Dataset Information

Genome-wide marker discovery in three South African indigenous cattle breeds (Afrikaner, Drakensberger and Nguni) using whole genome sequencing

ABSTRACT: The aim of this study was to perform genome-wide marker discovery in three South African indigenous cattle breeds through whole genome sequencing of pooled DNA samples, with specific objectives to search for new variants, validate newly identified variants using 1000 Bull Genomes Project data, perform functional annotation and enrichment analysis on identified SNPs, identify selective sweeps and a panel of breed-specific markers to discriminate between breeds

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Bos Indicus

SUBMITTER: Agricultural Research Council-Animal Production

PROVIDER: PRJEB31574 | EVA | 2021-03-06

REPOSITORIES: EVA

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			Action	DRS
	AFR2_novel.accessioned.vcf.gz	Vcf
	AFR2_novel.accessioned.vcf.gz.csi	Vcf
	AFR2_novel.accessioned.vcf.gz.tbi	Vcf
	AFR2_novel.vcf.gz	Vcf
	AFR2_novel.vcf.gz.tbi	Vcf

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Project description:Obese and lean pig breeds showed obvious phenotypic variations and physiological differences in skeletal muscle growth. Prenatal muscle development programs postnatal performance. In this study we initially conducted full transcriptional profiling of prenatal skeletal muscle from Tongcheng pigs (obese) and Landrace pigs (lean) at 33, 65 and 90 days post coitus (dpc), using long serial analysis of gene expression (LongSAGE). We subsequently sequenced 317,115 LongSAGE tags and identified 1400 and 1201 differentially expressed transcripts that showed eight expression patterns for Tongcheng and Landrace, respectively. These two breeds had more significant differences in their gene expression profiles at 65 than that at 33 and 90 dpc. We also identified 532, 653 and 459 transcripts that were differentially expressed at 33, 65 and 90 dpc between the two breeds, respectively. The cellular function of the differentially expressed transcripts that matched annotated genes revealed that each stage had a uniquely altered profile between the two breeds in various functional categories including muscle fiber constitute and contraction, apoptosis, protein synthesis, and signalling transduction. Our results suggest that skeletal muscle development potentially has a greater lag in its growth rate at 33-65 dpc in Tongcheng pigs when compared with their Landrace counterparts. Our analyses therefore not only will provide valuable resources in the further identification of candidate genes for meat production traits, but also assist in the elucidation of the development of prenatal skeletal muscle in pigs and other vertebrates. Keywords: comparative transcriptome analysis Three Tongcheng and Landrace sows were mated with the same boar of each corresponding breed, respectively. The sows were then sacrificed at a commercial slaughterhouse and the uteri containing the embryos were collected immediately. The longissimus muscle tissues were then rapidly dissected from each of the embryos at 33, 65 and 90 dpc for both the Tongcheng and Landrace pigs. These samples were snap-frozen in liquid nitrogen and stored at -80°C until further use in the LongSAGE experiments. For the skeletal muscles from the six different samples, that is, Tongcheng (T33, T65 and T90, respectively) and Landrace (L33, L65 and L90, respectively), equal quantities of total RNA from each individual (n=4) were pooled. Six LongSAGE libraries were subsequently generated using I-SAGETM Long kits (Invitrogen, USA) according to the manufacturer’s instructions. Transforming clones were sequenced with the help of an ABI PRIZM 3730 DNA sequencer.

Dataset Information

Genome-wide marker discovery in three South African indigenous cattle breeds (Afrikaner, Drakensberger and Nguni) using whole genome sequencing

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