Sequencing the mosaic genome of Brahman cattle identifies historic and recent introgression including polled

Koufariotis, Lambros T.; Hayes, Ben J.; Kelly, Matthew; Burns, B. M.; Lyons, Rebecca; Stothard, Paul; Chamberlain, Amanda J.; Moore, S. S.

doi:10.1038/s41598-018-35698-5

Cited by 41 publications

(57 citation statements)

References 56 publications

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“…In the USA, the import of zebu led to the development of the popular transboundary Brahman zebu breed, which has taurine mtDNA as well as an autosomal taurine ancestry of 9% (Koufariotis et al . 2018). Zavarez et al .…”

Section: Domestication Dispersal and Differentiation Of Breedsmentioning

confidence: 99%

Evolution and domestication of the Bovini species

et al. 2020

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Summary Domestication of the Bovini species (taurine cattle, zebu, yak, river buffalo and swamp buffalo) since the early Holocene (ca. 10 000 BCE) has contributed significantly to the development of human civilization. In this study, we review recent literature on the origin and phylogeny, domestication and dispersal of the three major Bos species – taurine cattle, zebu and yak – and their genetic interactions. The global dispersion of taurine and zebu cattle was accompanied by population bottlenecks, which resulted in a marked phylogeographic differentiation of the mitochondrial and Y‐chromosomal DNA. The high diversity of European breeds has been shaped through isolation‐by‐distance, different production objectives, breed formation and the expansion of popular breeds. The overlapping and broad ranges of taurine and zebu cattle led to hybridization with each other and with other bovine species. For instance, Chinese gayal carries zebu mitochondrial DNA; several Indonesian zebu descend from zebu bull × banteng cow crossings; Tibetan cattle and yak have exchanged gene variants; and about 5% of the American bison contain taurine mtDNA. Analysis at the genomic level indicates that introgression may have played a role in environmental adaptation.

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Section: Domestication Dispersal and Differentiation Of Breedsmentioning

confidence: 99%

Evolution and domestication of the Bovini species

et al. 2020

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“…A genome-wide alignment of DNA fragments from a B. taurus individual differs from the Herefordbased reference sequence at between 7 and 8 million single nucleotide polymorphisms (SNPs) and small (<50 bp) insertions and deletions (Indels) [12,13]. The number of differences is higher for DNA samples with greater divergence from the reference [14,15].…”

Section: Introductionmentioning

confidence: 99%

Bovine breed-specific augmented reference graphs facilitate accurate sequence read mapping and unbiased variant discovery

Crysnanto

Pausch

2019

Preprint

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BackgroundThe current bovine genomic reference sequence was assembled from the DNA of a Hereford cow.The resulting linear assembly lacks diversity because it does not contain allelic variation. Lack of diversity is a drawback of linear references that causes reference allele bias. High nucleotide diversity and the separation of individuals by hundreds of breeds make cattle ideally suited to investigate the optimal composition of variation-aware references. ResultsWe augment the bovine linear reference sequence (ARS-UCD1.2) with variants filtered for allele frequency in dairy (Brown Swiss, Holstein) and dual-purpose (Fleckvieh, Original Braunvieh) cattle breeds to construct either breed-specific or pan-genome reference graphs using the vg toolkit. We find that read mapping is more accurate to variation-aware than linear references if pre-selected variants are used to construct the genome graphs. Graphs that contain random variants do not improve read mapping over the linear reference sequence. Breed-specific augmented and pangenome graphs enable almost similar mapping accuracy improvements over the linear reference.We construct a whole-genome graph that contains the Hereford-based reference sequence and 14 million alleles that have alternate allele frequency greater than 0.03 in the Brown Swiss cattle breed.We show that our novel variation-aware reference facilitates accurate read mapping and unbiased sequence variant genotyping for SNPs and Indels. ConclusionsWe developed the first variation-aware reference graph for an agricultural animal: https://doi.org/10.5281/zenodo.3570312. Our novel reference structure improves sequence read mapping and variant genotyping over the linear reference. Our work is a first step towards the transition from linear to variation-aware reference structures in species with high genetic diversity and many sub-populations.

