Cassava haplotype map highlights fixation of deleterious mutations during clonal propagation

Article purchased; Published online: 17 April 2017Cassava (Manihot esculenta Crantz) is an important staple food crop in Africa and South America; however, ubiquitous deleterious mutations may severely decrease its fitness. To evaluate these deleterious mutations, we constructed a cassava haplotype map through deep sequencing 241 diverse accessions and identified >28 million segregating variants. We found that (i) although domestication has modified starch and ketone metabolism pathways to allow for human consumption, the concomitant bottleneck and clonal propagation have resulted in a large proportion of fixed deleterious amino acid changes, increased the number of deleterious alleles by 26%, and shifted the mutational burden toward common variants; (ii) deleterious mutations have been ineffectively purged, owing to limited recombination in the cassava genome; (iii) recent breeding efforts have maintained yield by masking the most damaging recessive mutations in the heterozygous state but have been unable to purge the mutation burden; such purging should be a key target in future cassava breeding

Utility of Ugandan genomic selection cassava breeding populations for prediction of cassava viral disease resistance and yield in West African clones

Open Access Journal; Published online: 23 Nov 2022Cassava (Manihot esculenta Crantz) is a staple crop for ~800 million people in sub-Saharan Africa. Its production and productivity are being heavily affected by the two viral diseases: cassava brown streak disease (CBSD) and cassava mosaic disease (CMD), impacting greatly on edible root yield. CBSD is currently endemic to central, eastern and southern Africa, if not contained could spread to West Africa the largest cassava producer and consumer in the continent. Genomic selection (GS) has been implemented in Ugandan cassava breeding for accelerated development of virus resistant and high yielding clones. This study leveraged available GS training data in Uganda for pre-emptive CBSD breeding in W. Africa alongside CMD and fresh root yield (FRW). First, we tracked genetic gain through the current three cycles of GS in Uganda. The mean genomic estimated breeding values (GEBVs), indicated general progress from initial cycle zero (C0) to cycle one (C1) and cycle two (C2) for CBSD traits and yield except for CMD. Secondly, we used foliar data of both CBSD and CMD, as well as harvest root necrosis and yield data to perform cross-validation predictions. Cross-validation prediction accuracies of five GS models were tested for each of the three GS cycles and West African (WA) germplasm as a test set. In all cases, cross-validation prediction accuracies were low to moderate, ranging from -0.16 to 0.68 for CBSD traits, -0.27 to 0.57 for CMD and -0.22 to 0.41 for fresh root weight (FRW). Overall, the highest prediction accuracies were recorded in C0 for all traits tested across models and the best performing model in cross-validation was G-BLUP. Lastly, we tested the predictive ability of the Ugandan training sets to predict CBSD in W. African clones. In general, the Ugandan training sets had low prediction accuracies for all traits across models in West African germplasm, varying from -0.18 to 0.1. Based on the findings of this study, the cassava breeding program in Uganda has made progress through application of GS for most target traits, but the utility of the training population for pre-emptive breeding in WA is limiting. In this case, efforts should be devoted to sharing Ugandan germplasm that possess resistance with the W. African breeding programs for hybridization to fully enable deployment of genomic selection as a pre-emptive CBSD breeding strategy in W. Africa

Cassava Brown Streak Disease response and association with agronomic traits in elite Nigerian cassava cultivars

