Hostname: page-component-cd9895bd7-jn8rn Total loading time: 0 Render date: 2024-12-23T02:37:50.216Z Has data issue: false hasContentIssue false
  • English
  • Français

Direct and indirect contributions of molecular genetics to farm animal welfare: a review

Published online by Cambridge University Press:  29 November 2021

Eymen Demir Open the ORCID record for Eymen Demir [Opens in a new window] ,
Umit Bilginer ,
Murat Soner Balcioglu  and
Taki Karsli
Eymen Demir
Affiliation:
Department of Animal Science, Faculty of Agriculture, Akdeniz University, Antalya, Turkey
Umit Bilginer
Affiliation:
Department of Animal Science, Faculty of Agriculture, Akdeniz University, Antalya, Turkey
Murat Soner Balcioglu
Affiliation:
Department of Animal Science, Faculty of Agriculture, Akdeniz University, Antalya, Turkey
Taki Karsli*
Affiliation:
Department of Animal Science, Faculty of Agriculture, Akdeniz University, Antalya, Turkey
*
Author for correspondence: Taki Karsli Department of Animal Science, Faculty of Agriculture, Akdeniz University, Antalya, Turkey. E-mail: [email protected]
Get access Rights & Permissions [Opens in a new window]

Abstract

Since domestication, farm animals have played a key role to increase the prosperity of humankind, while animal welfare (AW) is debated even today. This paper aims to comprehensively review the contributions of developing molecular genetics to farm animal welfare (FAW) and to raise awareness among both scientists and farmers about AW. Welfare is a complex trait affected by genetic structure and environmental factors. Therefore, the best welfare status can be achieved not only to enhance environmental factors such as management and feeding practices, but also the genetic structure of animals must be improved. In this regard, advances in molecular genetics have made great contributions to improve the genetic structure of farm animals, which has increased AW. Today, by sequencing and/or molecular markers, genetic diseases may be detected and eliminated in local herds. Additionally, genes related to diseases or adaptations are investigated by molecular techniques, and the frequencies of desired genotypes are increased in farm animals to keep welfare at an optimized level. Furthermore, stress on animals can be reduced with DNA extraction from stool and feather samples which reduces physical contact between animals and veterinarians. Together with molecular genetics, advances in genome editing tools and biotechnology are promising to improve FAW in the future.

Keywords

Climate changemolecular markersprosperitystresswell-being
Type
Review Article
Information
Animal Health Research Reviews , Volume 22 , Issue 2 , December 2021 , pp. 177 - 186
Check for updates
Copyright
Copyright © The Author(s), 2021. Published by Cambridge University Press

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Alaie, H, Mirhoseini, SZ, Mehdizadeh, M and Dalirsefat, SB (2012) Identification of complex vertebral malformation carriers in Holstein and Guilan native cow breeds in Iran using SSCP markers. Iranian Journal of Applied Animal Science 2, 319–322.Google Scholar
Aleman, M, Nieto, JE and Magdesian, KG (2009) Malignant hyperthermia associated with ryanodine receptor 1 (C7360G) mutation in Quarter Horses. Journal of Veterinary Internal Medicine 23, 329–334.CrossRefGoogle ScholarPubMed
Anvar, Z, Namavar-Jahromi, B, Ebrahimi, S and Gharesi-Fard, B (2015) Genomic DNA extraction from sperm. Journal of Advanced Medical Sciences and Applied Technologies 1, 120–121.CrossRefGoogle Scholar
Avanus, K and Altınel, A (2017) Comparison of allele-specific PCR created restriction-site PCR, and PCR with primer-introduced restriction analysis methods used for screening complex vertebral malformation carriers in Holstein cattle. Journal of Veterinary Science 18, 465.CrossRefGoogle ScholarPubMed
Becker, D, Tetens, J, Brunner, A, Bürstel, D, Ganter, M and Kijas, J (2010) Microphthalmia in Texel sheep is associated with a missense mutation in the paired-like homeodomain 3 (PITX3) gene. PLoS ONE 5, e8689.CrossRefGoogle ScholarPubMed
Bello, N, Francino, O and Sánchez, A (2001) Isolation of genomic DNA from feathers. Journal of Veterinary Diagnostic Investigation 13, 162–164.CrossRefGoogle ScholarPubMed
Bereżnicka, J and Pawlonka, T (2018) Meat consumption as an indicator of economic well-being-case study of a developed and developing economy. Acta Scientiarum Polonorum. Oeconomia 17, 17–26.CrossRefGoogle Scholar
