Department of Science and Vocational Studies

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Pyramiding Fusarium root rot resistance genes and validation of SSR PVBR87 in common bean
(RUFORUM, 2010) Obala, Jimmy; Rubaihayo, P.R; Mukankusi, C; Gibson, P
This study determined effectiveness of pyramided Fusarium root rot (FRR) resistance genes and validated association of SSR PVBR87 marker with FRR resistance in common bean. A double cross (DC) involving four resistance sources was used to accumulate FRR resistance genes into one background. The DC F1 and each resistant line were crossed to two susceptible cultivars. Parents, F1 and F2 populations were subjected to FSP-3 in a screenhouse. Two single cross (SC) F2 populations were screened with SSR PVBR87 marker. Five parent crosses performed better than single crosses. SSR PVBR87 marker showed association with FRR resistance in the two SC F2 populations.
Improvement of resistance to Fusarium root rot through gene pyramiding and validation of SSR PVBR87 marker in common bean
(Makerere University, 2011) Obala, Jimmy
Fusarium root rot caused by Fusarium solani f. sp. phaseoli is among the most serious diseases of the common bean in Uganda causing total crop loss in susceptible cultivars. Studies have indicated that 2-9 genes located at different loci govern resistance to Fusarium root rot among different resistance sources. Accumulation of several of these genes from the different sources into a single genetic background has been proposed to result in an increased level of resistance to Fusarium root rot, and more effective transfer of this resistance into consumer-preferred cultivars. Use of molecular markers together with phenotypic selection could speed up breeding progress for Fusarium root rot resistance. A simple sequence repeat (SSR) PVBR87 marker linked to Fusarium root rot resistance quantitative trait loci (QTL) was identified in a previous study but its use in identifying resistant genotypes outside the original two mapping populations has not been determined. This study estimated the number of pyramided Fusarium root rot resistance genes from four sources of resistance, their interaction and effectiveness in improving Fusarium root rot resistance levels. The study also validated the association of the SSR PVBR87 marker with resistance to Fusarium root rot in an additional population. The study was conducted at the International Centre for Tropical Agriculture (CIAT) based at the National Agricultural Research Laboratories – Kawanda, Uganda. Four Fusarium root rot resistant (R) inbred lines: MLB-48-89A (48), MLB-49-89A (49), G2333 (G2) and G685 (G6), and two susceptible (S) lines: K20 and Kanyebwa (Kan) were used in the study. A double cross (DC) was developed from the four resistant parents. The DC F1 and each resistant parent were crossed to the two susceptible cultivars to form five-parent crosses and single crosses, respectively. Parental, F1 and F2 populations were subjected to Fusarium solani f. sp. phasoeli isolate-3. Twenty one days xi after planting, symptom severity was assessed on a scale of 1-9 (varied at 1,2,3,4,5,6,7,8,9). Plants of each cross were grouped into resistant (score 1-4) and susceptible (score 5-9). F2 plants of K20 x G2 and 49 x Kan were screened with SSR PVBR87 marker. The estimated number of genes and gene interactions were determined using X2 goodness-of-fit test (P = 0.05) and means were compared by “Students t-test” (P = 0.05). The association of SSR PVBR87 marker to Fusarium root rot resistance was determined using X2 test of independence and single marker regression analysis (P = 0.05). Two to three genes segregated in the R x R single crosses and at least four genes segregated in the double cross population indicating three of the four resistant parents differed from each other by at least one gene and two of the four parents have at least one gene in common. Genetic effects among the crosses included additive and dominance effects and epistatic interactions. Five-parent crosses performed better than the single crosses, demonstrating the potential of using combined resistance in improving resistance to Fusarium root rot in susceptible bean cultivars. The SSR PVBR87 marker showed significant association to Fusarium root rot resistance in both K20 x G2 and Kan x 49 indicating its stability in different genetic background but still requires further validation in different environments and in additional genetic backgrounds to determine its use for marker-assisted breeding for improving resistance to Fusarium root rot. The genes responsible for the higher levels of Fusarium root rot resistance in the pyramids are not specifically known. It is necessary that these resistance genes be tagged with molecular markers. Tagging of the genes with molecular markers would provide knowledge of their genomic locations, the nature of their interactions and also facilitate the transfer of these genes or alleles, through molecular marker-assisted gene introgression, into other agronomically superior, but Fusarium root xii rot susceptible cultivars. Since no selection for Fusarium root rot resistance or any other desirable agronomic traits was practiced in this study, there is need to select between and within families from among the five-parent cross populations and the single crosses for resistance to Fusarium root rot. However, the predominance of non-additive gene effects for Fusarium root rot resistance, especially in the five-parent crosses suggests that selection for resistance would be more effective at advanced generations of selfing. The bean parents used in constructing the five-parent cross populations are of diverse seed character, growth habit, maturity period, and have varied response to several abiotic and biotic constraints. There is also need to select for these traits in the populations developed in this study as these traits eventually affect acceptability of any potential new variety. The amounts of phenotypic variation explained by the SSR PVBR87 in two populations were low; hence, there is still need to further validate the marker in additional populations and in several environments to determine its efficacy for marker-assisted breeding for Fusarium root rot resistance
IMPROVEMENT OF RESISTANCE TO FUSARIUM ROOT ROT THROUGH GENE PYRAMIDING IN COMMON BEAN
(African Crop Science Journal, 2012) OBALA, JIMMY; MUKANKUSI, C.; RUBAIHAYO, P.R.; GIBSON, P.; EDEMA, R.
