High-resolution linkage map and chromosome-scale genome assembly for cassava (Manihot esculenta Crantz) from 10 populations

Cassava (Manihot esculenta Crantz) is a major staple crop in Africa, Asia, and South America, and its starchy roots provide nourishment for 800 million people worldwide. Although native to South America, cassava was brought to Africa 400–500 years ago and is now widely cultivated across sub-Saharan Africa, but it is subject to biotic and abiotic stresses. To assist in the rapid identification of markers for pathogen resistance and crop traits, and to accelerate breeding programs, we generated a framework map for M. esculenta Crantz from reduced representation sequencing [genotyping-by-sequencing (GBS)]. The composite 2412-cM map integrates 10 biparental maps (comprising 3480 meioses) and organizes 22,403 genetic markers on 18 chromosomes, in agreement with the observed karyotype. We used the map to anchor 71.9% of the draft genome assembly and 90.7% of the predicted protein-coding genes. The chromosome-anchored genome sequence will be useful for breeding improvement by assisting in the rapid identification of markers linked to important traits, and in providing a framework for genomic selectionenhanced breeding of this important crop.Bill and Melinda Gates Foundation (BMGF) Grant OPPGD1493. University of Arizona. CGIAR Research Program on Roots, Tubers, and Bananas. Next Generation Cassava Breeding grant OPP1048542 from BMGF and the United Kingdom Department for International Development. BMGF grant OPPGD1016 to IITA. National Institutes of Health S10 Instrumentation Grants S10RR029668 and S10RR027303.http://www.g3journal.orghb201

Diallel analysis of field resistance to brown streak disease in cassava (Manihot esculenta Crantz) landraces from Tanzania

Published online: 13 June 2012Cassava brown streak disease (CBSD) is an economically important virus disease causing significant losses to cassava root yield and quality in east, central and southern Africa. Breeding for resistance in cassava requires an understanding of the underlying genetic control of CBSD resistance. Sources of CBSD resistance are available but little is known on the value of those varieties as parents for CBSD resistance breeding. Two resistant and two susceptible varieties were crossed in a half diallel design and 35 F1 progeny from each of the six families, plus parents, were screened at two locations in a randomised complete block design with four replications in warm sub-humid environments of coastal Tanzania in 2008. Screening for CBSD field resistance was done using disease severity scoring on a scale of 1–5. Significant variations in disease severity were observed for crosses, general combining ability (GCA) and specific combining ability (SCA) at both locations. The CBSD shoot symptom severity scores ranged from 1 to 4.4 while root necrosis ranged from 1.3 to 4.5. The contribution of GCA to the total sum of squares of crosses for disease scores ranged from 86.9 to 95.2 % compared to SCA that ranged from 4.8 to 14.2 %. Additive gene effects were more important than non-additive effects indicating that CBSD resistance is genetically determined and that selection should be successful to improve resistance. Selection of parents with good GCA effects will be important for success in CBSD resistance breeding

Mapping of QTL associated with resistance to Cassava Brown Streak and Mosaic Diseases in outcrossing cassava cultivars locally cultivated in Tanzania

Cassava brown streak (CBSD) and mosaic (CMD) diseases are the major cassava production constraints in the East African region. Efforts to control these diseases were initiated in northeastern Tanganyika in the 1930’s using conventional breeding methods. Despite these efforts, CBSD is spreading, threatening central and western Africa. Identification of molecular markers associated with observed plant resistance and tolerance would facilitate marker assisted breeding leading to efficient breeding, knowledge-based deployment of resistance genes and pre-emptive breeding in West Africa. QTL analysis using a bi-parental F1 mapping population was undertaken to identify QTL for CMD resistance in the variety ‘Albert’ and CBSD resistance in the variety ‘Namikonga’. A one-step genetic linkage map composed of 986 SNP markers and 18 linkage groups spanning 1826.3 cM was generated and used to create a framework map of 242 loci. Phenotyping data was obtained from two disease hotspots in Tanzania from 226 F1 progeny. Significant QTL were identified on chromosomes VIII, XV and I for CMD, CBSD foliar and root symptoms respectively. The maximum LOD score of 19.32 explained variation 34.9% of variation for CMD resistance. CBSD foliar and root symptoms revealed different QTL with moderate LOD scores of up to 5.09 and 7.33, explaining 10.7 and 16.2% respectively of variation. Several other minor significant QTL for all traits were also identified. Genes within QTL regions are being characterized

Candidate genes for field resistance to cassava brown streak disease revealed through the analysis of multiple data sources