Bermingham, ML, Bishop, SC, Woolliams, JA, Pong-Wong, R, Allen, AR, McBride, SH, Ryder, JJ, Wright, DM, Skuce, RA, McDowell, SWJ and Glass, EJ (2014) Genome-wide association study identifies novel loci associated with resistance to bovine tuberculosis. Heredity 112, 543–551.CrossRefGoogle ScholarPubMed
Bhattacharya, TK, Chatterjee, RN, Dange, M and Bhanja, SK (2019) Polymorphisms in GnRHI and GnRHII genes and their association with egg production and egg quality traits in chicken. British Poultry Science 60, 187–194.CrossRefGoogle ScholarPubMed
Biase, FH, Franco, MM, Goulart, LR and Antunes, RC (2002) Protocol for extraction of genomic DNA from swine solid tissues. Genetics and Molecular Biology 25, 313–315.CrossRefGoogle Scholar
Botreau, R, Veissier, I, Butterworth, A, Bracke, MB and Keeling, LJ (2007) Definition of criteria for overall assessment of animal welfare. ANIMAL Welfare-Potters Bar Then Wheathampstead 16, 225.Google Scholar
Bressani, FA, Tizioto, PC, Giglioti, R, Meirellhes, S, Coutinho, L, Benvenuti, CL, Malagó-Jr, W, Mudado, MA, Vieria, LS, Zaros, LG, Carrilho, E and Regitano, LDA (2014) Single nucleotide polymorphisms in candidate genes associated with gastrointestinal nematode infection in goats. Genetics and Molecular Research 13, 8530–8536.CrossRefGoogle ScholarPubMed
Breuer, K, Hemsworth, PH, Barnett, JL, Matthews, LR and Coleman, GJ (2000) Behavioural response to humans and the productivity of commercial dairy cows. Applied Animal Behaviour Science 66, 273–288.CrossRefGoogle ScholarPubMed
Carlson, DF, Lancto, CA, Zang, B, Kim, ES, Walton, M, Oldeschulte, D, Sonstegard, TS and Fahrenkrug, SC (2016) Production of hornless dairy cattle from genome-edited cell lines. Nature Biotechnology 34, 479–481.CrossRefGoogle ScholarPubMed
Castelhano-Carlos, MJ and Baumans, V (2009) The impact of light, noise, cage cleaning and in-house transport on welfare and stress of laboratory rats. Laboratory Animals 43, 311–327.CrossRefGoogle ScholarPubMed
Ceccobelli, S, Lasagna, E, Demir, E, Rovelli, G, Albertini, E, Veronesi, F, Francesca, MS and Rosellini, D (2020) Molecular identification of the ‘Facciuta Della Valnerina’ local goat population reared in the Umbria Region, Italy. Animals 10, 601.CrossRefGoogle ScholarPubMed
Chen, ZY, Gan, JK, Xiao, X, Jiang, LY, Zhang, XQ and Luo, QB (2013) The association of SNPs in Hsp90β gene 5′ flanking region with thermo tolerance traits and tissue mRNA expression in two chicken breeds. Molecular Biology Reports 40, 5295–5306.CrossRefGoogle ScholarPubMed
Clark, B, Stewart, GB, Panzone, LA, Kyriazakis, I and Frewer, LJ (2017) Citizens, consumers and farm animal welfare: a meta-analysis of willingness-to-pay studies. Food Policy 68, 112–127.CrossRefGoogle Scholar
Demir, E and Balcioğlu, MS (2019) Genetic diversity and population structure of four cattle breeds raised in Turkey using microsatellite markers. Czech Journal of Animal Science 64, 411–419.CrossRefGoogle Scholar
Demir, Y and Güneş, E (2017) The determination of milk consumption level in Ankara province. Soil Water Journal 6, 28–35.Google Scholar
Demir, E, Karsli, T, Fidan, HG, Karsli, BA, Aslan, M, Aktan, S, Kamanlı, S, Karabağ, K, Şahin Semerci, E and Balcıoğlu, MS (2020) Polymorphisms in some candidate genes associated with egg yield and quality in five different white layer pure lines. Kafkas Universitesi Veteriner Fakultesi Dergisi 26, 735–741.Google Scholar
De Volo, SB, Reynolds, RT, Douglas, MR and Antolin, MF (2008) An improved extraction method to increase DNA yield from molted feathers. The Condor 110, 762–766.CrossRefGoogle Scholar
Dillon, P, Berry, DP, Evans, RD, Buckley, F and Horan, B (2006) Consequences of genetic selection for increased milk production in European seasonal pasture based systems of milk production. Livestock Science 99, 141–158.CrossRefGoogle Scholar
Ding, Q, Strong, A, Patel, KM, Ng, SL, Gosis, BS, Regan, SN, Cowan, CA, Rader, DJ and Musunuru, K (2014) Permanent alteration of PCSK9 with in vivo CRISPR-Cas9 genome editing. Circulation Research 115, 488–492.CrossRefGoogle ScholarPubMed
Drobik-Czwarno, W, Wolc, A, Fulton, JE, Arango, J, Jankowski, T, O'Sullivan, NP and Dekkers, JCM (2018) Identifying the genetic basis for resistance to avian influenza in commercial egg layer chickens. Animal: An International Journal of Animal Bioscience 12, 1363–1371.CrossRefGoogle ScholarPubMed
Duncan, IJH (2004) Pain, fear and distress. Proceedings of Global Conference on Animal Welfare: an OIE initiative, 23–25.Google Scholar
Duncan, EJ, Dodds, KG, Henry, HM, Thompson, MP and Phua, SH (2007) Cloning, mapping and association studies of the ovine ABCG2 gene with facial eczema disease in sheep. Animal Genetics 38, 126–131.CrossRefGoogle ScholarPubMed
