Plant & Animal Genomes XIV Conference

January 14-18, 2006
Town & Country Convention Center
San Diego, CA

Development Of TRAP Markers In Pearl Millet For Genes Related To Nutritional Quality Of Straw, Terminal Drought Tolerance, And Salinity Stress Tolerance

Rupashree Mukhopadhyay^1,2 , V Rajaram^1,3 , Punna Ramu^1,2 , Ch Ashok Kumar¹ , PB Kavi Kishor² , S Sivaramakrishnan² , S Senthilvel¹ , B Jayashree¹ , C Tom Hash¹

¹  International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad 502 324, AP, India

²  Department of Genetics, Osmania University, Hyderabad 500 007, AP, India

³  Department of Agricultural Biotechnology, Acharya N.G. Ranga Agricultural University (ANGRAU), Rajendranagar, Hyderabad 500 030, AP, India

Target Region Amplification Polymorphism (TRAP) provides PCR-based markers for target sequence-related gene families. We developed TRAP markers using candidate genes for a major drought tolerance QTL and several QTLs associated with differences in ruminant nutritional values of grain crop residues (i.e., straw) in pearl millet. TRAP primer pairs were developed for the cinnamyl alcohol dehydrogenase gene (cad = brown midrib1 = Bm1) and caffeic acid O-methyltransferase gene (comt = brown midrib 3 = Bm3) of maize, as well as for the teosinte branched 1 (tb1) gene, which governs stress-responsive apical dominance. Pairs of fixed and arbitrary primers were tested for easily scorable PCR product banding polymorphism (presence/absence on silver-stained PAGE gels) among pearl millet mapping population parents. Seventeen of 18 candidate TRAP markers were mapped with the (841B x 863B)-derived mapping population. One, based on primers designed from the Bm3 sequence, coincided perfectly with a consistent QTL for pearl millet stover fraction digestibility, and three linked TRAP loci detected by tb1-based primer sequences coincided with the major pearl millet drought tolerance QTL. Similarly, TRAP primers were generated for delta-1-pyrolline-5-carboxylase synthase and two antioxidant enzymes (glutathione reductase and superoxide dismutase). Of 64 TRAP marker polymorphisms scored for these, 43 mapped onto the skeleton linkage map of pearl millet mapping population (Tift 23D2B1-P5 x WSIL-P8), based on parents expressing differential salinity tolerance.
TRAP successfully generated trait-specific markers. TRAP markers offer a potentially inexpensive means for preliminary evaluation of candidate genes during development of near-perfect selectable markers for species with limited sequence information.