Analysis of diversity among East African sweet potato cultivars (ipomoea batatas) using morphological and simple sequence repeats dna markers

A Thesis submitted in partial fulfillment of the requirements for the degree of master of science in molecular biology of Makerere University, Kampala. Full thesis.East Africa is considered to be a secondary centre of origin of sweet potato and it is suspected that the wide morphological variation observed indicates wide genetic diversity in the region. To conserve and utilize the germplasm, it is important that proper assessment of the diversity of the East African sweet potato germplasm be made.Identification by molecular technologies is more commonly used over morphological characters since the latter can be influenced by environmental factors. In this study, we used molecular and morphological markers to study the genetic diversity of the germplasm in the region. Collections of cultivars were made from selected locations of Uganda, Kenya and Tanzania and subsequently established in pots in a screen house at Makerere University. A total of 266 cultivars were collected. After 3 weeks, the cultivars were screened for morphological characters using the CIP Research Guide. Cluster analysis was done using UPGMA in Treecon (Version 1.3). Based on morphological grouping, 57 cultivars, which were morphologically diverse, were randomly selected for DNA extraction and further analysis was done. Cluster analysis revealed only two major groupings (A & B) of sweet potatoes with very low bootstrap support of 0-54 %. The key distinguishing morphological markers were triangular leaf outline and a cordate shaped leaf outline for group A & B respectively. In addition, there were no geographical distinct morphological types identified. No population structure was detected. However, within each country, a high variation was observed (97.65%), suggesting that a wide range of cultivars is being grown in each country. Microsatellite (SSR) reactions were performed using four SSR primer combinations. The polymerase chain reaction (PCR) products were resolved using a high resolution metaphor agarose gel electrophoresis. Genetic distance data matrices were subjected to Unweighted pair-group method of arithmetic averages (UPGMA) clustering using TREECON phylogenetic program Version 1.3 b. Two major sub-clusters were found by UPGMA at a bootstrap value of 54 %. Low bootstrap values (0-55 %) indicate absence of clusters and close genetic relationships among the cultivars. The majority of cultivars were in the range of 0.1-0.3 Nei's genetic distance from each other, which also shows close genetic relatedness. The clustering of sweet potato cultivars based on SSR markers showed that cultivars from Kenya, Uganda and Tanzania were grouping in group A. In sub-cluster B the cultivars were from Uganda and they seemed to form a unique group. However the Tanzanian cultivars seem to cluster closely together in various sub-clusters. Analysis of Molecular Variance (AMOVA) indicated that there is statistically measurable divergence between the sweet potato of Uganda-Kenya and the other East-African country, Tanzania with detectable difference between the cultivars of the three sources. The largest source of diversity comes from within-population variation, which accounts for 88.91 % of the total variance. The data from AMOVA analysis also indicated an F st value >0.05 which seems to suggest great genetic differentiation amongst the cultivars in the East African region and hence presence of a population structure. The gene flow values > 1 shows that there is high genetic drift amongst the cultivars in this region. In this study, the morphological analysis of sweet potato landraces indicated that there was not much variation in the East African sweet potato. However the investigation at genome level using PCR-based SSR markers was able to identify significant variation amongst the landraces and existence of a population structure. The major results in this study indicate that SSR markers are appropriate for the genotyping and revealing genetic relationship of East African sweetpotato cultivars. In addition, morphological