Dunisławska, A, Łachmańska, J, Sławińska, A and Siwek, M (2017) Next generation sequencing in animal science-a review. Animal Science Papers and Reports 35, 205–224.Google Scholar
Falker-Gieske, C, Blaj, I, Preuß, S, Bennewitz, J, Thaller, G and Tetens, J (2019) GWAS for meat and carcass traits using imputed sequence level genotypes in pooled F2-designs in pigs. G3: Genes, Genomes, Genetics 9, 2823–2834.CrossRefGoogle ScholarPubMed
Farm Animal Welfare Council (1992) FAWC updates the five freedoms. Veterinary Record 17, 357.Google Scholar
Fernandes, JN, Hemsworth, PH, Coleman, GJ and Tilbrook, AJ (2021) Costs and benefits of improving farm animal welfare. Agriculture 11, 104.CrossRefGoogle Scholar
Frantz, LA, Bradley, DG, Larson, G and Orlando, L (2020) Animal domestication in the era of ancient genomics. Nature Reviews Genetics 21, 449–460.CrossRefGoogle ScholarPubMed
Freebern, E, Santos, DJ, Fang, L, Jiang, J, Gaddis, KLP, Liu, GE, VanRaden, PM, Maltecca, C, Cole, JB and Ma, L (2020) GWAS and fine-mapping of livability and six disease traits in Holstein cattle. BMC Genomics 21, 1–11.CrossRefGoogle ScholarPubMed
Gao, Y, Wu, H, Wang, Y, Liu, X, Chen, L, Li, Q, Cui, C, Liu, X, Zhang, J and Zhang, Y (2017) Single Cas9 nickase induced generation of NRAMP1 knockin cattle with reduced off-target effects. Genome Biology 18, 1–15.CrossRefGoogle ScholarPubMed
Gardner, GE, Pethick, DW, Hopkins, DL, Hegarty, RS, Cake, MA, Boyce, M and Allingham, P (2006) The impact of carcase estimated breeding values on yield and quality of sheep meat. International Journal of Sheep and Wool Science 54, 50–56.Google Scholar
Gebreselassie, G, De, S, Mukherjee, A and Gohain, M (2019) Allele specific PCR based genotyping reveals lack of bovine leukocyte adhesion deficiency, bovine citrullinemia and complex vertebral malformation carriers in Indian cattle population. International Journal of Current Microbiology and Applied Sciences 8, 1581–1589.CrossRefGoogle Scholar
González-Recio, O, Ugarte, C and Alenda, R (2005) Genetic analysis of an artificial insemination progeny test program. Journal of Dairy Science 88, 783–789.CrossRefGoogle ScholarPubMed
Gouveia, JJ, Cunha, SMF, De Almeida, EM, Nogueira, JF, Souza Filho, JLP, Menezes, DR and Gouveia, GV (2016) Molecular and genealogical analyses reveal multiple sources of the mutation associated with dermatosparaxis in Brazilian White Dorper sheep. Small Ruminant Research 140, 46–49.CrossRefGoogle Scholar
Greeff, JC, Safari, E, Fogarty, NM, Hopkins, DL, Brien, FD, Atkins, KD, Mortimer, SI and Van Der Werf, JHJ (2008) Genetic parameters for carcass and meat quality traits and their relationships to liveweight and wool production in hogget Merino rams. Journal of Animal Breeding and Genetics 125, 205–215.CrossRefGoogle ScholarPubMed
Grindflek, E, Hansen, MH, Lien, S and van Son, M (2018) Genome-wide association study reveals a QTL and strong candidate genes for umbilical hernia in pigs on SSC14. BMC Genomics 19, 1–9.CrossRefGoogle ScholarPubMed
Guang-Xin, E, Hong, QH, Zhao, YJ, Ma, YH, Chu, MX, Zhu, L and Huang, YF (2019) Genetic diversity estimation of Yunnan indigenous goat breeds using microsatellite markers. Ecology and Evolution 9, 5916.Google Scholar
Guo, J, Tao, H, Li, P, Li, L, Zhong, T, Wang, L, Ma, J, Chen, X, Song, T and Zhang, H (2018) Whole-genome sequencing reveals selection signatures associated with important traits in six goat breeds. Scientific Reports 8, 1–11.CrossRefGoogle ScholarPubMed
Guo, L, Huang, W, Tong, F, Chen, X, Cao, S, Xu, H, Luo, W, Li, Z and Nie, Q (2020) Whole transcriptome analysis of chicken bursa reveals candidate gene that enhances the host's immune response to coccidiosis. Frontiers in Physiology 11, 573676.CrossRefGoogle ScholarPubMed
Hacıhasanoğlu Çakmak, NH and Yardibi, H (2019) Detection of allele and genotype frequencies of bovine leukocyte adhesion deficiency, factor XI deficiency and complex vertebral malformation disease genes in Holstein cattle. Ankara Universitesi Veteriner Fakultesi Dergisi 66, 311–316.Google Scholar
Häfliger, IM, Letko, A, Murgiano, L and Drögemüller, C (2020) De novo stop-lost germline mutation in FGFR3 causes severe chondrodysplasia in the progeny of a Holstein bull. Animal Genetics 51, 466–469.CrossRefGoogle ScholarPubMed
Hamadani, A, Ganai, NA, Khan, NN, Shanaz, S and Ahmad, T (2019) Estimation of genetic, heritability, and phenotypic trends for weight and wool traits in Rambouillet sheep. Small Ruminant Research 177, 133–140.CrossRefGoogle Scholar
