Favored single nucleotide variants identified using whole genome re-sequencing of Austrian and Chinese cattle breeds

Authors: NAJI, MAULANA - University Of Natural Resources And Life Sciences, Vienna; JIANG, YIFAN - China Agricultural University; UTSUNOMIYA, YURI - Sao Paulo State University (UNESP); Rosen, Benjamin - Ben; SOLKNER, JOHANN - University Of Natural Resources And Life Sciences, Vienna; WANG, CHUDUAN - China Agricultural University; JIANG, LI - China Agricultural University; ZHANG, QIN - China Agricultural University; ZHANG, YI - China Agricultural University; DING, XIANGDONG - China Agricultural University; MESZAROS, GABOR - University Of Natural Resources And Life Sciences, Vienna

Submitted to: Frontiers in Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/29/2022
Publication Date: 9/27/2022
Citation: Naji, M.M., Jiang, Y., Utsunomiya, Y.T., Rosen, B.D., Solkner, J., Wang, C., Jiang, L., Zhang, Q., Zhang, Y., Ding, X., Meszaros, G. 2022. Favored single nucleotide variants identified using whole genome re-sequencing of Austrian and Chinese cattle breeds. Frontiers in Genetics. https://doi.org/10.3389/fgene.2022.974787.
DOI: https://doi.org/10.3389/fgene.2022.974787

Interpretive Summary: Cattle have been essential for the development of human civilization since their first domestication a few thousand years ago. Throughout the generations, evolutionary processes such as natural and human selection have shaped the cattle genome with detectable signals. These genetic patterns are called signatures of selection and can they can point us towards traits that may have been important to the success of various breeds. Whole genome sequence data from Austrian Fleckvieh and Chinese indigenous breeds was used to identify single nucleotide variants. Signatures were identified in production, reproduction, and temperament traits in some breeds, while heat and parasites tolerance were identified in others.

Technical Abstract: The cattle genome has been shaped with detectable signals induced by various evolutionary processes. Previous studies used various methods to identify signatures of selection and normalize the outputs using specific windows, in kbp or based on the number of SNPs, to identify candidate regions. The recent method of iSAFE claimed for high accuracy in pinpointing the candidate SNPs. In this study, we analyzed whole-genome resequencing (WGS) data of ten individuals from Austrian Fleckvieh (Bos taurus taurus) and fifty individuals from 14 Chinese indigenous breeds (Bos taurus taurus, Bos taurus indicus, and admixed). Individual WGS reads were aligned to the cattle reference genome of ARS.UCD1.2 and subsequently undergone single nucleotide variants (SNVs) calling pipeline using GATK. Using these SNVs, we examined population structure and candidate selection using the iSAFE program and compared it with the classical iHS approach. Additionally, we ran Fst population differentiation from these two cattle groups. We found gradual changes of taurine in north China to admixed and indicine to the south. Based on the population structure, we grouped individuals to Fleckvieh, three Chinese taurines (Kazakh, Mongolian, Yanbian), admixed individuals (CHBI_Med), indicine individuals (CHBI_Low), and a combination of admixed and indicine (CHBI) for performing iSAFE and iHS tests. There are more significant SNVs identified using iSAFE than the iHS for the candidate of positive selection and more detectable signals in taurine than in indicine individuals. However, combining admixed and indicine individuals decreased the iSAFE signals. From both withinpopulation tests, significant SNVs are linked to the olfactory receptors, production, reproduction, and temperament traits in taurine cattle, while heat and parasites tolerance in the admixed individuals. Fst test suggests similar patterns of population differentiation between Fleckvieh and three Chinese taurine breeds against CHBI. Nevertheless, there are genes shared only among the Chinese taurine, such as PAX5, affecting coat color, which might drive the differences between these yellowish coated breeds, and those in the greater Far East region.