Zhaowuda Road, No.8 Teaching and Research Building, 010018 Hohhot City, Inner Mongolia Autonomous Region, China; Key Laboratory Of Mutton Sheep and Goat Genetics And Breeding, Ministry Of Agriculture And Rural Affairs, Zhaowuda Road, No.8 Teaching and Research Building, 010018, Hohhot City, Inner Mongolia Autonomous Region, China
| | - M X Lan
- Inner Mongolia Agricultural University Animal Science Department, Inner Mongolia Agricultural University, Zhaowuda Road, No.8 Teaching and Research Building, 010018 Hohhot City, Inner Mongolia Autonomous Region, China
| | - Z X Wang
- Inner Mongolia Agricultural University Animal Science Department, Inner Mongolia Agricultural University, Zhaowuda Road, No.8 Teaching and Research Building, 010018 Hohhot City, Inner Mongolia Autonomous Region, China
| | - S H Alatan
- East Ujumqin Sheep Original Breeding Farm, East Ujumqin Banner, China
| | - I Batu
- East Ujumqin Sheep Original Breeding Farm, East Ujumqin Banner, China
| | - X D Qi
- Inner Mongolia Huawen Technology and Information Co. Ltd, Alatan Street, Saihan District Hohhot, 010018, Hohhot City, Inner Mongolia Autonomous Region, China
| | - R Q Zhao
- Inner Mongolia Huawen Technology and Information Co. Ltd, Alatan Street, Saihan District Hohhot, 010018, Hohhot City, Inner Mongolia Autonomous Region, China
| | - J Q Li
- Inner Mongolia Agricultural University Animal Science Department, Inner Mongolia Agricultural University, Zhaowuda Road, No.8 Teaching and Research Building, 010018 Hohhot City, Inner Mongolia Autonomous Region, China
| | - B Y Wang
- Inner Mongolia Agricultural University College of Computer and Information Engineering, Inner Mongolia Agricultural University, Zhaowuda Road, No.8 Teaching and Research Building, 010018 Hohhot City, Inner Mongolia Autonomous Region, China
| | - Z H Liu
- Inner Mongolia Agricultural University Animal Science Department, Inner Mongolia Agricultural University, Zhaowuda Road, No.8 Teaching and Research Building, 010018 Hohhot City, Inner Mongolia Autonomous Region, China; Institute of Grassland Research of CAAS, No. 120 Ulanqab East Street, Saihan District, 010018, Hohhot City, Inner Mongolia Autonomous Region, China; Key Laboratory of Animal Biotechnology of Xinjiang, Xinjiang Academy of Animal Science, Urumqi 830000, China; Key Laboratory Of Mutton Sheep and Goat Genetics And Breeding, Ministry Of Agriculture And Rural Affairs, Zhaowuda Road, No.8 Teaching and Research Building, 010018, Hohhot City, Inner Mongolia Autonomous Region, China.
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Carvalho Filho I, Arikawa LM, Mota LFM, Campos GS, Fonseca LFS, Fernandes Júnior GA, Schenkel FS, Lourenco D, Silva DA, Teixeira CS, Silva TL, Albuquerque LG, Carvalheiro R. Genome-wide association study considering genotype-by-environment interaction for productive and reproductive traits using whole-genome sequencing in Nellore cattle. BMC Genomics 2024; 25:623. [PMID: 38902640 PMCID: PMC11188527 DOI: 10.1186/s12864-024-10520-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 06/13/2024] [Indexed: 06/22/2024] Open
Abstract
BACKGROUND The genotype-by-environment interaction (GxE) in beef cattle can be investigated using reaction norm models to assess environmental sensitivity and, combined with genome-wide association studies (GWAS), to map genomic regions related to animal adaptation. Including genetic markers from whole-genome sequencing in reaction norm (RN) models allows us to identify high-resolution candidate genes across environmental gradients through GWAS. Hence, we performed a GWAS via the RN approach using whole-genome sequencing data, focusing on mapping candidate genes associated with the expression of reproductive and growth traits in Nellore cattle. For this purpose, we used phenotypic data for age at first calving (AFC), scrotal circumference (SC), post-weaning weight gain (PWG), and yearling weight (YW). A total of 20,000 males and 7,159 females genotyped with 770k were imputed to the whole sequence (29 M). After quality control and linkage disequilibrium (LD) pruning, there remained ∼ 2.41 M SNPs for SC, PWG, and YW and ∼ 5.06 M SNPs for AFC. RESULTS Significant SNPs were identified on Bos taurus autosomes (BTA) 10, 11, 14, 18, 19, 20, 21, 24, 25 and 27 for AFC and on BTA 4, 5 and 8 for SC. For growth traits, significant SNP markers were identified on BTA 3, 5 and 20 for YW and PWG. A total of 56 positional candidate genes were identified for AFC, 9 for SC, 3 for PWG, and 24 for YW. The significant SNPs detected for the reaction norm coefficients in Nellore cattle were found to be associated with growth, adaptative, and reproductive traits. These candidate genes are involved in biological mechanisms related to lipid metabolism, immune response, mitogen-activated protein kinase (MAPK) signaling pathway, and energy and phosphate metabolism. CONCLUSIONS GWAS results highlighted differences in the physiological processes linked to lipid metabolism, immune response, MAPK signaling pathway, and energy and phosphate metabolism, providing insights into how different environmental conditions interact with specific genes affecting animal adaptation, productivity, and reproductive performance. The shared genomic regions between the intercept and slope are directly implicated in the regulation of growth and reproductive traits in Nellore cattle raised under different environmental conditions.
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Affiliation(s)
- Ivan Carvalho Filho
- Department of Animal Science, School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil
| | - Leonardo M Arikawa
- Department of Animal Science, School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil
| | - Lucio F M Mota
- Department of Animal Science, School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil.
