Molecular markers (GENETIC):

Molecular Markers

marker

Genetic markers act as ‘tags flag or sign that is located in close proximity to the gene i.e. tightly linked. The genetic differences between individual organisms and species are differentiated by genetic markers. Generally, target genes are not affected by them but they act as signs’ or ‘flags’. Molecular markers are not affected by various environmental conditions or plant phenology so these are also valuable for characterization and cultivar identification and can differentiate cultivars having similar phenotypes (Belaj et al., 2002). Therefore morphological traits, are not affected by such markers because they are closely linked or located near to genes of the trait. (Collard et al, 2009).

There are three types of genetic markers (1) morphological markers built on phenotypic traits or agronomical characters (2) molecular markers or genetic markers built on polymorphism in DNA and (3) biological markers constructed on gene product protein investigation like Isozyme markers (Market and Moller 1959) (Botstein et al., 1980; Welsh and McClelland, 1990; Williams et al., 1990; Adams et al., 1991; Jones et al., 1997). DNA-based markers are very useful and have wide applications, used for genotype identification, segregation of population for linked markers, population and pedigree analysis, phylogenetic analysis, restriction of a gene, and upgrading of plant genotypes by marker-assisted collection (Fracaro et al., 2005).

1. SSR Markers

The SSR markers have proven to be very useful due to their large quantity, polymorphism, and reproducibility (Weber and May 1989; Nybomand Weising, 2010). Due to their high degree of polymorphism, co-dominance, and correctness for automation, simple sequence repeat (SSR) markers have become valued molecular tools for genotype identification, mapping, and determination of genetic relatedness. Simple sequence repeats (SSR) markers have been used for genetic diversity, relationship, and cultivar identification of Pyrus (Yamamoto et al.,  2001, 2002a, b, 2004; Kimura et al., 2002; Wunsch and Hormaza 2007; Bao et al., 2007; Katayama et al., 2007; Bassil and Postman, 2010). Out of 133 putative alleles by using nine SSR markers fifty-eight (58) Asian pear lines were identified (Kimura et al., 2002) belonging to six Pyrus species. On the basis of SSR, a dendrogram was developed which shows three main groups, resembling Japanese, Chinese, and European Pears. These SSR loci were extremely heterozygous and thus effective in the differentiation of Asian Pears. Similarly (Bao et al., 2007) it is estimated that 98 Pear cultivars are native to East Asia, and were evaluated through six SSR loci.

Although in the early era, SSRs are well established for the investigation of human and mammalian genetic diversity, recently these markers have only recently become available in plant species. They have been identified in many plant genomes including those of maize (Senior and Heun, 1993; Shatuck-Eidens et al., 1990; Taramino and Tingey, 1996); soybean (Akkaya et al., 1992; Morgante and Olivieri, 1993); Brassicaspp. (Poulsen et al., 1993); rice (Wu and Tanksley 1993); barley (Saghai-Maroof et al., 1994); pearl millet (Chowdari et al., 1998a); Arabidopsis (Depeige et al., 1995); tomato (Broun and Tanksley, 1996); conifers (Tsumura et al., 1997); and sorghum (Brown et al., 1996; Taramino et al., 1997; Dean et al., 1999). Consequences of numerous works validated that the application of SSR markers delivers an unresolved new implement for the genetic study of plant species. Additionally, to Pear, the complete genome sequences of individual apples (Velasco et al., 2010) and strawberries (Shulaev et al., 2011) have been finished, making enormous genomic data of apple, pear, and strawberries in the aspect of molecular marker maps, uttered sequence tags (EST). Nevertheless, there is somewhat little genomic evidence accessible for other appreciated fruit tree members of the Rosacea family. Due to their co-dominant and frequently single-locus nature, SSR loci can be recognized, and their alleles can be identified in different varieties of similar species and repeatedly in those of other close lineages. This means that a specific set of SSRs can be used in different groups of genotypes or mapping populations, making them predominantly useful for inconsistency (MAS), map building, and proportional research (Mnejja et al. 2010). So, it is greatly appreciated to inspect the transferability of SSR markers from Pyrus, where they are easily established and assessed, to other Rosacea species. Transferability to relations subsidizes the wide applicability of SSRs established based on the Pear genome. Lately, there have been numerous information on the transferability of SSR markers in or crossways the genera midst Rosaceae fruit crops (Decroocq et al. 2003; Gasic et al., 2009; Gisbert et al., 2009; Sargent et al., 2009,2007; Yamamoto et al. 2004; Yao et al., 2010; Wünsch 2009; Mnejja et al. 2010; He et al. 2011; Bouvier et al., 2012.

2. Benefits of SSR markers

SSRs have become the markers of choice in both animal and plant species because of their abundance, high degree of polymorphism, and suitability for automation (Weber and May 1989). SSR markers have some benefits over other molecular markers which confirm a more reliable method for DNA fingerprinting. Among others, they exhibit a large number of alleles per locus, codominant type of inheritance, and are abundant in genomes.  

SSR markers have been issued for European  Pear (Bassils  et  al.,  2005;  Fernández-Fernández  et  al.,  2006)  as well as for  Asian  Pear species  (Kimura  et  al.,  2002;  Yamamoto  et  al., 2002).  Furthermore, SSR markers applied to apples have shown good transferability to European Pear (Yamamoto et al., 2001). (Sisko et al. 2009) between the Slovene Pear diversities with SSR investigation have explored the genetic relative in 7 microsatellite locus of 64 polymorphic alleles. The distribution of heterozygosity has been determined between 0.235. The expected heterozygosity with an average of 0.716 has ranged between 0.430(BGA35) and 0.824 (KU10). Further, at all loci expected and observed heterozygosity are observed, the highest and deepest differences have been unwavering 0.153 (CH01H10) and 0.055 (BGA35) respectively. Through SSR markers (Wolko et al., 2010) have been identified the genetic diversity of six cultivated Pears (P. communis) and two wild Pears, P. pyraster (Song et al., 2014) reported that for the establishment of genetic relationships in P. pyrifolia Pears 134 SSR markers should be used (Queiroz et al., 2005) carried out determined molecular analysis of Portugal pear types by evaluating 36 different genotypes and by using SSR markers. Significantly, high heterozygosity (0.806) was observed, and the highest number of alleles per locus was found (11.3). was an effective number of alleles was found within the range of 3.3 to 9.0 (Rana et al., 2015) genotype diversity was identified and examined 20 SSR primers and phylogenetic affinities of 48 Pears samples have its place to six species by discussing the 23 morphological characteristics.

3. Limitations

The present work is limited to the use of SSR markers for the molecular investigation of selected Pyrus genotypes belonging to Northern Pakistan.

1: Structure software shows the genetic relationship among 30 Pyrus genotypes.