Next generation sequencing technologies for next generation plant breeding

Ray, Soham; Satya, Pratik

doi:10.3389/fpls.2014.00367

Cited by 71 publications

(47 citation statements)

References 27 publications

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“…Thousands of polymorphic sites can be detected simultaneously in single run (Ray and Satya 2014). Both genic and non-genic marker sequences can be identified as the byproduct from the data generated from nuclear and organelle genome as well as transcriptome.…”

Section: Molecular Markers Miningmentioning

confidence: 99%

Renaissance in phytomedicines: promising implications of NGS technologies

Sharma

Shrivastava

2016

Planta

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Medicinal plant research is growing significantly in faith to discover new and more biologically compatible phytomedicines. Deposition of huge genome/trancriptome sequence data assisted by NGS technologies has revealed the new possibilities for producing upgraded bioactive molecules in medicinal plants. Growing interest of investors and consumers in the herbal drugs raises the need for extensive research to open the facts and details of every inch of life canvas of medicinal plants to produce improved quality of phytomedicines. As in agriculture crops, knowledge emergence from medicinal plant's genome/transcriptome, can be used to assure their amended quality and these improved varieties are then transported to the fields for cultivation. Genome studies generate huge sequence data which can be exploited further for obtaining information regarding genes/gene clusters involved in biosynthesis as well as regulation. This can be achieved rapidly at a very large scale with NGS platforms. Identification of new RNA molecules has become possible, which can lead to the discovery of novel compounds. Sequence information can be combined with advanced phytochemical and bioinformatics tools to discover functional herbal drugs. Qualitative and quantitative analysis of small RNA species put a light on the regulatory aspect of biosynthetic pathways for phytomedicines. Inter or intra genomic as well as transcriptomic interactive processes for biosynthetic pathways can be elucidated in depth. Quality management of herbal material will also become rapid and high throughput. Enrichment of sequence information will be used to engineer the plants to get more efficient phytopharmaceuticals. The present review comprises of role of NGS technologies to boost genomic studies of pharmaceutically important plants and further, applications of sequence information aiming to produce enriched phytomedicines. Emerging knowledge from the medicinal plants genome/transcriptome can give birth to deep understanding of the processes responsible for biosynthesis of medicinally important compounds.

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Section: Molecular Markers Miningmentioning

confidence: 99%

Renaissance in phytomedicines: promising implications of NGS technologies

Sharma

Shrivastava

2016

Planta

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“…This has encouraged the development of novel but still high-throughput and time-and cost-saving SNP discovery methods based on next-generation sequencing (NGS) technologies. Several strategies, methods and protocols for NGS-based genotyping have been developed so far [53,54]. We will go through some of these with a special focus on genotype-by-sequencing (GBS).…”

Section: Ngs-based Genotyping For Genetic Diversity Evaluationmentioning

confidence: 99%

NGS-Based Genotyping, High-Throughput Phenotyping and Genome-Wide Association Studies Laid the Foundations for Next-Generation Breeding in Horticultural Crops

D’Agostino¹,

Tripodi²

2017

Diversity

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Demographic trends and changes to climate require a more efficient use of plant genetic resources in breeding programs. Indeed, the release of high-yielding varieties has resulted in crop genetic erosion and loss of diversity. This has produced an increased susceptibility to severe stresses and a reduction of several food quality parameters. Next generation sequencing (NGS) technologies are being increasingly used to explore "gene space" and to provide high-resolution profiling of nucleotide variation within germplasm collections. On the other hand, advances in high-throughput phenotyping are bridging the genotype-to-phenotype gap in crop selection. The combination of allelic and phenotypic data points via genome-wide association studies is facilitating the discovery of genetic loci that are associated with key agronomic traits. In this review, we provide a brief overview on the latest NGS-based and phenotyping technologies and on their role to unlocking the genetic potential of vegetable crops; then, we discuss the paradigm shift that is underway in horticultural crop breeding.

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“…Ploidy is another challenge for sequencing projects, and results are dependent on many aspects, such as autopolyploid or allopolyploid character of the genome or the age of ploidization event. This complexity of the genomes had been a problem for a long time and it needed to be reduced involving sequencing library with partial representation of the genome using restriction enzymes or capturing sequences without enzyme digestion (Ray & Satya 2014). Many projects aimed to generate reference genome sequences for the species of interest.…”

Section: Reference Genomesmentioning

confidence: 99%

Application of next-generation sequencing in plant breeding

Vlk¹,

Řepková²

2017

CZECH J GENET PLANT

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In the past decade, next-generation sequencing (NGS) platforms have changed the impact of sequencing on our knowledge of crop genomes and gene regulation. These techniques are today acquiring a great potential in metagenomic and agrigenomic research while showing prospects for their utilization in plant breeding. We can now obtain new and beneficial information about gene regulation on the cellular as well as whole-plant level through RNA-sequencing and subsequent expression analyses of genes participating in plant defence reactions to pathogens and in abiotic stress tolerance. NGS has facilitated the development of methods to genotype very large numbers of single-nucleotide polymorphisms. Genotyping-by-sequencing and whole-genome resequencing can lead to the development of molecular markers suited to studies of genetic relationships among breeding materials, creation of detailed genetic mapping of targeted genes and genome-wide association studies. Plant genotyping can benefit plant breeding through selection of individuals resistant to climatic stress and to pathogens causing substantial losses in agriculture.

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Next generation sequencing technologies for next generation plant breeding

Cited by 71 publications

References 27 publications

Renaissance in phytomedicines: promising implications of NGS technologies

Renaissance in phytomedicines: promising implications of NGS technologies

NGS-Based Genotyping, High-Throughput Phenotyping and Genome-Wide Association Studies Laid the Foundations for Next-Generation Breeding in Horticultural Crops

Application of next-generation sequencing in plant breeding

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