Identification and characterisation of molecular markers linked to leaf rust resistance gene Lr41

Abstract

Wheat is one of the major food crops consumed by man and is grown in a wide range of environments. One constraint in the production of wheat is the different diseases attack the crop. One such a diseases is leaf rust. Leaf rust is caused by Pucdnia recondita f.sp. trifid and is the most widespread and regularly occurring rust on wheat. Researchers are continually searching for new resistance genes and to date 47 leaf rust resistance genes (Lr) have been designated in wheat. Three molecular techniques RAPDs (random amplified polymorphic DNA), AFLPs (amplified fragment length polymorphism) and SSRs (microsatellites) were used to identify and analyse the distances between different cereal genotypes. Four RAPD primers, three AFLP primers and two SSR primers were used to analyse the wheat genotypes, x-tritosecale and rye. The average polymorphisms obtained from the AFLPs were 100 polymorphisms per AFLP primer combination, and is much higher than with the RAPD primers (11-16 polymorphic loci). The four RAPD primers failed to identify unique molecular markers for the wheat genotypes. The AFLP primers were able to distinguished between the 'Kiewiet', rye, 'SA463/*4Palmiet', 'SA684', TA2460' and 'KG90WGRClO' genotypes. The SSR primer pair XGWM122150 was able to amplify a fragment from the A or B genome. The pairwise distances between the genotypes revealed that the wheat genotypes were genetically very close, with an average distance value of 0.29 between the genotypes. The genotypes, 'TA2460', 'TAMI07' and 'KS90WGRCI0', were not closely related to the South African wheat genotypes and were genetically very close to each other. The rye and 'Kiewiet' genotypes were grouped as an outgroup by the UPGMA analysis and were the least closely related to the cereal genotypes. RAPD (Random amplified polymorphic DNA) and AFLP (amplified fragment length polymorphism) analysis were used to identify molecular markers linked to leaf rust resistance gene Lr41. Bulk and parental lines were screened with 380 RAPD primers and 64 AFLP primer combinations. A total of 3190 RAPD and 1859 AFLP loci, respectively were screened for linkage to the resistance gene. Twelve fragments (seven RAPD and five AFLP), nine in coupling phase and three in repulsion phase, were identified as putative markers for the leaf rust resistance gene Lr41. Segregation analysis of these markers in a BC2F2 population revealed varying linkage distances that ranged from 2.8 to 33 cM. The coupling phase AFLP marker E-AAG:M-CTA300 was converted into a sequence characterised amplified region (SCAR) marker. AFLP markers have potential for marker assisted selection breeding programs, provided it can be converted into SCARs or equivalent marker typed systems.