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Open AccessJournal ArticleDOI

Translational genomics for plant breeding with the genome sequence explosion

TLDR
The strategies of translational genomics are reviewed and suggested perspectives on the current databases of genomic resources and the database structures of translated information on the new genome are suggested.
Abstract
The use of next-generation sequencers and advanced genotyping technologies has propelled the field of plant genomics in model crops and plants and enhanced the discovery of hidden bridges between genotypes and phenotypes. The newly generated reference sequences of unstudied minor plants can be annotated by the knowledge of model plants via translational genomics approaches. Here, we reviewed the strategies of translational genomics and suggested perspectives on the current databases of genomic resources and the database structures of translated information on the new genome. As a draft picture of phenotypic annotation, translational genomics on newly sequenced plants will provide valuable assistance for breeders and researchers who are interested in genetic studies.

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Journal ArticleDOI

The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution

TL;DR: It is found that the genomic architecture of flowering time has been shaped by the most recent whole-genome duplication, which suggests that ancient paralogues can remain in the same regulatory networks for dozens of millions of years.
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Crop Breeding Chips and Genotyping Platforms: Progress, Challenges, and Perspectives

TL;DR: It is proposed that future practical breeding platforms should adopt automated genotyping technologies, either array or sequencing based, target functional polymorphisms underpinning economic traits, and provide desirable prediction accuracy for quantitative traits, with universal applications under wide genetic backgrounds in crops.
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Accelerating the Domestication of New Crops: Feasibility and Approaches

TL;DR: It is suggested here that genome editing can be used as a new tool by breeders to accelerate the domestication of semi-domesticated or even wild plants, building a more varied foundation for the sustainable provision of food and fodder in the future.
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Photosynthetic Metabolism under Stressful Growth Conditions as a Bases for Crop Breeding and Yield Improvement

TL;DR: The current review aims to analyze, from a multi-perspective approach, the impact of changing environmental conditions on the performance of the photosynthetic apparatus and, consequently, plant growth.
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Recent advances in Cannabis sativa genomics research.

TL;DR: This review provides a comprehensive summary of key cannabis genomics resources and their applications, and discusses prospective applications of existing and emerging genomics technologies for accelerating the genetic improvement of cannabis.
References
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Journal ArticleDOI

Pfam: the protein families database.

TL;DR: Pfam as discussed by the authors is a widely used database of protein families, containing 14 831 manually curated entries in the current version, version 27.0, and has been updated several times since 2012.
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A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

TL;DR: A procedure for constructing GBS libraries based on reducing genome complexity with restriction enzymes (REs) is reported, which is simple, quick, extremely specific, highly reproducible, and may reach important regions of the genome that are inaccessible to sequence capture approaches.
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Functions of DNA methylation: islands, start sites, gene bodies and beyond

TL;DR: Improved genome-scale mapping of methylation allows us to evaluate DNA methylation in different genomic contexts: transcriptional start sites with or without CpG islands, in gene bodies, at regulatory elements and at repeat sequences.
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Phytozome: a comparative platform for green plant genomics

TL;DR: Phytozome provides a view of the evolutionary history of every plant gene at the level of sequence, gene structure, gene family and genome organization, while at the same time providing access to the sequences and functional annotations of a growing number of complete plant genomes.
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The NHGRI GWAS Catalog, a curated resource of SNP-trait associations

TL;DR: A number of recent improvements to theNHGRI Catalog of Published Genome-Wide Association Studies are presented, including novel ways for users to interact with the Catalog and changes to the curation infrastructure.
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