Potential mitochondrial diversity role in the productivity of three lines of Japanese quails
##plugins.themes.bootstrap3.article.sidebar##
Issue
Section
Articles
##plugins.themes.bootstrap3.article.main##
TAMADHUR HUSSEIN
MOHAMMED BAQUR S. AL-SHUHAIB
♥
TAHREER M. AL-THUWAINI
https://orcid.org/0000-0003-4534-2963
Abstract
Abstract. Hussein TH, Al-Shuhaib MBS, Al-Thuwaini TM. 2020. Potential mitochondrial diversity role in the productivity of three lines of Japanese quails. Biodiversitas 21: 2258-2265. This study was conducted to identify the mitochondrial D-loop genetic diversity in three lines of Japanese quails that differ in productive performance. A total of 223 quails consisting of 54, 84, and 85 of black (control line), white (egg-producing line), and brown (meat-producing line) quails respectively were genotyped by PCR-single strand conformation polymorphism (SSCP). The genetic and phylogenetic differences within and among quails’ populations were analyzed. Three different SSCP banding patterns were observed in black and brown quails, while white quails exhibited six different SSCP-banding patterns. Sequencing reactions confirmed the presence of 12 haplotypes with 48 variations distributed among the studied birds. The white line exhibited the most diverse nucleotide variability, followed by the brown, and black lines respectively. The mean diversity for all populations was mainly due to within-population variation (71.6%), while among-population variation accounted for much less value (28.4%). Tajima’s D test showed significant values for both productive white (2.45680) and brown (3.07723) lines. In conclusion, this study suggested a wide nucleic acid variation in the investigated egg productive line than the meat productive line respectively compared with the black line control, implying a positive correlation between mitochondrial variability and productive performance.
##plugins.themes.bootstrap3.article.details##
References
Al-Kafajy FR, Al-Shuhaib MBS, Al-Jashami GS, Al-Thuwaini TM. 2018. Comparison of Three Lines of Japanese Quails Revealed a Remarkable Role of Plumage Color in the Productivity Performance Determination. J World Poult Res 8(4): 111-119.
Al-Shuhaib M.B.S.A. 2017. A Universal, rapid, and inexpensive method for genomic DNA isolation from the whole blood of mammals and birds. J Genet 96(1): 171-176.
Al-Shuhaib MBS. 2018. A minimum requirements method to isolate large quantities of highly purified DNA from one drop of poultry blood. J Genet 97(4): e87-e94.
Al-Shuhaib MBS, Al-Kafajy FR, Badi MA, AbdulAzeez S, Marimuthu K, Al-Juhaishi HAI, Borgio JF. 2018. Highly deleterious variations in COX1, CYTB, SCG5, FK2, PRL and PGF genes are the potential adaptation of the immigrated African ostrich population. Comput Biol Med 100: 17-26.
Bottje WG. 2018. 270 Mitochondrial Physiology, Oxidative Stress, and Animal Production Efficiency. J Anim Sci 96(suppl 2): 145.
Byun SO, Fang Q, Zhou H, Hickford JGH. 2009. An effective method for silver-staining DNA in large numbers of polyacrylamide gels. Anal Biochem 385: 174-175.
Di Lorenzo P, Ceccobelli S, Panella F, Attard G, Lasagna E. 2015. The role of mitochondrial DNA to determine the origin of domestic chicken. World Poultry Sci J 71: 311-318.
Excoffier L, Laval G, Schneider S. 2005. Arlequin ver. 3.0: An integrated software package for population genetics data analysis. Evol Bioinform 1: 47-50.
French N, Yu S, Biggs P, Holland B, Fearnhead P, Binney B, Fox A, Grove-White D, Leigh JW, Miller W, Muellner P, Carter P. 2014. Evolution of Campylobacter species in New Zealand. In Sheppard, S. K. & Méric, G. (Eds.), Campylobacter Ecology and Evolution (pp. 221–240). Norfolk, England: Caister Academic Press.
