Cassava Mosaic Disease Resistance Research Articles

Developing Cassava Mosaic Disease resistant cassava varieties in Ghana using a marker assisted selection approach

Cassava is a major staple and food security crop in Africa which can produce a crop under uncertain rainfall and low fertility conditions. However, it suffers from several pests and diseases, with Cassava Mosaic Disease (CMD) being the main biotic constraint in production in sub-Saharan Africa. It is caused by cassava mosaic geminiviruses. Plants infected with CMD usually produce a few or no storage roots. Markers associated with resistance genes to CMD have been mapped, including a major dominant gene, CMD2. Eight CMD resistant genotypes from CIAT were used in crosses with three cassava landraces and one IITA breeding genotype. CMD evaluation was done on the parents and 525 F1 progenies comprising of individuals pre-selected for CMD resistance based on average severity scores of 1 and 2. Multiple marker analysis was used to screen for the CMD2 gene, where four markers associated with this gene were used. Of the tested genotypes 83 % showed at least one marker allele for the CMD2 gene. Two CIAT genotypes (CR52A-31 and AR14-10) had all four marker alleles. TMEII had three alleles associated with CMD2 while Dabodabo had one marker allele. This suggests that Dababo may have alternative genes than CMD2 for CMD resistance. The F1 families showed segregation for the CMD2 gene. A total of 88 individuals (17 %) had all four marker alleles associated with the CMD2 gene. A total of 179 individuals had between one to three marker alleles each associated with CMD2. A total of 91 individuals had no marker allele associated with the CMD2 gene.

Genetic Mapping Using Genotyping‐by‐Sequencing in the Clonally Propagated Cassava

ABSTRACTCassava (Manihot esculenta L.) is one of the most important food crops in the tropics, but yields are far below their potential. The gene pool of cassava contains natural genetic diversity relevant to many important breeding goals, but breeding progress has been slow, partly because of insufficient genomic resources. As a first step toward implementing genomewide genetic studies that will facilitate rapid genetic gain through breeding, we genotyped‐by‐sequencing a set of 182 full‐sibs population of cassava that segregated in several traits: resistance to the cassava mosaic disease (CMD) and yield under CMD pressure; increased carotenoid content in storage roots; color of stem exterior and anthocyanin pigmentation in the petioles, inner root skin, and apical leaves. Employing a rare‐cutting restriction enzyme, PstI, in a genotyping‐by‐sequencing (GBS) library preparation, we obtained 2478 segregating single nucleotide polymorphisms (SNPs), of which 1257 passed standard filtering for missing genotypes and deviation from expected genotypic frequencies. We mapped 772 SNPs across 19 linkage groups and anchored 313 unique scaffolds from the version 4.1 of the cassava genome assembly. Most of the studied morphological traits as well as resistance to CMD and root carotenoid content showed qualitative inheritance. As expected, quantitative trait loci analysis for these traits revealed single loci surrounded by small confidence intervals. Yield under CMD was associated with the CMD resistance locus. We show that GBS is a powerful genotyping tool that provides a sufficient number of markers for unraveling the genetic architecture of Mendelian traits in cassava in addition to the development of a robust genetic map that can help anchor unassembled genomic scaffolds.

English

Cassava mosaic disease (CMD), caused by cassava mosaic geminivirus (CMG) is the most-important disease threatening production of cassava (Manihot esculenta) in Ghana. The disease is best managed through host-plant resistance. The study was conducted to assess resistance of 38 cassava genotypes to CMD, determine the associated resistance gene, and to identify the strains of CMG infecting cassava in Ghana. Both morphological and molecular markers were used to screen 38 cassava accessions against CMG infection. Morphological studies revealed one genotype (Capevars) as highly resistant whilst three others (Adehye, Nkabom and KW085) were tolerant, showing mild symptoms. PCR analyses using strain specific primers, however, detected the virus in all the three tolerant genotypes, but absent in Capevars. However, the dominant CMD resistance gene, CMD2, was detected in both the resistant and the tolerant genotypes. Apart from Capevars, the other 37 cassava genotypes were infected by, at least, one of the four ACMV variants of ACMV1, ACMV2, ACMV-AL and ACMV3. It is, therefore, concluded that field screening for CMD resistance, should integrate phenotypic evaluation and detection of the virus.  Key words: Cassava, African cassava mosaic virus, simple sequence repeats, resistance.

