347
Views
6
CrossRef citations to date
0
Altmetric
Research Article

Revealing Genomic Footprints of Selection for Fiber and Production Traits in Three Indian Sheep Breeds

, ORCID Icon, , , , & show all
Pages 14963-14974 | Published online: 02 May 2022

References

  • Al Kalaldeh, M., J. Gibson, S. Hong Lee, C. Gondro, and J. H. J. van der Werf. 2019. Detection of genomic regions underlying resistance to gastrointestinal parasites in Australian sheep. Genetics, Selection, Evolution: GSE 51 (1):37. doi:10.1186/s12711-019-0479-1.
  • Álvarez, I., I. Fernández, A. Traoré, L. Pérez-Pardal, N. A. Menéndez-Arias, and F. Goyache, 2020. Genomic scan of selective sweeps in Djallonké (West African Dwarf) sheep shed light on adaptation to harsh environments. Sci Res 10(1): 1–13.
  • Bautista, D. M., J. Siemens, J. M. Glazer, P. R. Tsuruda, A. I. Basbaum, C. L. Stucky, S.-E. Jordt, and D. Julius. 2007. The menthol receptor TRPM8 is the principal detector of environmental cold. Nature 448 (7150):204–08. doi:10.1038/nature05910.
  • Bonhomme, M., C. Chevalet, B. Servin, S. Boitard, J. Abdallah, S. Blott, and M. SanCristobal. 2010. Detecting selection in population trees: The Lewontin and Krakauer test extended. Genetics 186 (1):241–62. doi:10.1534/genetics.110.117275.
  • Buzanskas, M. E., D. A. Grossi, D. B. Fernando Baldi, L. O. C. Silva, R. A. A. Torres Júnior, D. P. Munari, and M. M. Alencar. 2010. Genetic associations between stayability and reproductive and growth traits in Canchim beef cattle. Livestock Science 132 (1–3):107–12. doi:10.1016/j.livsci.2010.05.008.
  • Cesarani, A., T. Sechi, G. Gaspa, M. Graziano Usai, S. Sorbolini, N. Pietro Paolo Macciotta, and A. Carta. 2019. Investigation of genetic diversity and selection signatures between Sarda and Sardinian Ancestral black, two related sheep breeds with evident morphological differences. Small Ruminant Research 177:68–75. doi:10.1371/journal.pone.0103813.
  • Cheng, J. B., A. J. Sedgewick, A. I. Finnegan, P. Harirchian, J. Lee, S. Kwon, R. J. Cho . 2018. Transcriptional programming of normal and inflamed human epidermis at single-cell resolution. Cell Reports. 25(4):871–83. doi:10.1016/j.celrep.2018.09.006.
  • Chessa, B., F. Pereira, F. Arnaud, A. Amorim, F. Goyache, I. Mainland, R. R. Kao . 2009. Revealing the history of 325 sheep domestication using retrovirus integrations. Science. 324(5926):532–36. doi:10.1126/science.1170587.
  • DAHDF (Department of Animal husbandry, dairy and fisheries). 2020. Annual report of department of animal husbandry. dairying & fisheries, ministry of agriculture, Government of India. Retrieved April 20 2020, from http://dadf.gov.in/sites/default/filess/Annual%20Report.pdf
  • Dauda, A., H. Y. Abbaya, S. M. Shettima, S. Sinodo, A. A. Adekoya, S. Asiamah, and H. I. Malgwi. 2017. Computational algorithm to assess genetic relationship and functional analysis of non-synonymous substitution of HSP 70 gene of cattle, sheep and goat. J Dairy Vet Anim Res 5 (6):216–19.
  • Edea, Z., H. Dadi, T. Dessie, and K.-S. Kim. 2019. Genomic signatures of high-altitude adaptation in Ethiopian sheep populations. Genes & Genomics 41 (8):973–81. doi:10.1007/s13258-019-00820-y.
  • Eriksson, J., G. Larson, U. Gunnarsson, B. Bed’Hom, M. Tixier-Boichard, L. Strömstedt, D. Wright . 2008. Identification of the yellow skin gene reveals a hybrid origin of the domestic chicken. PLoS genetics. 4(2):e1000010. doi:10.1371/journal.pgen.1000010.
  • Estrada-Reyes, Z. M., Y. Tsukahara, R. R. Amadeu, A. L. Goetsch, T. A. Gipson, T. Sahlu, R. Puchala, Z. Wang, S. P. Hart, and R. G. Mateescu. 2019. Signatures of selection for resistance to Haemonchus contortus in sheep and goats. BMC Genomics 20 (1):1–14. doi:10.1186/s12864-019-6150-y.
  • Eydivandi, S., M. Amiri Roudbar, M. Osman Karimi, and G. Sahana. 2021. Genomic scans for selective sweeps through haplotype homozygosity and allelic fixation in 14 indigenous sheep breeds from Middle East and South Asia. Scientific Reports 11 (1):1–18. doi:10.1038/s41598-021-82625-2.
