Nasser K Yao - Academia.edu (original) (raw)

Papers by Nasser K Yao

Research Square (Research Square), Feb 18, 2022

Background: Future demand for cassava is expected to increase to mitigate climatic changes, susta... more Background: Future demand for cassava is expected to increase to mitigate climatic changes, sustain food security and provide raw materials for industry. To meet these demands, adoption of modern omics methods ensures reliability, precision and timely delivery of more productive and resilient varieties. Therefore the purpose of this study was to contribute towards accurate identi cation of cassava accessions from a mix of duplicate clones, diverse local landraces (LARs) and improved genotypes (IMGs) in farmer elds. This is vital for cassava breeding. Results: A total of 112 germplasms sampled through a eld survey in major cassava growing regions of Kenya, were genotyped using single nucleotide polymorphisms (SNPs) markers generated through genotyping-by-sequencing (GBS) approach. Of the 33672 SNPs, 88% were anchored onto chromosomes, 3% in scaffolds and 9% could not be mapped. LD pruning and identity by state matrix estimation revealed 5808 SNPs that were used for hierarchical clustering and ADMIXTURE analysis for ancestries. Considering a sub-population of 2-20, a 5-fold cross-validation procedure identi ed 14 subpopulations present in the population from which the population structure was modeled. Approximately 48% of the germplasms were classi ed into 17 independent clusters as identical clones or duplicates. The remaining 52% formed admixtures and hence unique or non-duplicated clones; reducing the total number of samples surveyed from 112 to 73. Of the duplicates, 10 clusters were formed from LARs, four from IMGs, and three from a mix of both LARs and IMGs. The major and minor clusters contained 8 and 2 accessions, respectively. About 71% of clusters contained accessions from the same geographical region while 29% had accessions from different regions. The results revealed genetic relationships amongst LARs and IMGs. Duplication of LARs was attributed to historical sharing or exchange of planting materials by farmers while duplicates of IMGs could be attributed to convergent evolution, selection, or sharing of common parentage. The high number of admixtures or unique clones implied minimal loss of genetic diversity. Geographical restriction of clusters adduced to the minimal movement of planting materials across the country, perhaps linked to either ine cient seed distribution system or disease-driven quarantine measures. Conclusions: GBS was successfully used to study the genetic relatedness of cassava genetic resources and variety identi cation in farmer elds. This omics approach and data herein generated could be adopted by breeders and other stakeholders in designing e cient and effective cassava improvement programs which might include the development of a core set of diagnostic markers for quality assurance, disease resistance, and targeted genomic pro ling in cassava.

Proceedings of the World Congress on Genetics Applied to Livestock Production, 2018

The main aim of the current study was to establish the genetic diversity of the Rwandese indigeno... more The main aim of the current study was to establish the genetic diversity of the Rwandese indigenous chicken (RIC) using microsatellite markers. This aim was investigated by sampling indigenous chicken genetic materials from 5 agro-ecological zones in Rwanda. The collected blood samples were subjected to DNA extraction, PCR amplification and genotyping. The data was analyzed for genetic variation and differentiation. The findings demonstrated that the RIC are broadly categorized into four gene pools, namely Central North and North West, Eastern, Central South and South West, and South West. The highest number of private alleles was found in the Eastern while North West had the least. This demonstrates low inflow of genes in Eastern as compared to North West. The Ho was similar to the He, hence no significant differences in F IS implying that the population is under Hardy-Weinberg equilibrium. It could be concluded that the RIC are genetically diverse and therefore important genetic resource for conservation and utilization through genetic improvement.

