Molecular Biotechnology

, Volume 50, Issue 3, pp 250–266 | Cite as

Emerging Knowledge from Genome Sequencing of Crop Species

  • Delfina Barabaschi
  • Davide Guerra
  • Katia Lacrima
  • Paolo Laino
  • Vania Michelotti
  • Simona Urso
  • Giampiero Valè
  • Luigi Cattivelli
Review

Abstract

Extensive insights into the genome composition, organization, and evolution have been gained from the plant genome sequencing and annotation ongoing projects. The analysis of crop genomes provided surprising evidences with important implications in plant origin and evolution: genome duplication, ancestral re-arrangements and unexpected polyploidization events opened new doors to address fundamental questions related to species proliferation, adaptation, and functional modulations. Detailed paleogenomic analysis led to many speculation on how chromosomes have been shaped over time in terms of gene content and order. The completion of the genome sequences of several major crops, prompted to a detailed identification and annotation of transposable elements: new hypothesis related to their composition, chromosomal distribution, insertion models, amplification rate, and evolution patterns are coming up. Availability of full genome sequence of several crop species as well as from many accessions within species is providing new keys for biodiversity exploitation and interpretation. Re-sequencing is enabling high-throughput genotyping to identify a wealth of SNP and afterward to produce haplotype maps necessary to accurately associate molecular variation to phenotype. Conservation genomics is emerging as a powerful tool to explain adaptation, genetic drift, natural selection, hybridization and to estimate genetic variation, fitness and population’s viability.

Keywords

Whole genome sequencing Whole genome duplication Transposable elements Biodiversity Re-sequencing 

Abbreviations

BAC

Bacterial artificial chromosome

CDPK

Calcium-dependent protein kinases

CI

Chromosome inversion

CNV

Copy-number variation

CSSL

Chromosome segment substitution line

DNA-TE

DNA transposable element

GWAS

Genome-wide association study

HapMap

Haplotype map

HT

Horizontal transfer

IDSR

Identical sequence region

InDel

Inversion deletion

LD

Linkage disequilibrium

LINE

Long interspersed nuclear element

LTR

Long terminal repeat

LTR-RE

Long terminal repeat retrotransposons

MULE

Mutator-like element

MYA

Million years ago

NAM

Nested association mapping

NBS–LRR

Nucleotide-binding site–leucine-rich repeat

NCF

Nested chromosome fusion

NGS

Next generation sequencing

NNGS

Next–next generation sequencing

OMAP

Oryza map alignment project

PAV

Presence–absence variation

QTL

Quantitative trait locus

RE

Retrotransposon

RefSeq

Reference sequence

RFLP

Restriction fragment-length-polymorphism

RIL

Recombinant inbred line

SNP

Single nucleotide polymorphism

TE

Transposable element

TIR

Terminal inverted repeat

WGD

Whole genome duplication

Notes

Acknowledgments

The authors would like to thank Dr. Giacomo Morreale for critical reading of the manuscript and to acknowledge the funding support from the Italian Ministry of Agriculture: “Physical Mapping of wheat chromosome 5A.”

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Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • Delfina Barabaschi
    • 1
  • Davide Guerra
    • 2
  • Katia Lacrima
    • 2
  • Paolo Laino
    • 2
  • Vania Michelotti
    • 2
  • Simona Urso
    • 2
  • Giampiero Valè
    • 2
    • 3
  • Luigi Cattivelli
    • 2
  1. 1.CRA, Viticolture Research CentreSuseganaItaly
  2. 2.CRA, Genomics Research CentreFiorenzuola d’ArdaItaly
  3. 3.CRA, Rice Research UnitVercelliItaly

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