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The objectives of the current study were to detect putative genomic loci and to identify candidate genes associated with milk production traits in Egyptian buffalo. A total number of 161 479 daily milk yield (DMY) records and 60 318 monthly measures for fat and protein percentages (FP and PP, respectively), along with fat and protein yields (FY and PY, respectively) from 1670 animals were used. Genotyping was performed using Axiom® Buffalo Genotyping 90 K array. Genome-wide association study (GWAS) for each trait was performed using PLINK. After Bonferroni correction, 47 SNPs were associated with one or more milk production traits. These SNPs were distributed over 36 quantitative trait loci (QTL) and located on 20 buffalo chromosomes (BBU). For the 47 SNPs, one was overlapped for three traits (DMY, FY, and PY), six were associated with two traits (one for PP and PY and five for FY and PY) while the rest were associated with only one trait. Out of 36 identified QTL, eleven were overlapped with previously reported loci in buffalo and/or cattle populations. Some of these SNPs are placed within or close to potential candidate genes, for example: TPD52, ZBTB10, RALYL and SNX16 on BBU15, ADGRD1 on BBU17, ESRRG on BBU5 and GRIP1 on BBU4. This is the first reported study between genome-wide markers and milk components in Egyptian buffalo. Our findings provide useful information to explore the genetic mechanisms and relevant genes contributing to the variation in milk production traits. Further confirmation studies with larger population size are necessary to validate the findings and detect the causal genetic variants.

Prenatal mortality is one of the most important causes of production losses in the livestock industry. This study shed lights on the prevalence of abortion and stillbirth, and postnatal mortality up to six months in five buffalo herds (6169 pregnancy cases) to determine the effect of some non-genetic factors on the incidence of the three disorders in five buffalo herds in Egypt. These factors included the effect of farm, year, season and parity on abortion as well as dam's weight at calving, and sex, weight and age (at death) of calves on stillbirth and mortality rate..Results showed that percentage of pre-and post-natal losses was 16%,, representing 1.33% abortion, 3.65% stillbirth and 11.05% for postnatal mortality upto six months of age. The incidence of abortion was affected (P<0.001) by season, year, dam's parity, and the farm. The same factors in addition to calf's weight exerted significant (P<0.001) effects on the rate of stillbirth but dam's weight at calving did not show any significant effect (P≥0.05). Incidence of mortality was significantly (P<0.001) affected by season, year, parity, dam's weight at calving, calf's age and weight at death, and farm.This study put more emphasis on the importance of non-genetic effects as the main contributors impacting productive and reproductive performance of buffaloes. Farm conditions, herd management and policy have pronounced effects on the incidence of abortion, stillbirths, and postnatal mortality. The results of this study could be useful to enhancing productive and reproductive performance in large or small sized buffalo herds.

The aim of the present genome-wide association study (GWAS) was to identify single nucleotide polymorphisms (SNPs) and candidate genes associated with lactose percentage (LP) and lactose yield (LY) in Egyptian buffalo. The phenotypic dataset included 60,318 monthly measures for LP and LY from 1481 animals. A total number of 114 animals with high and low deviated performance were selected for genotyping with Axiom Buffalo Genotyping 90K Array. Genome-wide analysis was performed using a single marker regression. The GWAS revealed 32 significant and seven suggestive SNPs for LP, however; only two suggestive SNPs were identified for LY. The identified genomic regions are overlapped with previously reported QTL in different cattle breeds. In addition, novel genomic loci were detected. The identified genomic regions harbored many candidate genes with biological roles associated with milk production traits, such as TPD52 and ZBTB10 on chromosome 15; AADAT and GALNTL6 on chromosome 3 and COL8A1 and PLOD2 on chromosome 1. Our findings provide the basis to uncover the key markers and candidate genes affecting lactose traits which facilitate the exploration of the genetic mechanisms that control lactose traits variation in Egyptian buffalo.

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