Molecular and phenotypic diversity of groundnut (Arachis hypogaea L.) cultivars in Togo.

Diversity assessment of 94 groundnut accessions from Togo and Senegal, using agro-morphological and SNP markers, revealed high variability for many quantitative traits such as late leaf spot (LLS) incidence, number of pods per plant and yield per plant. For qualitative traits, the Simpson Index showed high diversity for primary seed colour (0.75), stem pigmentation (0.60), and Growth habit (0.59). Principal component analysis underscored quantitative traits such as hundred seed weight, days to maturity, and LLS incidence, as the main traits contributing to the divergence. Correlation and path coefficient analysis showed that the number of pods per plant was the main yield-related trait positively affecting yield (r = 0.95, PC = 0.84; p = 0.01). Overall, 990 SNP markers revealed moderate genetic variability in the genotypes and the percentage of heterozygous genotypes varied from 0 to 50% for all loci. Analysis of molecular variance revealed that only 1.1% of the total molecular variance accounted for geographical contribution to the diversity. Co-analysis of phenotypic and SNP data delineated three clusters harbouring useful alleles and interesting phenotypic features such as LLS resistance, large number of pods per plant and early maturity indicating that differences observed at the phenotypic level are underlined by genotypic differences. The phenotypic and genotypic diversity observed could be exploited for the identification of parents with preferred traits for use in the breeding program. However, the low population structure highlights the necessity to improve groundnut diversity in Togo through introduction from various sources.

Characterization and diversity of rhizobia nodulating selected tree legumes in Ghana.

The study was conducted to assess the characteristics and diversity of the rhizobia that nodulate some prominent tree legumes in three soils of Ghana. Five introduced and/or indigenous tree legumes were initially assessed for nodulation in three Ghanaian soils. After 12 weeks of growth in nursery pots the 200 rhizobial strains isolated from their nodules were characterized culturally, metabolically and phenotypically. Sixty of these isolates were selected randomly and their genotypic characteristics determined using PCR-RFLP of 16S rRNA and intergenic spacer (ITS) genes. Each tree legume was nodulated by isolates classified as fast or very fast-growers or by isolates classified as slow- or very slow-growers with 54 % of all the 200 isolates belonging to fast- or very fast-growers. Morphologically, eighty five percent of the colonies formed on yeast extract mannitol agar were wet and gummy while 70 % were acid tolerant, i.e. they were able to grow at a pH of 3.5. Combined restriction of the 16S rRNA genes of the 60 rhizobial isolates with five restriction enzymes clearly distinguished seven different clusters at 80 % similarity level. The majority of A. lebbeck isolates were distinct from those of the Acacias and L. leucocephala. The M. thonningii isolates were related to L. leucocephala isolates. Simple PCR of the ITS DNA provided several distinct band sizes indicating great variation among the isolates and restriction of the ITS with three different enzymes did not yield many further differences. Molecular techniques revealed a great diversity among the rhizobia that nodulate tree legumes in the tropics and this may explain why many introduced and/or indigenous trees are able to form nodules with indigenous rhizobia in this region.

Genetic diversity and epidemic histories of rice yellow mottle virus in Ghana.

Rice yellow mottle virus (RYMV) has persisted as a major biotic constraint to rice production in Africa. However, no data on RYMV epidemics were available in Ghana, although it is an intensive rice-producing country. Surveys were performed from 2010 to 2020 in eleven rice-growing regions of Ghana. Symptom observations and serological detections confirmed that RYMV is circulating in most of these regions. Coat protein gene and complete genome sequencings revealed that RYMV in Ghana almost exclusively belongs to the strain S2, one of the strains covering the largest area in West Africa. We also detected the presence of the S1ca strain which is being reported for the first time outside its area of origin. These results suggested a complex epidemiological history of RYMV in Ghana and a recent expansion of S1ca to West Africa. Phylogeographic analyses reconstructed at least five independent RYMV introductions in Ghana for the last 40 years, probably due to rice cultivation intensification in West Africa leading to a better circulation of RYMV. In addition to identifying some routes of RYMV dispersion in Ghana, this study contributes to the epidemiological surveillance of RYMV and helps to design disease management strategies, especially through breeding for rice disease resistance.

