Researchers : A.J. Salces, J.B. Banayo, K.M. Umali and K.C.B. Tenorio

June 1, 2015 – May 31, 2016

UPLB-FI, USAID STRIDE

ABSTRACT

The project validated a genomic DNA extraction protocol from cattle hair and blood. Tail hair samples were obtained from 86 commercial hybrid cattle (SahiwalHolstein) from Real Fresh Dairy Farms, Inc., Bay, Laguna and 124 Siquijor native cattle from the Ubay Stock Farm, Ubay, Bohol. DNA were extracted successfully from hair follicles of Siquijor native cattle and the Sahiwal-Holstein hyrbid and was subsequently used for PCR-RFLP genotyping. The project also developed a PCR- RFLP protocol for cattle genotyping to select animals with superior cheese making properties (elite animals). The Siquijor native cattle group showed a higher frequency (0.93) of the B allele compared to the Sahiwal Holstein group. B variants of the betalactoglobulin gene has been found to be favourable for milk coagulation and cheese making (Allmere et al. 1998). Based on the combined kappa-casein and beta- lactoglobulin genotypes favorable for cheese production, we were able to rank the native animals. Of which, we further genotyped the top 25 using PCR-Sequencing technique to identify SNP markers present in select genes. Blood samples of native cattle from Batanes, Siquijor, Iloilo and Mindanao genetic groups were collected by needle puncture from the jugularvein using vacutainer with EDTA. DNA were succesfully extracted from blood samples of Batanes, Siquijor, Iloilo and Mindanao genetic groups using commercial DNA extraction kit. To analyze putative SSR markers, DNA from Philippine native cattle representing four genetic groups were sent for whole genome sequencing. DNA (2.5 μg) from each genetic group was sent to Australian Genome Research Facility (AGRF), however the Batanes group failed the AGRF QC test due to the low concentration of DNA. Library preparation was recently completed for two samples (Siquijor and Mindanao genetic groups) and forwarded to clustering step. The sequencing results is expected to arrive by July. Bioinformatics analysis will be done by Julian Villela from the Philippine Genome Center in Phase 2. Focused group discussions with the Siquijor farmers were conducted in order to identify problems and constraints in current dairy production practices and determine their selection criteria in dairying in order to develop breeding objectives for small hold dairy cattle breeding program.
Production environment survey and market survey were done to derive the economic values and come up with the breeding objectives for commercial dairy breeding program.