Hasenauer, FC, Rossi, UA, Caffaro, ME, Raschia, MA, Maurizio, E, Poli, MA and Rossetti, CA (2020) Association of TNF rs668920841 and INRA111 polymorphisms with caprine brucellosis: a case-control study of candidate genes involved in innate immunity. Genomics 112, 3925–3932.CrossRefGoogle ScholarPubMed
Hassan, FU, Nawaz, A, Rehman, MS, Ali, MA, Dilshad, SM and Yang, C (2019) Prospects of HSP70 as a genetic marker for thermo-tolerance and immuno-modulation in animals under climate change scenario. Animal Nutrition 5, 340–350.CrossRefGoogle ScholarPubMed
Hayes, BEN and Goddard, ME (2001) The distribution of the effects of genes affecting quantitative traits in livestock. Genetics Selection Evolution 33, 1–21.CrossRefGoogle ScholarPubMed
Herzog, A, Winckler, C and Zollitsch, W (2018) In pursuit of sustainability in dairy farming: a review of interdependent effects of animal welfare improvement and environmental impact mitigation. Agriculture, Ecosystems & Environment 267, 174–187.CrossRefGoogle Scholar
Holmbeg, M and Andersson-Eklund, L (2004) Quantitative trait loci affecting health traits in Swedish dairy cattle. Journal of Dairy Science 87, 2653–2659.CrossRefGoogle Scholar
Hong, YH, Kim, ES and Lillehoj, HS (2011) Identification of parental line specific effects of MLF2 on resistance to coccidiosis in chickens. BMC Proceedings 5, 1–4.CrossRefGoogle ScholarPubMed
Horback, K (2019) Applied cognition research to improve sheep welfare. Animal Sentience 4, 1–4.CrossRefGoogle Scholar
Hu, G, Do, DN, Gray, J and Miar, Y (2020) Selection for favorable health traits: a potential approach to cope with diseases in farm animals. Animals 10, 1717.CrossRefGoogle ScholarPubMed
Huang, H, Cao, J, Hanif, Q, Wang, Y, Yu, Y, Zhang, S and Zhang, Y (2019) Genome-wide association study identifies energy metabolism genes for resistance to ketosis in Chinese Holstein cattle. Animal Genetics 50, 376–380.CrossRefGoogle ScholarPubMed
Indu, S and Pareek, A (2015) A review: growth and physiological adaptability of sheep to heat stress under semi-arid environment. International Journal of Emerging Trends in Science and Technology 2, 3188–3198.Google Scholar
Jin, M, Lu, J, Fei, X, Lu, Z, Quan, K, Liu, Y, Chu, M, Di, R, Wang, H and Wei, C (2020) Genetic signatures of selection for cashmere traits in Chinese goats. Animals 10, 1905.CrossRefGoogle ScholarPubMed
Kaczor, U, Kucharski, M, Martyniuk, E and Krupinski, J (2015) Analiza polimorfizmu w genie FGFR3 u owiec rasy suffolk. Annales Universitatis Mariae Curie-Skłodowska. Sectio EE: Zootechnica 33, 11–15.Google Scholar
Kadarmideen, HN, Ali, AA, Thomson, PC, Müller, B and Zinsstag, J (2011) Polymorphisms of the SLC11A1 gene and resistance to bovine tuberculosis in African Zebu cattle. Animal Genetics 42, 656–658.CrossRefGoogle ScholarPubMed
Karsli, T, Şahin, E, Argun Karsli, B, Alkan, S and Balcioglu, MS (2011) Identification of alleles for factor XI (FXID) and uridine monophosphate synthase (DUMPS) deficiencies in Holstein cows reared in Antalya. Kafkas Universitesi Veteriner Fakultesi Dergisi 17, 503–505.Google Scholar
Karsli, T, Demir, E, Fidan, HG, Aslan, M, Karsli, BA, Arik, IZ, Semerci, ES, Karabag, K and Balcioglu, MS (2020) Determination of genetic variability, population structure and genetic differentiation of indigenous Turkish goat breeds based on SSR loci. Small Ruminant Research 190, 106147.CrossRefGoogle Scholar
Kaushik, AK, Kandavel, H, Nalpathamkalam, T and Pasman, Y (2021) Bovine neonate is deficient in innate immunity at birth. Molecular Immunology 133, 101–109.CrossRefGoogle ScholarPubMed
Kaya, M, Meydan, H, Kiyma, Z, Alan, M and Yildiz, MA (2016) Screening for bovine leukocyte adhesion deficiency, deficiency of uridine monophosphate synthase, bovine citrullinaemia and factor XI deficiency in Holstein cattle. Indian Journal of Animal Sciences 86, 900–903.Google Scholar
Keskin, M, Yilmaz, O, Gündüz, Z, Ata, N, Gül, S, Cemal, İ, Karaca, O and Önel, SE (2019) Microsatellite panels for parentage testing of Kilis goats reared in Turkey. Turkish Journal of Veterinary and Animal Sciences 43, 94–101.CrossRefGoogle Scholar
Kevorkian, SEM, Georgescu, SE, Manea, MA, Gavrila, MG, Hrinca, G and Costache, M (2010) The spider lamb syndrome absence in five Romanian sheep breeds. Lucrări Știinţifice 53, 254–258.Google Scholar
Kiyici, J, Arslan, K, Akyuz, B, Kaliber, M, Aksel, EG and Çinar, MU (2019) Relationships between polymorphisms of growth hormone, leptin and myogenic factor 5 genes with some milk yield traits in Holstein dairy cows. International Journal of Dairy Technology 72, 1–7.CrossRefGoogle Scholar
