Next-generation sequencing technologies and their implications for crop genetics and breeding.

By Rajeev K. Varshney, Spurthi N. Nayak, G. May, Scott A. Jackson. Trends in Biotechnology, 2009

867 citations recorded by the source corpus.

Using next-generation sequencing technologies it is possible to resequence entire plant genomes or sample entire transcriptomes more efficiently and economically and in greater depth than ever before. Rather than sequencing individual genomes, we envision the sequencing of hundreds or even thousands of related genomes to sample genetic diversity within and between germplasm pools. Identification and tracking of genetic variation are now so efficient and precise that thousands of variants can be tracked within large populations. In this review, we outline some important areas such as the large-scale development of molecular markers for linkage mapping, association mapping, wide crosses and alien introgression, epigenetic modifications, transcript profiling, population genetics and de novo genome/organellar genome assembly for which these technologies are expected to advance crop genetics and breeding, leading to crop improvement.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/83a7e813c6e14aa1435f093c8c92fefa13b9b47a

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Citations in the corpus

Characterization of a global germplasm collection and its potential utilization for analysis of complex quantitative traits in maize (2011, background): “With the development of next-generation sequencing techniques, the inexpensive cost of sequencing a genome (Varshney et al. 2009) may allow further detailed studies to achieve the final solution to this problem.”
The Complex Regulation of Senescence (2012, background): “…will be greatly facilitated by “next-” or “third-” (single-molecule)-generation sequencing techniques, some of which allow direct RNA sequencing (see Varshney et al., 2009, for a recent update); • Transcriptomic screens, especially with better temporal/spatial resolution (see below); these will…”
Marker‐Assisted Backcrossing to Introgress Resistance to Fusarium Wilt Race 1 and Ascochyta Blight in C 214, an Elite Cultivar of Chickpea (2014, background): “Marker-assisted backcrossing (MABC) aims at conversion of targeted lines with respect to one or two traits without disturbing remaining all other native traits of target variety (Varshney et al., 2009).”
Biological Nitrification Inhibition—A Novel Strategy to Regulate Nitrification in Agricultural Systems (2012, positive): “With the rapid advances in sequencing and data analysis capability (Varshney et al. 2009), transcriptomic approach could lead to identification of candidate genes associated with the BNI-function.”
Plant Breeding with Genomic Selection: Gain per Unit Time and Cost (2010, background): “Similar advances are being made in crop genotyping, as more species are being sequenced more quickly and new marker technologies are being applied to crops (Varshney et al., 2009).”
Genomic Selection in Plant Breeding (2011, methodology): “Details on the mechanisms of current NGS platforms, the available bioinformatics tools for sequence data analysis and SNP identification, and their impact on future genetics studies and crop improvement can be found in several recent review articles (Deschamps and Campbell, 2010; Mardis, 2008; Shend”
Plant tolerance to high temperature in a changing environment: scientific fundamentals and production of heat stress-tolerant crops (2013, background): “Association mapping or linkage disequilibrium mapping is a high resolution and relatively low cost methodology, that might likely be used to identify traits associated with abiotic stresses, in combination with high throughput marker genotyping platforms (Varshney et al., 2009).”
Translational Genomics in Agriculture: Some Examples in Grain Legumes (2015, background): “…a plant, Yield parameters QTL 3.78–40.10 (Gautami et al., 2012a; Liang et al., 2009; Ravi et al., 2011; Selvaraj et al., 2009; Shirasawa et al., 2012; Varshney et al., 2009b) (Continued on next page) TABLE 4 Summary of some trait mapping studies in select legumes (Continued) Trait Gene/ QTL ∗PVE (”
Genetic and Genomic Resources of Small Millets (2016, background): “wealth of nucleic acid sequence resources in various important agricultural crops (Varshney et al., 2009; Varshney, 2010).”
Single Nucleotide Polymorphism–based Genetic Diversity in the Reference Set of Peanut (Arachis spp.) by Developing and Applying Cost‐Effective Kompetitive Allele Specific Polymerase Chain Reaction Genotyping Assays (2013, background): “…tools (Gupta and Varshney, 2000), have enabled discrimination and assessment of genetic variation in peanut germplasm revealing very low to moderate levels of polymorphism in cultivated germplasm as compared to wild relatives (Gautami et al., 2009; Varshney et al., 2009a; Koppolu et al., 2010).”
Comprehending crystalline β-carotene accumulation by comparing engineered cell models and the natural carotenoid-rich system of citrus (2011, neutral): “The development of new high-throughput sequencing technologies provides the capacity for massively parallel re-sequencing of genomes, and thus can be used to develop single nucleotide polymorphism (SNP) markers for population genotyping (Mardis, 2008; Schuster, 2008; Varshney et al., 2009).”
Applications of next-generation sequencing to the study of biological invasions (2015, background): “490 Current Zoology Vol. 61 No. 3 (Varshney et al., 2009), among many more.”
Avoiding damage and achieving cold tolerance in rice plants (2013, background): “This is the basis of genomics-assisted breeding (Varshney et al. 2009).”