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Rajawat D, Nayak SS, Jain K, Sharma A, Parida S, Sahoo SP, Bhushan B, Patil DB, Dutt T, Panigrahi M. Genomic patterns of selection in morphometric traits across diverse Indian cattle breeds. Mamm Genome 2024:10.1007/s00335-024-10047-2. [PMID: 39014170 DOI: 10.1007/s00335-024-10047-2] [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: 02/09/2024] [Accepted: 06/09/2024] [Indexed: 07/18/2024]
Abstract
This study seeks a comprehensive exploration of genome-wide selective processes impacting morphometric traits across diverse cattle breeds, utilizing an array of statistical methods. Morphometric traits, encompassing both qualitative and quantitative variables, play a pivotal role in characterizing and selecting livestock breeds based on their external appearance, size, and physical attributes. While qualitative traits, such as color, horn structure, and coat type, contribute to adaptive features and breed identification, quantitative traits like body weight and conformation measurements bear a closer correlation with production characteristics. This study employs advanced genotyping technologies, including the Illumina BovineSNP50 Bead Chip and next-generation sequencing methods like Reduced Representation sequencing, to identify genomic signatures associated with these traits. We applied four intra-population methods to find evidence of selection, such as Tajima's D, CLR, iHS, and ROH. We found a total of 40 genes under the selection signature, that were associated with morphometric traits in five cattle breeds (Kankrej, Tharparkar, Nelore, Sahiwal, and Gir). Crucial genes such as ADIPDQ, DPP6, INSIG1, SLC35D2 in Kankrej, LPL, ATP6V1B2, CDC14B in Tharparkar, HPSE2, PLAG1 in Nelore, PCSK1, PRKD1 in Sahiwal, and GNAQ, HPCAL1 in Gir were identified in our study. This approach provides valuable insights into the genetic basis of variations in body weight and conformation traits, facilitating informed selection processes and offering a deeper understanding of the evolutionary and domestication processes in diverse cattle breeds.
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Affiliation(s)
- Divya Rajawat
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | - Karan Jain
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | - Anurodh Sharma
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | - Subhashree Parida
- Division of Pharmacology & Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | | | - Bharat Bhushan
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | | | - Triveni Dutt
- Livestock Production and Management Section, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | - Manjit Panigrahi
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India.
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Zhang W, Lu Z, Guo T, Yuan C, Liu J. Construction of a high-density genetic map and QTL localization of body weight and wool production related traits in Alpine Merino sheep based on WGR. BMC Genomics 2024; 25:641. [PMID: 38937677 PMCID: PMC11212225 DOI: 10.1186/s12864-024-10535-4] [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: 12/05/2023] [Accepted: 06/17/2024] [Indexed: 06/29/2024] Open
Abstract
BACKGROUND The Alpine Merino is a new breed of fine-wool sheep adapted to the cold and arid climate of the plateau in the world. It has been popularized in Northwest China due to its superior adaptability as well as excellent production performance. Those traits related to body weight, wool yield, and wool fiber characteristics, which are economically essential traits in Alpine Merino sheep, are controlled by QTL (Quantitative Trait Loci). Therefore, the identification of QTL and genetic markers for these key economic traits is a critical step in establishing a MAS (Marker-Assisted Selection) breeding program. RESULTS In this study, we constructed the high-density genetic linkage map of Alpine Merino sheep by sequencing 110 F1 generation individuals using WGR (Whole Genome Resequencing) technology. 14,942 SNPs (Single Nucleotide Polymorphism) were identified and genotyped. The map spanned 2,697.86 cM, with an average genetic marker interval of 1.44 cM. A total of 1,871 high-quality SNP markers were distributed across 27 linkage groups, with an average of 69 markers per LG (Linkage Group). Among them, the smallest genetic distance is 19.62 cM for LG2, while the largest is 237.19 cM for LG19. The average genetic distance between markers in LGs ranged from 0.24 cM (LG2) to 3.57 cM (LG17). The marker density in the LGs ranged from LG14 (39 markers) to LG1 (150 markers). CONCLUSIONS The first genetic map of Alpine Merino sheep we constructed included 14,942 SNPs, while 46 QTLs associated with body weight, wool yield and wool fiber traits were identified, laying the foundation for genetic studies and molecular marker-assisted breeding. Notably, there were QTL intervals for overlapping traits on LG4 and LG8, providing potential opportunities for multi-trait co-breeding and further theoretical support for selection and breeding of ultra-fine and meaty Alpine Merino sheep.
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Affiliation(s)
- Wentao Zhang
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Zengkui Lu
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Tingting Guo
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Chao Yuan
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China.
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China.
| | - Jianbin Liu
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China.
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China.
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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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Sheet S, Jang SS, Kim JH, Park W, Kim D. A transcriptomic analysis of skeletal muscle tissues reveals promising candidate genes and pathways accountable for different daily weight gain in Hanwoo cattle. Sci Rep 2024; 14:315. [PMID: 38172605 PMCID: PMC10764957 DOI: 10.1038/s41598-023-51037-9] [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: 08/08/2023] [Accepted: 12/29/2023] [Indexed: 01/05/2024] Open
Abstract
Cattle traits like average daily weight gain (ADG) greatly impact profitability. Selecting based on ADG considering genetic variability can lead to economic and genetic advancements in cattle breeding. This study aimed to unravel genetic influences on ADG variation in Hanwoo cattle at the skeletal muscle transcriptomic level. RNA sequencing was conducted on longissimus dorsi (LD), semimembranosus (SB), and psoas major (PM) muscles of 14 steers assigned to same feed, grouped by low (≤ 0.71 kg) and high (≥ 0.77 kg) ADG. At P ≤ 0.05 and log2fold > 1.5, the distinct pattern of gene expression was identified with 184, 172, and 210 differentially expressed genes in LD, SB, and PM muscles, respectively. Tissue-specific responses to ADG variation were evident, with myogenesis and differentiation associated JAK-STAT signaling pathway and prolactin signaling pathways enriched in LD and SB muscles, while adipogenesis-related PPAR signaling pathways were enriched in PM muscle. Key hub genes (AXIN2, CDKN1A, MYC, PTGS2, FZD5, SPP1) were upregulated and functionally significant in muscle growth and differentiation. Notably, DPP6, CDKN1A, and FZD5 emerged as possible candidate genes linked to ADG variation. These findings enhance our understanding of genetic factors behind ADG variation in Hanwoo cattle, illuminating skeletal muscle mechanisms influencing ADG.
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Affiliation(s)
- Sunirmal Sheet
- Animal Genomics and Bioinformatics Division, Rural Development Administration, National Institute of Animal Science, Wanju, 55365, Republic of Korea
| | - Sun Sik Jang
- Hanwoo Research Institute, National Institute of Animal Science, RDA, Pyeongchang, 25342, Republic of Korea
| | - Jae Hwan Kim
- Animal Genomics and Bioinformatics Division, Rural Development Administration, National Institute of Animal Science, Wanju, 55365, Republic of Korea
| | - Woncheoul Park
- Animal Genomics and Bioinformatics Division, Rural Development Administration, National Institute of Animal Science, Wanju, 55365, Republic of Korea.
| | - Dahye Kim
- Animal Genomics and Bioinformatics Division, Rural Development Administration, National Institute of Animal Science, Wanju, 55365, Republic of Korea.
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Alipanah M, Roudbari Z, Momen M, Esmailizadeh A. Impact of inclusion non-additive effects on genome-wide association and variance's components in Scottish black sheep. Anim Biotechnol 2023; 34:3765-3773. [PMID: 37343283 DOI: 10.1080/10495398.2023.2224845] [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: 06/23/2023]
Abstract
CONTEXT It's well-documented that most economic traits have a complex genetic structure that is controlled by additive and non-additive gene actions. Hence, knowledge of the underlying genetic architecture of such complex traits could aid in understanding how these traits respond to the selection in breeding and mating programs. Computing and having estimates of the non-additive effect for economic traits in sheep using genome-wide information can be important because; non-additive genes play an important role in the prediction accuracy of genomic breeding values and the genetic response to the selection. AIM This study aimed to assess the impact of non-additive effects (dominance and epistasis) on the estimation of genetic parameters for body weight traits in sheep. METHODS This study used phenotypic and genotypic belonging to 752 Scottish Blackface lambs. Three live weight traits considered in this study were included in body weight at 16, 20, and 24 weeks). Three genetic models including additive (AM), additive + dominance (ADM), and additive + dominance + epistasis (ADEM), were used. KEY RESULTS The narrow sense heritability for weight at 16 weeks of age (BW16) were 0.39, 0.35, and 0.23, for 20 weeks of age (BW20) were 0.55, 0.54, and 0.42, and finally for 24 weeks of age (BW24) were 0.16, 0.12, and 0.02, using the AM, ADM, and ADEM models, respectively. The additive genetic model significantly outperformed the non-additive genetic model (p < 0.01). The dominance variance of the BW16, BW20, and BW24 accounted for 38, 6, and 30% of the total phenotypic, respectively. Moreover, the epistatic variance accounted for 39, 0.39, and 47% of the total phenotypic variances of these traits, respectively. In addition, our results indicated that the most important SNPs for live weight traits are on chromosomes 3 (three SNPS including s12606.1, OAR3_221188082.1, and OAR3_4106875.1), 8 (OAR8_16468019.1, OAR8_18067475.1, and OAR8_18043643.1), and 19 (OAR19_18010247.1), according to the genome-wide association analysis using additive and non-additive genetic model. CONCLUSIONS The results emphasized that the non-additive genetic effects play an important role in controlling body weight variation at the age of 16-24 weeks in Scottish Blackface lambs. IMPLICATIONS It is expected that using a high-density SNP panel and the joint modeling of both additive and non-additive effects can lead to better estimation and prediction of genetic parameters.
