Selection and implementation of SNP markers for parentage analysis in a Chinese crossbred cattle population

Abstract

Background: In China, the widespread crossbreeding between Simmental and Holstein is a universal way so as to better improve the comprehensive benefits, as well as decline the inbreeding coefficient. However, the wrong parentage appeared frequently in this population than others due to not only the reasons in pure breeds, but more importantly, the lack of enough attention, which caused the lower accuracy of genetic parameter estimation and genetic evaluation in breeding systems. Single nucleotide polymorphism (SNP) panel in a certain population as a powerful tool for parentage assignment has been reported in numerous studies, especially in cattle. Therefore, the aim of this study was to build an SNP panel with sufficient power for parentage testing in the crossbred population of Simmental and Holstein in China. Results: In the present study, combining direct sequencing method in polymerase chain reaction (PCR) products of deoxyribonucleic acid (DNA) pooling and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) genotyping method in individuals, a panel comprising 50 highly informative single nucleotide polymorphisms (SNPs) for parentage analysis was developed in a crossbred Chinese cattle population. The average minor allele frequency (MAF) was 0.43 and the cumulative exclusion probability for single-parent and both-parent inference met 0.99797 and 0.999999, respectively. The maker-set was then used for parentage verification in a group of 81 trios with the likelihood-based parentage-assignment program of Cervus software. Compared with on-farm records, the results showed that this 50-SNP system could provide sufficient and reliable information for parentage testing with the parental mistakes for mother-offspring and sire-offspring being 8.6% and 18.5%, respectively.Conclusion: Knowledge of these results, we provided one set of low-cost and efficient SNPs for running paternity testing in the crossbred cattle population of Simmental and Holstein in China. Keywords: Parentage analysis, Single nucleotide polymorphism (SNP), Chinese crossbred cattle

Definición y análisis del panel de polimorfismos de nucleótido simple a utilizar en pruebas de paternidad para tres razas de bovinos

“…En México, las pruebas de paternidad se han implementado en las razas Brangus, Limousin y Hereford con base en el panel de SNP propuesto por la SIGA; no obstante, se requiere validar el panel de SNP a través de poblaciones, dado que la funcionalidad y veracidad de un MAGE en pruebas genéticas depende del equilibrio Hardy-Weinberg, el posible desequilibrio de ligamiento, el contenido de información polimórfica, entre otros componentes; además, en un conjunto de MAGE el poder de prueba es validado por la probabilidad de exclusión (14,15) . Al respecto, se han realizado estudios validando el panel de SNP desarrollado por la SIGA a utilizar en pruebas de paternidad de bovinos en Brasil (16) , Argentina (17) , China (18,19) , Estados Unidos (20,21) , Japón (22,23) y Europa (24,25,26) . Con base en lo anterior, los objetivos del presente estudio fueron validar el panel de SNP definido por la Sociedad Internacional de Genética Animal para pruebas genéticas en poblaciones de bovinos mexicanas.…”

“…Panetto et al (16) para la raza Sindhi de Brasil, con 71 SNP donde la FAM fue superior a 0.35, publicaron PNEC de 1 x 10 -8 . Zhang et al (18) en ganado Simmental con 50 SNP y FAM superior a 0.40, reportaron PEC superior a 0.9989; Hu et al (19) en bovinos cruzados de China, con 50 SNP donde el valor promedio de la FAM fue de 0.43, obtuvieron PEC de 0.99797 a 0.999999. PEC1= probabilidad de exclusión combinada, con un progenitor candidato y otro conocido.…”