Genomics Applied to Livestock and Aquaculture Breeding

Overview

Journal Evol Appl

Specialty Biology

Date 2022 May 4

PMID 35505887

Authors

Jose M Yanez

Peng Xu

Roberto Carvalheiro

Ben Hayes

Affiliations

Soon will be listed here.

Abstract

The increasing global demand for food, due to the continuous growth of human population, requires improvements in the efficiency and sustainability of animal production systems. In addition, several challenges facing farming of aquatic and terrestrial organisms need to be overcome to ensure food security in the upcoming decades, e.g. adaptation to climate change, reduced availability of conventional animal feed ingredients, emerging infectious and parasitic diseases, among others. Genomic technologies such as massive parallel sequencing, high-throughput genotyping, genome selection and gene editing, combined with highly efficient computational methods can accelerate the rate of genetic progress in animal breeding. Thus, such technologies can help us meet the needs for protein sources for human consumption in the upcoming years. This Special Issue aims at presenting current advancements in the field of genomic tools applied to aquatic and terrestrial farmed animal populations.

Citing Articles

Genome-wide detection of positive and balancing signatures of selection shared by four domesticated rainbow trout populations (Oncorhynchus mykiss).

Paul K, Restoux G, Phocas F Genet Sel Evol. 2024; 56(1):13.

PMID: 38389056 PMC: 10882880. DOI: 10.1186/s12711-024-00884-9.

Design and validation of a high-density single nucleotide polymorphism array for the Eastern oyster (Crassostrea virginica).

Xuereb A, Nahuelpi R, Normandeau E, Babin C, Laporte M, Mallet A G3 (Bethesda). 2023; 13(6).

PMID: 36966413 PMC: 10234413. DOI: 10.1093/g3journal/jkad071.

GWAS on Imputed Whole-Genome Sequence Variants Reveal Genes Associated with Resistance to in Rainbow Trout ().

Sanchez-Roncancio C, Garcia B, Gallardo-Hidalgo J, Yanez J Genes (Basel). 2023; 14(1).

PMID: 36672855 PMC: 9859203. DOI: 10.3390/genes14010114.

Aquaponics as a Promising Strategy to Mitigate Impacts of Climate Change on Rainbow Trout Culture.

Vasdravanidis C, Alvanou M, Lattos A, Papadopoulos D, Chatzigeorgiou I, Ravani M Animals (Basel). 2022; 12(19).

PMID: 36230264 PMC: 9559468. DOI: 10.3390/ani12192523.

Genomics applied to livestock and aquaculture breeding.

Yanez J, Xu P, Carvalheiro R, Hayes B Evol Appl. 2022; 15(4):517-522.

PMID: 35505887 PMC: 9046759. DOI: 10.1111/eva.13378.

References

Raymond B, Bouwman A, Schrooten C, Houwing-Duistermaat J, Veerkamp R . Utility of whole-genome sequence data for across-breed genomic prediction. Genet Sel Evol. 2018; 50(1):27. PMC: 5960108. DOI: 10.1186/s12711-018-0396-8. View

Agudelo J, Mastrochirico-Filho V, Borges C, Ariede R, Lira L, Neto R . Genomic selection signatures in farmed from tropical and subtropical regions in South America. Evol Appl. 2022; 15(4):679-693. PMC: 9046916. DOI: 10.1111/eva.13351. View

Palaiokostas C, Anjum A, Jeuthe H, Kurta K, Lopes Pinto F, de Koning D . A genomic-based vision on the genetic diversity and key performance traits in selectively bred Arctic charr (). Evol Appl. 2022; 15(4):565-577. PMC: 9046918. DOI: 10.1111/eva.13261. View

Naval-Sanchez M, McWilliam S, Evans B, Yanez J, Houston R, Kijas J . Changed Patterns of Genomic Variation Following Recent Domestication: Selection Sweeps in Farmed Atlantic Salmon. Front Genet. 2020; 11:264. PMC: 7147387. DOI: 10.3389/fgene.2020.00264. View

Marjanovic J, Mulder H, Ronnegard L, de Koning D, Bijma P . Capturing indirect genetic effects on phenotypic variability: Competition meets canalization. Evol Appl. 2022; 15(4):694-705. PMC: 9046766. DOI: 10.1111/eva.13353. View

