Home >Current Issue

Volume: 7, Issue: 1, Jan-Feb, 2019
DOI: 10.7324/JABB.2019.70112

Research Article

Morphological Trait, Molecular Genetic Evidence and Proteomic Determination of Different Chickens (Gallus gallus) Breeds


Wirot Likittrakulwong1, Pisit Poolprasert2, Sittiruk Roytrakul3

  Author Affiliations


Abstract

The phenotypic characterization, genetic variation and proteomic analysis of three main male chicken (Gallus gallus) breeds were investigated. These included hybrid red jungle fowl with the native chicken breed (KaiTor), white tail yellow chicken (WTYC) and commercial layer hen (HL). A phenetic analysis found that two major clades were observed in which the first two clades of Kai-Tor (clade A) and HL (clade B) were related. Meanwhile, WTYC was distinctly separated from the others. In terms of genetic diversity, three haplotypes were observed with 0.343 ± 0.097 of haplotypes diversity (Hd). The nucleotide diversity (Pi) of all samples was 0.00057 which conformed to low genetic diversity. In terms of protein characterization, two potential protein biomarkers were found in Kai-Tor serum samples namely 1) ATP-dependent RNA helicase DHX34 (DHX34; Accession number: XP_015128539.1) and 2) histone-lysine N-methyltransferase SETDB1 isoform X6 (SETDB1; Accession number: XP_015135538.1). Only one biomarker peptide was detected in HL (Cell division cycle 7-related protein kinase; CDC7; Accession number: XP_422347.5) as well as in WTYC (Bloom syndrome protein; BLM; Accession number: Q9I920).

Keywords:

Morphological character, mtDNA, Genetic variation, Protein identification.



Citation: Likittrakulwong W, Poolprasert P, Roytrakul S. Morphological Trait, Molecular Genetic Evidence and Proteomic Determination of Different Chickens (Gallus gallus) Breeds. J App Biol Biotech. 2018. Online first


Copyright: Author(s). This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License, which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited.

References

1. Darwin C. The variation of animals and plants under domestication.1st ed. London, UK: John Murray; 1868.

2. Hebert PD, Cywinska A, Shelley LB, Jeremy R. Biological identifications through DNA Barcodes. Proc R Soc Lond B Biol Sci 2003; 270: 313-321. https://doi.org/10.1098/rspb.2002.2218

3. Loftus RT, MacHugh DE, Bradley DG, Sharp PM, Cunningham P. Evidence for two independent domestications of cattle. Proc Natl Acad Sci USA 1994; 91: 2757-2761. https://doi.org/10.1073/pnas.91.7.2757

4. Luikart G, Gielly L, Excoffier L, Vigne JD, Bouvet J, Taberlet P. Multiple maternal origins and weak phylogeographic structure in domestic goats. Proc Natl Acad Sci USA 2001; 98: 5927-5932. https://doi.org/10.1073/pnas.091591198

5. Jansen T, Forster P, Levine MA, Oelke H, Hurles M, Renfrew C, Olek K. Mitochondrial DNA and the origins of the domestic horse. Proc Natl Acad Sci USA 2002; 99: 10905-10910. https://doi.org/10.1073/pnas.152330099

6. Komiyama T, Ikeo K, Gojobori T. The evolutionary origin of long-crowing chicken: its evolutionary relationship with fighting cocks disclosed by the mtDNA sequence analysis. Gene 2004; 333: 91-99. https://doi.org/10.1016/j.gene.2004.02.035

7. Sulandari S, Zein MSA, Sartika T. Molecular characterization of Indonesian Indigenous chickens based on Mitochondrial DNA Displacement (D)-loop Sequences. HAYATI J Biosci 2008; 15: 145 – 154. https://doi.org/10.4308/hjb.15.4.145

8. Cui H, Ibtisham F, Xu C, Huang H, Su Y. DNA barcoding of Chinese native chicken breeds through COI gene. Thai J Vet Med 2017; 47: 123-129.

9. Sneath PH, Sokal RR. Numerical Taxonomy. The principles and practice of numerical classification. Freeman, San Fransisco; 1973. 573.

10. Rohlf FJ. NTSYS-PC: Numerical taxonomy and multivariate analysis system version 2.02e. Exeter Software. New York;1997.

11. Kumar S, Stecher G, Tamura K. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33: 1870-1874. https://doi.org/10.1093/molbev/msw054

12. Librado P, Rozas J. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 2009; 25: 1451–1452. https://doi.org/10.1093/bioinformatics/btp187

13. Mi H, Muruganujan A, Casagrande JT, Thomas PD. Large-scale gene function analysis with the PANTHER classification system. Nat Protoc 2013; 8: 1551-1566. https://doi.org/10.1038/nprot.2013.092

14. Yamada T, Letunic I, Okuda S, Kanehisa M, Bork P. iPath2. 0: interactive pathway explorer. Nucleic Acids Res 2011; 39: 412-415. https://doi.org/10.1093/nar/gkr313

15. Boore JL. Animal mitochondrial genomes. Nucleic Acids Res 1999; 27: 1767-1780 https://doi.org/10.1093/nar/27.8.1767

16. Huang XH, Li GM, Chen X, Wu YJ, Li WN, Zhong FS, Wang WZ, Ding ZL. Identification of a novel mtDNA lineage B3 in chicken (Gallus gallus domesticus). Zool Res 2017; 38: 208–210.

17. Kimura MA. 1980. Simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16: 111–120. https://doi.org/10.1007/BF01731581

18. Teinlek P, Siripattarapravat K, Tirawattanawanich C. Genetic diversity analysis of Thai indigenous chickens based on complete sequences of mitochondrial DNA D-loop region. Asian-Australas J Anim Sci 2018; 31: 804-811. https://doi.org/10.5713/ajas.17.0611

19. Yushi G, Yunjie T, Haibing T, Kehua W, Kuanwei C, Rong G. DNA Barcoding application of mtDNA gene in Identifying Six indigenous chicken breeds in China. J Agric Biol 2007; 15: 924-930.

20. Sawai H, Kim HL, Kuno K, Suzuki S, Gotoh H, Takada M, Takahata N, Satta Y, Akishinonomiya F. The Origin and Genetic Variation of Domestic Chickens with Special Reference to Junglefowls Gallus g. gallus and G. varius . PLoS ONE 2010; 5: 10639. https://doi.org/10.1371/journal.pone.0010639

21. Trueb B, Zhuang L, Taeschler S, Wiedemann M. Characterization of FGFRL1, a novel fibroblast growth factor (FGF) receptor preferentially expressed in skeletal tissues. J Biol Chem 2003; 278: 33857-33865. https://doi.org/10.1074/jbc.M300281200

22. Toydemir RM, Rutherford A, Whitby FG, Jorde LB, Carey JC, Bamshad MJ. Mutations in embryonic myosin heavy chain (MYH3) cause Freeman-Sheldon syndrome and Sheldon-Hall syndrome. Nature genetics 2006; 38: 561. https://doi.org/10.1038/ng1775

23. Carraway KL, Perez A, Idris N, Jepson S, Arango M, Komatsu M, Carraway CAC. Muc4/sialomucin complex, the intramembrane Er6B2 ligand, in cancer and epithelia: to protect and to survive. Prog Nucleic Acid Res Mol Biol 2002; 71: 149-185. https://doi.org/10.1016/S0079-6603(02)71043-X

Article Metrics

Similar Articles