Koknaroglu, H and Akunal, T (2013) Animal welfare: an animal science approach. Meat Science 95, 821–827.CrossRefGoogle ScholarPubMed
Kroezen, V, Schenkel, FS, Miglior, F, Baes, CF and Squires, EJ (2018) Candidate gene association analyses for ketosis resistance in Holsteins. Journal of Dairy Science 101, 5240–5249.CrossRefGoogle ScholarPubMed
Kunz, E, Rothammer, S, Pausch, H, Schwarzenbacher, H, Seefried, FR, Matiasek, K, Seichter, D, Russ, I, Fries, R and Medugorac, I (2016) Confirmation of a non-synonymous SNP in PNPLA8 as a candidate causal mutation for Weaver syndrome in Brown Swiss cattle. Genetics Selection Evolution 48, 1–14.CrossRefGoogle ScholarPubMed
Lacetera, N (2019) Impact of climate change on animal health and welfare. Animal Frontiers 9, 26–31.CrossRefGoogle ScholarPubMed
Lee, S, Do, C, Choy, Y, Dang, C, Mahboob, A and Cho, K (2019) Estimation of the genetic milk yield parameters of Holstein cattle under heat stress in South Korea. Asian-Australasian Journal of Animal Sciences 32, 1–7.CrossRefGoogle ScholarPubMed
Lee, K, Uh, K and Farrell, K (2020) Current progress of genome editing in livestock. Theriogenology 150, 229–235.CrossRefGoogle ScholarPubMed
Lehner, S, Zerbin, I, Doll, K, Rehage, J and Distl, O (2018) A genome-wide association study for left-sided displacement of the abomasum using a high-density single nucleotide polymorphism array. Journal of Dairy Science 101, 1258–1266.CrossRefGoogle ScholarPubMed
Li, H, Sheng, C, Wang, S, Yang, L, Liang, Y, Huang, Y, Liu, H, Li, P, Yang, C, Yang, X, Jia, L, Xie, J, Wang, L, Hao, R, Du, X, Xu, D, Zhou, J, Li, M, Sun, Y, Tong, Y, Li, Q, Qiu, S and Song, H (2017) Removal of integrated hepatitis B virus DNA using CRISPR-Cas9. Frontiers in Cellular and Infection Microbiology 7, 1–9.CrossRefGoogle ScholarPubMed
Li, J, Zhang, Y, Zhang, Y, Yu, PL, Pan, H and Rollins, JA (2018) Introduction of large sequence inserts by CRISPR-Cas9 to create pathogenicity mutants in the multinucleate filamentous pathogen Sclerotinia sclerotiorum. MBio 9, 1–19.CrossRefGoogle ScholarPubMed
Lopes, FB, de los Reyes Borjas, A, da Silva, MC, Facó, O, Lôbo, RN, Fiorvanti, MCS and McManus, C (2012) Breeding goals and selection criteria for intensive and semi-intensive dairy goat system in Brazil. Small Ruminant Research 106, 110–117.CrossRefGoogle Scholar
Lopez, BI, Lee, SH, Park, JE, Shin, DH, Oh, JD, De Las Heras-Saldana, S, van der Werf, J, Chai, H, Park, W and Lim, D (2019) Weighted genomic best linear unbiased prediction for carcass traits in Hanwoo cattle. Genes 10, 1019.CrossRefGoogle ScholarPubMed
Mader, TL, Frank, KL, Harrington, JA, Hahn, GL and Nienaber, JA (2009) Potential climate change effects on warm-season livestock production in the Great Plains. Climatic Change 97, 529–541.CrossRefGoogle Scholar
Martinez, N, Sinedino, LDP, Bisinotto, RS, Ribeiro, ES, Gomes, GC, Lima, FS, Greco, LF, Risco, CA, Galvão, KN, Taylor-Rodriguez, D, Driver, JP, Thatcher, WW and Santos, JEP (2014) Effect of induced subclinical hypocalcemia on physiological responses and neutrophil function in dairy cows. Journal of Dairy Science 97, 874–887.CrossRefGoogle ScholarPubMed
Menchaca, A, Dos Santos-Neto, PC, Mulet, AP and Crispo, M (2020) CRISPR in livestock: from editing to printing. Theriogenology 150, 247–254.CrossRefGoogle ScholarPubMed
Meydan, H, Özkan, MM and Yildiz, MA (2013) Genetic risk assessment for atypical scrapie in Turkish native sheep breeds. Small Ruminant Research 111, 16–22.CrossRefGoogle Scholar
Meyers, SN, McDaneld, TG, Swist, SL, Marron, BM, Steffen, DJ, O'Toole, D, O'Connell, JR, Beever, JE, Sonstegard, TS and Smith, TP (2010) A deletion mutation in bovine SLC4A2 is associated with osteopetrosis in Red Angus cattle. BMC Genomics 11, 1–14.CrossRefGoogle ScholarPubMed
Molomo, M and Mumba, T (2014) Drivers for animal welfare policies in Africa. Revue Scientifique et Technique 33, 47–53.CrossRefGoogle ScholarPubMed
Mömke, S, Sickinger, M, Rehage, J, Doll, K and Distl, O (2012) Transcription factor binding site polymorphism in the motilin gene associated with left-sided displacement of the abomasum in German Holstein cattle. PLoS ONE 7, e35562.CrossRefGoogle ScholarPubMed
Mulder, M and Zomer, S (2017) Dutch consumers’ willingness to pay for broiler welfare. Journal of Applied Animal Welfare Science 20, 137–154.CrossRefGoogle ScholarPubMed
Murgiano, L, Jagannathan, V, Benazzi, C, Bolcato, M, Brunetti, B, Muscatello, LV, Dittmer, K, Piffer, C, Gentile, A and Drögemüller, C (2014) Deletion in the EVC2 gene causes chondrodysplastic dwarfism in Tyrolean Grey cattle. PLoS ONE 9, e94861.CrossRefGoogle ScholarPubMed