Combining ability of cassava genotypes for cassava mosaic disease and cassava bacterial blight, yield and its related components in two ecological zones in Ghana

Breeding for resistant genotypes is the best strategy to offset the destructive effects of cassava mosaic disease (CMD) and cassava bacterial blight (CBB). Two sets of diallel parents were selected for the forest and the savannah ecological zones in Ghana based on good levels of resistance to CMD and CBB. Both sets were crossed in a half-diallel design. The first set of seven progenitors and their 21 F1 progenies were planted in a randomised complete block design (RCBD) with three replications in two different locations for two seasons in the forest ecology. The second set of five progenitors and their 10 F1 progenies were planted in a RCBD with three replications in two locations in the coastal savannah ecological zone of Ghana. Both experiments were evaluated for CMD and CBB resistance, fresh root yield, dry root yield, root number, harvest index, dry matter content, plant height at maturity and height at first branching, levels of branching and plant vigour. Results of the combined analysis of variance revealed that the environment effect was significant for all the traits. General combining ability and specific combining ability effects were significant for most of the traits. Narrow sense heritability was significant for plant vigour, root number, CMD and CBB in both the zones. CMD and root number also had a predictability ratio of close to one, indicating the importance of additive gene effects.

Mapping New Genetic Markers Associated with CMD Resistance in Cassava (Manihot esculenta Crantz) Using Simple Sequence Repeat Markers

Cassava mosaic disease (CMD) is the most serious disease in cassava–in India where it is grown for food, starch and sago purpose. The disease is best kept under control by exploiting the available host plant resistance, which was introgressed from M. glaziovii to cassava and it is known to be polygenic control. In the present study, an attempt was made to construct the genetic linkage map of cassava using SSR markers with the objective of mapping genes associated with CMD. Using single marker analysis (SMA), four CMD resistance markers were detected viz. SSRY28, SSRY235, SSRY44 and NS136. SSRY28 and SSRY235 were located on linkage group G and SSRY44 and NS136 on linkage group P of cassava genetic map developed by Fregene et al. (1997). Among the four markers, three (SSRY235, SSRY44 and NS136) are new markers associated with CMD resistance. The detection of markers SSRY44 and NS136 having association with CMD resistance is a new report indicating the possibility of having another genetic loci for CMD resistance in cassava in addition to the already established on linkage group G. This finding supports the polygenic control of CMD resistance.

Genetic variability of cassava progenies developed through introgression of cassava mosaic disease resistance into Ghanaian landraces

Availability of genetic diversity is important in selecting suitable cultivars for crop improvement. Progenies of crosses between 19 farmer-preferred cassava landraces and Cassava Mosaic Disease (CMD)-resistant cultivar TME 11 were evaluated and compared with their maternal parents to assess their genetic variability and genetic gains based on CMD tolerance, some growth variables and root yield. The combined analysis of variance for the traits showed significant genotypic differences amongst the progenies and the parents. Apart from a few instances, the differences in replications and years were also significant. Genetic variability components showed high heritability ranging from 92.3 to 99.6% and moderately high genetic gains of 54.1 to 99.6% for the parental cultivars. Apart from canopy spread and plant height, heritability and genetic gains of the progenies were slightly lower than the parents indicating high variability within families of the progenies. The phenotypic coefficient of variation was slightly greater than genotypic coefficient of variation indicating minimal influence of environment on the genotypes. For most of the characters evaluated, the mean performance of the progenies was higher than their corresponding parental lines. Although the genotypes differed significantly (P < 0.001) for all traits evaluated, cultivars such as Afebankye, Bosome nsia, Cedi bankye, 262 Debor, Kwadaso 25, Nkaakom 57 and Sisipe were found to constitute a pool of germplasm with adequate variability. The negative correlation between CMD incidence and other traits evaluated showed significant progress made in the breeding program.

Molecular Marker Analysis and Validation of Resistance to Cassava Mosaic Disease in Elite Cassava Genotypes in Nigeria

ABSTRACTCassava (Manihot esculenta Crantz), a highly heterozygous crop, is devastated by cassava mosaic disease (CMD). The discovery of the CMD2 dominant gene is helpful in the genetic analysis of CMD resistance. Molecular markers for CMD2 gene were used to introgress CMD resistance into Latin American cassava genotypes and validated in the field for 4 yr for stability of resistance conferred by CMD2. Field screening identified 64 Latin American genotypes with stable resistance to CMD. Resistance to CMD of two Nigerian cassava cultivars (TMS 97/2205 and TMS 98/0505) was analyzed with markers and in the field. Molecular data indicated that CMD resistance in the two Nigerian cultivars was mediated by the CMD2 gene. Results showed TMS 97/2205 to be highly resistant to CMD in three ecological zones in Nigeria. Further genetic analysis of this genotype as a source of high level of resistance to CMD using a segregating F1 population derived from a TMS 97/2205 × NR 8083 cross was initiated using 530 simple sequence repeat (SSR) markers to identify quantitative trait loci (QTL) for CMD resistance. A marker (NS198) associated with a QTL for CMD resistance, explaining 11% of the phenotypic variance observed, was identified. The combined effect of this QTL and CMD2 may account for the high level of resistance of TMS 97/2205. The resistance profile of the evaluated CMD2 genotypes in growth cycle was not uniform and was affected by genetic background. The discovery of a new QTL (CMD3) for CMD resistance in TMS 97/2205 offers new opportunities for pyramiding CMD genes for enhanced durability of CMD resistance in cassava.