Goddard M, Hayes B . Mapping genes for complex traits in domestic animals and their use in breeding programmes. Nat Rev Genet. 2009; 10(6):381-91. DOI: 10.1038/nrg2575. View

Hou H, Wang X, Ding W, Xiao C, Cai X, Lv W . Whole-genome sequencing reveals the artificial selection and local environmental adaptability of pigeons (). Evol Appl. 2022; 15(4):603-617. PMC: 9046921. DOI: 10.1111/eva.13284. View

Carvalheiro R, Boison S, Neves H, Sargolzaei M, Schenkel F, Utsunomiya Y . Accuracy of genotype imputation in Nelore cattle. Genet Sel Evol. 2015; 46:69. PMC: 4192291. DOI: 10.1186/s12711-014-0069-1. View

Cadiz M, Lopez M, Diaz-Dominguez D, Caceres G, Marin-Nahuelpi R, Gomez-Uchida D . Detection of selection signatures in the genome of a farmed population of anadromous rainbow trout (Oncorhynchus mykiss). Genomics. 2021; 113(5):3395-3404. DOI: 10.1016/j.ygeno.2021.07.027. View

10.

Houston R, Bean T, Macqueen D, Gundappa M, Jin Y, Jenkins T . Harnessing genomics to fast-track genetic improvement in aquaculture. Nat Rev Genet. 2020; 21(7):389-409. DOI: 10.1038/s41576-020-0227-y. View

11.

VanRaden P . Symposium review: How to implement genomic selection. J Dairy Sci. 2020; 103(6):5291-5301. DOI: 10.3168/jds.2019-17684. View

12.

Georges M, Charlier C, Hayes B . Harnessing genomic information for livestock improvement. Nat Rev Genet. 2018; 20(3):135-156. DOI: 10.1038/s41576-018-0082-2. View

13.

Muniz M, Fonseca L, Scalez D, Vega A, Silva D, Ferro J . Characterization of novel muscle expression profiles associated with meat quality in beef cattle. Evol Appl. 2022; 15(4):706-718. PMC: 9046762. DOI: 10.1111/eva.13365. View

14.

Ni G, Cavero D, Fangmann A, Erbe M, Simianer H . Whole-genome sequence-based genomic prediction in laying chickens with different genomic relationship matrices to account for genetic architecture. Genet Sel Evol. 2017; 49(1):8. PMC: 5238523. DOI: 10.1186/s12711-016-0277-y. View

15.

Sun L, Liu S, Wang R, Jiang Y, Zhang Y, Zhang J . Identification and analysis of genome-wide SNPs provide insight into signatures of selection and domestication in channel catfish (Ictalurus punctatus). PLoS One. 2014; 9(10):e109666. PMC: 4196944. DOI: 10.1371/journal.pone.0109666. View

16.

Xia J, Bai Z, Meng Z, Zhang Y, Wang L, Liu F . Signatures of selection in tilapia revealed by whole genome resequencing. Sci Rep. 2015; 5:14168. PMC: 4570987. DOI: 10.1038/srep14168. View

17.

Xu J, Jiang Y, Zhao Z, Zhang H, Peng W, Feng J . Patterns of Geographical and Potential Adaptive Divergence in the Genome of the Common Carp (). Front Genet. 2019; 10:660. PMC: 6640160. DOI: 10.3389/fgene.2019.00660. View

18.

Cubric-Curik V, Novosel D, Brajkovic V, Rota Stabelli O, Krebs S, Solkner J . Large-scale mitogenome sequencing reveals consecutive expansions of domestic taurine cattle and supports sporadic aurochs introgression. Evol Appl. 2022; 15(4):663-678. PMC: 9046920. DOI: 10.1111/eva.13315. View

19.

Yoshida G, Lhorente J, Correa K, Soto J, Salas D, Yanez J . Genome-Wide Association Study and Cost-Efficient Genomic Predictions for Growth and Fillet Yield in Nile Tilapia (). G3 (Bethesda). 2019; 9(8):2597-2607. PMC: 6686944. DOI: 10.1534/g3.119.400116. View

20.

Paul K, DAmbrosio J, Phocas F . Temporal and region-specific variations in genome-wide inbreeding effects on female size and reproduction traits of rainbow trout. Evol Appl. 2022; 15(4):645-662. PMC: 9046919. DOI: 10.1111/eva.13308. View