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Variation in Recombination Rate and Its Genetic Determinism in Sheep Populations

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Variation in Recombination Rate and Its Genetic Determinism in Sheep Populations | INVESTIGATION Variation in Recombination Rate and Its Genetic Determinism in Sheep Populations Morgane Petit,* Jean-Michel Astruc,† Julien Sarry,* Laurence Drouilhet,* Stéphane Fabre,* Carole R. Moreno,* and Bertrand Servin*,1 *INRA, Génétique, Physiologie, Systèmes d’Elevage, and †Institut de l’Elevage, F-31326 Castanet-Tolosan, France ORCID IDs: 0000-0002-2498-0926 (C.R.M.); 0000-0001-5141-0913 (B.S.) ABSTRACT Recombination is a complex biological process that results from a cascade of multiple events during meiosis. Understanding the genetic determinism of recombination can help to understand if and how these events are interacting. To tackle this question, we studied the patterns of recombination in sheep, using multiple approaches and data sets. We constructed male recombination maps in a dairy breed from the south of France (the Lacaune breed) at a fine scale by combining meiotic recombination rates from a large pedigree genotyped with a 50K SNP array and historical recombination rates from a sample of unrelated individuals genotyped with a 600K SNP array. This analysis revealed recombination patterns in sheep similar to other mammals but also genome regions that have likely been affected by directional and diversifying selection. We estimated the average recombination rate of Lacaune sheep at 1.5 cM/Mb, identified 50,000 crossover hotspots on the genome, and found a high correlation between historical and meiotic recombination rate estimates. A genome-wide association study revealed two major loci affecting interindividual variation in recombination rate in Lacaune, including the RNF212 and HEI10 genes and possibly two other loci of smaller effects including the KCNJ15 and FSHR genes. The comparison of these new results to those obtained previously in a distantly related population of domestic sheep (the Soay) revealed that Soay and Lacaune males have a very similar distribution of recombination along the genome. The two data sets were thus combined to create more precise male meiotic recombination maps in Sheep. However, despite their similar recombination maps, Soay and Lacaune males were found to exhibit different heritabilities and QTL effects for interindividual variation in genome-wide recombination rates. This highlights the robustness of recombination patterns to underlying variation in their genetic determinism. KEYWORDS recombination rate; genetic maps; QTLs; evolution; sheep eiotic recombination is a fundamental biological pro- preventing the accumulation of deleterious mutations. Mcess that brings a major contribution to the genetic Over large evolutionary timescales, divergence in recombina- diversity and the evolution of eukaryotic genomes (Baudat tion landscapes can lead to speciation; the action of a key et al. 2013). During meiosis, recombination enables chromo- factor in the recombination process in many mammals, the somal alignment resulting in proper disjunction and segre- gene PRDM9, has been shown to have a major contribution gation of chromosomes, avoiding deleterious outcomes to the infertility between two mouse species, making it the such as aneuploidy (Hassold et al. 2007). Over generations, only known speciation gene in mammals today (Mihola et al. recombination contributes to shaping genetic diversity in 2009). a population by creating new allelic combinations and Genetics studies on recombination were first used to infer the organization of genes along the genome (Sturtevant Copyright © 2017 by the Genetics Society of America 1913). With advances in molecular techniques, more de- doi: https://doi.org/10.1534/genetics.117.300123 Manuscript received June 30, 2017; accepted for publication July 31, 2017; published tailed physical maps and eventually whole-genome assem- Early Online September 8, 2017. blies are now available in many species. The establishment Available freely online through the author-supported open access option. Supplemental material is available online at www.genetics.org/lookup/suppl/doi:10. of highly resolutive recombination maps remains of funda- 1534/genetics.117.300123/-/DC1. mental importance for the validation of the physical order- 1Corresponding author: INRA, Génétique, Physiologie, Systèmes d’Elevage, 24 Chemin de Borde Rouge, Auzeville-Tolosane, CS 52627, F-31326 Castanet-Tolosan, France. ing of markers obtained from sequencing experiments E-mail: [email protected] (Groenen et al. 2012; Jiang et al. 2014). From an evolutionary Genetics, Vol. 207, 767–784 October 2017 767 perspective, the relevant distance between loci is the genetic 2012) mice (Shifman et al. 2006; Brunschwig et al. 2012), distance and recombination maps are essential tools for the