Genetic Variation, Genotype by Environment Interactions and Grain Yield Stability Analysis in Finger Millet Accessions Resulted in the Release of an Improved Variety

The use of multiple data sets, such as morphological, biochemical and molecular in combination with appropriate statistical analysis tools are essential in  identifying inter and intra-species variation to develop improved cultivars. To this end, a total of 150 finger millet accessions, of which 105 were collected  from Ethiopia, 39 introduced from eastern and south eastern Africa and six commercially released Ethiopian varieties were evaluated at Arsi Negele and  Gute research sites in 2011. Among those, 138 accessions were genotyped using 20 Simple Sequence Repeat (SSR) markers at International Crop  Research Institute for Semi-Arid Tropics (ICRISAT), Nairobi, in 2012. Highly significant (P ≤ 0.01) variations were observed among the 150 accessions for  grain yield and other agronomic traits. A total of 199 alleles were recorded with an average of 9.95 alleles per microsatellite locus and polymorphism  information content (PIC) of 0.57 was observed. Hierarchical clustering based on major phenotypic traits revealed that the majority of accessions from  the same region and adjoining geographical region shared strong phenotypic similarity and thus grouped together. Weighted Neighbor Joining based on  SSR data grouped the test accessions into three major clusters that were not entirely based on geographical origin. Based on the magnitude of  phenotypic and genotypic diversity and blast disease tolerance, 30 finger millet genotypes were selected for further evaluation at multi-location (Arsi  Negele, Assosa, Bako and Gute) in the 2012 and 2013. Additive Main effect and Multiplicative Interaction (AMMI), and Genotype and Genotype by  Environment Interaction (GGI) biplot analysis revealed that Acc. 203544 was found to be the most stable and highest yielding (3.16 ton ha-1), with yield  advantage of 13.7% over the best standard check, Gute (2.78 ton ha-1). Thus, this accession was officially released with the name “Addis-01” and  recommended for production in the test environments and similar agro-ecologies in the country

Cross-Sectional Variations in Structure and Function of Coral Reef Microbiome With Local Anthropogenic Impacts on the Kenyan Coast of the Indian Ocean

Coral reefs face an increased number of environmental threats from anthropomorphic climate change and pollution from agriculture, industries and sewage. Because environmental changes lead to their compositional and functional shifts, coral reef microbial communities can serve as indicators of ecosystem impacts through development of rapid and inexpensive molecular monitoring tools. Little is known about coral reef microbial communities of the Western Indian Ocean (WIO). We compared taxonomic and functional diversity of microbial communities inhabiting near-coral seawater and sediments from Kenyan reefs exposed to varying impacts of human activities. Over 19,000 species (bacterial, viral and archaeal combined) and 4,500 clusters of orthologous groups of proteins (COGs) were annotated. The coral reefs showed variations in the relative abundances of ecologically significant taxa, especially copiotrophic bacteria and coliphages, corresponding to the magnitude of the neighboring human impacts in the respective sites. Furthermore, the near-coral seawater and sediment metagenomes had an overrepresentation of COGs for functions related to adaptation to diverse environments. Malindi and Mombasa marine parks, the coral reef sites closest to densely populated settlements were significantly enriched with genes for functions suggestive of mitigation of environment perturbations including the capacity to reduce intracellular levels of environmental contaminants and repair of DNA damage. Our study is the first metagenomic assessment of WIO coral reef microbial diversity which provides a much-needed baseline for the region, and points to a potential area for future research toward establishing indicators of environmental perturbations

Morphological Variation in the Wild-Weedy Complex of Sorghum bicolor In Situ in Western Kenya: Preliminary Evidence of Crop-to-Wild Gene Flow?

Crop wild relatives are important components of agroecosystems and have over the years been exploited in breeding programs as sources of genes for novel traits. Information on the extent and patterns of variability is important in formulating effective conservation and utilization strategies for existing crop wild relative populations. We conducted surveys and collections of wild and weedy accessions of Sorghum bicolor (L.) Moench in Lambwe Valley in western Kenya in order to investigate occurrence, distribution, and morphological variability in the wild-weedy complex of S. bicolor under local agroecological conditions. We also attempted to understand the role, if any, of crop-to-wild gene flow in structuring variability within and among populations. The morphological data presented here showed wide variability within wild-weedy sorghum populations with respect to habitats and morphotypes. True wild sorghum populations in national parks and the sugarcane belt were clearly distinguishable from the putative hybrids or intermediate forms found in sorghum fields, in sorghum field margins, and, to some extent, by the roadside near sorghum fields. The existence of these intermediate forms is empirical evidence of introgression between cultivated sorghum and its wild-weedy relatives. Extensive introgression, especially within in situ conservation areas and/or in areas of high diversity, would lead to genetic erosion and possible depletion of these important wild sorghum genetic resources

