Emmanuel Okogbenin

Genome mapping in cassava improvement: Challenges, achievements and opportunities

Breeding goals of yield increases, root quality improvement, and disease resistance in cassava are considerably slowed down by biological characteristics of the crop, which includes a long growth cycle, a heterozygous genetic background and a poor knowledge of the organization of crop diversity. These factors severely hamper the speed and ease of moving around useful genes in cassava. The consequences are that cassava production fails to keep up with demand, especially in regions where over90% of yield is consumed as food, leading to an increase in acreage of cassava fields mostly into marginal lands. The advent of molecular markers,genome studies and plant genetic transformation holds promise of providing ways around breeding obstacles in long growth cycle and heterozygous crops. A number of these new tools, including a molecular genetic map, markers linked to disease resistance genes, and marker-aided studies of complex traits now exist or are being developed for cassava at CIAT. Large scale sequencing and mapping of expressed sequence tags(ESTs) have been initiated, towards a transcript map of cassava and the implementation of the candidate-gene approach to complex trait mapping. A cassava bacterial artificial chromosome (BAC) library has also been constructed to expedite positional cloning of genes, known only by their phenotypes and their position relative to markers on a molecular genetic map and complementation studies of candidate loci. Studies of genes that control traits of agronomic importance, and their allelic diversity in nature,provides powerful tools for understanding the basis of crop performance and improvement.

Phenotypic approaches to drought in cassava: review

Cassava is an important crop in Africa, Asia, Latin America, and the Caribbean. Cassava can be produced adequately in drought conditions making it the ideal food security crop in marginal environments. Although cassava can tolerate drought stress, it can be genetically improved to enhance productivity in such environments. Drought adaptation studies in over three decades in cassava have identified relevant mechanisms which have been explored in conventional breeding. Drought is a quantitative trait and its multigenic nature makes it very challenging to effectively manipulate and combine genes in breeding for rapid genetic gain and selection process. Cassava has a long growth cycle of 12–18 months which invariably contributes to a long breeding scheme for the crop. Modern breeding using advances in genomics and improved genotyping, is facilitating the dissection and genetic analysis of complex traits including drought tolerance, thus helping to better elucidate and understand the genetic basis of such traits. A beneficial goal of new innovative breeding strategies is to shorten the breeding cycle using minimized, efficient or fast phenotyping protocols. While high throughput genotyping have been achieved, this is rarely the case for phenotyping for drought adaptation. Some of the storage root phenotyping in cassava are often done very late in the evaluation cycle making selection process very slow. This paper highlights some modified traits suitable for early-growth phase phenotyping that may be used to reduce drought phenotyping cycle in cassava. Such modified traits can significantly complement the high throughput genotyping procedures to fast track breeding of improved drought tolerant varieties. The need for metabolite profiling, improved phenomics to take advantage of next generation sequencing technologies and high throughput phenotyping are basic steps for future direction to improve genetic gain and maximize speed for drought tolerance breeding.

Genetic analysis and QTL mapping of early root bulking in an F1 population of non-inbred parents in cassava ( Manihot esculenta Crantz).

Abstract.The genetic basis of early bulking in cassava was studied in a replicated, multi-locational trial using 144 F1 progeny derived from an intra-specific cross between two non-inbred parents. A second, sequential harvest experiment examined the relative importance of eight yield-related traits on early bulking and their QTLs during the crop growth cycle. Our objectives were to identify traits, and genes controlling them, strongly associated with early yield as a first step to marker-assisted improvement of the trait. Multiple linear regression analysis and stepwise regression of early yield on eight yield-related traits revealed harvest index, dry foliage weight and root diameter as the most important factors associated with early yield. A total of 18 QTLs controlling early yield were identified in the first and second experiments and 27 QTLs, 2 for dry foliage weight, 8 for harvest index and 17 for root diameter, in the second experiment. The individual effects of alleles at these QTLs identified ranged from 7% to 33% of the phenotypic variance explained. Seven of 18 QTLs found for early yield (39%) coincided with QTLs associated with one or more traits with significant influence on early yield. The results show that sink and source capacities are very important in determining early yield. The identification of a number of QTLs with positive effect for increased early yield provides an opportunity for marker-assisted selection and improvement of early bulking potential in cassava.

Mapping wound-response genes involved in post-harvest physiological deterioration (PPD) of cassava (Manihot esculenta Crantz)

The genome locations of the wound-response genes that were expressedduring the post-harvest physiological deterioration (PPD) of cassava, suchas phenylalanine ammonia lyase, β-1.3 glucanase, hydroxyprolinerich glycoprotein, catalase, 1-aminocyclopropane 1-carboxylate, cysteineprotease inhibitor, aspartic protease, a partial cDNA for serine/threonineprotein kinase and peroxidase, have been identified on the frameworkmolecular genetic map of cassava. Also, molecular markers linked toputative quantitative trait loci (QTLs) influencing PPD of cassava weremapped using an F1mapping population derived from elite parentallines (TMS 30572 × cm 2177-2). A molecular linkage map previouslyconstructed based on the segregation of 240 RFLP, 100 RAPD, 85microsatellite and five isoenzyme markers on 144 F1 individuals wasused for the QTL mapping.A set of 10 molecular markers with a significant association with putativeQTLs for PPD were identified based on probability values < 0.005in order to minimize the detection of false positives. Based on single-markerregression, eight putative QTLs located on the linkage groups G, P, L, U,and X of the female-derived framework map were found to explain between 5–12% of the phenotypic variance of the PPD. In the male-derived frameworkmap, two putative QTLs on linkage groups C and L explained 13% and11% of this variance, respectively. This study thus identified the majorgenome regions of cassava related to physiological post-harvestdeterioration, thereby providing tools for the identification of gene(s)controlling this trait.

A global alliance declaring war on cassava viruses in Africa

James Legg & Eklou Attiogbevi Somado & Ian Barker & Larry Beach & Hernan Ceballos & Willmer Cuellar & Warid Elkhoury & Dan Gerling & Jan Helsen & Clair Hershey & Andy Jarvis & Peter Kulakow & Lava Kumar & Jim Lorenzen & John Lynam & Matthew McMahon & Gowda Maruthi & Doug Miano & Kiddo Mtunda & Pheneas Natwuruhunga & Emmanuel Okogbenin & Phemba Pezo & Eugene Terry & Graham Thiele & Mike Thresh & Jonathan Wadsworth & Steve Walsh & Stephan Winter & Joe Tohme & Claude Fauquet