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Affiliation(s)
- Masoud Alipanah
- Department of Plant Production, University of Torbat Heydarieh, Torbat-e Heydarieh, Iran
| | - Zahra Roudbari
- Department of Animal Science, University of Jiroft, Jiroft, Iran
| | - Mehdi Momen
- Department of Surgical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Ali Esmailizadeh
- Department of Animal Science, Shahid Bahonar University of Kerman, Kerman, Iran
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Cinar MU, Arslan K, Sohel MMH, Bayram D, Piel LMW, White SN, Daldaban F, Aksel EG, Akyüz B. Genome-wide association study of early liveweight traits in fat-tailed Akkaraman lambs. PLoS One 2023; 18:e0291805. [PMID: 37988399 PMCID: PMC10662757 DOI: 10.1371/journal.pone.0291805] [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: 09/27/2022] [Accepted: 09/06/2023] [Indexed: 11/23/2023] Open
Abstract
Small ruminants, especially sheep, are essential for sustainable agricultural production systems, future food/nutrition security, and poverty reduction in developing countries. Within developed countries, the ability of sheep to survive on low-quality forage intake could act as buffer against climate change. Besides sheep's importance in sustainable agricultural production, there has been less ongoing work in terms of sheep genetics in Near East, Middle East and in Africa. For lamb meat production, body weight and average daily gain (ADG) until weaning are critical economic traits that affects the profitability of the industry. The current study aims to identify single nucleotide polymorphisms (SNPs) that are significantly associated with pre-weaning growth traits in fat tail Akkaraman lambs using a genome-wide association study (GWAS). A total of 196 Akkaraman lambs were selected for analysis. After quality control, a total of 31,936 SNPs and 146 lambs were used for subsequent analyses. PLINK 1.9 beta software was used for the analyses. Based on Bonferroni-adjusted p-values, one SNP (rs427117280) on chromosome 2 (OAR2) had significant associations with weaning weight at day 90 and ADG from day 0 to day 90, which jointly explains a 0.8% and 0.9% of total genetic variation respectively. The Ovis aries natriuretic peptide C (NPPC) could be considered as a candidate gene for the defined significant associations. The results of the current study will help to increase understanding of the variation in weaning weight and ADG until weaning of Akkaraman lambs and help enhance selection for lambs with improved weaning weight and ADG. However, further investigations are required for the identification of causal variants within the identified genomic regions.
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Affiliation(s)
- Mehmet Ulas Cinar
- Faculty of Agriculture, Department of Animal Science, Erciyes University, Kayseri, Turkiye
- Department of Veterinary Microbiology & Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Korhan Arslan
- Faculty of Veterinary Medicine, Department of Genetics, Erciyes University, Kayseri, Turkiye
| | - Md Mahmodul Hasan Sohel
- Faculty of Veterinary Medicine, Department of Genetics, Erciyes University, Kayseri, Turkiye
- Department of Life Sciences, School of Environment and Life Sciences, Independent University, Dhaka, Bangladesh
| | - Davut Bayram
- Faculty of Veterinary Medicine, Department of Animal Science, Erciyes University, Kayseri, Turkiye
| | - Lindsay M. W. Piel
- USDA-ARS Animal Disease Res. 3003 ADBF, WSU Pullman, Pullman, Washington, United States of America
| | - Stephen N. White
- Department of Veterinary Microbiology & Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Fadime Daldaban
- Faculty of Veterinary Medicine, Department of Genetics, Erciyes University, Kayseri, Turkiye
| | - Esma Gamze Aksel
- Faculty of Veterinary Medicine, Department of Genetics, Erciyes University, Kayseri, Turkiye
| | - Bilal Akyüz
- Faculty of Veterinary Medicine, Department of Genetics, Erciyes University, Kayseri, Turkiye
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Selionova M, Aibazov M, Sermyagin A, Belous A, Deniskova T, Mamontova T, Zharkova E, Zinovieva N. Genome-Wide Association and Pathway Analysis of Carcass and Meat Quality Traits in Karachai Young Goats. Animals (Basel) 2023; 13:3237. [PMID: 37893961 PMCID: PMC10603756 DOI: 10.3390/ani13203237] [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: 08/14/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
Goats with diverse economic phenotypic traits play an important role in animal husbandry. However, the genetic mechanisms underlying complex phenotypic traits are unclear in goats. Genomic studies of variations provided a lens to identify functional genes. The work aimed to search for candidate genes related to body measurements and body weight of Karachai goats and develop an experimental PCR-RV test system for genotyping significant SNPs. Comparison of GWAS results for ages 4 and 8 months revealed 58 common SNPs for significant genotypes. 11 common SNPs were identified for body weight, 4 SNPs-for group of traits withers height, rump height, body length, 2 SNPs-for withers height and rump height, 1 SNP-for body length and chest depth. Structural annotation of genomic regions covering a window of ±0.20 Mb showed the presence of 288 genes; 52 of them had the described functions in accordance with gene ontology. The main molecular functions of proteins encoded by these genes are the regulation of transcription, cell proliferation, angiogenesis, body growth, fatty acid and lipid metabolism, nervous system development, and spermatogenesis. SNPs common to body weight and localized within a window of ±200 kb from the structural genes CRADD, HMGA2, MSRB3, FUT8, MAX, and RAB15 were selected to create a test system. The study of meat productivity after slaughter and chemical analysis of muscle tissue in Karachai goats at the age of 8 months of different genotypes according to the identified SNPs revealed that rs268269710 is the most promising for further research and use in breeding. The GG genotype is associated with a larger live weight of animals, a larger carcass yield, the content of the boneless part in it, and the ratio of protein and adipose tissue in meat preferred for dietary nutrition. These results will contribute to the genetic improvement of Karachai goats.
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Affiliation(s)
- Marina Selionova
- Subdepartment of Animal Breeding, Genetics and Biotechnology, Moscow Timiryazev Agricultural Academy, Russian State Agrarian University, Timiryazevskaya Street, 41, 127343 Moscow, Russia; (M.S.); (T.M.)
| | - Magomet Aibazov
- North Caucasian Agrarian Center, Zootechnicheski 15, 355017 Stavropol, Russia;
| | - Alexander Sermyagin
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy 60, 142132 Moscow, Russia; (A.S.); (A.B.); (T.D.); (N.Z.)
| | - Anna Belous
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy 60, 142132 Moscow, Russia; (A.S.); (A.B.); (T.D.); (N.Z.)
| | - Tatiana Deniskova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy 60, 142132 Moscow, Russia; (A.S.); (A.B.); (T.D.); (N.Z.)
| | - Tatiana Mamontova
- Subdepartment of Animal Breeding, Genetics and Biotechnology, Moscow Timiryazev Agricultural Academy, Russian State Agrarian University, Timiryazevskaya Street, 41, 127343 Moscow, Russia; (M.S.); (T.M.)
| | - Ekaterina Zharkova
- Subdepartment of Animal Breeding, Genetics and Biotechnology, Moscow Timiryazev Agricultural Academy, Russian State Agrarian University, Timiryazevskaya Street, 41, 127343 Moscow, Russia; (M.S.); (T.M.)
| | - Natalia Zinovieva
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy 60, 142132 Moscow, Russia; (A.S.); (A.B.); (T.D.); (N.Z.)