cattle (Sandor et al. 2012; Ma et al. 2015; Kadri et al. 2016), genetic studies of a species, for estimation of past demogra- and sheep (Johnston et al. 2016) have demonstrated phy (Li and Durbin 2011; Boitard et al. 2016), detection of that recombination exhibits interindividual variation and selection signatures (Sabeti et al. 2002; Voight et al. 2006), that this variation is partly determined by genetic factors. QTL mapping (Cox et al. 2009), and imputation of genotypes Two recombination phenotypes have been described: the (Howie et al. 2009) for genome-wide association studies number of crossovers per meiosis (genome-wide recombina- (GWAS) or genomic selection. Precise recombination maps tion rate, GRR herein) and the fine-scale localization of cross- can be estimated using different approaches. Meiotic recom- overs (Individual Hotspot Usage, IHU). GRR has been shown bination rates can be estimated from the observation of to be influenced by several genes. For example, a recent markers’ segregation in families. Although this is a wide- GWAS found evidence for association with six genome re- spread approach, its resolution is limited by the number of gions in cattle (Kadri et al. 2016). Among them, one of the meioses that can be collected within a population and the genomic regions consistently found associated with GRR in number of markers that can be genotyped. Consequently, mammals is an interval containing the RNF212 gene. In con- highly resolutive meiotic maps have been produced trast to GRR, the IHU phenotype seems mostly governed by a in situations where large segregating families can be studied single gene in most mammals: PRDM9. This zinc-finger pro- and genotyped densely (Shifman et al. 2006; Mancera et al. tein has a key role in recruiting SPO11, thereby directing DNA 2008; Groenen et al. 2009; Rockman and Kruglyak 2009; double-strand breaks (DSBs) that initiate meiotic recombina- Kong et al. 2010) or by focusing on specificgenomicre- tion. Because PRDM9 recognizes a specific DNA motif, the gions (Cirulli et al. 2007; Stevison and Noor 2010; Kaur crossover events happen in hotspots carrying this motif. How- and Rockman 2014). In livestock species, the recent availabil- ever, this PRDM9-associated process is not universal as it is ity of dense genotyping assays has fostered the production of only active in some mammals; canids, for example, do not highly resolutive recombination maps (Tortereau et al. 2012; carry a functional copy of PRDM9 and exhibit different pat- Johnston et al. 2016, 2017), particularly by exploiting refer- terns for the localization of recombination hotspots (Auton ence population data from genomic selection programs et al. 2013). (Sandor et al. 2012; Ma et al. 2015; Kadri et al. 2016). As mentioned above, recombination was studied recently Another approach to study the distribution of recombina- in sheep (Johnston et al. 2016), which lead to the production tion on a genome is to exploit patterns of correlation between of precise genome-wide recombination maps, revealed a sim- allele frequencies in a population (i.e., linkage disequilibrium, ilar genetic architecture of recombination rates in sheep as in LD) to infer past (historical) recombination rates (McVean other mammals, and identified two major loci affecting indi- et al. 2002; Li and Stephens 2003; Chan et al. 2012). Because vidual variation. Quite interestingly,one of the QTL identified the LD-based approach in essence exploits meioses accumu- in this study, localized near the RNF212 gene, was clearly lated over many generations, it can provide more precise demonstrated to have a sex-specific effect. This study was estimates of local variation on recombination rate. For exam- performed in a feral population of sheep that is quite distantly ple, until recently (Pratto et al. 2014; Lange et al. 2016) this related to continental populations (Kijas et al. 2012) and has was the only known indirect approach allowing the detection not been managed by humans for a long time. To understand of fine-scale patterns of recombination genome-wide in how recombination patterns and genetic determinism can species with large genomes. Several highly recombining in- vary across populations, in this work we conducted a study tervals (recombination hotspots) were detected from histor- in another sheep population, the Lacaune, from the south of ical recombination rate maps and confirmed or completed France. The Lacaune breed is the main dairy sheep popula- those discovered by sperm-typing experiments (Crawford tion in France, its milk being mainly used for the production et al. 2004; Myers et al. 2005). One important caveat of of Roquefort cheese. Starting in 2011, a large genotyping LD-based approaches is that their recombination rate esti- effort started in the breed to implement a genomic selection mates are affected by other evolutionary processes,
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