Narinc, D, Aksoy, T, Karaman, E, Aygun, A, Firat, MZ and Uslu, MK (2013) Japanese quail meat quality: characteristics, heritabilities, and genetic correlations with some slaughter traits. Poultry Science 92, 1735–1744.CrossRefGoogle ScholarPubMed
Nasiri, H, Forouzandeh, M, Rasaee, MJ and Rahbarizadeh, F (2005) Modified salting-out method: high-yield, high-quality genomic DNA extraction from whole blood using laundry detergent. Journal of Clinical Laboratory Analysis 19, 229–232.CrossRefGoogle ScholarPubMed
Oltenacu, PA and Broom, DM (2010) The impact of genetic selection for increased milk yield on the welfare of dairy cows. Animal Welfare 19, 39–49.Google Scholar
Öner, Y, Yılmaz, O, Eriş, C, Ata, N, Ünal, C and Koncagül, S (2019) Genetic diversity and population structure of Turkish native cattle breeds. South African Journal of Animal Science 49, 628–635.CrossRefGoogle Scholar
Özşensoy, Y, Kurar, E, Dogan, M, Bulut, Z, Nizamoglu, M, Isık, A, Camlıdag, A and Altunok, V (2019) Phylogenetic relationships of native Turkish cattle breeds using microsatellite markers. Turkish Journal of Veterinary and Animal Sciences 43, 23–29.CrossRefGoogle Scholar
Pacheco, HA, Da Silva, S, Sigdel, A, Mak, CK, Galvão, KN, Texeira, RA, Dias, LT and Peñagaricano, F (2018) Gene mapping and gene-set analysis for milk fever incidence in Holstein dairy cattle. Frontiers in Genetics 9, 465.CrossRefGoogle ScholarPubMed
Patel, RK, Singh, KM, Soni, KJ, Chauhan, JB and Rao, KS (2008) Screening of dairy bulls for weaver syndrome in India. Current Trends in Biotechnology and Pharmacy 2, 192–197.Google Scholar
Perini, F, Cendron, F, Rovelli, G, Castellini, C, Cassandro, M and Lasagna, E (2021) Emerging genetic tools to investigate molecular pathways related to heat stress in chickens: A review. Animals 11, 46.CrossRefGoogle Scholar
Petersen, B (2017) Basics of genome editing technology and its application in livestock species. Reproduction in Domestic Animals 52, 4–13.CrossRefGoogle ScholarPubMed
Pokorska, J, Kułaj, D, Dusza, M, Żychlińska-Buczek, J and Makulska, J (2016) New rapid method of DNA isolation from milk somatic cells. Animal Biotechnology 27, 113–117.CrossRefGoogle ScholarPubMed
Rashamol, VP, Sejian, V, Bagath, M, Krishnan, G, Archana, PR and Bhatta, R (2020) Physiological adaptability of livestock to heat stress: an updated review. Journal of Animal Behaviour and Biometeorology 6, 62–71.CrossRefGoogle Scholar
Rooney, NJ and Sargan, DR (2010) Welfare concerns associated with pedigree dog breeding in the UK. Animal Welfare 19, 133–140.Google Scholar
Sailo, L, Gupta, I, Verma, A, Singh, A, Vishwas, M, Chaudhari, RD, Das, R, Upadhyay, RC and Goswami, J (2015) Single nucleotide polymorphism in HSP90AB1 gene and its association with thermo-tolerance in Jersey crossbred cows. Animal Science 9, 43–49.Google Scholar
Sartelet, A, Stauber, T, Coppieters, W, Ludwig, CF, Fasquelle, C, Druet, T, Zhang, Z, Ahariz, N, Cambisano, N, Jentsch, TJ and Charlier, C (2014) A missense mutation accelerating the gating of the lysosomal Cl − /H + -exchanger ClC-7/Ostm1 causes osteopetrosis with gingival hamartomas in cattle. Disease Models and Mechanisms 7, 119–128.Google Scholar
Sasaki, K, Yamagishi, N, Kizaki, K, Devkota, B and Hashizume, K (2014) Microarray-based gene expression profiling of peripheral blood mononuclear cells in dairy cows with experimental hypocalcemia and milk fever. Journal of Dairy Science 97, 247–258.CrossRefGoogle ScholarPubMed
Seo, KS, Shen, YN, Salces, AJ, Yoon, DH, Lee, HG and Kim, SH (2006) Correlation analysis between the breeding value of carcass traits in Hanwoo (Korean Brown Cattle), Bos Taurus, L. and spot intensity on two-dimensional gel electrophoresis. Asian-Australasian Journal of Animal Sciences 19, 1404–1408.CrossRefGoogle Scholar
Sevane, N, Armstrong, E, Cortés, O, Wiener, P, Wong, RP, Dunner, S and Gemqual Consortium, (2013). Association of bovine meat quality traits with genes included in the PPARG and PPARGC1A networks. Meat Science 94, 328–335.CrossRefGoogle ScholarPubMed
Sinclair, KD, Rutherford, KMD, Wallace, JM, Brameld, JM, Stöger, R, Alberio, R, Sweetman, D, Gardner, DS, Perry, VEA, Adam, CL, Ashworth, CJ, Robinson, JE and Dwyer, CM (2016) Epigenetics and developmental programming of welfare and production traits in farm animals. Reproduction, Fertility and Development 28, 1443–1478.CrossRefGoogle Scholar
Singh, J, Birbian, N, Sinha, S and Goswami, A (2014) A critical review on PCR, its types and applications. International Journal of Advanced Research in Biological Sciences 1, 65–80.Google Scholar