Journal of Plant Sciences, Jan 7, 2017

Seventy-seven (77) potato accessions were collected from production areas in Western highlands of... more Seventy-seven (77) potato accessions were collected from production areas in Western highlands of Cameroon (5°10'-6°30'N and 9°30'-10° 80'E). Out of the 77 accessions, 69 were traditional and 8 were modern varieties. The genotypes were grown under Menoua (5°27'N, 10°04'E) ecological conditions. 23 morphological and agronomical traits from the internationally accepted descriptor list for potato were used. When considering 7 agronomic traits used in this study, there were no significant difference among collection zone and among altitudes; however, highly significant differences among the accessions were found. Dried matter content (21.25%), total tubers number (15.55), mean eyes number (10.46) and mean stem number (3.21) were significantly higher in traditional varieties than in modern varieties which however had the highest percentage of marketable tubers (84.89%). Significant correlations were found between marketable tuber number and plant height (r = 0.44; p ≤ 0.0001) and between dried matter content, mean stems number (r = 0.38; p ≤ 0.001), mean eyes number (r = 0.30; p ≤ 0.01) and total tubers number (r = 0.44; p ≤ 0.0001). Cluster analysis identified 2 distinct groups with high level of variation. Significant differences were observed on all agronomic traits between the 2 groups; the first group was made up of Forty-seven (47) individuals, all of them were traditional varieties out of the sixty-nine (69) collected; The second group comprised et mixture of local and exotic varieties. Implications of these results in connection with the potato breeding programs in Cameroon are discussed.

Global Journal of Science Frontier Research, Jul 31, 2020

Six bi-parental populations were evaluated in three seasons under artificial inoculation using a ... more Six bi-parental populations were evaluated in three seasons under artificial inoculation using a combination of MCMV and SCMV (Fig. 1) and genotyped with 156 to 289 polymorphic SNPs using the KASP assay (Semagn et al. 2014) and GBS (Elshire et al. 2011)  Five additional F 2 mapping populations were developed, genotyped with DART SNPs and phenotyped under artificial inoculation.  Three major QTLs on chromosomes 3 and 6 and a few minor QTL across other chromosomes were identified (Fig. 2)  Major MLN disease resistant QTL on chromosome 6 was validated by QTL seq and confirmed (Fig. 3)

Journal of agriculture and food research, Jun 1, 2021

β-amylase is a thermostable enzyme that hydrolyses starch during cooking of sweetpotato (Ipomoea ... more β-amylase is a thermostable enzyme that hydrolyses starch during cooking of sweetpotato (Ipomoea batatas) storage roots, thereby influencing eating quality. Its activity is known to vary amongst genotypes but the genetic diversity of the beta-amylase gene (Amyβ) is not well studied. Amyβ has a highly conserved region between exon V and VI, forming part of the enzyme's active site. To determine the gene diversity, a 2.3 kb fragment, including the conserved region of the Amyβ gene was sequenced from 25 sweetpotato genotypes. The effect of sequence variation on gene expression, enzyme activity, and firmness in cooked roots was determined. Six genotypes carrying several SNPs within exon V, linked with an AT or ATGATA insertion in intron V were unique and clustered together. The genotypes also shared an A336E substitution in the amino acid sequence, eight residues upstream of a substrate-binding Thr344. The genotypes carrying this allele exhibited low gene expression and low enzyme activity. Enzyme activity was negatively correlated with firmness (R ¼ À0.42) in cooked roots. This is the first report of such an allele, associated with low enzyme activity. These results suggest that genetic variation within the AmyB locus can be utilized to develop markers for firmness in sweetpotato breeding.

PLOS ONE, Sep 23, 2020

Garcinia kola (Heckel) is a versatile tree indigenous to West and Central Africa. All parts of th... more Garcinia kola (Heckel) is a versatile tree indigenous to West and Central Africa. All parts of the tree have value in traditional medicine. Natural populations of the species have declined over the years due to overexploitation. Assessment of genetic diversity and population structure of G. kola is important for its management and conservation. The present study investigates the genetic diversity and population structure of G. kola populations in Benin using ultra-high-throughput diversity array technology (DArT) single nucleotide polymorphism (SNP) markers. From the 102 accessions sampled, two were excluded from the final dataset owing to poor genotyping coverage. A total of 43,736 SNPs were reported, of which 12,585 were used for analyses after screening with quality control parameters including Minor allele frequency (� 0.05), call rate (� 80%), reproducibility (� 95%), and polymorphic information content (� 1%). Analysis revealed low genetic diversity with expected heterozygosity per population ranging from 0.196 to 0.228. Pairwise F-statistics (F ST) revealed low levels of genetic differentiation between populations while an Analysis of molecular variance (AMOVA) indicated that the majority of variation (97.86%) was within populations. Population structure analysis through clustering and discriminant analysis on principal component revealed two admixed clusters, implying little genetic structure. However, the model-based maximum likelihood in Admixture indicated only one genetic cluster. The present study indicated low genetic diversity of G. kola, and interventions are needed to be tailored towards its conservation.