Fusarium root rot (FRR), caused by Fusarium solani f.sp. phaseoli, is one of the most serious root rot diseases of common bean (Phaseolus vulgaris L.) throughout the world. Yield losses of up to 84% have been attributed to the disease. Development and deployment of resistant materials is the most feasible approach to managing the disease. The objective of this study was to estimate the number of pyramided Fusarium root rot resistance genes among the four resistant lines and determine their effectiveness in improving levels of resistance to Fusarium root rot in the susceptible bean cultivars. Crosses among four Fusarium root rot (Fusarium solani f.sp. phaseoli) resistant common bean (Phaseolus vulgaris) were developed. They involved six inbred lines, MLB-48-89A (M48), MLB-49-89A (M49), G2333 (G2) and G685 (G6), and two susceptible cultivars, K20 and Kanyebwa, The resistant lines were used to develop a double cross (DC) population. The DC F1 and each resistant parent were crossed to each of the two susceptible cultivars to form five-parent and single crosses, respectively. Developed populations were subjected to Fusarium solani f. sp. phasoeli isolate-3 under screenhouse conditions. There were segregation ratios of 15:1 (χ2 = 1.89, P = 0.17), 61:3 (χ2 = 0.18, P = 0.67) and 249:7 (χ2 = 1.74, P = 0.19) indicating that two, three and four genes independently condition resistance to F. solani in lines G2 x G6, M49 x M48 and (M49 x M48) x (G2 x G6). A good fit of only four genes in the double cross compared to two in the G2 x G6 , and three genes in the M49 x M48 cross suggests that at least one parent in the G2 x G6 cross have the same or closely linked genes as a parent in the M49 x M48 cross. The F1 means of the five-parent cross (FPC) involving either susceptible parent had lower disease scores, though not significantly (P > 0.05), than the single-crosses from that parent. The F2 of both FPC showed less disease than the single-cross (SC) means (P < 0.05) compared to the single-cross (SC) while the F2 of both FPC had a significant negative deviation (P < 0.05). The F2 frequency distributions also showed that the FPC in both Kanyebwa and K20 populations had higher proportions of resistant plants than any of the single crosses in the respective populations. The superior performance of the FPC over the SC demonstrates that combining resistance genes form different FRR resistance sources can provide a stable source of resistance than using single sources of resistance.
Forest resilience and tipping points at different spatio-temporal scales: approaches and challenges
(Journal of Ecology, 2015) Reyer, Christopher P. O.; Brouwers, Niels; Rammig, Anja; Brook, Barry W.; Epila, Jackie; Grant, Robert F.; Holmgren, Milena; Langerwisch, Fanny; Leuzinger, Sebastian; Lucht, Wolfgang; Medlyn, Belinda; Pfeifer, Marion; Steinkamp, Jorg; Vanderwel, Mark C.; Verbeeck, Hans; Villela, Dora M.
1. Anthropogenic global change compromises forest resilience, with profound impacts to ecosystem functions and services. This synthesis paper reflects on the current understanding of forest resilience and potential tipping points under environmental change and explores challenges to assessing responses using experiments, observations and models. 2. Forests are changing over a wide range of spatio-temporal scales, but it is often unclear whether these changes reduce resilience or represent a tipping point. Tipping points may arise from interactions across scales, as processes such as climate change, land-use change, invasive species or deforestation gradually erode resilience and increase vulnerability to extreme events. Studies covering interactions across different spatio-temporal scales are needed to further our understanding. 3. Combinations of experiments, observations and process-based models could improve our ability to project forest resilience and tipping points under global change. We discuss uncertainties in changing CO2 concentration and quantifying tree mortality as examples. 4. Synthesis. As forests change at various scales, it is increasingly important to understand whether and how such changes lead to reduced resilience and potential tipping points. Understanding the mechanisms underlying forest resilience and tipping points would help in assessing risks to ecosystems and presents opportunities for ecosystem restoration and sustainable forest management.
Genomics-assisted breeding for boosting crop improvement in pigeonpea (Cajanus cajan)
(Frontiers in plant science, 2015) Pazhamala, Lekha; Saxena, Rachit K.; Singh, Vikas K.; Sameerkumar, C. V.; Kumar, Vinay; Sinha, Pallavi; Patel, Kishan; Obala, Jimmy; Kaoneka, Seleman R.; Tongoona, P.; Shimelis, Hussein A.; Gangarao, N. V. P. R.; Odeny, Damaris; Rathore, Abhishek; Dharmaraj, P. S.; Yamini, K. N.; Varshney, Rajeev K.
Pigeonpea is an important pulse crop grown predominantly in the tropical and sub-tropical regions of the world. Although pigeonpea growing area has considerably increased, yield has remained stagnant for the last six decades mainly due to the exposure of the crop to various biotic and abiotic constraints. In addition, low level of genetic variability and limited genomic resources have been serious impediments to pigeonpea crop improvement through modern breeding approaches. In recent years, however, due to the availability of next generation sequencing and high-throughput genotyping technologies, the scenario has changed tremendously. The reduced sequencing costs resulting in the decoding of the pigeonpea genome has led to the development of various genomic resources including molecular markers, transcript sequences and comprehensive genetic maps. Mapping of some important traits including resistance to Fusarium wilt and sterility mosaic disease, fertility restoration, determinacy with other agronomically important traits have paved the way for applying genomics-assisted breeding (GAB) through marker assisted selection as well as genomic selection (GS). This would accelerate the development and improvement of both varieties and hybrids in pigeonpea. Particularly for hybrid breeding programme, mitochondrial genomes of cytoplasmic male sterile (CMS) lines, maintainers and hybrids have been sequenced to identify genes responsible for cytoplasmic male sterility. Furthermore, several diagnostic molecular markers have been developed to assess the purity of commercial hybrids. In summary, pigeonpea has become a genomic resources-rich crop and efforts have already been initiated to integrate these resources in pigeonpea breeding.
