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Li W, Wang X, Zhang X, Li F, Zhang D, Li X, Zhang Y, Zhao Y, Zhao L, Xu D, Cheng J, Wang J, Zhou B, Lin C, Wang W. Polymorphism of sheep PRKAA2 gene and its association with growth traits. Anim Biotechnol 2023; 34:1324-1330. [PMID: 34971343 DOI: 10.1080/10495398.2021.2021215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Small ruminants farming plays an important role in the livelihood of a large part of the population. Herein we aimed to analyze the effects of single nucleotide polymorphisms in PRKAA2 gene on the growth-related traits of Hu sheep and Dorper sheep. The body weight and body type of 1254 sheep were measured at 80, 100, 120, 140, 160 and 180d, and 37620 phenotypic data were collected. RT-qPCR analysis was performed to test PRKAA2 gene expressed in different tissues of sheep, with the highest expression level in spleen, followed by kidney. In the present study, the PRKAA2 gene sequencing revealed one polymorphism located on Chr1 (Oar_rambouillet_v1.0), termed as chr1:32832382 G > A, and were significantly associated with growth traits of sheep (p < 0.05). The body weight, body length, chest circumference, and cannon circumference of individuals with AA genotype were significantly higher than those with the GG and GA genotypes (p < 0.05). Our findings reveal that PRKAA2 gene could be used as a marker-assisted selection to improve the growth-related traits of sheep.
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Affiliation(s)
- Wenxin Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaojuan Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Fadi Li
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
- Engineering Laboratory of Sheep Breeding and Reproduction Biotechnology in Gansu Province, Minqin, China
| | - Deyin Zhang
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xiaolong Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yukun Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yuan Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Liming Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Dan Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jiangbo Cheng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jianghui Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Bubo Zhou
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Changchun Lin
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Weimin Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Lakhssassi K, Meneses C, Sarto MP, Serrano M, Calvo JH. Genome-wide analysis reveals that the cytochrome P450 family 7 subfamily B member 1 gene is implicated in growth traits in Rasa Aragonesa ewes. Animal 2023; 17:100975. [PMID: 37734362 DOI: 10.1016/j.animal.2023.100975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/16/2023] [Accepted: 08/25/2023] [Indexed: 09/23/2023] Open
Abstract
Sheep are very well adapted to changing environments and are able to produce and reproduce with low inputs in feed and water better than other domestic ruminants. Indeed, the ewe body condition score (BCS) and live weight (LW) play a significant role in productive and reproductive performance. This work conducts a genome-wide association study (GWAS) to detect genetic variants associated with growth traits in 225 adult ewes of the Rasa Aragonesa breed by using the genotypes from 50 k and HD Illumina Ovine BeadChip. These ewes were measured for LW, BCS and growth rate (GR) for 2 years, from January to September. Corrected phenotypes for BCS, LW and GR were estimated and used as input for the GWAS. Only one single nucleotide polymorphism (SNP) rs425509273 in chromosome 9 (OAR9), associated with the GR, overcame the genome-wise significance level. One, three and nine SNPs were associated at the chromosome-wise level (FDR 10%) for traits BCS, LW and GR, respectively. The cytochrome P450 family 7 subfamily B member 1 (CYP7B1) candidate gene, located 83 kb upstream from SNP rs425509273 in OAR9, was partially isolated and Sanger-sequenced. Fifteen polymorphisms comprising 12 SNPs, two indels and one polyC, were detected in promoter, exon 1, 3, 5, and intron 1-3 region. The SNP association analysis of the polymorphisms located close to the transcription start site (TSS) showed that a 22 bp insertion located at -58 nucleotides from the TSS (indel (-58)), a polyC (-25), and two A/G SNPs (SNP3 (-114) and SNP5 (-63)) were associated with the GR trait, whereas only the indel (-58) was associated with the BCS trait. The haplotype analysis confirmed these results. The functional characterisation of the polymorphisms at CYP7B1 gene in liver by real-time quantitative PCR analysis confirmed that the mutations in the promoter region affected CYP7B1 gene expression. Our results demonstrated the involvement of the CYP7B1 gene promoter on GR and BCS traits in Rasa Aragonesa. These findings suggest that variations in ovine CYP7B1 may serve as potential genetic markers to be used in breeding programmes to improve growth characteristics that could influence reproductive traits.
