Identification of quantitative trait loci for cane splitting in red raspberry (Rubus idaeus)

Cane splitting, a normal feature of raspberry growth, can lead to plant infestation by cane midge followed by fungal infection, with losses in yield of up to 50 % if left untreated. The extent of splitting in the Latham × Glen Moy reference mapping population was assessed over six years and in three environments and quantitative trait loci (QTL) were identified across linkage groups (LG) 2, 3, 5 and 6. Cane splitting QTL on LG 3 and 5 co-locate with QTL for plant vigour. The cane splitting QTL on LG 6 is associated with the QTL for resistance to root rot caused by Phytophthora rubi. Broad-sense heritability for cane splitting ranged from 25.6 % in 2007 to 49.1 % in 2008 in this population. Season and environment were also found to influence cane splitting in this population. Several genes involved in general plant growth and in defence responses lie within these QTL. This is a first step towards identifying the genetic basis of cane splitting in raspberry and the development of genetic markers for use in raspberry breeding programmes.     

The construction of a genetic linkage map of red raspberry (Rubus idaeus subsp. idaeus) based on AFLPs, genomic-SSR and EST-SSR markers

Breeding in raspberry is time-consuming due to the highly heterozygous nature of this perennial fruit crop, coupled with relatively long periods of juvenility. The speed and precision of raspberry breeding can be improved by genetic linkage maps, thus facilitating the development of diagnostic markers for polygenic traits and the identification of genes controlling complex phenotypes. A genetic linkage map (789 cM) of the red raspberry Rubus idaeus has been constructed from a cross between two phenotypically different cultivars; the recent European cultivar Glen Moy and the older North American cultivar Latham. SSR markers were developed from both genomic and cDNA libraries from Glen Moy. These SSRs, together with AFLP markers, were utilised to create a linkage map. In order to test the utility of the genetic linkage map for QTL analysis, morphological data based on easily scoreable phenotypic traits were collected. The segregation of cane spininess, and the root sucker traits of density and spread from the mother plant, was quantified in two different environments. These traits were analysed for significant linkages to mapped markers using MapQTL and were found to be located on linkage group 2 for spines and group 8 for density and diameter. The availability of co-dominant markers allowed heterozygosities to be calculated for both cultivars.     

Resistance to Botrytis cinerea in canes of Rubus idaeus and some related species

Mycelial inoculation of canes with Botrytis cinerea proved a useful method for assessing Rubus material for resistance. When canes were inoculated in summer resistant genotypes developed relatively small lesions which produced few small sclerotia in the following spring. The size of lesions in autumn generally provided the best discrimination between genotypes. Very strong resistance was found in several species, of which Rubus pileatus and R. occidentalis are the most useful for breeding; hybrids of raspberry with these species or with R. crataegifolius also had strong resistance. The resistance shown by a derivative of red raspberry cv. Chief was less strong, as was the resistance conferred by gene H, which determines cane pubescence.     

Resistance to raspberry cane midge (Resseliella theobaldi) and its association with wound periderm in Rubus crataegifolius and its red raspberry derivatives

Rubus parviflorus, R. odoratus and F₂ plants from the cross R. crataegifolius x R. idaeus were resistant to the raspberry cane midge (Resseliella theobaldi) when exposed to the pest in an insectary or in the field. Histological studies of R. crataegifolius and one of its hybrids with R. idaeus showed that resistance was associated with a wound periderm of suberised and lignified cells. These cells were formed from the primary cortex and phelloid cells of the polyderm as a rapid response to the occurrence of natural splits and wounds which are the oviposition sites of R. theobaldi. In the hybrid, new tissues from this wound periderm prevented the peeling of the mature primary cortex, thereby precluding serious midge attack, and resulted in a reticulate appearance on the cane surface, a distinctive cane feature useful for identifying resistant segregates.     

