Agriculture Reference
In-Depth Information
In this chapter, we emphasize the use of AM in tropical and sub-
tropical species of legumes, root, and tuber crops as well as review
results in cereals where the approach has been more widely applied. We
also discuss some applications in vegetables of more restricted produc-
tion as compared with these staples. In addition, we review the state of
the art in cereals, where studies of linkage disequilibrium started (Flint-
Garcia et al. 2003) and where the strategy has been widely applied (Flint-
Garcia et al. 2005; Breseghello and Sorrells 2006). There has been a new
interest in using AM for long-lived crops such as fruit trees or forestry
species (Khan et al. 2012), but there have been few examples so far in
tropical or subtropical species of these important plants.
In this chapter we will cover principles and methods of association
genetics and AM. Then, from the brief history of this science we will
summarize the types of studies that have been realized so far building on
the review from Zhu et al. (2008) who summarized the state of the art for
AM in various crops 5 years ago. Since then, there has been a steady
growth in knowledge about linkage disequilibrium and trait
marker
associations for a wide range of crops that we summarize in this chapter.
We thereafter list some practicalities, such as software developed for
population structure (PS) and AM analysis. We conclude by indicating
the limitations to AMwith genotype collections and present alternatives
that are useful for populations developed from controlled crosses and
breeding programs.
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II. ADVANTAGES OF ASSOCIATION MAPPING APPROACHES
Association mapping promises the possibility for high-resolution map-
ping of genes-controlling traits depending on the linkage disequilibrium
of the genomic region, the crop being studied, the type of trait, and the
marker density. Association studies also hold promise as a less time-
consuming approach for the discovery of marker
trait associations
compared with studies of mapping populations. These two advantages
of AM analysis should lead to the faster implementation of precision
breeding based on highly accurate marker selection and better trait
resolution.
Although association genetics approaches were de
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ned for human
genetics by Weir as early as 1988, it is only in the last decade that this
concept has been brought into wider practice and has started to be used in
crop genetics (Hill and Weir 1988). The ef
cient increases in obtaining
genotypic data and computational power available in present laboratory
computers have led to the widespread implementation of association
