Molecular Plant Breeding 2016, Vol.7, No.10, 1-17
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can be carried on large scale (Poland and Trevor, 2012). This methodology has been used in number of species of
cotton (
Gossypium hirsutum
L.), sorghum (Sorghum bicolor), following basic protocol (Poland et al., 2012) with
minor changes. Gore et al., (2014) developed genetic map in cotton having 841 SSR and SNP loci contributing to
half of the tetraploid cotton genome through execution of GBS together with fluorescent-based SSR genotyping.
GBS application is highly interweaved in cultivated cottons due complicated allotetraploid genetic constitution
and having repetitive DNA (Li et al., 2014).
15 Genome Wide Association (GWAS)
Exploration of genetic diversity available in germplasm, genetic map construction and QTL mapping for
economic and agronomic traits has been conducted by utilizing segregating populations through DNA marker
techniques (Chen et al., 2007; Zhang et al., 2008) which are essential for fastening marker assisted selection. It is
challenging for bi-parental population to detect closely linked markers for molecular breeding due to confined
crossing over. Moreover, the density of polymorphism in bi-parental population is restricted as some minor QTLs
are not detected.
There is a substitute methodology for QTL mapping that is called “association mapping” which relies on linkage
disequilibrium and utilizes cultivars having distinctive traits (Zhao et al., 2014). Association mapping relies on the
association of alleles among marker locus and phenotypic locus. This technique can be induced by mutation,
genetic drift, population selection etc and particularly in plants that the extent of inbreeding caused by
hybridization (Hart and Clark, 1997). Hereditary basis of the characters permitting exclusive selection of parents
and allowing successors for mutagenesis and transgenics through genome wide association (GWAS). This
technique elicits many obstacles of traditional genetic mapping due to furnishing increased resolution generally to
the locus and utilizing highly examined populations having genetic variation associated with phenotypic variation.
This technique relies upon linkage disequilibrium among the loci. It is compulsory in LD mapping to characterize
LD magnitude and pattern in population under observation for acquisition of desired objectives. Magnitude of
relation, extent of parental recombination and linkage disequilibrium in gene pool permits the selection of most appropriate
collection for association mapping (Lu et al., 2011).
Seed cotton yield, yield components and fiber quality traits in cotton has been studied by utilizing association
mapping by many scientists all over the world (Abdurakhmonov et al. 2008 and 2009). Association mapping has
enabled the scientists to study the variation found in the germplasm resources. With the discovery of single
nucleotide polymorphism, it is now possible to study the whole genome wide association with desired quantitative
trait loci for developing highly saturated mapping populations in plants (Waqas et al., 2014).
16 Linkage Maps
The chromosomes obtained from two different parents may be elucidated by using linkage maps (Paterson, 1996a).
The location and relative genetic distances in either side of markers across chromosomes, which is parallel to
signs along a roadway is manifested by linkage maps (Collard, et al., 2005). Genetic linkage maps are helpful in
introgression, examining genome structure and MAS in plant improvement studies owing to close association
with important agronomic characters (Bolek, 2003). Genetic information of a crop genome is usually presented in
framework of a genetic linkage map. Such maps are useful to locate or tag genes of interest, to facilitate MAS,
and to enable map-based cloning. Use of MAS to improve the resistance has become a choice for many breeding
programs.
The regions in genomes having genes linked with a quantitative trait are called quantitative trait loci, QTLs
(Collard et al., 2005) and QTL mapping is used for developing linkage maps and conducting QTL analysis (Paterson,
1996a). QTLmapping is accomplished by crossing over principal that allow the analysis of genes and markers in the
progeny (Paterson et al. 1998). These characters are often of oligogenic inheritance in nature. Although, for some
quality traits, few major QTLs or genes can account for a very high proportion of the phenotypic variation of the
trait (Pham et al., 2012). Many required traits are examined at the same time by manipulating marker