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Affiliation(s)
- K Lakhssassi
- Departamento de Ciencia Animal, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA-IA2), Avda. Montañana 930, 50059 Zaragoza, Spain; Research Unit of Animal Production, National Institute for Agronomic Research (INRA), BP 6356, Institutes 10101, Rabat, Morocco
| | - C Meneses
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), 28040 Madrid, Spain
| | - M P Sarto
- Departamento de Ciencia Animal, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA-IA2), Avda. Montañana 930, 50059 Zaragoza, Spain
| | - M Serrano
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), 28040 Madrid, Spain.
| | - J H Calvo
- Departamento de Ciencia Animal, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA-IA2), Avda. Montañana 930, 50059 Zaragoza, Spain; Aragonese Foundation for Research and Development (ARAID), 50018 Zaragoza, Spain
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Ma S, Li P, Liu H, Xi Y, Xu Q, Qi J, Wang J, Li L, Wang J, Hu J, He H, Han C, Bai L. Genome-wide association analysis of the primary feather growth traits of duck: identification of potential Loci for growth regulation. Poult Sci 2022; 102:102243. [PMID: 36334470 PMCID: PMC9636485 DOI: 10.1016/j.psj.2022.102243] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 10/05/2022] [Accepted: 10/05/2022] [Indexed: 11/28/2022] Open
Abstract
The feather is an important epidermal appendage, plays an important role in the life activities of avian specie, and has important economic value. Revealing the molecular regulation mechanism of feather growth has a significant meaning in studying adaptive evolution, physiology, and mating of avian species and also provides a theoretical reference for poultry breeding. In this study, the genome-wide association analysis (GWAS) of 358 ducks was based on primary feather length phenotypic data (28-60 d), length growth rates (LGRs), and maturity scores (60 d) to explore the genetic basis affecting feather growth and maturation. The results showed that, among the primary feather 1 to 5 in ducks, the mean LGR of primary feather 2 was the fastest, with the longest length. The primary feathers in males grew and matured slightly faster than in females. The mean maturity scores of primary feather 10∼7 were higher than primary feather 1 to 3 in ducks. GWAS further showed 116 SNPs associated with feather length traits. In addition, 2 candidate regions (Chr1: 127,407,230-127,524,879 bp and Chr21: 182,061,707-183,616,298 bp) were associated with LGR, which contain total 13 candidate genes (The extremely significant SNPs were mainly located in 2 genes: Chr1: REPS2 and Chr21: PTPRT). Four candidate regions (Chr1: 29,113,036-28,675,018 bp, Chr2: 18,253,612-149,111,290 bp, Chr15: 6,489,774 to 12,138,221 bp and Chr21: 6,578,021-8,472,904 bp) were associated with feather maturity, which contain total 24 candidate genes (The extremely significant SNPs were mainly located in 4 genes: Chr1: IMMP2L, DOCK4 and DDX10, Chr2: LDLRAD4). In conclusion, sex factors influence feather growth and maturity, and the genetic basis of the growth /maturity trait between different feathers is similar. REPS2, PTPRT genes, and IMMP2L, DOCK4, DDX10, and LDLRAD4 are important candidate genes that influence feather growth and maturity, respectively.