| | - Gabriel S Campos
- Department of Animal Science, School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil
| | - Larissa F S Fonseca
- Department of Animal Science, School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil
| | - Gerardo A Fernandes Júnior
- Department of Animal Science, School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil
| | - Flavio S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G2W1, Canada
| | - Daniela Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, 30602, USA
| | - Delvan A Silva
- Department of Animal Science, School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil
| | - Caio S Teixeira
- Department of Animal Science, School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil
| | - Thales L Silva
- Department of Animal Science, School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil
| | - Lucia G Albuquerque
- Department of Animal Science, School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil
- National Council for Science and Technological Development, Brasilia, DF, 71605-001, Brazil
| | - Roberto Carvalheiro
- Department of Animal Science, School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil
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Khazaei-Koohpar H, Gholizadeh M, Hafezian SH, Esmaeili-Fard SM. Weighted single-step genome-wide association study for direct and maternal genetic effects associated with birth and weaning weights in sheep. Sci Rep 2024; 14:13120. [PMID: 38849438 PMCID: PMC11161479 DOI: 10.1038/s41598-024-63974-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 06/04/2024] [Indexed: 06/09/2024] Open
Abstract
Body weight is an important economic trait for sheep meat production, and its genetic improvement is considered one of the main goals in the sheep breeding program. Identifying genomic regions that are associated with growth-related traits accelerates the process of animal breeding through marker-assisted selection, which leads to increased response to selection. In this study, we conducted a weighted single-step genome-wide association study (WssGWAS) to identify potential candidate genes for direct and maternal genetic effects associated with birth weight (BW) and weaning weight (WW) in Baluchi sheep. The data used in this research included 13,408 birth and 13,170 weaning records collected at Abbas-Abad Baluchi Sheep Breeding Station, Mashhad-Iran. Genotypic data of 94 lambs genotyped by Illumina 50K SNP BeadChip for 54,241 markers were used. The proportion of variance explained by genomic windows was calculated by summing the variance of SNPs within 1 megabase (Mb). The top 10 window genomic regions explaining the highest percentages of additive and maternal genetic variances were selected as candidate window genomic regions associated with body weights. Our findings showed that for BW, the top-ranked genomic regions (1 Mb windows) explained 4.30 and 4.92% of the direct additive and maternal genetic variances, respectively. The direct additive genetic variance explained by the genomic window regions varied from 0.31 on chromosome 1 to 0.59 on chromosome 8. The highest (0.84%) and lowest (0.32%) maternal genetic variances were explained by genomic windows on chromosome 10 and 17, respectively. For WW, the top 10 genomic regions explained 6.38 and 5.76% of the direct additive and maternal genetic variances, respectively. The highest and lowest contribution of direct additive genetic variances were 1.37% and 0.42%, respectively, both explained by genomic regions on chromosome 2. For maternal effects on WW, the highest (1.38%) and lowest (0.41%) genetic variances were explained by genomic windows on chromosome 2. Further investigation of these regions identified several possible candidate genes associated with body weight. Gene ontology analysis using the DAVID database identified several functional terms, such as translation repressor activity, nucleic acid binding, dehydroascorbic acid transporter activity, growth factor activity and SH2 domain binding.
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Affiliation(s)
- Hava Khazaei-Koohpar
- Department of Animal Science and Fisheries, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari, Iran
| | - Mohsen Gholizadeh
- Department of Animal Science and Fisheries, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari, Iran.
| | - Seyed Hasan Hafezian
- Department of Animal Science and Fisheries, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari, Iran
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Congiu M, Falchi L, Carta S, Cesarani A, Dimauro C, Correddu F, Macciotta NPP. Investigation of phenotypic, genetic and genomic background of Milk spectra in Sarda dairy sheep. J Anim Breed Genet 2024; 141:317-327. [PMID: 38148615 DOI: 10.1111/jbg.12843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 09/14/2023] [Accepted: 12/16/2023] [Indexed: 12/28/2023]
Abstract
Aim of this study was to analyse the genetic background of milk Fourier transform infrared (FTIR) spectra in dairy sheep. Individual milk FTIR spectra, with 1060 wavenumbers each, were available for 793 adult Sarda breed ewes genotyped at 45,813 SNP. The absorbance values of each wavenumber was analysed using a linear mixed model that included dim class, parity and lambing month as fixed effects and flock-test date and animal as random effects. The model was applied to estimate variance components and heritability and to perform a genome-wide association study for each wavenumber. Average h2 of wavenumbers absorbance was 0.13 ± 0.08, with the largest values observed in the regions associated with the characteristic bonds of carbonylic and methylenic groups of milk fat (h2 = 0.57 at 1724-1728 cm-1; and h2 = 0.34 at 2811-2834 cm-1, respectively). The absorbance values of wavenumbers were moderately correlated with the estimated heritabilities. After the Bonferroni correction, a total of nine markers were found to be significantly associated with 32 different wavenumbers. Of particular interest was the SNP s63269.1, mapped on chromosome 2, that was found to be associated with 27 wavenumbers. Genes previously found to be related to traits of interest (e.g. disease resistance, milk yield and quality, cheese firmness) are located close to the significant SNP. As expected, the heritability estimated for the absorbance of each wavenumbers seems to be associated with the related milk components.
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Affiliation(s)
- Michele Congiu
- Dipartimento di Agraria, University of Sassari, Sassari, Italy
| | - Laura Falchi
- Dipartimento di Agraria, University of Sassari, Sassari, Italy
| | - Silvia Carta
- Dipartimento di Agraria, University of Sassari, Sassari, Italy
| | - Alberto Cesarani
- Dipartimento di Agraria, University of Sassari, Sassari, Italy
- Department of Animal and Dairy Science, University of Georgia, Athens, Georgia, USA
| | - Corrado Dimauro
- Dipartimento di Agraria, University of Sassari, Sassari, Italy
| | - Fabio Correddu
- Dipartimento di Agraria, University of Sassari, Sassari, Italy
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Chang L, Zheng Y, Li S, Niu X, Huang S, Long Q, Ran X, Wang J. Identification of genomic characteristics and selective signals in Guizhou black goat. BMC Genomics 2024; 25:164. [PMID: 38336605 PMCID: PMC10854126 DOI: 10.1186/s12864-023-09954-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 12/29/2023] [Indexed: 02/12/2024] Open
Abstract
BACKGROUND Guizhou black goat is one of the indigenous black goat breeds in the southwest region of Guizhou, China, which is an ordinary goat for mutton production. They are characterized by moderate body size, black coat, favorite meat quality with tender meat and lower odor, and tolerance for cold and crude feed. However, little is known about the genetic characteristics or variations underlying their important economic traits. RESULTS Here, we resequenced the whole genome of Guizhou black goat from 30 unrelated individuals breeding in the five core farms. A total of 9,835,610 SNPs were detected, and 2,178,818 SNPs were identified specifically in this breed. The population structure analysis revealed that Guizhou black goat shared a common ancestry with Shaanbei white cashmere goat (0.146), Yunshang black goat (0.103), Iran indigenous goat (0.054), and Moroccan goat (0.002). However, Guizhou black goat showed relatively higher genetic diversity and a lower level of linkage disequilibrium than the other seven goat breeds by the analysis of the nucleotide diversity, linkage disequilibrium decay, and runs of homozygosity. Based on FST and θπ values, we identified 645, 813, and 804 selected regions between Guizhou black goat and Yunshang black goat, Iran indigenous goat, and cashmere goats. Combined with the results of XP-EHH, there were 286, 322, and 359 candidate genes, respectively. Functional annotation analysis revealed that these genes are potentially responsible for the immune response (e.g., CD28, CD274, IL1A, TLR2, and SLC25A31), humility-cold resistance (e.g., HBEGF, SOSTDC1, ARNT, COL4A1/2, and EP300), meat quality traits (e.g., CHUK, GAB2, PLAAT3, and EP300), growth (e.g., GAB2, DPYD, and CSF1), fertility (e.g., METTL15 and MEI1), and visual function (e.g., PANK2 and NMNAT2) in Guizhou black goat. CONCLUSION Our results indicated that Guizhou black goat had a high level of genomic diversity and a low level of linkage disequilibrium in the whole genome. Selection signatures were detected in the genomic regions that were mainly related to growth and development, meat quality, reproduction, disease resistance, and humidity-cold resistance in Guizhou black goat. These results would provide a basis for further resource protection and breeding improvement of this very local breed.