Gaur U, Tantia MS, Mishra B, Bharani Kumar ST, Vijh RK, Chaudhury A. 2018. Mitochondrial D-loop analysis for uncovering the population structure and genetic diversity among the indigenous duck (Anas platyrhynchos) populations of India. Mitochondrial DNA A DNA Mapp Seq Anal 29(2): 212-219.
Groeneveld LF, Lenstra JA, Eding H, Toro MA, Scherf B, Pilling D, Negrini R, Finlay EK, Jianlin H, Groeneveld E, Weigend S, Consortium GLOBALDIV. 2010. Genetic diversity in farm animals-a review. Anim Genet 41: 6-31.
Hashim HO, Al-Shuhaib MBS. 2019. Exploring the Potential and Limitations of PCR-RFLP and PCR-SSCP for SNP Detection: A Review. Appl Biotechnol Rep 6(4): 137-144.
Hood WR, Austad SN, Bize P, Jimenez AG, Montooth KL, Schulte PM, Scott GR, Sokolova I, Treberg JR, Salin K. 2018. The Mitochondrial Contribution to Animal Performance, Adaptation, and Life-History Variation. Integr Comp Biol 1;58(3): 480-485.
Hudson W. 2017. Whole-loop mitochondrial DNA D-loop sequence variability in Egyptian Arabian equine matrilines. PLoS ONE 12(8): e0184309.
Islam MA, Nishibori M. 2012. Phylogenetic analysis of native chicken from Bangladesh and neighboring Asian countries based on complete sequence of mitochondrial DNA D-loop region. J Poult Sci 49: 237-244.
Jeke A, Phiri C, Chitindingu K and Taru P. 2018. Ethnomedicinal use and pharmacological potential of Japanese quail (Coturnix coturnix japonica) birds` meat and eggs, and its potential implications on wild quail conservation in Zimbabwe: A review. Cogent Food Agric 4: 1507305.
Jimenez AG. 2018. The same thing that makes you live can kill you in the end’: exploring the effects of growth rates and longevity on cellular metabolic rates and oxidative stress in mammals and birds. Integr Comp Biol 1;58(3): 544-558.
Ladoukakis ED, Zouros E. 2017. Evolution and inheritance of animal mitochondrial DNA: rules and exceptions. J Biol Res (Thessalon) 31: 24:2.
Lancioni H, Di Lorenzo P, Ceccobelli S, Perego UA, Miglio A, Landi V, et al. 2013. Phylogenetic Relationships of Three Italian Merino-Derived Sheep Breeds Evaluated through a Complete Mitogenome Analysis. PLoS ONE 8(9): e73712.
Letunic I, Bork, P. 2019. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res 2;47(W1): W256-W259.
Librado P, Rozas J. 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451-1452.
Mansour A., da Silva, JAT, El-Araby E E. 2010. Molecular markers associated with the development of new phenotypes of Japanese quail in Egypt. Dyn Biochem Process Biotechnol Mol Biol 4(1): 79-84.?
Mariotti M, Valentini A, Marsan PA, Pariset L. 2013. Mitochondrial DNA of seven Italian sheep breeds shows faint signatures of domestication and suggests recent breed formation. Mitochondr DNA 24: 577-583.
Meydan H, Jang CP, Yildiz MA, Weigend S. 2016. Maternal Origin of Turkish and Iranian Native Chickens Inferred from Mitochondrial DNA D-loop Sequences. Asian-Australas J Anim Sci 29(11): 1547-1554.
Miller JM, Hallager S, Monfort SL, et al. 2011. Phylogeographic analysis of nuclear and mtDNA supports subspecies designations in the ostrich (Struthio camelus). Conserv Genet 12(2): 423-431.
Muchadeyi FC, Eding H, Simianer H, Wollny CBA, Groeneveld E, Weigend S. 2008. Mitochondrial DNA D-loop sequences suggest a Southeast Asian and Indian origin of Zimbabwean village chickens. Anim Genet 39: 615-622.