SSR genetic diversity assessment of popular pigeonpea varieties in Malawi reveals unique fingerprints

Background: Pigeonpea ( Cajanus cajan L. Millsp.) is a drought tolerant legume of the Fabaceae family and the only cultivated species in the genus Cajanus. It is mainly cultivated in the semi-arid tropics of Asia and Oceania, Africa and America. In Malawi, it is grown as a source of food and income and for soil improvement in intercropping systems. However, varietal contamination due to natural outcrossing causes significant quality reduction and yield losses. In this study, 48 polymorphic SSR markers were used to assess the diversity among all pigeonpea varieties cultivated in Malawi to determine if a genetic fingerprint could be identified to distinguish the popular varieties. Results: A total of 212 alleles were observed with an average of 5.58 alleles per marker and a maximum of 14 alleles produced by CCttc019 (Marker 40). Polymorphic information content (PIC), ranged from 0.03 to 0.89 with an average of 0.30. A neighbor-joining tree produced 4 clusters. The most commonly cultivated varieties, which include released varieties and cultivated land races, were well-spread across all the clusters observed, indicating that they generally represented the genetic diversity available in Malawi, although substantial variation was evident that can still be exploited through further breeding. Conclusion: Screening of the allelic data associated with the five most popular cultivated varieties, revealed 6 markers \u2013 CCB1, CCB7, Ccac035, CCttc003, Ccac026 and CCttc019 \u2013 which displayed unique allelic profiles for each of the five varieties. This genetic fingerprint can potentially be applied for seed certification to confirm the genetic purity of seeds that are delivered to Malawi farmers

Compilation of an informative microsatellite set for genetic characterisation of East African finger millet ( Eleusine coracana )

Background: Genetic diversity of finger millet ( Eleusine coracana ), a nutritious neglected staple cereal in Africa and South Asia is largely uncharacterized. This study analysed 82 published SSR markers for finger millet across 10 diverse accessions to compile an informative set for genetic characterisation. Extensive optimization compared single samples with bulked leaf or bulked DNA samples for capturing within accession genetic diversity. The markers were evaluated to determine (1) how efficiently they amplified target loci during high-throughput genotyping with a generic PCR protocol, (2) ease of scoring PCR products and (3) polymorphism and ability to discern genetic diversity within the tested finger millet germplasm. Results: Across 88 samples, the 52 markers that worked well amplified 274 alleles, ranging from 2 to 14 per locus with a mean of 4.89. Major allele frequency ranged from 0.18 to 0.93 with a mean of 0.57. Polymorphic Information Content (PIC) ranged from 0.13 to 0.88 with a mean of 0.5 and availability varied between 64 and 100% with a mean of 92.8%. Heterozygosity ranged from 0 to 1.0, with a mean of 0.26. Discussion: Five individual samples from an accession captured the largest number of alleles per locus compared to the four different bulked sampling strategies but this difference was not significant. The identified set comprised 20 markers: UGEP24, UGEP53, UGEP84, UGEP27, UGEP98, UGEP95, UGEP64, UGEP33, UGEP67, UGEP106, UGEP110, UGEP57, UGEP96, UGEP66, UGEP46, UGEP79, UGEP20, UGEP12, UGEP73 and UGEP5 and was since used to assess East African finger millet genetic diversity in two separate studies

