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Single-step genomic best linear unbiased predictor (ssGBLUP) is a method for jointly estimating breeding values (BV) for genotyped and non-genotyped animals. Genomic information in the Italian Mediterranean Buffalo (IMB) is now available and its inclusion in the genetic evaluation system could increase both accuracy and genetic progress of the traits of interest of the breed. The aim of this study was to test the feasibility of ssGBLUP and to present the first results of the implementation of a genomic evaluation for production and type traits in the IMB. Phenotypic information on production (270-day milk, mozzarella yield (MY), protein and fat kg and %, respectively) and morphology: feet and legs (FL) and mammary system (MS) were used for this study. Production records included 743,904 lactations from 276,451 buffalo cows born from 1984 to 2019. Morphological traits were from 91,966 buffalo cows from 2004 to 2022. Regarding the genotypes, a total of 2,017 buffalo cows and 133 bulls were used. Data were analysed fitting two multitrait animal models, a 6-trait model for production data and a 2-trait model for morphology data. According to the relationship matrix used, two models were fitted: (i) the BLUP with the numerator relationship matrix (A); (ii) the ssGBLUP where A and the genomic relationship matrix (G) are blended into H. BV were estimated with BLUP and ssGBLUP models. Three different scenarios were used, according to the cut-off year used to create the partial datasets, namely 2012, 2015 and 2017. In each scenario, correlation, accuracy, dispersion, and bias statistics were calculated (LR method). Both bulls (N=49) and cows (N=1288) were used for validations. On average, correlation between EBVs from partial and whole datasets estimated with BLUP and ssGBLUP increased from 6 to 49% and from 14 to 17% for production and type traits, respectively. Among the traits analysed, the ones most affected by the change were protein/fat content, MY, and AM. The accuracy increase for these traits was above 20% when using the ssGBLUP. All LR statistics improved also for non-genotyped females. These results showed that implementing ssGBLUP in the breeding program can generate more accurate predictions for important traits in dairy IMB than traditional BLUP.

The Italian Mediterranean Buffalo is the most important buffalo’s breeds for milk production and its derivatives, which has a selection program implemented more than 20 years ago. The selection is based on an aggregate index that includes dairy, mozzarella yield, and functional traits. The improvement of udder conformation (UC) traits is an aspect that plays an essential role in udder health and longevity; it is of great interest due to its direct relationship with economic losses caused by mastitis or poor milkability. The aim of this study was the development of an aggregate selection index (ASI) considering MP (milk production), MSCS150 (geometric mean of somatic cell score at 150 days in milk), and UC traits (fore udder attachment– FUA; rear udder width– RUW; rear legs height– RLH; teat direction – TD; teat length – TL and teat position – TP). The first step was to estimate the genetic (co)variances between the UC, MP, and MSCS150 traits and to estimate the relative weight for each UC trait. The phenotypic records of 15,275 females and a pedigree with 43,395 animals were used. A multitrait animal model that included CG (herd-year-calving season), calving month, and parity as fixed effects, and the animal as a random effect was used. The estimated heritability for MP and MSCS150 were 0.391 and 0.134, respectively, and varied between 0.11 and 0.23 for UC traits. Low negative genetic correlations were observed between MP and RLH (−0.119), the same pattern between MSCS150 and RLH (−0.350) and MSCS150 and FUA (−0.220). A positive correlation was found between FUA and MP (0.4272) and MP and RUW (0.645). Using ASI as selection criteria, an annual reduction of −0.03 is expected for MSCS150 and an increase of 0.26 kg for MP. During a selection period of ten years, the expected cumulative genetic gains would be -0.32 for MSCS150 and an increase of MP in 2.57 kg. Selective breeding programs aim to improve specific traits over time by selecting individuals with desirable genetic characteristics as parents of the next generation. According to the results, by focusing on RUW, RLH, and TD traits, genetic improvements are expected to lead to reduced severity of MSCS150 while maintaining or increasing milk production.