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Affiliation(s)
- Shengchao Ma
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, P. R. China,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. China,College of Animal Science, Xinjiang Agricultural University, P. R. China
| | - Pengcheng Li
- Berry Genomics Corporation, Beijing 100015, P. R. China
| | - Hehe Liu
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, P. R. China,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. China,Corresponding author:
| | - Yang Xi
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, P. R. China,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. China
| | - Qian Xu
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, P. R. China,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. China
| | - Jingjing Qi
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, P. R. China,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. China
| | - Jianmei Wang
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, P. R. China,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. China
| | - Liang Li
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, P. R. China,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. China
| | - Jiwen Wang
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, P. R. China,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. China
| | - Jiwei Hu
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, P. R. China,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. China
| | - Hua He
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, P. R. China,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. China
| | - Chunchun Han
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, P. R. China,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. China
| | - Lili Bai
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, P. R. China,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. China
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Zhao L, Zhang D, Li X, Zhang Y, Zhao Y, Xu D, Cheng J, Wang J, Li W, Lin C, Yang X, Ma Z, Cui P, Zhang X, Wang W. Comparative proteomics reveals genetic mechanisms of body weight in Hu sheep and Dorper sheep. J Proteomics 2022; 267:104699. [PMID: 35995385 DOI: 10.1016/j.jprot.2022.104699] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 08/06/2022] [Accepted: 08/08/2022] [Indexed: 10/15/2022]
Abstract
Body weight (BW) is a critical economic trait for meat production in sheep, and it is a complex trait affected by numerous elements. The aim of this study was to investigate the genetic mechanisms of sheep BW by a label-free proteomics approach. The result showed, a total of 27, 14, 61, and 65 differentially abundant proteins (DAPs) were identified in the Hu_HBW vs. Hu_LBW, DP_HBW vs. DP_LBW, Hu_HBW vs. DP_HBW, and Hu_LBW vs. DP_LBW comparisons, respectively. Five proteins (including ILK, AHCYL2, MLIP, CYB5A, and SMTNL1) related to fat synthesis and muscle development were detected in the Hu sheep group. In the Dorper sheep group, the screened DAPs strictly related to muscle development and fat synthesis were significantly enriched in MAP kinase activity (MAPK12), Arachidonic acid metabolism, and Steroid hormone biosynthesis (PGFS, LOC101107119) pathways. Several DAPs related to immune responses (SERPINA1, FGG, SERPINC1, and LOC101108131), fat deposition (APOH, GC, AHSG, SKP1, ACSL1, ACAT1, and ACADS), and muscle development (LMOD3 and LRRC39) were detected in the Hu vs. Dorper sheep comparison. These analyses indicated that the BW of sheep is regulated via a variety of pathways, and these DAPs can be further investigated as candidate markers for predicting the BW of sheep. SIGNIFICANCE: Body weight is one of the key traits in sheep and involves multiple coordinated regulatory mechanisms, but the genetic mechanism of BW is still unclear in sheep. In the current study, the label-free method was used to identify the proteins and pathways related to BW using LT muscle of Hu sheep and Dorper sheep with different BW. These findings will provide new candidate proteins and vital pathways into the molecular mechanisms involved growth traits in sheep.
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Affiliation(s)
- Liming Zhao
- 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
| | - Yukun Zhang
- 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
| | - 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
| | - Xiaobin Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Zongwu Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Panpan Cui
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Xiaoxue Zhang
- 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.
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6
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Ge L, Su P, Wang S, Gu Y, Cao X, Lv X, Wang S, Getachew T, Mwacharo JM, Haile A, Yuan Z, Sun W. New Insight into the Role of the Leucine Aminopeptidase 3 ( LAP3) in Cell Proliferation and Myogenic Differentiation in Sheep Embryonic Myoblasts. Genes (Basel) 2022; 13:genes13081438. [PMID: 36011349 PMCID: PMC9408374 DOI: 10.3390/genes13081438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/07/2022] [Accepted: 08/10/2022] [Indexed: 11/18/2022] Open
Abstract
Previous genome-wide association studies (GWAS) have found that LAP3 may have the potential function to impact sheep muscle development. In order to further explore whether LAP3 expression has an important role in the development of sheep embryonic myoblasts, we conducted the spatiotemporal expression profile analysis of LAP3 at the tissue and cellular level. Then we used small interfering RNA and eukaryotic recombinant vectors to perform gain/loss-of-function analysis of LAP3. CCK-8 detection, EdU staining, and flow cytometry were used to investigate the impact of LAP3 knockdown or overexpression on the proliferation of embryonic myoblasts. In addition, cell phenotype observation, MyHC indirect immunofluorescence, and quantitative detection of the expression changes of myogenic regulatory factors (MRFs) were used to explore the effect of LAP3 on myogenic differentiation. The results showed that the LAP3 expression level in muscle tissue of fetuses was significantly higher than that in newborn lambs and adult sheep, and its expression level on day 3 of differentiation was also significantly higher than that in the proliferation phase and other differentiation time points. LAP3 silencing could significantly increase cell viability and EdU-positive cells, as well as prolonging the length of S phase of myoblasts to promote proliferation, while the results were reversed when LAP3 was overexpressed. Moreover, LAP3 silencing significantly hindered myotube formation and down-regulated the expression levels of MRFs from day 5 to day 7 of terminal differentiation, while the results were reversed when LAP3 was highly expressed. Overall, our results suggested that the expression of LAP3 impacts on the development of sheep embryonic myoblasts which provides an important theoretical basis for molecular breeding of meat production in sheep.
