Identification of Genomic Regions and Candidate Genes Associated with Body Weight and Body Conformation Traits in Karachai Goats
Abstract
:1. Introduction
2. Materials and Methods
2.1. Animals, Sampling and Genotyping
2.2. Quality Control of Data
2.3. Principal Component Analysis
2.4. Phenotypic Traits
2.5. Genome-Wide Association Studies
2.6. Gene Analysis
3. Results
3.1. Population Stratification
3.2. Genome-Wide Association Studies
3.3. Identification of Significant SNPs
3.4. Candidate Genes
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
- Miller, B.A.; Lu, C.D. Current status of global dairy goat production: An overview. Asian Australas. J. Anim. Sci. 2019, 32, 1219. [Google Scholar] [CrossRef]
- Gama, L.T.; Bressan, M.C. Biotechnology applications for the sustainable management of goat genetic resources. Small Rumin. Res. 2011, 98, 133–146. [Google Scholar] [CrossRef]
- Skapetas, B.; Bampidis, V. Goat production in the world: Present situation and trends. Livest. Res. Rural Dev. 2016, 28, 1–6. [Google Scholar]
- Melnikova, E.V. Ovcevodstvo i kozovodstvo tendencii k razvitiyu. Simvol Nauki. 2016, 4, 61–64. [Google Scholar]
- Mamontova, T.; Gadzhiev, Z.; Aibazov, M. Productivity of indigenous Karachai goats. Sheep Goats Wool. Bus. 2012, 2, 25–28. [Google Scholar]
- Aibazov, M.M.; Selionova, M.I.; Mamontova, T.V. Exterior and some biological indicators of Karachay goats. Zootechnics 2019, 12, 5–9. [Google Scholar] [CrossRef]
- Wang, W.; Dong, Y.; Xie, M.; Jiang, Y.; Xiao, N.; Du, X.; Zhang, W.; Tosser-Klopp, G.; Wang, J.; Yang, S.; et al. Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). Nat. Biotechnol. 2013, 31, 135–141. [Google Scholar] [CrossRef]
- Iung, L.H.S.; Petrini, J.; Ramírez-Díaz, J.; Salvian, M.; Rovadoscki, G.A.; Pilonetto, F.; Dauria, B.D.; Machado, P.F.; Coutinho, L.L.; Wiggans, G.R.; et al. Genome-wide association study for milk production traits in a Brazilian Holstein population. J. Dairy Sci. 2019, 102, 5305–5314. [Google Scholar] [CrossRef]
- Matukumalli, L.K.; Lawley, C.T.; Schnabel, R.D.; Taylor, J.F.; Allan, M.F.; Heaton, M.P.; O’Connell, J.; Moore, S.S.; Smith, T.P.L.; Sonstegard, T.S.; et al. Development and Characterization of a High Density SNP Genotyping Assay for Cattle. PLoS ONE 2009, 4, e5350. [Google Scholar] [CrossRef]
- Martin, P.M.; Palhière, I.; Ricard, A.; Tosser-Klopp, G.; Rupp, R. Genome wide association study identifies new loci associated with undesired coat color phenotypes in Saanen goats. PLoS ONE 2016, 11, e0152426. [Google Scholar] [CrossRef]
- Jiang, L.; Liu, J.; Sun, D.; Ma, P.; Ding, X.; Yu, Y.; Zhang, Q. Genome wide association studies for milk production traits in Chinese Holstein population. PLoS ONE 2010, 5, e13661. [Google Scholar] [CrossRef]
- Tosser-Klopp, G.; Bardou, P.; Bouchez, O.; Cabau, C.; Crooijmans, R.; Dong, Y.; Donnadieu-Tonon, C.; Eggen, A.; Heuven, H.C.M.; Jamli, S.; et al. Design and characterization of a 52K SNP chip for goats. PLoS ONE 2014, 9, e86227. [Google Scholar] [CrossRef]
- Moaeen-ud-Din, M.; Danish Muner, R.; Khan, M.S. Genome wide association study identifies novel candidate genes for growth and body conformation traits in goats. Sci. Rep. 2022, 12, 1–12. [Google Scholar] [CrossRef]
- Lu, Z.; Yue, Y.; Yuan, C.; Liu, J.; Chen, Z.; Niu, C.; Sun, X.; Zhu, S.; Zhao, H.; Guo, T.; et al. Genome-wide association study of body weight traits in Chinese fine-wool sheep. Animals 2020, 10, 170. [Google Scholar] [CrossRef]