characterisation should be complemented with DNA –based characterisation using SSR markers to reveal genetic diversity of East African sweet potato cultivars.East Africa is considered to be a secondary centre of origin of sweet potato and it is suspected that the wide morphological variation observed indicates wide genetic diversity in the region. To conserve and utilize the germplasm, it is important that proper assessment of the diversity of the East African sweet potato germplasm be made.Identification by molecular technologies is more commonly used over morphological characters since the latter can be influenced by environmental factors. In this study, we used molecular and morphological markers to study the genetic diversity of the germplasm in the region. Collections of cultivars were made from selected locations of Uganda, Kenya and Tanzania and subsequently established in pots in a screen house at Makerere University. A total of 266 cultivars were collected. After 3 weeks, the cultivars were screened for morphological characters using the CIP Research Guide. Cluster analysis was done using UPGMA in Treecon (Version 1.3). Based on morphological grouping, 57 cultivars, which were morphologically diverse, were randomly selected for DNA extraction and further analysis was done. Cluster analysis revealed only two major groupings (A & B) of sweet potatoes with very low bootstrap support of 0-54 %. The key distinguishing morphological markers were triangular leaf outline and a cordate shaped leaf outline for group A & B respectively. In addition, there were no geographical distinct morphological types identified. No population structure was detected. However, within each country, a high variation was observed (97.65%), suggesting that a wide range of cultivars is being grown in each country. Microsatellite (SSR) reactions were performed using four SSR primer combinations. The polymerase chain reaction (PCR) products were resolved using a high resolution metaphor agarose gel electrophoresis. Genetic distance data matrices were subjected to Unweighted pair-group method of arithmetic averages (UPGMA) clustering using TREECON phylogenetic program Version 1.3 b. Two major sub-clusters were found by UPGMA at a bootstrap value of 54 %. Low bootstrap values (0-55 %) indicate absence of clusters and close genetic relationships among the cultivars. The majority of cultivars were in the range of 0.1-0.3 Nei's genetic distance from each other, which also shows close genetic relatedness. The clustering of sweet potato cultivars based on SSR markers showed that cultivars from Kenya, Uganda and Tanzania were grouping in group A. In sub-cluster B the cultivars were from Uganda and they seemed to form a unique group. However the Tanzanian cultivars seem to cluster closely together in various sub-clusters. Analysis of Molecular Variance (AMOVA) indicated that there is statistically measurable divergence between the sweet potato of Uganda-Kenya and the other East-African country, Tanzania with detectable difference between the cultivars of the three sources. The largest source of diversity comes from within-population variation, which accounts for 88.91 % of the total variance. The data from AMOVA analysis also indicated an F st value >0.05 which seems to suggest great genetic differentiation amongst the cultivars in the East African region and hence presence of a population structure. The gene flow values > 1 shows that there is high genetic drift amongst the cultivars in this region. In this study, the morphological analysis of sweet potato landraces indicated that there was not much variation in the East African sweet potato. However the investigation at genome level using PCR-based SSR markers was able to identify significant variation amongst the landraces and existence of a population structure. The major results in this study indicate that SSR markers are appropriate for the genotyping and revealing genetic relationship of East African sweetpotato cultivars. In addition, morphological characterisation should be complemented with DNA –based characterisation using SSR markers to reveal genetic diversity of East African sweet potato cultivars