GENETIC DIVERSITY AND ECO-GEOGRAPHICAL DISTRIBUTION OF ELEUSINE SPECIES COLLECTED FROM ETHIOPIA

Eleusine is a small grass genus with three basic chromosome numbers (x=8, 9 and 10) and comprises of eight species including E. coracana subsp. coracana, (finger millet), which is an important subsistence crop in Africa and India. Research on these species could assist the development of high yielding and multiple stress tolerant variety(s) of the cultivable species, and also guide development of strategic genetic resource management and utilisation of the genus. A total of 72 accessions, sampled from five major species, E. coracana (including both E. coracana subsp. coracana and E. coracana subsp. africana), E. intermedia, E. indica, E. multiflora and E. floccifolia were analysed for genetic variation and inter-relationships using 20 microsatellite markers. All the SSR markers displayed high genetic polymorphism, with polymorphic information content ranging from 0.46 (UGEP110) to 0.91 (UGEP66). A total of 286 alleles were observed with an average of 14.3 alleles per locus. Classic F-statistics revealed the highest intra-specific polymorphism recorded for E. africana (32.45%), followed by E. coracana (16.83%); implying that genetic polymorphism is higher in the cultivable subspecies and its wild relatives, than the other species. Allelic frequency based inter-species genetic distance analysis, showed wider genetic distance between E. indica and E. multiflora (0.719); a narrow genetic distance between E. coracana sub-species africana and E. coracana subspecies coracana (0.3297). The weighted neighbor joining-based clustering revealed that the majority of the accessions in a species share strong similarity and are grouped together than do accessions of inter species.Eleusine est une herbe avec trois nombres de chromosomes de base (x=8, 9 et 10) et comprend huit esp\ue8ces dont E. coracana subsp. coracana, (finger millet), qui est une culture de subsistence importante en Afrique et en Inde. La recherche sur ces esp\ue8ces pourrait aider dans le d\ue9veloppement des vari\ue9t\ue9s d\u2019esp\ue8ces cultivables \ue0 rendement \ue9lev\ue9 et de tol\ue9rance aux stress multiples, et guider le d\ue9veloppement de la gestion des ressources g\ue9n\ue9tiques strat\ue9giques et l\u2019utilisation du genus. Un total de 72 accessions \ue9chantillonn\ue9es de cinq esp\ue8ces majeurs \ue0 savoir E. coracana (incluant E. coracana subsp. coracana et E. coracana subsp. africana), E. intermedia, E. indica, E. multiflora et E. floccifolia \ue9taient analys\ue9es pour variation g\ue9n\ue9tique et relations mutuelles utilisant 20 marqueurs microsatellites. Tous les marquers SSR ont manifest\ue9 un polymorphisme g\ue9n\ue9tique \ue9lev\ue9, avec un contenu d\u2019information polymorphique allant de 0.46 (UGEP110) \ue0 0.91 (UGEP66). Un total de 286 all\ue8les \ue9tait observ\ue9 avec une moyenne de 14.3 all\ue8les par locus. Les statistiqies classiques F ont r\ue9v\ue9l\ue9 le polymorphisme intrasp\ue9cifique le plus \ue9lev\ue9 enregistr\ue9 pour le E. africana (32.45%), suivi de E. coracana (16.83%), ce qui implique que le polymorphisme g\ue9n\ue9tique est le plus \ue9lev\ue9 dans les sous esp\ue8ces cultivables et ses homologues sauvages que les autres esp\ue8ces. L\u2019analyse de la fr\ue9quence all\ue9lique de la distance g\ue9n\ue9tique entre esp\ue8ces a montr\ue9 une plus large distance g\ue9n\ue9tique entre E. indica et E. multiflora (0.719); une \ue9troite distance g\ue9n\ue9tique entre les sous esp\ue8ces Africana de E. coracana et les sous esp\ue8ces coracana de E. coracana (0.3297). La pond\ue9ration des groupements a r\ue9v\ue9l\ue9 que la majorit\ue9 des accessions au sein d\u2019une esp\ue8ce partage une forte similarit\ue9 et sont group\ue9es ensemble en comparaison aux accessions des intra-esp\ue8ces

Identification of groundnut (Arachis hypogaea) SSR markers suitable for multiple resistance traits QTL mapping in African germplasm

