**7. Genetic markers in cotton**

In cotton, various markers like restriction fragment length polymorphism (RFLP) [84], random amplified polymorphic DNA (RAPD) [85], amplified fragment length polymorphism (AFLP) [86], simple sequence repeats microsatellites (SSRs) [87, 88], sequence-related amplified polymorphism (SRAP) [89, 90], target region amplified polymorphism (TRAP) [91], inter simple sequence repeats (ISSRs) [92], expressed sequence tag-Simple Sequence Repeat (EST-SSRs) [93] and single nucleotide polymorphism (SNP) [94–97] have been used for various genomic studies with each marker system having its advantages and disadvantages. However, SSRs were initially thought that they were sufficiently polymorphic but with the advent of high throughput SNPs, they are being less used. In the era of sequencing, the availability of the cotton reference genome is a boon to cotton researchers as a large number of SNPs are identified using whole-genome re-sequencing and transcriptome sequencing. Further, reduction in cost and advent of reduced representation sequencing methods like Genotype by sequencing (GBS) and Specificlocus amplified fragment sequencing (SLAF) provide scope for high throughput genotyping. To date, in CottonGen, 7,870,031 SSRs and 17,224,361 SNP markers are available for researchers for various studies [98]. There are few SNP arrays developed in cotton like 63k cotton array [99], 80k SNP array [100], and 50k array by Samir Sawanth and I.S. Katageri (unpublished) which are being utilized for linkage and association mapping studies. However, the SNPs associated with various traits identified using different techniques can't be used in a minimalistic laboratory with minimal cost involved, thus it is necessary to exploit trait-associated SNPs through different marker systems like CAPS (Cleaved Amplified Polymorphic Sequences) and dCAPS (derived CAPS) which require minimal laboratory set up. CAPS and dCAPS can be used as dominant marker systems and can be carried out in simple agarose gel electrophoresis. They are highly stable as they are specifically

designed for certain genomic targets [101–103]. However, there are only a few CAPs and dCAPS markers developed in cotton. There are huge prospects for developing simple PCR-based markers in cotton so that the breeders working in a remote research station with minimal laboratory can take advantage of DNA markers in cotton.