Vigour control, an integrated approach to cane, pest and disease management in red raspberry (Rubus idaeus)

The first flush of young canes of red raspberry (Rubus idaeus) was removed at different dates in spring, using the contact herbicide dinoseb. In comparison with untreated plots, cane removal increased fruit yield, controlled excessive cane vigour, and improved the health status of vegetative canes in a plantation infested by raspberry cane midge (Resseliella theobaldi). At the end of the growing season vegetative canes on treated plots were shorter and thinner, and sustained less physical injury than those on untreated plots. Access to the fruit at harvest was also improved. Reduced competition between fruiting and vegetative canes increased yield in the year of treatment by an average of 35%. Yield was not affected by date of cane removal, but growth of replacement cane was reduced below optimum when first flush cane was removed after mid-May. The later the canes were removed, the less was the incidence of pest and diseases. Cankers and lobate vascular lesions (‘patches’) resulting, respectively, from the feeding of first and second generation midge larvae (with associated fungi) affected fewer canes in treated than in untreated plots. Significantly fewer live larvae of R. theobaldi were recovered in the following winter from soil in plots treated on or after 11 May than from untreated plots. The main effect of vigour control on R. theobaldi and midge blight was that replacement canes provided fewer egg-laying sites (natural splits) than did the first flush canes on untreated plots. The incidence of spreading vascular lesions (‘stripes’) attributed to Leptosphaeria coniothyrium infecting either physical wounds (cane blight) or midge feeding wounds (midge blight) was substantially less in treated than untreated plots. Cane botrytis (Botrytis cinerea) and spur blight (Didymella applanata) were also less common in treated plots. Interactions between vigour control and pest and disease incidence are discussed in relation to the efficient management of cv. Glen Clova in eastern Scotland.     

Further studies on resistance to Leptosphaeria coniothyrium in the red raspberry and related species

Rubus pileatus and its F₁ hybrids with raspberry (R. idaeus) were resistant to cane blight (Leptosphaeriu conioth-yriurn), but little resistance was obtained in subsequent backcross generations apart from a hybrid identified in the second backcross. Two hybrids from backcrossing R. coreanus to raspberry also showed resistance. R. pileatus and its F, hybrids produced hard growth, unlike that of raspberries, which may have been associated with a form of resistance that could not easily be transferred to commercial raspberry cultivars. Some of the genotypes used as parents showed intermediate levels of resistance and it is possible that the highly resistant genotype identified in the second backcross arose from a recombination of genes for resistance. Plants with pubescent canes (gene H) were up to 20% more resistant to mycelial inoculation than those with non-pubescent canes (gene h), and the percentage of machine-harvester inflicted wounds with disease symptoms that resulted from natural infection was also less in genotypes with pubescent canes. Many genotypes with intermediate levels of resistance suffered only limited damage from mycelial inoculation and so there are good prospects for breeding cultivars with an effective resistance, despite the limited value of R. pileatus as a donor species.     

Modifying glucosinolates in oilseed rape – Giamoustaris & Mithen (1995): a top‐twenty paper in the Annals of Applied Biology

Part of the reason for the under‐exploitation of physical resistance traits in plant breeding is that the genetic basis and heritability of these traits is poorly characterised, and any associations of particular traits with pest and disease resistances have yet to be determined. In raspberry, some associations between architectural traits and disease resistances have been demonstrated, for example cane hairs and resistance to cane diseases. The aim of this work is to examine a range of traits, including leaf trichomes, leaf density, cane density, bush density, lateral length and lateral numbers, to determine the heritability and therefore breeding potential of these traits. The effect of these traits against aphids and spider mites, two important pests in raspberry, was examined. Chromosomal regions with candidate genes regulating these traits were identified as the first step to understanding the genetic control.     

Identification,characterisation and mapping of simple sequence repeat (SSR) markers from raspberry root and bud ESTs

