Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Oluf Thesens vei 6, 1433, Ås, Norway.
Norsvin, Storhamargata 44, 2317, Hamar, Norway.
Genet Sel Evol. 2022 May 20;54(1):33. doi: 10.1186/s12711-022-00723-9.
Recombination is a fundamental part of mammalian meiosis that leads to the exchange of large segments of DNA between homologous chromosomes and is therefore an important driver of genetic diversity in populations. In breeding populations, understanding recombination is of particular interest because it can break up unfavourable linkage phases between alleles and produce novel combinations of alleles that could be exploited in selection. In this study, we used dense single nucleotide polymorphism (SNP) genotype data and pedigree information to analyse individual and sex-specific variation and genetic architecture of recombination rates within and between five commercially selected pig breeds.
In agreement with previous studies, recombination rates were higher in females than in males for all breeds and for all chromosomes, except 1 and 13, for which male rates were slightly higher. Total recombination rate differed between breeds but the pattern of recombination along the chromosomes was well conserved across breeds for the same sex. The autosomal linkage maps spanned a total length of 1731 to 1887 cM for males and of 2231 to 2515 cM for females. Estimates of heritability for individual autosomal crossover count ranged from 0.04 to 0.07 for males and from 0.08 to 0.11 for females. Fourteen genomic regions were found to be associated with individual autosomal crossover count. Of these, four were close to or within candidate genes that have previously been associated with individual recombination rates in pigs and other mammals, namely RNF212, SYCP2 and MSH4. Two of the identified regions included the PRDM7 and MEI1 genes, which are known to be involved in meiosis but have not been previously associated with variation in individual recombination rates.
This study shows that genetic variation in autosomal recombination rate persists in domesticated species under strong selection, with differences between closely-related breeds and marked differences between the sexes. Our findings support results from other studies, i.e., that individual crossover counts are associated with the RNF212, SYCP2 and MSH4 genes in pig. In addition, we have found two novel candidate genes associated with the trait, namely PRDM7 and MEI1.
重组是哺乳动物减数分裂的一个基本组成部分，导致同源染色体之间的大片段 DNA 交换，因此是群体遗传多样性的重要驱动因素。在选育群体中，了解重组特别重要，因为它可以打破等位基因之间不利的连锁阶段，并产生新的等位基因组合，这些组合可以在选择中得到利用。在这项研究中，我们使用密集的单核苷酸多态性（SNP）基因型数据和系谱信息，分析了五个商业选育猪品种中个体和性别特异性的重组率变化以及重组率的遗传结构。
与之前的研究一致，所有品种的雌性重组率均高于雄性，除了 1 号和 13 号染色体，雄性的重组率略高。总重组率在品种间存在差异，但同一性别染色体上的重组模式在品种间很好地保持一致。常染色体连锁图谱覆盖的总长度为雄性 1731 至 1887 厘摩，雌性 2231 至 2515 厘摩。个体常染色体交叉计数的遗传力估计值范围为雄性 0.04 至 0.07，雌性 0.08 至 0.11。发现 14 个基因组区域与个体常染色体交叉计数有关。其中，四个区域接近或位于候选基因内，这些候选基因以前与猪和其他哺乳动物的个体重组率有关，即 RNF212、SYCP2 和 MSH4。两个鉴定出的区域包括 PRDM7 和 MEI1 基因，这两个基因已知参与减数分裂，但以前与个体重组率的变化无关。
本研究表明，在强烈选择下，家养物种的常染色体重组率遗传变异仍然存在，近缘品种之间存在差异，性别之间存在显著差异。我们的研究结果支持了其他研究的结果，即个体交叉计数与猪的 RNF212、SYCP2 和 MSH4 基因有关。此外，我们还发现了两个与该性状相关的新候选基因，即 PRDM7 和 MEI1。
