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Ribes genomics

Genomics research in Ribes is focused in three main areas:

Linkage mapping

Linkage mapping in Ribes utilises AFLP, SSR (genomic and EST-derived) and SNP markers, and the first reported linkage map of blackcurrant (R. nigrum) was published in 2008 (Brennan et al. 2008). The mapping population used derives from a cross between two diverse Institute breeding lines (the 9328 population), and is segregating for a range of agronomic and fruit quality traits. In preparing the map, marker information has been combined with data on phenological, pathological and biochemical traits to estimate the positions of quantitative trait loci (QTLs) for these traits, notably ascorbic acid content, budbreak and flowering time, and to identify markers with potential utility in breeding (Figure 1). This is now used to provide a framework for the development of marker assisted breeding strategies for blackcurrant, to improve breeding efficiency and time to cultivar.

Figure 1: Linkage Group 1 from Ribes nigrum map, with parental types shown separately.

Figure 1: Linkage Group 1 from Ribes nigrum map, with parental types shown separately.

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Marker development

Although marker systems have been reported in berry fruit crop species, to date there have been virtually no reports of the use of marker-assisted breeding and none in blackcurrant. Various marker types have been developed in Ribes, including AFLPs (Lanham and Brennan 1999), SSRs (genomic (Brennan et al. 2002) and EST-derived (Brennan et al. 2008) and SNPs (Brennan et al. 2008). Several key traits in blackcurrant, with commercial relevance through the breeding of improved cultivars, have been mapped, including resistance to gall mite (Cecidophyopsis ribis Westw.) based on the Ce gene from R. grossularia, which mapped to linkage group 2 on the Ribes map (Brennan et al. 2008).

Using a bulk segregant analysis, 90 AFLP primer combinations were screened and a linkage map constructed around the resistance locus controlled by Ce. Sixteen of the primer combinations produced a fragment in the resistant bulked progeny and the gall mite-resistant parent, but not in the susceptible bulked progeny and parent; subsequent testing on individual progeny identified an AFLP fragment closely linked to gall mite resistance. This fragment, designated E41M88-280 (Figure 2), has been converted to a PCR-based marker based on sequence-specific primers, amplifying only in resistant individuals (Brennan et al. 2008).

Figure 2: AFLP markers on bulks from mite-resistant and mite-susceptible segregants in the 9328 mapping population. E41M88 shows linkage with resistant phenotype

Figure 2: AFLP markers on bulks from mite-resistant and mite-susceptible segregants in the 9328 mapping population. E41M88 shows linkage with resistant phenotype.

Validation of this marker across a range of susceptible and resistant blackcurrant germplasm with different genetic backgrounds confirmed its reliability in the identification of mite-resistant germplasm containing gene Ce. The conversion of the original AFLP fragment to a sequence-based PCR marker simplifies its application and therefore increases its utility for selection of mite-resistant germplasm in high-throughput breeding programmes for blackcurrant.

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Dormancy studies

The effects of warmer winters, with an associated reduction in chilling levels, is beginning to have a serious impact on the performance of some blackcurrant germplasm, with uneven budbreak and reduced fruit quality at harvest (Atkinson et al. 2005). As a result, there is increasing interest in the selection of germplasm with a reduced winter chilling requirement and it is known that there are wide variations in this character between germplasm from Europe and from low-chill environments such as New Zealand (Figure 3).

Figure 3: James Hutton Institute cv. Ben Alder growing in New Zealand, showing lack of budbreak due to low winter chilling levels (Photo courtesy of G. Langford, HortResearch, NZ).

Figure 3: James Hutton Institute cv. Ben Alder growing in New Zealand, showing lack of budbreak due to low winter chilling levels. (Photo courtesy of G. Langford, HortResearch, NZ).

In Rubus, microarrays were used to identify significant changes in gene expression at the time of budbreak (Mazzitelli et al. 2007), and a broadly similar approach is being undertaken in Ribes. By identifying changes in expression in key genes at budbreak (Figure 4), the available germplasm with known chilling requirement can be assessed for polymorphism, and ultimately markers can be developed. These will then be used to select genotypes with reduced chilling requirement, which will be better adapted to future climatic conditions. By comparison with the Rubus experiments, generic trends will also be sought for the effects of warmer winters on other woody species.

Figure 4: Changes in gene expression around dormancy break in Ribes – red = upregulated, green = downregulated. Blue arrow denotes winter period, yellow denotes spring.

Figure 4: Changes in gene expression around dormancy break in Ribes – red = upregulated, green = downregulated. Blue arrow denotes winter period, yellow denotes spring.

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References

Atkinson, C., Sunley, R., Jones, H., Brennan, R. and Darby, P. 2005. Winter Chill in Fruit. Defra Report No. CTC 0206.

Brennan, R., Jorgensen, L., Hackett, C., Woodhead, M., Gordon, S.L. and Russell, J. 2008. The development of a genetic linkage map of blackcurrant (Ribes nigrum L.) and the identification of regions associated with key fruit quality and agronomic traits. Euphytica 161, 19-34.

Brennan, R., Jorgensen, L., Woodhead, M. and Russell, J. 2002. Development and characterisation of SSR markers in Ribes species. Molecular Ecology Notes 2, 327-330.

Brennan, R., Jorgensen, L., Gordon, S., Loades, K., Hackett, C. and Russell, J. 2008. The development of a PCR-based marker linked to resistance to the blackcurrant gall mite (Cecidophyopsis ribis Acari: Eriophyidae). Theoretical and Applied Genetics 118(2), 205-11.

Lanham, P.G. and Brennan, R.M. 1999. Genetic characterisation of gooseberry (Ribes subgenus Grossularia) germplasm using RAPD, ISSR and AFLP markers. Journal of Horticultural Science and Biotechnology 74, 361-366.

Mazzitelli, L., Hancock, R.D., Haupt, S., Walker, P.G., Pont, S., McNicol, J., Cardle, L., Morris, J., Viola, R., Brennan, R., Hedley, P.E. and Taylor, M.A. 2007. Co-ordinated gene expression during phases of dormancy release in raspberry (Rubus idaeus L.) buds. Journal of Experimental Botany 58, 1035 - 1045.

Research

Areas of Interest


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The James Hutton Research Institute is the result of the merger in April 2011 of MLURI and SCRI. This merger formed a new powerhouse for research into food, land use, and climate change.