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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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9
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Li Y, Yang H, Guo J, Yang Y, Yu Q, Guo Y, Zhang C, Wang Z, Zuo P. Uncovering the candidate genes related to sheep body weight using multi-trait genome-wide association analysis. Front Vet Sci 2023; 10:1206383. [PMID: 37662987 PMCID: PMC10469697 DOI: 10.3389/fvets.2023.1206383] [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: 04/15/2023] [Accepted: 08/04/2023] [Indexed: 09/05/2023] Open
Abstract
In sheep, body weight is an economically important trait. This study sought to map genetic loci related to weaning weight and yearling weight. To this end, a single-trait and multi-trait genome-wide association study (GWAS) was performed using a high-density 600 K single nucleotide polymorphism (SNP) chip. The results showed that 43 and 56 SNPs were significantly associated with weaning weight and yearling weight, respectively. A region associated with both weaning and yearling traits (OARX: 6.74-7.04 Mb) was identified, suggesting that the same genes could play a role in regulating both these traits. This region was found to contain three genes (TBL1X, SHROOM2 and GPR143). The most significant SNP was Affx-281066395, located at 6.94 Mb (p = 1.70 × 10-17), corresponding to the SHROOM2 gene. We also identified 93 novel SNPs elated to sheep weight using multi-trait GWAS analysis. A new genomic region (OAR10: 76.04-77.23 Mb) with 22 significant SNPs were discovered. Combining transcriptomic data from multiple tissues and genomic data in sheep, we found the HINT1, ASB11 and GPR143 genes may involve in sheep body weight. So, multi-omic anlaysis is a valuable strategy identifying candidate genes related to body weight.
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Affiliation(s)
- Yunna Li
- College of Animal Science and Technology, Northeast Agricultural University,, Harbin, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science,, Shihezi, China
| | - Hua Yang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science,, Shihezi, China
| | - Jing Guo
- College of Animal Science and Technology, Northeast Agricultural University,, Harbin, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science,, Shihezi, China
| | - Yonglin Yang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science,, Shihezi, China
| | - Qian Yu
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science,, Shihezi, China
| | - Yuanyuan Guo
- College of Animal Science and Technology, Northeast Agricultural University,, Harbin, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science,, Shihezi, China
| | - Chaoxin Zhang
- College of Animal Science and Technology, Northeast Agricultural University,, Harbin, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science,, Shihezi, China
| | - Zhipeng Wang
- College of Animal Science and Technology, Northeast Agricultural University,, Harbin, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science,, Shihezi, China
| | - Peng Zuo
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science,, Shihezi, China
- College of Science, Northeast Agricultural University, Harbin, China
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10
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Oster N, Szewczuk MA, Zych S, Stankiewicz T, Błaszczyk B, Wieczorek-Dąbrowska M. Association between Polymorphism in the Janus Kinase 2 ( JAK2) Gene and Selected Performance Traits in Cattle and Sheep. Animals (Basel) 2023; 13:2470. [PMID: 37570280 PMCID: PMC10416845 DOI: 10.3390/ani13152470] [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: 05/31/2023] [Revised: 07/17/2023] [Accepted: 07/29/2023] [Indexed: 08/13/2023] Open
Abstract
The Janus Kinase 2 (JAK2) tyrosine kinase is an essential component of signal transduction of the class II cytokine receptors, including the growth hormone receptor. Therefore, it may play a crucial role in the signaling pathway of the somatotropic axis, which influences growth, development, and reproductive traits in ruminants. For this purpose, for three breeds of cattle (Hereford, Angus, and Limousin; a total of 781 individuals), two polymorphic sites located in exon 16 (rs210148032; p.Ile704Val, within pseudokinase (JH2)) and exon 23 (silent mutation rs211067160, within JH1 kinase domain) were analyzed. For two breeds of sheep (Pomeranian and Suffolk; 333 individuals in total), two polymorphic sites in exon 6 (rs160146162 and rs160146160; encoding the FERM domain) and one polymorphic site in exon 24 of the JAK2 gene (rs160146116; JH1 kinase domain) were genotyped. In our study, the associations examined for cattle were inconclusive. However, Hereford and Limousin cattle with genotypes AA (e16/RsaI) and AA (e23/HaeIII) tended to have the highest body weight and better daily gains (p ≤ 0.05). No clear tendency was observed in the selected reproductive traits. In the case of sheep, regardless of breed, individuals with the AA (e6/EarI), GG (e6/seq), and AA (e24/Hpy188III) genotypes had the highest body weights and daily gains in the study periods (p ≤ 0.01). The same individuals in the Pomeranian breed also had better fertility and lamb survival (p ≤ 0.01). To the best of our knowledge, these are the first association studies for all these polymorphic sites. Single-nucleotide polymorphisms in the JAK2 gene can serve as genetic markers for growth and selected reproductive traits in ruminants given that they are further investigated in subsequent populations and analyzed using haplotype and/or combined genotype systems.
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Affiliation(s)
- Nicola Oster
- Department of Monogastric Animal Science, Faculty of Biotechnology and Animal Husbandry, West Pommeranian University of Technology in Szczecin, 29 Klemensa Janickiego, 71-270 Szczecin, Poland;
| | - Małgorzata Anna Szewczuk
- Department of Monogastric Animal Science, Faculty of Biotechnology and Animal Husbandry, West Pommeranian University of Technology in Szczecin, 29 Klemensa Janickiego, 71-270 Szczecin, Poland;
| | - Sławomir Zych
- Laboratory of Chromatography and Mass Spectroscopy, Faculty of Biotechnology and Animal Husbandry, West Pomeranian University of Technology in Szczecin, 29 Klemensa Janickiego, 71-270 Szczecin, Poland
| | - Tomasz Stankiewicz
- Department of Animal Reproduction Biotechnology and Environmental Hygiene, Faculty of Biotechnology and Animal Husbandry, West Pomeranian University of Technology in Szczecin, 29 Klemensa Janickiego, 71-270 Szczecin, Poland; (T.S.); (B.B.)
| | - Barbara Błaszczyk
- Department of Animal Reproduction Biotechnology and Environmental Hygiene, Faculty of Biotechnology and Animal Husbandry, West Pomeranian University of Technology in Szczecin, 29 Klemensa Janickiego, 71-270 Szczecin, Poland; (T.S.); (B.B.)
| | - Marta Wieczorek-Dąbrowska
- National Research Institute of Animal Production, Kraków, Experimental Department, Kołbacz, 1 Warcisława Street, 74-106 Stare Czarnowo, Poland
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11
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Zhao Y, He S, Huang J, Liu M. Genome-Wide Association Analysis of Muscle pH in Texel Sheep × Altay Sheep F 2 Resource Population. Animals (Basel) 2023; 13:2162. [PMID: 37443959 DOI: 10.3390/ani13132162] [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: 05/08/2023] [Revised: 05/29/2023] [Accepted: 06/25/2023] [Indexed: 07/15/2023] Open
Abstract
pH was one of the important meat quality traits, which was an important factor affecting the storage/shelf life and quality of meat in meat production. In order to find a way to extend the storage/shelf life, the pH values (pH45min, pH24h, pH48h and pH72h) of the longissimus dorsi muscles in F2 individuals of 462 Texel sheep × Altay sheep were determined, genotyping was performed using Illumina Ovine SNP 600 K BeadChip and whole genome resequencing technology, a genome-wide association analysis (GWAS) was used to screen the candidate genes and molecular markers for pH values related to the quality traits of mutton, and the effects of population stratification were detected by Q-Q plots. The results showed that the pH population stratification analysis did not find significant systemic bias, and there was no obvious population stratification effect. The results of the association analysis showed that 28 SNPs significantly associated with pH reached the level of genomic significance. The candidate gene associated with pH45min was identified as the CCDC92 gene by gene annotation and a search of the literature. Candidate genes related to pH24h were KDM4C, TGFB2 and GOT2 genes. The candidate genes related to pH48h were MMP12 and MMP13 genes. The candidate genes related to pH72h were HILPDA and FAT1 genes. Further bioinformatics analyses showed 24 gene ontology terms and five signaling pathways that were significantly enriched (p ≤ 0.05). Many terms and pathways were related to cellular components, processes of protein modification, the activity of protein dimerization and hydrolase activity. These identified SNPs and genes could provide useful information about meat and the storage/shelf life of meat, thereby extending the storage/shelf life and quality of meat.
