692
Views
0
CrossRef citations to date
0
Altmetric
Animal Genetics and Breeding

Genome wide analyses reveal the population distinctiveness of the ‘Nera del Mela’ sheep

ORCID Icon, ORCID Icon, ORCID Icon, ORCID Icon, , , , , ORCID Icon, ORCID Icon & ORCID Icon show all
Pages 548-559 | Received 17 Feb 2023, Accepted 15 May 2023, Published online: 08 Jun 2023

References

  • Al-Mamun HA, Clark SA, Kwan P, Gondro C. 2015. Genome-wide linkage disequilibrium and genetic diversity in five populations of Australian domestic sheep. Genet Sel Evol. 47:90.
  • Alexander DH, Novembre J, Lange K. 2009. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19(9):1655–1664.
  • Ben Sassi-Zaidy Y, Mohamed-Brahmi A, Aloulou R, Charfi-Cheikhrouha F, Cendron F, Tormen N, Cassandro M. 2022. Genetic characterization and alternative preservation ways of locally adapted sheep breeds: cases of private and public sheep sectors in Tunisia and Italy. Biology. 11(11):1623.
  • Biscarini F, Cozzi P, Gaspa G, Marras G. 2018. detectRUNS: an R package to detect runs of homozygosity and heterozygosity in diploid genomes. CRAN (the Comprehensive R Archive Network). https://orca.cardiff.ac.uk/108906/.
  • Boettcher PJ, Hoffmann I, Baumung R, Drucker AG, McManus C, Berg P, Stella A, Nilsen LB, Moran D, Naves M, et al. 2014. Genetic resources and genomics for adaptation of livestock to climate change. Front Genet. 5:461.
  • Chang CC, Chow CC, Tellier LC, Vattikuti S, Purcell SM, Lee JJ. 2015. Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience. 4(1):7.
  • Chen ZH, Xu YX, Xie XL, Wang DF, Aguilar-Gomez D, Liu GJ, Li X, Esmailizadeh A, Rezaei V, Kantanen J, et al. 2021. Whole-genome sequence analysis unveils different origins of European and Asiatic mouflon and domestication-related genes in sheep. Commun Biol. 4(1):1307.
  • Ciani E, Crepaldi P, Nicoloso L, Lasagna E, Sarti FM, Moioli B, Napolitano F, Carta A, Usai G, D'Andrea M, et al. 2014. Genome-wide analysis of Italian sheep diversity reveals a strong geographic pattern and cryptic relationships between breeds. Anim Genet. 45(2):256–266.
  • Ciani E, Mastrangelo S, Da Silva A, Marroni F, Ferenčaković M, Ajmone-Marsan P, Baird H, Barbato M, Colli L, Delvento C, et al. 2020. On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools. Genet Sel Evol. 52(1):1–14.
  • Deniskova T, Dotsev A, Selionova M, Brem G, Zinovieva N. 2021. Biodiversity of Russian local sheep breeds based on pattern of runs of homozygosity. Diversity. 13(8):360.
  • Di Gerlando R, Mastrangelo S, Tolone M, Rizzuto I, Sutera AM, Moscarelli A, Portolano B, Sardina MT. 2022. Identification of copy number variations and genetic diversity in Italian insular sheep breeds. Animals. 12(2):217.
  • Do C, Waples RS, Peel D, Macbeth GM, Tillett BJ, Ovenden JR. 2014. NeEstimator v2: re-implementation of software for the estimation of contemporary effective population size (Ne) from genetic data. Mol Ecol Resour. 14(1):209–214.
  • Excoffier L, Lischer HE. 2010. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour. 10(3):564–567.
  • FAO. 2007. Global Plan of action for animal genetic resources and the Interlaken Declaration. Rome (Italy): FAO.
  • Ferenčaković M, Sölkner J, Curik I. 2013. Estimating autozygosity from high-throughput information: effects of SNP density and genotyping errors. Genet Sel Evol. 45(1):42.
  • Fu X, Yang Y, Yan Z, Liu M, Wang X. 2022. Transcriptomic study of spermatogenesis in the testis of Hu sheep and Tibetan sheep. Genes. 13(12):2212.
  • Gao X, Martin ER. 2009. Using allele sharing distance for detecting human population stratification. Hum Hered. 68(3):182–191.
  • Guo X, Sha Y, Pu X, Xu Y, Yao L, Liu X, He Y, Hu J, Wang J, Li S, et al. 2022. Coevolution of rumen epithelial circRNAs with their microbiota and metabolites in response to cold-season nutritional stress in Tibetan sheep. Int J Mol Sci. 23(18):10488.