Open Access Journal; Published online: 22 Nov 2021Cassava mosaic geminiviruses (CMGs) and cassava brown streak viruses (CBSVs) cause the highest yield losses in cassava production in Africa. In particular, cassava brown streak disease (CBSD) is and continues to be a significant constraint to optimal cassava production in Eastern and Southern Africa. While CBSD has not been reported in West Africa, its recent rapid spread and damage to cassava productivity in Eastern, and Southern Africa is alarming. The aim of this study was to evaluate Nigerian cassava genotypes in order to determine their responses to CBSD, in the event that it invades Nigeria, the world’s largest cassava producer. The study gathered information on whether useful CBSD resistance alleles are present in the elite Nigerian cassava accessions. A total of 1,980 full-sib cassava seedlings from 106 families were assessed in the field at the seedling stage for a year. A subset of 569 clones were selected and assessed for another year at the clonal stage in Namulonge, central Uganda, a known hotspot for CBSD screening. Results indicated that foliar and root incidences and severities varied significantly (p ≤ 0.01, p ≤ 0.001) except for CBSD foliar incidence at 6 months (CBSD6i). Highest and lowest plot-based heritability estimates for CBSD were registered for CBSD root severity (CBSDrs) (0.71) and CBSD6i (0.5). Positive and highly significant correlations were noted between CBSD root incidence (CBSDri) and CBSDrs (r = 0.90∗∗∗). Significant positive correlations were also noted between CBSD foliar severity at 3 months (CBSD3s) and CBSD foliar incidence at 6 months (CBSD6i ) (r = 0.77∗∗∗), CBSD3s and CBSDrs (r = 0.35∗∗∗). Fresh root weight (FreshRW) negatively correlated with CBSDri and CBSDrs, respectively (r = −0.21∗∗∗ and r = −0.22∗∗∗). Similarly, CBSD3s correlated negatively with cassava mosaic disease severity at 3 (CMD3s) and 6 months (CMD6s), respectively (r = −0.25∗∗∗ and r = −0.21∗∗∗). Fifteen clones were selected using a non-weighted summation selection index for further screening. In conclusion, results revealed that the elite Nigerian accessions exhibited significant susceptibility to CBSD within 2 years of evaluation period. It is expected that this information will aid future breeding decisions for the improvement of CBSD resistance among the Nigerian cassava varieties

Effect of self-pollination with heat-treated pollen on parthenocarpy and homozygosity in cassava

Cassava\u2019s ( Manihot esculenta Crantz) high heterozygosity complicates its genetic improvement via selective breeding. Double haploid (DH) technology can be used to improve the crop\u2019s heterozygosity, thereby improving the capacity for genetic improvement. The objective of this study was to evaluate the effect of self-pollination using heated pollen on pollen tube penetration, fruit set, seed and haploid embryo development in cassava genotypes for the production of haploid cassava. Pollen from two cassava genotypes, NASE3 and NASE14, was heated at 40, 50 and 60 oC for 0.5, 1.0 and 2.0 hr each. The heated pollen was used in six rounds of self-pollinations. Pollen tube penetration was monitored by fluorescent microscopy, followed by early embryo rescue and ovule culture. Ploidy and zygosity were assessed using flow