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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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Li C, Yan Y, Pan C, Adjei M, Shahzad K, Wang P, Pan M, Li K, Wang Y, Zhao W. Identification and analysis of differentially expressed (DE) circRNA in epididymis of yak and cattleyak. Front Vet Sci 2023; 10:1040419. [PMID: 36825227 PMCID: PMC9941329 DOI: 10.3389/fvets.2023.1040419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 01/18/2023] [Indexed: 02/09/2023] Open
Abstract
Circular RNAs (circRNAs), as endogenous non-coding RNA with unique closed ring structure, is closely related to animal reproduction, and understanding the expression of circRNA in yak and cattleyak epididymal tissues is of great significance for understanding cattleyak sterility. Based on this, we screened and identified the differentially expressed circRNA in the epididymis of three yaks and two cattleyak. A total of 1,298 circRNAs were identified in the epididymis of yak and cattleyak, of which 137 differentially expressed (DE) circRNAs and the functions of some of them were elucidated in this research, as well as qPCR verification to 6 circRNAs from the 137 DE circRNAs. Gene Ontology (GO) enrichment analysis suggested that DE circRNAs were mainly related to metabolic process, development process, immune system process, reproductive process, reproduction, biological adhesion and growth. COG classification analysis showed that the DE circRNAs derived genes were mainly related to replication, recombination and repair. KEGG pathway analysis suggested that DE circRNAs were mainly involved in RNA degradation. In addition, we also screened Bta-mir-103, which is a circRNA binding miRNA related to sperm activity.
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Affiliation(s)
- Chunhai Li
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Yan Yan
- College of Life Sciences, Yan'an University, Yan'An, Shaanxi, China
| | - Cheng Pan
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Michael Adjei
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Khuram Shahzad
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Peng Wang
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Meilan Pan
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Kerui Li
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Ye Wang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China,*Correspondence: Ye Wang ✉
| | - Wangsheng Zhao
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China,Wangsheng Zhao ✉
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de Souza TC, de Souza TC, da Cruz VAR, Mourão GB, Pedrosa VB, Rovadoscki GA, Coutinho LL, de Camargo GMF, Costa RB, de Carvalho GGP, Pinto LFB. Estimates of heritability and candidate genes for primal cuts and dressing percentage in Santa Ines sheep. Livest Sci 2022. [DOI: 10.1016/j.livsci.2022.105048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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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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Chen Q, Xu L, Zhang M, Zhang T, Yan M, Zhai M, Huang X. Whole genome resequencing reveals the genetic contribution of Kazakh and Swiss Brown cattle to a population of Xinjiang Brown cattle. Gene 2022; 839:146725. [PMID: 35840005 DOI: 10.1016/j.gene.2022.146725] [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: 05/03/2022] [Revised: 06/21/2022] [Accepted: 07/08/2022] [Indexed: 11/04/2022]
Abstract
Xinjiang Brown cattle is characterized by wide environmental adaptation from its female parent (Kazakh cattle) and good production performance from its male parent (Swiss Brown cattle). However, the genetic basis underlying these characteristics hasnotbeenexplored. Here we compared 50 genomes of Xinjiang Brown cattle to the genomes of other eight breeds worldwide to analyze patterns of genetic variation in the Xinjiang Brown cattle. We found canonical genomic characteristics of cross breed with the lowest linkage disequilibrium and the highest effective population size. At the global level, Xinjiang Brown cattle had 9.88% Kazakh cattle and 90.12% Swiss Brown cattle inheritance. Our local ancestry inference revealed the segments with the excess of Kazakh cattle blood enriched in genes or pathways involved in digestion,absorption,metabolism and disease. More importantly, we also observed the completely fixed haplotypes inherited from Swiss Brown cattle harboring genes (LCORL, GHR, MEF2D, PCSK1 and MSRB3), KEGG pathways, cattle QTLs or human NHGRIGWAS catalog related to body measurement and growth traits. Our findings will not only help understand the process of cross breeding but can provide basic materials for further QTL mapping and improvement of important traits in Xinjiang Brown cattle.
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Affiliation(s)
- Qiuming Chen
- College of Animal Science, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Lei Xu
- College of Animal Science, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Menghua Zhang
- College of Animal Science, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Tao Zhang
- College of Animal Science, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Mengjie Yan
- College of Animal Science, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Manjun Zhai
- College of Animal Science, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Xixia Huang
- College of Animal Science, Xinjiang Agricultural University, Urumqi, Xinjiang, China.
