Molecular Plant Breeding 2016, Vol.7, No.10, 1-17
8
methodology which utilize F
2
, recombinant inbred lines, back-cross populations, near isogenic lines and doubled
haploids (Jiang et al., 2007b). Centi Morgans (cM) transform recombination fractions into map units during mapping
analysis. The investigation of many segregating markers produces linkage map. Moreover, additional markers
mapping may saturate structure of maps. Marker types that produce multiple loci per primer combination like
AFLPs are desired for increasing marker density. The selection of additional markers tagged to precise chromosomal
regions may be observed by bulked-segregant analysis (Campbell et al., 2001). The researchers at global level has
constructed many linkage maps to map functional traits and markers which consists about 5000 markers in public
database inclusive 3300 restriction fragment length polymorphism (RFLP), 700 amplified length polymorphism (AFLP),
1000microsatellites and 100 single nucleotide polymorphism (Rahman et al., 2012).
Jiang et al. (1998) developed an RFLP map of 261 markers distributed among 26 linkage groups using F
2
plants
from an interspecific cross. Ulloa and Meredith (1998) constructed a map by employing RFLP markers and
identified 26 QTLs for agronomic and fiber quality. QTL mapping by RFLP was observed for chlorophyll contents
(Saranga et al., 2001). 75 BC1 (
G. hirsutum
×
G. barbadense
) plants were examined with 1014 markers (Lacape et
al., 2003) for the construction of map. The map included 888 loci, containing 465 AFLPs, 229 SSRs, 192 RFLPs
and 2 morphological markers, arranged in 37 linkage groups and covering 4400cM. 18 of the 26 long groups had a
single dense region as the loci were not evenly distributed on linkage groups and they assumed a partially modified
list of 13 homologous pairs of chromosomes of tetraploid cotton genome. Rahman et al. (2002) observed molecular
markers connected with nectariless, hairiness and red color spots. Saranga et al., (2001, 2004); Paterson et al.,
(2003); Chee et al., (2005b); Draye et al., (2005) developed linkage map having 432 QTLs (yield and fiber quality,
leaf and flower morphology, trichome density and their distribution etc.) and 3475 loci detected in 11 populations.
Execution of desired molecular assisted selection includes a dilemma, e.g breeding methodology, number of
individuals in a population, target loci desired etc (Bonnet et al.,2005) and also use inbreeding, F
2
enrichment and
backcrossing techniques. To obtain efficient and fast cotton improvement at global level with high seed cotton yield
and better fiber quality; cotton molecular assisted selection methodology has been explored vastly in genomics
(Zhang et al., 2008; Paterson et al., 2012; Wang et al., 2013) and a tremendous achievement has been accomplished.
High saturated map can be developed with the markers which are polymorphic between near isogenic lines and the
donor parent should express markers that are tagged to target gene. Stelly et al., 2005 produced alien chromosome
substitution lines in a near isogenic genetic background of TM-1 by implying hyponeuploid-based backcross. Moreover,
chromosome effects on enhancement in lint yield and fiber quality traits by using CS-B lines have been examined by
scientists (Saha et al., 2006; Jenkins et al., 2006).
Recently Cao et al. (2014) investigated the first practical use of chromosome segment introgression lines (CSILs) for
the transfer of fiber quality QTLs into upland cotton cultivars using SSR markers without severally effecting the
economic traits. Microsatellite sequences mutate frequently by slippage and proofreading errors during DNA
replication that primarily change the number of repeats and thus the length of the repeat string (Eisen, 1999). Recent
advances in next-generation sequencing technologies have provided cost effective platforms for direct detection of
high-quality single nucleotide polymorphisms (SNP) markers for genotyping of mapping populations (Schuster, 2008;
Varshney et al., 2009). Genotyping by sequencing derived genomic selection is a prominent technique for crop
improvement. The value of GBS data and cost effectiveness for improving the breeding techniques via genomic selection
are a lot.
17 Conclusion
Molecular markers have significant value in future cotton genetic-breeding. They offer a relatively simple method
of tracing genetic sources. Specific chromosome regions with important QTLs can be identified and utilized for
efficient selection strategies. Major concerns of decline in cotton productivity is genetic uniformity among cotton
cultivars which do not allow for making significant genetic improvement for yield related traits, effected by biotic
and abiotic stresses. This objective can be achieved by introgression and use of modern molecular technologies in
increasing genetic gain of economic traits. DNA markers are the prominent types of genetic markers for molecular