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Affiliation(s)
- Ling Ge
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou 225009, China
| | - Pengwei Su
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou 225009, China
| | - Shan Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou 225009, China
| | - Yifei Gu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou 225009, China
| | - Xiukai Cao
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou 225000, China
| | - Xiaoyang Lv
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou 225000, China
| | - Shanhe Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou 225009, China
| | - Tesfaye Getachew
- International Centre for Agricultural Research in the Dry Areas, Addis Ababa 999047, Ethiopia
| | - Joram M. Mwacharo
- International Centre for Agricultural Research in the Dry Areas, Addis Ababa 999047, Ethiopia
| | - Aynalem Haile
- International Centre for Agricultural Research in the Dry Areas, Addis Ababa 999047, Ethiopia
| | - Zehu Yuan
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou 225000, China
- Correspondence: (Z.Y.); (W.S.)
| | - Wei Sun
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou 225000, China
- Correspondence: (Z.Y.); (W.S.)
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7
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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: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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8
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Peng H, Hu M, Liu Z, Lai W, Shi L, Zhao Z, Ma H, Li Y, Yan S. Transcriptome Analysis of the Liver and Muscle Tissues of Dorper and Small-Tailed Han Sheep. Front Genet 2022; 13:868717. [PMID: 35480317 PMCID: PMC9035493 DOI: 10.3389/fgene.2022.868717] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 03/21/2022] [Indexed: 11/25/2022] Open
Abstract
It is well known that Dorper (DP) is a full-bodied, fast-growing and high dressing percentage breed, while the production performance of Small-tailed Han sheep (STH) is not so excellent, in contrast to DP. Therefore, in this study, a comparative transcriptomic analysis of liver and muscle tissues from DP and STH breeds was carried out to find differentially expressed genes (DEGs) that affect their growth and meat quality traits. The results showed that the total number of DEGs was 2,188 in the two tissues. There were 950, 160 up-regulated and 1,007, 71 down-regulated genes in the liver and muscle, respectively. Several DEGs such as TGFB1, TGFB3, FABP3, LPL may be associated with growth and development in DP. Also, several GO terms were found to be associated with muscle growth and development, such as developmental growth (GO:0048589), and myofibril (GO:0030016). Further validation of eight genes (6 up-regulated, and 2 down-regulated) was performed using quantitative RT-PCR. These findings will provide valuable information for studying growth and development as well as meat quality traits in sheep.
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Affiliation(s)
- Hongyang Peng
- College of Animal Science, Jilin University, Changchun, China
| | - Mingyue Hu
- College of Animal Science, Jilin University, Changchun, China
| | - Zhengxi Liu
- College of Animal Science, Jilin University, Changchun, China
| | - Weining Lai
- College of Animal Science, Jilin University, Changchun, China
| | - Lulu Shi
- College of Animal Science, Jilin University, Changchun, China
| | - Zhongli Zhao
- Institute of Animal Husbandry and Veterinary, Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Huihai Ma
- Institute of Animal Husbandry and Veterinary, Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Yumei Li
- College of Animal Science, Jilin University, Changchun, China
- *Correspondence: Yumei Li, ; Shouqing Yan,
| | - Shouqing Yan
- College of Animal Science, Jilin University, Changchun, China
- *Correspondence: Yumei Li, ; Shouqing Yan,
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9
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Zhao Y, Zhang X, Li F, Zhang D, Zhang Y, Li X, Song Q, Zhou B, Zhao L, Wang J, Xu D, Cheng J, Li W, Lin C, Yang X, Zeng X, Wang W. Whole Genome Sequencing Analysis to Identify Candidate Genes Associated With the rib eye Muscle Area in Hu Sheep. Front Genet 2022; 13:824742. [PMID: 35368668 PMCID: PMC8964300 DOI: 10.3389/fgene.2022.824742] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 02/14/2022] [Indexed: 11/22/2022] Open
Abstract
In sheep meat production, the rib eye area is an important index to evaluate carcass traits. However, conventional breeding programs have led to slow genetic progression in rib eye muscle area. Operationalizing molecular marker assisted breeding is an optimized breeding method that might improve this situation. Therefore, the present study used whole genome sequencing data to excavate candidate genes associated with the rib eye muscle. Male Hu lambs (n = 776) with pedigrees and 274 lambs with no pedigree were included. The genetic parameters of the rib eye area were estimated using a mixed linear mixed model. The rib eye area showed medium heritability (0.32 ± 0.13). Whole-genome sequencing of 40 large rib eye sheep [17.97 ± 1.14, (cm2)] and 40 small rib eye sheep [7.89 ± 0.79, (cm2)] was performed. Case-control genome-wide association studies and the fixation index identified candidate rib eye-associated genes. Seven single nucleotide polymorphisms (SNPs) in six genes (ALS2, ST6GAL2, LOC105611989, PLXNA4, DPP6, and COL12A1) were identified as candidates. The study population was expanded to 1050 lambs to perform KASPar genotyping on five SNPs, which demonstrated that SNPs in LOC105611989, DPP6, and COL12A1 correlated significantly with the rib eye area, which could be used as genetic markers for molecular breeding of the rib eye area. The results provided genetic parameters estimated on the rib eye area and information for breeding based on carcass traits in Hu sheep.
