Detection of genomic regions associated malformations in newborn piglets: a machine-learning approach.

Autor:	Bakoev S; Federal Research Center for Animal Husbandry named after Academy Member LK. Ernst, Dubrovitsy, Russia.; Centre for Strategic Planning and Management of Biomedical Health Risks, Moscow, Russia., Traspov A; Federal Research Center for Animal Husbandry named after Academy Member LK. Ernst, Dubrovitsy, Russia.; Centre for Strategic Planning and Management of Biomedical Health Risks, Moscow, Russia., Getmantseva L; Federal Research Center for Animal Husbandry named after Academy Member LK. Ernst, Dubrovitsy, Russia., Belous A; Federal Research Center for Animal Husbandry named after Academy Member LK. Ernst, Dubrovitsy, Russia., Karpushkina T; Federal Research Center for Animal Husbandry named after Academy Member LK. Ernst, Dubrovitsy, Russia., Kostyunina O; Federal Research Center for Animal Husbandry named after Academy Member LK. Ernst, Dubrovitsy, Russia., Usatov A; South Federal University, Rostov-on-Don, Russia., Tatarinova TV; Department of Biology, University of La Verne, La Verne, CA, United States of America.; Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.; Vavilov Institute for General Genetics, Moscow, Russia.; School of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, Russia.
Jazyk:	angličtina
Zdroj:	PeerJ [PeerJ] 2021 Jul 22; Vol. 9, pp. e11580. Date of Electronic Publication: 2021 Jul 22 (Print Publication: 2021).
DOI:	10.7717/peerj.11580
Abstrakt:	Background: A significant proportion of perinatal losses in pigs occurs due to congenital malformations. The purpose of this study is the identification of genomic loci associated with fetal malformations in piglets. Methods: The malformations were divided into two groups: associated with limb defects (piglet splay leg) and associated with other congenital anomalies found in newborn piglets. 148 Landrace and 170 Large White piglets were selected for the study. A genome-wide association study based on the gradient boosting machine algorithm was performed to identify markers associated with congenital anomalies and piglet splay leg. Results: Forty-nine SNPs (23 SNPs in Landrace pigs and 26 SNPs in Large White) were associated with congenital anomalies, 22 of which were localized in genes. A total of 156 SNPs (28 SNPs in Landrace; 128 in Large White) were identified for piglet splay leg, of which 79 SNPs were localized in genes. We have demonstrated that the gradient boosting machine algorithm can identify SNPs and their combinations associated with significant selection indicators of studied malformations and productive characteristics. Data Availability: Genotyping and phenotyping data are available at http://www.compubioverne.group/data-and-software/. Competing Interests: Tatiana Tatarinova is an Academic Editor for PeerJ. (©2021 Bakoev et al.)
Databáze:	MEDLINE
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