Reproduction performance and phenogram analysis of local swamp buffalo in East Java with a case of inbreeding based on phenotypic and DNA-RAPD characteristics

Abstract

This study identifies the phenotypic and reproduction performance of Indonesian swamp buffalo based on specific characteristics of skin color (gray, dark grey, albino or white, and red-brownish) found in East Java province, Indonesia. This phenotypic variation is thought to be the negative effect of inbreeding. The study included phenotypic identification and DNA characterization by RAPD (Random Amplified Polymorphic DNA) method using OPA 1–4 primers. A sampling from 3 heads of buffalo blood was isolated from Madura Island purposively and a comparison was done with 2 heads of gray buffalo from Malang Regency, East Java, which represented buffalo with normal and abnormal skin coloring. This study also sought to identify the reproductive performance of swamp buffalo in both locations. Data from RAPD–DNA with OPA 1–4 primers were used for genetic similarity analysis. The results showed that there were two heads of white skinned buffalo (7.14 %) in Madura and one head (1.54%) in Malang. Meanwhile, there were five heads of red-brownish buffalo and the rest were normal (gray and grey–dark black, n = 28 and 36 heads respectively). The abnormal phenotype may be a result of simple inheritance of a codominant gene associated with the appearance of the red-brownish phenotype and considered a recessive homozygote for white skin color or these characteristics may have appeared as a result of the qualitative character of the polygenes. The similarity of the red and white buffaloes was 88.9%, while both had a similarity of 85.4% with normal gray/dark grey/black buffalo groups. The availability of males, isolated location, and uncontrolled natural service allows for inbreeding pressure, with possible adverse recessive homozygote characteristics. Advanced DNA analysis is required to more accurately confirm the presence of a skin color inheritance control gene, and it is necessary for a continuous recording to be performed to obtain more evidence of the red or white buffalo skin character traits.