Murunga P, Kennedy GM, Imboma T, Malaki P, Kariuki D, Ndiema E, Obanda V, Agwanda B, Lichoti JK, Ommeh SC. Mitochondrial DNA D-Loop Diversity of the Helmeted Guinea Fowls in Kenya and Its Implications on HSP70 Gene Functional Polymorphism. BioMed Res Int 2018: 7314038.
Nasar A, Rahman A, Hoque N, Kumar Talukder A and Das ZC. 2016. A survey of Japanese quail (Coturnix coturnix japonica) farming in selected areas of Bangladesh. Vet World 9(9): 940-947.
Nunome M, Nakano M, Tadano R, Kawahara-Miki R, Kono T, Takahashi S, et al. 2017. Genetic Divergence in Domestic Japanese Quail Inferred from Mitochondrial DNA D-Loop and Microsatellite Markers. PLoS ONE 12(1): e0169978.
Rifki M, Dewanti R, Widyas N, Cahyadi M. 2018. Phylogenetic study of black and brown Japanese quails in Indonesia based on mitochondrial D-loop sequences. JABG 2(4): 237-244.
Siever F, Higgins DG. 2014. Clustal Omega, accurate alignment of very large numbers of sequences. Methods Mol Biol1079: 105-16.
Stier A, Bize P, Schull Q, Zoll J, Singh F, Geny B, Gros F, Royer C, Massemin S, Criscuolo F. 2013. Avian erythrocytes have functional mitochondria, opening novel perspectives for birds as animal models in the study of ageing. Front Zool.8;10(1): 33.
Stier A, Bize P, Hsu B-Y, Ruuskanen S. 2019. Plastic but repeatable: rapid adjustments of mitochondrial function and density during reproduction in a wild bird species. Cold Spring Harbor Laboratory.
Teinlek P, Siripattarapravat K, Tirawattanawanich C. 2018. Genetic diversity analysis of Thai indigenous chickens based on complete sequences of mitochondrial DNA D-loop region. Asian-Australas J Anim Sci 31(6): 804-811.
Vaughn SE. 2012. Review of the third edition of the Guide for the Care and Use of Agricultural Animals in Research and Teaching. J Am Assoc Lab Anim Sci 51(3): 298-300.
Wu YP, Huo JH, Xie JF, Liu LX, Wei QP, Xie MG, Kang ZF, Ji HY, Ma YH. 2014. Phylogeography and origin of Chinese domestic chicken. Mitochondr DNA 25(2): 126-130.?
Ye J, Coulouris G, Zaretskaya I, Cutcutache I, Rozen S, Madden TL. 2012. Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. BMC Bioinformatics 18;13: 134.
Yu C, Qiu M, Jiang X, Zhang Z, Du H, Li Q, Xia B, Song X, Hu C, Xiong X, Yang L, Peng H, Chen J, Wang Y, Yang C. 2019. Genetic Diversity and Phyletic Evolution of Eleven Chinese Indigenous and Three Commercial Chicken Breeds by mtDNA Sequences. Braz J Poult Sci 21(4): eRBCA-2018-0807.
Al-Shuhaib M.B.S.A. 2017. A Universal, rapid, and inexpensive method for genomic DNA isolation from the whole blood of mammals and birds. J Genet 96(1): 171-176.
Al-Shuhaib MBS. 2018. A minimum requirements method to isolate large quantities of highly purified DNA from one drop of poultry blood. J Genet 97(4): e87-e94.
Al-Shuhaib MBS, Al-Kafajy FR, Badi MA, AbdulAzeez S, Marimuthu K, Al-Juhaishi HAI, Borgio JF. 2018. Highly deleterious variations in COX1, CYTB, SCG5, FK2, PRL and PGF genes are the potential adaptation of the immigrated African ostrich population. Comput Biol Med 100: 17-26.
Bottje WG. 2018. 270 Mitochondrial Physiology, Oxidative Stress, and Animal Production Efficiency. J Anim Sci 96(suppl 2): 145.
