Genetic Basis of Dorper Sheep (Ovis aries) Revealed by Long-Read De Novo Genome Assembly

Abstract

Dorper sheep (Ovis aries) (DPS), developed in the 1930s by crossing Dorset Horn and Blackhead Persian sheep in South Africa, is a world-famous composite breed for mutton production. The genetic basis underlying this breed is yet to be elucidated. Here, we report the sequencing and assembly of a highly contiguous Dorper sheep genome via integration of Oxford Nanopore Technology (ONT) sequencing and Hi-C (chromatin conformation capture) approaches. The assembled genome was around 2.64 Gb with a contig N50 of 73.33 Mb and 140 contigs in total. More than 99.5% of the assembled sequences could be anchored to 27 chromosomes and they were annotated with 20,450 protein-coding genes. Allele-specific expression (ASE) genes of Dorper sheep were revealed through ASE analysis and they were involved in the immune system, lipid metabolism, and environmental adaptation. A total of 5,701 and 456 allelic sites were observed in the SNP and indels loci identified from relevant whole-genome resequencing data. These allelic SNP and INDEL sites were annotated in 1,002 and 294 genes, respectively. Moreover, we calculated the number of variant sites and related genes derived from the maternal and paternal ancestors, revealing the genetic basis of outstanding phenotypic performance of Dorper sheep. In conclusion, this study reports the first reference genome of Dorper sheep and reveals its genetic basis through ASE. This study also provides a pipeline for mining genetic information of composite breeds, which has an implication for future hybrid-breeding practices.

Chromosome-level assembly of the Rangifer tarandus genome and validation of cervid and bovid evolution insights

“…To date, animals for which complete chromosome-mapped genomes are available for reference purposes include humans (52), mice (53), Drosophila (54), zebra sh (55), chickens (56), cattle (57), swine (58), sheep (59), and goats (60). However, several wild species of conservation concern have not been fully chromosome-assembled (3,4,6,61).…”

Expression, Polymorphism, and Potential Functional Sites of the BMPR1A Gene in the Sheep Horn

“…Whole-genome sequencing (WGS) data consisted of publicly available and laboratory-collected data. The publicly available data for 3125 sheep were downloaded from NCBI, including PRJNA304478, PRJNA325682, PRJNA479525, PRJNA624020, PRJNA675420, PRJNA822017, PRJNA30931, PRJNA480684, PRJNA509694, PRJNA779188, and PRJNA783661 [ 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 ]. The sample of 3125 sheep was divided into horned and hornless sheep.…”

<strong>Recent Advances in the Genomic Resources for Sheep</strong>

“…Recent advances in long read sequencing technologies, and reductions in cost, have meant that in addition to a single reference genome per farmed animal species it is now possible to generate chromosome level genomes for many different breeds and populations. Many new chromosome level genomes including, for example, Hu sheep (Li et al, 2021), Dorper (Qiao et al, 2022), and Tibetan sheep (Li et al, 2022b) have recently been deposited in NCBI (Table 2). In addition, recently a pangenome for sheep was generated that included new long-read assemblies for 13 different breeds (Li et al, 2022a).…”

“…This is important because it can minimise reference mapping bias when working with short read whole genome sequencing data (Chen et al, 2021). For example, for a study investigating population genomics in sheep from the African continent using short read data, the Dorper (Qiao et al, 2022) a South African breed, would be a more appropriate reference assembly than the European Texel or Rambouillet. However, even when reference genome sequences for multiple different breeds are available the use of reference genome sequences that represent only a single individual, for understanding population diversity at genomic level are still limited.…”