Whole genome resequencing reveals the genetic contribution of Kazakh and Swiss Brown cattle to a population of Xinjiang Brown cattle

Xinjiang Brown cattle is characterized by wide environmental adaptation from its female parent (Kazakh cattle) and good production performance from its male parent (Swiss Brown cattle). However, the genetic basis un-derlying these characteristics has not been explored. Here we compared 50 genomes of Xinjiang Brown cattle to the genomes of other eight breeds worldwide to analyze patterns of genetic variation in the Xinjiang Brown cattle. We found canonical genomic characteristics of cross breed with the lowest linkage disequilibrium and the highest effective population size. At the global level, Xinjiang Brown cattle had 9.88% Kazakh cattle and 90.12% Swiss Brown cattle inheritance. Our local ancestry inference revealed the segments with the excess of Kazakh cattle blood enriched in genes or pathways involved in digestion, absorption, metabolism and disease. More importantly, we also observed the completely fixed haplotypes inherited from Swiss Brown cattle harboring genes (LCORL, GHR, MEF2D, PCSK1 and MSRB3), KEGG pathways, cattle QTLs or human NHGRI GWAS catalog related to body measurement and growth traits. Our findings will not only help understand the process of cross breeding but can provide basic materials for further QTL mapping and improvement of important traits in Xinjiang Brown cattle.

Automated summary

We compared the genomes of Xinjiang Brown cattle with eight other breeds and found that Xinjiang Brown cattle have typical genomic characteristics of cross breeds, with the lowest linkage disequilibrium and highest effective population size. Xinjiang Brown cattle inherit 9.88% of their genes from Kazakh cattle and 90.12% from Swiss Brown cattle. The study also identified fixed haplotypes from Swiss Brown cattle that carry genes, pathways, and QTLs related to body measurement and growth traits.