Cotton Genomic DNA Isolation and SSR Genotyping

The genomic DNA from cotton plant leaf tissues was isolated using the cetyltrimethylammonium bromide (CTAB) method [51 (link)]. The DNA concentration was calculated by measuring the absorbance of 1 µL of the samples at 260/280 nm using the NanoDrop Eight spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). DNA samples were diluted to a working concentration of 25 ng/µL. A total of 72 SSR (simple sequence repeat) markers were selected from CottonGen the cotton marker database (https://www.cottongen.org/data/markers) (accessed on 20 February 2022) [52 (link)]. PCR-based SSR genotyping was conducted as described previously [6 (link),53 (link),54 (link)]. The construction and visualization of the phylogenetic tree was performed using NCSS 12.

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Khidirov M.T., Ernazarova D.K., Rafieva F.U., Ernazarova Z.A., Toshpulatov A.K., Umarov R.F., Kholova M.D., Oripova B.B., Kudratova M.K., Gapparov B.M., Khidirova M.M., Komilov D.J., Turaev O.S., Udall J.A., Yu J.Z, & Kushanov F.N. (2023). Genomic and Cytogenetic Analysis of Synthetic Polyploids between Diploid and Tetraploid Cotton (Gossypium) Species. Plants, 12(24), 4184.

Publication 2023

NanoDrop Eight

Corresponding Organization : Agricultural Research Service

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Variable analysis

independent variables

DNA isolation method (CTAB)
Selection of SSR markers from CottonGen database

dependent variables

DNA concentration measured by NanoDrop spectrophotometer
SSR genotyping using PCR-based approach

control variables

Working concentration of DNA samples (25 ng/µL)

controls

No positive or negative controls were explicitly mentioned in the provided information.

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