Cassava (Manihot esculenta Crantz), a highly heterozygous crop, is devastated by cassava mosaic disease (CMD). The discovery of the CMD2 dominant gene is helpful in the genetic analysis of CMD resistance. Molecular markers for CMD2 gene were used to introgress CMD resistance into Latin American cassava genotypes and validated in the field for 4 yr for stability of resistance conferred by CMD2. Field screening identified 64 Latin American genotypes with stable resistance to CMD. Resistance to CMD of two Nigerian cassava cultivars (TMS 97/2205 and TMS 98/0505) was analyzed with markers and in the field. Molecular data indicated that CMD resistance in the two Nigerian cultivars was mediated by the CMD2 gene. Results showed TMS 97/2205 to be highly resistant to CMD in three ecological zones in Nigeria. Further genetic analysis of this genotype as a source of high level of resistance to CMD using a segregating F1 population derived from a TMS 97/2205 × NR 8083 cross was initiated using 530 simple sequence repeat (SSR) markers to identify quantitative trait loci (QTL) for CMD resistance. A marker (NS198) associated with a QTL for CMD resistance, explaining 11% of the phenotypic variance observed, was identified. The combined effect of this QTL and CMD2 may account for the high level of resistance of TMS 97/2205. The resistance profile of the evaluated CMD2 genotypes in growth cycle was not uniform and was affected by genetic background. The discovery of a new QTL (CMD3) for CMD resistance in TMS 97/2205 offers new opportunities for pyramiding CMD genes for enhanced durability of CMD resistance in cassava.

The study of quantitative trait's expression over time helps to understand developmental processes which occur in the course of the growing season. Temperature and other environmental factors play an important role. The dynamics of haulm senescence was observed in a diploid potato mapping population in two consecutive years (2004 and 2005) under field conditions in Finland. The available time series data were used in a smoothed generalized linear model to characterize curves describing the senescence development in terms of its onset, mean and maximum progression rate and inflection point. These characteristics together with the individual time points were used in a Quantitative trait loci (QTL) analysis. Although QTLs occurring early in the senescence process coincided with QTLs for onset of senescence, the analysis of the time points made it difficult to study senescence as a continuous trait. Characteristics estimated from the senescence curve allowed us to study it as a developmental process and provide a meaningful biological interpretation to the results. Stable QTLs in the two experimental years were identified for progression rate and year-specific QTLs were detected for onset of senescence and inflection point. Specific interactions between loci controlling senescence development were also found. Epistatic interaction between QTLs on chromosomes 4, 5 and 7 were detected in 2004 and pleiotopic effects of QTLs on chromosomes 3 and 4 were observed in 2005.

Several molecular marker systems have been developed for assessing genetic diversity in crop germplasm collections. A trade-off often exists between the number of loci that can feasibly be sampled by a marker system and the amount of information provided by each locus. We compared the usefulness of two marker systems for revealing genetic diversity and population structure in cassava (Manihot esculenta Crantz): simple sequence repeats (SSRs) and diversity array technology (DArT) markers. DArTs survey many more loci per reaction than do SSRs; however, as bi-allelic, dominant markers, DArTs provide less polymorphism information per locus. Genetic differentiation was assessed in a randomly selected set of 436 cassava accessions, consisting of 155 African and 281 Latin American accessions. A genome-wide set of 36 SSR markers and a DArT array of approximately 1000 polymorphic clones were used to assess genetic diversity and differentiation. Cluster analyses were performed using principal coordinate analysis (PCoA). Results were compared with a priori expectations of genetic differentiation based on previous genetic analyses. Analyses of the two datasets generated broadly similar clustering patterns. However, SSRs revealed greater differentiation than DArTs, and more effectively recovered patterns of genetic differentiation observed in previous analyses (differentiation between Latin American and African accessions, and some geographical differentiation within each of these groups). These results suggest that SSR markers, while low throughput in comparison with DArTs, are relatively better at detecting genetic differentiation in cassava germplasm collections. Nonetheless, DArTs will likely prove useful in ‘orphan crop’ species, where alternative molecular markers have not been developed.