Effects of Sex, Age, and Breed on Genetic Recombination Features in Cattle

Meiotic recombination is a fundamental biological process which generates genetic diversity, affects fertility, and influences evolvability. Here we investigate the roles of sex, age, and breed in cattle recombination features, including recombination rate, location and crossover interference. Using genotype data from 1,357,628 three-generation families of dairy cattle in four breeds, we measured recombination rates between SNP pairs based on over 22.4 and 7.7 million identified paternal and maternal recombination events, respectively. Our analysis reveals a number of sex, age, and breed differences in the total number and distribution of recombination events. Using recombination features as phenotype, we also performed GWAS and identified several associated SNPs in multiple cattle breeds. By using the Housworth–Stahl interference escape model, we estimated the strength of crossover interference in Holstein cows and bulls. Our results show that the levels of both cross-over interference and interference escape are higher in females than in males. In addition, we find that both of the estimates of interference and escape parameters vary considerably across the 29 autosomes. After dividing the data into groups based on maternal age, we observed a peak for both interference and escape parameters in 9 year old cows. Collectively, this large-scale analysis of cattle meiotic recombination provides useful insights into the variation in recombination due to sex, age and breed differences.