Genomics applied to livestock and aquaculture breeding

Yáñez, José M.; Xu, Peng; Carvalheiro, Roberto; Hayes, Ben J.

doi:10.1111/eva.13378

Cited by 16 publications

(8 citation statements)

References 66 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Genetic improvement via selective breeding is one of the most important approaches currently used to enhance production of farmed species ( Yáñez et al 2022b ). Selective breeding practices are widely used for genetic improvement of livestock but their adoption in aquaculture has been slower, especially for shellfish ( Gjedrem et al 2012 ; Houston et al 2020 ).…”

Section: Introductionmentioning

confidence: 99%

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

Xuereb

Marin-Nahuelpi

Normandeau

et al. 2023

G3: Genes, Genomes, Genetics

Self Cite

View full text Add to dashboard Cite

Dense single nucleotide polymorphism (SNP) arrays are an essential tool for rapid high-throughput genotyping for many genetic analyses, including genomic selection and high-resolution population genomic assessments. We present a high-density (200K) SNP array developed for the Canadian Eastern oyster (Crassostrea virginica), which is a species of significant aquaculture production and restoration efforts throughout its native range. SNP discovery was performed using low-coverage whole-genome sequencing of 435 F1 oysters from families from 11 founder populations in New Brunswick, Canada. An Affymetrix Axiom Custom array was created with 219,447 SNPs meeting stringent selection criteria and validated by genotyping more than 4000 oysters across two generations. In total, 144,570 SNPs had a call rate >90%, most of which (96%) were polymorphic and were distributed across the Eastern oyster reference genome, with similar levels of genetic diversity observed in both generations. Linkage disequilibrium (LD) was low (maximum r2 ∼0.32) and decayed moderately with increasing distance between SNP pairs. Taking advantage of our intergenerational dataset, we quantified Mendelian inheritance errors (MIEs) to validate SNP selection. Although most of SNPs exhibited low MIE rates overall, with 72% of called SNPs having an error rate of <1%, many loci had elevated MIE rates, potentially indicating the presence of null alleles. This SNP panel provides a necessary tool to enable routine application of genomic approaches, including genomic selection, in C. virginica selective breeding programs. As demand for production increases, this resource will be essential for accelerating production and sustaining the Canadian oyster aquaculture industry.

show abstract

Section: Introductionmentioning

confidence: 99%

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

Xuereb

Marin-Nahuelpi

Normandeau

et al. 2023

G3: Genes, Genomes, Genetics

Self Cite

View full text Add to dashboard Cite

show abstract

“…Moreover, C. zillii should not be considered for enhancing capture fisheries in non-native areas due to its slow growth and negative consequences to the ecosystem (Gu et al, 2018a). In its current state, it is not feasible to consider it for aquaculture; however, intensive research works in areas such as modern selective breeding approaches combined with genomic selection technologies may help to produce a strain with superior growth performance, which could be used in its native range (Lind et al, 2012;Houston et al, 2020;Yáñez et al, 2022).…”

Section: Discussionmentioning

confidence: 99%

Ecological niche and life-history traits of redbelly tilapia (Coptodon zillii, Gervais 1848) in its native and introduced ranges

Geletu,

Tang,

Xing

et al. 2024

Aquat. Living Resour.

View full text Add to dashboard Cite

Redbelly tilapia (Coptodon zillii) is a member of a group of fishes in the Cichlidae family endemic to the northern half of Africa and the Middle East. In the literature, the name C. zillii is mostly associated with a negative impact on the ecosystem and biodiversity in the areas to which it was introduced. In its native range, it is not a much-appreciated fish species from both fisheries and aquaculture perspectives because of its small size and difficulty to catch when compared to Nile tilapia, Oreochromis niloticus. Although C. zillii has several desirable aquaculture traits such as feeding at lower trophic levels, high fecundity, saltwater and cold tolerance, the attempts to capitalize on this potential are lacking. Moreover, comprehensive studies that characterize its ecological niche in its native range and adaptive mechanisms of invasiveness in introduced areas are also limited. Notwithstanding, it is a species of invasion concern that requires continuous monitoring and implementation of mitigation actions in non-native regions. Compilation of information regarding the environmental requirements, feeding, and reproductive biology of C. zillii may serve as a starting ingredient for further research and management of its invasiveness, which is highly required in the face of freshwater ecosystem modifications as a result of climate change. This paper also addresses the current state and potential of C. zillii for utilization in capture fisheries and fish farming.

show abstract

“…is needed in the context of a circular economy. Aquaponics, in combination with selective breeding and thermal acclimation, are promising management strategies that may contribute to the development of a new form of rainbow trout farming [ 47 , 48 , 155 , 156 , 157 ]. Nevertheless, climate change remains a difficult obstacle for examining the genetic diversity of rainbow trout populations, a species sensitive to climate change.…”

Section: The Potential Of Rainbow Trout Farming In Aquaponicsmentioning

confidence: 99%

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

Vasdravanidis

Alvanou

Lattos

et al. 2022

Animals

View full text Add to dashboard Cite

The impact of climate change on both terrestrial and aquatic ecosystems tends to become more progressively pronounced and devastating over the years. The sector of aquaculture is severely affected by natural abiotic factors, on account of climate change, that lead to various undesirable phenomena, including aquatic species mortalities and decreased productivity owing to oxidative and thermal stress of the reared organisms. Novel innovative technologies, such as aquaponics that are based on the co-cultivation of freshwater fish with plants in a sustainable manner under the context of controlled abiotic factors, represent a promising tool for mitigating the effect of climate change on reared fish. The rainbow trout (Oncorhynchus mykiss) constitutes one of the major freshwater-reared fish species, contributing to the national economies of numerous countries, and more specifically, to regional development, supporting mountainous areas of low productivity. However, it is highly vulnerable to climate change effects, mainly due to the concrete raceways, in which it is reared, that are constructed on the flow-through of rivers and are, therefore, dependent on water’s physical properties. The current review study evaluates the suitability, progress, and challenges of developing innovative and sustainable aquaponic systems to rear rainbow trout in combination with the cultivation of plants. Although not commercially developed to a great extent yet, research has shown that the rainbow trout is a valuable experimental model for aquaponics that may be also commercially exploited in the future. In particular, abiotic factors required in rainbow trout farming along, with the high protein proportion required in the ratios due to the strict carnivorous feeding behavior, result in high nitrate production that can be utilized by plants as a source of nitrogen in an aquaponic system. Intensive farming of rainbow trout in aquaponic systems can be controlled using digital monitoring of the system parameters, mitigating the obstacles originating from extreme temperature fluctuations.

show abstract

Genomics applied to livestock and aquaculture breeding

Cited by 16 publications

References 66 publications

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

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

Ecological niche and life-history traits of redbelly tilapia (Coptodon zillii, Gervais 1848) in its native and introduced ranges

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

Contact Info

Product

Resources

About