Ecophysiological assessment of drought vulnerability of the African tropical tree species Maesopsis eminii Engl
(Ghent University, 2016) Epila, Jackie
Africa is endowed with the second largest block of nature-engineered machinery to sequester carbon: forests. Sadly, the functional traits and responses of this machinery are poorly understood, under non-drought, current drought and projected drought. Controversy surrounds the response of Africa’s forest tree species to drought. Moreover, little is known on the mechanisms or strategies they evoke to cope with drought. In this PhD study, the drought coping strategies and mechanisms of an African pioneer semi-deciduous tree species Maesopsis eminii Engl. (M. eminii) is investigated. A review of published and unpublished data provided insights in the species’ associated functional traits, phenology and provenance. The species’ occurrence niche was then characterized by combining this information and occurrence data of M. eminii in Africa with data on climate, soils and vegetation. It was found that M. eminii established itself in different ecosystems with diverse soil types and precipitation amounts. However, M. eminii mostly preferred the tropical rainforest region with fertile soils and annual precipitation exceeding 1000 mm yr-1. M. eminii’s presence in areas with pronounced seasonal precipitation prompted ecophysiological studies under natural and greenhouse settings. The aim was to determine additional traits used by this species to cope with drought. Different from most other plants, M. eminii seedlings continued to grow for a few days after the onset of drought and were also found to have nocturnal sap flow, because of low transpirational control. On the one hand, this trait seemed useful during non-drought conditions, but accelerated dehydration during drought and the eventual death of the seedlings. Unexpectedly, fast growth of M. eminii was not linked to its photosynthetic rate, as this was rather low. Instead, autoradiographs indicated a leaf role partition with older leaves actively loading sugars into the phloem compared to the expected passive loading in younger ones. Regardless of the loading mechanism, severe drought halved M. eminii’s photosynthetic rate but increased relative leaf respiration compared to a non-drought situation. This might explain why its growth eventually declined after a few days into drought. The hydraulic conduits of M. eminii were wide, which increased the likelihood of airseeding and may make this species’ xylem inherently vulnerable to drought-induced cavitation. But M. eminii was found to additionally have a considerable amount of water in its wood structure as evidenced by its low wood density, high volumetric water content and substantial hydraulic capacitance. This water probably contributed to the observed hydraulic redistribution between leaves, by which M. eminii could cope with drought for a couple of more days. During this hydraulic redistribution, a few leaves are shed while others remained hydrated, which reduced water loss but maintained limited carbon fixation. We also observed that M. eminii has low hydraulic conduits connection, which may limit the spread of drought-induced cavitation. This research has revealed different novel mechanisms (i.e., nocturnal sap flow, active sugar loading into the phloem in adult leaves, and hydraulic redistribution in the leaves) that have substantially increased the knowledge on how M. eminii copes with drought. It also shows that more attention must be paid to understand how African trees and eventually forests will deal with drought, if we aspire to more accurately predict the impact of climate change on this terrestrial ecosystem.
Characterization and mapping of Dt1 locus which co‑segregates with CcTFL1 for growth habit in pigeonpea
(Theor Appl Genet, 2017) Saxena, Rachit K; Obala, Jimmy; Sinjushin, Andrey; Kumar, C.V. Sameer; Saxena, K.B.; Varshney, Rajeev K.
Pigeonpea (Cajanus cajan) is one of the most important legume crops grown in arid and semi-arid regions of the world. It is characterized with few unique features compared with other legume species, such as Lotus, Med icago, and Glycine. One of them is growth habit, an impor tant agronomic trait. In the present study, identifcation of mutations affecting growth habit accompanied by a pre cise analysis of phenotype has been done which will shed more light upon developmental regulation in pigeonpea. A genetic study was conducted to examine the inheritance of growth habit and a genotyping by sequencing (GBS)-based genetic map constructed using F2 mapping population derived from crossing parents ICP 5529 and ICP 11605. Inheritance studies clearly demonstrated the dominance of indeterminate (IDT) growth habit over determinate (DT) growth habit in F2 and F2:3 progenies. A total of 787 SNP markers were mapped in the genetic map of 1454 cM map length. Growth habit locus (Dt1) was mapped on the CcLG03 contributing more than 61% of total phenotypic variations. Subsequently, QTL analysis highlighted one gene, CcTFL1, as a candidate for determinacy in pigeon pea, since an Indel marker derived from this gene co-seg regated with the Dt1 locus. Ability of this Indel-derived marker to differentiate DT/IDT lines was also validated on 262 pigeonpea lines. This study clearly demonstrated that CcTFL1 is a candidate gene for growth habit in pigeonpea and a user-friendly marker was developed in the present study which will allow low-cost genotyping without need of automation.
