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

Locus Missing data No. of Alleles detected Allele size range (bp)
Ta144 156(5.2) 56 179-287
Ta42 104(3.5) 46 101-251
Ta176 134(4.5) 65 146-365
Ts45 142(4.7) 27 134-274
Ta11 256(8.5) 30 158-296
Ta78 88(2.9) 39 95-262
Ta194 54(1.8) 30 87-291
ICRISAT-HD Upadhyaya, SL Dwivedi, CLL Gowda, PM Gaur,
RK Varshney, DA Hoisington and S Chandra;
ICARDA- SM Udupa, M. Baum and BJ Furman
Milestone C.3.1.2: Sorghum composite set (3000 accessions) genotyped with SSR markers in collaboration with
CIRAD and CAAS (ICRISAT- CTH/SS/HDU/PR/DH; CIRAD-CB/JFR/MD/LG/RR; CAAS-YL/TW/PL, 2006)
A total of 3393 sorghum lines, including 10 duplicates, have been genotyped at 43 SSR loci (marker data
provided by CIRAD and ICRISAT; the SSR data provided by CAAS for an additional 5 SSR primer pairs has
not been included in the final data set). Some 6% of the 145,889 potential data points were missing, so several
SSRs and lines were removed from the analysis due to unacceptably high frequency of missing data, leaving
3365 sorghum lines and 39 SSR loci. This represents 87.5% of our original target of 3000 sorghum lines
genotyped at 50 SSR loci. The composite set of sorghum lines for which adequate marker data are available for
diversity analysis is comprised of 2.0% wild accessions, 8.6% breeding lines and released cultivars, and 98.4%
landrace accessions representing all five major races of sorghum and their 10 intermediates, as well as materials
originating from 13 sub-continents.
ICRISAT - CT Hash, HD Upadhyaya, Punna Ramu,and DA Hoisington;
CIRAD – C Billot, J-F Rami, L Gardes, R Rivalian,and M Deu;
CAAS – Y Li, T Wang and P Lu.
Milestone C.3.1.3: Reference collection of chickpea (300 accessions) established (HDU/ DH/RKV/CLLG/ PMG,
2006)
All allelic data for 50 SSR primers on 3000 accessions resulted in less than 5% missing data (i.e., marker x
genotype). The accessions with maximum missing values were removed and based on analysis on 2915
accessions, we have selected a reference set consisting of 300 accessions. This reference set consists of 211
accessions of mini core (Upadhyaya and Ortiz, 2001), which has been phenotyped for several traits including
drought tolerance traits, and another 89 accessions. The reference set captured 78% (1403 alleles) of the 1791
alleles detected in the 2915 accessions of composite collection. Biologically, the reference set consists of 267
landraces, 13 breeding lines/cultivars, 7 wild Cicer accessions, and 13 accessions with an unknown biological
status. Geographically it consists of accessions from Asia (198), Africa (21), Europe (3), Mediterranean (56),
Americas (10), Russian Federation (6), and 6 accessions whose geographical origin is not known. The reference
set has 195 desi, 88 kabuli, and 10 intermediate type (pea-shaped), and 7 wild Cicer accessions. The reference
set is diverse and can be used for extensive phenotyping for traits of interest and genotyping for association
studies and eventually for efficient allele mining.
HD Upadhyaya, DA Hoisington, RK Varshney, CLL Gowda and PM Gaur
Milestone C.3.1.4: Four hundred wild and cultivated Sorghums from 60 villages in Mali genotyped for 15 SSR.
Write up report (FS + NARS, 2006)
Sorghum diversity in Mali assessed by microsatellite markers: We collected wild, weedy (60 types) and
cultivated Sorghums (340 varieties) in 60 villages from all Sorghum agro-ecological regions in Mali (except the
“décrûe” Sorghums from Gao region). Sorghum seeds were germinated in a greenhouse. DNA was isolated
from fresh leaves collected on 1-3 week old seedling per variety following a modified CTAB protocol at the
University of Bamako (Mali). Fifteen SSR markers were chosen among those selected for their reliability and
scoring accuracy among laboratories, their level of polymorphism and genome coverage, for the Challenge
Program Generation. The M13-tails added to forward primers for each SSR were labeled with IRD700 or
IRD800 Xuorochromes. Plants were genotyped at the Montpellier Languedoc-Roussillon Genopole (France)
platform using Li-Cor automated sequencers. Saga GT v. 2.2 (Li-Cor) was used to determine allele sizes. First
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