Kamaldinov EV, Petrov AF, Narozhnykh KN, Palchikov PN.
Animal Husbandry and Fodder Production. 2024. Vol. 107, no 4. Р. 53-67.
doi:10.33284/2658-3135-107-4-53
Original article
Assessment of the quality of genealogical data in breeding enterprises of Western Siberia
Evgeny V Kamaldinov1, Alexey F Petrov2, Kirill N Narozhnykh3, Pavel N Palchikov4
1,2,3Novosibirsk State Agrarian University, Novosibirsk, Russia
4JSC Novosibirskagroplem, Yarkovo settlement, Novosibirsk region, Russia
1ekamaldinov@yandex.ru, https://orcid.org/0000-0002-0341-5055
2lexluterking@yandex.ru, https://orcid.org/0000-0002-7402-4107
3narozhnykh@nsau.edu.ru, https://orcid.org/0000-0002-1519-697X
4v.2899936@yandex.ru
Abstract. Analysis of genealogical databases containing more than 6 million records revealed a significant number of gaps in the data on the origin of animals, especially for sires. This complicates the implementation of automated parental pair selection technologies and reduces the effectiveness of inbreeding level control. It was found that on average 7% of records on ancestors up to the third row of the pedigree contain gaps, of which 85.5% are for sires. This is a serious problem in the creation of regional digital platforms for the automation of decision-making in breeding livestock, limits the possibilities of an objective assessment of the breeding value of animals and hinders the necessary pressure of targeted artificial selection and assignment of sires to breeding stock.
Methods for improving the quality of primary genealogical data are proposed, including using foreign sources. It is shown that automation of the decision-making process in purebred dairy breeding allows not only to speed up the detection of errors, but also to significantly reduce the time for their correction thanks to the created data aggregators. This process can become the basis for large-scale verification and validation of primary zootechnical accounting data with subsequent transfer to the Federal State Information and Analytical System of Breeding Resources (FGIAS PR). In addition, this will increase the efficiency of zootechnicians-breeders in large breeding and commercial farms, and will also allow selecting breeding bulls that are genetically compatible with the breeding stock of both a separate region and their totality.Keywords: dairy cattle, genealogical data, information and analytical system, breeding value, breeding, inbreeding, agriculture
For citation: Kamaldinov EV, Petrov AF, Narozhnykh KN, Palchikov PN. Assessment of the quality of genealogical data in breeding enterprises of Western Siberia. Animal Husbandry and Fodder Production. 2024;107(4):53-67. (In Russ). https://doi.org/10.33284/2658-3135-107-4-53
References
- Kamaldinov EV, Petrov AF, Shatohin KS, Narozhnyh KN, Marenkov VG, Zhigulin TA, Bogdanova OV, Palchikov PN, Plakhova AA. Reliability of primary zootechnical records in dairy farming. Bulletin of NSAU (Novosibirsk State Agrarian University). 2022;2(63):76-83. doi: 10.31677/2072-6724-2022-63-2-76-83
- Marinchenko TE. Improving of the of dairy breedings efficiency. Journal of VNIIMZH. 2019; 2(34):193-203.
- Poddubny VV, Shevelyov OG, Bormashov DA. Comparision of texts clusterization methods quality on the base of hypergeometrical criterion. Tomsk State University Journal. 2006;293:120-125.