Singh, B, Mal, G, Gautam, SK, and Mukesh, M (2019). Whole-Genome selection in livestock. In Advances in Animal Biotechnology. Cham: Springer, pp. 349–364.CrossRefGoogle Scholar
Soma, P, van Marle-Köster, E and Frylinck, L (2014) Frequency of the malignant hyperthermia gene in the South African pig industry. South African Journal of Animal Science 44, 384–387.CrossRefGoogle Scholar
Taggart, JB, Hynes, RA, Prodöuhl, PA and Ferguson, A (1992) A simplified protocol for routine total DNA isolation from salmonid fishes. Journal of Fish Biology 40, 963–965.CrossRefGoogle Scholar
Thomsen, B, Nissen, PH, Agerholm, JS and Bendixen, C (2010) Congenital bovine spinal dysmyelination is caused by a missense mutation in the SPAST gene. Neurogenetics 11, 175–183.CrossRefGoogle ScholarPubMed
Tohidi, R, Idris, IB, Panandam, JM and Bejo, MH (2013) The effects of polymorphisms in 7 candidate genes on resistance to Salmonella Enteritidis in native chickens. Poultry Science 92, 900–909.CrossRefGoogle ScholarPubMed
Torricelli, M, Sebastiani, C, Ciullo, M, Ceccobelli, S, Chiappini, B, Vaccari, G, Capocefalo, A, Conte, M, Giovanni, S, Lasagna, E, Sarti, FM and Biagetti, M (2021) PRNP polymorphisms in eight local goat populations/breeds from central and southern Italy. Animals 11, 1–13.CrossRefGoogle ScholarPubMed
Upadhyay, MR, Chen, W, Lenstra, JA, Goderie, CRJ, MacHugh, DE, Park, SDE, Magee, DE, Matassino, D, Ciani, F, Megens, HJ, van Arendonk, JAM and Groenen, MAM (2017) Genetic origin, admixture and population history of aurochs (Bos primigenius) and primitive European cattle. Heredity 118, 169–176.CrossRefGoogle ScholarPubMed
Venturini, GC, da CRUZ, VAR, Rosa, JO, Baldi, F, El Faro, L, Ledur, MC, Peixoto, JO and Munari, DP (2014) Genetic and phenotypic parameters of carcass and organ traits of broiler chickens. Genetics and Molecular Research 13, 10294–10300.CrossRefGoogle ScholarPubMed
von Borell, E, Baumgartner, J, Giersing, M, Jäggin, N, Prunier, A, Tuyttens, FAM and Edwards, SA (2009) Animal welfare implications of surgical castration and its alternatives in pigs. Animal: An International Journal of Animal Bioscience 3, 1488–1496.CrossRefGoogle ScholarPubMed
Wakchaure, R, Ganguly, S, Praveen, PK, Kumar, A, Sharma, S and Mahajan, T (2015) Marker assisted selection (MAS) in animal breeding: a review. Drug Metabolism, and Toxicology 6, e127.Google Scholar
Wang, C, Tong, Q, Hu, XZ, Yang, LG, Zhong, XQ, Yu, Y, Wu, JJ, Liu, WJ, Li, X, Hua, GH, Zhao, HQ and Zhang, SJ (2011a) Identification of complex vertebral malformation carriers in Holstein cattle in south China. Genetics and Molecular Research 10, 2443–2448.CrossRefGoogle Scholar
Wang, TY, Wang, L, Zhang, JH and Dong, WH (2011b) A simplified universal genomic DNA extraction protocol suitable for PCR. Genetics and Molecular Research 10, 519–525.CrossRefGoogle Scholar
Wang, S, Hao, H, Zhao, X, Zhu, H, Du, W, Wang, D, Liu, Y, Qin, T and Wang, Z (2012) A rapid mismatch polymerase chain reaction assay to detect carriers of complex vertebral malformation in Holstein cattle. Journal of Veterinary Diagnostic Investigation 24, 568–571.CrossRefGoogle ScholarPubMed
Wang, K, Ouyang, H, Xie, Z, Yao, C, Guo, N, Li, M, Jiao, H and Pang, D (2015) Efficient generation of myostatin mutations in pigs using the CRISPR/Cas9 system. Scientific Reports 5, 1–11.Google ScholarPubMed
Wang, K, Liu, X, Qi, T, Hui, Y, Yan, H, Qu, L, Lan, X and Pan, C (2021) Whole-genome sequencing to identify candidate genes for litter size and to uncover the variant function in goats (Capra hircus). Genomics 113, 142–150.CrossRefGoogle Scholar
Warren, HE, Scollan, ND, Enser, M, Hughes, SI, Richardson, RI and Wood, JD (2008) Effects of breed and a concentrate or grass silage diet on beef quality in cattle of 3 ages. I: animal performance, carcass quality and muscle fatty acid composition. Meat Science 78, 256–269.CrossRefGoogle ScholarPubMed
Weldenegodguad, M, Popov, R, Pokharel, K, Ammosov, I, Ming, Y, Ivanova, Z and Kantanen, J (2019) Whole-genome sequencing of three native cattle breeds originating from the northernmost cattle farming regions. Frontiers in Genetics 9, 728.CrossRefGoogle ScholarPubMed
Wolc, A, Arango, J, Settar, P, O'sullivan, NP, Olori, VE, White, IMS, Hill, WG and Dekkers, JCM (2012) Genetic parameters of egg defects and egg quality in layer chickens. Poultry Science 91, 1292–1298.CrossRefGoogle ScholarPubMed
Wu, H, Wang, Y, Zhang, Y, Yang, M, Lv, J, Liu, J and Zhang, Y (2015) TALE nickase-mediated SP110 knockin endows cattle with increased resistance to tuberculosis. Proceedings of the National Academy of Sciences 112, e1530–E1539.CrossRefGoogle ScholarPubMed
