SIMPLE SEQUENCE REPEAT ANALYSIS OF 2015 WHEAT STEM RUST PATHOGEN (Puccinia graminis f. sp. Tritici); (Pgt) POPULATION IN KENYA.

Abstract

Wheat (Triticum aestivium) production in Kenya is severely hampered by emerging and re-emerging pathogens, stem rust Ug99 and related race group being one of the major constraints. The challenge has been largely attributed due to rapid evolution of races within the Ug99 lineage defeating deployed resistance genes. The objectives of this study were to determine the level of genetic variation of Pgt population in Kenya (2015) whether it is single or multiple and the driving force of the level of genetic variation whether due to asexual mutations, sexual recombination or migration forces. A total of 536 single uredinial-pustules were collected from wheat fields in the four-main wheat growing regions: Mount Kenya (101 samples), Central Rift (171 samples), North Rift (108 samples) and South Rift (156 samples). Out of the total samples collected, 104 single uredinial-pustule collections were successfully genotyped using 10 Pgt Simple Sequence Repeats (SSR) markers. Allele frequency distribution ranged from 2 to 4 per locus with an average of 3.10 per locus. Observed heterozygosity (Ho) for each of the ten SSR loci were significantly different (P < 0.001) than the expected heterozygosity (He) with Fixation Index (F) ranging from (-0.083 to -0.765). Five SSR Multi-locus Genotypes (SSR-MLGs) were identified. Neighbour joining (NJ) tree analysis clustered the five SSR-MLGs based on samples chosen from wheat growing fields with clade I (Ug99 race group) and clade IV-B (race TKTTF/TTTTF) indicating 2015 Pgt population being single. Analysis of molecular variance (AMOVA) showed that the majority of the variation occurred within the samples (91%) rather than between regions (9%). Psex values from each SSR-MLGs were significantly different (P <0.001) than the simulated psex (1.60E-08) meaning they likely belong to the same genet and clonal in nature. This would confirm that the SSR-MLGs generated are as a result of asexual mutation.