  • Fariello, M. I., S. Boitard, H. Naya, M. SanCristobal, and B. Servin. 2013. Detecting signatures of selection through haplotype differentiation among hierarchically structured populations. Genetics 193 (3):929–41. doi:10.1534/genetics.112.147231.
  • Fariello M, Servin B, Tosser-Klopp G, Rupp R, Moreno C, San Cristobal M, Boitard S. 2014. Selection signatures in worldwide sheep populations. PLoS One 9(8): e103813. doi:10.1371/journal.pone.0103813
  • Gao, G., N. Gao, L. Sicheng, W. Kuang, L. Zhu, W. Jiang, Y. Weiwei, . 2021. Genome-wide association study of meat quality traits in a three-way crossbred commercial pig population. Frontiers in Genetics:12.
  • Geherin, S. A., M. H. Lee, R. Paul Wilson, and G. F. Debes. 2013. Ovine skin-recirculating γδ T cells express IFN-γ and IL-17 and exit tissue independently of CCR7. Veterinary Immunology and Immunopathology 155 (1–2):87–97. doi:10.1016/j.vetimm.2013.06.008.
  • Henry, H., G. Vaz Meirelles, F. R. da Silva, G. P. Telles, and R. Minghim. 2015. InteractiVenn: A web-based tool for the analysis of sets through Venn diagrams. BMC Bioinformatics 16 (1):1–7. doi:10.1186/s12859-014-0430-y.
  • Ioannis, K., A. Triantafyllidis, D. Ntelidou, P. Alexandri, H.-J. Megens, R. P. M. A. Crooijmans, M. A. M. Groenen, G. Tsoumakas, and I. Vlahavas. 2015. TRES: Identification of discriminatory and informative SNPs from population genomic data. Journal of Heredity 106 (5):672–76. doi:10.1093/jhered/esv044.
  • Kijas, J. W., J. A. Lenstra, B. Hayes, S. Boitard, L. R. Porto Neto, M. San Cristobal, B. Servin, 2012. Genome-wide analysis of the world’s sheep breeds reveals high levels of historic mixture and strong recent selection. PLoS Biology. 10(2):e1001258. doi:10.1371/journal.pbio.1001258.
  • Korneliussen, T. S., I. Moltke, A. Albrechtsen, and R. Nielsen. 2013. Calculation of Tajima’s D and other neutrality test statistics from low depth next-generation sequencing data. BMC Bioinformatics 14 (1):1–14. doi:10.1186/1471-2105-14-289.
  • Kreitman, M. 2000. Methods to detect selection in populations with applications to the human. Annual Review of Genomics and Human Genetics 1 (1):539–59. doi:10.1146/annurev.genom.1.1.539.
  • Kumar H, Panigrahi M, Chhotaray S, Parida S, Chauhan A, Bhushan B, Gaur G K, Mishra B P, Singh R K. (2021). Comparative analysis of five different methods to design a breed-specific SNP panel for cattle. Anim Biotechnol 32(1): 130–136. doi:10.1080/10495398.2019.1646266
  • Lawrence, K. M., P. E. McGovern, A. Mejaddam, A. C. Rossidis, H. Baumgarten, A. Kim, J. B. Grinspan . 2019. 365 Chronic intrauterine hypoxia alters neurodevelopment in fetal sheep. The Journal of Thoracic and Cardiovascular Surgery 157 (5):1982–91. doi:10.1016/j.jtcvs.2018.12.093.
  • Manunza, A., T. F. Cardoso, A. Noce, A. Martínez, A. Pons, L. A. Bermejo, V. Landi . 2016. Population structure of eleven Spanish ovine breeds and detection of selective sweeps with BayeScan and HapFLK. Scientific Reports 6:1. doi:10.1038/srep27296.
  • Martinez-Royo, A., J. Luis Alabart, P. Sarto, M. Serrano, B. Lahoz, J. Folch, and J. Hugo Calvo. 2017. Genome-wide association studies for reproductive seasonality traits in Rasa Aragonesa sheep breed. Theriogenology 99:21–29. doi:10.1016/j.theriogenology.2017.05.011.
  • Moradi, M. H., A. Nejati-Javaremi, M. Moradi-Shahrbabak, K. G. Dodds, and J. C. McEwan. 2012. Genomic scan of selective sweeps in thin and fat tail sheep breeds for identifying of candidate regions associated with fat deposition. BMC Genetics 13 (1):10. doi:10.1186/1471-2156-13-10.
  • Mousel, M. R., J. O. Reynolds, and S. N. White. 2015. Genome-wide association identifies SLC2A9 and NLN gene regions as associated with entropion in domestic sheep. PloS One 10 (6):e0128909. doi:10.1371/journal.pone.0128909.
