Molecular and farmer-based comparison of a wild-weed and landrace complex of watermelon in Zimbabwe

Traditional farming systems have been associated with the occurrence of intervarietal and interspecific natural crosses in many crop plants, thus contributing to the genetic diversity of the crop through genetic exchange. In this study, a combination of farmerpreferred morphological traits and RAPD markers were used to evaluate the dynamics of genetic diversity in 43 watermelon accessions collected at a single village level with a traditional farming system. The molecular variability assessed with RAPD markers and analyzed with multidimensional scaling and cluster analysis, demonstrated a substantial differentiation among the accessions. Population structure analysis also demonstrated the existence of three major forms of watermelon, identified by a set of alleles predominant within each form. Dendrograms based on RAPD data and on farmer-preferred traits data were positively correlated according to a Mantel test. Although cultivated cow-melons were genetically most similar to wild-weedy plants at molecular level, they grouped more similar to sweet watermelons based on farmer-preferred traits. The present study revealed limited gene flow between three forms of watermelon and provides insight into how the genetic differentiation corresponds to farmers’ classification of watermelon

Mapping resistance to the bird cherry-oat aphid and the greenbug in wheat using sequence-based genotyping

Citation: Crespo-Herrera, L. A., Akhunov, E., Garkava-Gustavsson, L., Jordan, K. W., Smith, C. M., Singh, R. P., & Åhman, I. (2014). Mapping resistance to the bird cherry-oat aphid and the greenbug in wheat using sequence-based genotyping. Theoretical and Applied Genetics, 127(9), 1963-1973.The aphids Rhopalosiphum padi and Schizaphis graminum are important pests of common wheat (Triticum aestivum L.). Characterization of the genetic bases of resistance sources is crucial to facilitate the development of resistant wheat cultivars to these insects. We examined 140 recombinant inbred lines (RILs) from the cross of the susceptible wheat Seri M82 with the synthetic hexaploid wheat CWI76364, resistant to both aphid species. The RILs were phenotyped for R. padi antibiosis and tolerance traits. Phenotyping of S. graminum resistance was based on leaf chlorosis in a greenhouse screening, and also on the number of S. graminum per tiller in a field trial. Seedling pubescence was scored in each RIL. Using a sequence-based genotyping method we located genomic regions associated to these resistance traits. One QTL for R. padi antibiosis was found in chromosome 4BL; it explained 10.2% of phenotypic variation and was located 14.6 cM apart from the pubescence locus. However, we did not find any association between plant pubescence and the other resistance traits. We found two QTLs for tolerance to R. padi in chromosomes 5AL and 5BL, with an epistatic interaction between a locus in chromosome 3AL and the tolerance QTL in 5AL. These genomic regions together explained about 35% of the phenotypic variation. We confirmed the location of a previously reported gene for S. graminum resistance (Gba) in 7DL and found an additional, novel QTL associated with the number of aphids per tiller in chromosome 2DL. This is the first report where resistance to R. padi in wheat is mapped and also where chromosome 2DL shown to be associated with S. graminum resistance

Evaluation and managing wheat seed-borne diseases: Options and suggestions from the case of Tajikistan

Wheat seed-borne diseases are among the major constraints reducing crop yield and the quality of seed and grain. In this study we aimed to evaluate the type and prevalence of fungal seed-borne diseases in Tajik wheat seed samples. Particular emphasis was given to common bunt resistance in advanced wheat breeding materials. Furthermore, we aimed to identify options for improving the seed quality. Seed samples collected from two different locations in Tajikistan were tested by conventional seed-health testing methods for presence of seed-borne diseases. Nineteen advanced wheat breeding lines and three varieties collected from the Tajik wheat breeding program were screened using an artificial inoculation test for their response to common bunt. Significant differences were found between the locations and genotypes concerning presence of common bunt and black point. Fourteen fungal species, where most of them are pathogenic for wheat, were identified in the seed samples. Tilletia laevis, T. tritici, Bipolaris sorokiniana, Stemphylium spp., and Drechslera spp. were the major pathogenic fungi observed in collected wheat samples. Common bunt was predominantly represented by T. laevis. No strong resistance was found in the studied Tajik wheat material, although a low percentage of infection was found in one line (SHARK/ F4105W2.1), while the material was evaluated for common bunt resistance. In managing seed-borne diseases, breeding of resistant varieties should be given a priority, while cultural practices such as preventing contamination and monitoring seed health status should also be considered, as a last resort the use of chemical seed treatments are advised

