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 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

Interactive effects of Potato virus Y and Potato leafroll virus infection on potato yields in Uganda

Potatoes are prone to attack by multiple viruses, which contribute greatly to yield and quality decline depending on the cultivar and the virus involved. This study investigated the effect of co-infection involving Potato virus Y (potyvirus) and Potato leafroll Virus (pelero virus) on productivity of five potato cultivars in Uganda and the nature of virus interaction during co-infection process. Variety response to virus infection by PVY, PLRV and co-infection (PVY + PLRV) varied across different varieties. The plants that were infected with PLRV had leaf rolling, stuntedness, leaf distortion, reduction in leaf size and mottling and light yellow mosaics, and in some cases, purple or red margins were observed, while single infection of PVY induced necrosis, leaf rugosity, crinkling, stunting, interveinal necrosis, blotching of the margins, leaf distortion and mottling. When the two viruses were combined during co-infection with PVY + PLRV, the symptoms were characterized by bright blotching and necrotic leaf margins with purpling of the leaf tips and leaf margins, stuntedness and leaf distortions. The virus disease severity was higher under mixed infected plants than single infected plants. The high disease severity culminated in a significant effect on yield, marketable tuber number per plant, plant growth height and plant vigor, which were different across the varieties. Co-infection involving PVY and PLRV caused a reduction in the marketable yield of 95.2% (Kinigi), 94% (Victoria), 89.5 (Rwagume), 45.3% (Royal) and 23.7% (Sifra). Single infection by PLRV caused a reduction in a marketable yield in Victoria (91.8%), Kinigi (84.8%), Rwagume (73.3%), Royal (47.2%) and Sifra 22.1%, while PVY caused a marketable yield reduction in Victoria (87.2%), Rwagume (85.9.7%), Kinigi (85.1%), Royal (37.4%) and Sifra (14.1%). The effects associated with the co-infection of PVY and PLRV were lower than the combined value of the single infections, suggesting that the two viruses were interacting to affect the potato productivity. The high yield loss suggested that effective resistance strategy targeting PVY, PLRV and their combination was required to save the potato industry in Uganda

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

Alignment of the 43 different RNase3 protein amino acid (aa) sequences of <i>Sweet</i><i>potato</i><i>chlorotic</i><i>stunt</i><i>virus</i>.

<p>Groups of isolates containing identical RNase3 aa sequences are represented each by a single isolate. Numbers on top of the alignment indicate the aa positions with reference to isolate Ug (AJ428554) whereas numbers on the right indicate the number of the last amino acid at that position for each isolate. Numbers at the bottom of the alignment indicate aa positions in the new unknown virus (KML33b) related to SPCSV and detected in this study. The class 1 RNase III signature motif at aa positions 36-44 in SPCSV isolates (aa 42-50 in KML33b) is boxed. Two aa sites predicted to be under positive selection are indicated with black shades. Names of isolates characterized from wild plants are in bold.</p

Volatile organic compound based markers for the aroma trait of rice grain

A study was conducted to determine the volatile organic compounds (VOCs) associated with rice grain aroma in 37 commonly grown lines within Uganda, as well as elites. The aim of the study was to identify potential volatile biochemical markers, if any, for the rice grain aroma trait. Certified rice seeds were obtained from the Uganda National Crops Resources Research Institute germplasm collection. The seeds were sown into experimental plots, under field conditions and the mature paddy harvested. Polished rice grains were heated to 80 oC and the liberated VOCs subjected to untargeted metabolite analysis using gas chromatography-time-of-flight mass spectrometry. In total, nine functional groups were present; hydrocarbons, alcohols, ketones, aldehydes, N-containing compounds, S-containing compounds, esters, oxygen heterocycles and carboxylic acids. More specifically, 148 VOCs were identified across the 37 rice lines, of which 48 (32.4%) including 2-acetyl-1-pyrroline (2-AP) appeared to elucidate the difference between non-aromatic and aromatic rice. Furthermore, 41 (27.7%) VOCs were found to be significantly correlated with 2-AP abundance, the principle rice aroma compound. Amongst the 41 VOCs, only ten compounds were found to contribute highly towards variation in 2-AP abundance, indicative of their possible modulation roles in regard to rice aroma. Within the ten influential volatiles, three aroma active compounds; toluene, 1-hexanol, 2-ethyl and heptane, 2,2,4,6,6-pentamethyl- were established as the most reliable biochemical surrogates to the rice aroma trait. Thus, the aforementioned compounds may be used in rice breeding programme for enhancing development of the grain aroma trait

Symptoms and virus accumulation in single or double infections with Sweet potato chlorotic stunt virus (SPCSV) and Sweet potato feathery mottle virus (SPFMV) in sweetpotato plants of cv.

