Babita Singh from the CSIR National Botanical Research Institute in India presented at London Calling 2023 on “Exploring targeted genetic diversity in the core Indian cotton germplasm using Oxford Nanopore platforms.” Singh spoke about the importance of cotton and that they are “unicellular epidermal trichomes of ovules.” Singh explained that the top cotton-producing countries are India, China, the US, and Pakistan. However, biotic stress sources affecting cotton are insects and pests. Singh noted that they are studying the core Indian germplasm to identify important genes for drought tolerance and quality. One example Singh shared was the design of primer sets for targeted amplicon sequencing. The approach was applied to 249 genotypes with 3-8 amplicons/gene. The research team has also collected phenotypic data from a multi-location field test. This allowed the researchers to correlate genetic variants with cotton fiber and drought-related conditions. I was curious how they prepared their libraries and used the PromethION flow cells for sequencing. In total, Singh shared they generated about 120 Gbases of data. The study combined genotyping and expression studies using a targeted approach.
