Population genetic structure, gene flow and recombination of Cochliobolus miyabeanus on cultivated wildrice (Zizania palustris)

Abstract

A collection of 168 Cochliobolus miyabeanus isolates was made from cultivated wildrice (Zizania palustris) paddies in Minnesota, USA, during 2007 and 2008. Analysis of 26 polymorphic amplified fragment length polymorphism (AFLP) markers generated with three primer-pair combinations indicated a moderate average gene diversity (Ĥ) of 0AE283. Genotypic diversity was high in all collection areas with the exception of a paddy in Itasca County. Significant population subdivision by collection site was found with AMOVA tests using both the entire fungal population data (F ST = 0AE29, P < 0AE001) and the clone-corrected data (F ST = 0AE08, P < 0AE001), and with a Markov chain Monte Carlo approach. Abundant immigrants, shared haplotypes and admixed genotypes were found in paddies in central-eastern areas. Although indirect tests did not support the hypothesis of random mating at the subpopulation level, sexual recombination nevertheless may be possible in areas where both mating type idiomorphs, MAT1-1 and MAT1-2, were found. These results may have implications in breeding for resistance and disease management.

Genome Assembly of the Fungus Cochliobolus miyabeanus, and Transcriptome Analysis during Early Stages of Infection on American Wildrice (Zizania palustris L.)

“…The C . miyabeanus strain TG12bL2 (hereafter referred to as Cm TG12bL2) was isolated from a wildrice leaf with FBS symptoms collected from a paddy in Aitkin, Minnesota, USA as previously described [ 29 ]. For DNA extraction, the fungus was grown in 2% (w/v) water agar (Bacto Agar, DIFCO) for approximately two weeks until spores were produced.…”

Population structure, genetic diversity, and sexual state of the rice brown spot pathogen Bipolaris oryzae from three Asian countries

“…Also, this information could have implications for effective disease management strategies and recommendations for breeding programmes. The genetic diversity of B. oryzae collections from diverse geographical origins and hosts has been analysed with a variety of molecular markers (Kamal & Mia, ; Castell‐Miller & Samac, ; Burgos et al ., ). For example, in a B. oryzae collection from the Philippines, population subdivision was found using variable number of tandem repeat (VNTR) markers, with the two major sources of variation being collection sites and rice varieties.…”

“…The DNA sequences of MAT1‐1 and MAT1‐2 are very dissimilar, and called idiomorphs, while outer DNA flanking areas are nearly identical between homologous chromosomes (Arie et al ., ; Turgeon, ). The idiomorphs have been identified in field isolates pathogenic on switchgrass, wild rice and rice (Krupinsky et al ., ; Castell‐Miller & Samac, ; Condon et al ., ). Frequency distribution of the two idiomorphs deviated from the 1:1 ratio in some field populations (Castell‐Miller & Samac, ), while they were found equally distributed in other populations (Tsuda & Ueyama, ; Castell‐Miller & Samac, ).…”

Primary metabolism plays a central role in moulding silicon‐inducible brown spot resistance in rice

“…Consistent with plant cell death facilitating C. miyabeanus infection, brown spot is especially prevalent in rainfed ecosystems in which plants are prone to premature senescence as a result of suboptimal growth conditions (Leung et al ., ; Ou, ; Zadoks, ). Although semi‐resistant rice cultivars are available, brown spot management still relies heavily on the application of hazardous fungicides (Castell‐Miller and Samac, ). In this context, the application of Si holds great potential for environmentally friendly, economically sound and sustainable control of brown spot disease.…”