<p>Tanzania. (<b>A</b>) A plant infected with SPFMV (isolate RUK73) shows no obvious virus symptoms 6 weeks post-inoculation. (<b>B</b>) Chlorosis and purpling of older leaves induced by SPCSV isolate HOM76. (<b>C</b>) Typical symptoms of sweetpotato virus disease (SPVD) including retarded growth, severe leaf strapping and puckering induced by co-infection with SPCSV isolate HOM76 and SPFMV. (<b>D</b>) Chlorosis and purpling of older leaves induced by SPCSV isolate SOR71, and (<b>E</b>) similar symptoms in a plant co-infected with SOR71 and SPFMV. Young leaves develop normally in (D) SOR71-infected plants and (E) plants co-infected with SOR71 and SPFMV. In both cases the plants display only mild chlorosis typical of SPCSV infection, which indicates that SOR71 is not able to induce SPVD in co-infection with SPFMV. (<b>F</b>) SPCSV RNA detected by dot blot hybridization with a digoxigenin-labelled RNA probe specific to the <i>RNase3</i> gene in (a) plants infected with SPCSV alone or (b) plants co-infected with the SPCSV and SPFMV. The amounts of total plant RNA dotted on the membrane are indicated. The SPCSV isolates tested were 1, KTK39; 2, KTK40; 3, KTK41; 4, SOR71; 5, MAS69; 6, SET5; 7, MSK7; 8, TOR16; and 9, HOM76. Isolates 1 to 4 are lacking the p22 gene. Note that SOR71 (4a and 4b) accumulates at very low concentrations in sweetpotato leaves and is barely detectable. H, non-inoculated healthy plant of cv. Tanzania. (<b>G</b>) SPFMV RNA detected by dot blot hybridization with a digoxigenin-labelled RNA probe specific to the CP-encoding region. Samples 1 to 9 are those co-infected with SPCSV and SPFMV and tested for SPCSV (i.e., samples 1b to 9b) in (F). Three additional samples co-infected with SPCSV (10, MAS46; 11, TOR14; and 12, MPG88) and SPFMV were included. Note that SOR71 synergises SPFMV, which is detected by the enhanced SPFMV concentrations (sample 4) as compared to the samples (FM) from cv. Tanzania infected with SPFMV only. H, non-inoculated healthy plant of cv. Tanzania.</p

Suppression of RNA silencing by the p22 and RNase3 proteins of SPCSV isolates and the RNase3-like protein of the new virus KML33b.

<p>Upper row of leaves: “Silencing on the spot” to induce “strong silencing” of the <i>gfp</i> gene for green fuorescent protein (GFP) was achieved by co-expressing <i>gfp</i> from one <i>A. tumefaciens</i> strain and double-stranded (hairpin) RNA homologous to <i>gfp</i> from another strain in coinfiltrated leaf tissue of <i>Nicotiana benthamiana</i>, and coinfiltration of a third strain expressing p22 protein to suppress gfp silencing. The p22 proteins of isolates ARU59 (<i>I. sinensis</i>) and HOM89 (sweetpotato) were compared with the previously characterized p22 protein of isolate Ug by expressing them at the opposite sites of the midrib in the same leaf. An <i>Agrobacterium</i> strain expressing ß-glucuronidae (GUS) was included as the negative control. Leaves were illuminated with UV light and photographed from the underside with a digital camera 3 days postinfiltration. Lower row of leaves: Cosuppression of <i>gfp</i> in transgenic <i>N. benthamiana</i> plants (line 16c) constitutively expressing <i>gfp</i> (note the green fluorescence in veins). The spots were co-infiltrated with a mixture of two <i>Agrobacterium</i> strains, one expressing <i>gfp</i> to achieve cosuppression (silencing) of <i>gfp</i> and another expressing RNase3 of isolate SOR71 (<i>I. obscura</i>), Ug, or the RNase3-like protein of the new virus KML33b (<i>I. sinensis</i>). Leaves were illuminated with UV light and photographed from the underside with a digital camera 6 days postinfiltration. </p

Phylogenetic analysis of genes coding for RNase3 of <i>Sweet</i><i>potato</i><i>chlorotic</i><i>stunt</i><i>virus</i> and the corresponding sequence of an unknown related virus (KML33b) detected in this study.

<p>The branch of KML33b is not fully depicted. Names of isolates characterized from wild plants are indicated in bold, whereas the ten SPCSV isolates lacking the p22 gene are indicated with a black triangle (▲). Numbers at branches represent bootstrap values of 1000 replicates. Only bootstrap values of ≥ 50% are shown. Scale indicates Kimura units in nucleotide substitutions per site [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0081479#B55" target="_blank">55</a>].</p