- Tao, L.; He, X.Y.; Jiang, Y.T.; Lan, R.; Li, M.; Li, Z.M.; Yang, W.F.; Hong, Q.H.; Chu, M.X. Combined approaches to reveal genes associated with litter size in Yunshang black goats. Anim. Genet. 2020, 51, 924–934. [Google Scholar] [CrossRef]
- Shi, S.Y.; Li, L.J.; Zhang, Z.J.; Wang, E.Y.; Wang, J.; Xu, J.W.; Liu, H.B.; Wen, Y.F.; He, H.; Lei, C.Z.; et al. Copy number variation of MYLK4 gene and its growth traits of Capra hircus (goat). Anim. Biotechnol. 2020, 31, 532–537. [Google Scholar] [CrossRef]
- Xu, Z.; Wang, X.; Zhang, Z.; An, Q.; Wen, Y.; Wang, D.; Liu, X.; Li, Z.; Lyu, S.; Li, L.; et al. Copy number variation of CADM2 gene revealed its association with growth traits across Chinese Capra hircus (goat) populations. Gene 2020, 741, 144519. [Google Scholar] [CrossRef]
- Gu, B.; Sun, R.; Fang, X.; Zhang, J.; Zhao, Z.; Huang, D.; Zhao, Y.; Zhao, Y. Genome-Wide Association Study of Body Conformation Traits by Whole Genome Sequencing in Dazu Black Goats. Animals 2022, 12, 548. [Google Scholar] [CrossRef]
- Wang, Z.; Wang, C.; Guo, Y.; She, S.; Wang, B.; Jiang, Y.; Bai, Y.; Song, X.; Li, L.; Shi, L.; et al. Screening of Deletion Variants within the Goat PRDM6 Gene and Its E ff ects on Growth Traits. Animals 2020, 10, 208. [Google Scholar] [CrossRef]
- Luigi-Sierra, M.G.; Landi, V.; Guan, D.; Delgado, J.V.; Castelló, A.; Cabrera, B.; Mármol-Sánchez, E.; Alvarez, J.F.; Gómez-Carpio, M.; Martínez, A.; et al. A genome-wide association analysis for body, udder, and leg conformation traits recorded in Murciano-Granadina goats. J. Dairy Sci. 2020, 103, 11605–11617. [Google Scholar] [CrossRef]
- Liu, X.; Ma, L.; Wang, M.; Wang, K.; Li, J.; Yan, H.; Zhu, H.; Lan, X. Two indel variants of prolactin receptor (PRLR) gene are associated with growth traits in goat. Anim. Biotechnol. 2020, 31, 314–323. [Google Scholar] [CrossRef]
- Zhang, L.; Wang, F.; Gao, G.; Yan, X.; Liu, H. Genome-Wide Association Study of Body Weight Traits in Inner Mongolia Cashmere Goats. Front. Vet. Sci. 2021, 8, 1–9. [Google Scholar] [CrossRef]
- VanRaden, P.M. Efficient methods to compute genomic predictions. J. Dairy Sci. 2008, 91, 4414–4423. [Google Scholar] [CrossRef] [Green Version]
- R Development Core Team. A Language and Environment for Statistical Computing; R Foundation for Statistical Computing: Vienna, Austria, 2018; Available online: https://www.R-project.org (accessed on 17 July 2022).
- Kinsella, R.J.; Kähäri, A.; Haider, S.; Zamora, J.; Proctor, G.; Spudich, G.; Almeida-King, J.; Staines, D.; Derwent, P.; Kerhornou, A.; et al. Ensembl BioMarts: A hub for data retrieval across taxonomic space. Database 2011, 2011, bar030. [Google Scholar] [CrossRef]
- Huang, D.W.; Sherman, B.T.; Lempicki, R.A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 2009, 4, 44–57. [Google Scholar] [CrossRef]
- Klein, R.J.; Zeiss, C.; Chew, E.Y.; Tsai, J.Y.; Sackler, R.S.; Haynes, C.; Henning, A.K.; SanGiovanni, J.P.; Mane, S.M.; Mayne, S.T.; et al. Complement factor H polymorphism in age-related macular degeneration. Science 2005, 308, 385–389. [Google Scholar] [CrossRef]
- Rahmatalla, S.A.; Arends, D.; Reissmann, M.; Wimmers, K.; Reyer, H.; Brockmann, G.A. Genome-wide association study of body morphological traits in Sudanese goats. Anim. Genet. 2018, 49, 478–482. [Google Scholar] [CrossRef]
- Igoshin, A.V.; Yudin, N.S.; Belonogova, N.M.; Larkin, D.M. Genome-wide association study for body weight in cattle populations from Siberia. Anim. Genet. 2019, 50, 250–253. [Google Scholar] [CrossRef]
