Characterization of recombination features and the genetic basis in multiple cattle breeds

Botong Shen,George E Liu,Jicai Jiang,Eyal Seroussi,Li Ma

doi:10.1186/s12864-018-4705-y

Abstract

BackgroundCrossover generated by meiotic recombination is a fundamental event that facilitates meiosis and sexual reproduction. Comparative studies have shown wide variation in recombination rate among species, but the characterization of recombination features between cattle breeds has not yet been performed. Cattle populations in North America count millions, and the dairy industry has genotyped millions of individuals with pedigree information that provide a unique opportunity to study breed-level variations in recombination.ResultsBased on large pedigrees of Jersey, Ayrshire and Brown Swiss cattle with genotype data, we identified over 3.4 million maternal and paternal crossover events from 161,309 three-generation families. We constructed six breed- and sex-specific genome-wide recombination maps using 58,982 autosomal SNPs for two sexes in the three dairy cattle breeds. A comparative analysis of the six recombination maps revealed similar global recombination patterns between cattle breeds but with significant differences between sexes. We confirmed that male recombination map is 10% longer than the female map in all three cattle breeds, consistent with previously reported results in Holstein cattle. When comparing recombination hotspot regions between cattle breeds, we found that 30% and 10% of the hotspots were shared between breeds in males and females, respectively, with each breed exhibiting some breed-specific hotspots. Finally, our multiple-breed GWAS found that SNPs in eight loci affected recombination rate and that the PRDM9 gene associated with hotspot usage in multiple cattle breeds, indicating a shared genetic basis for recombination across dairy cattle breeds.ConclusionsCollectively, our results generated breed- and sex-specific recombination maps for multiple cattle breeds, provided a comprehensive characterization and comparison of recombination patterns between breeds, and expanded our understanding of the breed-level variations in recombination features within an important livestock species.

Highlights

Crossover generated by meiotic recombination is a fundamental event that facilitates meiosis and sexual reproduction
Comparing to the previously reported Holstein recombination maps, we examined the similarities and differences between eight recombination maps and documented significant breedand sex-specific recombination hotspot regions, revealing both broad- and fine-scale recombination features that differed between cattle breeds
Identification of crossover events using genotyped cattle pedigree Using a similar approach to our previous studies in Holstein cattle [15, 30], we constructed three-generation families that included an offspring, parents, and grandparents from large pedigrees of three dairy cattle breeds

Summary

Introduction

Crossover generated by meiotic recombination is a fundamental event that facilitates meiosis and sexual reproduction. Comparative studies have shown wide variation in recombination rate among species, but the characterization of recombination features between cattle breeds has not yet been performed. Cattle populations in North America count millions, and the dairy industry has genotyped millions of individuals with pedigree information that provide a unique opportunity to study breed-level variations in recombination. As a fundamental biological process, the genetic mechanisms of meiotic recombination are conserved across all eukaryotic species [3]. Pedigree-based studies have discovered considerable variation in recombination rate in humans and mice [6, 7]. Males have more recombination events per meiosis in sheep [14] and cattle [15, 16]. Despite the extensive variation in recombination between species and sexes, only a few studies have examined the effect of

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