Molecular Plant Breeding 2016, Vol.7, No.10, 1-17
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many species as SNP-based markers overcome other markers, owing to the enormous persistent polymorphism in
the genome, both within and between (Berard et al., 2009). Quick detection of SNPs is based on sequence
information in EST libraries (Bundock et al., 2006) or on the basis of primer design for re-sequencing (Choi et al.,
2007) in species having no available genome sequence. Universally well-known method for SNP discovery is
mass spectrometry and sequenom (San Diego, USA), evolved an efficient genotyping technique (Buetow et al.,
1999); moreover, SNPs can be identified by SNP flow software (Weissensteiner et al., 2013).
SNPs have been detected in many species including model species such as
Arabidopsis thaliana
(Jander et al.,
2002), many field crops like maize (Ching et al., 2002), wheat (Ablet et al., 2006) and in humans (Sachidanandam
et al., 2001). SNPs furnish fast and efficient genotyping of enormous population by using next generation
sequencing methodology.
SNPs have been identified in cotton by scientists all over the world for analyzing genetic diversity, phylogenetic
analysis and genetic mapping in the
Gossypium
genome (Deynze et al., 2009). SNPs among two accessions of
Gossypium arboreum
were examined between 30 conserved regions of expressed sequence tags by Shaheen et al.,
(2010), and identified as a whole 27 SNPs consisting of six indels and 21 substitutions in 7804 bp having a
frequency of one SNP/371 bp and one indel after every 1300 bp; 52% transitions and 48% SNPs were
transversions in the observed SNPs. Affymetrix has developed “Gene Chip” for cotton genome array consisting of
239777 probe sets containing 21485 cotton transcripts which is in verification stage and then will be available
commonly. For SNP development the sequences are collected from Genbank, dbEST and RefSeq supplied by
partners all over the world. Roche 454 pyrosequencing technique in allotetraploid cotton produced more number
of SNPs through reduced representation library sequencing (Byers et al., 2012). Desirable SNPs were observed by
using conservative approach; KASPar assay was about 35.8% for conversion of SNPs. Genome map of 1688 cM
was developed in G. hirsutum using 367 SNP markers. Wang et al., (2013) developed linkage map by using SNPs
and QTLs were analyzed. A total of 15.971 markers, including gSSRs, EST-SSRs, SRAPs, and SSCP-SNPs. Gore
et al., (2014) produced a linkage map and conducted a quantitative trait locus (QTL) analysis of 10 agronomic and
fiber quality traits in a recombinant inbred mapping population and observed QTLs in introgressed population by
using SNPs. Hulse-Kemp et al., (2015) has developed inter- and intra-specific maps in cotton by using
CottonSNP63K, the most saturated map for cotton to-date. The array and maps provide a foundation for the genetic
dissection of agronomically and economically important traits, and crop improvement through genomics-assisted
selection. It will also foster positional cloning and genome assembly efforts. The fast growing contribution of portable
markers in cotton furnishes inexpensive way for gene isolation and linkage mapping for breeding cotton to obtain
desirable objectives.
14 Genotyping by Sequencing, GBS
For next generation sequencing multiplex libraries are prepared by utilizing restriction endonuclease for detecting
a minute section of the genome coupled with DNA barcoded adaptors through genotyping by sequencing (GBS).
This technique has manifested to be fast among the number of species and having ability of evolving enormous
markers (Elshire et al., 2011; Poland et al., 2012a). Ultimate goal of functional genomics is to screen better plant
types in crop improvement by sharing phenotypic information from phenotype to genotype. Genotyping by
sequencing, will evolve first to capture more sequence variants and then to whole-genome resequencing (Poland
and Trever, 2012). GBS technique has been modified right from start including restriction association DNA which
utilizes restriction enzymes for targeted reduction of genome complexity integrated with next generation
sequencing (Baird et al., 2008). The improved form of RAD; utilizes restriction enzymes that cut upstream and
downstream of target site (Wang et al., 2012) which allows marker intensity adjustment by producing same length
tags permitting about all the restriction sites to be analyzed. Genotyping by sequencing having a diverse capability
that can produce numerous SNPs in research and appropriate for gene pool maintenance, diversity analysis,
genomic selection, gene mapping and other plant improvement methodologies (Elshire et al., 2011). GBS
furnishes cost effective way for studying populations, helps in association mapping by which genomic selection