Raspberry breeding is a long, slow process in this highly heterozygous out-breeder. Selections for complex traits like fruit quality are broad-based and few simple methodologies and resources are available for glasshouse and field screening for key pest and disease resistances. Additionally, the timescale for selection of favourable agronomic traits requires data from different seasons and environmental locations before any breeder selection can proceed to finished cultivar. Genetic linkage mapping offers the possibility of a more knowledge-based approach to breeding through linking favourable traits to markers and candidate genes on genetic linkage maps. To further increase the usefulness of existing maps, a set of 25 polymorphic SSRs derived from expressed sequences (EST-SSRs) have been developed in red raspberry (Rubus idaeus). Two different types of expressed sequences were targeted. One type was derived from a root cDNA library as a first step in assessing sequences which may be involved in root vigour and root rot disease resistance and the second type were ESTs from a gene discovery project examining bud dormancy release and seasonality. The SSRs detect between 2 and 4 alleles per locus and were assigned to linkage groups on the existing ‘Glen Moy’ × ‘Latham’ map following genotyping of 188 progeny and examined for association with previously mapped QTL. The loci were also tested on a diverse range of Rubus species to determine transferability and usefulness for germplasm diversity studies and the introgression of favourable alleles.     

Mapping of A1 conferring resistance to the aphid Amphorophora idaei and dw (dwarfing habit) in red raspberry (Rubus idaeus L.) using AFLP and microsatellite markers

Background  

Raspberry breeding programmes worldwide aim to produce improved cultivars to satisfy market demands and within these programmes there are many targets, including increased fruit quality, yield and season, and improved pest and disease resistance and plant habit. The large raspberry aphid, Amphorophora idaei, transmits four viruses and vector resistance is an objective in raspberry breeding. The development of molecular tools that discriminate between aphid resistance genes from different sources will allow the pyramiding of such genes and the development of raspberry varieties with superior pest resistance. We have raised a red raspberry (Rubus idaeus) F₁ progeny from the cross 'Malling Jewel' × 'Malling Orion' (MJ × MO), which segregates for resistance to biotype 1 of the aphid Amphorophora idaei and for a second phenotypic trait, dwarf habit. These traits are controlled by single genes, denoted (A ₁) and (dw) respectively.     

Construction of an oilseed rape (Brassica napus L.) genetic map with SSR markers

We constructed a Brassica napus genetic map with 240 simple sequence repeats (SSR) primer pairs from private and public origins. SSR, or microsatellites, are highly polymorphic and efficient markers for the analysis of plant genomes. Our selection of primer pairs corresponded to 305 genetic loci that we were able to map. In addition, we also used 52 sequence-characterized amplified region primer pairs corresponding to 58 loci that were developed in our lab. Genotyping was performed on six F2 populations, corresponding to a total of 574 F2 individual plants, obtained according to an unbalanced diallel cross design involving six parental lines. The resulting consensus map presented 19 linkage groups ranging from 46.2 to 276.5 cM, which we were able to name after the B. napus map available at , thus enabling the identification of the A genome linkage groups originating from the B. rapa ancestor and the C genome linkage groups originating from the B. oleracea ancestor in the amphidiploid genome of B. napus. Some homoeologous regions were identified between the A and the C genomes. This map could be used to identify more markers, which would eventually be linked to genes controlling important agronomic characters in rapeseed. Furthermore, considering the good genome coverage we obtained, together with an observed homogenous distribution of the loci across the genome, this map is a powerful tool to be used in marker-assisted breeding. Electronic Supplementary Material Supplementary material is available for this article at     

Genetic linkage map of melon (<Emphasis Type="Italic">Cucumis melo</Emphasis> L.) and localization of a major QTL for powdery mildew resistance

Powdery mildew caused by Podosphaera xanthii has become a major problem in melon since it occurs all year round irrespective of the growing system. The TGR-1551 melon genotype was found to be resistant to several melon diseases, among them powdery mildew. However, the corresponding resistance genes have been never mapped. We constructed an integrated genetic linkage map using an F2 population derived from a cross between the multi-resistant genotype TGR-1551 and the susceptible Spanish cultivar ‘Bola de Oro’. The map spans 1,284.9 cM, with an average distance of 3.6 cM among markers, and consists of 354 loci (188 AFLP, 39 RAPD, 111 SSR, 14 SCAR/CAPS/dCAPS, and two phenotypic traits) distributed in 14 linkage groups. QTL analysis identified one major QTL (Pm-R) on LG V for resistance to races 1, 2, and 5 of powdery mildew. The PM4-CAPS marker is closely linked to the Pm-R QTL at a genetic distance of 1.9 cM, and the PM3-CAPS marker is located within the support interval of this QTL. These codominant markers, together with the map information reported here, could be used for melon breeding, and particularly for genotyping selection of resistance to powdery mildew in this vegetable crop species.     