  • Hu ZL, Park CA, Reecy JM. 2022. Animal QTLdb. [online database; Data release #49]. https://www.animalgenome.org/QTLdb.
  • Huson DH, Bryant D. 2006. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol. 23(2):254–267.
  • Kalaldeh MA, van der Werf JHJ, Gondro C. 2015. Identification of loci associated with parasite resistance in australian sheep. Proc Assoc Advmt Breed Genet. 21:69–72.
  • Kang X, Liu G, Liu Y, Xu Q, Zhang M, Fang M. 2013. Transcriptome profile at different physiological stages reveals potential mode for curly fleece in Chinese tan sheep. PLoS One. 8(8):e71763.
  • Kijas JW, Lenstra JA, Hayes B, Boitard S, Porto Neto LR, San Cristobal M, Servin B, McCulloch R, Whan V, Gietzen K, et al. 2012. Genome-wide analysis of the world’s sheep breeds reveals high levels of historic mixture and strong recent selection. PLoS Biol. 10(2):e1001258.
  • Kim ES, Elbeltagy AR, Aboul-Naga AM, Rischkowsky B, Sayre B, Mwacharo JM, Rothschild MF. 2016. Multiple genomic signatures of selection in goats and sheep indigenous to a hot arid environment. Heredity. 116(3):255–264.
  • Kirin M, McQuillan R, Franklin CS, Campbell H, McKeigue PM, Wilson JF. 2010. Genomic runs of homozygosity record population history and consanguinity. PLoS One. 5(11):e13996.
  • Li S, Chen W, Zheng X, Liu Z, Yang G, Hu X, Mou C. 2020. Comparative investigation of coarse and fine wool sheep skin indicates the early regulators for skin and wool diversity. Gene. 758:144968.
  • Li XY, He XY, Liu QY, Wang XY, Guo XF, Xia Q, Hu WP, Zhang XS, Zhang JL, Chu MX, et al. 2018. Expression pattern analysis of TAC1 and PRLR genes in different reproductive states of sheep. Acta Vet Zootech Sin. 49(2):253–262.
  • Lu Z, Chu M, Li Q, Jin M, Fei X, Ma L, Zhang L, Wei C. 2019. Transcriptomic analysis provides novel insights into heat stress responses in sheep. Animals. 9(6):387.
  • Luo Y, Liu C, Li W, Wang B, Dou L, Zhao L, Du R, Wang ZG, Jin Y. 2019. Effects of two different feeding patterns on umami substances and expression of related genes in Sunit sheep meat. Food Science. 40(13):8–13.
  • Marras G, Gaspa G, Sorbolini S, Dimauro C, Ajmone-Marsan P, Valentini A, Williams JL, Macciotta NP. 2015. Analysis of runs of homozygosity and their relationship with inbreeding in five cattle breeds farmed in Italy. Anim Genet. 46(2):110–121.
  • Mastrangelo S, Ciani E, Sardina MT, Sottile G, Pilla F, Portolano B, Bi O, Ita C. 2018. Runs of homozygosity reveal genome-wide autozygosity in Italian sheep breeds. Anim Genet. 49(1):71–81.
  • Mastrangelo S, Di Gerlando R, Tolone M, Tortorici L, Sardina MT, Portolano B. 2014. Genome wide linkage disequilibrium and genetic structure in Sicilian dairy sheep breeds. BMC Genet. 15:108.
  • Mastrangelo S, Portolano B, Di Gerlando R, Ciampolini R, Tolone M, Sardina MT. 2017. Genome-wide analysis in endangered populations: a case study in Barbaresca sheep. Animal. 11(7):1107–1116.
  • Mastrangelo S, Tolone M, Sardina MT, Sottile G, Sutera AM, Di Gerlando R, Portolano B. 2017. Genome-wide scan for runs of homozygosity identifies potential candidate genes associated with local adaptation in Valle del Belice sheep. Genet Sel Evol. 49(1):84.
  • Miao X, Luo Q, Xie L, Zhao H, Qin X. 2020. Comparative DNA methylome analysis of estrus ewes reveals the complex regulatory pathways of sheep fecundity. Reprod Biol Endocrinol. 18(1):77.
  • Milanesi M, Capomaccio S, Vajana E, Bomba L, Garcia JF, Ajmone-Marsan P, Colli L. 2017. BITE: an R package for biodiversity analyses. bioRxiv:181610.
  • Nosrati M, Asadollahpour Nanaei H, Javanmard A, Esmailizadeh A. 2021. The pattern of runs of homozygosity and genomic inbreeding in world-wide sheep populations. Genomics. 113(3):1407–1415.
