Harness the power of genomic selection and the potential of germplasm in crop breeding for global food security in the era with rapid climate change DOI Creative Commons
Tianhua He, Chengdao Li

The Crop Journal, Journal Year: 2020, Volume and Issue: 8(5), P. 688 - 700

Published: June 5, 2020

Crop genetic improvements catalysed population growth, which in turn has increased the pressure for food security. We need to produce 70% more meet demands of 9.5 billion people by 2050. Climate changes have posed challenges global supply, while narrow base elite crop cultivars further limited our capacity increase gain through conventional breeding. The effective utilization resources germplasm collections improvement is crucial increasing address supply. Genomic selection (GS) uses genome-wide markers and phenotype information from observed populations establish associations, followed predict phenotypic values test populations. Characterizing an extensive collection can serve a dual purpose GS, as reference predicting model, mining desirable variants incorporation into cultivars. New technologies, such high-throughput genotyping phenotyping, machine learning, gene editing, great potential contribute genome-assisted Breeding programmes integrating characterization, GS emerging technologies offer promise accelerating development with improved yield enhanced resistance tolerance biotic abiotic stresses. Finally, scientifically informed regulations on new breeding sharing resources, genomic data, bioinformatics expertise between developed developing economies will be key meeting rapidly changing climate demand food.

Language: Английский

Harnessing genomics to fast-track genetic improvement in aquaculture DOI
Ross D. Houston, Tim P. Bean, Daniel J. Macqueen

et al.

Nature Reviews Genetics, Journal Year: 2020, Volume and Issue: 21(7), P. 389 - 409

Published: April 16, 2020

Language: Английский

Citations

422
Bringing the Animal QTLdb and CorrDB into the future: meeting new challenges and providing updated services DOI Creative Commons

Zhi-Liang Hu,

Carissa A. Park,

James M. Reecy

et al.

Nucleic Acids Research, Journal Year: 2021, Volume and Issue: 50(D1), P. D956 - D961

Published: Oct. 22, 2021

Abstract The Animal QTLdb (https://www.animalgenome.org/QTLdb) and CorrDB (https://www.animalgenome.org/CorrDB) are unique resources for livestock animal genetics genomics research which have been used extensively by the international genome community. This is largely due to active development of databases over years keep up with rapid advancement sciences. ongoing has ensured that these provide researchers not only continually updated data but also new web tools disseminate data. Through our continued efforts, evolved from original Pig cross-experiment QTL comparisons an hosting 220 401 QTL, SNP association eQTL linking phenotype genotype 2210 traits. In addition, there 23 552 correlations 866 traits 4273 heritability on 1069 in CorrDB. All were curated 3157 publications cover seven species. Along curation, species, additional builds, functions features built into as well. Standardized procedures support mapping multiple species/genome builds ability browse based linked ontology terms highlights recent developments.

Language: Английский

Citations

246
Enhancing Genetic Gain through Genomic Selection: From Livestock to Plants DOI Creative Commons
Yunbi Xu, Xiaogang Liu, Junjie Fu

et al.

Plant Communications, Journal Year: 2019, Volume and Issue: 1(1), P. 100005 - 100005

Published: Oct. 17, 2019

Although long-term genetic gain has been achieved through increasing use of modern breeding methods and technologies, the rate needs to be accelerated meet humanity's demand for agricultural products. In this regard, genomic selection (GS) considered most promising improvement complex traits controlled by many genes each with minor effects. Livestock scientists pioneered GS application largely due livestock's significantly higher individual values greater reduction in generation interval that can GS. Large-scale plants refining field management improve heritability estimation prediction accuracy developing optimum models consideration genotype-by-environment interaction non-additive effects, along significant cost reduction. Moreover, it would more effective integrate other tools platforms accelerating process thereby further enhancing gain. addition, establishing an open-source network transdisciplinary approaches essential efficiency small- medium-sized enterprises research systems countries. New strategies centered on need developed.

Language: Английский

Citations

212
ABO genotype alters the gut microbiota by regulating GalNAc levels in pigs DOI Open Access
Hui Yang,

Jinyuan Wu,

Xiaochang Huang

et al.

Nature, Journal Year: 2022, Volume and Issue: 606(7913), P. 358 - 367

Published: April 27, 2022

Language: Английский

Citations

109
Genome‐wide association and genomic selection in aquaculture DOI Creative Commons
José M. Yáñez, Agustín Barría, María E. López

et al.

Reviews in Aquaculture, Journal Year: 2022, Volume and Issue: 15(2), P. 645 - 675

Published: Nov. 17, 2022

Abstract Recent advancements in genomic technologies have led to the discovery and application of DNA‐markers [e.g. single nucleotide polymorphisms (SNPs)] for genetic improvement several aquaculture species. The identification specific regions associated with economically important traits, using, example, genome‐wide association studies (GWAS), has allowed incorporation markers linked quantitative trait loci (QTL) into breeding programs through marker‐assisted selection (MAS). However, most traits economic relevance are expected be controlled by many QTLs, each one explaining only a small proportion variation. For under polygenic control, prediction merit animals based on sum effects at positions across entire genome (i.e. estimated values, GEBV, which used what become known as selection), been demonstrated speed rate gain breeding. aim this review was provide an overview development uncovering basis complex accelerating progress species, well providing future perspectives about deployment novel molecular selective coming years.

