Genomic insights into female productivity in limousine cattle: a single-step genome-wide association on longevity, fertility, and conformation traits

Abstract Background Improving female efficiency and resilience is a priority for beef cattle systems, where reproductive failure and early culling significantly affect sustainability and profitability. Longevity, fertility, and conformation traits provide complementary indicators of female performance, but their complex genetic architecture has limited progress in selection. This study aimed to investigate the genetic basis of these traits in the Italian Limousine population using a single-step genome-wide association approach, which integrates pedigree, phenotypic, and genomic information. Results The final dataset included 38,188 cows for longevity, 38,188 for fertility traits (age at first calving and first calving interval), and 32,316 for conformation traits, with 2,489 genotyped females included in the analyses. Heritability estimates were moderate for conformation (0.19–0.23) and for longevity at early parities (up to 0.21), lower for later parities (0.10–0.14), and low to moderate for fertility (0.18 for age at first calving, 0.14 for first calving interval). The single-step genome-wide association identified several genomic regions explaining more than 1% of the additive genetic variance, a subset of which was validated by a bootstrapping test. Key candidate genes overlapping across traits included KHDRBS2 (longevity and conformation), CPEB4 (longevity, fertility, and conformation), TOX (longevity, age at first calving, and conformation), and the LAP3–NCAPG–LCORL cluster (longevity and fertility). Functional annotation of overlapping quantitative trait loci highlighted pathways related to reproduction, health, and carcass quality, supporting pleiotropic effects across traits. Conclusions This study provides new insights into the genetic architecture of longevity, fertility, and conformation in Limousine cattle. The identification of pleiotropic loci and shared genomic regions supports the development of multi-trait genomic selection strategies. Targeting early indicators such as age at first calving, longevity at early parities, and conformation could accelerate genetic progress, reduce replacement costs, and enhance the sustainability, resilience, and profitability of beef production systems.