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Affiliation(s)
- Yuan Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Fadi Li
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
- Engineering Laboratory of Sheep Breeding and Reproduction Biotechnology in Gansu Province, Minqin, China
| | - Deyin Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yukun Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaolong Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Qizhi Song
- Linze County Animal Disease Prevention and Control Center of Gansu Province, Linze, China
| | - Bubo Zhou
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Liming Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jianghui Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Dan Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jiangbo Cheng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Wenxin Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Changchun Lin
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaobin Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiwen Zeng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Weimin Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- *Correspondence: Weimin Wang,
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10
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Saif R, Henkel J, Mahmood T, Ejaz A, Ahmad F, Zia S. Detection of whole genome selection signatures of Pakistani Teddy goat. Mol Biol Rep 2021; 48:7273-80. [PMID: 34609690 DOI: 10.1007/s11033-021-06726-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 09/27/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Natural and artificial selection tend to cause variability that contributes to shape the genome of livestock in a way that differentiates them among the animal kingdom. The particular aim here is to identify positive selection signatures with whole genome pooled-sequence data of Pakistani Teddy goat. METHODS AND RESULTS Paired-end alignment of 635,357,043 reads of Teddy goat with (ARS1) reference genome assembly was carried out. Pooled-Heterozygosity (Hp) and Tajima's D (TD) are applied for validation and getting better hits of selection signals, while pairwise FST statistics is conducted on Teddy vs. Bezoar (wild goat ancestor) for genomic differentiation, moreover annotation of regions under positive selection was also performed. Hp score with - ZHp > 5 detected six windows having highest hits on Chr. 29, 9, 25, 15 and 14 that harbor HRASLS5, LACE1 and AXIN1 genes which are candidate for embryonic development, lactation and body height. Secondly, - ZTD value of > 3.3 showed 4 windows with very strong hits on Chr.5 & 9 which harbor STIM1 and ADM genes related to body mass and weight. Lastly, - ZFST < - 5 generated four strong signals on Chr.5 & 12 harbor LOC102183233 gene. Other significant selection signatures encompass genes associated with wool production, prolificacy and coat colors traits in this breed. CONCLUSIONS In brief, this study identified the genes under selection in Pakistani Teddy goat that will be helpful to refining the marker-assisted breeding policies and converging required production traits within and across other goat breeds and to explore full genetic potential of this valued species of livestock.
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11
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Niu Q, Zhang T, Xu L, Wang T, Wang Z, Zhu B, Zhang L, Gao H, Song J, Li J, Xu L. Integration of selection signatures and multi-trait GWAS reveals polygenic genetic architecture of carcass traits in beef cattle. Genomics 2021; 113:3325-3336. [PMID: 34314829 DOI: 10.1016/j.ygeno.2021.07.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 05/05/2021] [Accepted: 07/22/2021] [Indexed: 11/18/2022]
Abstract
Carcass merits are widely considered as economically important traits affecting beef production in the beef cattle industry. However, the genetic basis of carcass traits remains to be well understood. Here, we applied multiple methods, including the Composite of Likelihood Ratio (CLR) and Genome-wide Association Study (GWAS), to explore the selection signatures and candidate variants affecting carcass traits. We identified 11,600 selected regions overlapping with 2214 candidate genes, and most of those were enriched in binding and gene regulation. Notably, we identified 66 and 110 potential variants significantly associated with carcass traits using single-trait and multi-traits analyses, respectively. By integrating selection signatures with single and multi-traits associations, we identified 12 and 27 putative genes, respectively. Several highly conserved missense variants were identified in OR5M13D, NCAPG, and TEX2. Our study supported polygenic genetic architecture of carcass traits and provided novel insights into the genetic basis of complex traits in beef cattle.