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Affiliation(s)
- Yilong Zhao
- College of Animal Science and Technology, Shihezi University, Shihezi 832000, China
- College of Animal Science and Technology, Xinjiang Agricultural Vocational and Technical College, Changji 831100, China
| | - Sangang He
- Biotechnology Institute, Xinjiang Academy of Animal Science, Urumqi 830013, China
| | | | - Mingjun Liu
- Biotechnology Institute, Xinjiang Academy of Animal Science, Urumqi 830013, China
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12
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Aixia Y, Xiaolei D, Yuan F, Ruiwen Z, Jianren Y. Genetic diversity and genome-wide association analysis of pine wood nematode populations in different regions of China. FRONTIERS IN PLANT SCIENCE 2023; 14:1183772. [PMID: 37426967 PMCID: PMC10327295 DOI: 10.3389/fpls.2023.1183772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 04/28/2023] [Indexed: 07/11/2023]
Abstract
Introduction Pine wilt disease (Bursaphelenchus xylophilus) was recently detected in Liaoning Province, which was previously considered an unfavourable area for B. xylophilus due to its low temperatures. This study aims to compare the reproductivity and genetic variations of B. xylophilus isolates from Liaoning Province and other parts of China to explore their phenotypic and genomic differences. Methods The samples from Liaoning, Anhui, Hubei, Henan, Zhejiang and Jiangsu were isolated and purified to obtain the strains. The reproductivity of the strains was determined at 15 °C. The genetic structure was analyzed by using SNP molecular markers, and the whole genome association analysis was carried out by integrating SNP information and feculence traits. Results A reproductivity experiment showed that Liaoning isolates have higher reproductive ability at 15 °C. Subsequent SNP profiling and population differentiation analysis revealed obvious genetic differentiation of Liaoning isolates from other isolates. A genome-wide association study showed that SNPs closely related to low-temperature tolerance were mainly located in GPCR, Acyl-CoA, and Cpn10, which are responsible for adaptation to environmental factors, such as temperature change. Discussion Pine wood nematodes likely adapted to the climate in Liaoning and maintained a certain reproductive capacity at low temperature via variants of adaptation-related genes. This study provides a theoretical basis for elucidating the prevalence and diffusion status of B. xylophilus in China.
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13
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Pinto B, Valente R, Caramelo F, Ruivo R, Castro LFC. Decay of Skin-Specific Gene Modules in Pangolins. J Mol Evol 2023:10.1007/s00239-023-10118-z. [PMID: 37249590 DOI: 10.1007/s00239-023-10118-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 05/10/2023] [Indexed: 05/31/2023]
Abstract
The mammalian skin exhibits a rich spectrum of evolutionary adaptations. The pilosebaceous unit, composed of the hair shaft, follicle, and the sebaceous gland, is the most striking synapomorphy. The evolutionary diversification of mammals across different ecological niches was paralleled by the appearance of an ample variety of skin modifications. Pangolins, order Pholidota, exhibit keratin-derived scales, one of the most iconic skin appendages. This formidable armor is intended to serve as a deterrent against predators. Surprisingly, while pangolins have hair on their abdomens, the occurrence of sebaceous and sweat glands is contentious. Here, we explore various molecular modules of skin physiology in four pangolin genomes, including that of sebum production. We show that genes driving wax monoester formation, Awat1/2, show patterns of inactivation in the stem pangolin branch, while the triacylglycerol synthesis gene Dgat2l6 seems independently eroded in the African and Asian clades. In contrast, Elovl3 implicated in the formation of specific neutral lipids required for skin barrier function is intact and expressed in the pangolin skin. An extended comparative analysis shows that genes involved in skin pathogen defense and structural integrity of keratinocyte layers also show inactivating mutations: associated with both ancestral and independent pseudogenization events. Finally, we deduce that the suggested absence of sweat glands is not paralleled by the inactivation of the ATP-binding cassette transporter Abcc11, as previously described in Cetacea. Our findings reveal the sophisticated and complex history of gene retention and loss as key mechanisms in the evolution of the highly modified mammalian skin phenotypes.
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Affiliation(s)
- Bernardo Pinto
- CIMAR/CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal
- Department of Biology, Faculty of Sciences, University of Porto (U. Porto), Rua Do Campo Alegre S/N, 4169-007, Porto, Portugal
| | - Raul Valente
- CIMAR/CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal
- Department of Biology, Faculty of Sciences, University of Porto (U. Porto), Rua Do Campo Alegre S/N, 4169-007, Porto, Portugal
| | - Filipe Caramelo
- CIMAR/CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal
- Department of Biology, Faculty of Sciences, University of Porto (U. Porto), Rua Do Campo Alegre S/N, 4169-007, Porto, Portugal
| | - Raquel Ruivo
- CIMAR/CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal.
| | - L Filipe C Castro
- CIMAR/CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal.
- Department of Biology, Faculty of Sciences, University of Porto (U. Porto), Rua Do Campo Alegre S/N, 4169-007, Porto, Portugal.
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14
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Zhao L, Wang W, Wang X, Zhang D, Li X, Zhao Y, Zhang Y, Xu D, Cheng J, Wang J, Li W, Lin C, Wu W, Zhang X, Zheng W. Identification of SNPs and expression patterns of ALB, AHSG and GC genes and their association with growth traits in Hu sheep. Gene 2023; 853:147100. [PMID: 36470483 DOI: 10.1016/j.gene.2022.147100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 10/20/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022]
Abstract
Growth traits are economically important traits in sheep breeding. This study was conducted to evaluate the polymorphisms of ALB, AHSG and GC genes and their association with growth traits in Hu sheep. We measured and recorded the body weight (BW), body height (BH), body length (BL) and feed conversion ratio (FCR) of 1418 male Hu sheep raised in the same environment from 80 to 180 days of age. The total of four SNPs in the ALB, AHSG and GC genes were identified by direct sequencing technology. The results of association analysis showed that two loci (g.8699 A>T and g.13458 T>C) of ALB gene significantly affect average daily gain (ADG; P < 0.05). The genotypes of SNP g.2454 T>C in AHSG gene were significantly associated with ADG and FCR (P < 0.05). There were significant associations between GC g.19484 A>C and BW, BH and BL (P < 0.05). The results of qRT-PCR showed that ALB, AHSG, and GC genes were extremely significantly higher in H_BW sheep compared with those in the L_BW sheep (P < 0.01). These results revealed that ALB-1 g.8699 A>T, ALB-2 g.13458 T>C, AHSG g.2454 T>C and GC g.19484 A>C loci are potential molecular markers for Hu sheep breeding.
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Affiliation(s)
- Liming Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Weimin Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China; The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou Gansu 730020, China
| | - Xiaojuan Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Deyin Zhang
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou Gansu 730020, China
| | - Xiaolong Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Yuan Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Yukun Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Dan Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Jiangbo Cheng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Jianghui Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Wenxin Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Changchun Lin
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Weiwei Wu
- Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, Xinjiang 830000, China
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China.
| | - Wenxin Zheng
- Institute of Animal Husbandry Quality Standards, Xinjiang Academy of Animal Sciences, Urumqi, Xinjiang 830000, China.
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Ramos Z, Garrick DJ, Blair HT, Vera B, Ciappesoni G, Kenyon PR. Genomic Regions Associated with Wool, Growth and Reproduction Traits in Uruguayan Merino Sheep. Genes (Basel) 2023; 14:167. [PMID: 36672908 PMCID: PMC9858812 DOI: 10.3390/genes14010167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 12/29/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
The aim of this study was to identify genomic regions and genes associated with the fiber diameter (FD), clean fleece weight (CFW), live weight (LW), body condition score (BCS), pregnancy rate (PR) and lambing potential (LP) of Uruguayan Merino sheep. Phenotypic records of approximately 2000 mixed-age ewes were obtained from a Merino nucleus flock. Genome-wide association studies were performed utilizing single-step Bayesian analysis. For wool traits, a total of 35 genomic windows surpassed the significance threshold (PVE ≥ 0.25%). The proportion of the total additive genetic variance explained by those windows was 4.85 and 9.06% for FD and CFW, respectively. There were 42 windows significantly associated with LWM, which collectively explained 43.2% of the additive genetic variance. For BCS, 22 relevant windows accounted for more than 40% of the additive genetic variance, whereas for the reproduction traits, 53 genomic windows (24 and 29 for PR and LP, respectively) reached the suggestive threshold of 0.25% of the PVE. Within the top 10 windows for each trait, we identified several genes showing potential associations with the wool (e.g., IGF-1, TGFB2R, PRKCA), live weight (e.g., CAST, LAP3, MED28, HERC6), body condition score (e.g., CDH10, TMC2, SIRPA, CPXM1) or reproduction traits (e.g., ADCY1, LEPR, GHR, LPAR2) of the mixed-age ewes.