BMC Plant Biology, Jan 2, 2020

Background: Continuous storage root formation and bulking (CSRFAB) in sweetpotato is an important... more Background: Continuous storage root formation and bulking (CSRFAB) in sweetpotato is an important trait from agronomic and biological perspectives. Information about the molecular mechanisms underlying CSRFAB traits is lacking. Results: Here, as a first step toward understanding the genetic basis of CSRFAB in sweetpotato, we performed a genome-wide association study (GWAS) using phenotypic data from four distinct developmental stages and 33,068 single nucleotide polymorphism (SNP) and insertion-deletion (indel) markers. Based on Bonferroni threshold (pvalue < 5 × 10 − 7), we identified 34 unique SNPs that were significantly associated with the complex trait of CSRFAB at 150 days after planting (DAP) and seven unique SNPs associated with discontinuous storage root formation and bulking (DCSRFAB) at 90 DAP. Importantly, most of the loci associated with these identified SNPs were located within genomic regions (using Ipomoea trifida reference genome) previously reported for quantitative trait loci (QTL) controlling similar traits. Based on these trait-associated SNPs, 12 and seven candidate genes were respectively annotated for CSRFAB and DCSRFAB traits. Congruent with the contrasting and inverse relationship between discontinuous and continuous storage root formation and bulking, a DCSRFAB-associated candidate gene regulates redox signaling, involved in auxin-mediated lateral root formation, while CSRFAB is enriched for genes controlling growth and senescence. Conclusion: Candidate genes identified in this study have potential roles in cell wall remodeling, plant growth, senescence, stress, root development and redox signaling. These findings provide valuable insights into understanding the functional networks to develop strategies for sweetpotato yield improvement. The markers as well as candidate genes identified in this pioneering research for CSRFAB provide important genomic resources for sweetpotato and other root crops.

Genetic Resources and Crop Evolution, Sep 14, 2019

Enset (Ensete ventricosum (Welw.) Cheesman), which feeds around 20 million Ethiopian people, is a... more Enset (Ensete ventricosum (Welw.) Cheesman), which feeds around 20 million Ethiopian people, is a unique crop; with all parts of the plant are utilizable. It is, arguably, less researched crop and the mode of production remained conventional. Understanding the extent of genetic diversity in the crop, especially making use of genotyping data, is a very important first step in the genetic improvement of the crop. Twelve polymorphic enset SSR markers were used to assess the genetic diversity and population structure of 79 cultivated landraces and four wild enset individuals collected from different enset growing locations of Ethiopia. The polymorphic information content of markers ranged from 0.62 to 0.77 with a mean value of 0.69. A total of 77 alleles were identified, and the average observed heterozygosity varied from 0.51 to 0.67. A mean gene diversity of 0.59 was recorded ranging from 0.55 to 0.62. The AMOVA revealed that within population allelic variations contributed more to the genetic diversity than among population variations. Discriminant Analysis of Principal Components and population structure analysis grouped the 83 enset germplasms into three major clusters, where the wild individuals clustered distinctly. Outcomes of this research provide valuable information for enset conservation and breeding strategies especially for development of resistance for bacterial wilt and nematode attacks.

Tropical Plant Pathology, Feb 14, 2023

bioRxiv (Cold Spring Harbor Laboratory), Oct 30, 2019

Rwanda has about 4.5 million of indigenous chicken (IC) that are very low in productivity. To ini... more Rwanda has about 4.5 million of indigenous chicken (IC) that are very low in productivity. To initiate any genetic improvement programme, IC needs to be accurately characterized. The key purpose of this study was to ascertain the genetic diversity of IC in Rwanda using microsatellite markers. Blood samples of IC sampled from 5 agro-ecological zones were collected from which DNA was extracted, amplified by PCR and genotyped using 28 microsatellite markers. A total of 325 (313 indigenous and 12 exotic) chicken were genotyped and revealed a total number of 305 alleles varying between 2 and 22 with a mean of 10.89 per locus. 186 distinct alleles and 60 private alleles were also observed. The frequency of private alleles was highest in samples from the Eastern region, whereas those from the North West had the lowest. The influx of genes was lower in the Eastern agro-ecological zone than the North West. The mean observed heterozygosity was 0.6155, whereas the average expected heterozygosity was 0.688. The overall inbreeding coefficient among the population was 0.040. Divergence from the Hardy-Weinberg equilibrium was significant in 90% of loci in all the populations. The analysis of molecular variance revealed that about 92% of the total variation originated from variation within populations. Additionally, the study demonstrated that IC in Rwanda could be clustered into four gene groups. In conclusion, there was considerable genetic diversity in IC in Rwanda, which represents a crucial genetic resource that can be conserved or optimized through genetic improvement. Gates Foundation (BMGF); the UK Department for International Development (DFID) and the Swedish International Development Cooperation Agency (SIDA).