- Brito, L.F.; Kijas, J.W.; Ventura, R.V.; Sargolzaei, M.; Porto-Neto, L.R.; Cánovas, A.; Feng, Z.; Jafarikia, M.; Schenkel, F.S. Genetic diversity and signatures of selection in various goat breeds revealed by genome-wide SNP markers. BMC Genom. 2017, 18, 1–20. [Google Scholar] [CrossRef]
- Zonaed Siddiki, A.M.A.M.; Miah, G.; Islam, M.S.; Kumkum, M.; Rumi, M.H.; Baten, A.; Hossain, M.A. Goat Genomic Resources: The Search for Genes Associated with Its Economic Traits. Int. J. Genom. 2020, 2020, 5940205. [Google Scholar] [CrossRef]
- Deniskova, T.E.; Dotsev, A.V.; Selionova, M.I.; Reyer, H.; Sölkner, J.; Fornara, M.S.; Aybazov, A.-M.M.; Wimmers, K.; Brem, G.; Zinovieva, N.A. SNP-Based Genotyping Provides Insight Into the West Asian Origin of Russian Local Goats. Front. Genet. 2021, 12, 1133. [Google Scholar] [CrossRef] [PubMed]
- Abousoliman, I.; Reyer, H.; Oster, M.; Murani, E.; Mohamed, I.; Wimmers, K. Genome-Wide Analysis for Early Growth-Related Traits of the Locally Adapted Egyptian Barki Sheep. Genes 2021, 12, 1243. [Google Scholar] [CrossRef] [PubMed]
- Pasandideh, M.; Gholizadeh, M.; Rahimi-Mianji, G. A genome-wide association study revealed five SNPs affecting 8-month weight in sheep. Anim. Genet. 2020, 51, 973–976. [Google Scholar] [CrossRef] [PubMed]
- Öner, Y.; Serrano, M.; Sarto, P.; Iguácel, L.P.; Piquer-Sabanza, M.; Estrada, O.; Juan, T.; Calvo, J.H. Genome-Wide Association Studies of Somatic Cell Count in the Assaf Breed. Animals 2021, 11, 1531. [Google Scholar] [CrossRef]
- Wang, F.H.; Zhang, L.; Gong, G.; Yan, X.C.; Zhang, L.T.; Zhang, F.T.; Liu, H.F.; Lv, Q.; Wang, Z.Y.; Wang, R.J.; et al. Genome-wide association study of fleece traits in Inner Mongolia Cashmere goats. Anim. Genet. 2021, 52, 375–379. [Google Scholar] [CrossRef]
- Bad Barin, N.; Mir Hosseini, S.; Rabeei, B.; Qavi Hossein Zadeh, N. A survey on chromosomes 1 and 5 for QTL controlling body weight in Markhoz goats. Agric. Biotechnol. J. 2015, 7, 1–10. [Google Scholar] [CrossRef]
- Wong, M.L.; Islas-trejo, A.; Medrano, J.F. Structural characterization of the mouse high growth deletion and discovery of a novel fusion transcript between suppressor of cytokine signaling-2 (Socs-2) and viral encoded semaphorin receptor (Plexin C1). Gene 2002, 299, 153–163. [Google Scholar] [CrossRef]
- Duan, H.; Dixit, V.M. RAIDD is a new ‘‘death’’ adaptor molecule. Nature 1997, 385, 86–89. [Google Scholar] [CrossRef]
- Horvat, S.; Medrano, J.F. Lack of Socs2 expression causes the high-growth phenotype in mice. Genomics 2001, 72, 209–212. [Google Scholar] [CrossRef]
- Ramos, A.M.; Pita, R.H.; Malek, M.; Lopes, P.S.; Guimarães, S.E.F.; Rothschild, M.F. Analysis of the mouse High-growth region in pigs. J. Anim. Breed. Genet. 2009, 126, 404–412. [Google Scholar] [CrossRef]
- Ashar, H.R.; Tkachenko, A.; Shah, P.; Chada, K. HMGA2 is expressed in an allele-specific manner in human lipomas. Cancer Genet. Cytogenet. 2003, 143, 160–168. [Google Scholar] [CrossRef]
- Falvo, J.V.; Thanos, D.; Maniatis, T. Reversal of intrinsic DNA bends in the IFNβ gene enhancer by transcription factors and the architectural protein HMG I(Y). Cell 1995, 83, 1101–1111. [Google Scholar] [CrossRef]
- Shi, Z.; Wu, D.; Tang, R.; Li, X.; Chen, R.; Xue, S.; Zhang, C.; Sun, X. Silencing of HMGA2 promotes apoptosis and inhibits migration and invasion of prostate cancer cells. J. Biosci. 2016, 41, 229–236. [Google Scholar] [CrossRef]
- Zhou, X.; Benson, K.F.; Ashar, H.R.; Chada, K. Mutation responsible for the mouse pygmy phenotype in the developmentally regulated factor HMGI-C. Nature 1995, 376, 771–774. [Google Scholar] [CrossRef] [PubMed]