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Affiliation(s)
- Zully Ramos
- School of Agriculture and Environment, Massey University, Palmerston North 4410, New Zealand
| | - Dorian J. Garrick
- School of Agriculture and Environment, Massey University, Palmerston North 4410, New Zealand
| | - Hugh T. Blair
- School of Agriculture and Environment, Massey University, Palmerston North 4410, New Zealand
| | - Brenda Vera
- National Research Program on Meat and Wool Production, Instituto Nacional de Investigación Agropecuaria, INIA Las Brujas, Ruta 48 Km 10, Canelones 90100, Uruguay
| | - Gabriel Ciappesoni
- National Research Program on Meat and Wool Production, Instituto Nacional de Investigación Agropecuaria, INIA Las Brujas, Ruta 48 Km 10, Canelones 90100, Uruguay
| | - Paul R. Kenyon
- School of Agriculture and Environment, Massey University, Palmerston North 4410, New Zealand
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Zsolnai A, Egerszegi I, Rózsa L, Mezőszentgyörgyi D, Anton I. Position of Hungarian Merino among other Merinos, within-breed genetic similarity network and markers associated with daily weight gain. Anim Biosci 2023; 36:10-18. [PMID: 35760405 PMCID: PMC9834658 DOI: 10.5713/ab.21.0459] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 05/18/2022] [Indexed: 01/27/2023] Open
Abstract
OBJECTIVE In this study, we aimed to position the Hungarian Merino among other Merino-derived sheep breeds, explore the characteristics of our sampled animals' genetic similarity network within the breed, and highlight single nucleotide polymorphisms (SNPs) associated with daily weight-gain. METHODS Hungarian Merino (n = 138) was genotyped on Ovine SNP50 Bead Chip (Illumina, San Diego, CA, USA) and positioned among 30 Merino and Merino-derived breeds (n = 555). Population characteristics were obtained via PLINK, SVS, Admixture, and Treemix software, within-breed network was analysed with python networkx 2.3 library. Daily weight gain of Hungarian Merino was standardised to 60 days and was collected from the database of the Association of Hungarian Sheep and Goat Breeders. For the identification of loci associated with daily weight gain, a multi-locus mixed-model was used. RESULTS Supporting the breed's written history, the closest breeds to Hungarian Merino were Estremadura and Rambouillet (pairwise FST values are 0.035 and 0.036, respectively). Among Hungarian Merino, a highly centralised connectedness has been revealed by network analysis of pairwise values of identity-by-state, where the animal in the central node had a betweenness centrality value equal to 0.936. Probing of daily weight gain against the SNP data of Hungarian Merinos revealed five associated loci. Two of them, OAR8_17854216.1 and s42441.1 on chromosome 8 and 9 (-log10P>22, false discovery rate<5.5e-20) and one locus on chromosome 20, s28948.1 (-log10P = 13.46, false discovery rate = 4.1e-11), were close to the markers reported in other breeds concerning daily weight gain, six-month weight, and post-weaning gain. CONCLUSION The position of Hungarian Merino among other Merino breeds has been determined. We have described the similarity network of the individuals to be applied in breeding practices and highlighted several markers useful for elevating the daily weight gain of Hungarian Merino.
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Affiliation(s)
- Attila Zsolnai
- Department of Animal Breeding, Institute of Animal Science, Hungarian University of Agriculture and Life Sciences, Kaposvár Campus, Herceghalom, 2053,
Hungary,National Centre for Biodiversity and Gene Conservation, Gödöllő, 2100,
Hungary,Corresponding Author: Attila Zsolnai, Tel: +36-70-491-7824, E-mail:
| | - István Egerszegi
- Department of Animal Husbandry Technology and Animal Welfare, Institute of Animal Science, Hungarian University of Agriculture and Life Sciences, Kaposvár Campus, Gödöllő, 2100,
Hungary
| | - László Rózsa
- Hungarian University of Agriculture and Life Sciences, Georgikon Campus, Keszthely, 8360,
Hungary
| | - Dávid Mezőszentgyörgyi
- Department of Animal Breeding, Institute of Animal Science, Hungarian University of Agriculture and Life Sciences, Kaposvár Campus, Herceghalom, 2053,
Hungary
| | - István Anton
- Department of Animal Breeding, Institute of Animal Science, Hungarian University of Agriculture and Life Sciences, Kaposvár Campus, Herceghalom, 2053,
Hungary
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17
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Easa AA, Selionova M, Aibazov M, Mamontova T, Sermyagin A, Belous A, Abdelmanova A, Deniskova T, Zinovieva N. Identification of Genomic Regions and Candidate Genes Associated with Body Weight and Body Conformation Traits in Karachai Goats. Genes (Basel) 2022; 13:genes13101773. [PMID: 36292658 PMCID: PMC9601913 DOI: 10.3390/genes13101773] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/23/2022] [Accepted: 09/28/2022] [Indexed: 11/04/2022] Open
Abstract
The objective of this study was to identify the SNPs and candidate genes related to body weight and seven body conformation traits at the age of 8 months in the Russian aboriginal Karachai goats (n = 269) by conducting genome-wide association studies (GWAS), using genotypes generated by Goat SNP BeadChip (Illumina Inc., USA). We identified 241 SNPs, which were significantly associated with the studied traits, including 47 genome-wide SNPs (p < 10−5) and 194 suggestive SNPs (p < 10−4), distributed among all goat autosomes except for autosome 23. Fifty-six SNPs were common for two and more traits (1 SNP for six traits, 2 SNPs for five traits, 12 SNPs for four traits, 20 SNPs for three traits, and 21 SNPs for two traits), while 185 SNPs were associated with single traits. Structural annotation within a window of 0.4 Mb (±0.2 Mb from causal SNPs) revealed 238 candidate genes. The largest number of candidate genes was identified at Chr13 (33 candidate genes for the five traits). The genes identified in our study were previously reported to be associated with growth-related traits in different livestock species. The most significant genes for body weight were CRADD, HMGA2, MSRB3, MAX, HACL1 and RAB15, which regulate growth processes, body sizes, fat deposition, and average daily gains. Among them, the HMGA2 gene is a well-known candidate for prenatal and early postnatal development, and the MSRB3 gene is proposed as a candidate gene affecting the growth performance. APOB, PTPRK, BCAR1, AOAH and ASAH1 genes associated with withers height, rump height and body length, are involved in various metabolic processes, including fatty acid metabolism and lipopolysaccharide catabolism. In addition, WDR70, ZBTB24, ADIPOQ, and SORCS3 genes were linked to chest width. KCNG4 was associated with rump height, body length and chest perimeter. The identified candidate genes can be proposed as molecular markers for growth trait selection for genetic improvement in Karachai goats.
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Affiliation(s)
- Ahmed A. Easa
- Timiryazev Agricultural Academy, Russian State Agrarian University-Moscow, Timiryazevskaya Street, 41, Moscow 127550, Russia
- Department of Animal and Poultry Production, Faculty of Agriculture, Damanhour University, Damanhour 22511, Egypt
- Correspondence: (A.A.E.); (N.Z.)
| | - Marina Selionova
- Timiryazev Agricultural Academy, Russian State Agrarian University-Moscow, Timiryazevskaya Street, 41, Moscow 127550, Russia
| | - Magomet Aibazov
- Timiryazev Agricultural Academy, Russian State Agrarian University-Moscow, Timiryazevskaya Street, 41, Moscow 127550, Russia
| | - Tatiana Mamontova
- Timiryazev Agricultural Academy, Russian State Agrarian University-Moscow, Timiryazevskaya Street, 41, Moscow 127550, Russia
| | - Alexander Sermyagin
- L K Ernst Federal Research Center for Animal Husbandry, Dubrovitsy 60, Podolsk Municipal District, Moscow 142132, Russia
| | - Anna Belous
- L K Ernst Federal Research Center for Animal Husbandry, Dubrovitsy 60, Podolsk Municipal District, Moscow 142132, Russia
| | - Alexandra Abdelmanova
- L K Ernst Federal Research Center for Animal Husbandry, Dubrovitsy 60, Podolsk Municipal District, Moscow 142132, Russia
| | - Tatiana Deniskova
- L K Ernst Federal Research Center for Animal Husbandry, Dubrovitsy 60, Podolsk Municipal District, Moscow 142132, Russia
| | - Natalia Zinovieva
- L K Ernst Federal Research Center for Animal Husbandry, Dubrovitsy 60, Podolsk Municipal District, Moscow 142132, Russia
- Correspondence: (A.A.E.); (N.Z.)
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18
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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: 10] [Impact Index Per Article: 5.0] [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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19
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Genome wide association study identifies novel candidate genes for growth and body conformation traits in goats. Sci Rep 2022; 12:9891. [PMID: 35701479 PMCID: PMC9197946 DOI: 10.1038/s41598-022-14018-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 05/31/2022] [Indexed: 11/08/2022] Open
Abstract
Pakistan is third largest country in term of goat population with distinct characteristics of breeds and estimated population of 78.2 million. Punjab province has 37% of country's total population with seven important documented goat breeds namely Beetal, Daira Din Pannah, Nachi, Barbari, Teddi, Pahari and Pothwari. There is paucity of literature on GWAS for economically important traits i.e., body weight and morphometric measurements. Therefore, we performed GWAS using 50 K SNP Chip for growth in term of age adjusted body weight and morphometric measurements in order to identify genomic regions influencing these traits among Punjab goat breeds. Blood samples were collected from 879 unrelated animals of seven goat breeds along with data for body weight and morphometric measurements including body length, body height, pubic bone length, heart girth and chest length. Genomic DNA was extracted and genotyped using 50 K SNP bead chip. Association of genotypic data with the phenotypic data was performed using Plink 1.9 software. Linear mixed model was used for the association study. Genes were annotated from Capra hircus genome using assembly ARS1. We have identified a number of highly significant SNPs and respective candidate genes associated with growth and body conformation traits. The functional aspects of these candidate genes suggested their potential role in body growth. Moreover, pleiotropic effects were observed for some SNPs for body weight and conformation traits. The results of current study contributed to a better understanding of genes influencing growth and body conformation traits in goat.
