Abstract
Next-generation sequencing (NGS) is a massively parallel sequencing technology that has revolutionized genomic research. The goal of genomics is outlining the genetic composition, collective characterization, and quantification to describe a particular phenotype. NGS has enabled the sequencing of thousands of genomes to study diversity within or between germplasm pools. Advancement in sequencing has also transformed the enhancement strategies in agriculture. The introduction of new platforms employing long-read sequencing ensured more efficient sequencing of large and complex genomes. NGS has replaced the traditional methods of genotyping and plant breeding and simplified the genetic enhancement and modification approaches with the availability of diverse genetic variants information. This review summarizes the available next-generation sequencing platforms and their utilization in agricultural genomics. Agri-genomics has become more efficient after the introduction of NGS technologies with broad applications in genome selection, parentage, genotyping, marker-assisted breeding, and genome editing. Data analysis of high throughput sequencing data allows the exploration of the horizons of evolution and diversity, molecular breeding, soil, and agricultural metagenomics. NGS has proved to be a boon for researchers and breeders, enabling cost-efficient identification of markers for desirable traits that have led to insect-resistant and more productive crops and livestock.
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Abbreviations
- NGS:
-
Next-generation sequencing
- SBS:
-
Sequencing by synthesis
- GS:
-
Genome sequencer
- SOLiD:
-
Sequencing by oligo ligation and detection
- PGM:
-
Ion personal genome machine
- ISFET:
-
Ion-sensitive field-effect transistor
- SMRT:
-
Single-molecule real-time
- ZMW:
-
Zero mode waveguide
- SMS:
-
True single molecule sequencing
- WGR:
-
Whole genome resequencing
- CNV:
-
Copy number variations
- PAV:
-
Presence/absence variation
- SNP:
-
Single nucleotide polymorphism
- ONT-:
-
Oxford nanopore technologies
- WGBS:
-
Whole-genome bisulfite sequencing
- ChIP-seq:
-
Chromatin immunoprecipitation sequencing
- NGG:
-
Next generation genotyping
- GBS:
-
Genotyping by sequencing
- PCR:
-
Polymerase chain reaction
- eDNA:
-
Environmental DNA
- ZFNs:
-
Zinc-finger nucleases
- TALENs:
-
Transcription activator-like effector nucleases
- CRISPR:
-
Clustered regularly interspaced short palindromic repeats
- SSNs:
-
Sequence-specific nucleases
- RILs:
-
Recombinant inbred lines
- QTL:
-
Quantitative trait loci
- GS:
-
Genomic selection
- GWAS:
-
Genome-wide association studies
- BSA:
-
Bulked segregant analysis
- GMO:
-
Genetically modified organisms
- TILLING:
-
Targeting induced local lesions in genomes
- DNA:
-
Deoxyribonucleic acid
- RNA:
-
Ribonucleic acid
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The authors extend their gratitude to the Director and Joint Director of ICAR—National Academy of Agricultural Research Management, Hyderabad, and the Department of Biotechnology (DBT) for providing the required infrastructure.
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This study was funded by the Director, ICAR- National Academy of Agricultural Research Management, Hyderabad.
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Marudamuthu, B., Sharma, T., Purru, S. et al. Next-generation sequencing technology: a boon to agriculture. Genet Resour Crop Evol 70, 353–372 (2023). https://doi.org/10.1007/s10722-022-01512-5
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DOI: https://doi.org/10.1007/s10722-022-01512-5