Exploitation of novel drought responsive EST-SSR markers in tetraploid cotton (Gossypium hirsutum L.)

Abstract

Drought is a major environmental challenge that affects the quality and yield of cotton fibres. The aim of the present study was to develop drought-responsive EST-SSRs from cotton transcriptome data. A total of 1946 functionally annotated EST-SSR markers were developed, with tri-nucleotide SSR repeats being the most abundant (40.7 %), followed by di-nucleotides (18.1 %). Gene Ontology (GO) associated with EST-SSR showed the presence of genes related to drought stress, such as PIP, CDK, LEA, etc. A set of 46 EST-SSRs was validated under In-vitro conditions on fourteen cotton genotypes, and 15 EST-SSRs were found to be polymorphic. The polymorphic EST-SSRs markers amplified a total of 44 loci with 32.6 % polymorphism. Genetic analysis revealed that the markers NAU-G-16, NAU-G-39, NAU-G-117 and NAU-G-142 amplified four unique alleles at 121, 163, 224 and 238 bp, respectively, only in drought-tolerant cotton genotypes. The effectiveness of the markers was demonstrated by their high polymorphism information content (PIC), which ranged from 0.35 to 0.89. The large number of markers, 60 %, had a PIC value of >0.6 and were classified as highly informative. The genetic similarity coefficients between cotton genotypes ranged from 0.409 to 0.89, indicating moderate genetic diversity. The Shannon index ranged from 0.21 to 0.65, while the Nei coefficient ranged from 0.12 to 0.46. Clustering and PCo analysis showed the distribution of genotypes into four main clusters, with drought-tolerant genotypes grouped into a single cluster. These drought-responsive markers are promising for the further development of marker-assisted breeding with the aim of increasing the productivity of cotton under drought-prone conditions.