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Zhao L, Zhou L, Hao X, Wang L, Han F, Liu L, Duan X, Guo F, He J, Liu N. Identification and Characterization of Circular RNAs in Association With the Deposition of Intramuscular Fat in Aohan Fine-Wool Sheep. Front Genet 2021; 12:759747. [PMID: 34938314 PMCID: PMC8685527 DOI: 10.3389/fgene.2021.759747] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/02/2021] [Indexed: 01/20/2023] Open
Abstract
Aohan fine-wool sheep (AFWS) is a high-quality fine-wool sheep breed that supplies wool and meat. Research is needed on the molecular mechanism behind intramuscular fat (IMF) deposition that greatly improves mutton quality. The widely expressed non-coding RNA is physiologically used in roles such as competitive endogenous RNA (ceRNA) that includes circular RNAs (circRNAs). Although circRNAs were studied in many fields, little research was devoted to IMF in sheep. We used the longissimus dorsi muscle of 2 and 12-month-old AWFS as research material to identify circRNAs related to IMF deposition in these sheep by RNA-seq screening for differentially expressed circRNAs in the two age groups. A total of 11,565 candidate circRNAs were identified, of which the 104 differentially expressed circRNAs in the two age groups were analyzed. Enrichment analysis was performed using Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes. The enriched pathways included lipid transport (GO:0006869), negative regulation of canonical Wnt signaling pathway (GO:0090090), fat digestion and absorption (ko04975), and sphingolipid metabolism (ko00600). The differentially expressed circRNAs included ciRNA455, circRNA9086, circRNA7445, circRNA4557, and others. The source genes involved in these pathways might regulate IMF deposition. We used the TargetScan and miRanda software for interaction analysis, and a network diagram of circRNA-miRNA interactions was created. CircRNA455-miR-127, circRNA455-miR-29a, circRNA455-miR-103, circRNA4557-mir149-5p, and circRNA2440-mir-23a might be involved in the IMF deposition process. The targeting relationship of circRNA4557-miR-149-5p was verified by a dual-luciferase reporter assay. The RT-qPCR results of seven randomly selected circRNAs were consistent with the sequencing results. This study provides additional information on circRNA regulation of IMF deposition in AFWS and is a useful resource for future research on this sheep breed.
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Affiliation(s)
- Le Zhao
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Lisheng Zhou
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Xiaojing Hao
- Qingdao Animal Husbandry and Veterinary Research Institute, Qingdao, China
| | - Lei Wang
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Fuhui Han
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Lirong Liu
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Xinming Duan
- Nongfayuan Zhejiang Agricultural Development Co. Ltd., Huzhou, China
| | - Feng Guo
- Tongliao Animal Agriculture Development Service Center, Tongliao, China
| | - Jianning He
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Nan Liu
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
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Novel InDels of GHR, GHRH, GHRHR and Their Association with Growth Traits in Seven Chinese Sheep Breeds. Animals (Basel) 2020; 10:ani10101883. [PMID: 33076416 PMCID: PMC7602648 DOI: 10.3390/ani10101883] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/08/2020] [Accepted: 10/12/2020] [Indexed: 12/18/2022] Open
Abstract
The GH growth axis plays an important role in the growth and development of animals and runs through the whole life of animals. Many studies have shown that molecular mutations in key genes of the GH axis will affect the growth and development of animals. The purpose of this study was to explore the distribution characteristics of InDels of GHR, GHRH, and GHRHR in seven Chinese sheep populations, and to further explore the relationship between InDels and sheep growth traits. GHR showed high variation in Chinese sheep, and GHR-53 showed the highest minimum allele frequency (MAF). There was only one InDel mutation site in both GHRH and GHRHR. The genotype frequencies of Hu sheep (HS), Tong sheep (TS), and Lanzhou fat-tail sheep (LFTS) were quite different from other breeds. The association between GHR, GHRH, and GHRHR InDels and body size traits in seven varieties were analyzed. The results showed that there was no significant relationship between GHRH and body size traits in the seven sheep populations. There was a positive association between GHR-21 and hip height of LFSH (p < 0.05). GHR-43 reduced body height and chest depth of Small tail han sheep (STHS) and hip width of TS. GHR-44 significantly affected the body weight of HS, the body height of STHS and the head depth of TS. GHR-53 significantly reduced cannon girth of HS, chest of STHS and forehead width of TS. GHRHR-2 significantly reduced the body weight of LFHS. To sum up, this study revealed the effects of GHR, GHRH, and GHRHR InDels on sheep phenotypic traits, which indicated their potential application prospects in the genetic improvement of mutton sheep.
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Gao Y, Huang B, Bai F, Wu F, Zhou Z, Lai Z, Li S, Qu K, Jia Y, Lei C, Dang R. Two Novel SNPs in RET Gene Are Associated with Cattle Body Measurement Traits. Animals (Basel) 2019; 9:E836. [PMID: 31640119 PMCID: PMC6826558 DOI: 10.3390/ani9100836] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/14/2019] [Accepted: 10/17/2019] [Indexed: 12/19/2022] Open
Abstract
The rearrangement of the transfection (RET) gene, which mediates the functions of the ganglion in the gastrointestinal tract, plays an important role in the development of the gastrointestinal nervous system. Therefore, the RET gene is a potential factor influencing animal body measurement. The aim of this study was to reveal the significant genetic variations in the bovine RET gene and investigate the relationship between genotypes and body measurement in two Chinese cattle breeds (Qinchuan and Nanyang cattle). In this study, two SNPs (c.1407A>G and c.1425C>G) were detected in the exon 7 of RET gene by sequencing. For the SNP1 and SNP2, the GG genotype was significantly associated with body height, hip height, and chest circumference in Qinchuan cattle (p < 0.05). Individuals with an AG-CC genotype showed the lowest value of all body measurement in both breeds. Our results demonstrate that the polymorphisms in the bovine RET gene were significantly associated with body measurement, which could be used as DNA marker on the marker-assisted selection (MAS) and improve the performance of beef cattle.
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Affiliation(s)
- Yuan Gao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi, China.
| | - Bizhi Huang
- Yunnan Academy of Grassland and Animal Science, Kunming 650212, China.
| | - Fuxia Bai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi, China.
| | - Fei Wu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi, China.
| | - Zihui Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi, China.
| | - Zhenyu Lai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi, China.
| | - Shipeng Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi, China.
| | - Kaixing Qu
- Yunnan Academy of Grassland and Animal Science, Kunming 650212, China.
| | - Yutang Jia
- Institute of Animal Science and Veterinary Medicine, Anhui Academy of Agriculture Science, Hefei 230001, China.
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi, China.
| | - Ruihua Dang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi, China.
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