Early Detection of Candidate Genes for Body Weight in Indonesian Cattle Breeds with Genome-Wide Association Study (GWAS)

1 Kementan RI: Livestock and animal health statistics 2022. 2022. [Jakarta]: Directorate General of Livestock and Animal Health. Search in Google Scholar

2 Kementan RI: Outlook of livestock commodities: beef. 2022 [Jakarta]: Data Center and Agricultural Information System of Ministry of Agriculture. Search in Google Scholar

3 Wiyatna MF: The ratio of meat index of Indonesian cattle (Bali, Madura PO) with Australian cattle (Australian Commercial Cross). JIT 2007, 7:22–25. Search in Google Scholar

4 Gurgul A, Semik E, Pawlina K, Szmatola T, Jasielczuk I, Bugno-Poniewierska M: The application of genome-wide SNP genotyping methods in studies of livestock genomes. J Appl Genetics 2014. Search in Google Scholar

5 Hartati H, Utsunomiya YT, Sonstegard TS, Garcia JF, Jakaria J, Muladno M: Evidence of Bos javanicus × Bos indicus hybridization and major QTLs for birth weight in Indonesian Peranakan Ongole cattle. BMC Genetics 2015, 16:75. Search in Google Scholar

6 Sudrajad P, Suhada H, Prasetyo D, Gariri PN, Eddianto E, Abiyoga AF, Kusminanto RY, Sukaryo S, Bramastya TA, Volkandari SD, Cahyadi M: Genome-wide association study of birth weight in Bali cattle (Bos javanicus). Trop Anim Sci J 2023, 46:151–156. Search in Google Scholar

7 Santana MHA, Utsunomiya YT, Neves HHR, Gomes RC, Garcia JF, Fukumasu H, Silva SL, Leme PR, Coutinho LL, Eler JP, Ferraz JBS: Genome-wide association study for feedlot average daily gain in Nellore cattle (Bos indicus). J Anim Breed Genet 2014, 131:210–216. Search in Google Scholar

8 Santana MHA, Gomes RC, Utsunomiya YT, Neves HHR, Novals FJ, Bonin MN, Fukumasu H, Garcia JF, Alexandre PA, Oliveira-Junior GA, Coutinho LL, Ferraz JBS: Genome-wide association with residual body weight gain in Bos indicus cattle. Genet Mol Res 2015, 14:5229–5233. Search in Google Scholar

9 Zepeda-Batista JL, Nunez-Dominguez R, Ramirez-Valverde R, Jahuey-Martinez FJ, Herrera-Ojeda JB, Parra-Bracamonte GM: Discovering of genomic variations associated with growth traits by GWAS in Braunvieh cattle. Genes 2012, 12:1666. Search in Google Scholar

10 Jahuey-Martinez FJ, Parra-Bracamonte GM, Sifuentes-Rincon AM, Martinez-Gonzalez JC, Gondro C, Garcia-Perez CA, Lopez-Bustamantes LA: Genome-wide association analysis of growth traits in Charolais beef cattle. J Anim Sci 2016, 94:4570–4582. Search in Google Scholar

11 Hardjosubroto W: Aplikasi pemuliabiakan ternak di lapangan. 1994 [Jakarta]: Gramedia Widiasarana. Search in Google Scholar

12 Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ, Sham PC: PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007, 81:559–575. Search in Google Scholar

13 Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES: TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 2007, 23:2633–2635. Search in Google Scholar

14 Trujano-Chavez MZ, Valerio-Hernandez JE, Lopez-Ordaz R, Ruiz-Flores A: Minor allele frequency in genomic prediction for growth traits in Braunvieh cattle. Revista Bio Ciencias 2021, 8:e1052. Search in Google Scholar

15 Becker GM, Burke JM, Lewis RM, Miller JE, Morgan JLM, Rosen BD, Tassell CPV, Notter DR, Murdoch BM: Variants within genes EDIL3 and ADGRB3 are associated with divergent fecal egg counts in Katahdin sheep at weaning. Front Genet 2022, 13:817319. Search in Google Scholar

16 Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, Jensen LJ, von Mering C: STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acid Res 2019, 47:D607–D613. Search in Google Scholar

17 Nei M, Kumar S: (2000). Molecular Evolution and Phylogenetics. 2000 [New York]: Oxford University Press. Search in Google Scholar

18 Hildebrand CE, Torney DC, Wagner RP: Informativeness of polymorphic DNA markers. Los Alamos Sci 1992, 20:100–102. Search in Google Scholar

19 Nei M, Tajima F: Genetic drift and estimation of effective population size. Genetics 1981, 98:625–640. Search in Google Scholar

20 Kaps M, Lamberson WR: Biostatistics for Animal Sciences. 2004. [London]: CABI Publishing. Search in Google Scholar

21 SPSS Inc. (2007). SPSS for Windows, Version 16.0. 2007. [Chicago]: SPSS Inc. Search in Google Scholar

22 Jahuey-Martinez FJ, Parra-Bracamonte GM, Sifuentes-Rincon AM, Martinez-Gonzalez JC, Gondro C, Garcia-Perez CA, Lopez-Bustamante LA: Genome-wide association analysis of growth traits in Charolais beef cattle. J Anim Sci 2016, 94:4570–4582. Search in Google Scholar

23 Zepeda-Batista JL, Nunez-Dominguez R, Ramirez-Valverde R, Jahuey-Martinez FJ, Herrera-Ojeda JB, Parra-Bracamonte GM: Discovering of genomic variations associated with growth traits by GWAS in Brauvieh cattle. Genes 2021, 12:1666. Search in Google Scholar

24 Igoshin AV, Yudin NS, Belonogova NM, Larkin DM: Genome-wide association study for body weight in cattle populations from Siberia. Anim Genet 2019, 50:250–253. Search in Google Scholar