Molecular mapping of seed protein content in pigeonpea – a drought tolerant crop of the semi-arid tropics
(: InterDrought, 2017) Obala, Jimmy; Saxena, R.K.; Singh, V.K; Kale, S.M.; Garg, V.; Kumar, V.; Sameer Kumar, C.V; Tongoona, P; Sibiya, J.; Saxena, K.B
Pigeonpea is a uniquely drought and heat tolerant crop that provides a major source of dietary protein to nearly a billion people in the tropical and semi-arid tropics of the world. Despite its importance as a source of dietary protein the genetic control of its seed protein content (SPC) is poorly understood. The present study used high density linkage maps to identify quantitative trait loci (QTL) associated with SPC and its relationship with 100-seed weight (HSW), seed yield (SY), days to first flower (DTFF) and growth habit (GH). Five F2 mapping populations segregating for SPS including ICP 11605 × ICP 14209, ICP 8863 × ICP 11605, HPL 24 × ICP 11605, ICP 5529 × ICP 11605 and ICP 8863 × ICPL 87119 were genotyped using genotyping-by-sequencing and phenotyped for the traits. The average inter-marker distance on the population-specific maps varied from 1.6cM to 3.5cM.On the basis of the population-specific and consensus linkage maps, 48main effect QTLs (M-QTLs)with phenotypic variance explained (PVE) ranging from 0.7 to 23.5% were detected across five populations, of which 15 M-QTLs were major (PVE≥10). Twenty seven of the M-QTLs could be collapsed into six consensus QTL regions. In addition, 34 epistatic QTLs (E-QTLs) with PVE ranging from 6.3% to 69.8% were detected across populations. Co-localization of M-QTLs and E-QTLs affecting SPC and the agronomic traits explained the genetic basis of the significant (P < 0.05) correlations of SPC with HSW (r2 = 0.22 to 0.30), SY (r2 = -0.18 to -0.28), DTFF (r2 = -0.17 to -0.31) and GH (r2 = 0.18 to 0.34). The quantitative nature of genetic control of SPC and its relationship with agronomic traits suggest that marker-assisted recurrent selection or genomic selection would be effective for the simultaneous improvement of SPC and other important traits
Plant measurements on African tropical Maesopsis eminii seedlings contradict pioneering water use behaviour
(Environmental and Experimental Botany, 2017) Epila, Jackie; Maesa, Wouter H.; Verbeeck, Hans; Campa, Janne Van; Okullod, John Bosco Lamoris; Steppe, Kathy
With increased drought events affecting forests globally, little is known about their future impact on Africa’s forests. In particular, we need to gain a better understanding of how key African forest species will respond to drought stress. In this study, we investigated functional traits and physiological responses to drought of the light-demanding pioneer species Maesopsis eminii Engl. The study involved an experiment on potted M. eminii seedlings with three different drought treatments in which sap flow (SF), stem diameter variation (SDV) and stomatal conductance (gs) were measured. Whereas low gs rates (39 30 mmol m 2 s 1) and pronounced SF-VPD (vapour pressure deficit) and gs-VPD hysteresis loops during well-watered conditions indicated conservative stomatal control on water loss, nocturnal sap flow implied M. eminii is not able to completely block transpiration. At the onset of drought, the pioneer seedlings retained high stem diameter growth despite highly reduced soil moisture (> 0.95 0.03 MPa) and SF rates, indicating that growth was prioritised. Contribution of stored stem water to daily water use was limited both during drought and control conditions, which was confirmed by the absence of time lags between photosynthetic active radiation (PAR)-SDV, PAR-SF and SDV-SF in all treatments. Below a soil water potential of 0.95 0.03 MPa, leaves were gradually shed, but diurnal and nocturnal SF did not turn zero, and absolute stem diameter kept decreasing for the entire experimental period (115 days), portraying that M. eminii seedlings can survive only limited drought periods. In sum, this study demonstrated that species-specific traits, as opposed to species ecological strategy, govern drought performance. For M. eminii, its leaf traits proved pivotal to its drought performance.
Study of inheritance and identification of molecular markers for seed protein content in pigeonpea (Cajanus cajan (L.) Millsp.)
