A review of the pangenome: how it affects our understanding of genomic variation, selection and breeding in domestic animals?

Y Gong, Y Li, X Liu, Y Ma, L Jiang - Journal of Animal Science and …, 2023 - Springer
As large-scale genomic studies have progressed, it has been revealed that a single
reference genome pattern cannot represent genetic diversity at the species level. While …

Assembly of a pangenome for global cattle reveals missing sequences and novel structural variations, providing new insights into their diversity and evolutionary …

Y Zhou, L Yang, X Han, J Han, Y Hu, F Li… - Genome …, 2022 - genome.cshlp.org
A cattle pangenome representation was created based on the genome sequences of 898
cattle representing 57 breeds. The pangenome identified 83 Mb of sequence not found in …

The application of genome-wide SNP genotyping methods in studies on livestock genomes

A Gurgul, E Semik, K Pawlina, T Szmatoła… - Journal of applied …, 2014 - Springer
Animal genomics is currently undergoing dynamic development, which is driven by the
flourishing of high-throughput genome analysis methods. Recently, a large number of …

[HTML][HTML] Pangenome obtained by long-read sequencing of 11 genomes reveal hidden functional structural variants in pigs

YF Jiang, S Wang, CL Wang, RH Xu, WW Wang… - Iscience, 2023 - cell.com
Long-read sequencing (LRS) facilitates both the genome assembly and the discovery of
structural variants (SVs). Here, we built a graph-based pig pangenome by incorporating 11 …

Towards the complete goat pan-genome by recovering missing genomic segments from the reference genome

R Li, W Fu, R Su, X Tian, D Du, Y Zhao, Z Zheng… - Frontiers in …, 2019 - frontiersin.org
It is broadly expected that next generation sequencing will ultimately generate a complete
genome as is the latest goat reference genome (ARS1), which is considered to be one of the …

The Bovine Pangenome Consortium: democratizing production and accessibility of genome assemblies for global cattle breeds and other bovine species

TPL Smith, DM Bickhart, D Boichard, AJ Chamberlain… - Genome biology, 2023 - Springer
Abstract The Bovine Pangenome Consortium (BPC) is an international collaboration
dedicated to the assembly of cattle genomes to develop a more complete representation of …

[HTML][HTML] Genetic resources, genome mapping and evolutionary genomics of the pig (Sus scrofa)

K Chen, T Baxter, WM Muir, MA Groenen… - International Journal of …, 2007 - ncbi.nlm.nih.gov
The pig, a representative of the artiodactyla clade, is one of the first animals domesticated,
and has become an important agriculture animal as one of the major human nutritional …

Genome-wide SNP data unveils the globalization of domesticated pigs

B Yang, L Cui, M Perez-Enciso, A Traspov… - Genetics Selection …, 2017 - Springer
Background Pigs were domesticated independently in Eastern and Western Eurasia early
during the agricultural revolution, and have since been transported and traded across the …

Building a sequence map of the pig pan-genome from multiple de novo assemblies and Hi-C data

X Tian, R Li, W Fu, Y Li, X Wang, M Li, D Du… - Science China Life …, 2020 - Springer
Pigs were domesticated independently in the Near East and China, indicating that a single
reference genome from one individual is unable to represent the full spectrum of divergent …

[HTML][HTML] Whole-genome resequencing analysis of Hanwoo and Yanbian cattle to identify genome-wide SNPs and signatures of selection

JW Choi, BH Choi, SH Lee, SS Lee, HC Kim, D Yu… - Molecules and cells, 2015 - Elsevier
Over the last 30 years, Hanwoo has been selectively bred to improve economically
important traits. Hanwoo is currently the representative Korean native beef cattle breed, and …