Nelson Morante

Prediction of carotenoids, cyanide and dry matter contents in fresh cassava root using NIRS and Hunter color techniques

Efforts are currently underway to improve carotenoids content in cassava roots through conventional breeding as a strategy to reduce vitamin A deficiency. However, only few samples can be quantified each day for total carotenoids (TCC) and β-carotene (TBC) contents, limiting the gains from breeding. A database with >3000 samples was used to evaluate the potential of NIRS and chromameter devices to predict root quality traits. Maximum TTC and TBC were up to 25.5 and 16.6 μg/g (fresh weight basis), respectively. NIRS predictions were highly satisfactory for dry matter content (DMC, R(2): 0.96), TCC (R(2): 0.92) and TBC (R(2): 0.93). NIRS could also distinguish roots with high or low cyanogenic potential (R(2): 0.86). Hunter color parameters could also be used for predictions, but with lower accuracy than NIRS. NIRS or chromameter improve selection protocols, allowing faster gains from breeding. Results also demonstrate that TBC and DMC can be improved simultaneously (required for the adoption of biofortified cassava).

Diallel inheritance of relevant traits in cassava (Manihot esculenta Crantz) adapted to acid-soil savannas

There is a limited knowledge on the inheritance of traits with agronomic relevance in cassava. A diallel study among 10 parental clones was conducted in the acid-soils environment in the eastern savannas of Colombia. Thirty clones were obtained for each F1 cross. Each clone was represented by six plants, which were distributed in three replications at two locations. Therefore, the same 30 genotypes of each F1 cross were planted in the three replications at the two locations. Analysis of variance suggested significant effects for five of the six variables analyzed (harvest index, dry matter content, height of first branching, reaction to super elongation disease, and plant type scores). Fresh root yield showed strong genotype × environment interaction and differences between crosses reached statistical significance in only one of the two environments analyzed. General and specific combining ability effects and their interaction with the environment were significant for most of the variables as well. Results suggested that dominance plays an important role particularly in the cases of fresh root yield and harvest index.

Within-family genetic variation and epistasis in cassava (Manihot esculenta Crantz) adapted to the acid-soils environment

Little is known about the inheritance of agronomic traits in cassava, or on the relative importance of epistasis for most crops. A group of 10 clones, adapted to the acid-soils environment was used as parents in a diallel study. Thirty genotypes were obtained from each F1 cross and cloned. Each clone was represented by six plants, which were distributed in three replications at two contrasting locations. Genetic variability concentrated in the within-family component, which was statistically significant for all the variables analyzed (fresh root yield (FRY), fresh foliage yield (FFY), harvest index, root dry matter content, and plant type score (PTS)) except for the reaction to super elongation disease (SED). Estimates of dominance variance were considerably larger than those of additive variance for fresh root and foliage yields. The reverse was observed for harvest index, dry matter content, PTS and SED score. Epistasis played an important role only for fresh root and foliage productions. These results agree with those from similar studies targeting different environments. The common assumption of absence of significant epistatic effects frequent in many quantitative genetic designs is, therefore, challenged from the results for these two variables. Alternative breeding approaches are suggested according to the results obtained from this study.

Biological implications in cassava for the production of amylose-free starch: Impact on root yield and related traits

Cassava (Manihot esculenta, Crantz) is an important food security crop, but it is becoming an important raw material for different industrial applications. Cassava is the second most important source of starch worldwide. Novel starch properties are of interest to the starch industry, and one them is the recently identified amylose-free (waxy) cassava starch. Waxy mutants have been found in different crops and have been often associated with a yield penalty. There are ongoing efforts to develop commercial cassava varieties with amylose-free starch. However, little information is available regarding the biological and agronomic implications of starch mutations in cassava, nor in other root and tuber crops. In this study, siblings from eight full-sib families, segregating for the waxy trait, were used to determine if the mutation has implications for yield, dry matter content (DMC) and harvest index in cassava. A total of 87 waxy and 87 wild-type starch genotypes from the eight families were used in the study. The only significant effect of starch type was on DMC (p < 0.01), with waxy clones having a 0.8% lower content than their wild type counterparts. There was no effect of starch type on fresh root yield (FRY), adjusted FRY and harvest index. It is not clear if lower DMC is a pleiotropic effect of the waxy starch mutation or else the result of linked genes introgressed along with the mutation. It is expected that commercial waxy cassava varieties will have competitive FRYs but special efforts will be required to attain adequate DMCs. This study contributes to the limited knowledge available of the impact of starch mutations on the agronomic performance of root and tuber crops.

Cassava Breeding I: The Value of Breeding Value

Breeding cassava relies on several selection stages (single row trial-SRT; preliminary; advanced; and uniform yield trials—UYT). This study uses data from 14 years of evaluations. From more than 20,000 genotypes initially evaluated only 114 reached the last stage. The objective was to assess how the data at SRT could be used to predict the probabilities of genotypes reaching the UYT. Phenotypic data from each genotype at SRT was integrated into the selection index (SIN) used by the cassava breeding program. Average SIN from all the progenies derived from each progenitor was then obtained. Average SIN is an approximation of the breeding value of each progenitor. Data clearly suggested that some genotypes were better progenitors than others (e.g., high number of their progenies reaching the UYT), suggesting important variation in breeding values of progenitors. However, regression of average SIN of each parental genotype on the number of their respective progenies reaching UYT resulted in a negligible coefficient of determination (r2 = 0.05). Breeding value (e.g., average SIN) at SRT was not efficient predicting which genotypes were more likely to reach the UYT stage. Number of families and progenies derived from a given progenitor were more efficient predicting the probabilities of the progeny from a given parent reaching the UYT stage. Large within-family genetic variation tends to mask the true breeding value of each progenitor. The use of partially inbred progenitors (e.g., S1 or S2 genotypes) would reduce the within-family genetic variation thus making the assessment of breeding value more accurate. Moreover, partial inbreeding of progenitors can improve the breeding value of the original (S0) parental material and sharply accelerate genetic gains. For instance, homozygous S1 genotypes for the dominant resistance to cassava mosaic disease (CMD) could be generated and selected. All gametes from these selected S1 genotypes would carry the desirable allele and 100% of their progenies would be resistant. Only half the gametes produced by the heterozygous S0 progenitor would carry the allele of interest. For other characteristics, progenies from the S1 genotypes should be, at worst, similar to those generated by the S0 progenitors.

