All traits (characteristics) are controlled by genes and the combination of alleles (versions) of the genes in the plant is known as the genotype. Red raspberry is diploid and therefore can have two alleles of each gene. The genotype, together with the environmental conditions in which the plant is grown, determines the phenotype (the way the plant looks and reacts to stresses etc).

The ultimate aim of plant genetics is to understand completely how genotype controls phenotype and this information can then be transferred to plant breeders in a way they can easily access and use. Significant progress in the development of strategies for relating genotype to phenotype has been achieved with the development of markers and genetic mapping in plants and the ability to use map based gene isolation approaches. Although a large number of gene sequences are available in data bases and held privately, little is known about what these genes do and how they influence phenotype.

With the availability of genetic linkage maps (which are simply a linear representation of the plant chromosomes) (Figure 1), through field and glasshouse evaluation of progeny the location of the genes controlling traits can be determined on the map. In the first instance this provides a marker for the trait and with more evaluation and study through, for example, DNA sequencing, large portions of DNA in the map region onto which the trait has been located, the genes themselves can be identified. For breeding purposes however the marker is sufficient to make a prediction on the likelihood of the presence of a trait of interest.

Figure 1: An example linkage map from Rubus showing quantitative trait loci

Figure 1: An example linkage map from Rubus showing quantitative trait loci

Molecular markers are DNA sequences (both known and unknown function) that are located near genes and inherited characteristics of interest (Antonius-Klemola 1999; Hokanson 2001), allowing selective breeding and identification of progeny with desired characteristics. Molecular markers have been rapidly adopted by researchers globally as an effective and appropriate tool for basic and applied studies addressing physiological traits.

Markers are most informative when integrated into genetic linkage maps (Bradshaw et al., 1994). These molecular markers are used as tools that identify DNA polymorphisms (variations at particular points in the sequence) between DNA samples of different individuals. These polymorphisms can be of many different types from single nucleotide changes, large or small insertions and deletions or length variation in repeat sequences (Graham et al., 2002; Graham et al., 2004; Lewers et al., 2004; Stafne et al., 2005; Graham et. al., 2006; Woodhead et al., 2008). All however provide information on a particular locus in the genome and importantly when that locus is known to be associated with a particular plant phenotype.

An important way of linking marker loci to a particular plant phenotype is through the use of genetic linkage maps. These maps when coupled with field trials and glasshouse or laboratory experiments to measure traits of interest in the population of individuals used for map construction can then be used to relate phenotypic data to marker data on linkage maps.

For map construction, individual marker loci are genetically characterised in a segregating population (progeny from the cross of two genetically diverse parents) and the recombination rate of alleles at each pair of loci can be determined using classical linkage analysis. Loci can then be ordered into a linkage map and distance between loci can be expressed as recombination units given in centiMorgans (cM) where one cM is equal to 1% recombination. Once a sufficient number of markers have been mapped, the number of linkage groups should equal the haploid number of chromosomes. Several computer programmes are available to quickly generate a map once markers have been applied to a segregating population.

In the initial phase of map creation genetically diverse parents are chosen which are known to segregate for the trait(s) of interest and depending on the biology of the crop an F1, F2 or backcross used for map construction. Once a map and segregating population have been developed attempts can be made to identify map locations of traits of interest. The speed and precision of crop enhancement can be improved by the development of genetic linkage maps which allow the development of diagnostic markers for polygenic traits and in the future, aid the identification of the genes behind the traits.

The developments in bioinformatics and genomics, especially in the construction, development and use of expressed sequence tag (EST) databases provide further tools to link genotype with phenotype.

One of the most important developments in genetic mapping has been the demonstration that quantitative trait loci (QTL) can be located near DNA markers with very high accuracy (Bradshaw and Stettler 1994). QTLs are stretches of DNA that are closely linked to the genes that underlie the trait in question. QTLs are often associated with traits of great economic importance that are usually difficult to manipulate in plant breeding programmes. Genetic maps based on DNA markers have allowed the dissection of some quantitative traits into single component loci which contribute to the phenotypic variation for a trait (Graham et al., 2006). Thus identification of DNA markers linked to specific QTLs offers the possibility of marker-assisted selection for such agronomically important traits. 

In raspberry significant progress has been made in QTL analysis and marker assisted breeding is now a reality with pest and disease and fruit quality markers currently used in the James Hutton Limited programme.



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Williams, D., Hackett, CA., Karley, A., McCallum, S., Smith, K., Britten, A., Graham, J. 2021. Seeing the wood for the trees: hyperspectral imaging for high throughput QTL detection in raspberry, a perennial crop species Fruit Research 2021 1:7

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Graham J., Smith K., MacKenzie K., Milne L., Jennings n., Mateos B., Hackett C. 2022. Developmental QTL in a red raspberry Promocane x biennial raspberry population that exhibit primocane fruiting Journal of horticulture J. Hortic, Vol. 9 Iss. 5 No: 308