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Affiliation(s)
- Lingle Chang
- Institute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Sciences and College of Animal Science, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Yundi Zheng
- Institute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Sciences and College of Animal Science, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Sheng Li
- Institute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Sciences and College of Animal Science, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Xi Niu
- Institute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Sciences and College of Animal Science, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Shihui Huang
- Institute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Sciences and College of Animal Science, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Qingmeng Long
- Guizhou Testing Center for Livestock and Poultry Germplasm, Guiyang, 550018, Guizhou, China
| | - Xueqin Ran
- Institute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Sciences and College of Animal Science, Guizhou University, Guiyang, 550025, Guizhou, China.
| | - Jiafu Wang
- Institute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Sciences and College of Animal Science, Guizhou University, Guiyang, 550025, Guizhou, China.
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Aydin KB, Bi Y, Brito LF, Ulutaş Z, Morota G. Review of sheep breeding and genetic research in Türkiye. Front Genet 2024; 15:1308113. [PMID: 38333619 PMCID: PMC10850221 DOI: 10.3389/fgene.2024.1308113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 01/11/2024] [Indexed: 02/10/2024] Open
Abstract
The livestock industry in Türkiye is vital to the country's agricultural sector and economy. In particular, sheep products are an important source of income and livelihood for many Turkish smallholder farmers in semi-arid and highland areas. Türkiye is one of the largest sheep producers in the world and its sheep production system is heavily dependent on indigenous breeds. Given the importance of the sheep industry in Türkiye, a systematic literature review on sheep breeding and genetic improvement in the country is needed for the development and optimization of sheep breeding programs using modern approaches, such as genomic selection. Therefore, we conducted a comprehensive literature review on the current characteristics of sheep populations and farms based on the most up-to-date census data and breeding and genetic studies obtained from scientific articles. The number of sheep has increased in recent years, mainly due to the state's policy of supporting livestock farming and the increase in consumer demand for sheep dairy products with high nutritional and health benefits. Most of the genetic studies on indigenous Turkish sheep have been limited to specific traits and breeds. The use of genomics was found to be incipient, with genomic analysis applied to only two major breeds for heritability or genome-wide association studies. The scope of heritability and genome-wide association studies should be expanded to include traits and breeds that have received little or no attention. It is also worth revisiting genetic diversity studies using genome-wide single nucleotide polymorphism markers. Although there was no report of genomic selection in Turkish sheep to date, genomics could contribute to overcoming the difficulties of implementing traditional pedigree-based breeding programs that require accurate pedigree recording. As indigenous sheep breeds are better adapted to the local environmental conditions, the proper use of breeding strategies will contribute to increased income, food security, and reduced environmental footprint in a sustainable manner.
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Affiliation(s)
- Kenan Burak Aydin
- School of Animal Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Ye Bi
- School of Animal Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - Zafer Ulutaş
- Department of Animal Science, Faculty of Agriculture, Ondokuz Mayis University, Samsun, Türkiye
| | - Gota Morota
- School of Animal Sciences, Virginia Tech, Blacksburg, VA, United States
- Center for Advanced Innovation in Agriculture, Virginia Tech, Blacksburg, VA, United States
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Xiao T, Li Y, Yue L, Lu Z, Yuan C, Song Y, Yang B, Liu J, Guo T. Correlation of 20 Single-Nucleotide Polymorphisms with Weight and Wool Traits in Alpine Merino Sheep. Animals (Basel) 2023; 14:127. [PMID: 38200858 PMCID: PMC10778225 DOI: 10.3390/ani14010127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/22/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
SNPs associated with important traits of fine-wool sheep that were previously obtained through genome-wide association analysis screening were verified and analyzed. A total of 20 SNPs related to birth weight, bundle strength, cleaning rate, and fiber diameter were screened using whole-genome resequencing, and the SNPshot assay was used to detect and analyze polymorphisms. This study found that, among the 20 SNPs associated with important traits in Alpine Merino sheep, 8 were monomorphic and 12 were polymorphic, of which 6 showed moderate polymorphisms and 6 showed low polymorphisms. The heterozygosity of the 12 polymorphic loci ranged from 0.10 to 0.49, the effective number of alleles ranged from 1.11 to 1.98, and the polymorphic information content ranged from 0.09 to 0.37. The chi-square test showed that only RHPN2:g.42678119T>G and RALYL:g.90030866A>G were in Hardy-Weinberg disequilibrium (p < 0.05); the other loci were in equilibrium (p > 0.05). These SNPs associated with important traits in Alpine Merino sheep provide a theoretical basis for genomic selection and molecular design breeding.
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Affiliation(s)
- Tong Xiao
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (T.X.); (Z.L.); (C.Y.); (Y.S.); (B.Y.)
| | - Yuhang Li
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China;
| | - Lin Yue
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (T.X.); (Z.L.); (C.Y.); (Y.S.); (B.Y.)
| | - Zengkui Lu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (T.X.); (Z.L.); (C.Y.); (Y.S.); (B.Y.)
- Sheep Breeding Engineering Technology Research Center, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Chao Yuan
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (T.X.); (Z.L.); (C.Y.); (Y.S.); (B.Y.)
- Sheep Breeding Engineering Technology Research Center, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Yali Song
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (T.X.); (Z.L.); (C.Y.); (Y.S.); (B.Y.)
| | - Bohui Yang
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (T.X.); (Z.L.); (C.Y.); (Y.S.); (B.Y.)
- Sheep Breeding Engineering Technology Research Center, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Jianbin Liu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (T.X.); (Z.L.); (C.Y.); (Y.S.); (B.Y.)
- Sheep Breeding Engineering Technology Research Center, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Tingting Guo
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (T.X.); (Z.L.); (C.Y.); (Y.S.); (B.Y.)
