Page 55 - RUT Publisher

Life Science Research and Sustainable Development ISBN: 978-98-84663-33-9

d27- D-27 11 P3-P6 frame shift Hao Lin,
ZF802 2009
mutant/Z
F802
(5200 F2)

GN, Grain number; GW, Grain weight; GS, grain size; TN, Tillers number; PL, Panicle length;
HI, Harvest index; GF, Grain filling.

6.Association mapping
Plant breeding and genetics rely on geneticmaps. These are made by analysis of
segregating plant populations derived by crossingparents with contrasting characteristics. The
hybridresulting from such a cross is then allowed toproduce offspring by selfing, and it is in
thissegregating family that genetic variation, causingdifferent physical attributes (known as
thephenotype), can be assessed. Regions of the plantchromosomes that contain important
geneticinformation governing interesting and heritablephenotypic traits are identified by co-
inheritancewith molecular DNA markers. Molecular markersare basically different length DNA
fragments that areall inherited in a simple Mendelian manner. During the reproductive phase,
recombination, orcross-over, occurs between the correspondingchromosomes from the two
parents in the cross. Thisleads to reshuffling of the genes from each parent sothat the
chromosomes in the offspring will consist ofmixtures, some parts of which are derived from
oneparent, and some from the other. The closer twopositions on the chromosome (loci) are
together, theless likely it is that a cross-over point is locatedbetween them. The closeness of the
linkage betweentwo loci can therefore be measured in a segregatingfamily by observing the
inheritance of molecularmarkers, which can then be ordered on the geneticmap. The association
or linkage of particularmolecular marker variants (alleles) with an heritablephenotypic trait
enables us to identify which regionof a particular chromosome is important for the phenotype.
This is important for plant varietydevelopment because it means that plant breederscan use
markers to test for the presence of importanttraits rather than testing for the traits themselves.This
is called marker assisted selection (MAS).Genetic linkage between two loci (genes or molecular
markers) on a genome is revealed by thefact that they are associated, or in LinkageDisequilibrium
(LD). This is a genetic term meaningthat the two loci are very closely associated and islocated
very close together on the chromosome
6.1 Population structure analysis
Pritchard et al. (2000) introduced the so-calledstructured association to reduce
confounding due topopulation structure. The approach is based onassigning individuals to
subpopulations by using amodel-based Bayesian clustering algorithm,STRUCTURE, and
carrying out all analyses asconditional on the inferred assignments. TheSTRUCTURE algorithm
is computationally intensiveand may be impractical on large datasets. Price et al. (2006) suggested
that a principal components analysisbe used to summarize genome-wide patterns ofrelatedness.
However, as the population is divided inmore subgroups, the probability of false positives
isreduced at the cost of a reduction in statistical power.Moreover, any method that effectively
removesconfounding also removes the true positives that arestrongly correlated with population
structure (Zhao et al., 2007). For instance, if the causal polymorphismsare perfectly correlated with
the underlying populationstructure, distinguishing between true and falsepositives statistically
is impossible, and any attempt toremove the latter will remove the former.The structured

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