Byun SO, Fang Q, Zhou H, Hickford JGH. 2009. An effective method for silver-staining DNA in large numbers of polyacrylamide gels. Anal Biochem 385: 174-175.
Di Lorenzo P, Ceccobelli S, Panella F, Attard G, Lasagna E. 2015. The role of mitochondrial DNA to determine the origin of domestic chicken. World Poultry Sci J 71: 311-318.
Excoffier L, Laval G, Schneider S. 2005. Arlequin ver. 3.0: An integrated software package for population genetics data analysis. Evol Bioinform 1: 47-50.
French N, Yu S, Biggs P, Holland B, Fearnhead P, Binney B, Fox A, Grove-White D, Leigh JW, Miller W, Muellner P, Carter P. 2014. Evolution of Campylobacter species in New Zealand. In Sheppard, S. K. & Méric, G. (Eds.), Campylobacter Ecology and Evolution (pp. 221–240). Norfolk, England: Caister Academic Press.
Gaur U, Tantia MS, Mishra B, Bharani Kumar ST, Vijh RK, Chaudhury A. 2018. Mitochondrial D-loop analysis for uncovering the population structure and genetic diversity among the indigenous duck (Anas platyrhynchos) populations of India. Mitochondrial DNA A DNA Mapp Seq Anal 29(2): 212-219.
Groeneveld LF, Lenstra JA, Eding H, Toro MA, Scherf B, Pilling D, Negrini R, Finlay EK, Jianlin H, Groeneveld E, Weigend S, Consortium GLOBALDIV. 2010. Genetic diversity in farm animals-a review. Anim Genet 41: 6-31.
Hashim HO, Al-Shuhaib MBS. 2019. Exploring the Potential and Limitations of PCR-RFLP and PCR-SSCP for SNP Detection: A Review. Appl Biotechnol Rep 6(4): 137-144.
Hood WR, Austad SN, Bize P, Jimenez AG, Montooth KL, Schulte PM, Scott GR, Sokolova I, Treberg JR, Salin K. 2018. The Mitochondrial Contribution to Animal Performance, Adaptation, and Life-History Variation. Integr Comp Biol 1;58(3): 480-485.
Hudson W. 2017. Whole-loop mitochondrial DNA D-loop sequence variability in Egyptian Arabian equine matrilines. PLoS ONE 12(8): e0184309.
Islam MA, Nishibori M. 2012. Phylogenetic analysis of native chicken from Bangladesh and neighboring Asian countries based on complete sequence of mitochondrial DNA D-loop region. J Poult Sci 49: 237-244.
Jeke A, Phiri C, Chitindingu K and Taru P. 2018. Ethnomedicinal use and pharmacological potential of Japanese quail (Coturnix coturnix japonica) birds` meat and eggs, and its potential implications on wild quail conservation in Zimbabwe: A review. Cogent Food Agric 4: 1507305.
Jimenez AG. 2018. The same thing that makes you live can kill you in the end’: exploring the effects of growth rates and longevity on cellular metabolic rates and oxidative stress in mammals and birds. Integr Comp Biol 1;58(3): 544-558.
Ladoukakis ED, Zouros E. 2017. Evolution and inheritance of animal mitochondrial DNA: rules and exceptions. J Biol Res (Thessalon) 31: 24:2.
Lancioni H, Di Lorenzo P, Ceccobelli S, Perego UA, Miglio A, Landi V, et al. 2013. Phylogenetic Relationships of Three Italian Merino-Derived Sheep Breeds Evaluated through a Complete Mitogenome Analysis. PLoS ONE 8(9): e73712.
Letunic I, Bork, P. 2019. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res 2;47(W1): W256-W259.
Librado P, Rozas J. 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451-1452.
Mansour A., da Silva, JAT, El-Araby E E. 2010. Molecular markers associated with the development of new phenotypes of Japanese quail in Egypt. Dyn Biochem Process Biotechnol Mol Biol 4(1): 79-84.?
