3. RADseq: Restriction-site Associated DNA markers
Uses Illumina sequencing technology
Based on digestion with restriction enzymes. An adapter binds to the restriction site and up to 5kb fragments are sequenced around the target size.
Bioinformatics work used to find SNPs on the amplified regions

4. MORPHOLOGICAL
RFLP
SSR
STS
DArT
SNP
RAD

5. Marker Usefulness
Informativeness - measured by the number of alleles and allele frequencies
heterozygosity (H)
polymorphic information content (PIC)
Throughput - multiplex ratio (number of simultaneously assayed loci)
Utility
reproducibility of the marker assay
clarity of the marker genotypes

6. Heterozygosity or Gene/Marker Diversity
pi is the frequency of the ith allele
k is the No. of alleles
(Nei 1973)
Outbred population
H estimates the probability that a randomly sampled individual is heterozygous
Inbred population
H estimates the probability that a randomly sampled pair of lines are homozygous for different alleles

7. The Hardy-Weinberg Principle
AA Aa Aa aa
p1 (freq. of A) = 0.5
p2 (freq of a) = 0.5
p12 (freq. of AA) = 0.25
p22 (freq. of aa) = 0.25
2 p1 p2 (freq. of Aa) = 0.50
p p1 p2 + p22 = 1.00
freq. of homozygotes = p12 + p22
freq. of heterozygotes = 1 - (p12 + p22)

8. Examples ABO alleles in humans SSR markers in sunflower
If p1 = 0.28 , p2 = 0.06 , and p3 = 0.66
H = 1 – ( ) = 0.48
SSR markers in sunflower
If p1 = 0.13 , p2 = 0.19 , p3 = 0.62 , and p4 = 0.06
H = 1 – ( ) = 0.56

9. Heterozygosity for a genetic marker with k equally frequent alleles
No. Alleles
Alleles 1 2 3 4 5 p1
1.0
0.95
0.90
0.85
0.92
0.50
0.33
0.25
0.20 p2
0.05
0.02 p3
0.34 p4 p5 H
0.0
0.10
0.19
0.27
0.15
0.67
0.75
0.80
Heterozygosity for a genetic marker with k equally frequent alleles

10. Polymorphism Information Content (PIC)
pi is the frequency of the ith allele
pj is the frequency of the jth allele
k is the No. of alleles
(Botstein et al. 1980)
A measure of the informativeness of a genetic marker for linkage analysis
Probability that a marker will be polymorphic in a set of untested genotypes

11. H vs. PIC
Heterozygocity and PIC for a genetic marker with k equally frequent alleles

12. Mean Heterozygosity Hj is the heterozygocity of the jth markers
n is the No. of genetic markers

13. Mean Heterozygosity
HT mean heterozygocity for polymorphic and monomorphic markers
Hp mean heterozygocity for polymorphic markers
Hj is the heterozygocity of the jth markers
np is the No. of polymorphic markers
nm is the No. of monomorphic markers
When averaging over polymorphic and non-polymorphic markers

14. Mean number of polymorphic genetic markers per assay
ma is the No. of bands produced by ath assay
b is the No. of assays
m is the mean No. of bands per assay
HT is the mean heterozygosity
Product of the mean number of bands per assay and mean heterozygocity