Molecular Plant Breeding 2016, Vol.7, No.10, 1-17
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contrary to RAPD primers, enabling elevated annealing temperature which produces high polymorphic bands
converse to RAPDs (Reddy et al., 2002). All over the globe the scientists are using ISSR markers vastly in cotton
improvement, phylogenetic study and for mapping (Bornet et al., 2002; Sica et al., 2005). ISSR provides easy way
for examining the polymorphic bands conversely to other molecular markers (Dongre et al., 2007). Noorulhamdi
et al., (2013) observed genetic diversity and studied agronomic traits in
Gossypium hirsutum
and F
2
progenies by
using ISSR.
8 Sequence Characterized Amplified Region (SCAR)
A technique in which DNA sequence is detected by using polymerase chain based marker having well defined pair of
oligonucleotide primers (Paran and Michelmore, 1993). SCARs are advantageous over RAPDs having capability to
recognize merely a single locus, the PCR reaction conditions are less manifested during amplification and mostly
transformed into co-dominant markers (Paran and Michelmore, 1993). These markers are more beneficial for genome
mapping being co-dominant contrary to dominant RAPDs and are having the ability to evaluate pooled genomic
libraries through PCR for map based cloning. The methodology of sequence characterized amplified region is
prominent among the researchers for mapping studies within closely related species (Michelmore et al., 1991; Tanaka
et al., 2006). SCAR markers have been used for disease and insect resistance and also utilized for restoration of
fertility in crops (Nair., 1995; Norio, 1997; Liu., 1999). SCAR marker is cost effective and highly polymorphic which
makes it suitable to be used for evaluating large numbers of mapping population in cotton (Guo et al., 2003).
9 Sequence Tagged Site (STS)
Sequence-tagged site (STS) are the markers which utilize polymerase chain reaction with particular primer that
produces a marker linked to desired character (Feng et al., 2005). Sequence tag site is manifested by a pair of
oligonucleotides that are developed by sequencing an RFLP probe representing a mapped low copy number
sequence (Blake et al., 1996). STS markers are simple to use, highly polymorphic, co-dominant and suitable for
high throughput sequencing (Remon and Jung, 2000). Breeders use STS markers for developing restorer parental
lines for hybrid cotton (Feng et al., 2005).
10 SSR (Simple Sequence Repeat) (Microsatellites)
Short tandem repeats are polymorphic bands found in DNA that contain 1-6 bp repeating units (Bidichandani, et al.,
1998). Especially if the tandem repeats are higher than 10, then this marker shows high level of inter and
intra-specific polymporhism (Queller et al., 1993). Repetitive sequences are found all over the genomes and chain of
mono, di and tri nucleotides repeats are known as microsatellites. These markers are multiallelic, co-dominant,
intensively changing and are distributed randomly all over the genome. During polymerase chain reaction precise
flanking fragments serve as primers that are utilized for the amplification of simple sequence repeats for observation.
During replication tandem repeats produce simple sequence repeats due to copy choice recombination (Viguera et al.,
2001) or dissimilarity occur in the specific nucleotide sequence due to unbalance crossing over (Yu and Kohel, 1999).
Simple sequence repeats play important role in germplasm characterization, screening of varieties, pedigree analysis
and genome mapping (Billotte et al., 1999). SSR markers are the desired type of markers in cotton as having higher
possibility for phylogenetic study (Zhang et al., 2008). SSR markers and their mapping information can be found in
substantial Cotton Gene database (
markers). SSR analysis needs small quantity of DNA,
not having precise quality and the inferences are discussed; SSRs are employed in plant breeding, conservation
biology and as forensics in population genetics, genetic diversity analysis and genetic mapping (Coetes and Byrne,
2005). For assisting the development of saturated and fully integrated saturated genetic map of cotton “The International
Cotton Genome Initiative” was launched that will furnish the way for the evolvement of a consensus map (Yu et al.,
2005).
Simple sequence repeats have been utilized for analyzing genetic diversity in cotton and closely related species
(Rungis et al., 2005; Liu et al., 2006), significant hindrance for use in cotton breeding due to limitation of genetic
variability (Iqbal et al., 2001; Liu et al., 2006). Many researchers have used SSRs for refinement of fiber traits (Ulloa
