Arithmetic Averages UPGMA. The analysis and dendrogram construction was performed using NTSYS-PC version 2.02 Rohlf 1999.
3.6.2. Agronomic Traits and Nutrient Content
Means were calculated on data for three replications. Mean value of the parents were calculated from all the replications of plants those were included in
the experimental set. Frequency distribution of each trait was analyzed using Qgene for Windows version 4.06 Nelson, 1997;
http:www.qgene.org .
Variance, covariance, and broad sense heritability were analyzed Kempthorne 1969; Table 6.
Table 6. Expected Components of Variances in a Completely Randomized Design. No Sourve of variation
df MS
EMS 1 Plants
n-1 MSP
σ
2 gx
+ σ
2 ex
2 Error nr-1 MSE
σ
2 ex
3 Total rn-1
Genotypic variance of variable x= σ
gx 2
=MS Plant – MSE3 Phenotype variance of variable x=
σ
Px 2
= σ
Gx 2
+ σ
2 ex
Heritability of the variable x :
2 2
2 2
x gx
gx x
H σ
σ σ
+ 3.6.3.
Quantitative Trait Loci
Quantitative Trait Loci analysis was done using 1 Single Marker Regression SMR; 2 Simple Interval Mapping SIM, and 3 Composite Interval Mapping
CIM. The QTL consistently detected by all the three analyses were selected. Quantitative Trait Loci analysis of backcross mapping population BC
1
F
1
included the test of F, R
2
, LOD, F Additive, and Additive Effect. QTL analysis of F
2
mapping population included the test of F, R
2
, LOD, F Additive, Additive Effect, F Dominant, and Dominant Effect. Threshold value of LOD was 3 or by 1000 times
permutation 5 and 1.
26
IV. RESULTS AND DISCUSSION 4.1. Assessment of Molecular Diversity
Microsatellite markers are the markers of choice for many breeding and genetic applications including assessment of genetic diversity because of several
reasons such as abundance, higher degree of polymorphism, cost-effectiveness, codominance and wide genomic distribution among others Panaud et al. 1995,
Akagi et al. 1996, Lapitan et al. 2007 and Edwards McCouch 2007. Furthermore, a saturated map of SSR markers in rice with 2240 validated and
another 52,845 SSR markers is available McCouch et al. 2002 and Zhang et al. 2007.
In this study promising germplasm possessing high zinc and iron content along with some nutritionally rich Korean cultivars and some popular indica rice
varieties were analyzed using SSR markers. The objectives of the present study were firstly to assess genetic diversity for grain nutritional traits amongst
promising germplasm and secondly to identify suitable parents for developing mapping populations aimed at studying the genetic control of these traits.
A total of 288 SSR markers were surveyed of which 183 were polymorphic Appendix 6. Number of SSR polymorphic markers varied from 8 to 28 for
chromosome 4 and 1 respectively. A total of 455 alleles were identified across 12 genotypes. The number of alleles varied widely for these SSR loci. For example,
the number of alleles ranged from 2 for 113 SSR loci to 6 for RM207 with an average value of 2.49. The PIC values representing allelic diversity and frequency
among genotypes varied from one locus to another. The PIC value was 0.49 per marker and it ranged from 0.08 RM563 to 0.75 RM264. PIC value varied from
one chromosome to another and was the highest 0.51 for chromosome 11 while it was the lowest 0.37 for chromosome 6. Our results both for number of alleles
and PIC values are comparable to those reported by Cho et al. 2000 but are lower than those reported by Yu et al. 2003, Thomson et al. 2007 and Lapitan
et al. 2007.
Simple Sequence Repeats loci amplifying di-nucleotide repeat motifs were in general more polymorphic with average values of alleles and PIC value 2.52
and 0.45 respectively than tri or tetra nucleotide repeat motifs. The number of
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