The effect of sprays of thiophanate–methyl on cane diseases and yield in red raspberry, with particular reference to cane blight (Leptosphaeria coniothyrium)

Spur blight (Didymella applanata), cane botrytis (Botrytis cinerea) and cane blight (Leptosphaeria coniothyrium) were studied in two consecutive seasons in unsprayed raspberries and in plots sprayed with thiophanate-methyl in the first season alone, (a) twice pre-harvest, (b) twice post-harvest, or (c) twice pre- plus twice post-harvest. Pre-harvest, but not post-harvest sprays, gave moderate control of both spur blight and cane botrytis; both diseases occurred mainly on the lower halves of canes, the latter being the less common. Cane blight occurred at the base of canes where they were wounded by old cane stubs. In the first year it was severe; 37% of canes died before harvest in the unsprayed plots. The three spray programmes all decreased cane death due to cane blight and they all increased yield by c. 45% even in those plots sprayed post-harvest where spur blight was severe and not controlled. Clearly this last disease, despite its high incidence, had no effect on potential yield in this experiment. In the second year cane blight was common but less severe and the incidence of its lesions was reduced similarly by all programmes, but only 4% of canes died in control plots. Analysis of the potential yield and the sizes of lesions caused by L. coniothyrium in canes inoculated at fortnightly intervals in the previous year showed that potential yield loss occurred only when lesions girdled canes. A bimodal distribution in the lesion sizes, measured by length or girdling, indicated some endogenous control of lesion development which might explain the marked differences in the effect of cane blight on potential yield in two seasons.     

Resistance to Didymella applanata in red raspberry and some related species

When raspberry canes were inoculated in summer with a mycelial inoculum of Didymella applanata resistant genotypes developed relatively small lesions which produced few fruiting bodies in the following spring. Scores of the frequency of these fruiting bodies provided the best discrimination between genotypes. Very strong resistance was found in R. pileatus, R. occidentalis and R. coreanus and in hybrids of these species with red raspberry. Hybrids with R. crataegifolius were less resistant. Resistance was also found in Malling 1473/35, a derivative of red raspberry cv. Chief, and in red raspberry segregates with gene H which determines cane pubescence. Both the expression of resistance and the ranking of resistance sources for their resistance was similar for D. applanata to that reported for Botrytis cinerea.     

An anchored linkage map for sugar beet based on AFLP,SNP and RAPD markers and QTL mapping of a new source of resistance to <Emphasis Type="Italic">Beet necrotic yellow vein virus</Emphasis>

Rhizomania, caused by Beet necrotic yellow vein virus (BNYVV), is an important sugar-beet disease worldwide and can result in severe losses of root yield and sugar content. We have identified a major QTL for BNYVV resistance from a new source in a segregating population of 158 individuals. The QTL explained an estimated 78% of the observed phenotypic variation and the gene conferring the partial resistance is referred to as Rz4. AFLP was used in combination with bulked segregant analysis (BSA) to develop markers linked to the resistance phenotype. AFLP marker analysis was extended to produce a linkage map that was resolved into nine linkage groups. These were anchored to the nine sugar-beet chromosomes using previously published SNP markers. This represents the first anchored sugar-beet linkage map to be published with non-anonymous markers. The final linkage map comprised 233 markers covering 497.2 cM, with an average interval between markers of 2.1 cM. The Rz4 QTL and an Rz1 RAPD marker were mapped to chromosome III, the known location of the previously identified BNYVV resistance genes Rz1, Rz2 and Rz3. The availability to breeders of new resistance sources such as Rz4 increases the potential for breeding durable disease resistance.     

An expressed sequence tag SSR map of tetraploid alfalfa (Medicago sativa L.)