Inheritance of resistance to common bacterial blight in four selected common bean (\u3ci\u3ePhaseolus vulgaris\u3c/i\u3e L.) genotypes

Common bacterial blight (CBB) is the most serious bacterial disease of common bean in Uganda. It causes severe yield losses of up to 62%. Genetic resistance is the most effective option for controlling CBB in smallholder common bean production systems. This study was carried out to determine the inheritance pattern of CBB resistance in leaf and pod of four new resistance sources. The four resistant and four susceptible genotypes were crossed in a half-diallel mating design. F1 individuals were advanced to F2 and evaluated with the parents, in a randomized complete block design replicated twice. Combining ability analysis was performed according to Griffing\u27s (1956) method IV and model 1 using Genstat 12th. General combining ability effects were significant whereas specific combining ability was not suggesting that resistance to CBB in leaf and pod was primarily controlled by additive genes effects. The estimated narrow sense coefficient of genetic determination was moderately high (0.65) for the resistance in leaf and high (0.83) for resistance in pod suggesting that early-generation selection would be effective. Baker’s ratio estimates were relatively high for resistance in leaf (0.79) and pod (0.9) suggesting that hybrids’ performance can be predicted based on the parents’ general combining ability (GCA) effects

Genetic Variability and Evolutionary Implications of RNA Silencing Suppressor Genes in RNA1 of Sweet Potato Chlorotic Stunt Virus Isolates Infecting Sweetpotato and Related Wild Species

Peer reviewe

Genetic Gains for Yield and Virus Disease Resistance of Cassava Varieties Developed Over the Last Eight Decades in Uganda

Achieving food security for an ever-increasing human population requires faster development of improved varieties. To this end, assessment of genetic gain for key traits is important to inform breeding processes. Despite the improvements made to increase production and productivity of cassava in Uganda at research level, there has been limited effort to quantify associated genetic gains. Accordingly, a study was conducted in Uganda to assess whether or not genetic improvement was evident in selected cassava traits using cassava varieties that were released from 1940 to 2019. Thirty-two varieties developed during this period, were evaluated simultaneously in three major cassava production zones; central (Namulonge), eastern (Serere), and northern (Loro). Best linear unbiased predictors (BLUPs) of the genotypic value for each clone were obtained across environments and regressed on order of release year to estimate annual genetic gains. We observed that genetic trends were mostly quadratic. On average, cassava mosaic disease (CMD) resistance increased by 1.9% per year, while annual genetic improvements in harvest index (0.0%) and fresh root yield (−5 kg per ha or −0.03% per ha) were non-substantial. For cassava brown streak disease (CBSD) resistance breeding which was only initiated in 2003, average annual genetic gains for CBSD foliar and CBSD root necrosis resistances were 2.3% and 1.5%, respectively. It’s evident that cassava breeding has largely focused on protecting yield against diseases. This underpins the need for simultaneous improvement of cassava for disease resistance and high yield for the crop to meet its current and futuristic demands for food and industry

Genetic diversity and population structure of Peronosclerospora sorghi isolates of Sorghum in Uganda

Sorghum is the third most important staple cereal crop in Uganda after maize and millet. Downy mildew disease is one of the most devastating fungal diseases which limits the production and productivity of the crop. The disease is caused by an obligate fungus, Peronosclerospora sorghi (Weston & Uppal) with varying symptoms. Information on the genetic diversity and population structure of P.sorghi in sorghum is imperative for the screening and selection for resistant genotypes and further monitoring possible mutant(s) of the pathogen. Isolates of P. sorghi infecting sorghum are difficult to discriminate when morphological descriptors are used. The use of molecular markers is efficient, and reliably precised for characterizing P. sorghi isolates. This study was undertaken to assess the level of genetic diversity and population structure that exist in P. sorghi isolates in Uganda. A total of 195 P. sorghi isolates, sampled from 13 different geographic populations from 10 different regions (agro-ecological zones) was used. Eleven (11) molecular markers, comprising of four Random amplified microsatellite (RAM) and seven (7) Inter-Simple Sequence Repeat (ISSR) markers were used in this study. The analysis of molecular variation (AMOVA) based on 11 microsatellite markers showed significant (P < 0.001) intra-population (88.9 %, PhiPT = 0.111) and inter-population (8.4 %, PhiPR = 0.083) genetic variation, while the genetic variation among regions (2.7 %, PhiRT = 0.022) was not significant. The highest genetic similarity value (0.987 = 98.7 %) was recorded between Pader and Lira populations and the lowest genetic similarity (0.913 = 91.3 %) was observed between Namutumba and Arua populations. The mean Nei's genetic diversity index (H) and Shannon Information Index (I) were 0.308 and 0.471 respectively. Seven distinct cluster groups were formed from the 195 P. sorghi isolates based on their genetic similarity. Mantel test revealed no association between genetic differentiation and geographical distance (R2 = 0.0026, p = 0.02) within the 13 geographic populations

Genetic basis of maize resistance to multiple insect pests: integrated genome-wide comparative mapping and candidate gene prioritization

