An understanding of the level of genetic diversity is a prerequisite for designing efficient breeding programs. Fifty-one cultivars of four cotton species (Gossypium hirsutum, G. barbadense, G. herbaceum and G. arboreum) representing core collections at four major cotton research stations with a wide range of eco-geographical regions in India were examined for the level of genetic diversity, distinct subpopulations and the level of linkage disequilibrium (LD) using 1100 amplified fragment length polymorphism (AFLP) markers with 16 primer pairs combinations. The AFLP markers enabled a reliable assessment of inter- and intra-specific genetic variability with a heterogeneous genetic structure. Higher genetic diversity was noticed in G. herbaceum, followed by G. arboreum. The genetic diversity in tetraploid cotton species was found to be less than that in the diploid species. The genotypes VAGAD, RAHS14, IPS187, 221 557, Jayhellar of G. herbaceum and 551, DLSA17, 221 566 of G. arboreum were identified as the most diverse parents, useful for quantitative trait loci (QTL) analysis in diploid cotton. Similarly, LRA 5166, AS3 and MCU5 of G. hirsutum and B1, B3, Suvin of G. barbadense were most diverse to develop mapping populations for fibre quality. The internal transcribed spacer sequences were sufficient to resolve different species and subspecies of diploid cotton. Low level of genome-wide LD was detected in the entire collection (r2 = 0.07) as well as within the four species (r2 = 0.11–0.15). A strong agreement was noticed between the clusters constructed on the basis of morphological and genotyping data.

Sucrose is the key economic trait in sugarcane which is a highly polyploid multi-species hybrid and shows a complex pattern of trait inheritance. The excessively large genome of sugarcane is comparatively less explored through Next Generation Sequencing tools for creating superior varieties. In this study, RNAseq libraries of two extreme bulks from a segregating full-sib population and its parents were used to identify 9905 condition-specific non-synonymous genetic variants (NSVs), out of which 43 had a very high degree of differential enrichment (Δf >0.5) for contrasting sucrose accumulating conditions. The statistical model used in this study which was able to quantify the relative effect of NSVs on the trait detected highly significant positive and negative effect NSVs located in the coding regions of genes involved in sucrose metabolism, photosynthesis, mitochondrial electron transport, glycolysis and transcription. In addition, a few differential pre-mature stop codons that could result in production of truncated proteins were also detected in genes coding for aquaporin, GAPDH, aldolase, cytochrome C-oxidase, chlorophyll synthase and plant plasma membrane intrinsic proteins. Additionally, a total of 2140 differentially expressed genes (DEGs) linked to high sucrose accumulation were identified. Among the DEGs, sucrose phosphate synthase III, genes involved in transport, auxin signal transduction, etc., were upregulated, while those involved in electron transfer, cytochrome P450, etc., were downregulated in high sucrose accumulation conditions. This study was able to give finer insights in to the role of allelic heterozygosity on sucrose accumulation and the identified NSVs and DEGs could be useful as candidate markers in marker-assisted breeding for developing high sugar varieties.