A genetic map constructed from a population segregating for a trait of interest is required for QTL identification. The goal of this study was to construct a molecular map of tetraploid alfalfa (Medicago sativa.) using simple sequence repeat (SSR) markers derived primarily from expressed sequence tags (ESTs) and bacterial artificial chromosome (BAC) inserts of M. truncatula. This map will be used for the identification of drought tolerance QTL in alfalfa. Two first generation backcross populations were constructed from a cross between a water-use efficient, M. sativa subsp. falcata genotype and a low water-use efficient M. sativa subsp. sativa genotype. The two parents and their F₁ were screened with 1680 primer pairs designed to amplify SSRs, and 605 single dose alleles (SDAs) were amplified. In the F₁, 351 SDAs from 256 loci were mapped to 41 linkage groups. SDAs not inherited by the F₁, but transmitted through the recurrent parents and segregating in the backcross populations, were mapped to 43 linkage groups, and 44 of these loci were incorporated into the composite maps. Homologous linkage groups were joined to form eight composite linkage groups representing the eight chromosomes of M. sativa. The composite maps consist of eight composite linkage groups with 243 SDAs from M. truncatula EST sequences, 38 SDAs from M. truncatula BAC clone sequences, and five SDAs from alfalfa genomic SSRs. The total composite map length is 624 cM, with average marker density per composite linkage group ranging from 1.5 to 4.4 cM, and an overall average density of 2.2 cM. Segregation distortion was 10%, and distorted loci tended to cluster on individual homologues of several linkage groups. Electronic Supplementary Material Supplementary material is available for this article at     

A Microsatellite Linkage Map of Striped Bass (Morone saxatilis) Reveals Conserved Synteny with the Three-Spined Stickleback (Gasterosteus aculeatus)

The striped bass (Morone saxatilis) and its relatives (genus Morone) are of great importance to fisheries and aquaculture in North America. As part of a collaborative effort to employ molecular genetics technologies in striped bass breeding programs, we previously developed nearly 500 microsatellite markers. The objectives of this study were to construct a microsatellite linkage map of striped bass and to examine conserved synteny between striped bass and three-spined stickleback (Gasterosteus aculeatus). Of 480 microsatellite markers screened for polymorphism, 289 informative markers were identified and used to genotype two half-sib mapping families. Twenty-six linkage groups were assembled, and only two markers remain unlinked. The sex-averaged map spans 1,623.8 cM with an average marker density of 5.78 cM per marker. Among 287 striped bass microsatellite markers assigned to linkage groups, 169 (58.9%) showed homology to sequences on stickleback chromosomes or scaffolds. Comparison between the stickleback genome and the striped bass linkage map revealed conserved synteny between these two species. This is the first linkage map for any of the Morone species. This map will be useful for molecular mapping and marker-assisted selection of genes of interest in striped bass breeding programs. The conserved synteny between striped bass and stickleback will facilitate fine mapping of genome regions of interest and will serve as a new resource for comparative mapping with other Perciform fishes such as European sea bass (Dicentrarchus labrax), gilthead sea bream (Sparus aurata), and tilapia (Oreochromis ssp.).     

The Ficus erecta genome aids Ceratocystis canker resistance breeding in common fig (F. carica)

Ficus erecta, a wild relative of the common fig (F. carica), is a donor of Ceratocystis canker resistance in fig breeding programmes. Interspecific hybridization followed by recurrent backcrossing is an effective method to transfer the resistance trait from wild to cultivated fig. However, this process is time consuming and labour intensive for trees, especially for gynodioecious plants such as fig. In this study, genome resources were developed for F. erecta to facilitate fig breeding programmes. The genome sequence of F. erecta was determined using single‐molecule real‐time sequencing technology. The resultant assembly spanned 331.6 Mb with 538 contigs and an N50 length of 1.9 Mb, from which 51 806 high‐confidence genes were predicted. Pseudomolecule sequences corresponding to the chromosomes of F. erecta were established with a genetic map based on single nucleotide polymorphisms from double‐digest restriction‐site‐associated DNA sequencing. Subsequent linkage analysis and whole‐genome resequencing identified a candidate gene for the Ceratocystis canker resistance trait. Genome‐wide genotyping analysis enabled the selection of female lines that possessed resistance and effective elimination of the donor genome from the progeny. The genome resources provided in this study will accelerate and enhance disease‐resistance breeding programmes in fig.     