- Sheep Breeding Engineering Technology Research Center, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
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9
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Unlusoy I. Determination of declined genetic diversity of Holstein stud bulls based on microsatellite markers. Anim Biotechnol 2023; 34:4627-4633. [PMID: 36847656 DOI: 10.1080/10495398.2023.2176866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Semen importing countries are trying to select the most suitable studs according to their breeding goals, while the globally widespread use of common genetic material has been turning the loss of genetic diversity into a possible danger. The aim of this study was to evaluate the genetic diversity of 304 high-yielding Holstein stud bulls whose semen were produced in Turkiye, Europe and the Americas. The values of allele frequencies, expected heterozygosity (He), observed heterozygosity (Ho), Hardy-Weinberg (HW) Equilibrium, the number of alleles per locus (Na), allelic richness (Rs), polymorphic information content (PIC) and F-statistics were calculated and compared the results with similar studies. It was observed that some indicator values of the genetic diversity were decreased compared to the values of the other studies in Holstein breed. Especially the decrease in some values of SPS115 locus was statistically significant. It is thought that this could be as a result of SPS115 to be close to possible QTL regions associated with traits which indicates overall potential of selection in stud bulls. Therefore, while applying a selection program to populations, national genetic resource management strategies that maintain genetic diversity should not be forgotten besides gaining high yield.
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Affiliation(s)
- Ilke Unlusoy
- Department of Animal Breeding and Genetics, International Center for Livestock Research and Training, Ankara, Turkiye
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10
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Yuan Z, Ge L, Su P, Gu Y, Chen W, Cao X, Wang S, Lv X, Getachew T, Mwacharo JM, Haile A, Sun W. NCAPG Regulates Myogenesis in Sheep, and SNPs Located in Its Putative Promoter Region Are Associated with Growth and Development Traits. Animals (Basel) 2023; 13:3173. [PMID: 37893897 PMCID: PMC10603679 DOI: 10.3390/ani13203173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/02/2023] [Accepted: 10/07/2023] [Indexed: 10/29/2023] Open
Abstract
Previously, NCAPG was identified as a candidate gene associated with sheep growth traits. This study aimed to investigate the direct role of NCAPG in regulating myogenesis in embryonic myoblast cells and to investigate the association between single-nucleotide polymorphisms (SNPs) in its promoter region and sheep growth traits. The function of NCAPG in myoblast proliferation and differentiation was detected after small interfering RNAs (siRNAs) knocked down the expression of NCAPG. Cell proliferation was detected using CCK-8 assay, EdU proliferation assay, and flow cytometry cell cycle analysis. Cell differentiation was detected via cell immunofluorescence and the quantification of myogenic regulatory factors (MRFs). SNPs in the promoter region were detected using Sanger sequencing and genotyped using the improved multiplex ligation detection reaction (iMLDR®) technique. As a result, a notable decrease (p < 0.01) in the percentage of EdU-positive cells in the siRNA-694-treated group was observed. A significant decrease (p < 0.01) in cell viability after treatment with siRNA-694 for 48 h and 72 h was detected using the CCK-8 method. The quantity of S-phase cells in the siRNA-694 treatment group was significantly decreased (p < 0.01). After interfering with NCAPG in myoblasts during induced differentiation, the relative expression levels of MRFs were markedly (p < 0.05 or p < 0.01) reduced compared with the control group on days 5-7. The myoblast differentiation in the siRNA-694 treatment group was obviously suppressed compared with the control group. SNP1, SNP2, SNP3, and SNP4 were significantly (p < 0.05) associated with all traits except body weight measured at birth and one month of age. SNP5 was significantly (p < 0.05) associated with body weight, body height, and body length in six-month-old sheep. In conclusion, interfering with NCAPG can inhibit the proliferation and differentiation of ovine embryonic myoblasts. SNPs in its promoter region can serve as potential useful markers for selecting sheep growth traits.
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Affiliation(s)
- Zehu Yuan
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (Z.Y.); (L.G.); (P.S.); (Y.G.); (W.C.); (X.C.); (S.W.); (X.L.)
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China
| | - Ling Ge
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (Z.Y.); (L.G.); (P.S.); (Y.G.); (W.C.); (X.C.); (S.W.); (X.L.)
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Pengwei Su
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (Z.Y.); (L.G.); (P.S.); (Y.G.); (W.C.); (X.C.); (S.W.); (X.L.)
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Yifei Gu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (Z.Y.); (L.G.); (P.S.); (Y.G.); (W.C.); (X.C.); (S.W.); (X.L.)
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Weihao Chen
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (Z.Y.); (L.G.); (P.S.); (Y.G.); (W.C.); (X.C.); (S.W.); (X.L.)
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Xiukai Cao
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (Z.Y.); (L.G.); (P.S.); (Y.G.); (W.C.); (X.C.); (S.W.); (X.L.)
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China
| | - Shanhe Wang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (Z.Y.); (L.G.); (P.S.); (Y.G.); (W.C.); (X.C.); (S.W.); (X.L.)
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Xiaoyang Lv
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (Z.Y.); (L.G.); (P.S.); (Y.G.); (W.C.); (X.C.); (S.W.); (X.L.)
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China
| | - Tesfaye Getachew
- International Centre for Agricultural Research in the Dry Areas, Addis Ababa 999047, Ethiopia; (T.G.); (J.M.M.); (A.H.)
| | - Joram M. Mwacharo
- International Centre for Agricultural Research in the Dry Areas, Addis Ababa 999047, Ethiopia; (T.G.); (J.M.M.); (A.H.)
| | - Aynalem Haile
- International Centre for Agricultural Research in the Dry Areas, Addis Ababa 999047, Ethiopia; (T.G.); (J.M.M.); (A.H.)
| | - Wei Sun
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (Z.Y.); (L.G.); (P.S.); (Y.G.); (W.C.); (X.C.); (S.W.); (X.L.)