cytometry and single-nucleotide polymorphism analysis, respectively. Pollen germinated on the stigma, grew within the style through the nucellar beak, but did not reach the embryo sac, thus achieving no fertilisation in all the 5756 self-pollinated flowers. There was a reduction in pollen germination (in vitro and in vivo), pollen tube penetration and fruit set with increasing temperature. Heat-treated pollen stimulated division of the egg cell and induced development of parthenocarpic fruits. Up to 6 embryoids per ovule were observed and all regenerated plantlets were diploid, with up to 93.0% increased homozygosity. For the first time, plant regeneration from ovules, pollinated with fresh pollen at 14 days after pollination, was achieved indicating improved speed in plant regeneration. The data generated are important for the development of protocols for cassava DH plant production.La forte h\ue9t\ue9rozygotie du manioc ( Manihot esculenta Crantz) complique son am\ue9lioration g\ue9n\ue9tique par s\ue9lection s\ue9lective. La technologie d\u2018 haplo\uefde double (DH) peut \ueatre utilis\ue9e pour am\ue9liorer l\u2019h\ue9t\ue9rozygotie de la culture, am\ue9liorant ainsi la capacit\ue9 d\u2019am\ue9lioration g\ue9n\ue9tique. L\u2019objectif de cette \ue9tude \ue9tait d\u2019\ue9valuer l\u2019effet de l\u2019auto-pollinisation \ue0 l\u2019aide de pollen chauff\ue9 sur la p\ue9n\ue9tration du tube pollinique, la nouaison, le d\ue9veloppement des graines et des embryons haplo\uefdes dans les g\ue9notypes de manioc pour la production de manioc haplo\uefde. Le pollen de deux g\ue9notypes de manioc, NASE3 et NASE14, a \ue9t\ue9 chauff\ue9 \ue0 40, 50 et 60 oC pendant 0,5, 1,0 et 2,0 heure (s) chacun. Le pollen chauff\ue9 a \ue9t\ue9 utilis\ue9 dans six cycles d\u2019auto-pollinisation. La p\ue9n\ue9tration du tube pollinique a \ue9t\ue9 surveill\ue9e par microscopie fluorescente, suivie d\u2019un sauvetage pr\ue9coce des embryons et d\u2019une culture d\u2019ovules. La plo\uefdie et la zygosit\ue9 ont \ue9t\ue9 \ue9valu\ue9es \ue0 l\u2019aide de la cytom\ue9trie en flux et de l\u2019analyse du polymorphisme mononucl\ue9otidique, respectivement. Le pollen a germ\ue9 sur le stigmate, s\u2019est d\ue9velopp\ue9 dans le style \ue0 travers le bec nucellaire, mais n\u2019a pas atteint le sac embryonnaire, n\u2019obtenant ainsi aucune f\ue9condation dans toutes les 5756 fleurs autogames. Il y avait une r\ue9duction de la germination du pollen (in vitro et in vivo), de la p\ue9n\ue9tration du tube pollinique et de la nouaison avec l\u2019augmentation de la temp\ue9rature. Le pollen trait\ue9 thermiquement a stimul\ue9 la division de l\u2019ovule et induit le d\ue9veloppement de fruits parth\ue9nocarpiques. Les 6 embryo\uefdes par ovule ont \ue9t\ue9 observ\ue9s et toutes les plantules r\ue9g\ue9n\ue9r\ue9es \ue9taient diplo\uefdes, avec 93,0% d\u2018augmentation d\u2019homozygotie. Pour la premi\ue8re fois, la r\ue9g\ue9n\ue9ration des plantes \ue0 partir des ovules, pollinis\ue9es avec du pollen frais 14 jours apr\ue8s la pollinisation, a \ue9t\ue9 r\ue9alis\ue9e, indiquant une vitesse am\ue9lior\ue9e de r\ue9g\ue9n\ue9ration des plantes. Les donn\ue9es g\ue9n\ue9r\ue9es sont importantes pour l\u2019\ue9laboration de protocoles de production de plantes de manioc de DH