Several species of herbivores feed on maize in field and storage setups, making the development of multiple insect resistance a critical breeding target. In this study, an association mapping panel of 341 tropical maize lines was evaluated in three field environments for resistance to fall armyworm (FAW), whilst bulked grains were subjected to a maize weevil (MW) bioassay and genotyped with Diversity Array Technology’s single nucleotide polymorphisms (SNPs) markers. A multi-locus genome-wide association study (GWAS) revealed 62 quantitative trait nucleotides (QTNs) associated with FAW and MW resistance traits on all 10 maize chromosomes, of which, 47 and 31 were discovered at stringent Bonferroni genome-wide significance levels of 0.05 and 0.01, respectively, and located within or close to multiple insect resistance genomic regions (MIRGRs) concerning FAW, SB, and MW. Sixteen QTNs influenced multiple traits, of which, six were associated with resistance to both FAWandMW, suggesting a pleiotropic genetic control. Functional prioritization of candidate genes (CGs) located within 10–30 kb of the QTNs revealed 64 putative GWAS-based CGs (GbCGs) showing evidence of involvement in plant defense mechanisms. Only one GbCG was associated with each of the five of the six combined resistance QTNs, thus reinforcing the pleiotropy hypothesis. In addition, through in silico co-functional network inferences, an additional 107 network-based CGs (NbCGs), biologically connected to the 64 GbCGs, and di erentially expressed under biotic or abiotic stress, were revealed within MIRGRs. The provided multiple insect resistance physical map should contribute to the development of combined insect resistance in maize

Factors influencing genomic prediction accuracies of tropical maize resistance to fall armyworm and weevils

Genomic selection (GS) can accelerate variety improvement when training set (TS) size and its relationship with the breeding set (BS) are optimized for prediction accuracies (PAs) of genomic prediction (GP) models. Sixteen GP algorithms were run on phenotypic best linear unbiased predictors (BLUPs) and estimators (BLUEs) of resistance to both fall armyworm (FAW) and maize weevil (MW) in a tropical maize panel. For MW resistance, 37% of the panel was the TS, and the BS was the remainder, whilst for FAW, random-based training sets (RBTS) and pedigree-based training sets (PBTSs) were designed. PAs achieved with BLUPs varied from 0.66 to 0.82 for MW-resistance traits, and for FAW resistance, 0.694 to 0.714 for RBTS of 37%, and 0.843 to 0.844 for RBTS of 85%, and these were at least two-fold those from BLUEs. For PBTS, FAW resistance PAs were generally higher than those for RBTS, except for one dataset. GP models generally showed similar PAs across individual traits whilst the TS designation was determinant, since a positive correlation (R = 0.92***) between TS size and PAs was observed for RBTS, and for the PBTS, it was negative (R = 0.44**). This study pioneered the use of GS for maize resistance to insect pests in sub-Saharan Africa

Heritability Studies of Major Chemical Attributes of Soybean Seed

67 p.Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 1972.U of I OnlyRestricted to the U of I community idenfinitely during batch ingest of legacy ETD

Crystalline and pasting properties of cassava starch are influenced by its molecular properties

This study was undertaken to detail starch characteristics among cassava varieties and compare them to their improved progenies. Cassava starch was extracted from roots of both the parents and progenies of two popular Ugandan local varieties (Bamunanika and Nyaraboke) and three popular elite varieties (NASE 10, TME 14 and 95/SE/00036) and their properties compared. The pasting and rheological properties showed a unique pasting curve in the progenies compared to the parents with significantly low peak viscosities among the progenies. Percentage crystallinity as determined by X-ray crystallography was on average four points higher in parents compared to progenies. There were no significant differences in the average amylose contents (17 - 20%) and starch contents (about 81%) in both the progenies and their parents. Significant relationships were observed between crystalline and pasting properties of the starch among the clones and parents. The above differences suggest possible variations in the amylopectin chain structure and starch molecular properties attributable to differences in the starch branching enzyme among the progenies and their parents.This work was supported under the BIO-EARN program, with a grant from the Swedish International Cooperation Agency/Department for Research Cooperation (Sida/ SAREC)