Genetic analysis of a major international collection of cultivated apple varieties reveals previously unknown historic heteroploid and inbred relationships

Domesticated apple (Malus x domestica Borkh.) is a major global crop and the genetic diversity held within the pool of cultivated varieties is important for the development of future cultivars. The aim of this study was to investigate the diversity held within the domesticated form, through the analysis of a major international germplasm collection of cultivated varieties, the UK National Fruit Collection, consisting of over 2,000 selections of named cultivars and seedling varieties. We utilised Diversity Array Technology (DArT) markers to assess the genetic diversity within the collection. Clustering attempts, using the software STRUCTURE revealed that the accessions formed a complex and historically admixed group for which clear clustering was challenging. Comparison of accessions using the Jaccard similarity coefficient allowed us to identify clonal and duplicate material as well as revealing pairs and groups that appeared more closely related than a standard parent-offspring or full-sibling relations. From further investigation, we were able to propose a number of new pedigrees, which revealed that some historically important cultivars were more closely related than previously documented and that some of them were partially inbred. We were also able to elucidate a number of parent-offspring relationships that had resulted in a number of important polyploid cultivars. This included reuniting polyploid cultivars that in some cases dated as far back as the 18th century, with diploid parents that potentially date back as far as the 13th century

Genetic diversity in a collection of apple (Malus x domestica Borkh.) cultivars as revealed by RAPD markers

A collection of 151 apple cultivars was investigated with 7 RAPD primers generating 71 informative bands, to evaluate genetic variability and relatedness. All cultivars presumably derived through genetic recombination were distinguished whereas identical DNA profiles indicated that some cultivars had arisen as sports. A cluster analysis and a PCO did not reveal any distinct geographic patterns, but there was a weak tendency for Swedish and foreign cultivars to differentiate.. Many cultivars however clustered together with either one of their parents or with siblings. Overall genetic diversity among the 151 cultivars was estimated with Nei's diversity index (H), 0.269, and with Shannon's index (H'), 0.594. The cultivars were also analysed in six groups, according to time of origination and country of origin, with an average H = 0.262 and H' = 0.546. No major differences in genetic diversity were observed over time or space, although the group with recent, foreign cultivars had the lowest diversity (FL = 0.235, H' = 0.493). Comparison between the entire material and a subset with 94 mandate cultivars chosen for preservation in Sweden, showed similar genetic diversity: HFN.rj1E = 0.268, frE,NTIRE, = 0.593 and HMANDATE = 0.263, WMANDATE = 0.575. No major differences in band frequencies were observed between these two sets, but 5 RAPD bands were missing in the set with mandate cultivars

Fire blight (Erwinia amylovora) resistance in apple varieties associated with molecular markers

The invasive bacterial disease fire blight, caused by Erwinia amylovora has the potential to destroy fruit tree orchards all over Europe. Effective plant protection methods are lacking in many countries, highlighting the increasing importance placed on identification of germplasm with heritable disease resistance. Recent l y. a promising QTL (quantitative trait locus) was identified on linkage group 7 in the apple cultivar 'Fiesta· which is derived from ·cox's Orange Pippin' . I n the present study, 144 Swedish and foreign apple cultivars were analysed with the SCAR markers AE I 0-375 and GE-8019. which flank-. this QTL. Twenty-nine of the analysed cultivars had both markers. 78 had either AE I 0-375 or GE-8019, and 37 cultivars did not carry an) of the two markers. Seventeen cultivars. 7 with both markers and I 0 not having either of the two markers, were then inocoluted with the bacterium in a 4uaran1i ne greenhouse test. Cultivars carrying both DNA markers were significantly less susceptible than cultivars lacking the markers, P<0.001. Cultivars that were most resistant had both markers and had 'Cox· in their pedigree. Unrelated cultivars with the markers may still lack the QTL

