Research Article
PDF EndNote BibTex Cite

Pedigrili Hayvanlarda Paydan Akrabalık Matrisini Hesaplamaya Yönelik Bir Visual Basic Uygulaması Yaklaşımı: EasyNRM

Year 2019, Volume 22, Issue , 418 - 423, 31.12.2019
https://doi.org/10.18016/ksutarimdoga.vi.571575

Abstract

Hayvancılıkta akrabalık ve akrabalı yetiştirme ayrıcalıklı öneme sahip kavramlardır. Bu nedenle yaygın kullanılan Microsoft Excel ortamında adı geçen değerleri hesaplamak üzere ücretsiz ve özgün bir yazılım geliştirilmiştir. Programda soykütüğüne dayalı tablo yöntemi uygulanmıştır. Yazılım EasyNRM olarak adlandırılmış ve bu konuda kaynaklar tarafından bilinen Comet isimli boğanın pedigrisi ile denenmiştir. Sonuç olarak Excel sayfalarında paydan akrabalık matrisi ve akrabalı yetiştirme katsayıları hesaplanmış ve bu bulgular literatür ile teyit edilmiştir. Bu yazılımın damızlık değer tahmininde akrabalık ilişkilerini de dikkate almak isteyen araştırmacılar ve yetiştiriciler için yararlı olacağı kanaatine varılmıştır.

References

  • Aguilar I, Misztal I 2008. Recursive algorithm for inbreeding coefficients assuming nonzero inbreeding of unknown parents. Journal of Dairy science, 91(4): 1669-1672.
  • Bıyıkoğlu MK 1973. Hayvancılıkta Uygulanan Yetiştirme Sistemleri (in Turkish). Erzurum, Turkey: Atatürk Üniversitesi Yayınları.
  • Boichard D 2002. PEDIG: A Fortran package for pedigree analysis suited for large populations. Proceedings of the 7th world congress on genetics applied to livestock production, Montpellier, France.
  • Bourdon RM 2013. Understanding Animal Breeding 2nd ed. Pearson Education Limited, Essex, England.
  • Cole JB 2007. PyPedal: A computer program for pedigree analysis. Computers and Electronics in Agriculture, 57 (1): 107-113. Doi: 10.1016/j.compag. 2007.02.002
  • Cruden D 1949. The computation of inbreeding coefficients for closed populations. Journal of Heredity, 40 (9): 248-251.
  • Emik LO, Terrill CE 1949. Systematic procedures for calculating inbreeding coefficients. Journal of Heredity, 40 (2): 51-55. doi: 10.1093/oxfordjournals. jhered.a105986
  • García-Cortés LA, Martínez-Ávila JC, Toro MA 2010. Fine decomposition of the inbreeding and the coancestry coefficients by using the tabular method. Conservation Genetics, 11 (5): 1945-1952. doi: 10.1007/s10592-010-0084-x
  • Gutiérrez JP, Goyache F 2005. A note on ENDOG: a computer program for analysing pedigree information. Journal of Animal Breeding and Genetics, 122 (3): 172-176. Doi: 10.1111/j.1439-0388.2005. 00512.x
  • Henderson CR 1976. A simple method for computing the inverse of a numerator relationship matrix used in prediction of breeding values. Biometrics, 32 (1): 69-83. Doi: 10.2307/2529339
  • Kaygısız A, Kösetürkmen E 2011. İsviçre Esmeri Sığırlarda Akrabalı Yetiştirme Düzeyi ve Akrabalı Yetiştirmenin Süt Verim Özellikleri Üzerine Etkileri (in Turkish). Kahramanmaraş Sütçü İmam Üniversitesi Doğa Bilimleri Dergisi, 14(2): 1-6.
  • Kerr RJ, Li L, Tier B, Dutkowski GW, McRae TA 2012. Use of the numerator relationship matrix in genetic analysis of autopolyploid species. Theoretical and Applied Genetics, 124 (7): 1271-1282. Doi: 10.1007/s00122-012-1785-y
  • Kim B, Beavis WD, Léon J 2016. Numericware N: numerator relationship matrix calculator. Journal of Heredity, 107 (7): 686-690. Doi: 10.1093/jhered/ esw057
  • Legates JE, Warwick EJ 1990. Breeding and Improvement of Farm Animals. McGraw Hill Inc, New York, USA.
  • Lush JL 2011. Animal breeding plans (Second Edition). Breiningsville, PA USA.
  • Nicholas F 2010. Introduction to Veterinary Genetics. 1st ed. Wiley-Blackwell, Singapore.
  • Sargolzaei M, Iwaisaki H, Colleau JJ 2006. CFC: A tool for monitoring genetic diversity. 8th World Congress Genetics Applied Livestock Producion, Belo Horizonte, Brazil.
  • StackOverflow-community, Test or check if sheet exists, https://stackoverflow.com/questions/ 6688131/test-or-check-if-sheet-exists, 2019.
  • Strandén I, Vuori K 2006. RelaX2: pedigree analysis programme. In Proceedings of the 8th World Congress on Genetics Applied to Livestock Production, Belo Horizonte, Minas Gerais, Brazil, 13-18 August, 2006 (pp. 27-30). Instituto Prociência.
  • Tekerli M 2018. Pedigri Yıldızı, Excel based unpublished pedigree software.
  • Tier B 1990. Computing inbreeding coefficients quickly. Genetics Selection Evolution, 22 (4): 419-430. Doi:10.1186/1297-9686-22-4-419
  • VanRaden PM 1992. Accounting for inbreeding and crossbreeding in genetic evaluation of large populations. Journal of Dairy Science, 75(11): 3136-3144.
  • Van Vleck LD, Pollak EJ, Oltenacu EA 1987. Genetics for the Animal Sciences. W.H. Freeman and Company, New York, USA.
  • Wright S 1922. Coefficients of Inbreeding and Relationship. The American Naturalist 56 (645): 330-338. Retrieved from http://www.jstor.org/ stable/2456273
  • Yazgan K 2018. RE-NUM-OR: Python-based renumbering and reordering software for pedigree files. Czech Journal of Animal Science, 63(2): 70-77.