Yadav, AK, Tomar, SS, Jha, AK and Singh, J (2017) Importance of molecular markers in livestock improvement: a review. International Journal of Agriculture Innovations and Research 5, 614–622.Google Scholar
Yakovlev, AF (2018) Epigenetic effects in livestock breeding. Russian Journal of Genetics 54, 897–909.CrossRefGoogle Scholar
Yaman, Y, Aymaz, R, Keleş, M, Bay, V, Hatipoğlu, E, Kaptan, C, Başkurt, A, Yilmaz, O and Heaton, MP (2021) Evaluation of CD109, PCP4 and SEMA3D genes for their association with Ovine Johne's disease in Turkish sheep. Animal Biotechnology, 32, 1–10.CrossRefGoogle ScholarPubMed
Yan, Z, Huang, H, Freebern, E, Santos, DJ, Dai, D, Si, J, Ma, C, Cao, J, Guo, G, Liu, GE, Ma, L, Fang, L and Zhang, Y (2020) Integrating RNA-Seq with GWAS reveals novel insights into the molecular mechanism underpinning ketosis in cattle. BMC Genomics 21, 1–12.CrossRefGoogle ScholarPubMed
Yang, F, Cao, H, Xiao, Q, Guo, X, Zhuang, Y, Zhang, C, Wang, T, Lin, H, Song, Y, Hu, G and Liu, P (2016) Transcriptome analysis and gene identification in the pulmonary artery of broilers with ascites syndrome. PLoS ONE 11, e0156045.CrossRefGoogle ScholarPubMed
Yatkın, S, Özdil, F, Ünal, EÖ, Genç, S, Kaplan, S, Gürcan, EK, Arat, S and Soysal, Mİ (2020) Genetic characterization of native donkey (Equus asinus) populations of Turkey using microsatellite markers. Animals 10, 1093.CrossRefGoogle ScholarPubMed
Zahra, W, Imran, M, Zahoor, MY, Ashraf, K, Jaffry, KH, Nadeem, A, Rashid, I, Younas, M, Akhtar, M and Shehzad, W (2020) Molecular screening of complex vertebral malformation and Citrullinemia carriers in Pakistani Nili-Ravi buffalo (Bubalus bubalis) breeding bulls. The Journal of Animal and Plant Sciences 30, 619–626.Google Scholar
Zeder, MA (2012) The domestication of animals. Journal of Anthropological Research 68, 161–190.CrossRefGoogle Scholar
Zeng, L, Cao, Y, Wu, Z, Huang, M, Zhang, G, Lei, C and Zhao, Y (2019) A missense mutation of the HSPB7 gene associated with heat tolerance in Chinese Indicine cattle. Animals 9, 554.CrossRefGoogle ScholarPubMed
Zepeda-Batista, JL, Parra-Bracamonte, GM, Núñez-Domínguez, R, Ramírez-Valverde, R and Ruíz-Flores, A (2019) Screening genetic diseases prevalence in Braunvieh cattle. Tropical Animal Health and Production 51, 25–31.CrossRefGoogle ScholarPubMed
Zhang, BW, Li, M, Ma, LC and Wei, FW (2006) A widely applicable protocol for DNA isolation from fecal samples. Biochemical Genetics 44, 494.CrossRefGoogle ScholarPubMed
Zhang, Y, Wang, Z, Lei, H, Wang, Z, Su, R, Zhang, W, Zhou, J, Wei, Y, Meng, R, Wang, R and Li, J (2014) Estimates of genetic parameters and genetic changes for fleece traits in Inner Mongolia cashmere goats. Small Ruminant Research 117, 41–46.CrossRefGoogle Scholar
Zhang, Z, Xu, ZQ, Luo, YY, Zhang, HB, Gao, N, He, JL, Ji, CL, Zhang, DX, Li, JQ and Zhang, XQ (2017) Whole genomic prediction of growth and carcass traits in a Chinese quality chicken population. Journal of Animal Science 95, 72–80.CrossRefGoogle Scholar
Zhang, T, Lu, Y, Song, S, Lu, R, Zhou, M, He, Z, Yuan, T, Yan, K and Cheng, Y (2019) ‘Double-muscling’ and pelvic tilt phenomena in rabbits with the cystine-knot motif deficiency of myostatin on exon 3. Bioscience Reports 39, 1–13.Google ScholarPubMed
Zhang, X, Hirschfeld, M, Beck, J, Kupke, A, Köhler, K, Schütz, E and Brenig, B (2020) Osteogenesis imperfecta in a male Holstein calf associated with a possible oligogenic origin. Veterinary Quarterly 40, 58–67.CrossRefGoogle Scholar
Zhao, X, Onteru, SK, Piripi, S, Thompson, KG, Blair, HT, Garrick, DJ and Rothschild, MF (2012) In a shake of a lamb's tail: using genomics to unravel a cause of chondrodysplasia in Texel sheep. Animal genetics 43, 9–18.CrossRefGoogle Scholar
Zhao, X, Dittmer, KE, Blair, HT, Thompson, KG, Rothschild, MF and Garrick, DJ (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, e21739.CrossRefGoogle ScholarPubMed
Zhi, D, Da, L, Liu, M, Cheng, C, Zhang, Y, Wang, X, Li, X, Tian, Z, Yang, Y, He, T, Long, X, Wei, W and Cao, G (2018) Whole genome sequencing of Hulunbuir short-tailed sheep for identifying candidate genes related to the short-tail phenotype. G3: Genes, Genomes, Genetics 8, 377–383.CrossRefGoogle Scholar
Zhu, Y, Zeng, Q, Li, F, Fang, H, Zhou, Z, Jiang, T, Yin, C, Wei, Q, Wang, Y, Ruan, J and Huang, J (2020) Dysregulated H3K27 acetylation is implicated in fatty liver hemorrhagic syndrome in chickens. Frontiers in Genetics 11, 1–15.Google ScholarPubMed