  • NBAGR (National Bureau of Animal Genetic Resources). 2020. Registered breeds of cattle. Retrieved April 20 2020, from http://www.nbagr.res.in/regcat.html#
  • Pavlidis, P., D. Živkovic, A. Stamatakis, and N. Alachiotis. 2013. SweeD: likelihood-based detection of selective sweeps in thousands of genomes. Molecular Biology and Evolution 30 (9):2224–34. doi:10.1093/molbev/mst112.
  • Polley, S., S. De, Batabyal, S., Kaushik, R., Yadav, P., Arora, J.S., S. Batabyal, R. Kaushik, P. Yadav, J. S. Arora, and S. Goswami, 2009. Polymorphism of fecundity genes (BMPR1B, BMP15 and GDF9) in the Indian prolific Black Bengal goat. Small Rumin 85(2–3): 122–129.
  • Purcell, S., B. Neale, K. Todd-Brown, L. Thomas, M. A. R. Ferreira, D. Bender, J. Maller . 2007. PLINK: A tool set for whole-genome association and population-based linkage analyses. The American Journal of Human Genetics 81 (3):559–75. doi:10.1086/519795.
  • Qanbari, S., and H. Simianer. 2014. Mapping signatures of positive selection in the genome of livestock. Livestock Science 166:133–43. doi:10.1016/j.livsci.2014.05.003.
  • Rajawat D, Panigrahi M, Kumar H, Nayak S Sonejita, Parida S, Bhushan B, Gaur G K, Dutt T, Mishra B P. 2022. Identification of important genomic footprints using eight different selection signature statistics in domestic cattle breeds. Gene 816: 146165. doi:10.1016/j.gene.2021.146165
  • Raschia, M. A., M. Valeria Donzelli, P. Daniel Medus, B. M. Cetrá, D. O. Maizon, V. H. Suarez, R. Pichler, K. Periasamy, and M. A. Poli. 2021. Single nucleotide polymorphisms from candidate genes associated with nematode resistance and resilience in corriedale and pampinta sheep in Argentina. Gene 770 (145345):145345. doi:10.1016/j.gene.2020.145345.
  • Reid, S. J., S. Patassini, R. R. Handley, S. R. Rudiger, C. J. McLaughlan, A. Osmand, J. C. Jacobsen . 2013. Further molecular characterisation of the OVT73 transgenic sheep model of Huntington’s disease identifies cortical aggregates. Journal of Huntington’s Disease. 2(3):279–95. doi:10.3233/JHD-130067.
  • Ren, S., Z. Huang, Y. Jiang, and T. Wang. 2018. DTBC1D7 regulates systemic growth independently of TSC through Insulin signaling. The Journal of Cell Biology 217 (2):517–26. doi:10.1083/jcb.201706027.
  • Reynolds J, Weir B S, Cockerham C C. 1983. Estimation of the coancestry coefficient: basis for a short-term genetic distance. Genetics 105(3): 767–79. doi:10.1093/genetics/105.3.767
  • Rocha, R. D. F. B., M. Moura Baena, A. de Cássia Estopa, I. Carvalho Gervásio, A. Mércia Guaratini Ibelli, T. Ramalho Santos Gionbelli, M. Pies Gionbelli, R. T. F. de Freitas, and S. L. C. Meirelles. 2019. Differential expression of HSF1 and HSPA6 genes and physiological responses in Angus and Simmental cattle breeds. Journal of Thermal Biology 84:92–98. doi:10.1016/j.jtherbio.2019.06.002.
  • Rochus, C. M., F. Tortereau, F. Plisson-Petit, G. Restoux, C. Moreno-Romieux, G. Tosser-Klopp, and B. Servin. 2018. Revealing the selection history of adaptive loci using genome-wide scans for selection: an example from domestic sheep. BMC Genomics 19 (1):71. doi:10.1186/s12864-018-4447-x.
  • Rogde, S., B. Olaisen, P. Teisberg, and J. Sodetz. 1991. A BamHI RFLP of the C8A Gene. Nucleic Acids Research 19 (13):3762. doi:10.1093/nar/19.13.3762-a.
  • Rosa, H. J. D., and M. J. Bryant. 2003. Seasonality of reproduction in sheep. Small Ruminant Research: The Journal of the International Goat Association 48 (3):155–71. doi:10.1016/s0921-4488(03)00038-5.
  • Saravanan, K. A., M. Panigrahi, H. Kumar, B. Bhushan, T. Dutt, and B. P. Mishra. 2020. Selection signatures in livestock genome: a review of concepts, approaches and applications. Livestock Science 241 (104257):104257. doi:10.1016/j.livsci.2020.104257.