- Zhou, X.; Chada, K. HMGI family proteins: Architectural transcription factors in mammalian development and cancer. Keio J. Med. 1998, 47, 73–77. [Google Scholar] [CrossRef]
- Federico, A.; Forzati, F.; Esposito, F.; Arra, C.; Palma, G.; Barbieri, A.; Palmieri, D.; Fedele, M.; Pierantoni, G.M.; De Martino, I.; et al. Hmga1/Hmga2 double knock-out mice display a “superpygmy” phenotype. Biol. Open 2014, 3, 372–378. [Google Scholar] [CrossRef]
- Lee, M.O.; Li, J.; Davis, B.W.; Upadhyay, S.; Al Muhisen, H.M.; Suva, L.J.; Clement, T.M.; Andersson, L. Hmga2 deficiency is associated with allometric growth retardation, infertility, and behavioral abnormalities in mice. G3 Genes Genom. Genet. 2022, 12, jkab417. [Google Scholar] [CrossRef]
- Hodge, J.C.; Cuenco, K.T.; Huyck, K.L.; Somasundaram, P.; Panhuysen, C.I.M.; Stewart, E.A.; Morton, C.C. Uterine leiomyomata and decreased height: A common HMGA2 predisposition allele. Hum. Genet. 2009, 125, 257–263. [Google Scholar] [CrossRef]
- Yang, T.; Guo, Y.; Zhang, L.; Tian, Q.; Yan, H.; Guo, Y. HMGA2 Is Confirmed To Be Associated with Human Adult Height. Ann. Hum. Genet. 2010, 74, 11–16. [Google Scholar] [CrossRef]
- Quan, J.; Ding, R.; Wang, X.; Yang, M.; Yang, Y.; Zheng, E.; Gu, T.; Cai, G.; Wu, Z.; Liu, D.; et al. Genome-wide association study reveals genetic loci and candidate genes for average daily gain in Duroc pigs. Asian-Australas. J. Anim. Sci. 2018, 31, 480–488. [Google Scholar] [CrossRef]
- Xiaokai, L.; Quankui, H.; Lingki, F.; Yafeng, G.; Jing, L.; Ganqiu, L. Sequence and expression differences of BMP2 and, FGFR3 genes in Guangxi Bama mini pig and Landrace pig. Guangxi Agric. Sci. 2021, 52, 1709–1718. [Google Scholar]
- Wanbo, L.; Yaling, Z.; Huashui, A.; Tianfu, G. Identifying signatures of Selection Related to Small Body Size in Pigs. Chin. J. Anim. Vet. Sci. 2016, 47, 1839. [Google Scholar] [CrossRef]
- Kwak, G.H.; Kim, T.H.; Kim, H.Y. Down-regulation of MsrB3 induces cancer cell apoptosis through reactive oxygen species production and intrinsic mitochondrial pathway activation. Biochem. Biophys. Res. Commun. 2017, 483, 468–474. [Google Scholar] [CrossRef]
- Zhang, L.C.; Liang, J.; Pu, L.; Zhang, Y.B.; Wang, L.G.; Liu, X.; Yan, H.; Wang, L.X. mRNA and protein expression levels of four candidate genes for ear size in Erhualian and Large White pigs. Genet. Mol. Res. 2017, 16, gmr16029252. [Google Scholar] [CrossRef]
- Paris, J.M.; Letko, A.; Häfliger, I.M.; Ammann, P.; Drögemüller, C. Ear type in sheep is associated with the MSRB3 locus. Anim. Genet. 2020, 51, 968–972. [Google Scholar] [CrossRef]
- Saatchi, M.; Schnabel, R.D.; Taylor, J.F.; Garrick, D.J. Large-effect pleiotropic or closely linked QTL segregate within and across ten US cattle breeds. BMC Genom. 2014, 15, 1–17. [Google Scholar] [CrossRef]
- Breed, A.A.; Wu, M.; Li, S.; Zhang, G.; Fan, Y.; Gao, Y.; Huang, Y.; Lan, X.; Lei, C.; Ma, Y.; et al. Exploring insertions and deletions (indels) of MSRB3 gene and their association with growth traits in four Chinese indigenous cattle breeds. Arch. Anim. Breed. 2019, 62, 465–475. [Google Scholar]
- Blazevits, O.; Bolshette, N.; Vecchio, D.; Guijarro, A.; Croci, O.; Campaner, S.; Grimaldi, B. MYC-Associated Factor MAX is an Essential Regulator of the Clock Core Network. SSRN Electron. J. 2019. [Google Scholar] [CrossRef]
- GeneCards. Available online: https://www.genecards.org/cgi-bin/carddisp.pl?gene=MAX (accessed on 19 September 2022).