LOCAL Regression Algorithm Improves near Infrared Spectroscopy Predictions When the Target Constituent Evolves in Breeding Populations

The CGIAR Harvest Plus Challenge Program began in the mid-2000s to support the genetic improvement of nutritional quality in various crops, including the carotenoids content of cassava roots. Successful conventional breeding requires a large number of segregating progenies. However, only a few samples can be quantified by high performance liquid chromatography each day for total carotenoids (TCC) and β-carotene (TBC) contents, limiting the gains from breeding. This study describes the usefulness of near infrared (NIR) spectroscopy and the efficiency of a large database coupled to a LOCAL regression algorithm to reach accurate TCC/TBC predictions on fresh cassava roots. The cassava database (6026 samples) was built over six years. TCC values ranged from 0.11 μg g−1 to 29.0 μg g−1, whereas TBC ranged from negligible values up to 20.1 μg g−1. All values were measured and expressed on a fresh weight basis. Between 2009 and 2014 increases in TCC and TBC were 86% and 122%, respectively. A comparison of calibrations using partial least squares (PLS) regression and LOCAL regression was done. The standard error of prediction were 1.82 μg g−1 for TCC and 1.28 μg g−1 for TBC using PLS model and 1.38 μg g−1 and 1.02 μg g−1, respectively, using LOCAL regression. The specificity of the data, with increasing content of the constituent of interest year after year, clearly showed the limitation of the classical partial least squares regression approach. The LOCAL regression algorithm takes advantage of large databases; this study highlighted the efficiency of this concept. NIR spectroscopy coupled to LOCAL regression led to efficient models for breeding programmes aiming at increasing carotenoids content in fresh cassava roots. NIR spectroscopy can also be used to predict other important constituents such as dry matter content and cyanogenic glucosides.

Genetic distance and specific combining ability in cassava

Cassava (Manihot esculenta Crantz) is an important source of energy in the tropics. Its starchy roots are valuable for food security as well as for different industries. Cassava is an outcrossing crop and its breeding is based on the use of heterozygous progenitors. Non-additive genetic effects are important for fresh root yield (FRY) and can be exploited through reciprocal recurrent selection. Results from three diallel studies (with 9-10 progenitors), conducted at three different environments (sub-humid, acid soils and mid-altitude valleys) in Colombia, have already been published for FRY. In this article, phenotypic analysis of dry matter yield (DMY) was also conducted. Specific combining ability effects and actual FRY and DMY data was linked to Nei’s genetic distances which were estimated through a set of 95 SNPs diagnostic of the cassava diversity. Results from regression analyses indicated inconsistent and generally weak associations between genetic distances and performance of the F1 families per se (r2 values ranging from 0.01 to 0.10) and specific combining ability effects (r2 values ranging from 0.00 to 0.28) for the two variables analyzed.

Cassava Breeding II: Phenotypic Correlations through the Different Stages of Selection

Breeding cassava relies on a phenotypic recurrent selection that takes advantage of the vegetative propagation of this crop. Successive stages of selection (single row trial–SRT; preliminary yield trial–PYT; advanced yield trial–AYT; and uniform yield trials UYT), gradually reduce the number of genotypes as the plot size, number of replications and locations increase. An important feature of this scheme is that, because of the clonal, reproduction of cassava, the same identical genotypes are evaluated throughout these four successive stages of selection. For this study data, from 14 years (more than 30,000 data points) of evaluation in a sub-humid tropical environment was consolidated for a meta-analysis. Correlation coefficients for fresh root yield (FRY), dry matter content (DMC), harvest index (HIN), and plant type score (PTS) along the different stages of selection were estimated. DMC and PTS measured in different trials showed the highest correlation coefficients, indicating a relatively good repeatability. HIN had an intermediate repeatability, whereas FRY had the lowest value. The association between HIN and FRY was lower than expected, suggesting that HIN in early stages was not reliable as indirect selection for FRY in later stages. There was a consistent decrease in the average performance of clones grown in PYTs compared with the earlier evaluation of the same genotypes at SRTs. A feasible explanation for this trend is the impact of the environment on the physiological and nutritional status of the planting material and/or epigenetic effects. The usefulness of HIN is questioned. Measuring this variable takes considerable efforts at harvest time. DMC and FRY showed a weak positive association in SRT (r = 0.21) but a clearly negative one at UYT (r = −0.42). The change in the relationship between these variables is the result of selection. In later stages of selection, the plant is forced to maximize productivity on a dry weight basis either by maximizing FRY or DMC, but not both. Alternatively, the plant may achieve high dry root yield by simultaneously attaining “acceptable” (but not maximum) levels of FRY and DMC.