Mariotti M, Valentini A, Marsan PA, Pariset L. 2013. Mitochondrial DNA of seven Italian sheep breeds shows faint signatures of domestication and suggests recent breed formation. Mitochondr DNA 24: 577-583.
Meydan H, Jang CP, Yildiz MA, Weigend S. 2016. Maternal Origin of Turkish and Iranian Native Chickens Inferred from Mitochondrial DNA D-loop Sequences. Asian-Australas J Anim Sci 29(11): 1547-1554.
Miller JM, Hallager S, Monfort SL, et al. 2011. Phylogeographic analysis of nuclear and mtDNA supports subspecies designations in the ostrich (Struthio camelus). Conserv Genet 12(2): 423-431.
Muchadeyi FC, Eding H, Simianer H, Wollny CBA, Groeneveld E, Weigend S. 2008. Mitochondrial DNA D-loop sequences suggest a Southeast Asian and Indian origin of Zimbabwean village chickens. Anim Genet 39: 615-622.
Murunga P, Kennedy GM, Imboma T, Malaki P, Kariuki D, Ndiema E, Obanda V, Agwanda B, Lichoti JK, Ommeh SC. Mitochondrial DNA D-Loop Diversity of the Helmeted Guinea Fowls in Kenya and Its Implications on HSP70 Gene Functional Polymorphism. BioMed Res Int 2018: 7314038.
Nasar A, Rahman A, Hoque N, Kumar Talukder A and Das ZC. 2016. A survey of Japanese quail (Coturnix coturnix japonica) farming in selected areas of Bangladesh. Vet World 9(9): 940-947.
Nunome M, Nakano M, Tadano R, Kawahara-Miki R, Kono T, Takahashi S, et al. 2017. Genetic Divergence in Domestic Japanese Quail Inferred from Mitochondrial DNA D-Loop and Microsatellite Markers. PLoS ONE 12(1): e0169978.
Rifki M, Dewanti R, Widyas N, Cahyadi M. 2018. Phylogenetic study of black and brown Japanese quails in Indonesia based on mitochondrial D-loop sequences. JABG 2(4): 237-244.
Siever F, Higgins DG. 2014. Clustal Omega, accurate alignment of very large numbers of sequences. Methods Mol Biol1079: 105-16.
Stier A, Bize P, Schull Q, Zoll J, Singh F, Geny B, Gros F, Royer C, Massemin S, Criscuolo F. 2013. Avian erythrocytes have functional mitochondria, opening novel perspectives for birds as animal models in the study of ageing. Front Zool.8;10(1): 33.
Stier A, Bize P, Hsu B-Y, Ruuskanen S. 2019. Plastic but repeatable: rapid adjustments of mitochondrial function and density during reproduction in a wild bird species. Cold Spring Harbor Laboratory.
Teinlek P, Siripattarapravat K, Tirawattanawanich C. 2018. Genetic diversity analysis of Thai indigenous chickens based on complete sequences of mitochondrial DNA D-loop region. Asian-Australas J Anim Sci 31(6): 804-811.
Vaughn SE. 2012. Review of the third edition of the Guide for the Care and Use of Agricultural Animals in Research and Teaching. J Am Assoc Lab Anim Sci 51(3): 298-300.
Wu YP, Huo JH, Xie JF, Liu LX, Wei QP, Xie MG, Kang ZF, Ji HY, Ma YH. 2014. Phylogeography and origin of Chinese domestic chicken. Mitochondr DNA 25(2): 126-130.?
Ye J, Coulouris G, Zaretskaya I, Cutcutache I, Rozen S, Madden TL. 2012. Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. BMC Bioinformatics 18;13: 134.
Yu C, Qiu M, Jiang X, Zhang Z, Du H, Li Q, Xia B, Song X, Hu C, Xiong X, Yang L, Peng H, Chen J, Wang Y, Yang C. 2019. Genetic Diversity and Phyletic Evolution of Eleven Chinese Indigenous and Three Commercial Chicken Breeds by mtDNA Sequences. Braz J Poult Sci 21(4): eRBCA-2018-0807.