- Wang, X.; Kadarmideen, H.N. Metabolomics analyses in high-low feed efficient dairy cows reveal novel biochemical mechanisms and predictive biomarkers. Metabolites 2019, 9, 151. [Google Scholar] [CrossRef]
- Zhang, S.; Li, H.; Shi, H. Single marker and haplotype analysis of the chicken apolipoprotein B gene T123G and D 9 500D 9- polymorphism reveals association with body growth and obesity. Poult. Sci. 2006, 85, 178–184. [Google Scholar] [CrossRef] [PubMed]
- Decai, X.; Zhiyong, Z.; Bin, Z.; Zhongcheng, H.; Quanshu, W.; Jing, L. Correlation analysis of relative expression of apob, adfp and fatp1 with lipid metabolism in daweishan mini chickens. Braz. J. Poult. Sci. 2017, 19, 151–157. [Google Scholar] [CrossRef]
- Bagatoli, A.; de Melo, A.L.P.; Gasparino, E.; Rodrigues, M.T.; Ferreira, L.; Garcia, O.S.R.; Soares, M.A.M. Association between polymorphisms of APOB, SLC27A6, AGPAT6 and PRLR genes and milk production and quality traits in goats. Small Rumin. Res. 2021, 203, 106484. [Google Scholar] [CrossRef]
- Braz, C.U.; Taylor, J.F.; Bresolin, T.; Espigolan, R.; Feitosa, F.L.B.; Carvalheiro, R.; Baldi, F.; De Albuquerque, L.G.; De Oliveira, H.N. Sliding window haplotype approaches overcome single SNP analysis limitations in identifying genes for meat tenderness in Nelore cattle. BMC Genet. 2019, 20, 1–12. [Google Scholar] [CrossRef]
- Daetwyler, H.D.; Swan, A.A.; Van Der Werf, J.H.; Hayes, B.J. Accuracy of pedigree and genomic predictions of carcass and novel meat quality traits in multi-breed sheep data assessed by cross-validation. Genet. Sel. Evol. 2012, 44, 33. [Google Scholar] [CrossRef]
- Cesar, A.S.M.; Regitano, L.C.A.; Reecy, J.M.; Poleti, M.D.; Oliveira, P.S.N.; de Oliveira, G.B.; Moreira, G.C.M.; Mudadu, M.A.; Tizioto, P.C.; Koltes, J.E.; et al. Identification of putative regulatory regions and transcription factors associated with intramuscular fat content traits. BMC Genom. 2018, 19, 1–20. [Google Scholar] [CrossRef] [Green Version]
- Diniz, W.J.S.; Mazzoni, G.; Coutinho, L.L.; Banerjee, P.; Geistlinger, L.; Cesar, A.S.M.; Bertolini, F.; Afonso, J.; De Oliveira, P.S.N.; Tizioto, P.C.; et al. Detection of co-expressed pathway modules associated with mineral concentration and meat quality in nelore cattle. Front. Genet. 2019, 10, 210. [Google Scholar] [CrossRef]
- Feng, J.; Jiang, W.; Cheng, X.; Zou, B.; Varley, A.W.; Liu, T.; Qian, G.; Zeng, W.; Tang, J.; Zhao, Q.; et al. A host lipase prevents lipopolysaccharide-induced foam cell formation. iScience 2021, 24, 103004. [Google Scholar] [CrossRef]
- Lucki, N.C.; Bandyopadhyay, S.; Wang, E.; Merrill, A.H.; Sewer, M.B. Acid ceramidase (ASAH1) is a global regulator of steroidogenic capacity and adrenocortical gene expression. Mol. Endocrinol. 2012, 26, 228–243. [Google Scholar] [CrossRef]
- Liu, A.; Wang, Y.; Sahana, G.; Zhang, Q.; Liu, L.; Lund, M.S.; Su, G. Genome-wide Association Studies for Female Fertility Traits in Chinese and Nordic Holsteins. Sci. Rep. 2017, 7, 1–12. [Google Scholar] [CrossRef]
