Crop Breeding Chips and Genotyping Platforms: Progress, Challenges, and Perspectives
Awais Rasheed,Yuanfeng Hao,Xianchun Xia,Awais Khan,Yunbi Xu,Yunbi Xu,Rajeev K. Varshney,Zhonghu He,Zhonghu He +8 more
TLDR
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.About:
This article is published in Molecular Plant.The article was published on 2017-08-07 and is currently open access. It has received 338 citations till now. The article focuses on the topics: Molecular breeding & Cost effectiveness.read more
Citations
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Journal ArticleDOI
Fast-Forwarding Genetic Gain
TL;DR: Combining speed breeding and other leading-edge plant breeding technologies with strategic global partnerships has the potential to achieve the genetic gain targets required to deliver the authors' future crops.
Journal ArticleDOI
Genomic Selection in Aquaculture: Application, Limitations and Opportunities With Special Reference to Marine Shrimp and Pearl Oysters.
Kyall R. Zenger,Mehar S. Khatkar,David B. Jones,Nima Khalilisamani,Nima Khalilisamani,Dean R. Jerry,Herman W. Raadsma,Herman W. Raadsma +7 more
TL;DR: The technical advances, practical requirements, and commercial applications that have made genomic selection feasible in a range of aquaculture industries are discussed, with a particular focus on molluscs and marine shrimp.
Journal ArticleDOI
The Wheat 660K SNP array demonstrates great potential for marker-assisted selection in polyploid wheat.
TL;DR: The Wheat 660K SNP array could act as a substitute for other 6 arrays and shows promise for a wide range of possible applications and may be the best choice for targeted genotyping and marker‐assisted selection in wheat genetic improvement.
Journal ArticleDOI
5Gs for crop genetic improvement
Rajeev K. Varshney,Pallavi Sinha,Vikas K. Singh,Arvind Kumar,Qifa Zhang,Jeffrey L. Bennetzen +5 more
TL;DR: 5G breeding approach brings precision and enhances efficiency in breeding programs and multi-disciplinary team of scientists need to be trained to deploy 5G breeding in developing countries.
Journal ArticleDOI
Toward the sequence-based breeding in legumes in the post-genome sequencing era
Rajeev K. Varshney,Manish K. Pandey,Abhishek Bohra,Vikas K. Singh,Mahendar Thudi,Rachit K. Saxena +5 more
TL;DR: A sequence-based breeding approach which includes use of independent or combination of parental selection, enhancing genetic diversity of breeding programs, forward breeding for early generation selection, and genomic selection using sequencing/genotyping technologies is proposed.
References
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Journal ArticleDOI
A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species
Robert J. Elshire,Jeffrey C. Glaubitz,Qi-ying Sun,Jesse Poland,Ken Kawamoto,Edward S. Buckler,Edward S. Buckler,Sharon E. Mitchell +7 more
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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Potential etiologic and functional implications of genome-wide association loci for human diseases and traits
Lucia A. Hindorff,Praveen Sethupathy,Heather Junkins,Erin M. Ramos,Jayashri P. Mehta,Francis S. Collins,Teri A. Manolio +6 more
TL;DR: An online catalog of SNP-trait associations from published genome-wide association studies for use in investigating genomic characteristics of trait/disease-associated SNPs (TASs) is developed, well-suited to guide future investigations of the role of common variants in complex disease etiology.
Development and Validation of A
TL;DR: The results suggest that the LJQ is a reliable and valid instrument for evaluating LJ.
Journal ArticleDOI
Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers
Nathan A. Baird,Paul D. Etter,Tressa S. Atwood,Mark Currey,Anthony L. Shiver,Zachary A. Lewis,Eric U. Selker,William A. Cresko,Eric A. Johnson +8 more
TL;DR: The sequencing of restriction-site associated DNA (RAD) tags was described, which identified more than 13,000 SNPs, and three traits in two model organisms were mapped, using less than half the capacity of one Illumina sequencing run.
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Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species
TL;DR: This modified RADseq approach requires no prior genomic knowledge and achieves per-site and per-individual costs below that of current SNP chip technology, while requiring similar hands-on time investment, comparable amounts of input DNA, and downstream analysis times on the order of hours.
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