**8. Summary remarks**

ogy to perform cluster analysis of 77 accessions, of which 73 *Hippophae rhamnoides* were clas‐ sified into 2 groups and 4 *H. salicifolia*, into 1 group. They associated SRAP markers with dried-shrink disease (DSD) resistance and suggested SRAP markers are useful for breeding new sea buckthorn lines with resistance to DSD. Feng et al., (2009a) reported on the genetic diversity analysis of *Pinus koraiensis* using SRAP markers. They obtained 24 to 33 loci per primer combination and used 143 SRAP markers to analyze 480 samples collected from 24 provinces in China. They found that there was no significant difference in genetic diversity among provinces. However, genetic variation of intra population accounted for 93.355% of

In fungi, Sun et al., (2006) used SRAP markers to classify *Ganoderma lucidum* strains. They performed genetic diversity analysis with 31 accessions collected from several countries. Us‐ ing 75 polymorphic loci, they classified all 31 accessions into five groups. The results showed that *G. lucidum* strains were significantly different from *G. sinense* and *G. lucidum* in China, also different from *G. lucidum* in Yugoslavia. They suggested that SRAP markers are useful in taxonomy and systematics of Ganoderma strains within basidiomycetes. In anoth‐ er fungus, Tang et al., (2010) analyzed Chinese *Auricularia auricula* strains using SRAP and ISSR markers. They found both SRAP and ISSR markers were abundant in *A. auricula* and could be used to effectively distinguish all tested strains. After phylogenetic analysis, they classified 34 *A. auricula* strains into four or five major groups using the UPGMA method. They suggested that genetic diversity information would be used in *A. auricula* breeding programs to develop new medicinal mushroom. Fu et al., (2010) performed genetic diversity analysis in 23 elite *Lentinula edodes* strains from China using RAPD, ISSR and SRAP markers. In total, they used 16 RAPD primers, 5 ISSR primers and 23 SRAP primer combinations to produce 138, 77 and 144 bands, respectively. After UPGMA clustering analysis, they classi‐ fied all 23 *L. edodes* strains into three or four groups. However, all groups showed high lev‐

els of similarity, showing a low level of genetic diversity in all tested strains.

SRAP amplification is actually a small portion of all possible sampling of a genome. So SRAP can be used to produce a reduced genome samples when multiple SRAP reactions are pooled. As described previously, pooled SRAP produces can be directly sequenced using next generation sequencing technologies. When replacing genomic DNA with cDNA samples, SRAP is adequate to perform gene expression profiling and also con‐

More recently, Yu et al., (2012) used SRAP markers to distinguish fertile somatic hybrids of *G. hirsutum L.* and *G. trilobum* produced by protoplast fusion. They obtained fertile somatic hybrids by symmetric electrofusion of protoplasts of tetraploid upland cotton *G. hirsutum* and wild cotton *G. trilobum.* These hybrids were confirmed using morphological characteris‐ tics, flow cytometric analysis, and molecular markers including RAPD, SRAP and AFLP.

the total variation.

36 Plant Breeding from Laboratories to Fields

**7. Other applications**

struct cDNA genetic maps.

SRAP was first used to construct a genetic map and tag genes in *Brassica oleracea* in 2001 (Li and Quiros, 2001). This molecular marker technology is simply performed with one round PCR to amplify multiple or occasionally over a hundred loci in a genome. In its PCR reaction mixture, two random primers are included, which leads to maximum flexi‐ bility in primer designing and primer labelling. There is no limitation on primer combi‐ nations and one labelled primer may be combined with any number of unlabelled primers. Most SRAP products fall into a size range of 100 to 1000 base pairs, which can be separated in both polyacrylamide and agarose gels. In automatized detection, one SRAP primer is fluorescently labelled and SRAP products can be analyzed using ad‐ vanced instruments such as an ABI genetic analyzer, which dramatically increases throughput of SRAP molecular marker detection.

There is a wide range of applications of SRAP technology such as genetic map construction, genetic diversity analysis, gene tagging and cloning. Since SRAP detects multiple loci in one reaction, it is feasible to construct ultradense genetic maps with over 10,000 SRAP molecular markers. SRAP has advantages over other molecular detection techniques in gene tagging and cloning and allows screening thousands of loci shortly to pinpoint the genetic position underlying the trait of interest. Sequencing SRAP products enhances the applications of SRAP technology. In well characterized genomes, SRAP sequences are used to identify the chromosomal region of mapped genes while in species without a known whole genome se‐ quence, sequences of SRAP markers on a genetic map allow arranging sequence contigs and assembly of a whole genome sequence.

SRAP molecular technology is very useful in plant breeding. In QTL mapping, common QTL for the same trait of interest can be effectively identified. Since SRAP has a high throughput feature, multiple mapping populations can be analyzed effectively to construct several genetic maps. In addition, the same set of SRAP primers allows detection of the same genetic loci, which can used to align several genetic maps. SRAP is effective and effi‐ cient in marker assisted selection in plant breeding since thousands of samples can be ana‐ lyzed inexpensively. SRAP technology has been commonly used in analysis of genetic diversity of many plant species. Currently, SRAP are used in most crops, tree species, orna‐ mental and medicinal plants.

## **Author details**

Genyi Li1 , Peter B. E. McVetty1 and Carlos F. Quiros2

