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Genomics

  • P. M. Priyadarshan
Chapter

Abstract

Genomics is the study on how the complex sets of genes are expressed in cells (the term genomics was coined by Tom Roderick, a geneticist at the Jackson Laboratory, Bar Harbor, USA, in 1986). It’s a discipline in genetics that applies recombinant DNA, DNA sequencing methods and bioinformatics to sequence, assemble and analyse the structure and function of genomes. Though the term genetic engineering is modification of plants and animals through recombinant DNA technology, human beings have been actually practising genetic engineering for thousands of years. The rate of crop improvement was increased because of an in-depth understanding of genetics during the beginning of the twentieth century. Introduction of hybrid corn was the most dramatic agricultural development. But highly inbred lines gave decreased yield because of homozygous deleterious recessive alleles. As per the observation of George Harrison Shull, crossing of two different inbred lines gave progeny with “hybrid vigour”, with fourfold yield. Hybrid rice of the International Rice Research Institute in the Philippines gave 20% extra yield. Currently, breeders are looking for genes to optimize nutritional quality like golden rice. Rice is staple food for almost half the world’s population, but it lacks vitamin A. Vitamin A deficiency causes reduced vision and immunity. Genetically engineered golden rice is with vitamin A. It has been named golden rice because of the gold-coloured beta-carotene, a precursor to vitamin A. The intensity of golden colour increases with the presence of pro-vitamin A. The commencement of the twenty-first century made new ways to understand genomes. The complexity of plant genomes is multi-fold compared to eukaryotic genomes with evolutionary flips and turns of DNA sequences. Chromosome numbers ploidy levels are also widely different. The size of plant genomes (both number of chromosomes and total nucleotide base pairs) shows the greatest variation in the biological world. As an example, wheat contains over 110 times more DNA compared to Arabidopsis thaliana. Plant DNA contains sequence repeats, sequence inversions or transposable element insertions that modify the genetic content further.

Keywords

Genetic structure of plant genomes Nuclear genomes and their size Chemical and physical composition of plant DNA The packaging of the genome The genomic DNA sequence Model plant species Genome co-linearity/genome evolution Whole genome sequencing Transposable elements DNA microarrays Genomics-assisted breeding Genome sequencing and sequence-based markers High-throughput phenotyping Marker-trait association for genomics-assisted breeding From genotype to phenotype Post-transcriptional gene silencing (PTGS) The new systems biology 

Abbreviations

bp, kbp

Base pairs, kilobase pairs

ddNTPs

Dideoxynucleotide triphosphates

DH

Doubled haploid

DiGE

Difference gel electrophoresis

DNA

Deoxyribonucleic acid

DSB

Double-strand break

dsRNA

Double-stranded RNAs

ELISA

Enzyme-linked immunosorbent assay

FT-MS

Fourier transform mass spectrometry

GBSS

Granule-bound starch synthase

GC

Gas chromatography

GFP

Green fluorescent protein

GM

Genetically modified

GMM

Genetically modified microorganism

GMO

Genetically modified organism

GUS

Beta-glucuronidase gene

GVA

Grapevine virus A

HILIC

Hydrophilic interaction chromatography

HPLC

High-performance liquid chromatography

hpRNA

Hairpin RNA

HR

Homologous recombination

HRM

High-resolution melting

LC

Liquid chromatography

LFD

Lateral flow devices

LNA

Locked nucleic acids

LOD

Limit of detection

LOQ

Limit of quantification

MALDI

Matrix-assisted laser-desorption ionization

MAS

Marker-assisted selection

miRNA

MicroRNA

mRNA

Messenger RNA

MS

Mass spectrometry

MS-HRM

Methylation-sensitive high-resolution melting

ncRNA

Non-coding RNA

NHEJ

Non-homologous end-joining

NMR

Nuclear magnetic resonance

NOS

Nopaline synthase

NPTII

Neomycin phosphotransferase gene

nt

Nucleotides

NTTF

New Techniques Task Force

NTWG

New Techniques Working Group

ODM

Oligonucleotide-directed mutagenesis

OECD

Organisation for Economic Co-operation and Development

ORF

Open reading frames

PAGE

Polyacrylamide gel electrophoresis

PAT

Phosphinothricin phosphotransferase

PCR

Polymerase chain reaction

PCT

Patent Cooperation Treaty

PEG

Polyethylene glycol

PTA

Plate-trapped antigen

PTGS

Post-transcriptional gene silencing

RdDM

RNA-dependent DNA methylation

RNAi

RNA interference

RP

Reversed-phase

rRNA

Ribosomal RNA

RT qPCR

Real-time quantitative PCR

siRNA

Small interfering RNA

SNPs

Single-nucleotide polymorphisms

TALEN

Transcription activator-like effector nucleases

TAS

Triple antibody sandwich

T-DNA

Transfer DNA

TFO

Triple helix-forming oligonucleotide

TGS

Transcriptional gene silencing

TOF

Time of flight

tRNA

Transfer RNA

UHPLC

Ultra-high-performance liquid chromatography

UV

Ultra-violet

ZFN

Zinc finger nuclease

Further Reading

  1. Bolger ME et al (2014) Plant genome sequencing – applications for crop improvement. Curr Opin Biotechnol 26:31–37CrossRefGoogle Scholar
  2. Chakradhar T (2017) Genomic-based-breeding tools for tropical maize improvement. Genetica 145:525–539.  https://doi.org/10.1007/s10709-017-9981-yCrossRefPubMedGoogle Scholar
  3. Kang YJ et al (2015) Translational genomics for plant breeding with the genome sequence explosion. Plant Biotechnol J:1–13.  https://doi.org/10.1111/pbi.12449CrossRefGoogle Scholar
  4. Ronald PC (2014) Lab to farm: applying research on plant genetics and genomics to crop improvement. PLoS Biol 12:e1001878.  https://doi.org/10.1371/journal.pbio.1001878CrossRefPubMedPubMedCentralGoogle Scholar
  5. Songstad DD et al (2017) Genome editing of plants. Crit Rev Plant Sci 36:1–23.  https://doi.org/10.1080/07352689.2017.1281663CrossRefGoogle Scholar
  6. Zhang X, Zhu Y, Wu H, Guo H (2016) Post-transcriptional gene silencing in plants: a double-edged sword. Sci China Life Sci 59:271–276.  https://doi.org/10.1007/s11427-015-4972-7CrossRefPubMedGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2019

Authors and Affiliations

  • P. M. Priyadarshan
    • 1
  1. 1.Erstwhile Deputy DirectorRubber Research Institute of IndiaKottayamIndia

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