25 Karacaoren B: Across-breed genomic prediction for body weight in Siberian cattle population. Turk J Vet Anim Sci 2020, 44:675–680. Search in Google Scholar

26 Terakado APN, Costa RB, de Camargo GMF, Irano N, Bresolin T, Takada L, Carvalho CVD, Oliveira HN, Carvalheiro R, Baldi F, de Albuquerque LG: Genome-wide association study for growth traits in Nelore cattle. Animal 2018, 12:1358–1362. Search in Google Scholar

27 Buzanskaz ME, Grossi DA, Ventura RV, Schenkel FS, Sargolzaei M, Meireles SLC, Mokry FB, Higa RH, Mudadu MA, da Silva MVGB, Niciura SCM, Torres Jr RAA, Alencar MM, Regitano LCA, Munari DP: Genome-wide association for growth traits in Canchim cattle. PloS ONE 2014, 9:e94802. Search in Google Scholar

28 Abdelmanova AS, Sermyagin AA, Dotsev AV, Bardukov NV, Fornara MS, Brem G, Zinovieva NA: Genome-wide screening for SNPs associated with stature in diverse cattle breeds. Diversity 2022, 14:692. Search in Google Scholar

29 Martinez R, Bejarano D, Gomez Y, Dasoneville R, Jimenez A, Even G, Solkner J, Meszaros G: Genome-wide association study for birth, weaning and yearling weight in Colombian Brahman cattle. Genet Mol Biol 2017, 40:453–459. Search in Google Scholar

30 Lu D, Miller S, Sargolzaei M, Kelly M, Voort GV, Caldwell T, Wang Z, Plastow G, Moore S: Genome-wide association analyses for growth and feed efficiency traits in beef cattle. J Anim Sci 2013, 91:3612–3633. Search in Google Scholar

31 Andersen RO, Turnbull DW, Johnson EA, Doe CQ: Sgt1 acts via an LKB1/AMPK pathway to establish cortical polarity in larval neuroblasts. Dev Biol 2012, 363:258–265. Search in Google Scholar

32 Pausch H, Schwarzenbacher H, Burgstaller J, Flisikowski K, Wurmser C, Jansen S, Jung S, Schnieke K, Wittek T, Fries R: Homozygous haplotype deficiency reveals deleterious mutations compromising reproductive and rearing success in cattle. BMC Genomics 2015, 16:312. Search in Google Scholar

33 Yun HJ, Kwon J, Seol W: Specific inhibition of transcriptional activity of the constitutive androstane receptor (CAR) by the splicing factor SF3a3. Biol Chem 2008, 389:1313–1318. Search in Google Scholar

34 Peedicayil A, Vierkant RA, Hartmann LC, Fridley BL, Fredericksen ZS, White KL, Elliott EA, Phelan CM, Tsai YY, Berchuck A, Iversen ES, Couch FJ, Peethamabaran P, Larson MC, Kalli KR, Kosel ML, Shridhar V, Rider DN, Liebow M, Cunningham JM, Schildkraut JM, Sellers TA, Goode EL: Risk of ovarian cancer and inherited variants in relapse-associated genes. PloS ONE 2010, 5:e8884. Search in Google Scholar

35 Agarwala KL, Nakamura S, Tsutsumi Y, Yamakawa K: Down syndrome cell adhesion molecule DSCAM mediates homophilic intercellular adhesion. Brain Res. Brain Res 2000, 79:118–126. Search in Google Scholar

36 Lu YJ, Yu WW, Cui MM, Yu XX, Song HL, Bai MR, Wu WJ, Gu BL, Wang J, Cai W, Chu X: Association analysis of variants of DSCAM and BACE2 with Hirschsprung disease susceptibility in Han Chinese and functional evaluation in zebrafish. Front. Cell Dev Biol 2021, 9:641152. Search in Google Scholar

37 Fuerst P, Koizumi A, Masland R, Burgess R: Neurite arborization and mosaic spacing in the mouse retina require DSCAM. Nature 2008, 451:470–474 Search in Google Scholar

38 Yimlamai D, Konnikova L, Moss L, Jay D: The zebrafish down syndrome cell adhesion molecule is involved in cell movement during embryogenesis. Dev Biol 2005, 279:44–57. Search in Google Scholar

39 Shen H, Li C, He M, Huang Y, Wang J, Wang M, Yue B, Zhang X: Immune profiles of male giant panda (Ailuropoda melanoleuca) during the breeding season. BMC Genomics 2021, 22:143. Search in Google Scholar

40 Liao S, Du R, Wang L, Qu Z, Cui X, Li C, Liu F, Huang M, Wang J, Chen J, Gao M, Yu S, Tang Z, Li DWC, Jiang T, Liu M: BCAS2 interacts with HSF4 and negatively regulates its protein stability via ubiquitination. Int J Biochem Cell Biol 2015, 68:78–86. Search in Google Scholar

41 Purohit AA, Li W, Qu C, Dwyer T, Shao Q, Guan KL, Liu G: Down syndrome cell adhesion molecule (DSCAM) associates with uncoordinated-5C (UNC5C) in Netrin-1-mediated growth cone collapse. J Biol Chem 2012, 287:27126–27138. Search in Google Scholar

42 Suhendro I, Noor RR, Jakaria J, Priyanto R, Manalu W, Andersson G: Association of heat-shock protein 70.1 gene with physiological and physical performance of Bali cattle. Vet World 2024,17:17–25. Search in Google Scholar

43 Prakash V, Bhattacharya TK, Jyotsana B, Pandey OP: Molecular cloning, characterization, polymorphism, and association study of the Interleukin-2 gene in Indian crossbred cattle. Biochem Genet 2011, 49:638–644. Search in Google Scholar