Effects of gamma irradiation and ethyl methane sulphonate on morphometric traits and prevalence of common viral diseases and whiteflies in cassava

Cassava ( Manihot esculenta Crantz) is an important staple and food security crop for millions of people in Africa. However, its nutritional value is limited; yet its productivity is constrained by several pests and diseases. Induced mutagenesis is one approach with the potential to overcome such biotic stresses. The objective of this study was to assess the variability in morphometric traits and prevalence of common viral diseases and whiteflies in cassava to different doses and concentrations of gamma irradiation and ethyl methane sulphonate (ems) treatments. The effects were assessed on seed germination and growth of stakes, as well as foliar viral disease symptoms and whitefly counts. Radio-sensitivity tests revealed LD50 for sprouting as 37.6Gy for \u3b3-irradiation and 0.08% for EMS treatment. There was notable decrease in sprout, epicotyl length, shoot height, petiole length and number of leaf lobes, with increasing \u3b3-ray doses and EMS concentrations. Contrastingly, total chlorophyll content increased with increasing doses of \u3b3-rays and EMS concentrations. Basing on foliar whitefly counts and disease symptoms, there was a general increase in susceptibility to whitefly infestation and cassava mosaic disease (CMD) incidence. Significantly varying levels of resistance or tolerance to whiteflies and CMD were observed among plantlets derived from irradiated and EMS treated stems, compared to the controls. These findings lay a foundation for more future research on breeding for various traits, including disease resistance in cassava using induced mutagenesis approach.Le manioc ( Manihot esculenta Crantz) est une culture de base et de la s\ue9curit\ue9 alimentaire importante pour des millions de personnes en Afrique. Cependant, sa valeur nutritionnelle est limit\ue9e; pourtant, sa productivit\ue9 est limit\ue9e par plusieurs ravageurs et maladies. La mutagen\ue8se induite est une approche ayant le potentiel de surmonter de tels stress biotiques. L\u2019objectif de cette \ue9tude \ue9tait d\u2019\ue9valuer la variabilit\ue9 des traits morphom\ue9triques et la pr\ue9valence des maladies virales courantes et des aleurodes du manioc en raison de l\u2019exposition \ue0 diff\ue9rentes doses et concentrations des traitements par l\u2018 irradiation gamma et \ue9thyl m\ue9thane sulfonate (EMS). Les effets ont \ue9t\ue9 \ue9valu\ue9s sur la germination des graines et la croissance des tuteurs, ainsi que sur les sympt\uf4mes de la maladie virale foliaire et le nombre des aleurodes. Les tests de radiosensibilit\ue9 ont r\ue9v\ue9l\ue9 que la DL50 pour la germination \ue9tait de 37,6 Gy pour l\u2019irradiation et de 0,08 % pour le traitement EMS. Il y avait une diminution notable de la pousse, de la longueur de l\u2019\ue9picotyle, de la hauteur des pousses, de la longueur du p\ue9tiole et du nombre des lobes foliaires, avec l\u2019augmentation des doses de rayons et des concentrations EMS. En revanche, la teneur totale en chlorophylle augmentait avec l\u2019augmentation des doses de rayons et des concentrations EMS. Sur la base des d\ue9nombrements foliaires des aleurodes et des sympt\uf4mes de la maladie, il y avait une susceptibilit\ue9 g\ue9n\ue9ralement accrue \ue0 l\u2019infestation des aleurodes et \ue0 l\u2019incidence de la maladie de la mosa\uefque du manioc (CMD). Des niveaux significativement variables de r\ue9sistance ou de tol\ue9rance aux aleurodes et \ue0 la CMD ont \ue9t\ue9 observ\ue9s parmi les plantules d\ue9riv\ue9es de tiges irradi\ue9es et trait\ue9es par EMS, par rapport aux t\ue9moins. Ces r\ue9sultats jettent les bases des autres recherches futures sur la s\ue9lection pour les divers caract\ue8res, y compris la r\ue9sistance aux maladies du manioc en utilisant une approche de mutagen\ue8se induite

Estimates for heritability and consumer-validation of a penetrometer method for phenotyping softness of cooked cassava roots