Language: Английский

Citations

74
HIBLUP: an integration of statistical models on the BLUP framework for efficient genetic evaluation using big genomic data DOI Creative Commons
Lilin Yin, Haohao Zhang, Zhenshuang Tang

et al.

Nucleic Acids Research, Journal Year: 2023, Volume and Issue: 51(8), P. 3501 - 3512

Published: Feb. 22, 2023

Abstract Human diseases and agricultural traits can be predicted by modeling a genetic random polygenic effect in linear mixed models. To estimate variance components predict effects of the model efficiently with limited computational resources has always been primary concern, especially when it involves increasing genotype data scale current genomic era. Here, we thoroughly reviewed development history statistical algorithms used evaluation theoretically compared their complexity applicability for different scenarios. Most importantly, presented computationally efficient, functionally enriched, multi-platform user-friendly software package named ‘HIBLUP’ to address challenges that are faced currently using big data. Powered advanced algorithms, elaborate design efficient programming, HIBLUP computed fastest while lowest memory analyses, greater number individuals genotyped, benefits from HIBLUP. We also demonstrated is only tool which accomplish analyses UK Biobank-scale dataset within 1 h proposed ‘HE + PCG’ strategy. It foreseeable will facilitate research human, plants animals. The user manual accessed freely at https://www.hiblup.com.

Language: Английский

Citations

46
Comprehensive analyses of 723 transcriptomes enhance genetic and biological interpretations for complex traits in cattle DOI Creative Commons
Lingzhao Fang, Wentao Cai, Shuli Liu

et al.

Genome Research, Journal Year: 2020, Volume and Issue: 30(5), P. 790 - 801

Published: May 1, 2020

By uniformly analyzing 723 RNA-seq data from 91 tissues and cell types, we built a comprehensive gene atlas studied tissue specificity of genes in cattle. We demonstrated that tissue-specific significantly reflected the tissue-relevant biology, showing distinct promoter methylation evolution patterns (e.g., brain-specific evolve slowest, whereas testis-specific fastest). Through integrative analyses those with large-scale genome-wide association studies, detected relevant tissues/cell types candidate for 45 economically important traits cattle, including blood/immune system CCDC88C ) male fertility, brain TRIM46 RAB6A milk production, multiple growth-related FGF6 CCND2 body conformation. validated these findings by using epigenomic across major somatic sperm. Collectively, our provided novel insights into genetic biological mechanisms underlying complex transcriptome can serve as primary source interpretation, functional validation, studies adaptive evolution, genomic improvement livestock.

Language: Английский

Citations

137
Current status of genomic evaluation DOI Creative Commons
I. Misztal, Daniela Lourenço, Andrés Legarra

et al.

Journal of Animal Science, Journal Year: 2020, Volume and Issue: 98(4)

Published: April 1, 2020

Early application of genomic selection relied on SNP estimation with phenotypes or de-regressed proofs (DRP). Chips 50k seemed sufficient for an accurate effects. Genomic estimated breeding values (GEBV) were composed index parent average, direct value, and deduction a parental to eliminate double counting. Use weighting increased accuracy small data sets but had minimal no impact large sets. Efforts include potentially causative derived from sequence high-density chips showed limited gain in accuracy. After the implementation selection, EBV by BLUP became biased because preselection DRP computed based required adjustments, creation females is hard subject was greatly simplified single-step (ssGBLUP). This method combining pedigree relationships automatically creates all sources information, can use any combination male female genotypes, accounts preselection. To avoid biases, especially under strong ssGBLUP requires that are compatible. Because inversion relationship matrix (G) becomes costly more than 100k genotyped animals, computations solved exploiting dimensionality due effective population size. With such ranging 4k chickens about 15k cattle, inverse G be created directly (e.g., algorithm proven young) at linear cost. Due its simplicity accuracy, routinely used major chicken, pig, beef industries. Single step derive effects indirect prediction genome-wide association studies, including P-values. Alternative formulations exist animals. Although genomics new standard genetics, there still some problems need solved. involves validation procedures unaffected parameter strategies address reduction genetic variances after implemented.

Language: Английский

Citations

130
From FAANG to fork: application of highly annotated genomes to improve farmed animal production DOI Creative Commons
Emily L. Clark, Alan Archibald, Hans D. Daetwyler

et al.

Genome biology, Journal Year: 2020, Volume and Issue: 21(1)

Published: Nov. 24, 2020

Language: Английский

Citations

116
Research advances in the genomics and applications for molecular breeding of aquaculture animals DOI
Xinxin You, Xinxin Shan, Qiong Shi

et al.

Aquaculture, Journal Year: 2020, Volume and Issue: 526, P. 735357 - 735357

Published: April 10, 2020

Language: Английский

Citations

115