Cassava (Manihot esculenta Crantz) is a food and industrial storage root crop with substantial potential to contribute to managing risk associated with climate change due to its inherent resilience and in providing a biodegradable option in manufacturing. In Africa, cassava production is challenged by two viral diseases, cassava brown streak disease (CBSD) and cassava mosaic disease. Here we detect quantitative trait loci (QTL) associated with CBSD in a biparental mapping population of a Tanzanian landrace, Nachinyaya and AR37-80, phenotyped in two locations over three years. The purpose was to use the information to ultimately facilitate either marker-assisted selection or adjust weightings in genomic selection to increase the efficiency of breeding. Results from this study were considered in relation to those from four other biparental populations, of similar genetic backgrounds, that were phenotyped and genotyped simultaneously. Further, we investigated the co-localization of QTL for CBSD resistance across populations and the genetic relationships of parents based on whole genome sequence information. Two QTL on chromosome 4 for resistance to CBSD foliar symptoms and one on each of chromosomes 11 and 18 for root necrosis were of interest. Of significance within the candidate genes underlying the QTL on chromosome 4 are Phenylalanine ammonia-lyase (PAL) and Cinnamoyl-CoA reductase (CCR) genes and three PEPR1-related kinases associated with the lignin pathway. In addition, a CCR gene was also underlying the root necrosis-resistant QTL on chromosome 11. Upregulation of key genes in the cassava lignification pathway from an earlier transcriptome study, including PAL and CCR, in a CBSD-resistant landrace compared to a susceptible landrace suggests a higher level of basal lignin deposition in the CBSD-resistant landrace. Earlier RNAscope®in situ hybridisation imaging experiments demonstrate that cassava brown streak virus (CBSV) is restricted to phloem vessels in CBSV-resistant varieties, and phloem unloading for replication in mesophyll cells is prevented. The results provide evidence for the involvement of the lignin pathway. In addition, five eukaryotic initiation factor (eIF) genes associated with plant virus resistance were found within the priority QTL regions

Application of molecular marker-assisted selection in breeding for improved farmer/market preferred cassava varieties in Tanzania

Tanzania is the fifth largest producer of cassava in Africa, the eighth largest producer in the world with an estimated average yields of about 10.4 t/ha, which is far below the potential yield of the crop. The low yield is caused by a number of factors including susceptibility of commonly grown varieties to major diseases and pests including susceptibility of local varieties to major diseases and pests such as cassava mosaic diseases (CMD), caused principally by East African Cassava Mosaic Virus (EACMV), its Ugandan variant (UgV), and African Cassava Mosaic virus (ACMV), Cassava Brown Streak Disease (CBSD), Cassava Bacterial Blight (CBB), Cassava Green Mite (CGM) and Cassava Mealy Bug (CMB). A project entitled, ‘Molecular Marker-Assisted Selection (MAS) and Farmer Participatory Improvement of Cassava Germplasm for Farmer/Market Preferred Traits in Tanzania’ was initiated to speed up the process of improving local cassava germplasm for resistance to pests and diseases in Tanzania. Improved genotypes with resistance to CMD, CGM, and CBB were introduced to Tanzania in 2003 from the International Centre for Tropical Agriculture (CIAT) Colombia and crossed with susceptible, farmer preferred varieties from the Eastern and Southern zone of Tanzania. A total of 26,590 F1 genotypes were obtained, of which 13,320.were from controlled crosses and the remaining from open pollination. The F1 genotypes were phenotypically evaluated for CMD resistance under high disease pressure at Chambezi Experimental Station in Tanzania; and at 6 six months after planting (MAP) 18,017 plants were surviving in the field, of which 11,606 were from controlled pollination and 6,411 from open pollination. About one third of the plants (6,000) did not show any CMD, CGM and CBSD symptoms. These were then subjected to marker assisted selection using four molecular markers associated with resistance to CMD, namely RME1, RME4, NS158 and NS169. The MAS results revealed that the percentage of individuals having marker alleles associated with CMD2 for 2 markers ranged between 69.8 and 89.5% in the controlled crosses and 69.1 and 83.8 in the open pollinated crosses. The results showed that 80% of all individuals selected as resistant using phenotypic evaluation were found to be resistant by MAS. This suggests that broad sense heritability for CMD resistance at the Chambezi Station during the first year evaluation was about 0.8. Although Chambezi is a very high CMD intensity site, MAS could still increase selection efficiency for CMD resistance by 20%

Molecular marker-assisted selection for starchy staples

<p>Tree A was inferred for the region defined by positions 1–219 & 721–1496. Tree B was inferred for the region defined by positions 220–720. ML trees inferred with PAUP* have identical topology to the trees shown here. Phylogenetic relationships in these trees do not support a hypothesis of homologous recombination. Other features as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010434#pone-0010434-g001" target="_blank">Figure 1</a>.</p

Genetic diversity of cassava (Manihot esculenta Crantz) landraces and cultivars from southern, eastern and central Africa

Studies to quantify genetic variation in cassava germplasm, available within the national breeding programmes in Africa, have been limited. Here, we report on the nature and extent of genetic variation that exists within 1401 cassava varieties from seven countries: Tanzania (270 genotypes); Uganda (268); Kenya (234); Rwanda (184); Democratic Republic of Congo (DRC; 177); Madagascar (186); Mozambique (82). The vast majority of these genotypes do not exist within a formal germplasm conservation initiative and were derived from farmers' fields and National Agricultural Research Systems breeding programmes. Genotypes were assayed using 26 simple sequence repeat markers. Moderate genetic variation was observed with evidence of a genetic bottleneck in the region. Some differentiation was observed among countries in both cultivars and landraces. Euclidean distance revealed the pivotal position of Tanzanian landraces in the region, and STRUCTURE analysis revealed subtle and fairly complex relationships among cultivars and among landraces and cultivars analysed together. This is likely to reflect original germplasm introductions, gene flow including farmer exchanges, disease pandemics, past breeding programmes and the introduction of cultivars from the International Institute of Tropical Agriculture – Nigeria. Information generated from this study will be useful to justify and guide a regional cassava genetic resource conservation strategy, to identify gaps in cassava diversity in the region and to guide breeding strategies