The selection and breeding of good meat rabbit breeds are fundamental to their industrial development, and genomic selection (GS) can employ genomic information to make up for the shortcomings of traditional phenotype-based breeding methods. For the practical implementation of GS in meat rabbit breeding, it is necessary to assess different marker densities and GS models. Here, we obtained low-coverage whole-genome sequencing (lcWGS) data from 1515 meat rabbits (including parent herd and half-sibling offspring). The specific objectives were (1) to derive a baseline for heritability estimates and genomic predictions based on randomly selected marker densities and (2) to assess the accuracy of genomic predictions for single- and multiple-trait linear mixed models. We found that a marker density of 50 K can be used as a baseline for heritability estimation and genomic prediction. For GS, the multi-trait genomic best linear unbiased prediction (GBLUP) model results in more accurate predictions for virtually all traits compared to the single-trait model, with improvements greater than 15% for all of them, which may be attributed to the use of information on genetically related traits. In addition, we discovered a positive correlation between the performance of the multi-trait GBLUP and the genetic correlation between the traits. We anticipate that this approach will provide solutions for GS, as well as optimize breeding programs, in meat rabbits.

Embryo genomic selection (EGS) is a contemporary breeding strategy that combines genomic selection (GS) methodology with embryo biotechnology. By conducting genotyping and genomic prediction at the pre-implantation stage, embryos with superior breeding value can be identified for transfer, markedly increasing breeding efficiency while reducing the uncertainty and temporal expenditure associated with conventional GS. This study establishes a reliable embryo biopsy-based GS pipeline for sheep, incorporating optimized whole-genome amplification and microcell genotyping techniques. We developed a high-efficiency in vitro sheep embryo production platform compatible with embryo biopsy. Systematic comparison of Multiple Displacement Amplification (MDA) and Multiple Annealing and Looping Based Amplification Cycles (MALBAC) whole-genome amplification systems yielded high-quality genotypes from biopsy samples of embryos containing as few as 10 cells. Imputation using 10× whole-genome sequencing data significantly increased both genotype call rates and accuracy. High concordance was observed between embryo and lamb genotypes, and genomic estimated breeding values (GEBVs) for key growth traits exhibited strong correlations (R²: 0.91–0.98). This system enables accurate preimplantation genomic evaluation and provides an efficient strategy to accelerate genetic improvement in sheep breeding programs.

The efficiency of the laparoscopic ovum pick-up and in vitro embryo production (LOPU-IVEP) system in sheep is governed by a complex interplay of genetic and environmental factors. This study comprehensively evaluated the effects of breed, season, and their interaction on oocyte retrieval, embryonic development, and pregnancy outcomes in a commercial setting. A 20-month longitudinal analysis of a large commercial cohort revealed that breed was the dominant factor determining oocyte quantity, whereas season exerted a stronger influence on developmental competence. Specifically, autumn and winter provided optimal conditions, resulting in significantly higher cleavage rate and blastocyst rate (p < 0.05). A significant breed-by-season interaction further identified synergistic combinations, such as Black-headed Suffolk in autumn or winter, which achieved superior embryo production outcomes. Importantly, correlation analysis revealed that oocyte quantity was not predictive of developmental potential or pregnancy success. These findings underscore the necessity of a precision management strategy that aligns LOPU schedules with breed-specific seasonal advantages to maximize annual embryo production efficiency.

In vitro maturation (IVM) of oocytes remains suboptimal due to oxidative stress and disrupted cumulus–oocyte communication. Oocyte-derived factors (ODFs) are key mediators of this crosstalk and crucial for oocyte competence. Here, we provide systematic evidence that ephrin-A5 (EFNA5) is an oocyte-derived membrane ligand capable of regulating oocyte quality during IVM. Cross-species transcriptomic analysis revealed that EFNA5 is stably enriched in mammalian oocytes but markedly reduced in in vitro-matured oocytes compared with in vivo counterparts. Using the ovine IVM model, supplementation with recombinant EFNA5 significantly improved blastocyst formation, increased total cell numbers, and reduced apoptosis. Mechanistically, EFNA5 promoted cumulus–oocyte complex expansion, reduced reactive oxygen species accumulation, activated NRF2-dependent antioxidant signaling, and suppressed NF-κB-driven inflammation. RNA-seq and functional validation further confirmed that EFNA5 enhanced redox homeostasis and decreased DNA damage, collectively improving oocyte developmental potential. These findings establish EFNA5 as a novel and conserved ODF that alleviates oxidative and inflammatory stress to enhance oocyte quality and embryo development, providing mechanistic insight and a potential strategy for improving assisted reproductive technologies.

In vitro maturation (IVM) of oocytes remains suboptimal due to oxidative stress and disrupted cumulus–oocyte communication. Oocyte-derived factors (ODFs) are key mediators of this crosstalk and crucial for oocyte competence. Here, we provide systematic evidence that EFNA5 is an oocyte-derived membrane ligand capable of regulating oocyte quality during IVM. Cross-species transcriptomic analysis revealed that EFNA5 is stably enriched in mammalian oocytes but markedly reduced in in vitro–matured oocytes compared with in vivo counterparts. Using the ovine IVM model, supplementation with recombinant EFNA5 significantly improved blastocyst formation, increased total cell numbers, and reduced apoptosis. Mechanistically, EFNA5 promoted cumulus–oocyte complex expansion, reduced reactive oxygen species accumulation, activated NRF2-dependent antioxidant signaling, and suppressed NF-κB–driven inflammation. RNA-seq and functional validation further confirmed that EFNA5 enhanced redox homeostasis, and decreased DNA damage, collectively improving oocyte developmental potential. These findings establish EFNA5 as a novel and conserved ODF that alleviates oxidative and inflammatory stress to enhance oocyte quality and embryo development, providing mechanistic insight and a potential strategy for improving assisted reproductive technologies.

The efficiency of the laparoscopic ovum pick-up and in vitro embryo production (LOPU-IVEP) system in sheep is influenced by a complex interplay of genetic and environmental factors. This study comprehensively evaluated the effects of breed, season, and their interaction on oocyte retrieval, embryonic development, and pregnancy outcomes. A 20-month longitudinal analysis was conducted on a large commercial cohort comprising five breeds: Black-headed Suffolk (n = 3,024), White-headed Suffolk (n = 699), Australian White (n = 760), Black-headed Dorper (n = 1,109), and East Friesian (n = 1,077). We found that breed was the predominant factor affecting oocyte quantity and initial quality, with East Friesian yielding the highest number of total and available COCs. In contrast, season exerted a stronger influence on developmental competence, with autumn and winter providing optimal conditions, resulting in the highest cleavage rates (64.05%), blastocyst rates (59.02%), and pregnancy rates for single embryo transfer (73.04-75.31%). A significant breed-by-season interaction further identified Black-headed Suffolk in autumn/winter as a superior combination for embryo production. Correlation analysis revealed that oocyte quantity parameters were not predictive of developmental potential or pregnancy success. Our findings advocate for a precision management strategy that aligns the LOPU schedule with breed-specific seasonal advantages to maximize annual embryo production efficiency.