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- “Innovative China” “Belt and Road” International Agricultural Technology Innovation Institute for Evaluation, Protection, and Improvement on Sheep Genetic Resource, Yangzhou 225009, China
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11
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Xie S, Isaacs K, Becker G, Murdoch BM. A computational framework for improving genetic variants identification from 5,061 sheep sequencing data. J Anim Sci Biotechnol 2023; 14:127. [PMID: 37779189 PMCID: PMC10544426 DOI: 10.1186/s40104-023-00923-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 08/01/2023] [Indexed: 10/03/2023] Open
Abstract
BACKGROUND Pan-genomics is a recently emerging strategy that can be utilized to provide a more comprehensive characterization of genetic variation. Joint calling is routinely used to combine identified variants across multiple related samples. However, the improvement of variants identification using the mutual support information from multiple samples remains quite limited for population-scale genotyping. RESULTS In this study, we developed a computational framework for joint calling genetic variants from 5,061 sheep by incorporating the sequencing error and optimizing mutual support information from multiple samples' data. The variants were accurately identified from multiple samples by using four steps: (1) Probabilities of variants from two widely used algorithms, GATK and Freebayes, were calculated by Poisson model incorporating base sequencing error potential; (2) The variants with high mapping quality or consistently identified from at least two samples by GATK and Freebayes were used to construct the raw high-confidence identification (rHID) variants database; (3) The high confidence variants identified in single sample were ordered by probability value and controlled by false discovery rate (FDR) using rHID database; (4) To avoid the elimination of potentially true variants from rHID database, the variants that failed FDR were reexamined to rescued potential true variants and ensured high accurate identification variants. The results indicated that the percent of concordant SNPs and Indels from Freebayes and GATK after our new method were significantly improved 12%-32% compared with raw variants and advantageously found low frequency variants of individual sheep involved several traits including nipples number (GPC5), scrapie pathology (PAPSS2), seasonal reproduction and litter size (GRM1), coat color (RAB27A), and lentivirus susceptibility (TMEM154). CONCLUSION The new method used the computational strategy to reduce the number of false positives, and simultaneously improve the identification of genetic variants. This strategy did not incur any extra cost by using any additional samples or sequencing data information and advantageously identified rare variants which can be important for practical applications of animal breeding.
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Affiliation(s)
- Shangqian Xie
- Department of Animal, Veterinary & Food Sciences, University of Idaho, Moscow, ID, USA
| | | | - Gabrielle Becker
- Department of Animal, Veterinary & Food Sciences, University of Idaho, Moscow, ID, USA
| | - Brenda M Murdoch
- Department of Animal, Veterinary & Food Sciences, University of Idaho, Moscow, ID, USA.
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12
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Adeniyi OO, Medugorac I, Grochowska E, Düring RA, Lühken G. Single-Locus and Multi-Locus Genome-Wide Association Studies Identify Genes Associated with Liver Cu Concentration in Merinoland Sheep. Genes (Basel) 2023; 14:genes14051053. [PMID: 37239413 DOI: 10.3390/genes14051053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/02/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
Abstract
Economic losses due to copper intoxication or deficiency is a problem encountered by sheep farmers. The aim of this study was to investigate the ovine genome for genomic regions and candidate genes responsible for variability in liver copper concentration. Liver samples were collected from slaughtered lambs of the Merinoland breed from two farms, and used for measurement of copper concentration and genome-wide association study (GWAS). A total of 45,511 SNPs and 130 samples were finally used for analysis, in which single-locus and several multi-locus GWAS (SL-GWAS; ML-GWAS) methods were employed. Gene enrichment analysis was performed for identified candidate genes to detect gene ontology (GO) terms significantly associated with hepatic copper levels. The SL-GWAS and a minimum of two ML-GWAS identified two and thirteen significant SNPs, respectively. Within genomic regions surrounding identified SNPs, we observed nine promising candidate genes such as DYNC1I2, VPS35, SLC38A9 and CHMP1A. GO terms such as lysosomal membrane, mitochondrial inner membrane and sodium:proton antiporter activity were significantly enriched. Genes involved in these identified GO terms mediate multivesicular body (MVB) fusion with lysosome for degradation and control mitochondrial membrane permeability. This reveals the polygenic status of this trait and candidate genes for further studies on breeding for copper tolerance in sheep.
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Affiliation(s)
- Olusegun O Adeniyi
- Institute of Animal Breeding and Genetics, Justus Liebig University Giessen, Ludwigstrasse 21, 35390 Giessen, Germany
| | - Ivica Medugorac
- Population Genomics Group, Department of Veterinary Sciences, Ludwig Maximilian University Munich, Lena-Christ-Str. 48, 82152 Martinsried, Germany
| | - Ewa Grochowska
- Department of Animal Biotechnology and Genetics, Bydgoszcz University of Science and Technology, Mazowiecka 28 St., 85-084 Bydgoszcz, Poland
| | - Rolf-Alexander Düring
- Institute of Soil Science and Soil Conservation, Interdisciplinary Research Center for Biosystems, Land Use and Nutrition (IFZ), Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Gesine Lühken
- Institute of Animal Breeding and Genetics, Justus Liebig University Giessen, Ludwigstrasse 21, 35390 Giessen, Germany
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13
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Liu M, Lan Q, Yang L, Deng Q, Wei T, Zhao H, Peng P, Lin X, Chen Y, Ma H, Wei H, Yin Y. Genome-Wide Association Analysis Identifies Genomic Regions and Candidate Genes for Growth and Fatness Traits in Diannan Small-Ear (DSE) Pigs. Animals (Basel) 2023; 13:ani13091571. [PMID: 37174608 PMCID: PMC10177038 DOI: 10.3390/ani13091571] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/13/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
In the livestock industry, the growth and fatness traits are directly related to production efficiency and economic profits. As for Diannan small-ear (DSE) pigs, a unique indigenous breed, the genetic architecture of growth and fatness traits is still elusive. The aim of this study was to search the genetic loci and candidate genes associated with phenotypic traits in DSE pigs using GWAS based on the Geneseek Porcine 50K SNP Chip data. A total of 22,146 single nucleotide polymorphisms (SNPs) were detected in 265 DSE pigs and used for Genome-wide association studies (GWAS) analysis. Seven SNPs were found to be associated with back height, chest circumference, cannon bone circumference, and backfat thickness at the suggestive significance level. Based on gene annotation results, these seven SNPs were, respectively, mapped to the following candidate genes, VIPR2, SLC10A2, NUCKS1, MCT1, CHCHD3, SMOX, and GPR1, which are mainly involved with adipocyte differentiation, lipid metabolism, skeletal muscle development, and average daily weight gain. Our work offers novel insights into the genetic architecture of economically important traits in swine and may play an important role in breeding using molecular markers in the DSE breed.
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Affiliation(s)
- Mei Liu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Qun Lan
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Long Yang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Qiuchun Deng
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Taiyun Wei
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming 650201, China
| | - Heng Zhao
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming 650201, China
| | - Peiya Peng
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Xiaoding Lin
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Yuhan Chen
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Haiming Ma
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Hongjiang Wei
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming 650201, China
| | - Yulong Yin
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
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Liu Y, Mu Y, Wang W, Ahmed Z, Wei X, Lei C, Ma Z. Analysis of genomic copy number variations through whole-genome scan in Chinese Qaidam cattle. Front Vet Sci 2023; 10:1148070. [PMID: 37065216 PMCID: PMC10103646 DOI: 10.3389/fvets.2023.1148070] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 03/01/2023] [Indexed: 04/03/2023] Open
Abstract
Qaidam cattle (CDM) are indigenous breed inhabiting Northwest China. In the present study, we newly sequenced 20 Qaidam cattle to investigate the copy number variants (CNVs) based on the ARS-UMD1.2 reference genome. We generated the CNV region (CNVR) datasets to explore the genomic CNV diversity and population stratification. The other four cattle breeds (Xizang cattle, XZ; Kazakh cattle, HSK; Mongolian cattle, MG; and Yanbian cattle, YB) from the regions of North China embracing 43 genomic sequences were collected and are distinguished from each of the other diverse populations by deletions and duplications. We also observed that the number of duplications was significantly more than deletions in the genome, which may be less harmful to gene formation and function. At the same time, only 1.15% of CNVRs overlapped with the exon region. Population differential CNVRs and functional annotations between the Qaidam cattle population and other cattle breeds revealed the functional genes related to immunity (MUC6), growth (ADAMTSL3), and adaptability (EBF2). Our analysis has provided numerous genomic characteristics of some Chinese cattle breeds, which are valuable as customized biological molecular markers in cattle breeding and production.
