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IDENTIFYING GENETIC VARIATION IN GOSSYPIUM BASED ONSINGLE NUCLEOTIDE POLYMORPHISM

SAGHIR AHMAD¹, TIANZHEN ZHANG³, NOOR-UL-ISLAM⁴, TAYYABA SHAHEEN⁵ AND MEHBOOB-UR-RAHMAN⁵

Abstract: Various molecular markers such as RAPD, RFLP, AFLP, SSR and EST-SSR are being employed to detect genetic diversity and for marker-assisted selection (MAS) in cotton. But little information is available regarding the use of Single Nucleotide Polymorphisms (SNPs) in this crop. In the present study, polymorphism in the FIF1 gene, important in regulating cotton fiber development in Gossypium barbadense L., was studied among G. hirsutum cv. TM-1 and G. barbadense cv. Hai7124.  FIF1 genes from G. hirsutum cv. TM-1 and G. barbadense cv. Hai7124 were cloned on the basis of its reported sequence in G. arboreum L.  Three bases substitutions were detected at the 188-, 283-, 413-bp position of the FIF1 sequence of G. barbadense while G. hirsutum has the same sequence as in G. arboreum. The first base change (188 T-C) is located in the non-coding region, and the second (283 A-T) and the third (413 C-T) in the coding region, in which AGG (Arg) is changed to a TGG (Trp) in 283-SNP, and CCA (Pro) to a CTA (Leu) in 413-SNP. Thus it could be concluded that SNP molecular marker can be used to identify minute difference (which may or may not morphologically express) in germplasm of cotton.

¹Cotton Botanist, Cotton Research Station, Vehari, Pakistan,
¹Department of Botany, University of Agriculture, Faisalabad, Pakistan,
³Director, Cotton Institute, Vice-Dean Agriculture College, Nanjing Agriculture University China,

⁴Director, Cotton Institute, Faisalabad, Pakistan and

⁵Senior Scientific Officer, NIBGE, Faisalabd, Pakistan