Comparative analysis of infected cassava root transcriptomics reveals candidate genes for root rot disease resistance.

Cassava root-rot incited by soil-borne pathogens is one of the major diseases that reduces root yield. Although the use of resistant cultivars is the most effective method of management, the genetic basis for root-rot resistance remains poorly understood. Therefore, our work analyzed the transcriptome of two contrasting genotypes (BRS Kiriris/resistant and BGM-1345/susceptible) using RNA-Seq to understand the molecular response and identify candidate genes for resistance. Cassava seedlings (resistant and susceptible to root-rot) were both planted in infested and sterilized soil and samples from Initial-time and Final-time periods, pooled. Two controls were used: (i) seedlings collected before planting in infested soil (absolute control) and, (ii) plants grown in sterilized soil (mock treatments). For the differentially expressed genes (DEGs) analysis 23.912 were expressed in the resistant genotype, where 10.307 were differentially expressed in the control treatment, 15 DEGs in the Initial Time-period and 366 DEGs in the Final Time-period. Eighteen candidate genes from the resistant genotype were related to plant defense, such as the MLP-like protein 31 and the peroxidase A2-like gene. This is the first model of resistance at the transcriptional level proposed for the cassava × root-rot pathosystem. Gene validation will contribute to screening for resistance of germplasm, segregating populations and/or use in gene editing in the pursuit to develop most promising cassava clones with resistance to root-rot.

Genome-wide association study and selection for field resistance to cassava root rot disease and productive traits.

Cassava root rot disease is caused by a complex of soil-borne pathogens and has high economic impacts because it directly affects the tuberous roots, which are the main commercial product. This study aimed to evaluate cassava genotypes for resistance to root rot disease in a field with a previous history of high disease incidence. It also aimed to identify possible genomic regions associated with field resistance based on genome-wide association studies. A total of 148 genotypes from Embrapa Mandioca and Fruticultura were evaluated over two years, including improved materials and curated germplasms. Analysis of phenotypic data was conducted, as well as a genomic association analysis, based on the general linear model, mixed linear model, and fixed and random model circulating probability unification. The observed high disease index (ω) was directly correlated with genotype survival, affecting plant height, shoot yield, and fresh root yield. The genotypes were grouped into five clusters, which were classified according to level of root rot resistance (i.e., extremely susceptible, susceptible, moderately susceptible, moderately resistant, and resistant). The 10 genotypes with the best performance in the field were selected as potential progenitors for the development of segregating progenies. Estimates of genomic kinship between these genotypes ranged from -0.183 to 0.671. The genotypes BGM-1171 and BGM-1190 showed the lowest degree of kinship with the other selected sources of resistance. The genotypes BGM-0209, BGM-0398, and BGM-0659 showed negative kinship values with most elite varieties, while BGM-0659 presented negative kinship with all landraces. A genome-wide association analysis detected five significant single nucleotide polymorphisms related to defense mechanisms against biotic and abiotic stresses, with putative association with fresh root yield in soil infested with root rot pathogens. These findings can be utilized to develop molecular selection for root rot resistance in cassava.

Colletotrichum species causing cassava (Manihot esculenta Crantz) anthracnose in different eco-zones within the Recôncavo Region of Bahia, Brazil.

A survey to investigate the occurrence of cassava anthracnose disease (CAD) and distribution of Colletotrichum spp. in cassava plantations in different eco-zones of the Reconcavo Region in Bahia, Brazil, investigated during the rainy season of 2014. A total of 50 cassava fields distributed among 18 municipalities were visited and intensity of anthracnose evaluated. The highest disease incidence (DI) (83.3%) was in samples collected in São Félix, and the lowest (34.4%), in Varzedo. Municipalities that presented the highest values for DI were located within the 'Af' Köppen-Geiger eco-zone, also presenting the highest values for the estimated McKinney disease index. Based on previous studies of multilocus phylogeny, seven different species of Colletotrichum were identified (Colletotrichum fructicola, Colletotrichum tropicale, Colletotrichum gloeosporioides s.s, Colletotrichum theobromicola, Colletotrichum siamense, Colletotrichum brevisporum and Colletotrichum plurivorum) and a new approach based on ERIC-PCR was used aiming to group the 82 isolates according to these findings. The highest percentage of genetic variance (> 78%) was among isolates within fields. Based on the survey and genetic analysis, C. fructicola is probably the main causal agent of cassava anthracnose in the Recôncavo Region, since this species was present with highest incidence in all eco-zones, 47.61, 42.86 and 57.14% for Af (tropical rainforest climate), As (tropical dry savanna climate) and Aw (tropical wet savanna climate), respectively. This study is the first report of C. fructicola lineages as the most likely pathogen causing anthracnose disease of cassava in Brazil, and these findings may be used to guide the selection of resistant varieties.

A novel seed treatment-based multiplication approach for cassava planting material.

Cassava (Manihot esculenta Crantz) is an important food security crop in many parts of the developing world. The crop's high yield potential and multitude of uses-both for nutrition and processing-render cassava a promising driver for the development of rural value chains. It is traditionally propagated from stem cuttings of up to 30 cm in length, giving a multiplication rate as low as 1:10. Propagating cassava traditionally is very inefficient, which leads to challenges in the production and distribution of quality planting material and improved cultivars, greatly limiting the impact of investments in crop breeding. The work described in the present study aimed to develop a seed treatment approach to facilitate the use of shorter seed pieces, increasing the multiplication rate of cassava and thus making the crop's seed systems more efficient. After several tests, formulation was identified, consisting of thiamethoxam 21 g ha-1, mefenoxam 1.0 g ha-1, fludioxonil 1.3 g ha-1, thiabendazole 7.5 g ha-1 and Latex 2% as a binder. Plant growing from seed pieces treated with this formulation displayed increased crop establishment and early crop vigor, leading to an improved productivity throughout a full growing cycle. This allowed to reduce the cassava seed piece size to 8 cm with no negative effects on germination and crop establishment, leading to yields comparable to those from untreated 16 cm pieces. This, in turn, will allow to increase the multiplication ratio of cassava by a factor of up to 3. Notably, this was possible under regular field conditions and independently of any specialised treatment facilities. Compared with existing seed production protocols, the increased multiplication rates allowed for efficiency gains of between 1 to 1.9 years compared to conventional five-year cycles. We believe that the technology described here holds considerable promise for developing more reliable and remunerative delivery channels for quality cassava planting material and improved genetics.