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Affiliation(s)
- Yangkai Liu
- Plateau Livestock Genetic Resources Protection and Innovative Utilization Key Laboratory of Qinghai Province, Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
- Key Laboratory of Animal Genetics and Breeding on Tibet Plateau, Ministry of Agriculture and Rural Affairs, Xining, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Yanan Mu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Wenxiang Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Zulfiqar Ahmed
- Faculty of Veterinary and Animal Sciences, University of Poonch Rawalakot, Rawalakot, Pakistan
| | - Xudong Wei
- Plateau Livestock Genetic Resources Protection and Innovative Utilization Key Laboratory of Qinghai Province, Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
- Key Laboratory of Animal Genetics and Breeding on Tibet Plateau, Ministry of Agriculture and Rural Affairs, Xining, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
- Chuzhao Lei
| | - Zhijie Ma
- Plateau Livestock Genetic Resources Protection and Innovative Utilization Key Laboratory of Qinghai Province, Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
- Key Laboratory of Animal Genetics and Breeding on Tibet Plateau, Ministry of Agriculture and Rural Affairs, Xining, China
- *Correspondence: Zhijie Ma
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15
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Arzik Y, Kizilaslan M, Behrem S, White SN, Piel LMW, Cinar MU. Genome-Wide Scan of Wool Production Traits in Akkaraman Sheep. Genes (Basel) 2023; 14:genes14030713. [PMID: 36980985 PMCID: PMC10048666 DOI: 10.3390/genes14030713] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 12/26/2022] [Accepted: 03/10/2023] [Indexed: 03/17/2023] Open
Abstract
The objective of this study was to uncover the genetic background of wool quality, a production trait, by estimating genomic heritability and implementing GWAS in Akkaraman sheep. The wool characteristics measured included fibre diameter (FD) and staple length (SL) at the age of 8 months and yearling fibre diameter (YFD), yearling staple length (YSL) and yearling greasy fleece weight (YGFW) at 18 months of age. Animals were genotyped using the Axiom 50 K Ovine Genotyping Array. Maximum likelihood estimations of a linear mixed model (LMM) were used to estimate genomic heritability, where GWAS was conducted following a score test of each trait. Genomic heritability estimates for the traits ranged between 0.22 and 0.63, indicating that phenotypes have a moderate range of heritability. One genome- and six chromosome-wide significant SNPs were associated with the wool traits in Akkaraman lambs. Accordingly, TRIM2, MND1, TLR2, RNF175, CEP290, TMTC3, RERE, SLC45A1, SOX2, MORN1, SKI, FAAP20, PRKCZ, GABRD, CFAP74, CALML6 and TMEM52 genes as well as nine uncharacterized regions (LOC101118971, LOC105609137, LOC105603067, LOC101122892, LOC106991694, LOC106991467, LOC106991455, LOC105616534 and LOC105609719) were defined as plausible candidates. The findings of this study shed light on the genetics of wool quality and yield for the Akkaraman breed and suggests targets for breeders during systematic breeding programmes.
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Affiliation(s)
- Yunus Arzik
- Department of Animal Science, Faculty of Agriculture, Erciyes University, 38039 Kayseri, Türkiye
- International Center for Livestock Research and Training Center, Ministry of Agriculture and Forestry, 06852 Ankara, Türkiye
| | - Mehmet Kizilaslan
- Department of Animal Science, Faculty of Agriculture, Erciyes University, 38039 Kayseri, Türkiye
- International Center for Livestock Research and Training Center, Ministry of Agriculture and Forestry, 06852 Ankara, Türkiye
- Correspondence: ; Tel.: +90-553-6725986
| | - Sedat Behrem
- Department of Animal Science, Faculty of Veterinary Medicine, Aksaray University, 68100 Aksaray, Türkiye
| | - Stephen N. White
- Department of Veterinary Microbiology & Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
| | - Lindsay M. W. Piel
- USDA-ARS Animal Disease Research 3003 ADBF, Washington State University, Pullman, WA 99164, USA
| | - Mehmet Ulas Cinar
- Department of Animal Science, Faculty of Agriculture, Erciyes University, 38039 Kayseri, Türkiye
- Department of Veterinary Microbiology & Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
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Gul S, Arzik Y, Kizilaslan M, Behrem S, Keskin M. Heritability and environmental influence on pre-weaning traits in Kilis goats. Trop Anim Health Prod 2023; 55:85. [PMID: 36800041 DOI: 10.1007/s11250-023-03509-3] [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: 06/01/2022] [Accepted: 02/11/2023] [Indexed: 02/18/2023]
Abstract
Birth and weaning weights, average daily weight gain, and Kleiber ratio are important indicator traits in selection decision. The phenotypic expression of these traits is determined by the genetic background, environmental effects, and their interactions. The objective of this study was to estimate genetic parameters regarding birth (BW) and weaning weights (WW) and average daily weight gain (ADWG), Kleiber ratio (KR), and obtain the effects of sex, birth type, herd, and year. The data consisted of 2274 Kilis goats with pedigree information obtained from 53 bucks and 774 does in 4 generations. The restricted maximum likelihood (REML) procedure was conducted with an animal linear mixed model. Sex, birth type, herd, and year were found to be statistically significant (p value < 0.001) for all traits. Moderate direct heritabilities (ha2) for BW, WW, ADW, and KR were found to be as 0.18 ± 0.03, 0.50 ± 0.04, 0.47 ± 0.04, and 0.37 ± 0.05, respectively. The proportion of maternal permanent environmental effect (c2) to the total phenotypic variance (σ2p) was estimated as 0.00 ± 0.00, 0.12 ± 0.02, 0.11 ± 0.02, and 0.18 ± 0.03 for BW, WW, ADWG, and KR, respectively. The genetic, phenotypic, and environmental correlations between the pre-weaning growth traits were found to be ranging from - 0.02 to 0.99. Thus, our study suggests moderate heritabilities and positive and relatively high genetic correlations among the observed pre-weaning growth traits. These results have implications in terms of providing rapid genetic progress for these traits in breeding programs of Kilis goats.
