Molecular Plant Breeding 2016, Vol.7, No.10, 1-17
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et al., 2002; Zhang et al., 2003; Lin et al., 2005; Frelichowski et al., 2006; Zhang et al., 2013). Several genes for
disease resistance have been observed in cotton through applying SSR markers; including root knot nematode
[
Meloidogyne incognita
(Kofoid and White)] (Ynturi et al., 2006), verticillium wilt (
Verticillium dahliae
Kleb.)
(Bolek et al., 2005), bacterial blight [
Xanthomonas axonopodis
pv. malvacearum] (Rungis., 2002; Xiao., 2010);
cotton leaf curl virus (Aslam et al., 1999) have been tagged by SSR molecular markers. Commonly the null-alleles
are found which are not polymorphic, diverse microsatellites are examined to overcome null alleles using
population studies having enormous SSR primers (Weising et al., 2005). Association mapping performed in
Chinese cotton germplasm and QTLs for seed cotton yield and fiber quality observed by using SSRs which will
provide good parents for developing good cultivars (Zhang et al., 2013). Qin et al., (2015) employed SSR markers
used for the association mapping of 241 Upland cotton collections, results provide new useful markers for
marker-assisted selection in breeding programs and new insights for understanding the genetic basis of upland
cotton yields and fiber quality traits at the whole-genome level. Species specific SSRs are generally employed for
introgression, but with extending genetic distance the extent of loci that successfully amplify may be reduced.
11 Expressed Sequence Tags (EST-SSRs)
Transcribed regions of the DNA (EST- SSRs) are mostly maintained throughout the species compared to genomic
SSRs from the untranslated regions (Cuadrado and Schwarzacher, 1998), and are having more substitution to
genomic SSRs. The evolution of enormous expressed sequence tags produces a valuable origin of PCR-based
markers for targeting SSRs. Among divergent species in plants about 1-5% of the expressed sequence tags have
tandem repeats having acceptable length for the development of markers (Kantety et al., 2002). During gene
expression EST-SSRs have more chances of being functionally linked with variations than genomic SSRs (Gao et
al, 2004). Different genome analysis techniques provide increased quantity of ESTs which facilitated in the
recognition of SSRs domains from the ESTs. Moreover, many attempts done for the development of EST-SSRs in
cotton (Qureshi et al., 2004); for phylogenetic analysis (Arunita et al., 2010) and genomic map construction (Guo
et al., 2007; Lin et al., 2009). Genic SSRs have some intrinsic advantages over genomic SSRs because they are
quickly obtained by electronic sorting, and are present in expressed regions of the genome (Varshney et al., 2005).
However, EST-SSRs exhibit low level of polymorphism than conventional SSRs. Wang et al., (2015) utilized
EST-SSRs for developing genetic linkage map in cotton, and observed that marker development was very useful
for the saturation of the allotetraploid genetic linkage map, genome evolution studies and comparative genome
mapping.
12CleavedAmplifiedPolymorphic Sequence (CAPs)
The integration of RFLP and PCR (Semgan et al., 2006b) through which DNA particles are amplified using PCR,
followed by restriction enzyme digestion is accomplished by CAPs. Cleaved amplified polymorphic sequences derive
polymorphic markers from monomorphic markers which are mostly co-dominantly transferred (Karaca and Gul, 2011)
and show high polymorphism among closely related accessions. CAPs primers developed from ESTs are more useful
as genetic markers for comparative mapping study than those markers derived from non-functional sequences such as
genomic microsatellite markers (Matsumoto and Tsumura, 2004). These markers are helpful for evolving patents in
cotton and applicable in characterization of germplasm, genetic diversity analysis for utilization in breeding programs
and genome mapping (Karaca and Gul, 2011).
13 Single Nucleotide Polymorphism (SNP)
Precise and elucidated location at chromosome having fragment of DNA among two accessions demarcated by a
single base is called single nucleotide polymorphism; due to mutation either transition or transversion and deletion
or insertion abnormality (Ayeh, 2008; Hearne et al., 2008). SNPs are highly secured markers as furnish phenotype
directly (Batley and Edwards, 2007). They are the easiest type of markers as having minor heredity entity as alone
base and can produce large number of markers. SNPs are frequently found in plants and animals (Xiao et al.,
2010). SNPs are co-dominant, normally assigned and connected with morphological changes as used as a marker
(Lindbeld et al., 2000). Now a day’s researchers all over the world have thirst for single nucleotide markers for