(University of KwaZulu-Natal, Pietermaritzburg, Republic of South Africa, 2017) Obala, Jimmy
Pigeonpea is an important source of protein to the vegetarian and poor families around the globe, however, very little is known about the genetic control of seed protein content (SPC) and how it relates with other traits of agronomic importance in the crop. Availability of genomic resources such as a reference genome and whole genome resequencing data of germplasm lines in pigeonpea coupled with recent advances in next generation sequencing technologies provide opportunity to dissect the genetic architecture of SPC in the crop. The objectives of this study were to: (i) determine variation of SPC and its relationship with agronomic traits of importance in a set of breeding lines and landraces, (ii) study the inheritance of SPC and its relationship with seed weight and seed yield, (iii) identify quantitative trait loci (QTLs) conditioning SPC, and (iv) identify candidate genes involved in the accumulation of SPC using whole genome sequencing approach. To determine variation in SPC and its relationship with some agronomic traits in pigeonpea, 23 pigeonpea genotypes were used. The genotypes are parents of different mapping populations presently being developed at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India. The 23 genotypes were evaluated under field conditions at ICRISAT in 2014-2015 growing season. The experiment was carried out in RCB design with two replications. Data were recorded on SPC, number of days to first flowering (DTF), plant height (PH) at maturity, number of pods per plant (NPP), number of seeds per pod (NSP), 100- seed weight (SW) and seed yield per plant (SY). Seed protein content ranged from 19.3 to 25.5%, DTF (48 to 156 days), PH (67.5 to 230 cm), NPP (31.7 to 582 pods), NSP (2.9 to 4.6 seeds/pod), SW (6.2 to 20.8 g) and SY (7.9 to 333.4 g). There were significant differences among genotypes for all traits. Broad-sense heritability was 0.693 for SPC and ranged from 0.517 to 0.999 among the agronomic traits. Genetic advance (GA) was 2.4 % for SPC but ranged from 1.2 % to 141. % among the agronomic traits. Genetic gain, which is GA expressed as a percentage of the trait’s grand mean, was 11.0 % for SPC but ranged from 56.4 to 713.4 % among the agronomic traits. Simple correlation indicated that SPC is generally negatively associated with all measured traits but only significantly with SW. However, path coefficient analysis revealed that, in addition to SW, NPP also had a strong negative direct influence on SPC, whereas SY had strong positive direct effect on SPC. Indirect effects of the agronomic ii traits on SPC were also noticeable with NPP and SW having strong negative and positive effects, respectively on SPC via SY. To investigate inheritance pattern of SPC in pigeonpea, four elite germplasm lines of varying SPC were used to develop three crosses. Six generations (P1, P2, F1, F2, BC1P1 and BC1P2) were generated. Generation mean analysis (GMA) revealed the importance of dominance and epistatic effects for SPC. Duplicate and negative additive × additive epistasis were predominant. Transgressive segregation for SPC was conspicuous. Additive genetic variance component was higher than the environmental and dominance components. Broad-sense heritability ranged from 0.52 to 0.60. Predicted genetic gain after one cycle of selection was highest at 5% selection intensity. Seed weight and yield were positively and negatively correlated with SPC, respectively. The results suggests that careful selection of parents, and recurrent selection procedure targeting transgressive segregants should be effective for improving SPC in pigeonpea. For the identification of QTLs associated with SPC and its relationship with some agronomic traits, five F2 mapping populations segregating for SPC were developed, genotyped using genotyping-by-sequencing and phenotyped for SPC, 100-seed weight (SW), seed yield (SY), days to first flower (DTF) and growth habit (GH) under field conditions. The average inter marker distance in the population-specific maps varied from 1.6 cM to 3.5 cM. On the basis of the population-specific and consensus linkage maps, a total of 196 main effect QTLs (M QTLs) across all traits were detected that explained 0.7 to 91.3% of the phenotypic variation for the five traits across the five F2 mapping populations. In the case of SPC as the core trait in the present study, a total of 48 main effect QTLs (M-QTLs) with phenotypic variance explained (PVE) ranging from 0.7 to 23.5% were detected across five populations of which 15 M-QTLs were major (PVE≥10). Twenty seven of the M-QTLs from the five F2 mapping populations could be projected into six consensus M-QTL regions. Out of 573 epistatic QTLs (E-QTLs) detected with PVE ranging from 6.3 to 99.4% across traits and populations, 34 involved SPC with PVE ranging from 6.3 to 69.8%. Several co-localization of M-QTLs and E-QTLs affecting SPC and the agronomic traits were also detected and could explain the genetic basis of the significant (P < 0.05) correlations of SPC with SW (r2 = 0.22 to 0.30), SY iii (r2 = -0.18 to -0.28), DTF (r2 = -0.17 to -0.31) and GH (r2 = 0.18 to 0.34). The quantitative nature of genetic control of SPC and its relationship with agronomic traits suggest that marker assisted recurrent selection or genomic selection would be effective for the simultaneous improvement of SPC and other important traits. To identify candidate variants and genes associated with SPC, whole genome resequencing (WGRS) data with an average of 12× coverage per genotype when compared to the Asha (ICPL 87119) reference genome was used. By combining a common variant (CV) filtering strategy with knowledge of gene functions in relation to SPC, 108 sequence variants whose presence lead to protein change were selected. The variants were found in 57 genes spread over all chromosomes except CcLG05. Identified genes were assigned to 19 categories based on gene ontology molecular function with fifty six percent of the identified genes belonging to only two functional categories. Sanger sequencing confirmed the presence of 52 (75.4%) sequence variants in 37 genes between low and high SPC genotypes. Fifty nine variants were converted into CAPS/dCAPS markers and assayed for polymorphism. Highest level of polymorphism was in low by high SPC parental pairs, while the lowest was in high by high parental pairs. Assay of 16 polymorphic CAPS/dCAPS markers on an F2 segregating population of the cross ICP 5529 × ICP 11605 (high × low), resulted in 11 of the markers being incorporated into a GBS-derived SNPs genetic map. Single marker analysis (SMA) indicated four of the 16 CAPS/dCAPS markers to be significantly correlated with SPC. Three out of the four markers were positioned at <10.0 cM distance away from main effect SPC QTLs all on CcLG02. All the three markers found in close proximity to SPC QTL positions and those with significant association to SPC were derived from mutations in the same genes including NADH-GOGAT, copper transporter and BLISTER all on CcLG02. Results from this study provide a foundation for future basic research and marker-assisted breeding of pigeonpea for increased SPC. In general, the complex nature of the genetic architecture of SPC as revealed by classical quantitative genetic analysis, QTL analysis and candidate gene analysis suggests that breeding approaches that target genome wide variations for crop improvement would be more appropriate in achieving larger genetic gains for SPC in shorter periods than using conventional phenotype-based selection
The ecology of Maesopsis eminii Engl. in tropical Africa
(African Journal of Ecology, 2017) Epila, Jackie; Verbeeck, Hans; Otim-Epila, Thomas; Okullo, Paul; Kearsley, Elizabeth; Steppe, Kathy
Maesopsis eminii is referred to as one of the most widely distributed African tree species. However, its occurrence in Africa has never been mapped and little is known as to how this species can sustain in different environments. To gain insight into Maesopsis’ ecology, we (i) made a synthesis of its functional trait data from the literature, (ii) investigated phenological patterns using data on four M. eminii trees from Yangambi, DR Congo, (iii) assessed an empirical provenance trial from Uganda on 600 Maesopsis trees and (iv) synthesized geo-referenced point location maps of Maesopsis entailing WorldClim precipitation and temperature and FAO soils, rainfall and ecological zones for Africa. We found M. eminii to straddle the equator equidistantly in terms of latitude (10.97°N and 10.98°S) covering five forest types where twenty soil types and variable rainfall regimes support complex plant biodiversity. Maesopsis eminii was, however, largely concentrated in the tropical rainforest ecosystem which contains fertile Orthic Ferralsol soils. More than 97% of the point locations were found where annual precipitation was >1000 mm, and 82% occurred where average annual temperature was 22–28°C. Its functional traits, phenology and provenance trial findings explained its occurrence in Africa.