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Affiliation(s)
- Sabri Gul
- Agriculture Faculty, Mustafa Kemal University, Hatay, Turkey.
| | - Yunus Arzik
- International Centre for Livestock Research and Training, Ankara, Turkey
| | - Mehmet Kizilaslan
- International Centre for Livestock Research and Training, Ankara, Turkey
| | - Sedat Behrem
- Veterinary Faculty, Aksaray University, Aksaray, Turkey
| | - Mahmut Keskin
- Agriculture Faculty, Mustafa Kemal University, Hatay, Turkey
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17
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Cis-eQTL Analysis and Functional Validation of Candidate Genes for Carcass Yield Traits in Beef Cattle. Int J Mol Sci 2022; 23:ijms232315055. [PMID: 36499383 PMCID: PMC9736101 DOI: 10.3390/ijms232315055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/19/2022] [Accepted: 11/21/2022] [Indexed: 12/04/2022] Open
Abstract
Carcass yield traits are of considerable economic importance for farm animals, which act as a major contributor to the world’s food supply. Genome-wide association studies (GWASs) have identified many genetic variants associated with carcass yield traits in beef cattle. However, their functions are not effectively illustrated. In this study, we performed an integrative analysis of gene-based GWAS with expression quantitative trait locus (eQTL) analysis to detect candidate genes for carcass yield traits and validate their effects on bovine skeletal muscle satellite cells (BSCs). The gene-based GWAS and cis-eQTL analysis revealed 1780 GWAS and 1538 cis-expression genes. Among them, we identified 153 shared genes that may play important roles in carcass yield traits. Notably, the identified cis-eQTLs of PON3 and PRIM2 were significantly (p < 0.001) enriched in previous GWAS loci for carcass traits. Furthermore, overexpression of PON3 and PRIM2 promoted the BSCs’ proliferation, increased the expression of MYOD and downregulated the expression of MYOG, which indicated that these genes may inhibit myogenic differentiation. In contrast, PON3 and PRIM2 were significantly downregulated during the differentiation of BSCs. These findings suggested that PON3 and PRIM2 may promote the proliferation of BSCs and inhibit them in the pre-differentiation stage. Our results further contribute to the understanding of the molecular mechanisms of carcass yield traits in beef cattle.
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18
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Arzik Y, Kizilaslan M, White SN, Piel LMW, Çınar MU. Genomic Analysis of Gastrointestinal Parasite Resistance in Akkaraman Sheep. Genes (Basel) 2022; 13:2177. [PMID: 36553445 PMCID: PMC9778220 DOI: 10.3390/genes13122177] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/15/2022] [Accepted: 11/19/2022] [Indexed: 11/23/2022] Open
Abstract
Genome-wide association studies (GWAS) have been used as an effective tool to understand the genetics of complex traits such as gastrointestinal parasite (GIP) resistance. The aim of this study was to understand the genetics of gastrointestinal parasite (nematodes, Moniezia spp., Eimeria spp.) resistance in Akkaraman sheep by performing genomic heritability estimations and conducting GWAS to uncover responsible genomic regions. This is one of the first studies to examine the genetic resistance of Akkaraman sheep to the tapeworm parasite. The samples from 475 animals were genotyped using the Axiom 50K Ovine Genotyping Array. Genomic heritability estimates ranged from 0.00 to 0.34 for parasite resistance traits. This indicates that measured phenotypes have low to moderate heritability estimates. A total of two genome-wide significant SNP associated with TNEM3 and ATRNL1 genes and 10 chromosome-wide significant SNPs related with 10 genes namely NELL1, ST6GALNAC3, HIPK1, SYT1, ALK, ZNF596, TMCO5A, PTH2R, LARGE1, and SCG2 were suggested as candidates for parasite resistance traits. The majority of these candidate genes were involved in several basic biological processes that are essential and important for immune system functions and cellular growth; specifically, inflammatory responses, cellular transport, cell apoptosis, cell differentiation, histone de-acetylation, and endocytosis. These results have implications for animal breeding program studies due to the effect that the genetic background has on parasite resistance, which underlies many productive, health, and wellness-related traits.
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Affiliation(s)
- Yunus Arzik
- Department of Animal Science, Faculty of Agriculture, Erciyes University, Kayseri 38039, Turkey
- International Center for Livestock Research and Training, Ministry of Agriculture and Forestry, Ankara 06852, Turkey
| | - Mehmet Kizilaslan
- Department of Animal Science, Faculty of Agriculture, Erciyes University, Kayseri 38039, Turkey
- International Center for Livestock Research and Training, Ministry of Agriculture and Forestry, Ankara 06852, Turkey
| | - Stephen N. White
- Department of Veterinary Microbiology & Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
| | - Lindsay M. W. Piel
- USDA-ARS Animal Disease Research, 3003 Animal Disease Biotech Facility, Washington State University, Pullman, WA 99164, USA
| | - Mehmet Ulaş Çınar
- Department of Animal Science, Faculty of Agriculture, Erciyes University, Kayseri 38039, Turkey
- Department of Veterinary Microbiology & Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
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19
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Estimates of genomic heritability and genome-wide association studies for blood parameters in Akkaraman sheep. Sci Rep 2022; 12:18477. [PMID: 36323871 PMCID: PMC9630504 DOI: 10.1038/s41598-022-22966-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022] Open
Abstract
The aim of this study was to estimate genomic heritability and the impact that genetic backgrounds have on blood parameters in Akkaraman sheep by conducting genome-wide association studies and regional heritability mapping analysis. Genomic heritability estimates for blood parameters ranged from 0.00 to 0.55, indicating that measured phenotypes have a low to moderate heritability. A total of 7 genome- and 13 chromosome-wide significant SNPs were associated with phenotypic changes in 15 blood parameters tested. Accordingly, SCN7A, SCN9A, MYADM-like, CCDC67, ITGA9, MGAT5, SLC19A1, AMPH, NTRK2, MSRA, SLC35F3, SIRT6, CREB3L3, and NAV3 genes as well as three undefined regions (LOC101117887, LOC106991526 and LOC105608461) were suggested as candidates. Most of the identified genes were involved in basic biological processes that are essential to immune system function and cellular growth; specific functions include cellular transport, histone deacetylation, cell differentiation, erythropoiesis, and endocytosis. The top significant SNP for HCT, MCH, and MCHC was found within a genomic region mainly populated by the MYADM-like gene family. This region was previously suggested to be under historical selection pressure in many sheep breeds from various parts of the world. These results have implications on animal breeding program studies due to the effect that the genetic background has on blood parameters, which underlying many productive and wellness related traits.