In buffalo breeding, calves require special attention and housing systems that provide thermal comfort, good air quality, brightness, and adequate space. Overcrowding, poor ventilation, high temperatures, or improper management of animals can result in increased concentrations of environmental gases such as ammonia (NH3), carbon dioxide (CO 2 ), and hydrogen sulfide (H2 S), altered microclimate parameters, and worsened air quality. The increase in these gases can be problematic for the environment and the calves, whose stress levels can increase and adversely affect the buffalo calves´ nutrition, health, and physiological parameters. During the late spring and early summer season, gas monitoring was carried out in 7 buffalo calf housing spaces in the Campania region, and special measuring instruments were used to measure CO 2 (Portable indoor air quality CO2 meter, Extech instruments), H 2 S and NH3 (Pro gas badge, Industrial scientific) produced by calves. The recording of perceived data was performed continuously and over 15 minutes. Measurements were taken early in the morning before the morning milk feed, and the instruments were positioned at the height of the calves. The calves analysed are all housed in completely closed structures equipped with doors and windows, usually left open in the summer, and closed in the winter. Furthermore, the age range of the animals housed ranges from 0 to 90 days of life, during which the calf mainly takes on reconstituted milk and then is sent towards weaning in the last few weeks. The m 2 available per calf varies on each farm, and all the calves are housed individually. On average, the available space is approximately 100 cm x 1.40 cm. In all structures, the litter used is straw, mandatory for the first two weeks of the calf’s life. In addition, the “Health score” of 300 calves was also evaluated. Score 0 indicated no cough; normal serous discharge or a small amount of unilateral turbid discharge; normal eyes or a small amount of ocular discharge; normal ear, flick ear, or head shake; normal or semi-formed feces; forelimbs entirely covered by bedding when calf lying down. Score 1 indicates coughs on movement; bilateral, excessive, or mucopurulent mucus discharge; moderate or heavy ocular discharge; head tilt or unilateral/bilateral droop; loose or watery feces sifts through the bedding; partially visible or visible forelimbs when the calf is lying down. Each parameter has its score and is considered independent of the other. Finally, as regards the state of cleanliness of the litter, rather than in the calf score, the state of cleanliness of the litters was considered in the data collection regarding the management of the calf house, expressing a judgment such as: “The litter is: kept in good condition; fairly well kept; it is not kept in good condition”. The data collected show that in all calf housing spaces, the estimated NH3 concentrations were in the range of 0 ppm. Only in one particularly overcrowded, the maximum concentration was 1 ppm. For CO 2 levels, the values recorded also never exceeded 1,000 ppm, ranging from a minimum of 678 ppm to a maximum of 946 ppm, and the H 2 S values were 0 ppm in each one. In addition, all buffalo calves evaluated with the calf health score had a score of 0, indicating optimal health conditions. The monitored seven buffalo farms showed adequate attention to environmental conditions, and all the raised buffalo calves showed optimal health status.

Single-step genomic best linear unbiased predictor (ssGBLUP) is a method for jointly estimating breeding values (BV) for genotyped and non-genotyped animals. Genomic information in the Italian Mediterranean Buffalo (IMB) is now available. Its inclusion in the genetic evaluation system could increase both the accuracy and genetic progress of the traits of interest of the breed. The study aimed to test the feasibility of ssGBLUP and show the first results of implementing a genomic evaluation for production and type traits in the IMB. Phenotypic information on production (270-day milk, mozzarella yield (MY), protein and fat kg and %, respectively) and morphology: feet and legs (FL) and mammary system (MS) were used for this study. Production records included 743,904 lactations from 276,451 buffalo cows born from 1984 to 2019. Morphological traits were from 91,966 buffalo cows from 2004 to 2022. Regarding the genotypes, 2,017 buffalo cows and 133 bulls were used. Data were analyzed fitting two multi-trait animal models, a 6-trait model for production data and a 2-trait model for morphology data. According to the relationship matrix used, two models were fitted: (i) the BLUP with the numerator relationship matrix (A) and (ii) the ssGBLUP where A and the genomic relationship matrix (G) are blended into H. BVs were estimated with BLUP and ssGBLUP models. The cutoff year used to create the partial data set was 2012. The correlation, accuracy, dispersion, and bias statistics were calculated (LR method). Both bulls (N=49) and cows (N=1288) were used for validations. On average, the correlation between EBVs from partial and whole datasets estimated with BLUP and ssGBLUP increased from 6 to 49% and from 14 to 17% for production and type traits, respectively. Among the traits analyzed, the most affected by the change were protein/fat content, MY, and AM. The accuracy increase for these traits was above 20% when using the ssGBLUP. All LR statistics also improved for non-genotyped females. These results showed that implementing ssGBLUP in the breeding program can generate more accurate predictions for essential traits in dairy IMB than traditional BLUP.