- Vasilev NP, Protopopova LD, Dayanova GI, Krylova AN, Nikitina NN. Formation of a unified digital platform for the region’s agriculture. International agricultural Journal. 2024;1(397):53-56. doi: 10.55186/25876740_2024_67_1_53
- Sheveleva OM, Svyazhenina MA. The influence of bulls on the productive qualities of progeny. Animal Husbandry and Fodder Production. 2023;106(4):40-56. doi: 10.33284/2658-3135-106-4-40
- Aggarwal CC. Outlier analysis: advanced concepts. In: Data Mining. Springer, Cham; 2015:265-83. doi: 10.1007/978-3-319-14142-8_9
- Aguilar I, Fernandez EN, Blasco A, Ravagnolo O, Legarra A. Effects of ignoring inbreeding in model-based accuracy for BLUP and SSGBLUP. J Anim Breed Genet. 2020;137(4):356-3 doi: 10.1111/jbg.12470
- Bivand R. R packages for analyzing spatial data: a comparative case study with areal data. Geographical Analysis. 2022;54(3):488- doi: 10.1111/gean.12319
- Brito LF, Oliveira HR, McConn BR, Schinckel AP, Arrazola A, Marchant-Forde JN, et al. Large-scale phenotyping of livestock welfare in commercial production systems: a new frontier in animal breeding. Front Genet. 2020;11:793. doi: 10.3389/fgene.2020.00793
- Cañas–Álvarez JJ, Ossa-Saraz GA, Garcés-Blanquiceth JL, Burgos–Paz WO. Genealogical structure of the Colombian Romosinuano Creole cattle. Trop Anim Health Prod. 2023;55(5):292. doi: 10.1007/s11250-023-03694-1
- Castro-Vásquez R, Vásquez-Loaiza M, Cruz-Méndez A, Domínguez-Viveros J, Camacho-Sandoval J, Saborío-Montero A. Genealogical information analysis of Gyr and Nelore cattle from Costa Rica. Cienc Rural. 2023;53(10):e20220236. doi: 1590/0103-8478cr20220236
- Cavani L, Silva RM de O, Carreño LOD, Ono RK, Bertipaglia TS, Farah MM, et al. Genetic diversity of Brazilian Brahman cattle by pedigree analysis. Pesq Agropec Bras. 2018;53(1):74-79. doi: 10.1590/s0100-204x2018000100008
- Canadian Networck for Dairy Excelence. [Internet] Available from: https://www.cdn.ca/home.php (accessed 2024 November 27).
- Chen TY. New Chebyshev distance measures for Pythagorean fuzzy sets with applications to multiple criteria decision analysis using an extended ELECTRE approach. Expert Systems with Applications. 2019;147(2):113164. doi: 1016/j.eswa.2019.113164
- Cole JB, Dürr JW, Nicolazzi EL. Invited review: The future of selection decisions and breeding programs: What are we breeding for, and who decides? Journal of Dairy Science. 2021;104(5):5111-24. doi: 10.3168/jds.2020-19777
- Cole JB, Eaglen SAE, Maltecca C, Mulder HA, Pryce JE. The future of phenomics in dairy cattle breeding. Animal Frontiers. 2020;10(2):37-44. doi: 10.1093/af/vfaa007
- Fioretti M, Negrini R, Biffani S, Quaglia A, Valentini A, Nardone A. Demographic structure and population dynamics of Maremmana cattle local breed after 35 years of traditional selection. Livestock Science. 2020;232:103903. doi: 10.1016/j.livsci.2019.103903
- Gaikadi S, Kumar SV. Is ward-level calculation of urban green space availability important?—A case study on Vellore city, India, using the histogram-based spectral discrimination approach. Front Sustain Cities. 2024;6:1393156. doi: 10.3389/frsc.2024.1393156
- Georges M, Charlier C, Hayes B. Harnessing genomic information for livestock improvement. Nat Rev Genet. 2019;20(3):135-156. doi: 10.1038/s41576-018-0082-2
- Giorgi FM, Ceraolo C, Mercatelli D. The R language: an engine for bioinformatics and data science. Life (Basel). 2022;12(5):648. doi: 10.3390/life12050648
- International Bull Evaluation Service Official Website. [Internet] Available from: https://interbull.org/index (accessed 2024 November 27).
- Irnawati I, Riswanto FDO, Riyanto S, Martono S, et al. The use of software packages of R factoextra and FactoMineR and their application in principal component analysis for authentication of oils. Indonesian Journal of Chemometrics and Pharmaceutical Analysis. 2021;1(1):1-10. doi: 10.22146/ijcpa.482
- Little RJA. A test of missing completely at random for multivariate data with missing values. Journal of the American Statistical Association. 1988;83(404):1198-202.
