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SNP-Based Improvement of a Microsatellite Marker Associated with Karnal Bunt Resistance in Wheat

^a Dale Bumpers National Rice Research Center, USDA ARS, 2890 Hwy 130 E. (P.O. Box 1090), Stuttgart, AR 72160
^b Department of Plant Pathology, Kansas State University, Manhattan, KS 66506
^c USDA ARS, Plant Science Research Unit, North Carolina State University, Raleigh, NC 27606

View larger version (47K): [in a new window]   Fig. 1. Panel A; Lanes 1– 6. Fragments generated when the microsatellite gwm538 associated with Karnal bunt resistance was used to evaluate genotypes HD29 (resistant parent), WL711 (susceptible parent) and KB RILs #31 and #134 (heterozygotes). Panel B; Lanes 7– 12. Fragment profiles for HD29(R), WL711(S) and KB RILs #31 and #134 (H) generated with the SNP marker. Panel C; Lanes 13– 18. Physical mapping of microsatellite gwm538 fragments in Chinese Spring (control), N4AT4D (nullisomic for 4A), N4BT4D (nullisomic for 4B) and N4DT4B (nullisomic for 4D). Size standard HyperLadder IV (Bioline, Randolph, MA), with 100- and 200-bp markers indicated in Lanes 1, 7, and 13. Negative (no template DNA) controls in Lanes 6, 12, and 18.

View larger version (9K): [in a new window]   Fig. 2. AssemblyLIGN sequence alignment of the three fragments amplified from Chinese Spring derived nullisomic-tetrasomic lines (N4BT4D and N4DT4B) using gwm538F and gwm538R primers. Fragments are labeled by size in nucleotides. Nucleotide positions are indicated at top of the figure. Primer sequences for gwm538F, gwm538R and gwm538snpF1 are included for comparison. Black arrows indicate SNPs (in bold text) occurring outside the microsatellite region. The SNP indicated at Position 18 was designed as a mismatch to all three fragments (see results) and does not ‘naturally’ occur there. Period ‘.’ characters are used as pads to allow justification for the alignment of different size fragments.