LEARNING The objectives of BIOS 781 are to present: OBJECTIVES: 1. basic population and quantitative genetic principles, including classical genetics, chromosomal theory of inheritance, and meiotic recombination 2. an exposure to QTL mapping methods of complex quantitative traits and linkage methods to detect co-segregation with disease 3. methods for assessing marker-disease linkage disequilibrium, including case-control approaches 4. methods for genome-wide association and stratification control.

Genetic Data Analysis

Domestication of livestock species and a long history of migrations, selection and adaptation have created an enormous variety of breeds. Conservation of these genetic resources relies on demographic characterization, recording of production environments and effective data management. In addition, molecular genetic studies allow a comparison of genetic diversity within and across breeds and a reconstruction of the history of breeds and ancestral populations. This has been summarized for cattle, yak, water buffalo, sheep, goats, camelids, pigs, horses, and chickens. Further progress is expected to benefit from advances in molecular technology.

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Genetic diversity in farm animals--a review.

Handbook of enzyme electrophoresis in human genetics

Genetic variation at 59 protein coding loci (16 polymorphic) and 25 microsatellite loci was analysed for 11 indigenous south-east Asian goat populations, and the Australian feral population, to determine the magnitude of genetic differentiation and the genetic relationships among the populations. Significant deviations from Hardy–Weinberg equilibrium were detected in one or more populations for eight of the nine protein loci with codominant alleles, and for microsatellites for all except the two Sri Lankan populations and for all but four loci. For both marker types, average inbreeding coefficients (FIS) were exceptionally high. Heterogeneity of deviations from Hardy–Weinberg equilibrium for the microsatellites showed no differences for among loci within populations as compared with among populations within loci. For protein loci, however, the former was higher, indicating selection affecting allele frequencies at some loci. The variance among protein loci was significantly higher than among microsatellite loci, further indicating selection at some protein loci. There was significant differentiation among populations for both protein and microsatellite loci, most likely reflecting the geography of south-east Asia, and the presumed spread of goats throughout the region. Phylogenies derived from pair-wise genetic distance estimates show some similar clustering for the microsatellite and protein based trees, but bootstrap support was generally low for both. A phylogeny based on the combined set of 38 protein and microsatellite loci showed better consistency with geography and higher bootstrap values. The genetic distance phylogeny and the Weitzman diversity tree derived from microsatellite data showed some identical clusters, and both identified the Ujung Pandang and Australia populations as contributing most to overall genetic diversity.

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Genetic variation within and relationships among populations of Asian goats (Capra hircus)

Twenty-seven microsatellite loci were used to define genetic variation and relationships among eight Indian riverine buffalo breeds. The total number of alleles ranged from 166 in the Toda breed to 194 each in the Mehsana and the Murrah. Significant departures from the Hardy–Weinberg equilibrium were observed for 26 locus-breed combinations due to heterozygote deficiency. Breed differentiation was analysed by estimation of FST index (values ranging from 0.75% to 6.00%) for various breed combinations. The neighbour-joining tree constructed from chord distances, multidimensional scaling (MDS) display of FST values and Bayesian clustering approach consistently identified the Toda, Jaffarabadi, and Pandharpuri breeds as one lineage each, and the Bhadawari, Nagpuri, Surati, Mehsana and Murrah breeds as admixture. Analysis of molecular variance refuted the earlier classification of these breeds proposed on the basis of morphological and geographical parameters. The Toda buffaloes, reared by a tribe of the same name, represent an endangered breed from the Nilgiri hills in South India. Divergence time of the Toda buffaloes from the other main breeds, calculated from Nei's standard genetic distances based on genotyping data on seven breeds and 20 microsatellite loci, suggested separation of this breed approximately 1800–2700 years ago. The results of the present study will be useful for development of rational breeding and conservation strategies for Indian buffaloes.

Genetic variation and relationships among eight Indian riverine buffalo breeds.