Molecular Breeding, Nov 1, 2020

Wheat (Triticum aestivum L.) is a major staple crop in East Africa (EA) providing 9% and 10% of d... more Wheat (Triticum aestivum L.) is a major staple crop in East Africa (EA) providing 9% and 10% of daily calories and protein intake, respectively. However, EA countries depend on import to meet 55% of their domestic wheat supplies due to increasing demands and low domestic yields. To determine the beneficial gene pool currently exploited for wheat improvement in EA, we examined the allelic diversity of 39 genes of breeding importance in a collection of 239 wheat cultivars and breeding lines from Kenya and Ethiopia using KASP markers. The assayed genes have been shown to control variations in plant height, thousand kernel weight (TKW), grain protein content, pre-harvest sprouting (PHS), disease resistance, and flowering time. We observed the beneficial alleles of some major genes including Gpc-B1, Yr5, Yr15, Sr26, and Fhb1 to be missing or present at low frequencies in this population. Furthermore, we validated the effects of the major Rht-1 alleles and TaCKX-D1 in controlling variation in plant height and thousand kernel weight, respectively, under EA conditions. Our results uncover hitherto unexploited allelic diversity that can be used to improve the genetic potential of EA wheat germplasm. This will inform strategies to rapidly mobilize these beneficial alleles for wheat improvement in EA.

Scientific Reports, Feb 2, 2021

Cassava mosaic disease (CMD) is a serious threat to cassava production in sub-Saharan Africa. The... more Cassava mosaic disease (CMD) is a serious threat to cassava production in sub-Saharan Africa. The use of genomic-assisted selection at the seedling trial stage would help to reduce the time for release, breeding cost, and resources used, hence increase selection efficiency in cassava breeding programs. Five cassava populations were screened for resistance to CMD during the seedling evaluation trial at 1, 3, and 5 months after planting using a scale of 1-5. The genotypes in the five populations were also screened using six molecular markers linked to the CMD2 gene. The correlation between the phenotypic and marker data was estimated. Based on Cassava Mosaic Disease Severity Score (CMDSS), between 53 and 82% of the progenies were resistant across the populations with an average of 70.5%. About 70% of the progenies were identified to be resistant to the disease across the populations with a range of 62-80% using the marker data. With both marker data and CMDSS combined, 40-60% of the progenies in each population, with an average of 52%, were identified to be resistant to CMD. There was a fairly significant correlation between the marker data and CMDSS in each cassava population with correlation coefficients ranging from 0.2024 to 0.3460 suggesting that novel genes not associated to the markers used might be involved in the resistance to CMD. The resistant genotypes identified in this study with potential for other desirable traits were selected for evaluation at the advanced trial stage thereby shortening the period required for the breeding program. Cassava (Manihot esculenta Crantz) is an important subsistence and food security crop for resource-poor households in about 40 African countries where it is a mainstay of over 200 million people 1-5. It is said to be the fourth most important source of food calories for humans in the tropics 6. Globally, Nigeria is the leading producer of cassava roots with production estimated at 59.5 million metric tonnes 7. In Nigeria, cassava is ranked among the major food crops supplying 70% of the total calorie intake of about half of the population 8. However, CMD, a devastating and debilitating disease caused by cassava mosaic begomoviruses (CMBs) is constraining cassava cultivation in all cassava growing areas 5,9-12. Some of the improved cassava varieties currently cultivated in Nigeria are susceptible to CMD. It was reported that African cassava mosaic virus (ACMV) greatly decreased the growth and yield of susceptible varieties 13,14. Strategies for controlling the disease include the use of resistant varieties 15-18. The resistance to CMD is known to be polygenic; the International Center for Tropical Agriculture (CIAT) has mapped two CMD resistance genes namely CMD1 (recessive gene) and CMD2 (major dominant gene) 11,19 and three molecular markers associated with CMD2, namely RME1, SSRY28, and NS158, were developed 20. These markers are very useful and hold great promise in fast-tracking improvement of cassava for CMD-resistance 21. The molecular markers were used by Bi et al. 21 to screen some varieties of cassava for resistance to CMD. In

Frontiers in Plant Science, May 3, 2021

American Journal of Biochemistry and Biotechnology

This open-access article is distributed under a Creative Commons Attribution (CC-BY) 4.0 license.