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Affiliation(s)
- Qunhao Niu
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Tianliu Zhang
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ling Xu
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Tianzhen Wang
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zezhao Wang
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Bo Zhu
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lupei Zhang
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huijiang Gao
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jiuzhou Song
- Department of Animal and Avian Science, University of Maryland, College Park, USA
| | - Junya Li
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Lingyang Xu
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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12
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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13
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Tao L, He XY, Wang FY, Pan LX, Wang XY, Gan SQ, Di R, Chu MX. Identification of genes associated with litter size combining genomic approaches in Luzhong mutton sheep. Anim Genet 2021; 52:545-549. [PMID: 34002409 DOI: 10.1111/age.13078] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2021] [Indexed: 12/12/2022]
Abstract
Litter size is one of the most important reproductive traits of sheep, which has pronounced effects on the profit of husbandry enterprises and enthusiasm of breeders. Despite the importance of litter size, the underlying genetic mechanisms have not been entirely elucidated. Therefore, based on a high-density SNP chip, genome-wide comparative analysis was performed between two groups with different fecundity to reveal candidate genes linked to litter size via detection of homozygosity and selection signatures in Luzhong mutton sheep. Consequently, nine promising genes were identified from six runs of homozygosity islands, and functionally linked to reproduction (ACTL7A, ACTL7B, and ELP1), embryonic development (KLF5 and PIBF1), and cell cycle (DACH1, BORA, DIS3, and MZT1). A total of 128 genes were observed under selection, of which HECW1 and HTR1E were related to total lambs born, GABRG3, LRP1B, and MACROD2 to teat number, and AGBL1 to reproductive seasonality. Additionally, the presence of inbreeding depression implies the urgency of reasonable mating system to increase litter size in the present herd. These findings provide a comprehensive insight to the genetic makeup of litter size, and also contribute to implementation of marker-assisted selection in 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
| | - X Y He
- 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
| | - L X Pan
- Ji'nan Laiwu Yingtai Agriculture and Animal Husbandry Technology Co., Ltd, Ji'nan, Shandong, 271114, China
| | - X 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
| | - S Q Gan
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, Xinjiang, 832000, 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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14
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Sutera AM, Moscarelli A, Mastrangelo S, Sardina MT, Di Gerlando R, Portolano B, Tolone M. Genome-Wide Association Study Identifies New Candidate Markers for Somatic Cells Score in a Local Dairy Sheep. Front Genet 2021; 12:643531. [PMID: 33828586 PMCID: PMC8019815 DOI: 10.3389/fgene.2021.643531] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/01/2021] [Indexed: 12/13/2022] Open
Abstract
In the Mediterranean basin countries, the dairy sheep production is usually based on local breeds, which are very well-adapted to their production systems and environments and can indeed guarantee income, employment, and economic viability in areas where production alternatives are scarce or non-existent. Mastitis is still one of the greatest problems affecting commercial milk production. However, genetic evaluation of mastitis is particularly difficult because of its low heritability and the categorical nature of the trait. The aim of this study was to identify genomic regions putatively associated with somatic cells count (SCC) in the local economically important Valle del Belice sheep breed using of deregressed breeding values (DEBV) as response variables. All the samples were genotyped using the Illumina OvineSNP50K BeadChip. Genome-wide association analysis was carried out based on regression of DEBV. A total of eight markers were found to be significantly associated with log-transformed SCC. Several candidate genes associated with SCC were identified related to immunity system and udder conformation. The results can help improving the competitiveness of the local Valle del Belìce breed. Further studies considering a higher sample size or independent population will be needed to confirm our results.