AbstractBackgroundThis study aimed to identify and select informative Simple Sequence Repeat (SSR) markers that may be linked to resistance to important groundnut diseases such as Early Leaf Spot, Groundnut Rosette Disease, rust and aflatoxin contamination. To this end, 799 markers were screened across 16 farmer preferred and other cultivated African groundnut varieties that are routinely used in groundnut improvement, some with known resistance traits.ResultsThe SSR markers amplified 817 loci and were graded on a scale of 1 to 4 according to successful amplification and ease of scoring of amplified alleles. Of these, 376 markers exhibited Polymorphic Information Content (PIC) values ranging from 0.06 to 0.86, with 1476 alleles detected at an average of 3.7 alleles per locus. The remaining 423 markers were either monomorphic or did not work well. The best performing polymorphic markers were subsequently used to construct a dissimilarity matrix that indicated the relatedness of the varieties in order to aid selection of appropriately diverse parents for groundnut improvement. The closest related varieties were MGV5 and ICGV-SM 90704 and most distant were Chalimbana and 47–10. The mean dissimilarity value was 0.51, ranging from 0.34 to 0.66.DiscussionOf the 376 informative markers identified in this study, 139 (37%) have previously been mapped to the Arachis genome and can now be employed in Quantitative Trait Loci (QTL) mapping and the additional 237 markers identified can be used to improve the efficiency of introgression of resistance to multiple important biotic constraints into farmer-preferred varieties of Sub-Saharan Africa

Identification of SNP and SSR Markers in Finger Millet Using Next Generation Sequencing Technologies

Finger millet is an important cereal crop in eastern Africa and southern India with excellent grain storage quality and unique ability to thrive in extreme environmental conditions. Since negligible attention has been paid to improving this crop to date, the current study used Next Generation Sequencing (NGS) technologies to develop both Simple Sequence Repeat (SSR) and Single Nucleotide Polymorphism (SNP) markers. Genomic DNA from cultivated finger millet genotypes KNE755 and KNE796 was sequenced using both Roche 454 and Illumina technologies. Non-organelle sequencing reads were assembled into 207 Mbp representing approximately 13% of the finger millet genome. We identified 10,327 SSRs and 23,285 non-homeologous SNPs and tested 101 of each for polymorphism across a diverse set of wild and cultivated finger millet germplasm. For the 49 polymorphic SSRs, the mean polymorphism information content (PIC) was 0.42, ranging from 0.16 to 0.77. We also validated 92 SNP markers, 80 of which were polymorphic with a mean PIC of 0.29 across 30 wild and 59 cultivated accessions. Seventy-six of the 80 SNPs were polymorphic across 30 wild germplasm with a mean PIC of 0.30 while only 22 of the SNP markers showed polymorphism among the 59 cultivated accessions with an average PIC value of 0.15. Genetic diversity analysis using the polymorphic SNP markers revealed two major clusters; one of wild and another of cultivated accessions. Detailed STRUCTURE analysis confirmed this grouping pattern and further revealed 2 sub-populations within wild E. coracana subsp. africana. Both STRUCTURE and genetic diversity analysis assisted with the correct identification of the new germplasm collections. These polymorphic SSR and SNP markers are a significant addition to the existing 82 published SSRs, especially with regard to the previously reported low polymorphism levels in finger millet. Our results also reveal an unexploited finger millet genetic resource that can be included in the regional breeding programs in order to efficiently optimize productivity

Cross-Sectional Variations in Structure and Function of Coral Reef Microbiome With Local Anthropogenic Impacts on the Kenyan Coast of the Indian Ocean

Coral reefs face an increased number of environmental threats from anthropomorphic climate change and pollution from agriculture, industries and sewage. Because environmental changes lead to their compositional and functional shifts, coral reef microbial communities can serve as indicators of ecosystem impacts through development of rapid and inexpensive molecular monitoring tools. Little is known about coral reef microbial communities of the Western Indian Ocean (WIO). We compared taxonomic and functional diversity of microbial communities inhabiting near-coral seawater and sediments from Kenyan reefs exposed to varying impacts of human activities. Over 19,000 species (bacterial, viral and archaeal combined) and 4,500 clusters of orthologous groups of proteins (COGs) were annotated. The coral reefs showed variations in the relative abundances of ecologically significant taxa, especially copiotrophic bacteria and coliphages, corresponding to the magnitude of the neighboring human impacts in the respective sites. Furthermore, the near-coral seawater and sediment metagenomes had an overrepresentation of COGs for functions related to adaptation to diverse environments. Malindi and Mombasa marine parks, the coral reef sites closest to densely populated settlements were significantly enriched with genes for functions suggestive of mitigation of environment perturbations including the capacity to reduce intracellular levels of environmental contaminants and repair of DNA damage. Our study is the first metagenomic assessment of WIO coral reef microbial diversity which provides a much-needed baseline for the region, and points to a potential area for future research toward establishing indicators of environmental perturbations