Identification of Genomic Regions Associated with Agronomic and Disease Resistance Traits in a Large Set of Multiple DH Populations.

Breeding maize lines with the improved level of desired agronomic traits under optimum and drought conditions as well as increased levels of resistance to several diseases such as maize lethal necrosis (MLN) is one of the most sustainable approaches for the sub-Saharan African region. In this study, 879 doubled haploid (DH) lines derived from 26 biparental populations were evaluated under artificial inoculation of MLN, as well as under well-watered (WW) and water-stressed (WS) conditions for grain yield and other agronomic traits. All DH lines were used for analyses of genotypic variability, association studies, and genomic predictions for the grain yield and other yield-related traits. Genome-wide association study (GWAS) using a mixed linear FarmCPU model identified SNPs associated with the studied traits i.e., about seven and eight SNPs for the grain yield; 16 and 12 for anthesis date; seven and eight for anthesis silking interval; 14 and 5 for both ear and plant height; and 15 and 5 for moisture under both WW and WS environments, respectively. Similarly, about 13 and 11 SNPs associated with gray leaf spot and turcicum leaf blight were identified. Eleven SNPs associated with senescence under WS management that had depicted drought-stress-tolerant QTLs were identified. Under MLN artificial inoculation, a total of 12 and 10 SNPs associated with MLN disease severity and AUDPC traits, respectively, were identified. Genomic prediction under WW, WS, and MLN disease artificial inoculation revealed moderate-to-high prediction accuracy. The findings of this study provide useful information on understanding the genetic basis for the MLN resistance, grain yield, and other agronomic traits under MLN artificial inoculation, WW, and WS conditions. Therefore, the obtained information can be used for further validation and developing functional molecular markers for marker-assisted selection and for implementing genomic prediction to develop superior elite lines.

Genetic variability and genotype by environment interaction of two major cassava processed products in multi-environments.

Conversion of cassava (Manihot esculenta) roots to processed products such as gari and fufu before consumption is a common practice worldwide by cassava end-user for detoxification, prolonged shelf life or profitability. Fresh root and processed product yield are supposed to be equivalent for each genotype, however, that is not the case. Developing genotypes with high product conversion rate is an important breeding goal in cassava as it drives the adoption rates of new varieties. The objective of this study was to quantify the contribution of genetic and genotype-by-environment interaction (GEI) patterns on cassava root conversion rate to gari and fufu. Sixty-seven advanced breeding genotypes from the International Institute of Tropical Agriculture (IITA) were evaluated across eight environments in Nigeria. Root conversion rate means across trials ranges from 14.72 to 22.76% for gari% and 16.96-24.24% for fufu%. Heritability estimates range from 0.17 to 0.74 for trial bases and 0.71 overall environment for gari% and 0.03-0.65 for trial bases and 0.72 overall environment for fufu% which implies that genetic improvement can be made on these traits. Root conversion rate for both gari and fufu% showed a negative but insignificant correlation with fresh root yield and significant positive correlation to Dry Matter content. For all fitted models, environment and interaction had explained more of the phenotypic variation observed among genotypes for both product conversion rates showing the presence of a strong GEI. Wrickle ecovalence (Wi) stability analysis and Geometric Adaptability index (GAI) identified G40 (TMS14F1285P0006) as part of top 5 genotypes for gari% but no overlapping genotype was identified by both stability analysis for fufu%. This genotypic performance across environments suggests that it is possible to have genotype with dual-purpose for high gari and fufu conversion rate.

Mapping chromosomal regions associated with anther indehiscence with exerted stigmas in CRI-48 and Jasmine 85 cross of rice (Oryza sativa L).