Capacitive water release and internal leaf water relocation delay drought-induced cavitation in African Maesopsis eminii
(Tree physiology, 2017) Epila, Jackie; De Baerdemaeker, Niels J.F.; Vergeynst, Lidewei L.; Maes, Wouter H.; Beeckman, Hans; Steppe, Kathy
The impact of drought on the hydraulic functioning of important African tree species, like Maesopsis eminii Engl., is poorly understood. To map the hydraulic response to drought-induced cavitation, sole reliance on the water potential at which 50% loss of xylem hydraulic conductivity (ψ50) occurs might be limiting and at times misleading as the value alone does not give a comprehensive overview of strategies evoked by M. eminii to cope with drought. This article therefore uses a methodological framework to study the different aspects of drought-induced cavitation and water relations in M. eminii. Hydraulic functioning of wholebranch segments was investigated during bench-top dehydration. Cumulative acoustic emissions and continuous weight measurements were used to quantify M. eminii’s vulnerability to drought-induced cavitation and hydraulic capacitance. Wood structural traits, including wood density, vessel area, diameter and wall thickness, vessel grouping index, solitary vessel index and vessel wall reinforcement, were used to underpin observed physiological responses. On average, M. eminii’s ψ50 (±SE) was −1.9 ± 0.1 MPa, portraying its xylem as drought vulnerable, just as one would expect for a common tropical pioneer. However, M. eminii additionally employed an interesting desiccation delay strategy, fuelled by internal relocation of leaf water, hydraulic capacitance and the presence of parenchyma around the xylem vessels. Our findings suggest that exclusive dependence on ψ50 would have misdirected our assessments of M. eminii’s drought stress vulnerability. Hydraulic capacitance linked to anatomy and leaf-water relocation behaviour was equally important to better understand M. eminii’s drought survival strategies. Because our study was conducted on branches of 3-year-old greenhouse-grown M. eminii seedlings, the findings cannot be simply extrapolated to adult M. eminii trees or their mature wood, because structural and physiological plant properties change with age. The techniques and methodological framework used in this study are, however, transferable to other species regardless of age.
Drought Effects on Photosynthesis and Implications of Photoassimilate Distribution in 11C-Labeled Leaves in the African Tropical Tree Species Maesopsis eminii Engl.
(Forests, 2018) Epila, Jackie; Hubeau, Michiel; Steppe, Kathy
Photoassimilate distribution inside leaves is less studied than photosynthesis, and yet the topic is important as it gives insights into the vital roles played by leaves in plant survival. We combined greenhouse measurements of light response curves with 11C-labelling using leaves of 3-year-old potted Maesopsis eminii Engl. trees to improve our understanding of its leaf carbon physiology. This fast-growing pioneer tree species showed low photosynthetic rates for a common tropical pioneer during well-watered reference conditions (5.0 0.7 mol m􀀀2 s􀀀1), which further decreased in response to drought. 11C-autoradiography indicated active phloem loading and/or rapid phloem transport rates. Active loading is uncommon in tree species, but might be related to deciduousness traits and continuous investment in growth, like in herbaceous active loaders. Active loading involves higher carbon allocation to growth, which might explain why low photosynthetic rates were observed in this fast-growing species. These findings suggest that examining photoassimilate distribution and transport may be critical for understanding the role tree physiology plays in terrestrial carbon cycling.
Genetic variation and relationships of total seed protein content with some agronomic traits in pigeonpea (Cajanus cajan (L.) Millsp.)
(Australian Journal of Crop Science, 2018) Obala, Jimmy; Saxena, Rachit K.; Singh, Vikas K.; Vechalapu, Suryanarayana; Das, Roma; Rathore, Abhishek; Sameer-Kumar, Chanda V; Saxena, Kulbhushan; Tongoona, Pangirayi; Sibiya, Julia; Varshney, Rajeev K.