Starch content and cassava mosaic disease genetic diversity with relation to yield in south Indian cassava (Manihot esculenta Crantz) germplasm

Cassava, family Euphorbiaceae, is the fifth most important staple food crop. The study of variability and diversity present in diverse cassava accessions maintained at the field genebank of TCRS, TNAU is essential to design the breeding program of cassava in TNAU. Hence, a study was carried out to assess the genetic diversity based on morphological traits and Simple Sequence Repeat (SSR) markers, identifying the SSR markers linked to a cassava mosaic disease-resistant QTL region. Genetic diversity among cassava germplasm accessions was estimated using 28 morphological traits and three SSR markers. The polymorphic information content (PIC) result gives high information for all the SSR markers. Morphological traits revealed 10 clusters and the SSR markers revealed 13 clusters at a similarity coefficient of 2.514 and 0.75, respectively. The SSR marker diversity revealed that the most promising clusters (II and XII) possessing accessions with yield attributing traits and cluster IX were grouped together due to low yield and CMD susceptibility. Morphological descriptors revealed variance for yield contributing traits. The first three principle components accounted for 10.8, 9.1, and 8.4%, respectively. Correlation studies showed significant correlation among yield and yield-attributing traits, which in turn influences yield. The morphological traits diversity reveals that cluster VI was the most promising cluster in which genotypes ME209 and ME460 possess higher yield and starch content with cassava mosaic disease (CMD) resistance. Most of the accessions grouped under cluster X belong to selection from International Centre for Tropical Agriculture (CIAT) collections and the cultivars under clusters I and II were true cassava seed (TCS) selections of India. The CMD-linked SSR marker which is reported in the previous studies have generated eight alleles and each were regressed with CMD resistance and resulted in non-significant linkage to CMD resistance.

Genetic Gains from 30 Years of Cassava Breeding in Nigeria for Storage Root Yield and Disease Resistance in Elite Cassava Genotypes

ABSTRACT Cassava (Manihot esculenta Crantz) is crucial for both food security and poverty alleviation in Sub-Saharan Africa (SSA). Cassava improvement for SSA started at the International Institute of Tropical Agriculture in 1970, and several improved lines with different characteristics have been developed to date. The primary focus of breeding work has been to increase root yield, early bulking, tolerance to biotic and abiotic stresses, and increased dry matter content. This paper represents a study of 112 varieties cloned and introduced between 1970 and 2000, and evaluated in 2003 and 2004 to quantify genetic gains in root yield and disease resistance. The genetic gain per year was 1.3% for fresh root yield, 1.2% for dry root yield, 0.65% for cassava mosaic disease resistance, 0.21% for cassava anthracnose disease resistance, and -0.03% for cassava bacterial blight disease resistance. Though there was no statistical significance in the net negative genetic gain in cassava bacterial blight resistance, it is essential that more emphasis be placed on improving this trait to enhance stability and productivity in African environments.

Marker‐Assisted Introgression of Resistance to Cassava Mosaic Disease into Latin American Germplasm for the Genetic Improvement of Cassava in Africa

The gene pools for breeding cassava (Manihot esculenta Crantz) in Africa currently contain only a fraction of the existing genetic variation found in Latin America where the crop originates. Our research aimed to broaden the genetic base in Africa by introducing Latin American (LA) germplasm. The first set of introductions comprised sexual seeds that led to the evaluation of 20,032 seedlings in Nigeria between 1990 and 1994. A second set comprised in vitro cultures, where the dominant CMD2 gene for cassava mosaic disease (CMD) resistance was introgressed into LA germplasm through marker‐assisted selection (MAS). Through MAS 156 genotypes were preselected for the gene and evaluated in Nigeria between 2004 and 2006. Initial results from the first set of introductions indicated that LA germplasm was highly susceptible to CMD, minimizing its usefulness in African cassava‐breeding programs. In the second set of introductions from LA, introgression of the CMD2 gene resulted in high CMD resistance under African field conditions. Now at advanced stages in the African breeding program, 14 genotypes combining CMD resistance and high yield are being evaluated. Marker‐assisted introgression of CMD resistance into LA germplasm has improved the potential value of LA germplasm for Africa and enhanced the prospect of elite LA genotypes being released as improved varieties in Africa.