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Affiliation(s)
- Anna Maria Sutera
- Dipartimento Scienze Veterinarie, University of Messina, Messina, Italy
| | - Angelo Moscarelli
- Dipartimento di Scienze Agrarie Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Maria Teresa Sardina
- Dipartimento di Scienze Agrarie Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Rosalia Di Gerlando
- Dipartimento di Scienze Agrarie Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Baldassare Portolano
- Dipartimento di Scienze Agrarie Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Marco Tolone
- Dipartimento di Scienze Agrarie Alimentari e Forestali, University of Palermo, Palermo, Italy
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15
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Tao L, He X, Wang F, Zhong Y, Pan L, Wang X, Gan S, Di R, Chu M. Luzhong mutton sheep: inbreeding and selection signatures. J Anim Sci Technol 2020; 62:777-789. [PMID: 33987559 PMCID: PMC7721573 DOI: 10.5187/jast.2020.62.6.777] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/11/2020] [Accepted: 10/02/2020] [Indexed: 01/13/2023]
Abstract
Intense artificial selection has been imposed to Luzhong mutton sheep population
in the past years. Improvements on growth and reproductive performance are two
breeding goals in the present herd. Although some progresses were phenotypically
observed possibly due to inbreeding induced by strong selection in terms of
these traits, the genomic evaluation was poorly understood. Therefore, a
high-density SNP array was used to characterize the pattern of runs of
homozygosity (ROH), estimate inbreeding and inbreeding depressions on early
growth performance and litter size based upon ROH, and scan positive selection
signatures of recent population. Consequently, a low inbreeding level was
observed which had negative effects on litter size, but not on early growth
performance. And 160 genes were under selection, of which some were reported to
be linked to several traits of sheep including body weight, litter size, carcass
and meat quality, milk yield and composition, fiber quality and health, and the
top genes were associated with growth (growth hormone [GH]- growth hormone
receptor [GHR]- Insulin-like growth factor 1 [IGF1] axis) and litter size (bone
morphogenic proteins [BMPs]-associated). The effectiveness of previous breeding
measures was highlighted, but purging selection was proposed to alleviate the
inbreeding depression on litter size, providing some genomic insights to
breeding management of Luzhong mutton sheep.
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Affiliation(s)
- Lin 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
| | - Xiaoyun He
- 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
| | - Fengyan 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
| | - Yingjie Zhong
- 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
| | - Linxiang Pan
- Ji'nan Laiwu Yingtai Agriculture and Animal Husbandry Technology, Ji'nan, Shandong 271114, China
| | - Xiangyu 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
| | - Shangquan Gan
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, Xinjiang 832000, China
| | - Ran 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
| | - Mingxing 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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Cao Y, Song X, Shan H, Jiang J, Xiong P, Wu J, Shi F, Jiang Y. Genome-Wide Association Study of Body Weights in Hu Sheep and Population Verification of Related Single-Nucleotide Polymorphisms. Front Genet 2020; 11:588. [PMID: 32719712 PMCID: PMC7350885 DOI: 10.3389/fgene.2020.00588] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 05/14/2020] [Indexed: 12/14/2022] Open
Abstract
Body weight (BW) is a critical economic trait for meat production in sheep. The current study aimed to perform a genome-wide association study (GWAS) to detect significant single-nucleotide polymorphisms (SNPs) that are associated with BW in Hu sheep. The comparison and analysis of the G1 and G2 generations of a nucleus meat Hu sheep breeding herd revealed four SNPs identified by GWAS. The subsequent verification of the significant SNP loci in the Hu sheep G3 generation nucleus herd also detected nine SNPs in significant SNP regions. Two SNPs were significantly associated with the BW of Hu sheep (p < 0.05). OARX_76354330.1 and s64890.1 could be identified as functional SNPs for the growth traits of Hu sheep. CAPN6, as a candidate gene, was significantly different in the biceps femoris and longissimus dorsi muscles of weaning (60-day) and 6-month sheep, which facilitated the discovery of causal variants for BW and contributed to the marker-assisted selection breeding of Hu sheep.
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Affiliation(s)
- Yuhao Cao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.,Institute of Animal Husbandry and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xuemei Song
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, China
| | - Huili Shan
- Institute of Animal Husbandry and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Junfang Jiang
- Institute of Animal Husbandry and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Pei Xiong
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.,Institute of Animal Husbandry and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jianliang Wu
- Institute of Animal Husbandry and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Fangxiong Shi
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yongqing Jiang
- Institute of Animal Husbandry and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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