EasyNRM: A Visual Basic Application Approach for Computing Numerator Relationship Matrix of Pedigreed Animals

Year 2019, Volume 22, Issue , 418 - 423, 31.12.2019
https://doi.org/10.18016/ksutarimdoga.vi.571575

Abstract

The relationship and inbreeding are special concepts in animal breeding, for this reason, a free of charge VBA software was developed to calculate the coefficients of relationship and inbreeding in Microsoft Excel. The tabular method algorithm was implemented by using pedigree. The software was called as EasyNRM and verified with the inclusion of bull Comet's pedigree. Finally, the numerator relationship matrix was created and certified with the results of the literature. It would be beneficial for EasyNRM to be used by researchers and breeders in estimating the breeding values of animals. 

References

  • Aguilar I, Misztal I 2008. Recursive algorithm for inbreeding coefficients assuming nonzero inbreeding of unknown parents. Journal of Dairy science, 91(4): 1669-1672.
  • Bıyıkoğlu MK 1973. Hayvancılıkta Uygulanan Yetiştirme Sistemleri (in Turkish). Erzurum, Turkey: Atatürk Üniversitesi Yayınları.
  • Boichard D 2002. PEDIG: A Fortran package for pedigree analysis suited for large populations. Proceedings of the 7th world congress on genetics applied to livestock production, Montpellier, France.
  • Bourdon RM 2013. Understanding Animal Breeding 2nd ed. Pearson Education Limited, Essex, England.
  • Cole JB 2007. PyPedal: A computer program for pedigree analysis. Computers and Electronics in Agriculture, 57 (1): 107-113. Doi: 10.1016/j.compag. 2007.02.002
  • Cruden D 1949. The computation of inbreeding coefficients for closed populations. Journal of Heredity, 40 (9): 248-251.
  • Emik LO, Terrill CE 1949. Systematic procedures for calculating inbreeding coefficients. Journal of Heredity, 40 (2): 51-55. doi: 10.1093/oxfordjournals. jhered.a105986
  • García-Cortés LA, Martínez-Ávila JC, Toro MA 2010. Fine decomposition of the inbreeding and the coancestry coefficients by using the tabular method. Conservation Genetics, 11 (5): 1945-1952. doi: 10.1007/s10592-010-0084-x
  • Gutiérrez JP, Goyache F 2005. A note on ENDOG: a computer program for analysing pedigree information. Journal of Animal Breeding and Genetics, 122 (3): 172-176. Doi: 10.1111/j.1439-0388.2005. 00512.x
  • Henderson CR 1976. A simple method for computing the inverse of a numerator relationship matrix used in prediction of breeding values. Biometrics, 32 (1): 69-83. Doi: 10.2307/2529339
  • Kaygısız A, Kösetürkmen E 2011. İsviçre Esmeri Sığırlarda Akrabalı Yetiştirme Düzeyi ve Akrabalı Yetiştirmenin Süt Verim Özellikleri Üzerine Etkileri (in Turkish). Kahramanmaraş Sütçü İmam Üniversitesi Doğa Bilimleri Dergisi, 14(2): 1-6.
  • Kerr RJ, Li L, Tier B, Dutkowski GW, McRae TA 2012. Use of the numerator relationship matrix in genetic analysis of autopolyploid species. Theoretical and Applied Genetics, 124 (7): 1271-1282. Doi: 10.1007/s00122-012-1785-y
