It has been speculated that Indonesian cattle originated from indigenous Bali cattle and that its genetic structure was modified by the successive migration of Indian cattle. In order to study the genetic structure in Indonesian native cattle, the blood protein polymorphism in Bali cattle, Java cattle, Madura cattle, and Filial Ongole cattle were studied. Ten of the 25 loci examined, serum albumin (Alb), serum transferrin (Tf), serum post transferrin (P-tf), serum ceruloplasmin (Cp), serum amylase-I (Am-I), cell carbonic anhydrase (CA), hemoglobin α (Hb-α), hemoglobin β (Hb-β), cell NADH-diaphorase II (Dia-II), and cell peptidase-B (Pep-B) were found to be polymorphic.
The proportion of polymorphic loci and average heterozygosity among the Bali cattle were lower than those among the other Indonesian cattle populations (Madura, Java and Filial Ongole) . The phylogenetic trees and principal component analysis revealed that the Bali cattle were clustered separately from the other three populations. However, specific alleles that were identified in Bali cattle were also found among the Madura, Java and Filial Ongole cattle. We suggest that Bali cattle had introgressed to other indigenous cattle widespread in Indonesia.

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In this paper, for a crossbred population with the pedigree including non-inbred founder groups, an approach to predicting breeding values of animals as a selection criterion in marker-assisted selection is described. The current approach uses trait phenotype and flanking marker information. It allows best linear unbiased estimation of fixed effects such as macroenvironmental effects and best linear unbiased prediction of the random additive effects of the quantitative trait locus marked by flanking markers and of the remaining polygenes. A numerical example is given to illustrate how predicted breeding values for animals can be obtained with the current approach. The current approach could theoretically be a fundamental procedure of choice in genetically evaluating candidate animals for marker-assisted selection for quantitative traits in the crossbred population of concern.

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