Molecular Breeding

, Volume 29, Issue 4, pp 833–854 | Cite as

Whole-genome strategies for marker-assisted plant breeding

  • Yunbi XuEmail author
  • Yanli Lu
  • Chuanxiao Xie
  • Shibin Gao
  • Jianmin Wan
  • Boddupalli M. Prasanna


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.


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 



Consultative Group on International Agricultural Research


International Maize and Wheat Improvement Center


Doubled haploid


Expression quantitative trait locus/loci




Genomic estimated breeding value


Genotype-by-environment interaction


Geographic information system


Genomic selection


Genome-wide association


Haplotype map


International Plant Phenomics Network


Lycopene epsilon cyclase


Linkage disequilibrium


Marker-assisted backcrossing


Multiparent advanced generation inter-cross


Marker-assisted recurrent selection


Marker-assisted selection


Metabolite quantitative trait locus/loci


Nested association mapping


Next-generation sequencing


Quantitative trait locus/loci


Protein quantitative trait locus/loci


Phenotypic quantitative trait locus/loci


Pathways of distinction analysis


Restriction enzyme


Recombinant inbred line


Southern corn leaf blight


Single nucleotide polymorphism


Targeting induced local lesions IN genomes


Training population



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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© Springer Science+Business Media B.V. 2012

Authors and Affiliations

  • Yunbi Xu
    • 1
    Email author
  • Yanli Lu
    • 2
  • Chuanxiao Xie
    • 3
  • Shibin Gao
    • 2
  • Jianmin Wan
    • 3
  • Boddupalli M. Prasanna
    • 4
  1. 1.Institute of Crop Sciences/International Maize and Wheat Improvement Center (CIMMYT), The National Key Facility for Crop Gene Resources and Genetic ImprovementChinese Academy of Agricultural SciencesBeijingChina
  2. 2.Maize Research InstituteSichuan Agricultural UniversityWenjiangChina
  3. 3.Institute of Crop Sciences, The National Key Facility for Crop Gene Resources and Genetic ImprovementChinese Academy of Agricultural SciencesBeijingChina
  4. 4.International Maize and Wheat Improvement Center (CIMMYT), ICRAF HouseNairobiKenya

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