Although breeders have made significant progress in the genetic improvement of cassava ( Manihot esculenta Crantz) for agronomic traits, lack of information on heritability and limited testing of high-throughput phenotyping methods are major limitations to improving root quality traits, such as softness after cooking, which rank high among Ugandan consumers. The objectives of this study were to determine heritability for softness of cooked cassava roots, and quantify the relationship between penetrometer and consumer testing methods for phenotyping softness of cassava roots. Softness defined as the maximum force (N) needed to penetrate cooked root samples using a penetrometer, was evaluated at four cooking time intervals: 15, 30, 45, and 60 min on 268 cassava genotypes. Estimates of broad-sense heritability (repeatability) ranged from 0.17 to 0.37, with the highest value observed at 45 min of cooking time interval. In the second study involving 135 cassava consumers from Kibaale district in Uganda, penetrometer measurements of cooked roots from six cassava varieties were found to be in strong agreement (r2 = 0.91; P-value = 0.003) with ordinal scores of root softness from consumer testing. These results suggest that: (a) softness of cooked cassava roots is a trait amenable for evaluation and selection; and (b) a penetrometer can readily be used for assessment of cooked root softness. These findings form the basis for operationalising the routine assessment of root softness in cassava breeding trials, an output that will enhance ongoing efforts to breed for desired end-user root quality traits.Les s\ue9lectionneurs ont fait des progr\ue8s consid\ue9rables dans l\u2019am\ue9lioration g\ue9n\ue9tique des caract\ue8res agronomiques du manioc ( Manihot esculenta Crantz). Cependant un manque de m\ue9thodes de ph\ue9notypage haut-d\ue9bit adapt\ue9es aux caract\ue8res de qualit\ue9s tel que la fermet\ue9 de la racine apr\ue8s cuisson, essentiel pour les consommateurs Ougandais. Cette \ue9tude ambitionne a) de determiner l\u2019h\ue9ritabilit\ue9 de la fermete de racine cuite b) de quantifier la relation entre l \ue9valuation de la fermet\ue9 de racine cuite au p\ue9n\ue9trom\ue8tre et un panel consommateurs. Cette \ue9valuation a \ue9t\ue9 realisee a quatre intervals de temps: 15, 30, 45 et 60 minutes sur 268 genotypes de manioc. Pour d\ue9finir l\u2019h\ue9ritabilit\ue9 de la fermet\ue9 de la racine, celle ci a \ue9t\ue9 d\ue9finie par la force maximum (N) n\ue9cessaire pour p\ue9n\ue9trer des \ue9chantillons de racines incluant diff\ue8rent temps de cuisson (15, 30, 45, and 60 min) a l\u2019aide d\u2019un p\ue9n\ue9trom\ue8tre. L\u2019h\ue9ritabilit\ue9 au sens large (ou r\ue9p\ue9tabilit\ue9) observ\ue9e varie de 0.17 a 0.37, la valeur la plus \ue9lev\ue9 \ue9tant observ\ue9e pour un temps de cuisson de 45 minutes. Dans une seconde \ue9tude impliquant 135 consommateurs du district de Kibaale (Ouest de l\u2019Ouganda), les mesures au p\ue9n\ue9trom\ue8tre de racines cuites de six vari\ue9t\ue9s ont confirm\ue9es la forte correlation (r2 = 0.91; P-value = 0.003) avec les valeurs ordinales de fermet\ue9 de racine du panel consommateur. Les r\ue9sultats de cette \ue9tude indiquent que cette m\ue9thodologie de ph\ue9notypage est a) utile pour l\u2019 \ue9valuation de la fermet\ue9 sur des racines cuites en selection et b) d\ue9montre que l\u2019usage du p\ue9n\ue9trom\ue8tre est efficace pour celle ci. Ces r\ue9sultats offrent aux s\ue9lectionneurs une methode d\u2019 \ue9valuation de routine de la qualite de racine pour les essais experimentaux. Ceux ci contribueront aux efforts actuels pour l\u2019am\ue9lioration des caract\ue8res qualit\ue9s chers aux consommateurs

Molecular-assisted selection for resistance to cassava mosaic disease in Manihot esculenta Crantz

The geminivirus complex known as cassava mosaic disease (CMD) is one of the most devastating viruses for cassava (Manihot esculenta Crantz). The aim of this study was to use molecular-assisted selection (MAS) to identify CMD-resistant accessions and ascertain promising crosses with elite Brazilian varieties. One thousand two hundred twenty-four accessions were genotyped using five molecular markers (NS169, NS158, SSRY028, SSRY040 and RME1) that were associated with resistance to CMD, along with 402 SNPs (single-nucleotide polymorphism). The promising crosses were identified using a discriminant analysis of main component (DAPC), and the matrix of genomic relationship was estimated with SNP markers. The CMD1 gene, previously described in M. glaziovii, was not found in M. esculenta. In contrast, the CMD2 gene was found in 5, 4 and 5 % of cassava accessions, with flanking markers NS169+RME1, NS158+RME1 and SSRY28+RME1, respectively. Only seven accessions presented all markers linked to the CMD resistance. The DAPC of the seven accessions along with 17 elite cassava varieties led to the formation of three divergent clusters. Potential sources of resistance to CMD were divided into two groups, while the elite varieties were distributed into three groups. The low estimates of the genomic relationship (ranging from -0.167 to 0.681 with an average of 0.076) contributed to the success in identifying contrasting genotypes. The use of MAS in countries where CMD is a quarantine disease constitutes a successful strategy not only for identifying the resistant accessions but also for determining the promising crosses

Quantification of starch physicochemical characteristics in a cassava segregating population