Fire blight (Erwinia amylovora) resistance in apple varieties associated with molecular markers

The invasive bacterial disease fire blight, caused by Erwinia amylovora has the potential to destroy fruit tree orchards all over Europe. Effective plant protection methods are lacking in many countries, highlighting the increasing importance placed on identification of germplasm with heritable disease resistance. Recent l y. a promising QTL (quantitative trait locus) was identified on linkage group 7 in the apple cultivar 'Fiesta· which is derived from ·cox's Orange Pippin' . I n the present study, 144 Swedish and foreign apple cultivars were analysed with the SCAR markers AE I 0-375 and GE-8019. which flank-. this QTL. Twenty-nine of the analysed cultivars had both markers. 78 had either AE I 0-375 or GE-8019, and 37 cultivars did not carry an) of the two markers. Seventeen cultivars. 7 with both markers and I 0 not having either of the two markers, were then inocoluted with the bacterium in a 4uaran1i ne greenhouse test. Cultivars carrying both DNA markers were significantly less susceptible than cultivars lacking the markers, P<0.001. Cultivars that were most resistant had both markers and had 'Cox· in their pedigree. Unrelated cultivars with the markers may still lack the QTL

Approaches for evaluation of resistance to European canker (Neonectria ditissima) in apple

European canker is caused by the fungus Neonectria ditissima (Neonectria galligena, formerly Nectria galligena). The disease causes significant losses to apple production in Sweden and many other countries with a temperate wet climate. Application of fungicides and good horticultural practices do not prevent canker damage in nurseries and orchards. Disease outbreaks damage and even completely destroy trees. To date, complete resistance to N. ditissima is not known in apple, but cultivars differ considerably in their level of partial resistance. To be able to conduct breeding for resistance to European canker, reliable plant tests are urgently needed. Differences in resistance to N. ditissima (colonization rate; CR) in apple cultivars were evaluated by wound inoculations with a standardized number of conidia on cut shoots from mature trees placed in a climate chamber and on potted trees in an unheated greenhouse. Infection percentage (Inf%) was assessed by 'natural' inoculations in leaf scars under high infection pressure in the field. All the experiments were carried out over 2 years. Lengths of lesions were measured at regular time intervals on five occasions for shoots and seven occasions for trees. Considerable differences in CR and Inf% were found among the cultivars. The relative levels of resistance obtained are consistent with previous reports for most cultivars. Assessment of CR (area under curve) and Inf% thus proved to be useful tools for evaluation of resistance to European canker. Also, some potentially new sources of resistance were identified.</p

Screening of apple cultivars for resistance to European canker, Neonectria ditissima

European canker, caused by the fungus Neonectria ditissima, is a severe problem in apple production both in Sweden and in many other northern European countries. Even when applying fungicides and good horticultural practices, canker damage occurs almost yearly in nurseries and orchards. Some years, devastating outbreaks destroy numerous trees. To date, complete resistance to N. ditissima is not known in apple. For further research and plant breeding, heritable variation in quantitative resistance should be investigated by phenotyping large sets of cultivars. In the present project, 55 apple cultivars were screened for resistance to N. ditissima. One-year-old shoots from mature trees were inoculated in the greenhouse with a standardized volume and concentration of conidia suspension using different inoculation methods. Two-year-old trees of five cultivars were inoculated in the field. Length of the occurring cankers was measured at regular intervals throughout a period of up to three months. The investigated cultivars showed considerable differences in colonization rate. In cultivars known to be highly resistant, i.e., ‘Santana’, lesions progressed much slower compared to susceptible cultivars like ‘Cox’s Orange Pippin’ and ‘James Grieve’. Since the inoculation-based phenotyping is demanding in labour and time (duration), especially when the test is performed on grafted trees, qPCR-based assessment of fungal biomass at early stages of infection was explored as an alternative or complementary approach for phenotyping