here - First Legume Society Conference (LSC1)

Book of Abstracts First Legume Society Conference 2013: A Legume Odyssey Novi Sad, Serbia, 9-11 May 2013
_________________________________________________________________________________________
Translating Medicago truncatula genome sequence information for the development of
PCR based markers and discovery of single nucleotide polymorphisms for genome
analysis in legumes
HC Lohithaswa 1 , KR Sunil Kumar 2 , HB Shilpa 2 , K Jyothi 2 , K Vinutha 1 , B Rabiya 1 , Shailaja
Hittalmani 2
1 Division of Crop Improvement, V.C. Farm, Mandya, India
2 Department of Genetics and Plant Breeding, University of Agricultural Sciences, GKVK, Bangalore,
Karnataka, India
Compared to cereal crops, legumes are less well characterized at the genomic level and rightly
referred as ‘orphan crops’. Transfer of knowledge between model and crop legumes allows
development of orthologous pan-taxon genomic tools to benefit research on resource poor taxa.
Here, we developed 1180 Intron flanking gene specific markers by BLAST aligning common
bean (Phaseolus vulgaris L.) ESTs with complete genome sequence of Medicago truncatula. Primers
were designed from conserved exon borders in Medicago with near-perfect conservation (0-1
mismatch) to maximize (intronic) polymorphism discovery rates within a taxon. A random 384
PCR primer pairs representing loci from 8 chromosomes of Medicago were tested on members of
legume family. The single copy amplification rates of 86.2% (Medicago truncatula), 69.5% (Pigeon
pea), 83.6% (Cowpea), 82.0% (Horsegram), 80.9% (Chickpea), 69.3% (Urdbean), 82.7%
(Common bean), 77.3% (Field bean), 46.6% (Groundnut) and 75.2% (Soybean) signifies the
success of cross taxon primers and suggested their potential use in comparative legume genomics.
Genetic diversity was assessed in 27 cowpea genotypes using 236 intron flanking markers which
revealed 131 polymorphic markers with PIC values ranging from 0.054 to 0.59. The PCR
products of different varieties of pigeon pea, cowpea and chickpea were sequenced and aligned
using ClustalW2 to find putative SNPs. Potential SNPs detected were converted to size variation
for genotyping in pigeon pea, cowpea and chickpea. Integration of these newly developed
markers into genetic maps in resource poor legumes will not only aid in the map saturation but
also in designing successful marker assisted selection programs.
160