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20
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Liu Z, Bai C, Shi L, He Y, Hu M, Sun H, Peng H, Lai W, Jiao S, Zhao Z, Ma H, Yan S. Detection of selection signatures in South African Mutton Merino sheep using whole-genome sequencing data. Anim Genet 2022; 53:224-229. [PMID: 35099062 DOI: 10.1111/age.13173] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 12/31/2021] [Accepted: 01/10/2022] [Indexed: 12/12/2022]
Abstract
The South African Mutton Merino (SAMM), a dual-purpose (meat and wool) sheep breed, is characterized by its excellent performance on growth, carcass traits and meat quality compared to other fine-wool Merino breeds. Nowadays, the SAMM breed has been widely used to cross with commercial and indigenous fine-wool or coarse-wool breeds to improve the growth and meat performance in many countries. To date, however, little is known about the genetic basis for its prominent characteristics. In this study, whole-genome sequences of 10 SAMM were sequenced and the selection signatures were analyzed together with those of 39 Australian Merino and Chinese Merino (wool-type Merino) by FST , iHS, and XP-EHH methods. In total, 313 genes in 277 regions were identified by at least 2 methods with the signal of selection and 21 of them were identified by all three methods. We highlighted a list of interesting genes, including GHR, LCORL, SMO, NCAPG, DCC, IBSP, PPARGC1A, PACRGL, PRDM5, XYLB, AHCYL2, TEFM, AFG1L, and FAM184B, which have been shown to be involved in growth, carcass traits, and meat quality by previous studies. Herein, GHR, encoding a transmembrane receptor for growth hormone, is the most notable one. We report the first study on selection signatures analysis of SAMM at whole-genome sequence level. These results provide new insights into the genetic mechanisms underlying the growth and carcass traits in SAMM.
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Affiliation(s)
- Zhengxi Liu
- College of Animal Science, Jilin University, Changchun, China
| | - Chunyan Bai
- College of Animal Science, Jilin University, Changchun, China
| | - Lulu Shi
- College of Animal Science, Jilin University, Changchun, China
| | - Yu He
- College of Animal Science, Jilin University, Changchun, China
| | - Mingyue Hu
- College of Animal Science, Jilin University, Changchun, China
| | - Hao Sun
- College of Animal Science, Jilin University, Changchun, China
| | - Hongyang Peng
- College of Animal Science, Jilin University, Changchun, China
| | - Weining Lai
- College of Animal Science, Jilin University, Changchun, China
| | - Shuyu Jiao
- College of Animal Science, Jilin University, Changchun, China
| | - Zhongli Zhao
- Institute of Animal Husbandry and Veterinary, Jilin Academy of Agricultural Sciences, Gongzhuling, Jilin, China
| | - Huihai Ma
- Institute of Animal Husbandry and Veterinary, Jilin Academy of Agricultural Sciences, Gongzhuling, Jilin, China
| | - Shouqing Yan
- College of Animal Science, Jilin University, Changchun, China
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21
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Zhang L, Wang F, Gao G, Yan X, Liu H, Liu Z, Wang Z, He L, Lv Q, Wang Z, Wang R, Zhang Y, Li J, Su R. Genome-Wide Association Study of Body Weight Traits in Inner Mongolia Cashmere Goats. Front Vet Sci 2021; 8:752746. [PMID: 34926636 PMCID: PMC8673091 DOI: 10.3389/fvets.2021.752746] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/27/2021] [Indexed: 11/13/2022] Open
Abstract
Objective: Body weight is an important economic trait for a goat, which greatly affects animal growth and survival. The purpose of this study was to identify genes associated with birth weight (BW), weaning weight (WW), and yearling weight (YW). Materials and Methods: In this study, a genome-wide association study (GWAS) of BW, WW, and YW was determined using the GGP_Goat_70K single-nucleotide polymorphism (SNP) chip in 1,920 Inner Mongolia cashmere goats. Results: We discovered that 21 SNPs were significantly associated with BW on the genome-wide levels. These SNPs were located in 10 genes, e.g., Mitogen-Activated Protein Kinase 3 (MAPK3), LIM domain binding 2 (LDB2), and low-density lipoprotein receptor-related protein 1B (LRP1B), which may be related to muscle growth and development in Inner Mongolia Cashmere goats. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that these genes were significantly enriched in the regulation of actin cytoskeleton and phospholipase D signaling pathway etc. Conclusion: In summary, this study will improve the marker-assisted breeding of Inner Mongolia cashmere goats and the molecular mechanisms of important economic traits.
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Affiliation(s)
- Lei Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China.,Inner Mongolia Jinlai Livestock Technology Co., Ltd, Hohhot, China
| | - Fenghong Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Gong Gao
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Xiaochun Yan
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Hongfu Liu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Zhihong Liu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Hohhot, China.,Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hohhot, China.,Engineering Research Center for Goat Genetics and Breeding, Hohhot, China
| | - Zhixin Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Hohhot, China.,Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hohhot, China
| | - Libing He
- Inner Mongolia Jinlai Livestock Technology Co., Ltd, Hohhot, China
| | - Qi Lv
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Zhiying Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Ruijun Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Yanjun Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Hohhot, China.,Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hohhot, China.,Engineering Research Center for Goat Genetics and Breeding, Hohhot, China
| | - Jinquan Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Hohhot, China.,Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hohhot, China.,Engineering Research Center for Goat Genetics and Breeding, Hohhot, China
| | - Rui Su
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
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22
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Insight into the Candidate Genes and Enriched Pathways Associated with Height, Length, Length to Height Ratio and Body-Weight of Korean Indigenous Breed, Jindo Dog Using Gene Set Enrichment-Based GWAS Analysis. Animals (Basel) 2021; 11:ani11113136. [PMID: 34827868 PMCID: PMC8614278 DOI: 10.3390/ani11113136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/21/2021] [Accepted: 10/28/2021] [Indexed: 12/14/2022] Open
Abstract
As a companion and hunting dog, height, length, length to height ratio (LHR) and body-weight are the vital economic traits for Jindo dog. Human selection and targeted breeding have produced an extraordinary diversity in these traits. Therefore, the identification of causative markers, genes and pathways that help us to understand the genetic basis of this variability is essential for their selection purposes. Here, we performed a genome-wide association study (GWAS) combined with enrichment analysis on 757 dogs using 118,879 SNPs. The genomic heritability (h2) was 0.33 for height and 0.28 for weight trait in Jindo. At p-value < 5 × 10-5, ten, six, thirteen and eleven SNPs on different chromosomes were significantly associated with height, length, LHR and body-weight traits, respectively. Based on our results, HHIP, LCORL and NCAPG for height, IGFI and FGFR3 for length, DLK1 and EFEMP1 for LHR and PTPN2, IGFI and RASAL2 for weight can be the potential candidate genes because of the significant SNPs located in their intronic or upstream regions. The gene-set enrichment analysis highlighted here nine and seven overlapping significant (p < 0.05) gene ontology (GO) terms and pathways among traits. Interestingly, the highlighted pathways were related to hormone synthesis, secretion and signalling were generally involved in the metabolism, growth and development process. Our data provide an insight into the significant genes and pathways if verified further, which will have a significant effect on the breeding of the Jindo dog's population.