Predicting spring oviposition by raspberry cane midge from accumulated derived soil temperatures

An accumulated soil temperature model is described which calculates the first oviposition date for overwintered populations of the raspberry cane midge (Resseliella theobaldi). The model uses values for mean 10 cm soil temperature, derived from daily maximum and minimum air temperatures and 10 cm soil temperature at 0900 GMT. It was developed by minimising the variation between observed dates for the start of oviposition over an 8-yr period and accumulated air or soil temperature, using a series of base temperatures. The best fit was obtained with soil temperatures accumulated above a base temperature of 4°C. Oviposition was predicted to start when the daily accumulated soil temperature reached 339°C days above a base temperature of 4°C. Field observations and model predictions suggested that emergence and oviposition dates were influenced by the direction of the slope of raspberry plantations. To compensate for this, an empirical correction has been incorporated into the model to advance or retard the predicted oviposition date by adjusting the estimated maximum soil temperature to allow for aspect. The geographical variation between dates for first oviposition was simulated by running the model for nine meteorological sites in the UK in 1985 and 1986.     

Identification and mapping of AFLP markers linked to peanut (<Emphasis Type="Italic">Arachis hypogaea</Emphasis> L.) resistance to the aphid vector of groundnut rosette disease

Groundnut rosette disease is the most destructive viral disease of peanut in Africa and can cause serious yield losses under favourable conditions. The development of disease-resistant cultivars is the most effective control strategy. Resistance to the aphid vector, Aphis craccivora, was identified in the breeding line ICG 12991 and is controlled by a single recessive gene. Bulked segregant analysis (BSA) and amplified fragment length polymorphism (AFLP) analysis were employed to identify DNA markers linked to aphid resistance and for the development of a partial genetic linkage map. A F_2:3 population was developed from a cross using the aphid-resistant parent ICG 12991. Genotyping was carried out in the F₂ generation and phenotyping in the F₃ generation. Results were used to assign individual F₂ lines as homozygous-resistant, homozygous-susceptible or segregating. A total of 308 AFLP (20 EcoRI+3/MseI+3, 144 MluI+3/MseI+3 and 144 PstI+3/MseI+3) primer combinations were used to identify markers associated with aphid resistance in the F_2:3 population. Twenty putative markers were identified, of which 12 mapped to five linkage groups covering a map distance of 139.4 cM. A single recessive gene was mapped on linkage group 1, 3.9 cM from a marker originating from the susceptible parent, that explained 76.1% of the phenotypic variation for aphid resistance. This study represents the first report on the identification of molecular markers closely linked to aphid resistance to groundnut rosette disease and the construction of the first partial genetic linkage map for cultivated peanut.     

RFLP markers for sugar beet breeding: chromosomal linkage maps and location of major genes for rhizomania resistance, monogermy and hypocotyl colour

An RFLP linkage map for the nine chromosomes of sugar beet (Beta vulgaris L. ssp. vulgaris var. altissima Doell) was constructed by using a segregating population from a cross between two plants which were heterozygous for several agronomically interesting characters. One hundred and eleven RFLP loci have been mapped to nine linkage groups using 92 genomic markers. The current RFLP map covers a total length of 540 cM. Evidence for the existence of a major gene for rhizomania resistance (Rr1) is given, together with its map position on linkage group IV in the interval between loci GS44 and GS28a. The presence of an RFLP fragment at the GS3d locus is, until now, the best molecular marker for rhizomania-resistant genotypes in segregating populations of sugar beet; GS3d is linked to Rr1 with 6.7 cM. The gene MM, controlling the polygerm/monogerm seed type, has been mapped on linkage group IX in a distal position at 4.2 cM from the locus GS7. The gene R controlling the hypocotyl colour maps to linkage group VII and does not recombine with the RFLP locus GS42. The inheritance of a group of RFLP loci revealed the possible presence of a translocation in the population used to establish the map. The data presented are discussed in relation to the possibility of using RFLP markers in sugar beet breeding.