Recent Major Advances of Biotechnology and Sustainable Aquaculture in China

Xiang, Jianhai

doi:10.2174/2211550105666151105190012

Cited by 14 publications

(7 citation statements)

References 67 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, this benefit of the technology has not been fully realized in a number of animal species (e.g., meat and dairy sheep, Raoul et al, 2017 ; most of aquaculture species, Wang et al, 2017 ). The main reasons contributing to a slow adaptation of the technology in selective breeding programs include: 1) non-existence of commercially available large SNP panels due to the lack of quality reference genome sequences (Xiang, 2015 ); (2) the lack of breeding programs in which GS can be implemented (Xiang, 2015 ) and (3) the high cost associated with the need to genotype large numbers of individuals in reference populations for genomic prediction of target populations. Although rapid development of high-throughput technologies, commercial costs of genotyping a high density SNP panel per individual animal has been reducing at a fast speed, developing cost-effective methods for applying low-density SNP panels to build breeding populations for genomic selection still has profound impacts on many industries.…”

Section: Introductionmentioning

confidence: 99%

Genomic Prediction of Breeding Values Using a Subset of SNPs Identified by Three Machine Learning Methods

et al. 2018

View full text Add to dashboard Cite

The analysis of large genomic data is hampered by issues such as a small number of observations and a large number of predictive variables (commonly known as “large P small N”), high dimensionality or highly correlated data structures. Machine learning methods are renowned for dealing with these problems. To date machine learning methods have been applied in Genome-Wide Association Studies for identification of candidate genes, epistasis detection, gene network pathway analyses and genomic prediction of phenotypic values. However, the utility of two machine learning methods, Gradient Boosting Machine (GBM) and Extreme Gradient Boosting Method (XgBoost), in identifying a subset of SNP makers for genomic prediction of breeding values has never been explored before. In this study, using 38,082 SNP markers and body weight phenotypes from 2,093 Brahman cattle (1,097 bulls as a discovery population and 996 cows as a validation population), we examined the efficiency of three machine learning methods, namely Random Forests (RF), GBM and XgBoost, in (a) the identification of top 400, 1,000, and 3,000 ranked SNPs; (b) using the subsets of SNPs to construct genomic relationship matrices (GRMs) for the estimation of genomic breeding values (GEBVs). For comparison purposes, we also calculated the GEBVs from (1) 400, 1,000, and 3,000 SNPs that were randomly selected and evenly spaced across the genome, and (2) from all the SNPs. We found that RF and especially GBM are efficient methods in identifying a subset of SNPs with direct links to candidate genes affecting the growth trait. In comparison to the estimate of prediction accuracy of GEBVs from using all SNPs (0.43), the 3,000 top SNPs identified by RF (0.42) and GBM (0.46) had similar values to those of the whole SNP panel. The performance of the subsets of SNPs from RF and GBM was substantially better than that of evenly spaced subsets across the genome (0.18–0.29). Of the three methods, RF and GBM consistently outperformed the XgBoost in genomic prediction accuracy.

show abstract

Section: Introductionmentioning

confidence: 99%

Genomic Prediction of Breeding Values Using a Subset of SNPs Identified by Three Machine Learning Methods

et al. 2018

View full text Add to dashboard Cite

show abstract

“…Biotechnological research on all forms of aquaculture, including shellfish processing, is very well documented [111][112][113][114][115] and it is important to appreciate as a fact that fears that action to deal with climate change is impossibly costly are not true for the biotechnology of aquaculture [116][117][118]. Clearly it will take time, perhaps several decades, to amplify calcifier cultivation globally to levels that remove decisive quantities of CO2 from our atmosphere on an annual basis but gains from this activity are not restricted to some far off uncertain future.…”

Section: Solution For Today: Cultivate Shellfish On Industrial Scale ...mentioning

confidence: 99%

An Assessment of the Potential Value for Climate Remediation of Ocean Calcifiers in Sequestration of Atmospheric Carbon

