Agriculture Reference
In-Depth Information
simpler because most of the bioinformatic tools are designed for dip-
loids. Given the high heterozygosity, the genetic analysis of potatoes is
equivalent to some analysis in human genetics and can use some of the
same software. Even though diploids are less complicated, tools to work
with tetraploids are available and the work with diploids might serve as
a model to extrapolate to tetraploids that are the most important types of
potatoes at the commercial level.
Other root and tuber crops are lacking association studies, although
germplasm collections have been characterized in cassava, the second
most important root and tuber crop by area and production. Sweet
potatoes, yams, and taro have not been analyzed for trait
marker asso-
ciations, even though each has a wealth of novel characteristics including
vitamin and phytohormone production. Most of these tropical roots and
tubers are highly heterozygous; and many are polyploid species while
others are ancestral cryptic polyploids (i.e., behaving as diploids with
disomic inheritance, but with gene duplication across their genomes).
Although high heterozygosity is an obstacle for mapping genes and
breeding, this heterozygosity canbe valuable forAMbecausemany alleles
are present, and usually in HWE. Rare alleles found in seed-propagated
crops are less likely to be found in clonal crops, especially the polyploids,
in which rare or recessive alleles that are not ef
×
ciently selected against
can survive. Given the clonal nature of most root and tuber crops, one
advantage for AM is that clone replicates are stable genetically and
eld
replications represent true environmental variability rather than hetero-
geneity sometimes found in accessions of seed crops.
Where association studies have been carried out for dicotyledenous
crops, most have started with association of markers with simpler
quantitative traits as was done in the early stages of cereal studies. In
addition, for many of the dicotyledenous plants, the priority traits have
been disease resistance where the value of GWA and CG approaches are
still being validated. Examples are association studies for dieback
disease resistance in lettuce (Simko et al. 2009) and late-blight resistance
in potatoes (Gebhardt 2004; Gebhardt et al. 2004). Other phenotyping
studies in the dicotyledenous species have involved high-impact traits
for breeding programs and for productivity. For example, in potato, tuber
bruising and enzymatic discoloration were analyzed (Urbany et al.
2011).
Maximum AM studies attempt to analyze the most important oligo
and sometimes multigenic traits based on the economic relevance of the
trait. A good example is the study on cotton where
fiber traits were
analyzed by associations of microsatellite markers with the phenotypes
of 335 accessions (Abdurakhmonov et al. 2009). However, in many
