**3. Marker assisted selection**

Due to the inverse relationship between seedcotton yield and fiber quality, and the complicated involvement of multiple genes in traits demand breeders to evolve varieties through more useful methods. In the past textile industry flourished principally via selection of new recombinants among germplasm entries with traditional breeding approaches [37, 38]. Elite grown cotton genotypes have narrow genetic base, therefore it has been thought that germplasm should be used for improvement of traits. Some of popular characters such as disease and insect resistance have been enhanced by introgression [39]. The advent of DNA markers paved the way for plant breeders to fasten breeding process through fast, authentic and substitutive techniques instead of the traditional methods for the selection to develop both agronomic and economic characters of plants [40].

Molecular marker is a specific DNA portion with a known position on the chromosome [41], or a gene whose phenotypic expression is frequently easily distinguished and used to detect an individual [42, 43]. DNA markers are having the property of polymorphism which can be used for the differentiation of homozygotes and heterozygotes [44]. Marker assisted selection has a great amount of advantages over conventional breeding, reviewed by many researchers [45–47]. Plant breeders utilize DNA markers for selection of desirable traits on molecular basis in spite of observing them phenotypically [48], furnishing the basis for using the molecular assisted selection [49–51]. Molecular markers are desired for improving traits in many essential crops; rice [52], wheat [53], maize [54, 55] and barley [56, 57]. Cotton is an important cash crop at global level and marker assisted selection has not got desired goals because of compatibility barriers through historic domestication and insufficient polymorphism [58–60].

Molecular characterization is the way to transfer required traits into modern genotypes [45, 61–64]. Quantitative trait loci (QTLs) allow gene pyramiding for yield and fiber quality through evolution of linkage maps. Association mapping using linkage disequilibrium on genome wide level is the most valuable strategy among scientists for searching QTLs in crop sciences. The association among trait of interest and germplasm entries is observed using population construction information and linkage disequilibrium (LD) with association mapping [65]. LD mapping is highly popular thanks to the sophistication of mathematical methods and accessibility of large number of DNA markers.

The traits controlled by multiple genes such as fiber quality can be studied more precisely with linkage maps after the availability of new genomic data of *Gossypium* spp. like *Gossypium raimondii* Ulbrich [66, 67], *Gossypium arboreum* L. [68] and *Gossypium hirsutum* L. [69, 70]. [71] revealed that tetraploid species derived from crossing of two diploid species *Gossypium arboreum* L. (A genome) and *Gossypium raimondii* Ulbrich (D genome) about 1–2 million years ago. Moreover, it may pave the way for fiber improvements as higher number of QTLs assigned to the Dt subgenome compared to At sub-genome in hawian cotton [72–74].

Many researchers have observed QTLs for seedcotton yield and its components [9, 70, 75–79]. But, mostly filial generations were used for QTLs. Quantitative trait loci are highly effected by low heritability and more experimental error which are high in such plant materials, hence it is need of the day that a useful way should be

employed for the development of stable populations for overcoming these obstacles. The accuracy of QTL determination relies upon allelic frequency among QTL of the desired character and related marker [80]. Molecular breeding methods designed with the information obtained through quantitative trait loci analysis in association mapping creates valuable genetic variation from stable populations [81].
