Molecular dissection of a quantitative trait locus: a phenylalanine-to-tyrosine substitution in the transmembrane domain of the bovine growth hormone receptor is associated with a major effect on milk yield and composition.

Genetic effects for many dairy traits and for total economic merit are evenly distributed across all chromosomes. A high-density scan using 38,416 single nucleotide polymorphism markers for 5,285 bulls confirmed 2 previously known major genes on Bos taurus autosomes (BTA) 6 and 14 but revealed few other large effects. Markers on BTA18 had the largest effects on calving ease, several conformation traits, longevity, and total merit. Prediction accuracy was highest using a heavy-tailed prior assuming that each marker had an effect on each trait, rather than assuming a normal distribution of effects as in a linear model, or that only some loci have nonzero effects. A prior model combining heavy tails with finite alleles produced results that were intermediate compared with the individual models. Differences between models were small (1 to 2%) for traits with no major genes and larger for heavy tails with traits having known quantitative trait loci (QTL; 6 to 8%). Analysis of bull recessive codes suggested that marker effects from genomic selection may be used to identify regions of chromosomes to search in detail for candidate genes, but individual single nucleotide polymorphisms were not tracking causative mutations with the exception of diacylglycerol O-acyltransferase 1. Additive genetic merits were constructed for each chromosome, and the distribution of BTA14-specific estimated breeding value (EBV) showed that selection primarily for milk yield has not changed the distribution of EBV for fat percentage even in the presence of a known QTL. Such chromosomal EBV also may be useful for identifying complementary mates in breeding programs. The QTL affecting dystocia, conformation, and economic merit on BTA18 appear to be related to calf size or birth weight and may be the result of longer gestation lengths. Results validate quantitative genetic assumptions that most traits are due to the contributions of a large number of genes of small additive effect, rather than support the finite locus model.

Distribution and location of genetic effects for dairy traits.

The present study was carried out to identify genome-wide genetic markers and variants in candidate genes for production and reproduction traits in Sahiwal cattle using a cost-effective reduced representation sequencing method. A total of 258,231 genome-wide SNPs were identified in Sahiwal cattle with reference to Bos indicus genome, of which 150,231 were novel SNPs. Among the high-confidence SNPs identified, 91.86% and 27.30% were genotyped in 50% and 100% of the samples. Mapping of the identified SNPs revealed 525 SNPs in candidate genes related to production traits while 333 SNPs were mapped to candidate genes related to reproduction traits. The SNPs identified in this study will facilitate further insights on tropical adaptation, domestication history and population structure of indigenous cattle. The variants in candidate genes identified in this study will serve as useful genetic tools, in the quest for phenotype modifying nucleotide change and help in designing appropriate genetic improvement programs.

Genome-wide discovery of SNPs in candidate genes related to production and fertility traits in Sahiwal cattle

Genomic diversity and selection sweeps identified in Indian swamp buffaloes reveals it's uniqueness with riverine buffaloes.

Genomic and transcriptomic landscape of the Indian Water Buffalo (Bubalus bubalis)

Genomewide identification and annotation of SNPs in Bubalus bubalis.

The present study focused upon identification of genome-wide SNPs through the reduced representation approach and to study the genomic divergence of the Indian yak populations. A total of 80 samples belonging to Arunachali yak (N = 20), Himachali yak (N = 20), Ladakhi yak (N = 20) and Sikkimi yak (N = 20) of India were used in the study. The results of the study revealed a total of 579575 high quality SNPs along with 50319 INDELs in the Indian yaks. The observed heterozygosity was found to be high in Himachali yak, followed by Arunachali yak, Ladakhi yak and Sikkimi yaks. The Sikkimi yaks was found to be genetically distant, followed by Ladakhi yaks which was observed to have some few individuals from Arunachali and Himachali yaks. Arunachali and Himachali yaks are found to get clustered together and are genetically similar. The study provides evidence about the genomic diversity in the Indian yak populations and information generated in the present study may help to formulate a suitable breeding plan for endangered Indian yaks. Moreover, the unique yak populations identified in the study will further help to focus attention for future characterization and prioritization of the animals for conservation purposes through the ddRAD approach.

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M. S. Tantia

Papers

Genomewide identification and annotation of SNPs in Bubalus bubalis.

Genome-wide discovery of SNPs in candidate genes related to production and fertility traits in Sahiwal cattle

Genomic divergence reveals unique populations among Indian Yaks.