Seed protein content (SPC) is an important grain quality trait, which impacts the nutritional importance of pigeonpea seed in the diet of over a billion people globally. The present study was carried out to determine variation in SPC and its relationships with some agronomic traits among 23 parental lines of different types of pigeonpea mapping populations. The parental lines were evaluated under field conditions during 2014-2015 growing season. A randomised complete block design in two replications was used. Data were recorded on SPC, days to first flower (DTF), plant height at maturity (PltH), number of pods per plant (NPP), number of seeds per pod (NSP), hundred-seed weight (SW) and seed yield per plant (SY). There were significant differences among genotypes for all traits. Broad-sense heritability was 0.693 for SPC but ranged from 0.519 (NPP) to 0.999 (DTF) while genetic advance was 2.4% for SPC but ranged from 1.2 % (NSP) to 141.2 % (SY), and genetic gain ranged from 11.0 % (SPC) to 230.0 % (SY). Simple correlation showed that SPC is only significantly but negatively correlated with SW (r = -0.30, P < 0.05), while path analyses revealed that SPC is negatively associated SW and NPP but positively with DTF, PltH, NSP and SY. It is concluded that genetic variation for SPC and agronomic traits exist among pigeonpea genotypes studied. The variation is accompanied by both favourable and unfavourable relationships of SPC with the agronomic traits.
Effect of improved seed system on potato yields in Uganda
(RUFORUM Working Document Series, 2018) Kigambo, M; Wasswa, P; Obala, Jimmy; Mugisha, J
Potato seed quality is an important determinant of crop performance, final yield and quality. The quality of seed used by farmers depend on the existing seed system. In Uganda, since the formal sector has limited capacity to produce and deliver certified potato seed, the informal sector prevails providing over 93% of potato seed used by farmers. The informal sector is not regulated thus informal seed that is often used by farmers is usually of poor quality which has stagnated national yields at 7.5 t ha-1. This review looks at the general potato seed system in Uganda with an emphasis on potato seed quality while giving recommendations on how this problem can be alleviated. This is a narrative review organized under sub-topics to give the reader a comprehensive overview and easier tracking of the afore mentioned reviewed topic. In summary, this review revealed that although intervention have been used to improve quality and quantity of potato seed, a big gap still exists thus more interventions are needed both in the formal and informal sector. In addition, it revealed that if the quality of potato seed used by farmers can be improved either by making certified seed more available and affordable or improving the quality of seed obtained from the informal sector, it would be possible to increase potato yields in Uganda substantially.
Development of sequence-based markers for seed protein content in pigeonpea
(Molecular Genetics and Genomics, 2019) Obala, Jimmy; Saxena, Rachit K.; Singh, Vikas K.; Kumar, C. V. Sameer; Saxena, K. B.; Tongoona, Pangirayi; Sibiya, Julia; Varshney, Rajeev K.
Pigeonpea is an important source of dietary protein to over a billion people globally, but genetic enhancement of seed protein content (SPC) in the crop has received limited attention for a long time. Use of genomics-assisted breeding would facilitate accelerating genetic gain for SPC. However, neither genetic markers nor genes associated with this important trait have been identified in this crop. Therefore, the present study exploited whole genome re-sequencing (WGRS) data of four pigeonpea genotypes (~ 12X coverage) to identify sequence-based markers and associated candidate genes for SPC. By combining a common variant filtering strategy on available WGRS data with knowledge of gene functions in relation to SPC, 108 sequence variants from 57 genes were identified. These genes were assigned to 19 GO molecular function categories with 56% belonging to only two categories. Furthermore, Sanger sequencing confirmed presence of 75.4% of the variants in 37 genes. Out of 30 sequence variants converted into CAPS/dCAPS markers, 17 showed high level of polymorphism between low and high SPC genotypes. Assay of 16 of the polymorphic CAPS/dCAPS markers on an F2 population of the cross ICP 5529 (high SPC)×ICP 11605 (low SPC), resulted in four of the CAPS/dCAPS markers significantly (P<0.05) co-segregated with SPC. In summary, four markers derived from mutations in four genes will be useful for enhancing/regulating SPC in pigeonpea crop improvement programs
11C-autoradiographs to image phloem loading
(Frontiers in Forests and Global Change, 2019) Hubeau, Michiel; Mincke, Jens; Vanhove, Christian; Gorel, Anaïs Pasiphaé; Fayolle, Adeline; Epila, Jackie; Leroux, Olivier; Vandenberghe, Stefaan; Steppe, Kathy
Generally, tree species load photoassimilates passively into the phloem, while herbaceous species load actively. These phloem loading strategies have implications for phloem sugar concentration and growth potential. Whereas, in previous research, phloem loading identification was performed with 14C-autoradiography, we suggest 11C-autoradiography, because of its compatibility with plant-PET (positron emission tomography) scans. Because 11C-autoradiography has been hardly used in plant sciences so far, it was tested in contrasting plant species: one temperate tree species, Populus tremula L., three tropical tree species, Erythrophleum suaveolens (Guill. & Perr.) Brenan, E. ivorense A. Chev., and Maesopsis eminii Engl., and two herbaceous crop species Solanum lycopersicum L. and S. tuberosum L. Our results confirmed that P. tremula is a passive loader, and Solanum spp. are active loaders. Erythrophleum spp. and young leaves of M. eminii showed the expected passive loading strategy, but the mature leaves of M. eminii showed an uncommon pattern. Images corrected for leaf tissue thickness supported that mature leaves of M. eminii used active phloem loading, which is linked to continuous investment in growth and new leaves, supporting the lower carbon storage levels often observed in tropical tree species. With this study, we demonstrate that 11C-autoradiography is a powerful tool to acquire detailed tracer distribution in leaves to typify phloem loading strategies in plant species.
