ICRISAT Archival Report 2006 - The seedlings of success in the ...

throughput assay (ICRISAT: ABI3700 and ICARDA: ABI3100) and 50 SSR markers. ICRISAT generated data
on 35 SSR loci and ICARDA on 15 SSR loci on 3000 accessions (Table 5).
Identification of Markers: Identified 50 polymorphic SSRs for genotyping the global composite collection
from preliminary screening of 288 diverse chickpea germplasm accessions with 200 SSRs in 2004. Three di-and
tri-nucleoid repeat motifs markers were of 174-241 (bp) allele size at annealing temperature of 60-65 o C (Huttel
et al., 1999), 42 di-and tri-nucleoid repeat motifs markers were of 132-436 (bp) allele size at annealing
temperature of 55- 65 o C (Winter et al., 1999), and 5 di- nucleoid repeat motifs markers were of 195-306 (bp)
allele size at annealing temperature of 60-65 o C (Niroj et al., 2003).
Data Generated: ICRISAT and ICARDA were involved in genotyping of the composite collection using high
throughput assay and 50 SSR markers. ICRISAT generated 35 SSR loci data and provided sufficient and good
quality DNA for the 3000 accessions to ICARDA. ICARDA generated 15 SSR loci data.
All allelic data for 50 SSR primers on 3000 accessions resulted in less than 5% missing data (i.e., marker x
genotype). The dataset was then analyzed using the allele-binning algorithm of Idury and Cardon (1997) called
“Allelobin”. The quality index of the markers was calculated based on missing data recorded for each of the
markers and also to see if there was any allelic drift for these markers. Except for TA21, TA22, TA28, and
TA58 (data not shown), all markers produced an allele size expected on the basis of SSR repeat motif.
Data templates consisting of 105000 (3000 x 35) data points generated at ICRISAT has been delivered to GCP
repository. Data templates consisting of 45000 data points (3000 x 15) generated at ICARDA are currently
being checked for completeness will be delivered to repository soon after verification by ICARDA
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