Imputation accuracy for genomic selection using embryo biopsy samples in Gir

The aim of this study was to establish a platform for genomic selection of in vitro-fertilized (IVF) Gir embryos. Multiple displacement amplification (MDA)-based embryo biopsy samples were genotyped, and genomic estimated breeding values (GEBV) for milk yield (305MY) were calculated. The concordance of GEBV and accuracy between embryo biopsies and the respective liveborn were assessed. Imputation was performed using two panels (Z-Chip and Bovine HD, Illumina) based on a database of 73,110 lactating cow's database and pedigree files from 147,131 animals. Biopsied embryos had similar pregnancy rates (39% vs 40%), pregnancy loss rates (18% vs 20%), and pregnancy length compared to Control embryos. After genotyping, low call rate means were detected for biopsy samples compared to the respective calf samples (0.80 vs 0.98). Imputation presented 0.83 (Z-Chip) and 0.96 (HD) accuracy (CORRanim). Embryo GEBV accuracy levels were higher in BovineHD imputation (0.82) than Z-Chip imputation (0.55) or no imputation (0.62), and the correlation between embryo/calf pairs' accuracy was 0.85 for BovineHD imputation, 0.11 for Z-Chip imputation, and 0.02 for no imputation. GEVB estimates correlation between embryo/calf pairs was 0.87 for BovineHD imputation, 0.80 for Z-Chip imputation, and 0.41 before imputation. The call rate of embryo samples did not affect the correlation between embryo/calf pairs for accuracy and GEBV before and after BovineHD imputation. Embryos obtained on the same farm presented GEBV 305MY differences of up to 800 kg, emphasizing the expected impact of embryo genomic selection for the Gir breed.

Outstanding Gir oocyte donors: How does individual factor affect in vitro embryo production efficiency?

The oocyte donor plays a pivotal role in bovine in vitro embryo production (IVP) success. The individual factor affects blastocyst/oocyte ratio and determine the existence of outstanding performing animals. The aim of this study was to assess the extent of individual factor effect to IVP efficiency, in a population of Gir oocyte donors. Extreme (high or low IVP efficiency based on blastocyst/oocyte ratio) animals were selected out of a population of 250 oocyte donors (1,734 observations) to form high (>0.48, n = 40), average (0.17-0.48, n = 168), and low (<0.17, n = 42) efficiency donor groups. Cumulus-oocyte complex indicators (total number, IVF-grade number, and IVF-grade/total ratio) were lower (p < 0.05) in high efficiency donors. The number of blastocysts per OPU was analyzed for highest performing bull, and an increase (p < 0.05) in high efficiency donors and a decrease (p < 0.05) in low efficiency donors were noticed, compared to average efficiency donors. The number of pregnancies obtained per OPU was affected (p = 0.017) by donor's efficiency (low:0.60 ± 0.09 $$ 0.60\pm 0.09 $$ , average:1.17 ± 0.07 $$ 1.17\pm 0.07 $$ , high:2.57 ± 0.26 $$ 2.57\pm 0.26 $$ ), being 4.3-fold higher in high than in low efficiency donors. We conclude that producing embryos from high efficiency blastocyst/oocyte ratio donors increases blastocyst and pregnancy numbers by OPU, being an important indicator for donor selection in IVP programs.

Genomic breed composition of pure registered Brazilian Gir

INTRODUCTION

Gir is a Bos indicus breed originally from India, first imported to Brazil in 1850. High-performance Dairy Gir has been systematically selected in Brazil from its arrival. Since the major phenotypic difference between Gir in India and Brazil is a higher milk production in the former, it is speculated that Brazilian Gir was strategically crossed with Holstein or another Bos taurus to improve milk yield. This study evaluated the purity of Brazilian Gir breed stocks from BASA Farms in Brazil, trying to identify possible admixture events with other cattle breeds based on DNA analysis.

MATERIALS AND METHODS

The population included 1061 pure registered individuals genotyped using two commercial platforms with 37 k and 25 k SNPs. Admixture analysis was performed individually to estimate levels of genomic composition derived from six different reference populations, three indicine and three taurine breeds.

RESULTS

A Gir ancestry of 99% or higher was found for 94.2% of the population, while the remaining showed levels of non-Gir ancestry up to 6.8%. Only five individuals were identified with possible taurine ancestry, all of them exhibiting levels lower than 2%. The remaining non-Gir ancestry identified was derived from indicine breeds. The levels of admixture observed in the population were from low to non-detectable. No consistent patterns of admixture were observed indicating sustained introgression of taurine lines as means of genetic improvement.

CONCLUSION

According to these results, genetic improvement achieved by Brazilian Gir breeders is the result of within-breed selection methods applied intensively over the past five decades, rather than the result from sustained introgression.

Likelihood of pregnancy after the transfer of embryos derived from follicle aspiration and in vitro embryo production sessions with different relative efficiencies

The aim of the present study was to evaluate the likelihood of pregnancy of in vitro-produced (IVP) embryos from batches with distinct relative efficiencies. Data were retrospectively analyzed from 605 transvaginal ultrasonic-guided follicle aspiration sessions (OPU) followed by in vitro embryo production (IVEP) and 2456 fresh embryo transfers (ET), performed between 2008 and 2012 in individuals of the Gir (dairy Bos indicus) breed. The OPU and IVEP were performed using standard procedures by a single group of technicians at the same laboratory facility. Records were stratified into quartiles (I to IV) according to the total of cumulus-oocytes complexes (COC) produced per donor, or in percentile ranges (0%-25%, 26%-50%, 51%-75%, and 76%-100%) for endpoints related to COC quality or efficiency of embryo production. Pregnancy per embryo transfer (P/ET) was compared among quartiles or ranges using the chi-squared test. Donors producing a greater number of total COC (quartile I) also had more viable and grade I COC, and a greater number of embryos than donors ranked in quartiles II, III or IV, respectively (P < 0.0001). Nevertheless, P/ET did not differ (P > 0.05) among embryos produced by donors ranked in Quartiles I to IV. Similarly, there was no difference (P > 0.05) in P/ET for embryos derived from OPU sessions with a relatively greater or lesser percentage of viable or Grade I COC. Cleavage and blastocyst rates within each IVEP batch had no effect (P > 0.05) on P/ET. In conclusion, data suggest that there is no relationship among oocyte yield after OPU, or efficiency of IVEP, and the likelihood of pregnancy after ET of fresh IVP embryos.