Seed protein content and its relationships with agronomic traits in pigeonpea is controlled by both main and epistatic efects QTLs
(Scientific Reports, 2020) Obala, Jimmy; Saxena, Rachit K.; Singh, Vikas K.; Kale, Sandip M.; Garg, Vanika; Kumar, C.V. Sameer; Saxena, K. B.; Tongoona, Pangirayi; Sibiya, Julia; Varshney, Rajeev K.
The genetic architecture of seed protein content (SPC) and its relationships to agronomic traits in pigeonpea is poorly understood. Accordingly, fve F2 populations segregating for SPC and four agronomic traits (seed weight (SW), seed yield (SY), growth habit (GH) and days to frst fowering (DFF)) were phenotyped and genotyped using genotyping-by-sequencing approach. Five high-density population-specifc genetic maps were constructed with an average inter-marker distance of 1.6 to 3.5cM, and subsequently, integrated into a consensus map with average marker spacing of 1.6cM. Based on analysis of phenotyping data and genotyping data, 192 main efect QTLs (M-QTLs) with phenotypic variation explained (PVE) of 0.7 to 91.3% were detected for the fve traits across the fve populations. Major efect (PVE≥10%) M-QTLs included 14 M-QTLs for SPC, 16 M-QTLs for SW, 17 M-QTLs for SY, 19 M-QTLs for GH and 24 M-QTLs for DFF. Also, 573 epistatic QTLs (E-QTLs) were detected with PVE ranging from 6.3 to 99.4% across traits and populations. Colocalization of M-QTLs and E-QTLs explained the genetic basis of the signifcant (P<0.05) correlations of SPC with SW, SY, DFF and GH. The nature of genetic architecture of SPC and its relationship with agronomic traits suggest that genomics-assisted breeding targeting genome-wide variations would be efective for the simultaneous improvement of SPC and other important traits.
Economic Feasibility of Iodine Agronomic Biofortification
(sustainability, 2021) Olum, Solomon; Gellynck, Xavier; Wesana, Joshua; Odongo, Walter; Onek Aparo, Nathaline; Aloka, Bonny; Ongeng, Duncan; De Steur, Hans
Cost–benefit analysis of (iodine) biofortification at farm level is limited in the literature. This study aimed to analyze the economic feasibility of applying iodine-rich fertilizers (agronomic biofortification) to cabbage and cowpea in Northern Uganda. Data on costs and revenues were obtained from a survey of 100 farmers, and benefits that would accrue from using iodine fertilizers were elicited using consumers’ willingness to pay (WTP) for the iodine-biofortified vegetables. The cost–benefit analysis demonstrated iodine agronomic biofortification as a highly profitable effort, generating average benefit–cost ratios (BCRs) of 3.13 and 5.69 for cabbage and cowpea production, respectively, higher than the conventional production practice. However, the projective analysis showed substantive variations of economic gains from iodine biofortification among farmers, possibly due to differences in farming practices and managerial capabilities. For instance, only 74% of cabbage farmers would produce at a BCR above 1 if they were to apply iodine fertilizer. Furthermore, a sensitivity analysis to estimate the effect of subsidizing the cost of iodine fertilizer showed that a higher proportion of farmers would benefit from iodine biofortification. Therefore, as biofortification is considered a health policy intervention targeting the poor and vulnerable, farmers could be supported through fertilizer subsidies to lower the production cost of iodine-biofortified foods and to avoid passing on the price burden to vulnerable consumers.
QTL-seq for the identification of candidate genes for days to flowering and leaf shape in pigeonpea
(Heredity, 2022) Singh, Vikas; Sinha, Pallavi; Obala, Jimmy; Khan, Aamir W.; Chitikinen, Annapurna; Saxena, Rachit K.; Varshney, Rajeev K.
To identify genomic segments associated with days to flowering (DF) and leaf shape in pigeonpea, QTL-seq approach has been used in the present study. Genome-wide SNP profiling of extreme phenotypic bulks was conducted for both the traits from the segregating population (F2) derived from the cross combination- ICP 5529 × ICP 11605. A total of 126.63 million paired-end (PE) whole-genome resequencing data were generated for five samples, including one parent ICP 5529 (obcordate leaf and late flowering plant), early and late flowering pools (EF and LF) and obcordate and lanceolate leaf shape pools (OLF and LLS). The QTL seq identified two significant genomic regions, one on CcLG03 (1.58 Mb region spanned from 19.22 to 20.80 Mb interval) for days to flowering (LF and EF pools) and another on CcLG08 (2.19 Mb region spanned from 6.69 to 8.88 Mb interval) for OLF and LLF pools, respectively. Analysis of genomic regions associated SNPs with days to flowering and leaf shape revealed 5 genic SNPs present in the unique regions. The identified genomic regions for days to flowering were also validated with the genotyping-by-sequencing based classical QTL mapping method. A comparative analysis of the identified seven genes associated with days to flowering on 12 Fabaceae genomes, showed synteny with 9 genomes. A total of 153 genes were identified through the synteny analysis ranging from 13 to 36. This study demonstrates the usefulness of QTL-seq approach in precise identification of candidate gene(s) for days to flowering and leaf shape which can be deployed for pigeonpea improvement.

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