Abstract
Harvesting high quality lint, a long-awaited breeding goal—accomplished partly, can be achieved by identifying DNA markers which could be used for diagnosing cotton plants containing the desired traits. In the present studies, a total of 185 cotton genotypes exhibiting diversity for lint traits were selected from a set of 546 genotypes evaluated for fiber traits in 2009. These genotypes were extensively studied for three consecutive years (2011–2013) at three different locations. Significant genetic variations were found for average boll weight, ginning out turn (GOT), micronaire value, staple length, fiber bundle strength, and uniformity index. IR-NIBGE-3701 showed maximum GOT (43.63%). Clustering of genotypes using Ward's method was found more informative than that of the clusters generated by principal component analysis. A total of 382 SSRs were surveyed on 10 Gossypium hirsutum genotypes exhibiting contrasting fiber traits. Out of these, 95 polymorphic SSR primer pairs were then surveyed on 185 genotypes. The gene diversity averaged 0.191 and the polymorphic information content (PIC) averaged 0.175. Unweighted pair group method with arithmetic mean (UPGMA), principal coordinate analysis (PCoA), and STRUCTURE software grouped these genotypes into four major clusters each. Genetic distance within the clusters ranged from 0.0587 to 0.1030. A total of 47 (25.41%) genotypes exhibited shared ancestry. In total 6.8% (r2 ≥ 0.05) and 4.4% (r2 ≥ 0.1) of the marker pairs showed significant linkage disequilibrium (LD). A number of marker-trait associations (in total 75) including 13 for average boll weight, 18 for GOT percentage, eight for micronaire value, 18 for staple length, three for fiber bundle strength, and 15 for uniformity index were calculated. Out of these, MGHES-51 was associated with all the traits. Most of the marker-trait associations were novel while few validated the associations reported in the previous studies. High frequency of favorable alleles in cultivated varieties is possibly due to fixation of desirable alleles by domestication. These favorable alleles can be used in marker assisted breeding or for gene cloning using next generation sequencing tools. The present studies would set a stage for harvesting high quality lint without compromising the yield potential—ascertaining natural fiber security.
Highlights
Cotton, a leading natural textile fiber crop, is comprised of 52 species (Li et al, 2014)
The present study was conducted in Plant Genomic & Molecular Breeding Lab (PGMB), Agricultural Biotechnology Division (ABD), National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad affiliated with Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore Islamabad
In the current competitive scenario, it has been realized that conscious efforts should be made to improve the lint quality as well as ginning out turn (GOT) percentage without compromising the yield
Summary
A leading natural textile fiber crop, is comprised of 52 species (Li et al, 2014). High quantity and quality lint production remained the major goal of almost all breeding research institutes—resulted in marginal success. Marker-Trait Associations for Lint Traits in improvement of fiber traits is the complex genetics as well as negative correlations occur among quality traits (Zhang and Percy, 2007; Rahman et al, 2014). New statistical methodologies coupled with a parallel evolution in computational tools paved the way for studying the genetic variability among the cotton genotypes in multiple locations. Multivariate analysis has been deployed to assess the genetic variability among cotton genotypes (Guan et al, 2012; Zhu et al, 2013)
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