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“…Here we demonstrate a new approach that yielded haplotype-resolved Brahman and Angus cattle genomes from an F1 hybrid of the two subspecies. Our analyses demonstrated that previous studies which mapped indicine sequences onto the taurine reference UMD3.1.1 4,11 likely inflated the number of genetic variants that are present between the two subspecies by up to 4%.…”

Section: Discussionmentioning

confidence: 58%

“…Here we demonstrate a new approach that yielded highly contiguous, haplotype-resolved Brahman and Angus cattle genomes from an F1 hybrid of the two subspecies. Our analyses demonstrated that previous studies which mapped indicine sequences onto the taurine reference UMD3.1.1 4,11 likely inflated the number of genetic variants that are present between the two subspecies by up to 4%. Calling SNPs in transcripts from a diploid hybrid with both haplo-genomes decoded provides accurately phased transcripts for studies on the role of allele-specific expression in, e.g., hybrid vigor or heterosis.…”

Section: Discussionmentioning

confidence: 58%

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Haplotype-Resolved Cattle Genomes Provide Insights Into Structural Variation and Adaptation

Tearle

et al. 2019

Preprint

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We present high quality, phased genome assemblies representative of taurine and indicine cattle, subspecies that differ markedly in productivity-related traits and environmental adaptation. We report a new haplotype-aware scaffolding and polishing pipeline using contigs generated by the trio binning method to produce haplotype-resolved, chromosomelevel genome assemblies of Angus (taurine) and Brahman (indicine) cattle breeds. These assemblies were used to identify structural and copy number variants that differentiate the subspecies and we found variant detection was sensitive to the specific reference genome chosen. Six gene families with immune related functions are expanded in the indicine lineage. The very high quality of the assemblies from both sub-species enabled transcripts to be phased to detect allele-specific expression, and to study genome-wide selective sweeps. An indicus-specific extra copy of fatty acid desaturase is under positive selection and may contribute to indicine adaptation to heat and drought. MainAbout 10,000 years ago, cattle were domesticated from the aurochs which ranged across Eurasia and North Africa but are now extinct 1 . Modern day cattle belong to two subspecies, the humped zebu or indicine breeds (Bos taurus indicus) and the humpless taurine breeds (Bos taurus taurus), which arose from independent domestication events of genetically distinct aurochs populations 2 .During the last century, taurine breeds have been intensively selected for production traits, particularly milk and/or meat yield and quality, and generally have higher fertility than indicine breeds. European taurine breeds, such as Angus, have excellent carcass and meat quality, high fertility, and reach puberty early. These breeds have been imported by farmers around the world to improve or replace less-productive breeds. However, while European taurine animals are well adapted to temperate environments, they do not thrive and perform in hot, humid tropical environments with high disease and parasite burden.Indicine breeds originate from the Indus valley and later spread to Africa and across southeast Asia 3 . Between 1854 and 1926, the four indicine breeds, Ongole, Krishna, Gir and Gujarat, were imported into the United States and crossed with European taurine cattle to create the Brahman breed. Current US Brahman cattle retain ~10% of their genome of taurine origin 4 . Brahman have short, thick, glossy coat that reflects sunlight and loose skin that increases the body surface area exposed for cooling. While the Brahman are less productive and have lower fertility than taurine breeds, they have desirable traits, such as heat tolerance, and lower susceptibility to parasites such as ticks, and are disease and drought resistant 5 .We previously demonstrated a novel trio binning approach to assemble haplotypes of diploid individuals at the contig level. The quality of the contigs exceeded those of the best livestock reference genomes 6 . Here we present chromosome-level taurine (Angus) and indicine (Brahman) cattle ge...

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Sequencing the mosaic genome of Brahman cattle identifies historic and recent introgression including polled

Cited by 41 publications

References 56 publications

Evolution and domestication of the Bovini species

Evolution and domestication of the Bovini species

Bovine breed-specific augmented reference graphs facilitate accurate sequence read mapping and unbiased variant discovery

Haplotype-Resolved Cattle Genomes Provide Insights Into Structural Variation and Adaptation

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