BAC derived new SSRs for use in cotton (Gossypium spp) improvement

Structural Genomics

oral

Tabbasam, Nabila; Tabbasam, Nabila; Rahman, Mehboob-ur-; Zafar, Yusuf; Paterson, Andrew H

Tabbasam, Nabila; Tabbasam, Nabila

Tabbasam, Nabila; Tabbasam, Nabila

BAC derived new SSRs for use in cotton (Gossypium spp) improvement Authors: Nabila Tabbassam1*, Yusuf Zafar1, Andrew H Paterson2 and Mehboob-ur-Rahman1 1National Institute for Biotechnology & Genetic Engineering (NIBGE), PO Box 577 Jhang Road Faisalabad Pakistan Affiliation: 2Plant Genome Mapping Laboratory, University of Georgia, USA * Email: nabeela_pgmb@yahoo.com A new set of SSRs with di-, tri-, tetra-, penta- and hexa-nucleotide repeats were fished out from BAC ends and BAC clone sequences of Gossypium raimondii. A total of 1303 SSRs were designed: 766 from BAC end sequences and 537 from BAC clone sequences. These primer pairs were named with the alpha code PR-GR-BESS and PR-GR-BS (PR for the last name of the both principal investigators, GR for Gossypium raimondii, BES for BAC end sequences, B for BAC clone and S for simple sequence repeat).This new set of G. raimondii derived BAC-SSRs were tested for their transferability to other important cotton genomes including cultivated tetraploids (G. hirsutum, G. barbadense, G. raimondii and G. arboreum). In the present study, G. raimondii was used as a control for PCR amplification. BAC-gSSRs contained diverse types of repeat motifs. The large number of repeats were dinucleotide (731, 56.10%), followed by tri (397, 30.46%), tera (118, 9.05%), hexa (40, 3.06%) and penta (17, 1.30%). Hexa nucleotide repeats had the highest level of polymorphism (42.4%) followed by penta (35.29%), tetra (30.50%), tri (23.25%) and di (19.0%). More than 30 % of SSRs amplified two fragments, separated using high resolution agarose metaphor gel electrophoresis. A total of 30% of the total primers were unable to amplify clear fragments in G. arboreum species. These primers produced some private alleles in G. raimondii and AD genome species indicating the specificity of these SSRs for D genome. For genetic diversity assessment PIC values were calculated. Average PIC value was 0.39 with a range of 0.12 to 0.85. G. arboreum was found 0.57 and 0.63, genetically similar with G. hirsutum and G. barbadense, respectively while G. raimondii was more genetically close to G. hirsutum (0.642) and G. barbadense (0.667). This study was found to be instrumental in transferring genetic information for desired traits existing in wild species (G. raimondii) like resistance/tolerance to biotic and abiotic stresses to the cultivated species, which would lead to initiate marker-assisted selection in cotton.