Whole-genome strategies for marker-assisted plant breeding

An Erratum to this article was published on 14 March 2012

Abstract

Molecular breeding for complex traits in crop plants requires understanding and manipulation of many factors influencing plant growth, development and responses to an array of biotic and abiotic stresses. Molecular marker-assisted breeding procedures can be facilitated and revolutionized through whole-genome strategies, which utilize full genome sequencing and genome-wide molecular markers to effectively address various genomic and environmental factors through a representative or complete set of genetic resources and breeding materials. These strategies are now increasingly based on understanding of specific genomic regions, genes/alleles, haplotypes, linkage disequilibrium (LD) block(s), gene networks and their contribution to specific phenotypes. Large-scale and high-density genotyping and genome-wide selection are two important components of these strategies. As components of whole-genome strategies, molecular breeding platforms and methodologies should be backed up by high throughput and precision phenotyping and e-typing (environmental assay) with strong support systems such as breeding informatics and decision support tools. Some basic strategies are discussed in this article, including (1) seed DNA-based genotyping for simplifying marker-assisted selection (MAS), reducing breeding cost and increasing scale and efficiency, (2) selective genotyping and phenotyping, combined with pooled DNA analysis, for capturing the most important contributing factors, (3) flexible genotyping systems, such as genotyping by sequencing and arraying, refined for different selection methods including MAS, marker-assisted recurrent selection and genomic selection (GS), (4) marker-trait association analysis using joint linkage and LD mapping, and (5) sequence-based strategies for marker development, allele mining, gene discovery and molecular breeding.

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Abbreviations

CGIAR:

Consultative Group on International Agricultural Research

CIMMYT:

International Maize and Wheat Improvement Center

DH:

Doubled haploid

eQTL:

Expression quantitative trait locus/loci

GBS:

Genotyping-by-sequencing

GEBV:

Genomic estimated breeding value

GEI:

Genotype-by-environment interaction

GIS:

Geographic information system

GS:

Genomic selection

GWA:

Genome-wide association

HapMap:

Haplotype map

IPPN:

International Plant Phenomics Network

LYCE :

Lycopene epsilon cyclase

LD:

Linkage disequilibrium

MABC:

Marker-assisted backcrossing

MAGIC:

Multiparent advanced generation inter-cross

MARS:

Marker-assisted recurrent selection

MAS:

Marker-assisted selection

mQTL:

Metabolite quantitative trait locus/loci

NAM:

Nested association mapping

NGS:

Next-generation sequencing

QTL:

Quantitative trait locus/loci

pQTL:

Protein quantitative trait locus/loci

phQTL:

Phenotypic quantitative trait locus/loci

PoDA:

Pathways of distinction analysis

RE:

Restriction enzyme

RIL:

Recombinant inbred line

SLB:

Southern corn leaf blight

SNP:

Single nucleotide polymorphism

TILLING:

Targeting induced local lesions IN genomes

TP:

Training population

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Acknowledgments

Genomics and molecular breeding research at CIMMYT, Mexico, and China has been funded by the Rockefeller Foundation, the Bill and Melinda Gates Foundation, and the European Community, and through other attributed or unrestricted funds provided by the members of the Consultative Group on International Agricultural Research (CGIAR) and national governments of USA, Japan, and UK. Research at the Institute of Crop Sciences, Chinese Academy of Agricultural Sciences is supported by the National High Technology Research and Development Program of China and International Collaboration Project, Ministry of Science and Technology of China (2011DFA31140).

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Correspondence to Yunbi Xu.

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An erratum to this article can be found at http://dx.doi.org/10.1007/s11032-012-9724-9.

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Xu, Y., Lu, Y., Xie, C. et al. Whole-genome strategies for marker-assisted plant breeding. Mol Breeding 29, 833–854 (2012). https://doi.org/10.1007/s11032-012-9699-6

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Keywords

  • Molecular breeding
  • Whole-genome strategies
  • Marker-assisted selection
  • Marker-assisted recurrent selection
  • Genomic selection
  • Genotyping platform
  • Precision phenotyping
  • Environmental assay (e-typing)
  • Breeding informatics
  • Decision support tools