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Emerging Knowledge from Genome Sequencing of Crop Species

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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.

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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

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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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Authors and Affiliations

  1. CRA, Viticolture Research Centre, Via Casoni 13/A, 31058, Susegana, TV, Italy

    Delfina Barabaschi

  2. CRA, Genomics Research Centre, Via S. Protaso 302, 29017, Fiorenzuola d’Arda, PC, Italy

    Davide Guerra, Katia Lacrima, Paolo Laino, Vania Michelotti, Simona Urso, Giampiero Valè & Luigi Cattivelli

  3. CRA, Rice Research Unit, S.S. 11 to Torino, Km 2.5, 13100, Vercelli, Italy

    Giampiero Valè

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  1. Delfina Barabaschi
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  2. Davide Guerra
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  3. Katia Lacrima
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  4. Paolo Laino
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  8. Luigi Cattivelli
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Correspondence to Luigi Cattivelli.

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Barabaschi, D., Guerra, D., Lacrima, K. et al. Emerging Knowledge from Genome Sequencing of Crop Species. Mol Biotechnol 50, 250–266 (2012). https://doi.org/10.1007/s12033-011-9443-1

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