  • Saravanan, K. A., M. Panigrahi, H. Kumar, B. Bhushan, T. Dutt, and B. P. Mishra. 2021a. Genome-Wide Analysis of Genetic Diversity and Selection Signatures in Three Indian Sheep Breeds. Livestock Science 243 (104367):104367. doi:10.1016/j.livsci.2020.104367.
  • Saravanan, K. A., M. Panigrahi, H. Kumar, S. Parida, G. K. G. Bharat Bhushan, B. P. M. Triveni Dutt, and R. K. Singh. 2021b. Genomic scans for selection signatures revealed candidate genes for adaptation and production traits in a variety of cattle breeds. Genomics 113 (3):955–63. doi:10.1016/j.ygeno.2021.02.009.
  • Scheet, P., and M. Stephens. 2006. A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. The American Journal of Human Genetics 78 (4):629–44. doi:10.1086/502802.
  • Shameek, B., and J. M. Akey. 2006. Genomic insights into positive selection. TRENDS in Genetics 22 (8):437–46. doi:10.1016/j.tig.2006.06.005.
  • Stephan, W. 2016. Signatures of positive selection: from selective sweeps at individual loci to subtle allele frequency changes in polygenic adaptation. Molecular Ecology 25 (1):79–88. doi:10.1111/mec.13288.
  • Tajima, F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123 (3):585–95. doi:10.1093/genetics/123.3.585.
  • Tripurani, S. K., K.-B. Lee, L. Wang, G. Wee, G. W. Smith, Y. S. Lee, K. E. Latham, and J. Yao. 2011. A novel functional role for the oocyte-specific transcription factor newborn ovary homeobox (NOBOX) during early embryonic development in cattle. Endocrinology 152 (3):1013–23. doi:10.1210/en.2010-1134.
  • Tromer, E. C., T. A. Wemyss, P. Ludzia, R. F. Waller, and B. Akiyoshi. 2021. Repurposing of synaptonemal complex proteins for kinetochores in kinetoplastida. Open Biology 11 (5):210049. doi:10.1098/rsob.210049.
  • Wang, Z., H. Zhang, H. Yang, S. Wang, E. Rong, W. Pei, L. Hui, and N. Wang. 2014. Genome-wide association study for wool production traits in a Chinese merino sheep population. PloS One 9 (9):e107101. doi:10.1371/journal.pone.0107101.
  • Yao X, Ei-Samahy M A, Yang H, Feng X, Li F, Meng F, Nie H, Wang F. 2018. Age-associated expression of vitamin D receptor and vitamin D-metabolizing enzymes in the male reproductive tract and sperm of Hu sheep. Anim Reprod Sci 190: 27–38. doi:10.1016/j.anireprosci.2018.01.003
  • Yao, Y., A. Reheman, X. Yefei, and L. Qifa. 2019. MiR-125b contributes to ovarian granulosa cell apoptosis through targeting BMPR1B, a major gene for sheep prolificacy. Reproductive Sciences 26(2):295–305. Thousand Oaks, Calif. doi:10.1177/1933719118770544.
  • Zeder, M. A. 1982. The domestication of animals. Reviews in Anthropology 9 (4):321–27. doi:10.1080/00988157.1982.9977605.
  • Zhang, L., M. R. Mousel, W. Xiaolin, J. J. Michal, X. Zhou, B. Ding, M. V. Dodson, N. K. El-Halawany, G. S. Lewis, and Z. Jiang. 2013. Genome-wide genetic diversity and differentially selected regions among suffolk, rambouillet, Columbia, Polypay, and targhee sheep. PloS One 8 (6):e65942. doi:10.1371/journal.pone.0065942.
  • Zhang, L., M. Xiaomeng, J. Xuan, H. Wang, Z. Yuan, W. Mingming, R. Liu . 2016. Identification of MEF2B and TRHDE gene polymorphisms related to growth traits in a new ujumqin sheep population. PloS One 11 (7):e0159504. doi:10.1371/journal.pone.0159504.
  • Zhao, X., K. E. Dittmer, H. T. Blair, K. G. Thompson, M. F. Rothschild, and D. J. Garrick. 2011. A novel nonsense mutation in the DMP1 gene identified by a genome-wide association study is responsible for inherited rickets in corriedale sheep. PloS One 6 (7):e21739. doi:10.1371/journal.pone.0021739.
  • Zhou, S.et al . (2018). Generation of gene-edited sheep with a defined Booroola fecundity gene (FecBB) mutation in bone morphogenetic protein receptor type 1B (BMPR1B) via clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas) 9. Reprod Fertil Dev, 30(12), 1616–1621. doi:10.1071/RD18086
  • Zhou, G. L., H. G. Jin, L. C. Z. Zhou, Y. F. Song, and Y. Cao. 2016. Cloning, expression and polymorphisms of the 3’ UTR of ovine NOBOX gene. Indian Journal of Animal Research. doi:10.18805/ijar.v0iof.4558.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.