Resistance profile of improved cassava germplasm to cassava mosaic disease in Nigeria

Cassava mosaic disease (CMD) caused by a group of begomoviruses and transmitted by whitefly vector is a serious disease in all the cassava-growing areas of Africa. Field evaluation with replication was conducted in 2003 and 2004 in three agroecologies in Nigeria to study the response of 40 cassava genotypes to CMD and to investigate genotype × environment (GE) interactions on their reactions to CMD, using the rank-sum classification and site regression analysis model. The 40 genotypes were separated into resistant (n = 17), moderately resistant (n = 6), moderately susceptible (n = 2) and susceptible (n = 15) groups. Environments, genotypes and GE interactions were all highly significant (P < 0.0001) for the virus disease contributing 9.5%, 71.36% and 19.14%, respectively to total variation. More than 40% of the genotypes were identified as resistant to the disease. Genotypes TMS 98/0581, TMS 99/3073, TMS 97/4763, TMS M98/0040, TMS 98/0505, TMS 97/0211, TMS 97/4769, TMS 99/2123, TMS M98/0068 and TMS 97/0162 were shown to have high resistance to CMD. The study also identified Umudike, in south-east Nigeria, as having high disease severity and the most appropriate site for CMD resistance screening of genotypes. Most of the genotypes exhibited stable resistance to CMD. The implication that the availability of these resistant genotypes as identified in this study could be a source of CMD resistance for further breeding is discussed.

Molecular markers associated with a new source of resistance to the cassava mosaic disease

The predominant source of resistance to the cassava mosaic disease (CMD) is known to be polygenic requiring evaluation in multiple environments to characterise resistant genotypes, which makes the detection of genes for resistance using segregation analysis inefficient. Recently, some landraces have been identified which exhibit high levels of resistance to CMD. In this study, molecular markers associated with resistance to CMD in a resistant landrace were identified, using F1 progenies derived from a cross between the CMD resistant landrace TME7 and the susceptible line TMS30555, as a first step in marker assisted breeding for CMD resistance. Bulk segregant analysis (BSA) on the parents, resistant and susceptible DNA pools, using simple sequence repeat (SSR) and amplified fragment length polymorphism (AFLP) markers revealed that an SSR marker, SSRY28-180, donated by the resistant parent was linked with resistance to CMD. Marker-trait association detected by regression analysis showed that the marker, accounted for 57.41% of total phenotypic variation for resistance. The analysis further showed that another SSR marker, SSRY106-207 and an AFLP marker, E-ACC/M-CTC-225, accounted for 35.59% and 22.5% of the total phenotypic variation for resistance, respectively. The implication of the results in breeding for resistance to CMD is discussed.

Variants of East African cassava mosaic virus and Its Distribution in Double Infections with African cassava mosaic virus in Nigeria.

In a survey for cassava mosaic begomoviruses conducted in 1997 and 1998 in Nigeria, East African cassava mosaic virus (EACMV) was detected by the polymerase chain reaction together with African cassava mosaic virus (ACMV) in 27 out of 290 cassava leaf samples of infected plants from 254 farmers' fields in five agroecological zones. One plant was infected with EACMV only. Five variant isolates of EACMV were observed based on their reactions to primers that could detect Cameroonian and East African strains of EACMV. Isolates of variants 1 and 3 occurred mostly in the derived or coastal and southern Guinea savannahs, while variants 4 and 5 predominated in the humid forest region. Isolates of variant 2 were widely distributed across the three agroecologies. EACMV was not detected in the northern Guinea savannah and arid and semiarid zones. Most doubly infected plants showed more severe symptoms than plants with single infection. Occurrence of EACMV variants together with ACMV detection and information about their distribution in Nigeria could be used for the selection of cassava clones in cassava mosaic disease resistance programs.

Genetic mapping of a dominant gene conferring resistance to cassava mosaic disease.

Cassava mosaic disease (CMD) is the most-important disease of cassava ( Manihot esculenta) in Africa, and is a potential threat to Latin American (LA) cassava production. Although this viral disease is still unknown in LA, its vector - the whitefly - has recently been found. The disease is best controlled through host-plant resistance, which was first found in third backcross derivatives of an interspecific cross between cassava and Manihot glaziovii, and is thought to be polygenic. Recently, high levels of resistance were also found in several Nigerian cassava landraces. Classical genetic analysis and molecular genetic-mapping of the landraces showed that a major dominant gene confers this resistance. Bulk segregant analysis (BSA) was used to quickly identify a simple sequence repeat (SSR) marker linked to the CMD-resistance gene. The marker, SSRY28, is located on linkage group R of the male-parent-derived molecular genetic map. The gene, designated as CMD2, is flanked by the SSR and RFLP marker GY1 at 9 and 8 cM, respectively. To our knowledge, this is the first report of qualitative virus resistance in cassava, and of molecular markers that tag CMD resistance in cassava. We discuss the use of markers linked to CMD2 for marker-assisted breeding of CMD resistance in Latin America and for increasing the cost-effectiveness of resistance breeding in Africa.