Working group session:
Structural Genomics
Presentation type:
oral
Authors:
Tabbasam, Nabila; Zafar, Yusuf; Paterson, Andrew H; Rahman, Mehboob-ur-
Presenter:
Tabbasam, Nabila
Correspondent:
Tabbasam, Nabila
Abstract:
A molecular mapping F2 population was derived from an interspecific cross of G. hirsutum cv. FH-1000 (high yielding) and G. barbadense germplasm accession PGMB-36 (superior fiber quality). Field data were recorded for 18 productivity traits including yield and yield component for F2, F2:3 and F2:4 generations. A new set of SSRs (1294) designed at PGMB lab, NIBGE, Pakistan, fished out from BAC ends (560) and BAC clone sequences of Gossypium raimondii (734). These sequences were kind provided by Prof. Andrew H. Paterson PGML, UGA, USA. 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). These SSRs contained diverse types of repeat motifs. The large number of repeats were dinucleotide (722, 55.79%), followed by tri (397, 30.46%), tera (118, 9.05%), hexa (40, 3.06%) and penta (17, 1.30%). First these SSRs were used to assess their transferability to other cotton species i.e. G. hirsutum (FH-1000), G. barbadense (PGMB-36), G. raimondii (as control) and G. arboreum and genetic diversity between these species. The 30% of primers could not amplify clear fragments in G. arboreum while produced some private alleles in G. raimondii and AD genome species indicating the specificity of these SSRs for D genome. 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).
The 235 SSRs were found polymorphic between parental species. Out of these 73 were used to assay the entire F2 population consisting of 131 individuals. Linkage analysis resulted in mapping of 61 loci on 9 different linkage groups (LG) ranging from 12.0 to 92.7 cM in length. In this study we tried to assign chromosome number to linkage groups through blast search of sequences from which these SSRs were designed against whole genome shotgun sequence (WGS) of G. raimondii. Only two linkage groups could assign chromosome number while, rest of 7 linkage groups were not assigned chromosome number because markers of these linkage groups showed homology with the sequences of more than one chromosome. The map spanned a total of 322.9cM, covering ~8% of the total G. hirsutum (2.5 Gb) genome, and the average distance between adjacent markers was 5.3 cM. For QTL mapping “Interval mapping” and “Composite interval mapping” were used. Interval mapping analysis yielded 7 QTLs for six traits while composite interval mapping depicted 4 QTLs for 3 traits. Significant QTLs detected in this study can be employed in MAS for molecular breeding programs aiming at developing cotton cultivars with superior fiber quality.