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

A microsatellite or SSR (simple sequence repeat) enriched genomic DNA library of chickpea (ICC4958) has
been constructed using pGEM-3Zf (+) vector in collaboration with the University of Frankfurt, Germany (Dr
Peter Winter). The library has been enriched for (GA)n and (TAA)n microsatellites and a total of 359 clones
have been collected. The plasmid DNA, however could be isolated for about 300 clones. These clones were
sequenced for both strands, using T7 promater primer and SP6 primer of the pGEM-3Zf (+) vector. Analysis of
sequence data with the MIcrosSAtellite (MISA) search module provided about 220 clones containing at least one
SSR. Based on the conserved flanking regions of the SSRs, the primer pairs are being designed and optimized.
RK Varshney, P Winter and DA Hoisington
In the case of pigeonpea, efforts have been initiated to generate the SSR enriched library from the pigeonpea
variety “Asha”. The genomic DNA library is being enriched for (CT)n and (TCG)n SSRs.
RK Varshney, C Prathima and DA Hoisington
Milestone D.4.1.2: Novel set of microsatellite markers developed and characterized for pearl millet
(RKV/CTH/SS/DAH, 2008)
Development of microsatellite markers for pearl millet is in progress in collaboration with Centre for Cellular
and Molecular Biology (CCMB), Hyderabad (Dr Ramesh Aggarwal). By using an SSR enrichment method,
developed at CCMB, >1000 genomic DNA clones enriched for SSRs have been developed. The isolation of
plasmid DNA and sequencing is in progress. Sequencing of about 120 clones has already been completed and
about 80 clones containing at least one SSR have been identified. The primer pairs have been designed for 64
SSRs based on the conserved flanking regions and are being optimized for amplification of SSR loci in pearl
millet.
RK Varshney, R Aggarwal, T Mahender and DA Hoisington
Activity D.4.2: Development of molecular genetic maps
Milestone D.4.2.1: Molecular genetic maps and consensus maps based on SSRs, DArTs and EST-based markers
developed for chickpea, pigeonpea and groundnut (RKV/DAH/PMG/KBS/SNN/HDU, 2010)
For developing the genetic maps in chickpea, currently three recombinant inbred line (RIL) mapping
populations i.e. one interspecific (C. arietinum ICC4958 x C. reticulatum PI 489777) and two intraspecific
(ICC4958 x ICC1882; ICC283 x ICC8261) are being used with newly developed SSR or existing SSR markers
for identification of the polymorphic markers. The polymorphic markers will be used for genotyping the
respective mapping populations.
RK Varshney, PM Gaur, J Kashiwagi and DA Hoisington
In pigeonpea, an interspecific F 2 population developed after crossing C. cajan (ICP28) x C. scarabaeoides
(ICPW94) has been screened with the SSR markers developed at ICRISAT. About 30 polymorphic SSR
markers have been identified between the parental genotypes of the mapping population. These genotypes are
being screened with DArT (Diversity Array Technology) markers in collaboration with Dr Andrzej Killian
(Australia) for identification of larger number of polymorphic loci.
RK Varshney, HD Upadhyaya and DA Hoisington
The RIL mapping population of groundnut (ICGV86031 x TAG24) is being used for developing the genetic
map for cultivated groundnut. All the existing SSR markers for groundnut as well as unpublished markers from
some research groups e.g. David Bertioli (Catholic University/EMBRAPA, Brazil) and Steve Knapp (University
of Georgia, USA) have been screened on the parental genotypes of the mapping population. However, so far
about 120 polymorphic SSR markers. These polymorphic markers are being used for genotyping of the mapping
population.
RK Varshney, V Vadez, SN Nigam, R Aruna and DA Hoisington
Milestone D.4.2.2: Molecular genetic maps and consensus maps based on SSRs, DArTs and EST-based markers
developed for pearl millet (RKV/CTH/SS/DAH, 2010)
A total of 627 markers (100 genomic SSRs, 60 EST-SSRs, 100 pearl millet SSCP-SNPs, 57 wheat SSCP-SNPs,
310 CISP-SNPs) were screened on 24 genotypes including parental genotypes of 11 mapping populations (H
77/833-2 x PRLT 2/89-33; ICMB 841-P2 x 863-P3; Tift 23D2B1-P5 x WSIL-P8; PT 732B-P2 x P1449-2-P1;
LGD 1-B-10 x ICMP 85410-P7; 81B-P6 x ICMP 451-P8; 81B-P6 x ICMP 451-P8; ICMP 451-P6 x H 77/833-2-
P5 (OT); W 504-1-P1 x P310-17; IP 18293-P152 x Tift 238D1-P158; ICMB 89111-P6 x ICMB 90111-P6 and
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