Genome-wide Association Study Identifies Loci Associated With Temperament Traits In Yunling Cattle And Brahman Cattle

Cattle temperament is a complex trait defined as a set of response towards handling by human and challenging situations.Owing to its correlation to productive efficiency,labor safety and animal welfare,cattle temperament is one of the most interesting traits.Because it is technically difficult to measure cattle temperament,the research on the genetic basis underlying the individual difference is at the beginning.Brahman cattle is one of Bos indicus breeds which are relatively flighty compared with Bos taurus breeds.Yunling cattle is a typical hybrid cattle breed in Brahman bull × Murray Grey bull/Yunnan indigenous cross cow.This research took Brahman cattle and Yunling cattle as the research object,collected flight distance in 211 cattles,crush score and flight speed in 361 cattles,five neurotransmitter concentrations in 157 cattles,15 traits of open filed test and 14 trait of novel object test in 234 cattles,whereas the intersection of testing individuals was large.More importantly,we sequenced the genomes of 31 Brahman cattle and 131 Yunling cattle with most of phenotypic traits.For the genome-wide association study of the above-mentioned traits,the results were as follows:1.By comparing the sequenced genomes and downloaded genomes of possible ancestry of Yunling cattle,we found the crossbreed Yunling cattle harbored the ancestry with 44% European taurine,48% Indian indicine and 8% Chinese indicine blood,suggesting that Yunling cattle is an ideal material for exploring the genetic basis of complex traits(e.g.,temperament trait).The local-ancestry inference revealed the European taurine,Indian indicine and Chinese indicine excessive segments in which the proportions inherited from corresponding ancestry were significantly higher than in the whole-genome level.The gene annotation and KEGG enrichment analysis showed that the European taurine,Indian indicine and Chinese indicine excessive segments might contribute to the rapid growth,immune resistance and indigenous adaptation,respectively,in Yunling cattle.2.For the phenotypic analysis of flight reaction traits(flight distance,crush score and flight speed),the results showed that the flight reaction traits had negative correlation with body measurement traits,and the flight reaction traits in Yunling cattle were significantly higher than those in Brahman cattle.For GWAS on flight reaction traits,we identified nine genomic loci,implicated eight genes,including five genes related to cognition(LOC789753,LRP6,CTIF,SLC9A9 and ZEB1),a cadherin(CDH8)involved in synaptic adhesion),and a gamma-aminobutyric acid receptor(GABRG2).3.For the phenotypic analysis of neurotransmitter concentration,we found that ACTH concentration was positively correlated with body weight,cannon circumference and hip width(P < 0.05).For GWAS on neurotransmitter concentration,we identified 20 genomic loci,implicated eighteen genes,including PCCA involved in dopamine synthesis,SLC18A2 involved in dopamine transport,MCHR1 involved in glutamate release,SLC6A9 involved in glutamate transport and HTR1 F involved in ACTH release.4.For the phenotypic analysis of temperament traits in open filed test and novel object test,the results showed that five traits of open filed test and two traits of novel object test in Yunling cattle were significantly lower than those in Brahman cattle,and most of temperament traits were negatively correlated with body measurement traits.For further principal component analysis,we found that the first principal component(PC1)explained 50% and 51% of the variability in open field and novel object test,respectively.For GWAS on temperament traits in open filed test and novel object test,we identified 37 and 29 genome-wide significant loci,respectively.Gene set analysis implicated the neuroactive ligand-receptor interaction pathway.Analysis in tissue specific expressions showed enrichment in the brain.For PC1,the most significant loci were assigned to SORCS3(a neuronal receptor)and SESTD1(a synapse protein)in an open field and novel object test,respectively.This is the first identification of loci associated with temperament traits using GWAS from whole genome sequence data in cattle.The identification of SNP markers associated with temperament traits will provide genomic targets for the genetic improvement of temperament traits by means of marker assisted selection.The revelation of implicated KEGG pathways and specifically-expressed tissues will guide the exploration of genetic mechanism underlying temperament traits.The descriptions of some important candidate genes are helpful for future fine mapping studies to identify causal variants explaining the difference in temperament traits.