Plant Genetic Resources: Characterization and Utilization

Being difficult to regenerate and maintain the seeds, the oleaginous bottle gourd was investigate... more Being difficult to regenerate and maintain the seeds, the oleaginous bottle gourd was investigated using nine agromorphological traits and 31 amplified fragment length polymorphism (AFLP) markers. Specifically, the study was conducted to determine the intra-specific variability of a total of 173 accessions, which were identified from five agro-ecological regions from Côte d'Ivoire (Centre, East, North and South). Then, the genetic diversity and relationships within accessions were studied using AFLP markers. This characterization using both morphological and AFLP markers was realized in order to ultimately build a reliable core collection. The discriminant analysis, using nine quantitative traits, reveals plant length and seeds number per fruit as discriminating characteristics. From the accessions used for the agromorphological study, 148 were able to be differentiated by the AFLP markers. A range of 52 to 113 bands were amplified per primer combination. As revealed by the anal...

Frontiers in Genetics, 2021

A chicken genome has several regions with quantitative trait loci (QTLs). However, replication an... more A chicken genome has several regions with quantitative trait loci (QTLs). However, replication and confirmation of QTL effects are required particularly in African chicken populations. This study identified single nucleotide polymorphisms (SNPs) and putative genes responsible for body weight (BW) and antibody response (AbR) to Newcastle disease (ND) in Rwanda indigenous chicken (IC) using genome-wide association studies (GWAS). Multiple testing was corrected using chromosomal false detection rates of 5 and 10% for significant and suggestive thresholds, respectively. BioMart data mining and variant effect predictor tools were used to annotate SNPs and candidate genes, respectively. A total of four significant SNPs (rs74098018, rs13792572, rs314702374, and rs14123335) significantly (p ≤ 7.6E−5) associated with BW were identified on chromosomes (CHRs) 8, 11, and 19. In the vicinity of these SNPs, four genes such as pre-B-cell leukaemia homeobox 1 (PBX1), GPATCH1, MPHOSPH6, and MRM1 wer...

Global Journal of Science Frontier Research, 2020

Soybean (Glycine max (L.) Merrill) is a highly nutritious legume with enormous potential to impro... more Soybean (Glycine max (L.) Merrill) is a highly nutritious legume with enormous potential to improve dietary quality for humans and livestock. However, the development of varieties with improved nutritional traits has been affected by the negative correlation that exists among the different traits and the high cost of the phenotypic assessment. The objectives of this study were: (1) to quantify the total protein, total oil and fatty acids of 52 soybean genotypes from different sources, (2) to identify correlations among total protein, total oil content and fatty acids. The total protein content was determined using the Modified Folin-Lowry Method. In contrast, the total oil and fatty acids methyl esters were determined using the chloroform/methanol gravimetric method and Gas Chromatography–Mass Spectrometry. The analysis of variance revealed that the studied traits varied significantly depending on genotypes and origin.

Accurate identification of varieties is paramount to optimizing efficiencies in the management an... more Accurate identification of varieties is paramount to optimizing efficiencies in the management and conservation of genetic resources. A relatively inexpensive, rapid methodology is required to identify putative duplicates from any collection, when morphological traits give insufficient discrimination. Here we select a panel of 36 SNPs, visualized using the Kompetitive Allele-specific PCR (KASP) system. We used a panel of 95 cassava genotypes from Côte d’Ivoire to identify varieties that are not duplicates and few potential duplicates which could be put forward for further verification. The genetic variability and population structure of the germplasm is also described. 36 SNPs were polymorphic across the panel of 95 varieties with polymorphic information contents ranging from 0.23 to 0.37. Using these SNPs, we were able to identify 66 unique genotypes from the panel of 95 genotypes, discriminate three sets of known duplicates and identify 11 sets of unknown putative duplicates which...