- Sun, X.; Jiang, J.; Wang, G.; Zhou, P.; Li, J.; Chen, C.; Liu, L.; Li, N.; Xia, Y.; Ren, H. Genome-wide association analysis of nine reproduction and morphological traits in three goat breeds from Southern China. Anim. Biosci. 2022, 41, 1–23. [Google Scholar] [CrossRef]
- Wang, L.; Xue, K.; Wang, Y.; Niu, L.; Li, L.; Zhong, T.; Guo, J.; Feng, J.; Song, T.; Zhang, H. Molecular and functional characterization of the adiponectin (AdipoQ) gene in goat skeletal muscle satellite cells. Asian-Australas. J. Anim. Sci. 2018, 31, 1088–1097. [Google Scholar] [CrossRef]
- Xie, G.; Wang, Y.; Xu, Q.; Hu, M.; Zhu, J.; Bai, W.; Lin, Y. Knockdown of adiponectin promotes the adipogenesis of goat intramuscular preadipocytes. Anim. Biotechnol. 2022, 33, 408–416. [Google Scholar] [CrossRef]
- Wang, Y.; Xiao, X.; Wang, L. In vitro characterization of goat skeletal muscle satellite cells. Anim. Biotechnol. 2020, 31, 115–121. [Google Scholar] [CrossRef]
Trait | Max | Min | Mean | Var | Std. Dev | CV |
---|---|---|---|---|---|---|
BW | 49.5 kg | 27.1 kg | 36.35 kg | 13.1 | 3.62 | 9.95 |
WH | 60.4 cm | 47.5 cm | 52.78 cm | 7.3 | 2.70 | 5.11 |
RH | 60.5 cm | 48.0 cm | 53.48 cm | 8.1 | 2.84 | 5.31 |
BL | 61.5 cm | 48.1 cm | 54.14 cm | 8.4 | 2.90 | 5.35 |
CP | 68.9 cm | 52.2 cm | 60.60 cm | 10.0 | 3.17 | 5.23 |
CW | 14.0 cm | 8.0 cm | 10.21 cm | 1.5 | 1.22 | 11.94 |
CD | 26.4 cm | 18.0 cm | 21.54 cm | 2.7 | 1.63 | 7.57 |
RW | 13.9 cm | 9.5 cm | 11.30 cm | 0.6 | 0.78 | 6.86 |
Trait | Genome-Wide SNPs (p < 10−5) | Suggestive SNPs (p < 10−4) | ||
---|---|---|---|---|
n | Chr | n | Chr | |
BW | 5 | 5, 6, 10, 16 | 22 | 1, 5, 10, 16, 18, 20, 24, 25, 26 |
WH | 7 | 1, 3, 8, 9, 10, 13, 18 | 42 | 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 15, 16,17, 20, 26, 29 |
RH | 9 | 1, 3, 8, 9, 10, 13, 18, 26, 29 | 46 | 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 20, 26, 27, 29 |
BL | 6 | 3, 10, 13, 18, 29 | 42 | 1, 2, 3, 5, 6, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 20, 21, 26, 27, 28, 29 |
CP | 4 | 9, 10, 18, 19 | 18 | 4, 5, 6, 7, 9, 10, 12, 13, 17 |
CW | 30 | 1, 2, 3, 4, 5, 7, 9, 10, 12, 17,18, 20, 21, 22, 24, 26, 28 | 101 | 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29 |
CD | 1 | 18 | 7 | 9, 13, 17 |
RW | 3 | 1, 2, 3 | 11 | 4, 8, 9, 12, 14, 16, 18, 20, 25, |
Chr | SNP | Position * | Trait | p-Value | R2 | Genes ** |
---|---|---|---|---|---|---|
1 | snp36273-scaffold435-778554 | 76 791 560 | WH | 3.66 × 10−6 | 0.069 | CLDN16, CLDN1, P3H2 |
CW | 5.67 × 10−6 | 0.048 | ||||
RH | 7.62 × 10−6 | 0.069 | ||||
1 | snp40557-scaffold519-2601256 | 80 175 337 | CW | 7.04 × 10−6 | 0.110 | ST6GAL, ADIPOQ, RFC4, EIF4A2, MIR1248, KNG1, TBCCD1, DNAJB11, CRYGS, FETUB, AHSG, HRG |
1 | snp46677-scaffold65-1704757 | 105 833 294 | RW | 7.14 × 10−6 | 0.002 | - |
2 | snp37767-scaffold464-4950066 | 37 437 223 | CW | 8.29 × 10−6 | 0.023 | - |
2 | snp40316-scaffold515-741525 | 48 011 875 | RW | 2.15 × 10−6 | 0.021 | - |
3 | snp41843-scaffold545-952728 | 19 599 119 | CW | 7.17 × 10−6 | 0.016 | - |
3 | snp48395-scaffold687-2186794 | 39 664 309 | RW | 7.09 × 10−6 | 0.028 | UBE2U, ROR1 |