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23
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Zhao H, Zhu S, Guo T, Han M, Chen B, Qiao G, Wu Y, Yuan C, Liu J, Lu Z, Sun W, Wang T, Li F, Zhang Y, Hou F, Yue Y, Yang B. Whole-genome re-sequencing association study on yearling wool traits in Chinese fine-wool sheep. J Anim Sci 2021; 99:6319907. [PMID: 34255028 PMCID: PMC8418636 DOI: 10.1093/jas/skab210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 07/10/2021] [Indexed: 12/11/2022] Open
Abstract
To investigate single nucleotide polymorphism (SNP) loci associated with yearling wool traits of fine-wool sheep for optimizing marker-assisted selection and dissection of the genetic architecture of wool traits, we conducted a genome-wide association study (GWAS) based on the fixed and random model circulating probability unification (FarmCPU) for yearling staple length (YSL), yearling mean fiber diameter (YFD), yearling greasy fleece weight (YGFW), and yearling clean fleece rate (YCFR) by using the whole-genome re-sequenced data (totaling 577 sheep) from the following four fine-wool sheep breeds in China: Alpine Merino sheep (AMS), Chinese Merino sheep (CMS), Qinghai fine-wool sheep (QHS), and Aohan fine-wool sheep (AHS). A total of 16 SNPs were detected above the genome-wise significant threshold (P = 5.45E-09), and 79 SNPs were located above the suggestive significance threshold (P = 5.00E-07) from the GWAS results. For YFD and YGFW traits, 7 and 9 SNPs reached the genome-wise significance thresholds, whereas 10 and 12 SNPs reached the suggestive significance threshold, respectively. For YSL and YCFR traits, none of the SNPs reached the genome-wise significance thresholds, whereas 57 SNPs exceeded the suggestive significance threshold. We recorded 14 genes located at the region of ±50-kb near the genome-wise significant SNPs and 59 genes located at the region of ±50-kb near the suggestive significant SNPs. Meanwhile, we used the Average Information Restricted Maximum likelihood algorithm (AI-REML) in the “HIBLUP” package to estimate the heritability and variance components of the four desired yearling wool traits. The estimated heritability values (h2) of YSL, YFD, YGFW, and YCFR were 0.6208, 0.7460, 0.6758, and 0.5559, respectively. We noted that the genetic parameters in this study can be used for fine-wool sheep breeding. The newly detected significant SNPs and the newly identified candidate genes in this study would enhance our understanding of yearling wool formation, and significant SNPs can be applied to genome selection in fine-wool sheep breeding.
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Affiliation(s)
- Hongchang Zhao
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Shaohua Zhu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Tingting Guo
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Mei Han
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Bowen Chen
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Guoyan Qiao
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Yi Wu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Chao Yuan
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Jianbin Liu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Zengkui Lu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Weibo Sun
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Tianxiang Wang
- Gansu Provincial Sheep Breeding Technology Extension Station, Sunan, 734031, China
| | - Fanwen Li
- Gansu Provincial Sheep Breeding Technology Extension Station, Sunan, 734031, China
| | - Yajun Zhang
- Xinjiang Gongnaisi Breeding Sheep Farm, Xinyuan, 835808, China
| | - Fujun Hou
- Aohan Banner Breeding Sheep Farm, Chifeng, 024300, China
| | - Yaojing Yue
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Bohui Yang
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
- Corresponding author:
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24
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Yilmaz O, Kizilaslan M, Arzik Y, Behrem S, Ata N, Karaca O, Elmaci C, Cemal I. Genome-wide association studies of preweaning growth and in vivo carcass composition traits in Esme sheep. J Anim Breed Genet 2021; 139:26-39. [PMID: 34331347 DOI: 10.1111/jbg.12640] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 07/06/2021] [Accepted: 07/22/2021] [Indexed: 01/15/2023]
Abstract
Sheep are considered as a major contributor of global food security. Moreover, sheep preweaning growth traits as well as in vivo carcass composition traits such as ultrasonic measurements of Longissimus dorsi muscle depth (UMD) and back-fat thickness (UFD) are crucially important indicators of meat yield and hot carcass composition. Despite their relative importance for productivity and profitability of a sheep production system, detected QTL for these traits are quite scarce. Therefore, we implemented GWAS for these traits using animal mixed model-based association approach provided by GenABEL in Esme sheep. Three genome-wide and 14 individual chromosome-wide associated SNPs were discovered. As a result, ESRP1, LOC105613082, ZNF641, DUSP5, TEAD1, SMOX, PTPRT, RALYL, POM121C, PHIP, LOC101106051, ZIM3, PEG3, TRPC7, FBXL4, LOC105610397, LOC105616489 and DNAAF2 were suggested as candidates. Some of the discovered genes and involved pathways were already annotated to contribute growth and development in various species including human, mice and cattle. All in all, the results of this study are expected to strongly contribute to shed a light on the underlying molecular mechanisms behind growth and carcass composition traits, with potential implications on studies aiming faster genetic improvement, targeted low-resolution SNP panel designs and genome-editing studies.
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Affiliation(s)
- Onur Yilmaz
- Department of Animal Science, Faculty of Agriculture, Aydin Adnan Menderes University, Aydin, Turkey
| | - Mehmet Kizilaslan
- Department of Animal Breeding and Genetics, International Center for Livestock Research and Training, Ankara, Turkey
| | - Yunus Arzik
- Department of Animal Breeding and Genetics, International Center for Livestock Research and Training, Ankara, Turkey
| | - Sedat Behrem
- Department of Animal Breeding and Genetics, International Center for Livestock Research and Training, Ankara, Turkey
| | - Nezih Ata
- Department of Animal Science, Faculty of Agriculture, Aydin Adnan Menderes University, Aydin, Turkey
| | - Orhan Karaca
- Department of Animal Science, Faculty of Agriculture, Aydin Adnan Menderes University, Aydin, Turkey
| | - Cengiz Elmaci
- Animal Science Department, Agriculture Faculty, Bursa Uludag University, Bursa, Turkey
| | - Ibrahim Cemal
- Department of Animal Science, Faculty of Agriculture, Aydin Adnan Menderes University, Aydin, Turkey
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25
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Genome-Wide Association Study Identifies 12 Loci Associated with Body Weight at Age 8 Weeks in Korean Native Chickens. Genes (Basel) 2021; 12:genes12081170. [PMID: 34440344 PMCID: PMC8394794 DOI: 10.3390/genes12081170] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/24/2021] [Accepted: 07/26/2021] [Indexed: 02/07/2023] Open
Abstract
Meat from Korean native chickens (KNCs) has high consumer demand; however, slow growth performance and high variation in body weight (BW) of KNCs remain an issue. Genome-wide association study (GWAS) is a powerful method to identify quantitative trait-associated genomic loci. A GWAS, based on a large-scale KNC population, is needed to identify underlying genetic mechanisms related to its growth traits. To identify BW-associated genomic regions, we performed a GWAS using the chicken 60K single nucleotide polymorphism (SNP) panel for 1328 KNCs. BW was measured at 8 weeks of age, from 2018 to 2020. Twelve SNPs were associated with BW at the suggestive significance level (p < 2.95 × 10−5) and located near or within 11 candidate genes, including WDR37, KCNIP4, SLIT2, PPARGC1A, MYOCD and ADGRA3. Gene set enrichment analysis based on the GWAS results at p < 0.05 (1680 SNPs) showed that 32 Gene Ontology terms and two Kyoto Encyclopedia of Genes and Genomes pathways, including regulation of transcription, motor activity, the mitogen-activated protein kinase signaling pathway, and tight junction, were significantly enriched (p < 0.05) for BW-associated genes. These pathways are involved in cell growth and development, related to BW gain. The identified SNPs are potential biomarkers in KNC breeding.
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26
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Tao L, Liu YF, Zhang H, Li HZ, Zhao FP, Wang FY, Zhang RS, Di R, Chu MX. Genome-wide association study and inbreeding depression on body size traits in Qira black sheep (Ovis aries). Anim Genet 2021; 52:560-564. [PMID: 34096079 DOI: 10.1111/age.13099] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2021] [Indexed: 12/24/2022]
Abstract
Qira black sheep is a famous indigenous sheep breed in China. The objectives of this study are to identify candidate genes related to body size, and to estimate the level of inbreeding depression on body size based on runs of homozygosity in Qira black sheep. Here, 188 adult Qira black sheep were genotyped with a high density (630 K) SNP chip and genome-wide association study for body weight and body size traits (including withers height, body slanting length, tail length, chest girth, chest width, and chest depth) were performed using an additive linear model. In consequence, 12 genome- and chromosome-wide significant SNPs and, accordingly, six candidate genes involved in muscle differentiation, metabolism and cell processes were identified. Of them, ZNF704 (zinc finger protein 704) was identified for body weight; AK2 (adenylate kinase 2) and PARK2 (parkin RBR E3 ubiquitin protein ligase) for tail length; MOCOS (molybdenum cofactor sulfurase) and ELP2 (elongator acetyltransferase complex subunit 2) for chest width; and MFAP1 (microfibril associated protein 1) for chest girth. Additionally, inbreeding depressions on body size were observed in the current herd. These results will provide insightful understandings into the genetic mechanisms of adult body size, and into the conservation and utilization of Qira black sheep.