  • Kim B, Beavis WD, Léon J 2016. Numericware N: numerator relationship matrix calculator. Journal of Heredity, 107 (7): 686-690. Doi: 10.1093/jhered/ esw057
  • Legates JE, Warwick EJ 1990. Breeding and Improvement of Farm Animals. McGraw Hill Inc, New York, USA.
  • Lush JL 2011. Animal breeding plans (Second Edition). Breiningsville, PA USA.
  • Nicholas F 2010. Introduction to Veterinary Genetics. 1st ed. Wiley-Blackwell, Singapore.
  • Sargolzaei M, Iwaisaki H, Colleau JJ 2006. CFC: A tool for monitoring genetic diversity. 8th World Congress Genetics Applied Livestock Producion, Belo Horizonte, Brazil.
  • StackOverflow-community, Test or check if sheet exists, https://stackoverflow.com/questions/ 6688131/test-or-check-if-sheet-exists, 2019.
  • Strandén I, Vuori K 2006. RelaX2: pedigree analysis programme. In Proceedings of the 8th World Congress on Genetics Applied to Livestock Production, Belo Horizonte, Minas Gerais, Brazil, 13-18 August, 2006 (pp. 27-30). Instituto Prociência.
  • Tekerli M 2018. Pedigri Yıldızı, Excel based unpublished pedigree software.
  • Tier B 1990. Computing inbreeding coefficients quickly. Genetics Selection Evolution, 22 (4): 419-430. Doi:10.1186/1297-9686-22-4-419
  • VanRaden PM 1992. Accounting for inbreeding and crossbreeding in genetic evaluation of large populations. Journal of Dairy Science, 75(11): 3136-3144.
  • Van Vleck LD, Pollak EJ, Oltenacu EA 1987. Genetics for the Animal Sciences. W.H. Freeman and Company, New York, USA.
  • Wright S 1922. Coefficients of Inbreeding and Relationship. The American Naturalist 56 (645): 330-338. Retrieved from http://www.jstor.org/ stable/2456273
  • Yazgan K 2018. RE-NUM-OR: Python-based renumbering and reordering software for pedigree files. Czech Journal of Animal Science, 63(2): 70-77.

Details

Primary Language English
Subjects Agriculture
Journal Section RESEARCH ARTICLE
Authors

Samet ÇİNKAYA> (Primary Author)
FACULTY OF VETERINARY
0000-0003-0736-4571
Türkiye


Mustafa TEKERLİ>
FACULTY OF VETERINARY
0000-0002-8634-1193
Türkiye


Mustafa DEMİRTAŞ This is me
FACULTY OF VETERINARY
0000-0002-8349-9649
Türkiye


Koray ÇELİKELOĞLU>
FACULTY OF VETERINARY
0000-0002-1610-2226
Türkiye

Publication Date December 31, 2019
Application Date May 29, 2019
Acceptance Date July 18, 2019
Published in Issue Year 2019, Volume 22, Issue

Cite

APA Çinkaya, S. , Tekerli, M. , Demirtaş, M. & Çelikeloğlu, K. (2019). EasyNRM: A Visual Basic Application Approach for Computing Numerator Relationship Matrix of Pedigreed Animals . Kahramanmaraş Sütçü İmam Üniversitesi Tarım ve Doğa Dergisi , Cilt 22 (Ek Sayı 2) , 418-423 . DOI: 10.18016/ksutarimdoga.vi.571575

21082





Uluslararası Hakemli Dergi (International Peer Reviewed Journal)

       Dergimiz, herhangi bir başvuru veya yayımlama ücreti almamaktadır (Free submission and publication).

      Yılda 6 sayı yayınlanır. (Published 6 times a year)

      88x31.png Bu web sitesi Creative Commons Atıf 4.0 Uluslararası Lisansı ile lisanslanmıştır.

                 



Kahramanmaraş Sütçü İmam Üniversitesi Tarım ve Doğa Dergisi
e-ISSN: 2619-9149