A Comprehensive Genetic Map of the Cattle Genome Based on 3802 Microsatellites

TLDR

A high‑density microsatellite map enables fine mapping of hereditary traits, meiosis characterization, and serves as a foundation for physical map construction. The study aimed to develop a comprehensive cattle genetic map using over 880,000 genotypes from USDA MARC reference families, targeting 0.8 cM resolution. The map was constructed by incorporating 2,325 microsatellites via sex‑averaged two‑point LOD linkage analysis (>3.0), with 2,293 fine‑mapped using multipoint linkage. The resulting 3,160‑cM map contains 3,960 markers across 29 autosomal and one X‑chromosome linkage groups, with an average interval of 1.4 cM, 51 % of the map covered by intervals ≤2.0 cM, and a maximum gap of 10.2 cM on the X group, accelerating fine mapping and positional cloning in cattle and related livestock.

Abstract

A microsatellite-based high-density genetic map facilitates for fine mapping of hereditary traits of interest, characterization of meiosis, and providing a foundation for physical map construction. Here, we developed a comprehensive genetic map on the basis of >880,000 genotypes across the USDA MARC cattle reference families with a potential genetic resolution of 0.8 cM at the 95% confidence level (∼800 kb in the bovine genome). We incorporated 2325 microsatellites into the second-generation genetic map by linkage analysis based on sex-averaged two-point LOD scores (>3.0), of which 2293 were fine-mapped by multipoint linkage analysis. The new 3160-cM map comprised of 29 sex-averaged autosomal linkage groups and a sex-specific X-chromosome linkage group includes 3960 markers with 2389 positions, resulting in an average interval size of 1.4 cM. More than half (51%) of the total length of the map is covered with intervals of 2.0 cM or less, and the largest gap is a 10.2-cM interval on the X-linkage group. The new map should accelerate fine mapping and positional cloning of genes for genetic diseases and economically important traits in cattle, as well as related livestock species, such as sheep and goat.