Culinary cassava ( Manihot esculenta L.) qualities that make a variety popular are a function of starch physicochemical properties. Hence, in response to inferior root qualities in some released cassava varieties in Uganda compared to the local germplasm, a study was undertaken to examine: (i) starch physicochemical characteristics in both introduced and local varieties; and (ii) the variation in the starch properties of their F1 progenies. The local varieties included Bao, Nyaraboke, Kakwale, and Bamunanika; and the introduced genotypes SE/95/00036, NASE 10, NASE 12, TME 5, and TME 14. Of the generated 7000 F1 seedlings, 1077 seedlings were selected, cloned (6-8 plants per genotype) and established in a single-row trial. Root samples were collected per clone and examined for starch physicochemical properties. Considerable variations were observed in the F1 families compared to the parental lines with weak correlations in most starch properties (r < 0.25). Amylose content ranged from 10 to 25%, with the amylose: amylopectin ratio between 1:3 and 1:9. Among the F1 families, solubility and swelling power ranged from 1-15g100g-1 and 40-140g100 starch at 60°C, respectively. In the parents, it ranged between 1.3-8.6 and 50-67g100g-1 starch at 60°C, respectively. Fresh root starch yield ranged from 18 to 34%, with dry matter content varying from 19-47% in both the F1 families and the parents. Ash and lipid content varied among the F1 families and parents with ranges 0.05-0.29% for ash and 0.1-0.32% for lipids. In both the parents and the F1 families, the reducing sugar and protein content ranged between 0.7-1.7 and 0.23-0.43%, respectively. These findings demonstrate: (i) existence of considerable genetic variations in starch physicochemical properties in both local and introduced cassava genotypes and their progenies, and (ii) potential utilisation of cassava starches for various applications based on the inherent differences in physicochemical characteristics.Les qualités qui rendent le manioc culinaire ( Manihot esculenta L.) une variété populaire sont fonction des propriétés physico-chimiques de l&apos;amidon. Ainsi, en réponse aux qualités inférieures des racines dans certaines variétés de manioc diffusées en Ouganda en comparaison avec les matériels génétiques locaux, une étude avait était menée dans le but d&apos;examiner: (i) les caractéristiques physico-chimiques de l&apos;amidon aussi bien dans les variétés locales que dans les variétés exotiques introduites; en plus (ii) la variation dans les propriétés de l&apos;amidon des progenies F1. Les variétés locales sont Bao, Nyaraboke, Kakwale, Bamunanika et les génotypes exotiques SE/95/ 00036, NASE 10, NASE 12, TME 5 et TME 14. De 7000 F1plantules générées, 1077 plantules ont été sélectionnées, clonées (6-8 plants par génotype) et établies dans un essai en ligne unique. Les échantillons des racines avaient été collectées par clone et examinées pour les propriétés physico-chimiques de l&apos;amidon. Les variations considérables avaient été observées dans les familles F1 comparativement aux lignés parentales avec faibles corrélations dans la plupart de propriétés de l&apos;amidon (r < 0.25). Le contenu en amylose était de 10 à 25%, pour l&apos;amylose : rapport d&apos;amylopectin entre 1: 3 et 1: 9. Parmi les familles F1, la solubilité et le pouvoir de gonflement variaient respectivement de 1-15g100g-1 et 40-140 g 100 g-1 d&apos;amidon à 600C; tandis que dans les parents ils variaient respectivement entre 1,3-8.6 et l&apos;amidon 50-67g100g-1 à 60°C. Le rendement en amidon des racines fraîches était de 18 à 34 %, la teneur en matière sèche allant de 19-47 % au sein des familles F1 et les parents. Le contenu en cendres et lipides variait dans les familles F1 et les parents dans un intrvalle de 0,05- 0,29 % pour les cendres et de 0,32-0,1 % pour les lipides. Dans aussi bien les parents que les familles F1, le contenu en sucre reduit et en protéines variait respectivement entre 0,7- 1,7 et 0,23-0,43%. Ces conclusions demontrent: (i) l&apos;existence de variations génétiques considérables dans les propriétés physicochimiques de l&apos;amidon aussi bien pour les génotypes exotiques de manioc que traditionnels, ainsi que leurs progenies, et (ii) l&apos;utilisation potentielle des amidons du manioc pour diverses applications basées sur les différences inhérentes aux caractéristiques physico-chimiques