Moore

Heilweck

Fears³

et al. 2022

Preprint

View full text Add to dashboard Cite

Today’s marine calcifiers (coccolithophore algae, Foraminifera [protists], Mollusca, Crustacea, Anthozoa [corals], Echinodermata) remove carbon dioxide (CO 2) from the atmosphere, converting it into solid calcium carbonate (CaCO 3) which is stable for geological periods of time. These organisms could serve as a biotechnological carbon capture and storage mechanism to control climate change. Two criticisms made about this are: (i) ocean acidification has allegedly been shown to cause reduced shell formation in calcifiers; (ii) the calcification reaction that precipitates CaCO 3 crystals into the shells is alleged to return CO 2 to the atmosphere. In this review we assess the evidence concerning such criticisms and find reasons to doubt both. Experiments showing that ocean acidification is damaging to calcifiers have all used experimental pH levels that are not projected to be reached in the oceans until the next century or later; today’s oceans, despite recent changes, are alkaline in pH. Claiming precipitation of CaCO 3 during calcification as a net source of CO 2 to the atmosphere is an oversimplification of ocean chemistry that is true only in open water environments. Living calcifiers do not carry out the calcification reaction in an open water environment in equilibrium with the atmosphere. The chemistry that we know as life takes place on the surfaces of enzymatic polypeptides, within organelles that have phospholipid membranes, contained in a cell enclosed within another phospholipid bilayer membrane specifically to isolate the chemistry of life from the open water environment. Ignoring what is known about the biology, physiology, and molecular cell biology of living organisms, calcifiers of all types especially, leads to erroneous conclusions and deficient advice about the potential for calcifier biotechnology to contribute to atmosphere remediation. Net removal of CO 2 from the atmosphere by calcifiers is only achieved by the CaCO 3 stored in the shell, coccoliths, or foram tests that are left when they die. To capitalise on this requires a change in paradigm towards cultivating calcifiers for their CaCO 3 rather than their meat or other products. We conclude that the world’s aquaculture industries already operate the biotechnology that, with massive and immediate global expansion, can contribute to sustainably controlling atmospheric CO 2 levels at reasonable cost and with several positive benefits in addition to carbon sequestration.

show abstract

“…Extrapolating the figures in Table 1 suggests that this year's global aquaculture farming will remove about 5.5 million tonnes of CO2 from the atmosphere. Biotechnological research on aquaculture is well established (e.g., Rasmussen & Morrissey, 2007;Xiang, 2015); as is practical knowhow advice (Lovatelli, 1990;Utting & Spencer, 1991;Helm et al, 2004).…”

Section: Cultivate Shellfish: Save the Atmospherementioning

confidence: 99%

Saving the planet with appropriate biotechnology: 2. Cultivate shellfish to remediate the atmosphere

Moore¹,

Heilweck²,

Petros³

2021

Mexjbiotechnol

View full text Add to dashboard Cite

Shellfish cultivation is the only industry on the planet that (a) feeds us, (b) permanently removes CO2 from our atmosphere, and, with care, could (c) engineer our marine habitats to maintain the health and biodiversity of those ecosystems into the future. About 30-50% of shellfish biomass is represented by the animals’ shells, and shellfish shell is made by converting atmospheric CO2 into crystalline calcium carbonate which is stable for geological periods of time. The human tradition of eating shellfish is recorded in the ancient middens of shellfish shells that track migrations of early humans around the world. Recent history shows increasing exploitation of marine resources by an ever-growing human population. By the end of the 19th century oysters had become a cheap staple food on both sides of the Atlantic, but this oyster dredging destroyed 85% of the world’s oyster beds. In the tropics, Giant Clams have also been fished to extinction in many Indian Ocean and Pacific waters. In the 21st century, these animals deserve to have the same vigour applied to their restoration and conservation as we applied to dredging them from the seabed. In return they will cleanse our atmosphere by permanently sequestering its excess CO2 into limestone. And we must start now, before Homo sapiens is added to the list of organisms driven to extinction by humanity’s follies.

show abstract

Recent Major Advances of Biotechnology and Sustainable Aquaculture in China

Cited by 14 publications

References 67 publications

Genomic Prediction of Breeding Values Using a Subset of SNPs Identified by Three Machine Learning Methods

Genomic Prediction of Breeding Values Using a Subset of SNPs Identified by Three Machine Learning Methods

An Assessment of the Potential Value for Climate Remediation of Ocean Calcifiers in Sequestration of Atmospheric Carbon

Saving the planet with appropriate biotechnology: 2. Cultivate shellfish to remediate the atmosphere

Contact Info

Product

Resources

About