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Li X, Yuan L, Wang W, Zhang D, Zhao Y, Chen J, Xu D, Zhao L, Li F, Zhang X. Whole genome re-sequencing reveals artificial and natural selection for milk traits in East Friesian sheep. Front Vet Sci 2022; 9:1034211. [PMID: 36330154 PMCID: PMC9623881 DOI: 10.3389/fvets.2022.1034211] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 09/30/2022] [Indexed: 08/23/2023] Open
Abstract
The East Friesian sheep is one of the important high-yielding dairy sheep breeds, but still little is known about their genetic and genomic variation during domestication. Therefore, we analyzed the genomic data of 46 sheep with the aim of identifying candidate genes that are closely related to milk production traits. Our genomic data consisted of 20 East Friesian sheep and 26 Asian Mouflon wild sheep. Finally, a total of 32590241 SNPs were identified, of which 0.61% (198277) SNPs were located in exonic regions. After further screening, 122 shared genomic regions in the top 1% of F ST and top 1% of Nucleotide diversity ratio were obtained. After genome annotation, these 122 candidate genomic regions were found to contain a total of 184 candidate genes. Finally, the results of KEGG enrichment analysis showed four significantly enriched pathways (P < 0.05): beta-Alanine metabolism (SMOX, HIBCH), Pathways in cancer (GLI2, AR, TXNRD3, TRAF3, FGF16), Non-homologous end-joining (MRE11), Epstein-Barr virus infection (TRAF3, PSMD13, SIN3A). Finally, we identified four important KEGG enrichment pathways and 10 candidate genes that are closely related to milk production in East Friesian sheep. These results provide valuable candidate genes for the study of milk production traits in East Friesian sheep and lay an important foundation for the study of milk production traits.
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Affiliation(s)
- Xiaolong Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Lvfeng Yuan
- Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Weimin Wang
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Deyin Zhang
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Yuan Zhao
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Jiangbo Chen
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Dan Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Liming Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Fadi Li
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
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Kizilaslan M, Arzik Y, White SN, Piel LMW, Cinar MU. Genetic Parameters and Genomic Regions Underlying Growth and Linear Type Traits in Akkaraman Sheep. Genes (Basel) 2022; 13:genes13081414. [PMID: 36011330 PMCID: PMC9407525 DOI: 10.3390/genes13081414] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/06/2022] [Accepted: 08/08/2022] [Indexed: 02/07/2023] Open
Abstract
In the current study, the genetic architecture of growth and linear type traits were investigated in Akkaraman sheep. Estimations of genomic heritability, genetic correlations, and phenotypic correlations were implemented for 17 growth and linear type traits of 473 Akkaraman lambs by the univariate and multivariate analysis of animal mixed models. Correspondingly, moderate heritability estimates, as well as high and positive genetic/phenotypic correlations were found between growth and type traits. On the other hand, 2 genome-wide and 19 chromosome-wide significant single nucleotide polymorphisms were found to be associated with the traits as a result of animal mixed model-based genome-wide association analyses. Accordingly, we propose several genes located on different chromosomes (e.g., PRDM2, PTGDR, PTPRG, KCND2, ZNF260, CPE, GRID2, SCD5, SPIDR, ZNF407, HCN3, TMEM50A, FKBP1A, TLE4, SP1, SLC44A1, and MYOM3) as putative quantitative trait loci for the 22 growth and linear type traits studied. In our study, specific genes (e.g., TLE4, PTGDR, and SCD5) were found common between the traits studied, suggesting an interplay between the genetic backgrounds of these traits. The fact that four of the proposed genes (TLE4, MYOM3, SLC44A1, and TMEM50A) are located on sheep chromosome 2 confirms the importance of these genomic regions for growth and morphological structure in sheep. The results of our study are therefore of great importance for the development of efficient selection indices and marker-assisted selection programs, as well as for the understanding of the genetic architecture of growth and linear traits in sheep.
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Affiliation(s)
- Mehmet Kizilaslan
- Department of Animal Science, Faculty of Agriculture, Erciyes University, Kayseri 38039, Turkey
- International Center for Livestock Research and Training Center, Ministry of Agriculture and Forestry, Ankara 06852, Turkey
| | - Yunus Arzik
- Department of Animal Science, Faculty of Agriculture, Erciyes University, Kayseri 38039, Turkey
- International Center for Livestock Research and Training Center, Ministry of Agriculture and Forestry, Ankara 06852, Turkey
| | - Stephen N. White
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
| | - Lindsay M. W. Piel
- USDA-ARS Animal Disease Research, Washington State University Pullman, Pullman, WA 991646630, USA
| | - Mehmet Ulas Cinar
- Department of Animal Science, Faculty of Agriculture, Erciyes University, Kayseri 38039, Turkey
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
- Correspondence: ; Tel.: +90-352-2076666-38601
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22
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Liu TY, Feng H, Yousuf S, Xie LL, Miao XY. Genome-Wide Analysis of microRNAs Identifies the Lipid Metabolism Pathway to Be a Defining Factor in Adipose Tissue From Different Sheep. Front Vet Sci 2022; 9:938311. [PMID: 35880040 PMCID: PMC9308008 DOI: 10.3389/fvets.2022.938311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
microRNAs are a class of important non-coding RNAs, which can participate in the regulation of biological processes. In recent years, miRNA has been widely studied not only in humans and mice, but also in animal husbandry. However, compared with other livestock and poultry breeds, the study of miRNA in subcutaneous adipose tissue of sheep is not comprehensive. Transcriptome analysis of miRNAs in subcutaneous adipose tissue of Duolang sheep, and Small Tail Han sheep was performed using RNA-Seq technology. Differentially expressed miRNAs were screened between different breeds. Target genes were predicted, and then the joint analysis of candidate genes were conducted based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment. Finally, the RNA-Seq data were verified by real-time quantitative polymerase chain reaction (qRT-PCR). Herein, we identified 38 differentially expressed miRNAs (9 novel miRNAs and 29 known miRNAs). In addition, a total of 854 target genes were predicted by miRanda software. GO and KEGG pathway analysis demonstrated that regulation of lipolysis in adipocytes plays a key role in the deposition of subcutaneous adipose tissue in Duolang sheep and Small Tail Han sheep. The miRNAs might regulate fat deposits by regulating genes involved in regulation of lipolysis in adipocytes. Specifically, NC_ 040278.1_ 37602, oar-mir-493-3p, NC_ 040278.1_ 37521 and NC_ 040255.1_ 11627 might target PTGS2, AKT2, AKT3, and PIK3CA, respectively, and then play critical regulatory role. In conclusion, all the results provide a good idea for further revealing the mechanism of subcutaneous adipose tissue deposition and improving the meat production performance of sheep, and lay a foundation for promoting the development of animal husbandry.
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