Genome-wide recombination map construction from single sperm sequencing in cattle

Abstract

Background Meiotic recombination is one of the important phenomena contributing to gamete genome diversity. However, except for human and a few model organisms, it is not well studied in livestock, including cattle. Results To investigate their distributions in the cattle sperm genome, we sequenced 143 single sperms from two Holstein bulls. We mapped meiotic recombination events at high resolution based on phased heterozygous single nucleotide polymorphism (SNP). In the absence of evolutionary selection pressure in fertilization and survival, recombination events in sperm are enriched near distal chromosomal ends, revealing that such a pattern is intrinsic to the molecular mechanism of meiosis. Furthermore, we further validated these findings in single sperms with results derived from sequencing its family trio of diploid genomes and our previous studies of recombination in cattle. Conclusions To our knowledge, this is the first large-scale single sperm whole-genome sequencing effort in livestock, which provided useful information for future studies of recombination, genome instability, and male infertility.

Predicting recombination frequency from map distance

“…Although crossovers and the resultant recombinations have been studied for more than a hundred years (Sturtevant 1913;Sturtevant 1915), many related questions remain unanswered. Due to their profound importance in sexual reproduction, substantial research efforts have focused on better understanding the amongorganism and individual variation of crossover rate (e.g., Stapley et al 2017;Haenel et al 2018), and on the other hand, recent technologies have been utilized for detecting recombinations at the gamete level (Dréau et al 2019;Bell et al 2020;Yang et al 2022). Crossovers also have implications for statistical properties essential in population genetics, such as the variance of genetic relatedness (Veller et al 2020).…”

Predicting recombination frequency from map distance

“…Although crossovers and the resultant recombinations have been studied for more than a hundred years (Sturtevant 1913), many related questions remain unanswered. Due to their profound importance in sexual reproduction, substantial research efforts have focused on better understanding the among-organism and individual variation of crossover rate (e.g., Stapley et al 2017, Haenel et al 2018), and on the other hand, recent technologies have been utilized for detecting recombinations at the gamete level (Dréau 2019, Bell et al 2020, Yang et al 2022). Crossovers also have implications for statistical properties essential in population genetics, such as the variance of genetic relatedness (Veller et al 2020).…”

Mapping restricted introgression across the genomes of admixed indigenous African cattle breeds

“…Regions of low intra-specific recombination may be highly differentiated among populations and harbour an excess of genomic incompatibilities. In order to relate the results for cline steepness and within-Africa genetic differentiation (F ST ) to patterns of taurine recombination, we used estimates of recombination rate from single sperm sequencing of two Holstein bulls [63], which were presented as the number of crossover events for each 1-Mb region across the genome. We divided the genome into three region categories: high recombination, low recombination and all other regions.…”

“…We divided the genome into three region categories: high recombination, low recombination and all other regions. We defined regions of high recombination as the hotspots, defined by Yang et al [63] (segments with a recombination rate of 2.5 × standard deviation greater than the mean), that were shared by the two sires (Table S10 in Yang et al [63]). We defined regions of low recombination as those that showed no recombination events in blocks of three or more 1-Mb segments in either sire ("coldspots") (results shown in Fig.…”

“…We defined regions of low recombination as those that showed no recombination events in blocks of three or more 1-Mb segments in either sire ("coldspots") (results shown in Fig. 2C in Yang et al [63] and details provided by the authors). Linear regression with ln(v) and F ST as response variables were performed to test for differences between the three categories of genomic regions.…”