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Allele frequencies between Bos taurus and Bos indicus
Data related to Naval-Sanchez et al. 2019 "Selection Signatures in heat-resistant cattle reveal missense mutations in damage response gene HELB".
Whole genome sequences from the 1000 Bull Genomes Project (Run6, Bos taurus, and Bos indicus) for breeds chosen as a reference for imputation were retrieved (Daetwyler et al. 2014; Haye... mores and Daetwyler 2018). This results in 440 whole-genome sequences across 18 cattle breeds.
Breeds were grouped in accordance to their phenotypes and reported genomic crosses as taurine (humpless), indicine (with hump), admixed or African sanga, the two latter being stabilized composite breeds (Rege J 1999; Hanotte et al. 2002; Rege J et al. 2007; Mwai et al. 2015; Felius, Marleen et al. 2016).
The dataset contains 186 European Taurine, 102 Asiatic indicine and 80 cross-bred genomes as well as a set of African samples composed of 12 taurine, 41 sanga and 19 indicine.
Population, Ecological and Evolutionary Genetics
Mapping variant detection and imputation:
Genetic variants from the sequenced animals were extracted and filtered to only keep bi-allelic variants with minimally four copies of the minor allele. Genomes of filtered variants were phased using Eagle (Loh et al. 2016) and imputed using FImpute 2.2 (Sargolzaei et al. 2014). The analysis resulted in the detection of 39,679,303 high-quality SNPs, being 24,080,747 considered common SNPs (MAF >=0.05).
Marina Naval-Sanchez, Laercio R. Porto-Neto, Ben J. Hayes, Hans d. Daetwyler, Antonio Reverter.
Creative Commons Attribution 4.0 International Licence
Agriculture Victoria, AgriBio, Centre for AgriBioscience (Australia), CSIRO (Australia), Queensland Alliance for Agriculture and Food Innovation, The University of Queensland (Australia), School of Applied Systems Biology, La Trobe University (Australia)
Naval Sanchez, Marina; Porto Neto, Laercio; Daetwyler, Hans; Hayes, Ben; Reverter-Gomez, Toni (2019): Allele frequencies between Bos taurus and Bos indicus. v2. CSIRO. Data Collection.
All Rights (including copyright) CSIRO 2019.
The metadata and files (if any) are available to the public.
Bos primigenous taurus; Bos primingenous indicus
Genomic Analytics in the Realm of Big Data (OCE Post-Doc)
SELECTION SIGNATURES IN HEAT-RESISTANT CATTLE REVEAL MISSENSE MUTATIONS IN DAMAGE RESPONSE GENE HELB
Distinct domestication events, adaptation to different climatic zones and divergent selection in productive traits have shaped the genomic differences between taurine and indicine cattle. Here we assessed the impact of artificial selection and envi... moreronmental adaptation by comparing whole-genome sequences from European taurine and Asian indicine breeds as well as in African cattle. Next, we studied the impact of divergent selection making use of predicted and experimental functional annotation in the cattle genome. This revealed regions under selection in indicine cattle displayed significant enrichment for promoters and coding genes. Finally, we studied the impact of selection at nucleotide resolution by measuring allele frequency divergence between European taurine and Asian indicine populations. This identified a total of 10 coding region nucleotides fixed for different alleles between subspecies, nine of which were located within DNA Helicase B (HELB). HELB is involved in damage response including ultra-violet light and related to reproductive traits and yearling weight in Tropical cattle. Mining information from the 1000 Bull Genomes Project, we concluded that HELB carries indicine specific mutations also found in ‘drought’ resistant taurine cattle, including N’Dama, Anatolian Red, Marchigiana, Chianina, Piedmontese. Therefore, HELB is likely to have contributed to the adaptation of cattle to their harsh environment.
Marina Naval Sanchez
Laercio Porto Neto