Genetic variation at 53 protein-coding loci (25 polymorphic) was analysed for 17 water buffalo populations-12 swamp, three Lankan and two of the Murrah breed (river type), to determine the magnitude of genetic differentiation and the genetic relationships among the populations. In accord with previous cytological studies, the Lankan buffalo clearly are river type. Significant deviations from Hardy-Weinberg equilibrium were shown for a number of locus-population combinations, with all populations but one showing significant heterogeneity in these deviations among loci. By contrast, heterogeneity among populations for each locus was much less, indicating locus-specific deviations, which suggest selection affecting allele frequencies at some loci. There was significant genetic differentiation among populations of both the swamp and river types. The differentiation among the swamp populations may reflect the geography of south-east Asia and the presumed spread of the swamp buffalo through this region. Phylogenies derived from pairwise genetic distance estimates show the clear separation of swamp and river types, but the topology of the swamp populations shows rather poor consistency with their geographic locations. For at least one population (Australia), it is clear that bottleneck effects have distorted the phylogenetic topology. Average genetic distances for both the swamp and river types, as compared with previous studies of livestock breeds, show that the genetic differentiation of each of these sets of populations is of the same order of magnitude as that among well-recognized and established breeds of other species.

Genetic variation within and relationships among populations of Asian water buffalo (Bubalus bubalis)

We have developed the methodologies for typing and family studies to establish the modes of inheritance of water buffalo red cell acid phosphatase (Acp), protease inhibitor (Pi), and group-specific component (Gc) on isoelectric focusing and albumin (Alb), red cell alpha-esterase-3 (Est-3), and catalase (Cat) on polyacrylamide gel electrophoresis. Family studies showed that Pi, Gc, Alb, and Cat are coded by autosomal genes with two codominant alleles, while Est-3 is autosomal with two codominant alleles and a recessive null allele and Acp exhibits three codominant alleles.

Genetic studies of water buffalo blood markers. I. Red cell acid phosphatase, albumin, catalase, red cell alpha-esterase-3, group-specific component, and protease inhibitor.

Nine populations of three species ofNephotettix (Insecta: Hemiptera) from Peninsular Malaysia were analysed for nine enzymes comprising 11 loci. Nei's (Genetics 89, 583, 1978) genetic distance,D, betweenN. virescens andN. malayanus was 0.181, that betweenN. virescens andN. nigropictus was 0.283, and that betweenN. malayanus andN. nigropictus was 0.203. The genetic distance betweenN. nigropictus from rice plant and from the weed-grassL. hexandra at Universiti Pertanian Malaysia was 0.004 and their genetic identity was 0.996, thus indicating that this insect species feeds on both host plants. The proportion of polymorphic loci and the observed heterozygosities were higher inN. nigropictus, with a wider range of host plants, than inN. virescens andN. malayanus, restricted to rice andL. hexandra, respectively.

Biochemical genetic studies on wild populations of three species of green leafhoppers,Nephotettix, from peninsular Malaysia

To determine the genetic diversity of water buffaloes Bubalus bubalis, which underpins their genetic well-being over time, as well as efforts to improve their meat and milk yields, it is necessary first to estimate the genetic distances within and between populations of various geographical locations. Electrophoretic techniques provide the means to do this by estimating gene frequencies for polymorphic genetic markers. Cellulose acetate electrophoresis, the technique employed in this study, allows rapid and efficient screening for the presence of polymorphism in an enzyme (Tan et al., 1989). Makaveev (1978) has shown, using starch gel electrophoresis and family studies, that water buffalo malate dehydrogenase is encoded by a locus with two codominant alleles, M D H A and M D H B. Iorio and Annunziata (1986), using cellulose acetate electrophoresis, reported that the three water buffalo carbonic anhydrase phenotypes they observed were encoded by codominant alleles, CA F and CA s, but no family study was done to confirm this interpretation. Esterase D of water buffaloes was reported by Tan et al. (1980) to be polymorphic and encoded by two codominant alleles, E S D V and E S D s, on starch gel electrophoresis but no family data were available. In this paper family studies on animals with known pedigrees were conducted to ascertain whether the polymorphic genetic markers that we

O. S. Selvaraj

Papers

Genetic variation within and relationships among populations of Asian water buffalo (Bubalus bubalis)

Genetic studies of water buffalo blood markers. I. Red cell acid phosphatase, albumin, catalase, red cell alpha-esterase-3, group-specific component, and protease inhibitor.

Biochemical genetic studies on wild populations of three species of green leafhoppers,Nephotettix, from peninsular Malaysia

Genetic studies of water buffalo blood markers. II. Carbonic anhydrase, esterase D, malate dehydrogenase, and malic enzyme.