Vector backbone integration in transgenic cassava is significantly correlated to T-DNA copy number

Multiple T-DNA integrations often occur with transgenic technology, resulting in complex integration patterns and transgene silencing. This study, investigates the correlation coefficient of T-DNA copy number on vector backbone (VBB) integration in transgenic cassava using Dot blot and PCR analysis. Thirty-nine, fifty-one and thirty-eight transgenic cassava plant lines recovered from transformations of cassava friable embryogenic callus with A. tumefaciens strain LBA4404 independently carrying p8016, p8052, and p900 were randomly selected and evaluated for VBB integration and T-DNA copy number. The occurrences of events with low (1-2) and high (≥ 3) T-DNA copy numbers were correlated with the presence and absence of VBB integration. Seventy-two to ninety-eight percent of VBB-free events were low copy number events while 2 to 28% of same where high copy number events. Correlation coefficient of the data revealed that the number of VBB-free events showed a significant positive correlation (r = 0.821, n = 9, p = 0.01) for events with low T-DNA copy number and a significant negative correlation (r = -0.739, n =9, p = 0.02) for high copy number events. This shows that the recovery of events with low T-DNA copy number increases the chances of recovering VBB-free events thereby enhancing the production of quality transgenic events. Key words: Copy number, DsRed, T-DNA, transformation, transgenic cassava, vector backbone integration

Opportunities and challenges for biofortification of cassava to address iron and zinc deficiency in Nigeria

Open Access Article; Published online: 24 Jan 2021Nigeria is the world's largest producer of cassava (Manihot esculenta), and its production is important to the country's economy. Cassava's edible storage roots act as a critical staple food for over 180 million Nigerians. Micronutrient deficiency presents a major public health issue in Nigeria and correlates with cassava consumption level across six-agro-ecological zones within the country. Though high in caloric value, cassava roots are deficient in minerals, placing populations that rely on this crop at risk of hidden hunger. Micronutrient deficiencies, especially iron and zinc, affect an estimated 6 million children in Nigeria under five years of age. Supplementation, fortification and food-based diversification are being employed to tackle micronutrient deficiencies. However, in order to achieve wider impact and sustainability, biofortification of staple foods such as cassava is also being explored. Conventional breeding of cassava is unlikely to achieve elevated storage root mineral content at nutritionally significant levels due to lack of genetic diversity for these traits within the existing germplasm. Biofortification by genetic modification provides a potential solution to this challenge. Proof of concept has demonstrated that transgenic biofortification is a reality and can produce foodstuffs with increased mineral content that could beneficially impact the health of consumers in Nigeria and elsewhere. This review is targeted towards understanding the dynamics of micronutrient deficiency across Nigeria and addresses opportunities and challenges for deploying iron and zinc biofortified cassava

Towards closing cassava yield gap in West Africa : Agronomic efficiency and storage root yield responses to NPK fertilizers

Nutrient management of cassava has received little attention compared with cereal crops. We evaluated cassava yield potential and nutrient use efficiency when supplied with nitrogen, phosphorus and potassium at high rates and when supplied with increasing rates of K. On-farm experiments were conducted at six locations in Nigeria across the major cassava growing agro-ecologies of Western Africa (Tropical Rainforest – Cross River, Forest Transition Savanna – Edo, and Guinea Savanna – Benue) during two seasons (2016–2017 and 2017–2018). Nitrogen, P and K fertilizers were applied at various rates, including treatments with and without added secondary and micronutrients. Storage root dry matter (DM) yields ranged between 11 and 35 t DM ha−1. The largest yields were obtained with a mean agronomic efficiency of 60, 162 and 51 kg DM of storage roots per kg of N, P and K applied, with average uptakes of 364, 44 and 242 kg N, P and K ha−1 respectively. Storage root yield responses to applied N, P and K fertilizers (2–18, 3–16 and 3–22 t DM ha−1, respectively) varied across the locations, reflecting variability in potential yields and applied NPK ratios. Addition of a mixture of secondary and micronutrients did not affect cassava yields. We found that the caloric energy yield of cassava per kg of N applied is 2.7 times larger than the value reported for maize. Increasing the supply of K gave a high agronomic efficiency of N even when supplied at high rates, supporting the theory of “increasing returns to scale” of De Wit. We conclude that cassava has a major role in future food security of sub-Saharan Africa, with potentially larger DM yields, a better recovery of applied nutrients and larger energy yield per kg of applied N fertilizer when compared with grains.</p