3 | snp42136-scaffold55-4190633 | 57 469 911 | CW | 9.16 × 10−6 | 0.006 | - |
3 | snp24555-scaffold2498-324452 | 103 535 122 | WH | 2.93 × 10−7 | 0.058 | INTS3, SLC27A3, NPR1, CHTOP, ILF2, SNAPIN, NUP210L, DENND4B, RAB13, GATAD2B, CREB3L4, CRTC2, JTB, RPS27 |
RH | 2.36 × 10−6 | 0.058 | ||||
BL | 4.80 × 10−6 | 0.051 | ||||
CW | 9.93 × 10−6 | 0.017 | ||||
4 | snp56760-scaffold9-422861 | 56 008 260 | CW | 9.16 × 10−6 | 0.017 | - |
4 | snp31180-scaffold345-2038562 | 64 439 198 | CW | 2.69 × 10−6 | 0.016 | - |
4 | snp44315-scaffold603-2039906 | 104 315 554 | CW | 6.79 × 10−6 | 0.043 | - |
5 | snp17488-scaffold1809-252855 | 9 865 450 | CW | 9.13 × 10−8 | 0.004 | - |
5 | snp38426-scaffold486-2412676 | 23 345 368 | BW | 4.83 × 10−6 | 0.067 | CRADD |
6 | snp40083-scaffold511-2344051 | 62 949 329 | BW | 3.01 × 10−6 | 0.085 | - |
6 | snp40053-scaffold511-1070977 | 64 228 064 | BW | 6.44 × 10−6 | 0.065 | - |
7 | snp50806-scaffold735-500181 | 27 813 856 | CW | 6.75 × 10−6 | 0.002 | - |
8 | snp12933-scaffold1499-1805970 | 68 115 674 | RH | 2.88 × 10−6 | 0.074 | - |
WH | 2.98 × 10−6 | 0.076 | - | |||
9 | snp3895-scaffold1122-1069822 | 23 117 311 | CW | 2.93 × 10−6 | 0.024 | - |
9 | snp10101-scaffold1358-1351350 | 27 999 512 | CW | 1.38 × 10−6 | 0.030 | - |
9 | snp59091-scaffold969-2758702 | 30 398 000 | CW | 6.58 × 10−6 | 0.013 | - |
9 | snp29395-scaffold318-901939 | 53 346 107 | CP | 4.65 × 10−6 | 0.066 | PTPRK, THEMIS |
9 | snp3575-scaffold1110-924176 | 59 047 836 | WH | 8.69 × 10−6 | 0.071 | EYA4, TBPL1, TCF21 |
10 | snp43119-scaffold572-3093664 | 5 115 781 | CP | 4.28 × 10−6 | 0.051 | - |
10 | snp1448-scaffold104-1147808 | 25 854 668 | BW | 4.56 × 10−6 | 0.049 | MAX, RAB15, GPX2 |
10 | snp38108-scaffold475-788703 | 38 683 034 | WH | 2.60 × 10−6 | 0.066 | - |
RH | 3.50 × 10−6 | 0.062 | - | |||
BL | 6.24 × 10−6 | 0.069 | - | |||
10 | snp57312-scaffold912-2276709 | 53 713 433 | CW | 2.79 × 10−7 | 0.062 | - |
10 | snp33139-scaffold388-418538 | 61 359 453 | CW | 1.67 × 10−6 | 0.001 | - |
10 | snp17716-scaffold184-400952 | 74 860 568 | CW | 8.56 × 10−6 | 0.005 | - |
10 | snp16269-scaffold1711-397417 | 78 944 115 | CW | 2.87 × 10−7 | 0.018 | - |
12 | snp35954-scaffold431-1932104 | 37 043 670 | CW | 2.17 × 10−7 | 0.022 | - |
13 | snp31438-scaffold348-1638233 | 77 996 024 | RH | 1.60 × 10−7 | 0.108 | PTPN1, RIPOR3 |
WH | 7.62 × 10−7 | 0.108 | ||||
BL | 2.13 × 10−6 | 0.107 | ||||
16 | snp8624-scaffold131-2001386 | 57 408 452 | BW | 8.21 × 10−6 | 0.047 | - |
17 | snp35564-scaffold428-2794282 | 38 994 171 | CW | 5.81 × 10−6 | 0.024 | - |
17 | snp21166-scaffold207-2532534 | 52 935 461 | CW | 9.81 × 10−6 | 0.003 | - |
18 | snp6168-scaffold1217-1985930 | 3 837 951 | CW | 1.25 × 10−6 | 0.166 | BCAR1, LDHD, BCNT, P97BCNT |
18 | snp41877-scaffold546-944746 | 11 898 552 | CD | 1.45 × 10−6 | 0.067 | KCNG4, NECAB2, TAF1C, HSDL1, MBTPS1, DNAAF1, ADAD2, ATP2C2, WFDC1, MEAK7 |
BL | 1.56 × 10−6 | 0.063 | ||||
WH | 1.57 × 10−6 | 0.055 | ||||
RH | 2.71 × 10−6 | 0.055 | ||||
CP | 5.63 × 10−6 | 0.071 | ||||
