Affiliations: Bioinformatics and Biometrics Unit, International
Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502
324, Andhra Pradesh, India. E-mail:
{b.jayashree,r.punna,p.prasad,s.chandra}@cgiar.org | Applied Genomics Laboratory, International Crops
Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324,
Andhra Pradesh, India. E-mail: [email protected],
{c.hash,d.hoisington,r.k.varshney}@cgiar.org
Note: [] Corresponding author
Abstract: Simple sequence repeats (SSRs) or microsatellites are an important
class of molecular markers for genome analysis and plant breeding applications.
In this paper, the SSR distributions within ESTs from the legumes soybean
(Glycine max, representing 135.86 Mb), medicago (Medicago truncatula,
121.1 Mb) and lotus (Lotus japonicus, 45.4 Mb) have been studied relative
to the distributions in cereals such as sorghum (Sorghum bicolor, 98.9
Mb), rice (Oryza sativa, 143.9 Mb) and maize (Zea mays, 183.7 Mb).
The relative abundance, density, composition and putative annotations of di-,
tri-, tetra- and penta-nucleotide repeats have been compared and SSR containing
ESTs (SSR-ESTs) have been clustered to give a non-redundant set of EST-SSRs,
available in a database. Further, a subset of such candidate EST-SSRs from
sorghum have been tested for their ability to detect polymorphism between
Striga-susceptible, stay-green drought tolerant mapping population parent 'E
36-1' and its Striga-resistant, non-stay-green counterpart 'N13'. Primer
sets for 64% of the EST-SSRs tested produced a clear and specific PCR
product band and 34% of these detected scorable polymorphism between the N13
and E 36-1 parental lines. Over half of these markers have been genotyped on 94
RILs from the (N13 × E 36-1)-based mapping population, with 42 markers
mapping onto the ten sorghum linkage groups. This establishes the value of this
database as a resource of molecular markers for practical applications in
cereal and legume genetics and breeding. The primer pairs for non-redundant
EST-SSRs have been designed and are freely available through the database
(http://intranet.icrisat.org/gt1/ssr/ssrdatabase.html).
Keywords: EST-SSRs, microsatellite markers, conserved orthologous sets, tri-nucleotide repeats, class I repeats, class II repeats, cereals and legumes
