Agriculture Reference
In-Depth Information
when there is large genotypic diversity and low LD for the germplasm being
investigated. This methodology was initially applied in human genetics, espe-
cially to understand the genetic basis of many complex traits, especially the
inheritance of susceptibility to some diseases. Previously, most quantitative trait
analyses for crop species were done exclusively by linkage mapping, but now
AM offers an alternative that uses raw germplasm or breeding populations that
are of interest to seed bank curators and plant improvement programs. AM has
been most widely used in cereals whose wide diversity and low LD have allowed
fine mapping of candidate and noncandidate genes. In this chapter, we discuss
the advantages and disadvantages of association genetics and mapping espe-
cially in dicotyledonous crops of the Fabaceae and Solanaceae with various
genome sizes and reproductive strategies (clonal versus sexual). The main
objective of this chapter is to highlight the uses of association genetics in major
and minor crop species and species that have trouble being analyzed for QTL
with classical methods. We discuss the utility of the approach for accelerating
breeding in tropical crops, especially in the developing world.
KEYWORDS:
association mapping; candidate genes; genome-wide association
scans; genomic selection; linkage disequilibrium; population structure
ABBREVIATIONS
I. INTRODUCTION
II. ADVANTAGES OF ASSOCIATION MAPPING APPROACHES
A. Principles of Association Genetics and Association Mapping
B. Principles of Linkage Disequilibrium
III. METHODS OF ASSOCIATION GENETICS
A. Sampling or Selection of Individuals for Population Analysis
B. Population Genotyping
C. Phenotypic Characterization of the Population for the Trait of Interest
D. Assessment of the Association Between Genotypes and Phenotypes
E. Determining the Level and In
uence of Population Structure
1. Genome Control in Association Mapping
2. Structured Association and Model-Based Methods
IV. EXAMPLES OF ASSOCIATION MAPPING
A. Cereals
B. Dicotyledenous Crops
V. SOFTWARE FOR DATA ANALYSIS
A. Population Structure Determination
B. Software Used for Population Association Mapping
VI. ASSOCIATION MAPPING COMPAREDWITH LINKAGE MAPPING
A. Limitations
B. Alternatives
VII. GENOME-WIDE SELECTION AND GENOMIC SELECTION
VIII. OUTLOOK
ACKNOWLEDGMENTS
LITERATURE CITED
