Molecular Breeding

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

Whole-genome strategies for marker-assisted plant breeding

  • Yunbi Xu
  • Yanli Lu
  • Chuanxiao Xie
  • Shibin Gao
  • Jianmin Wan
  • Boddupalli M. Prasanna
Article

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.

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 

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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© Springer Science+Business Media B.V. 2012

Authors and Affiliations

  • Yunbi Xu
    • 1
  • 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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