- Martin P, Baes C, Houlahan K, Richardson CM, Jamrozik J, Miglior F. Genetic correlations among selected traits in Canadian Can J Anim Sci. 2019; 99(4):693-704. doi: 10.1139/CJAS-2018-0190
- Mrode R, Ojango JMK, Okeyo AM, Mwacharo JM. Genomic selection and use of molecular tools in breeding programs for indigenous and crossbred cattle in developing countries: current status and future prospects. Front Genet. 2019;9:694. doi:10.3389/fgene.2018.00694
- Nader N, El-Gamal FEZ, El-Sappagh S, Kwak KS, Elmogy M. Kinship verification and recognition based on handcrafted and deep learning feature-based techniques. PeerJ Computer Science. 2021;7:e735. doi: 10.7717/peerj-cs.735
- Nilforooshan MA, Saavedra-Jiménez LA. ggroups: an R package for pedigree and genetic groups data. Hereditas. 2020;157(1):17. doi: 10.1186/s41065-020-00124-2
- Nyman S, Johansson AM, Palucci V, Schönherz AA, Guldbrandtsen B, Hinrichs D, et al. Inbreeding and pedigree analysis of the European red dairy cattle. Genet Sel Evol. 2022;54(1):70. doi: 10.1186/s12711-022-00761-3
- Schaeffer L. Strategy for applying genome-wide selection in dairy cattle. Journal of Animal Breeding and Genetics. 2006;123(4):218-23. doi: 10.1111/j.1439-0388.2006.00595.x
- Select Star SA. [Internet] Available from: https://www.selectstar.ch/de/index.htm. (accessed: 2024 November 27).
- Silva MHMA da, Malhado CHM, Kern EL, Daltro D dos S, Cobuci JA, Carneiro PLS. Inbreeding depression in Holstein cattle in Brazil. R Bras Zootec. 2019;48:e20170212. doi: 1590/rbz4820170212
- Suwanda R, Syahputra Z, Zamzami EM. Analysis of euclidean distance and manhattan distance in the k-means algorithm for variations number of Centroid K. Journal of Physics: Conference Series. 2020;1566(1):012058. doi: 1088/1742-6596/1566/1/012058
- Toghiani S, VanRaden PM. National Index Correlations and Actual vs. Expected Use of Foreign Sires. Interbull Bulletin. Leeuwarden, The Netherlands, 2021, April 26-30. 2021;56:52-9.
- Wickham H, Grolemund G. R for Data Science. Gravenstein Highway North, Sebastopol, CA: O’Reilly; 2017: 520 p.
- Wiggans GR, Carrillo JA. Genomic selection in United States dairy cattle. Front Genet. 2022;9(13):994466.
- Wiggans GR, Vanraden PM, Cooper TA. The genomic evaluation system in the United States: past, present, future. J Dairy Sci. 2011;94(6):3202-11. doi: 10.3168/jds.2010-3866
Information about the authors:
Evgeny V Kamaldinov, Dr Sci. (Biology), Associate Professor, Head of the Department of Applied Bioinformatics, Novosibirsk State Agrarian University, 160 Dobrolyubova str., 630039, Novosibirsk.
Alexey F Petrov, Head of the Laboratory of Applied Bioinformatics, Novosibirsk State Agrarian University, 160 Dobrolyubova str., 630039, Novosibirsk.
Kirill N Narozhnykh, Cand. Sci. (Biology), Associate Professor of the Department of Applied Bioinformatics, Novosibirsk State Agrarian University, 160 Dobrolyubova str., 630039, Novosibirsk.
Pavel N Palchikov, Director, JSC "Novosibirsk Agroplem", 630522, NSO, Novosibirsk district, MO Yarkovsky village Council along the Ordynsky highway in the territory of the district 1.5 km from the village of Yarkovo.
The article was submitted 18.10.2024; approved after reviewing 05.12.2024; accepted for publication 16.12.2024.
Download