Anther indehiscence in certain wide crosses combines male sterility with stigma exertion, a phenomenon that is desirable for hybrid rice seed production. This study sought to identify chromosomal region(s) that combine anther indehiscence with exerted stigmas. A mapping population consisting of 189 BC1F1 plants was derived from a cross between CRI-48 and Jasmine 85 and backcrossing the resulting F1 to Jasmine 85. Contrary to the three complementary genes mode of inheritance reported earlier, a single locus (AI6-1) was mapped on chromosome 6 at 27.4 cM for anther indehiscence with exerted stigmas through a mixed model-based composite interval mapping (MCIM). This locus was flanked by two single nucleotide polymorphism (SNP) markers, K_ID6002884 and K_ID6003341 within a range of 23.1-28.9 cM. The allele at the locus was contributed by the CRI-48 parent which has Oryza glaberrima ancestry. This locus is suggested to control anther indehiscence and stigma exertion through pleiotropic gene action or cluster of genes.

Genetic diversity and population structure analysis of Ghanaian and exotic cassava accessions using simple sequence repeat (SSR) markers.

Genetic diversity is fundamentally important in crop improvement and provides plants with the capacity to meet the demands of changing environments. This work was carried out to assess the diversity and the extent of genetic relatedness among a number of assembled cassava (Manihot esculenta Crantz) accessions. We conducted a microsatellite marker analysis of 89 cassava accessions collected from Ghanaian and exotic sources. These accessions were assayed using 35 simple sequence repeat (SSR) markers. A total of 167 alleles were detected from 35 polymorphic markers with an average of 4.77 alleles per locus. High allelic frequency was detected across the accessions, ranging from 0.32 to 0.99 with an average of 0.62 per marker. Observed heterozygosity ranged from 0.03 - 0.97 across the accessions. Polymorphism information content (PIC) ranged from 0.03 to 0.78 with a mean of 0.45, indicating high level of polymorphism across the accessions. Comparatively, higher number of alleles, gene diversity and observed heterozygosity were detected among the local accessions compared with the exotic accessions indicating rich genetic diversity among them. Population structure analysis based on STRUCTURE identified two subpopulations and a large number of admixtures. Cluster analysis based on the neighbour joining algorithim further separated the collection into seven sub-groupings irrespective of geographical origin. This indicates the possible sharing of common genomic regions occurring across the accessions. High allelic frequency differences and levels of heterozygosity were observed among the germplasm. These findings indicated significant genetic variability in the germplasm to warrant selection.

Groundnut production constraints and farmers' trait preferences: a pre-breeding study in Togo.

BACKGROUND: Groundnut is an important legume crop in Togo. However, groundnut yield has been steadily decreasing for decades as a result of lack of organized breeding program to address production constraints. Though, low yielding varieties and late leaf spot have been often reported as the most important constraints, there is no documented evidence. Identifying and documenting the major production constraints is a prerequisite for establishing a good breeding program with clearly defined priority objectives and breeding strategies. Thus, the objectives of this study were to identify groundnut production constraints and assess farmers' preferred traits. METHODS: A participatory rural appraisal approach was used to collect data on agronomic practices, farmers' preferences, and possible threats to production through individual and group interviews. Three regions and three villages per region were selected based on the representativeness of groundnut production systems. In each village, 20 farmers were randomly selected and interviewed; thus, a total of 180 farmers were interviewed. Content analysis was carried out for qualitative data and for quantitative data generated within and across regions, comparative descriptive statistics were carried out. Differences in perception and preferences were assessed using chi-square tests. RESULTS: The study has revealed that, though there were some variation across the regions, traits pertaining to yield such as pod yield (66.66%) and pod size (12.12%) were the most important. Leaf spot diseases, rosette and peanut bud necrosis (37.77%) and insects such as pod sucking bug and bruchid (27.77%) were considered to be the most important constraints limiting groundnut production. Among diseases, farmers in all the three regions indicated that late leaf spot is of economic importance which they associated to various causes such as maturity, drought, or insects. No gender differences were observed for the perception of constraints and groundnut traits preferences. Land size is significantly influenced by age and gender. Besides, farmers have pointed the lack of improved varieties and the unavailability of groundnut seeds highlighting the necessity of a sustainable groundnut seed system linked with a strong breeding program. CONCLUSION: This study has enabled understanding of the farming practices, constraints, and farmers preferred characteristics, thus providing the basis for a participatory breeding program in Togo which should consider that farmers perceive low yielding varieties and diseases as major constraints to production.