Gene duplication is an important mechanism for acquiring new genes and creating genetic novelty in organisms. Many new gene functions have evolved through gene duplication and it has contributed tremendously to the evolution of developmental programmes in various organisms. Gene duplication can result from unequal crossing over, retroposition or chromosomal (or genome) duplication. Understanding the mechanisms that generate duplicate gene copies and the subsequent dynamics among gene duplicates is vital because these investigations shed light on localized and genomewide aspects of evolutionary forces shaping intra-specific and inter-specific genome contents, evolutionary relationships, and interactions. Based on whole-genome analysis of Arabidopsis thaliana, there is compelling evidence that angiosperms underwent two whole-genome duplication events early during their evolutionary history. Recent studies have shown that these events were crucial for creation of many important developmental and regulatory genes found in extant angiosperm genomes. Recent studies also provide strong indications that even yeast (Saccharomyces cerevisiae), with its compact genome, is in fact an ancient tetraploid. Gene duplication can provide new genetic material for mutation, drift and selection to act upon, the result of which is specialized or new gene functions. Without gene duplication the plasticity of a genome or species in adapting to changing environments would be severely limited. Whether a duplicate is retained depends upon its function, its mode of duplication, (i.e. whether it was duplicated during a whole-genome duplication event), the species in which it occurs, and its expression rate. The exaptation of preexisting secondary functions is an important feature in gene evolution, just as it is in morphological evolution.

Use of morphological differences, between true hybrids and off types in grow out test (GOT) for genetic purity analysis, are not always apparent and cannot be recognised easily. Further, morphological traits are costly, tedious to score and environment sensitive. Alternatively, it is suggested that recent breakthrough in molecular markers can be employed in genetic purity analysis. The genetic purity of three cotton hybrids (TCHB 4510, TCHB 2310 and TCHB 213) that are widely cultivated in Tamil Nadu, India were assessed by GOT and molecular markers. A total of 400 individuals from each one of the three hybrids were raised in the field and morphological traits were recorded. Results of this GOT have shown that TCHB 2310 had lowest genetic purity (62.5%) followed by TCHB 4510 (78.2%) and TCHB 213 (95.2%). Simple sequence repeats (SSR) marker analysis of parents that were involved in the production of all the three hybrids have shown that 45 out of 150 SSRs were polymorphic among the parents. From this set of polymorphic SSRs, BNL686, BNL1679, BNL3971, BNL3955, CIR407 and CIR413 were selected to test the genetic purity of hybrid seeds since they have produced clear, scorable and unambiguous polymorphic bands among the parents. All the three hybrids were clearly distinguished from their selfed females and off types using these six SSRs. Hence, it is proposed that these SSR markers can be used in efficient analysis of hybrid seed purity since this technique is simple to use, more accurate and not affected by environment when compared with GOT.

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The dawdling development in genetic improvement of cotton with conventional breeding program is chiefly due to lack of complete knowledge on and precise manipulation of fiber productivity and quality. Naturally available cotton continues to be a resource for the upcoming breeding program, and contemporary technologies to exploit the available natural variation are outlined in this paper for further improvement of fiber. Particularly emphasis is given to application, obstacles, and perspectives of marker-assisted breeding since it appears to be more promising in manipulating novel genes that are available in the cotton germplasm. Deployment of system quantitative genetics in marker-assisted breeding program would be essential to realize its role in cotton. At the same time, role of genetic engineering and in vitro mutagenesis cannot be ruled out in genetic improvement of cotton.

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