  • Paim TDP, Alves dos Santos C, Faria DAD, Paiva SR, McManus C. 2022. Genomic selection signatures in Brazilian sheep breeds reared in a tropical environment. Livest Sci. 258:104865.
  • Persichilli C, Senczuk G, Pasqualino L, Anzalone DA, Negrini R, Ajmone Marsan P, Colli L, Pilla F, Mastrangelo S. 2021. Genome-wide diversity of Pagliarola sheep residual population and its conservation implication. Ital J Anim Sci. 20(1):1695–1705.
  • Portolano N. 1987. La pecora della Valle Del Belice. In: pecore e Capre Italiane. Bologna (Italia): Edagricole; p. 117–124.
  • Rafeie F, Abdoli R, Hossein-Zadeh NG, Talebi R, Szmatoła T. 2023. Interaction networks and pathway analysis of genetic resistance to gastrointestinal nematodes in sheep. Trop Anim Health Prod. 55(1):34.
  • Rangwala SH, Kuznetsov A, Ananiev V, Asztalos A, Borodin E, Evgeniev V, Joukov V, Lotov V, Pannu R, Rudnev D, et al. 2021. Accessing NCBI data using the NCBI Sequence Viewer and Genome Data Viewer (GDV). Genome Res. 31(1):159–169.
  • Ronchi B, Nardone A. 2003. Contribution of organic farming to increase sustainability of Mediterranean small ruminants livestock systems. Livest Prod Sci. 80(1–2):17–31.
  • Scintu MF, Piredda G. 2007. Typicity and biodiversity of goat and sheep milk products. Small Ruminant Res. 68(1–2):221–231.
  • Somenzi E, Ajmone-Marsan P, Barbato M. 2020. Identification of ancestry informative marker (AIM) panels to assess hybridisation between feral and domestic sheep. Animals. 10(4):582.
  • Tolone M, Sardina MT, Senczuk G, Chessari G, Criscione A, Moscarelli A, Riggio S, Rizzuto I, Di Gerlando R, Portolano B, et al. 2022. Genomic tools for the characterization of local animal genetic resources: application in Mascaruna goat. Animals. 12(20):2840.
  • Tsartsianidou V, Sanchez-Molano E, Kapsona VV, Basdagianni Z, Chatziplis D, Arsenos G, Triantafyllidis A, Banos G. 2021. A comprehensive genome-wide scan detects genomic regions related to local adaptation and climate resilience in Mediterranean domestic sheep. Genet Sel Evol. 53(1):90.
  • Vastola A. 2015. The sustainability of agro-food and natural resource systems in the Mediterranean Basin. London: Springer Open.
  • Wanjala G, Kusuma Astuti P, Bagi Z, Kichamu N, Strausz P, Kusza S. 2023. A review on the potential effects of environmental and economic factors on sheep genetic diversity: consequences of climate change. Saudi J Biol Sci. 30(1):103505.
  • Wanjala G, Astuti PK, Bagi Z, Kichamu N, Strausz P, Kusza S. 2023. Assessing the genomics structure of Dorper and white Dorper variants, and Dorper populations in South Africa and Hungary. Biology. 12(3):386.
  • Waples RS, Do C. 2010. Linkage disequilibrium estimates of contemporary Ne using highly variable genetic markers: a largely untapped resource for applied conservation and evolution. Evol Appl. 3(3):244–262.
  • Wen Y, Hu J, Wang J, Liu X, Li S, Luo Y. 2021. Effect of glycolysis and heat shock proteins on hypoxia adaptation of Tibetan sheep at different altitude. Gene. 803:145893.
  • Wickham H. 2016. ggplot2: elegant Graphics for Data Analysis. New York (NY): Springer-Verlag New York. https://ggplot2.tidyverse.org.
  • Xu H, Sun W, Pei S, Li W, Li F, Yue X. 2021. Identification of key genes related to postnatal testicular development based on transcriptomic data of testis in Hu sheep. Front Genet. 12:773695.
  • Xu L, Zhang WG, Shen HX, Zhang Y, Zhao YM, Jia YT, Gao X, Zhu B, Xu LY, Zhang LP, et al. 2018. Genome-wide scanning reveals genetic diversity and signatures of selection in Chinese indigenous cattle breeds. Livest Sci. 216:100–108.
  • Yoshida GM, Caceres P, Marin-Nahuelpi R, Koop BF, Yanez JM. 2020. Estimates of autozygosity through runs of homozygosity in farmed Coho salmon. Genes. 11(5):490.
  • Zhang Q, Guldbrandtsen B, Bosse M, Lund MS, Sahana G. 2015. Runs of homozygosity and distribution of functional variants in the cattle genome. BMC Genom. 16(1):542.