London Calling 2023: Exploring targeted genetic diversity in the core Indian cotton germplasm using Oxford Nanopore platforms

Global climate changes pose enormous challenges for plant breeders to maintain and further enhance yield in varying environments. Cotton is one of the most economically important crops in the world. Among the four cultivated cotton species (Gossypium hirsutum, G. arboreum, G. herbaceum, and G. barbadense), G. hirsutum contributes 90% of global production. Despite the larger area under cotton cultivation in India,  productivity still needs significant improvement compared to other cotton-growing countries. In India, cotton is cultivated in three distinct agro-climatic zones: the North, Central, and South. These zones have several significant constraints and stress conditions like poor soil health, biotic (insects, pests, etc.), and abiotic stresses (drought, salinity, etc.). During the reproductive growth stage, yield reduction and fiber quality compromises are inescapable when biotic and abiotic stress conditions override the plant’s protective mechanisms.

Next-generation sequencing and functional genomics studies on economically essential plants assume greater importance due to their ability to unravel the complexities of key traits of interest and harness such traits for crop breeding and improvement. Our group has identified a few critical genes that may play a vital role in cotton fiber development and drought tolerance in G. hirsutum. We are exploring genetic variations of these potential genes through targeted sequencing of 320 core sets of G. hirsutum using Oxford Nanopore technology. Thus, we sequenced entire genomic loci of 24 targeted genes using ~1.5 kb overlapping amplicon. Therefore, 104 amplicons encompassing 24 genes were sequenced in 320 genotypes to generate 120 Gb of raw data, which was an average of 700x coverage of raw data for each gene. Our data analysis identifies high-confidence SNP variations in the targeted genes. We have also  performed a multi-location trial of 320 core germplasm of G. hirsutum at three locations and collected high-quality phenotypic data related to agronomically important traits in cotton. Thus, associations of SNPs in targeted genes and phenotypic data are expected to provide insights into the genetic basis of fiber yield-related traits and stress tolerance in cotton, which will also help us develop SNP markers for molecular-assisted breeding of high-yield and stress-resistance varieties under climate changes.