Association between basal stem rot disease and simple sequence repeat markers in oil palm, Elaeis guineensis Jacq.

The oil palm is badly affected by basal stem rot (BSR) disease in Southeast Asia. BSR disease is caused by the fungus Ganoderma boninense, which is a major threat to oil palm compared with other Ganoderma spp. Molecular markers associated with BSR disease will accelerate the identification process of resistant breeding materials in screening of plants for tolerance to the disease at the nursery stage. In this study, 58 simple sequence repeat markers were utilized with three progeny types, namely, KA4G1, KA4G8, and KA14G8, to perform a comparative molecular mapping for association with BSR. A total of 319 alleles were identified with an average of 5.51 alleles per locus. Five markers, mEgCIR0793:180, mEgCIR0894:200, mEgCIR03295:210, mEgCIR3737:146 and mEgCIR3785:299 were found to be associated with Ganoderma disease with P values of 0.018, 0.033, 0.037, 0.034 and 0.037, respectively, in single progeny analysis. However, in pooled data (KA4G1, KA4G8 and KA14G8), only two alleles, mEgCIR0804:213 (P value = 0.001) and mEgCIR3292:183 (P value = 0.001), were found to be associated with Ganoderma disease. These analyses confirmed that progeny type KA4G1 was tolerant, whereas the other two were susceptible progeny types. These markers and KA4 progeny will be useful in future works on BSR disease resistance in oil palm

Fungal diseases affecting oil palm

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The route to the development of basal stem rot resistance in oil palm (Elaeis guineensis) via the discovery of lignin degradation process in the pathogen Ganoderma boninense

International audienceAlthough the oil palm (Elaeis guineensis) is the oil crop bearing the highest oil yield ha(-1) in South-East Asia, it is facing a deadly disease, the basal stem rot (BSR) which is caused by Ganoderma boninense a fungus found commonly in the soil and air. The actual mode of infection by G. boninense still remains unclear. Meanwhile, some suspected cases of BSR can result from root infection, presumably following root contact with soil inoculum or other infected roots. Hence, oil palm plantations are suffering significant loss of palms at the early stages, thus directly reducing their potential oil yield. In the present study, we selected 3 isolates of G. boninense with various degree of pathogenicity (low, medium and high) which were identified through nursery trials and we cultured these isolates on two different media (carbon rich culture and carbon rich culture incorporating oil palm saw dust). The purpose of culturing isolates in the latter medium is to mimic the presence of the host tissue as compared to the former which was used as a control. Transcriptome sequencing was conducted via an Illumina platform and we investigated the expression profiles exhibited by the 3 G. boninense isolates grown under different media. We hypothesized that cell wall degradation was one of the possible modes of infection by the pathogen, hence, transcripts involved in lignin degradation process - and particularly those associated to laccase genes - were studied in detail. Concurrently, a separate analysis (not reported here) identified 33 laccase genes based on our de novo G. boninense genome assembly. All these laccase genes (de novo) contain the laccase specific four domain sequence signature encompassing cysteine and histidine residues which are involved in copper binding. Through transcriptomic analyses, in which isolates are compared under different conditions, there is no significant gene transcript detected for the isolate showing the weakest pathogenicity. Forty-five transcripts were found to be up-regulated in the G. boninense isolate with medium pathogenicity. In the most pathogenic isolate we found 409 unique transcripts which were down-regulated and 376 unique transcripts which were up-regulated and one laccase-related transcript. As we investigated further for the isolates (between medium and most pathogenic) cultivated on carbon medium supplemented with oil palm saw dust, we found that 6,551 transcripts were up-regulated (7 transcripts were found to be associated with laccase) as compared to 6,964 transcripts which were down-regulated, of which 18 transcripts were differentially expressed between two isolates cultivated on carbon medium supplemented with oil palm saw dust

Identification and development of new polymorphic microsatellite markers using genome assembly for Ganoderma boninense, causal agent of oil palm basal stem rot disease

International audienceGanoderma boninense is a telluric lignicolous basidiomycete and the causal agent of basal stem rot, one of the most devastating diseases of the oil palm (Elaeis guineensis). While the fight against G. boninense is of major concern in Southeast Asia, little information is available regarding the genetic diversity and evolutionary history of the fungus. In this context, the development of an informative molecular marker set to characterize the diversity of G. boninense is a key step towards understanding the biology of this pathogen. A G. boninense draft genome sequence of 63 Mbp, assembled using 454 and Illumina sequencing technology, was used to identify and develop a set of microsatellite markers (simple sequence repeats, SSRs). A total of 2487 SSRs were identified, for which 145 SSR primer pairs were designed. These SSRs are characterized by di- to hexanucleotide motifs with 5 to 34 repetitions. Ninety-seven SSR loci were successfully amplified on an initial small set of G. boninense isolates from Indonesia. A collection of 107 isolates from several regions in Southeast Asia were screened to characterize each locus for allele number, polymorphism information criterion and the presence or absence of null alleles at each locus. These results allowed us to propose an effective set of 17 SSRs for studying genetic diversity within G. boninense

About Ganoderma boninense in oil palm plantations of Sumatra and peninsular Malaysia: Ancient population expansion, extensive gene flow and large scale dispersion ability

International audienceWood rot fungi form one of the main classes of phytopathogenic fungus. The group includes many species, but has remained poorly studied. Many species belonging to the Ganoderma genus are well known for causing decay in a wide range of tree species around the world. Ganoderma boninense, causal agent of oil palm basal stem rot, is responsible for considerable yield losses in Southeast Asian oil palm plantations. In a large-scale sampling operation, 357 sporophores were collected from oil palm plantations spread over peninsular Malaysia and Sumatra and genotyped using 11 SSR markers. The genotyping of these samplesmade it possible to investigate the population structure and demographic history of G. boninense across the oldest known area of interaction between oil palm and G. boninense. Results show that G. boninense possesses a high degree of genetic diversity and no detectable genetic structure at the scale of Sumatra and peninsular Malaysia. The fact that few duplicate genotypes were found in several studies including this one supports the hypothesis of spore dispersal in the spread of G. boninense. Meanwhile, spatial autocorrelation analysis shows that G. boninense is able to disperse across both short and long distances. These results bring new insight into mechanisms by which G. boninense spreads in oil palm plantations. Finally, the use of approximate Bayesian computation (ABC) modelling indicates that G. boninense has undergone a demographic expansion in the past, probably before the oil palm was introduced into Southeast Asia