**8. Molecular mapping and quantitative trait mapping**

The Quantitative Trait Loci identification helps in finding the association between a marker and measurable phenotype at the genomic level or understanding the genetics of traits under study. Various types of populations like F2 [104], Recombinant inbred lines (RILs) [105], Backcross inbred lines (BILs) [106] and Multi-parent Advanced Generation Inter Cross (MAGIC) [107] are commonly used in cotton. Bi-parental RIL Mapping is one of the most common methodologies successfully employed for identifying QTLs in cotton for various traits. Genome-wide association study is also used for developing genetic maps and developing an association between the trait and DNA markers in cotton germplasm. This technique allows detecting association among various markers and traits through assessing Linkage disequilibrium (LD-mapping). In cotton the construction of linkage maps and detection of QTLs for various economic traits has been in progress since 1994 with the first RFLP linkage map [84] being published after which many maps have been constructed [94, 96, 97, 105, 108]. Many genome-wide association studies have also been carried out [95, 107, 109]. Currently, there are around 249 QTL mapping and association studies using various populations and germplasm (**Table 4**), QTLs identified using Bi-parental mapping/GWAS are presented in **Table 5**. However, QTLs discovered for various studies indicate that Chromosomes 5, 7, 10 and 25 are harboring many QTLs for fiber length, similarly Chromosomes 7 and 21, for fiber strength. For yield (Seed cotton yield/Lint yield) Chromosomes 1, 13 and 26 seem to be very important. For


#### **Table 4.**

*Number of Documented Quantitative Mapping studies in cotton.*


#### **Table 5.**

*Number of QTLs identified for major quality and yield traits in cotton.*

**Figure 6.** *QTLs identified for fiber length, strength, boll weight and yield in cotton.*

boll weight, Chromosomes 7 and 13 harbor many QTLs as reported from various studies. For Boll number, Chromosome 25 and for Lint percentage Chromosomes 16 and 13 are over represented (**Figure 6**). Efforts have been made to develop linkage maps in wild species like *G. hirsutum* X *G. anomalum* [110], *G. trilobum* X *G. raimondii* [111], *G. nelsonii* x *G. austral* [112], *G. hirsutum* X *G. darwinii* [113], *G. hirsutum* X *G. mustelinum* [114], *G. darwinii* X *G. darwinii* [115], *G. klotzschianum* X *G. davidsonii* [116], *G. hirsutum* x *G. tomentosum* [117–119] and *G. thurberi* x *G. trilobum* [104]. QTLs after validation can be used directly for marker-assisted selection. Transfer of QTL/pyramiding of QTLs is one way of realizing targeted trait introgression [120] or these QTLS can be utilized for fine mapping and map-based cloning before markerassisted selection. However, only a few validation studies are done for the Virescent gene in Virescent mutants [121, 122], the fuzzless gene in the fuzzless mutant [123], traits like fiber length [124], Fiber strength [125], leaf shape [126] and QTL affecting root-knot nematode multiplication [127] etc. Though fine-mapping is done it would require still more concentrated efforts to dissect out the traits. There are no successful cotton cultivars deployed in the field that are developed using the identified QTLs unlike in crops like Rice (MAS 946-1, Swarna Sub-1 and Cadet) and Wheat (Patwin, Expresso and AGS2026). Now that the marker development and QTL mapping has been done to a greater depth in cotton, at least for major traits like fiber quality and yield, the focus around the world should now be on utilizing all the major QTLs identified in fine mapping and then in marker assisted selection.