19 | snp32196-scaffold3643-64285 | 50 562 838 | CP | 5.91 × 10−6 | 0.076 | - |
20 | snp52283-scaffold776-291202 | 36 698 503 | CW | 3.55 × 10−6 | 0.079 | WDR70, GDNF |
20 | snp46145-scaffold637-12802 | 46 398 322 | CW | 4.28 × 10−6 | 0.012 | - |
21 | snp38794-scaffold492-1318578 | 41 944 739 | CW | 4.60 × 10−6 | 0.014 | - |
22 | snp55997-scaffold870-361893 | 58 798 676 | CW | 8.19 × 10−6 | 0.050 | - |
24 | snp1555-scaffold1042-1068020 | 33 188 152 | CW | 6.31 × 10−6 | 0.079 | LAMA3, ANKRD29, NPC1 |
24 | snp13566-scaffold1525-519249 | 61 541 989 | CW | 6.43 × 10−6 | 0.048 | - |
26 | snp34795-scaffold413-993146 | 2 502 077 | RH | 6.66 × 10−6 | 0.040 | GLRX3 |
26 | snp55577-scaffold861-1367391 | 26 021 230 | CW | 6.25 × 10−6 | 0.060 | SORCS3 |
28 | snp12240-scaffold1457-284782 | 43 341 968 | CW | 7.51 × 10−7 | 0.016 | - |
29 | snp19092-scaffold192-2366 | 16 138 152 | BL | 6.40 × 10−6 | 0.080 | TENM4 |
RH | 6.49 × 10−6 | 0.081 | ||||
29 | snp14507-scaffold1585-179608 | 22 176 436 | BL | 2.65 × 10−6 | 0.034 | ANO5 |
RH | 5.99 × 10−6 | 0.039 |
Category | GO Term | n | p-Value | FE 1 | FDR 2 | Genes | |
---|---|---|---|---|---|---|---|
Annotation cluster 1: Enrichment Score: 4.76 | |||||||
GOTERM_MF_ DIRECT | GO:0004869~cysteine-type endopeptidase inhibitor activity | 6 | 5.60 × 10−6 | 22.39 | 0.0015 | AHSG, FETUB, HRG, CST7, KNG1 | SPOCK1 |
SMART | SM00043:CY | 5 | 2.64 × 10−5 | 27.13 | 0.0031 | ||
INTERPRO | IPR000010:Proteinase inhibitor I25, cystatin | 5 | 3.49 × 10−5 | 25.67 | 0.0171 | ||
Annotation cluster 2: Enrichment Score: 1.66 | |||||||
UP_KW_BIOLOGICAL_PROCESS | KW-0132~Cell division | 6 | 0.0033 | 22.39 | 0.0015 | OIP5, CHFR, DIS3L2, AURKA | ANKLE2, PARD3 |
UP_KW_BIOLOGICAL_PROCESS | KW-0131~Cell cycle | 7 | 0.0136 | 27.13 | 0.0031 | ANKLE2, BRINP2, PARD3 | |
UP_KW_BIOLOGICAL_PROCESS | KW-0498~Mitosis | 4 | 0.0629 | 25.67 | 0.0171 | ||
GOTERM_BP_DIRECT | GO:0051301~cell division | 5 | 0.0839 | 43.72 | 1 | ANKLE2 |
Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations. |
© 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
Share and Cite
Easa, A.A.; 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 2022, 13, 1773. https://doi.org/10.3390/genes13101773
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. 2022; 13(10):1773. https://doi.org/10.3390/genes13101773
Chicago/Turabian StyleEasa, Ahmed A., Marina Selionova, Magomet Aibazov, Tatiana Mamontova, Alexander Sermyagin, Anna Belous, Alexandra Abdelmanova, Tatiana Deniskova, and Natalia Zinovieva. 2022. "Identification of Genomic Regions and Candidate Genes Associated with Body Weight and Body Conformation Traits in Karachai Goats" Genes 13, no. 10: 1773. https://doi.org/10.3390/genes13101773
APA StyleEasa, A. A., Selionova, M., Aibazov, M., Mamontova, T., Sermyagin, A., Belous, A., Abdelmanova, A., Deniskova, T., & Zinovieva, N. (2022). Identification of Genomic Regions and Candidate Genes Associated with Body Weight and Body Conformation Traits in Karachai Goats. Genes, 13(10), 1773. https://doi.org/10.3390/genes13101773