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Affiliation(s)
- L Tao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Y F Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,College of Life Science and Food Engineering, Hebei University of Engineering, Handan, 056038, China
| | - H Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,College of Life Science and Food Engineering, Hebei University of Engineering, Handan, 056038, China
| | - H Z Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - F P Zhao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - F Y Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - R S Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - R Di
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - M X Chu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
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Bitaraf Sani M, Zare Harofte J, Banabazi MH, Esmaeilkhanian S, Shafei Naderi A, Salim N, Teimoori A, Bitaraf A, Zadehrahmani M, Burger PA, Landi V, Silawi M, Taghipour Sheshdeh A, Faghihi MA. Genomic prediction for growth using a low-density SNP panel in dromedary camels. Sci Rep 2021; 11:7675. [PMID: 33828208 PMCID: PMC8027435 DOI: 10.1038/s41598-021-87296-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 03/26/2021] [Indexed: 11/29/2022] Open
Abstract
For thousands of years, camels have produced meat, milk, and fiber in harsh desert conditions. For a sustainable development to provide protein resources from desert areas, it is necessary to pay attention to genetic improvement in camel breeding. By using genotyping-by-sequencing (GBS) method we produced over 14,500 genome wide markers to conduct a genome- wide association study (GWAS) for investigating the birth weight, daily gain, and body weight of 96 dromedaries in the Iranian central desert. A total of 99 SNPs were associated with birth weight, daily gain, and body weight (p-value < 0.002). Genomic breeding values (GEBVs) were estimated with the BGLR package using (i) all 14,522 SNPs and (ii) the 99 SNPs by GWAS. Twenty-eight SNPs were associated with birth weight, daily gain, and body weight (p-value < 0.001). Annotation of the genomic region (s) within ± 100 kb of the associated SNPs facilitated prediction of 36 candidate genes. The accuracy of GEBVs was more than 0.65 based on all 14,522 SNPs, but the regression coefficients for birth weight, daily gain, and body weight were 0.39, 0.20, and 0.23, respectively. Because of low sample size, the GEBVs were predicted using the associated SNPs from GWAS. The accuracy of GEBVs based on the 99 associated SNPs was 0.62, 0.82, and 0.57 for birth weight, daily gain, and body weight. This report is the first GWAS using GBS on dromedary camels and identifies markers associated with growth traits that could help to plan breeding program to genetic improvement. Further researches using larger sample size and collaboration of the camel farmers and more profound understanding will permit verification of the associated SNPs identified in this project. The preliminary results of study show that genomic selection could be the appropriate way to genetic improvement of body weight in dromedary camels, which is challenging due to a long generation interval, seasonal reproduction, and lack of records and pedigrees.
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Affiliation(s)
- Morteza Bitaraf Sani
- Animal Science Research Department, Yazd Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education & Extension Organization (AREEO), 8915813155, Yazd, Iran.
| | - Javad Zare Harofte
- Animal Science Research Department, Yazd Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education & Extension Organization (AREEO), 8915813155, Yazd, Iran
| | - Mohammad Hossein Banabazi
- Department of Biotechnology, Animal Science Research Institute of IRAN (ASRI), Agricultural Research, Education & Extension Organization (AREEO), 3146618361, Karaj, Iran
| | - Saeid Esmaeilkhanian
- Department of Biotechnology, Animal Science Research Institute of IRAN (ASRI), Agricultural Research, Education and Extension Organization (AREEO), 3146618361, Karaj, Iran
| | - Ali Shafei Naderi
- Animal Science Research Department, Yazd Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education & Extension Organization (AREEO), 8915813155, Yazd, Iran
| | - Nader Salim
- Organization of Agriculture - Jahad -Yazd, Ministry of Agriculture-Jahad, 8916713449, Yazd, Iran
| | - Abbas Teimoori
- Organization of Agriculture - Jahad -Yazd, Ministry of Agriculture-Jahad, 8916713449, Yazd, Iran
| | - Ahmad Bitaraf
- Animal Science Research Department, Yazd Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education & Extension Organization (AREEO), 8915813155, Yazd, Iran
| | | | - Pamela Anna Burger
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, 1160, Vienna, Austria
| | - Vincenzo Landi
- Departement of Veterinary Medicine, Università Di Bari "Aldo Moro", Bari, Italy
| | - Mohammad Silawi
- Persian BayanGene Research and Training Center, 7134767617, Shiraz, Iran
| | | | - Mohammad Ali Faghihi
- Persian BayanGene Research and Training Center, 7134767617, Shiraz, Iran.,Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, 33136, USA
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28
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Yaman Y, Şenlik B, Özüiçli M, Keleş M, Aymaz R, Bay V, Hatipoğlu E, Koncagül S, Öner Y, Ün C. Detecting fecal egg count (FEC) for gastrointestinal nematodes of adult Turkish sheep with different scrapie related PRNP haplotypes. Anim Biotechnol 2020; 32:381-387. [PMID: 33356831 DOI: 10.1080/10495398.2020.1862136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Scrapie is a transmissible spongiform encephalopathy caused by prions and leads to neurodegeneration in the Central Nervous System (CNS) of sheep and goats. Genetic resistance/susceptibility to scrapie is well studied and it is known that the variations of 136th, 154th and 171st codons at the ovine PRNP gene have a major effect on the development of the disease. Many studies demonstrated that selection for PRNP genotypes has not influenced other performance traits, nevertheless, there is a knowledge gap about the possible link between the PRNP gene and the status of the other important diseases that affect the sheep population worldwide. In the present study, we tested whether there is an association between scrapie-related PRNP genotypes and fecal egg count (FEC) of gastrointestinal nematodes in seven adult Turkish sheep breeds. For this purpose, FEC scores of studied sheep (n = 253) were determined and the same animals were genotyped for the PRNP gene. Finally, an association analysis was performed for scrapie resistant (ARR), susceptible (VRQ), and wild-type (ARQ) haplotypes. Based on our statistical analysis, it is concluded that PRNP genotypes have no positive or negative effect on the FEC scores of adult sheep.
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Affiliation(s)
- Yalçın Yaman
- Department of Biometry and Genetics, Sheep Breeding and Research Institute, Bandirma, Turkey
| | - Bayram Şenlik
- Veterinary Faculty, Department of Parasitology, Uludag University, Bursa, Turkey
| | - Mehmet Özüiçli
- Veterinary Faculty, Department of Parasitology, Uludag University, Bursa, Turkey
| | - Murat Keleş
- Department of Biometry and Genetics, Sheep Breeding and Research Institute, Bandirma, Turkey
| | - Ramazan Aymaz
- Department of Biometry and Genetics, Sheep Breeding and Research Institute, Bandirma, Turkey
| | - Veysel Bay
- Department of Biometry and Genetics, Sheep Breeding and Research Institute, Bandirma, Turkey
| | - Ecem Hatipoğlu
- Department of Biometry and Genetics, Sheep Breeding and Research Institute, Bandirma, Turkey
| | - Seyrani Koncagül
- Agricultural Faculty, Departments of Animal Science, Ankara University, Ankara, Turkey
| | - Yasemin Öner
- Agricultural Faculty, Department of Biometry and Genetics, Uludag University, Bursa, Turkey
| | - Cemal Ün
- Faculty of Science, Department of Biology, Ege University, İzmir, Turkey
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29
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Sweet-Jones J, Yurchenko AA, Igoshin AV, Yudin NS, Swain MT, Larkin DM. Resequencing and signatures of selection scan in two Siberian native sheep breeds point to candidate genetic variants for adaptation and economically important traits. Anim Genet 2020; 52:126-131. [PMID: 33107621 DOI: 10.1111/age.13015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2020] [Indexed: 12/12/2022]
Abstract
Russian sheep breeds represent an important economic asset by providing meat and wool, whilst being adapted to extreme climates. By resequencing two Russian breeds from Siberia: Tuva (n = 20) and Baikal (n = 20); and comparing them with a European (UK) sheep outgroup (n = 14), 41 million variants were called, and signatures of selection were identified. High-frequency missense mutations on top of selection peaks were found in genes related to immunity (LOC101109746) in the Baikal breed and wool traits (IDUA), cell differentiation (GLIS1) and fat deposition (AADACL3) in the Tuva breed. In addition, genes found under selection owing to haplotype frequency changes were related to wool traits (DSC2), parasite resistance (CLCA1), insulin receptor pathway (SOCS6) and DNA repair (DDB2) in the Baikal breed, and vision (GPR179) in the Tuva breed. Our results present candidate genes and SNPs for future selection programmes, which are necessary to maintain and increase socioeconomic gain from Siberian breeds.
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Affiliation(s)
- J Sweet-Jones
- Royal Veterinary College, University of London, London, NW1 0TU, UK
| | - A A Yurchenko
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, 630090, Russia
| | - A V Igoshin
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, 630090, Russia
| | - N S Yudin
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, 630090, Russia
| | - M T Swain
- Institute of Biological, Environmental and Rural Sciences, University of Aberystwyth, Aberystwyth, SY23 3DA, UK
| | - D M Larkin
- Royal Veterinary College, University of London, London, NW1 0TU, UK.,The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, 630090, Russia
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