A recalibrated and tested LINTUL-Cassava simulation model provides insight into the high yield potential of cassava under rainfed conditions

Accurate assessments of the yield potential of cassava are needed to analyse yield gaps, define yield targets and set benchmarks for actual yields in Nigeria. This study evaluated the crop model LINTUL-Cassava under assumed potential growth and water-limited conditions in Nigeria. On-farm experiments were conducted at six locations across the three major cassava growing agro-ecologies of Western Africa (Tropical Rainforest – Ogoja and Ikom in Cross River state, Rainforest Transition Savanna – Ekpoma in Edo state and Guinea Savanna – Otukpo in Benue state) during two subsequent seasons (2016 – 2018). Treatments included fertilizer rates calculated to support the assumed potential yields of 90 t fresh storage root yield ha−1 y−1 (equivalent to 32 t DM ha−1, produced in a growing season of 12 months). Light interception (LI) and leaf area index (LAI) were measured each month. The weights of leaves, stems and storage roots were measured at 4 and 8 months after planting and at harvest, and radiation use efficiency (RUE) calculated. The Edo experiment from 2016 was without drought stress and was used to parameterise LINTUL-Cassava and calibrate assimilate partitioning as function of temperature sums. The average fraction of light intercepted during the season was 80 %, with a light extinction coefficient of 0.67 and a RUE of 2.8 g DM MJ−1 intercepted photosynthetically active radiation (IPAR). After calibration, the LINTUL-Cassava model described the crop growth and observed patterns of LAI well in the experiments in Cross River and Edo (2017). Simulated and observed storage root yield at 4 MAP (vegetative period), 8 MAP (mid-season) and at harvest were strongly correlated (R2 of 0.92), with a RMSE of 4.93 t DM ha−1. We ascertained that RUE of cassava was much higher than previously observed in Africa, with an average storage root yield of 39 ± 7 t DM ha−1. Consequently, potential yields are greater and yield gaps larger than expected or previously reported. We conclude that the LINTUL-Cassava model can provide an adequate estimate of storage root yield across major cassava growing agroecological zones in Nigeria under rainfed conditions.</p

Chromosome evolution and the genetic basis of agronomically important traits in greater yam

The nutrient-rich tubers of the greater yam Dioscorea alata L. provide food and income security for millions of people around the world. Despite its global importance, however, greater yam remains an “orphan crop.” Here we address this resource gap by presenting a highly-contiguous chromosome-scale genome assembly of greater yam combined with a dense genetic map derived from African breeding populations. The genome sequence reveals an ancient lineage-specific genome duplication, followed by extensive genome-wide reorganization. Using our new genomic tools we find quantitative trait loci for susceptibility to anthracnose, a damaging fungal pathogen of yam, and several tuber quality traits. Genomic analysis of breeding lines reveals both extensive inbreeding as well as regions of extensive heterozygosity that may represent interspecific introgression during domestication. These tools and insights will enable yam breeders to unlock the potential of this staple crop and take full advantage of its adaptability to varied environments

Morphological variation and isozyme diversity in Dioscorea alata L. landraces from Vale do Ribeira, Brazil

Traditional growers of the Vale do Ribeira, São Paulo State, grow and make use of several D. alata landraces. This study assessed the genetic diversity of 16 landraces, using isozymatic and morphological markers and comparing them with 19 commercial varieties of D. alata. Their distribution in different levels of organization such as households and communities of the Vale do Ribeira was evaluated. Isozymatic analyses were performed with polyacrylamide (six systems) and starch gels (one system), while the morphological analyses were carried out with 24 traits. Due to the polyploid nature of this species, the isozymatic bands were scored as binary data. Morphological traits were also scored as binary data. Principal coordinates and cluster analyses were conducted for both markers, using for the later the Jaccard´s similarity coefficient and UPGMA method. The separation of the landraces from the commercial varieties, which showed lower genetic diversity, was reported for both markers. No correlation between genetic and geographical distances was found for both data, which suggests that the observed variability is not spatially structured. Also, no correlation was found between both markers. The analysis of molecular variance (AMOVA) indicated that genetic diversity was mainly found within households for both isozymatic (54%) and morphological (70%) markers. The results obtained for both markers revealed the importance of traditional agriculturists in the Vale do Ribeira in maintaining high diversity for D. alata, even higher than the varieties commercialized in São Paulo State, contributing for the in situ/on farm conservation of this crop