Recent insights into cotton functional genomics: progress and future perspectives

Abstract

Functional genomics has transformed from futuristic concept to well-established scientific discipline during the last decade. Cotton functional genomics promise to enhance the understanding of fundamental plant biology to systematically exploit genetic resources for the improvement of cotton fibre quality and yield, as well as utilization of genetic information for germplasm improvement. However, determining the cotton gene functions is a much more challenging task, which has not progressed at a rapid pace. This article presents a comprehensive overview of the recent tools and resources available with the major advances in cotton functional genomics to develop elite cotton genotypes. This effort ultimately helps to filter a subset of genes that can be used to assemble a final list of candidate genes that could be employed in future novel cotton breeding programme. We argue that next stage of cotton functional genomics requires the draft genomes refinement, re-sequencing broad diversity panels with the development of high-throughput functional genomics tools and integrating multidisciplinary approaches in upcoming cotton improvement programmes.

Keywords: CRISPR/Cas9; biotic and abiotic stresses; cotton databases; cotton improvement; gene discovery tools; genome sequencing.

Figure 1

A scheme of the sequential research processes from whole‐genome sequencing to practical functional genomics in cotton. This figure shows the integrative approach of comprehensive information flows from the whole‐genome sequencing to practical functional genomics in cotton. It systematically represents the typical data evaluation path with bioinformatics tools in genomics, transcriptomics and epigenomics technologies to analyse the genomic mutations, differential gene expression and regulation of epigenetic signalling tools. It also incorporates protein expression data into appropriate genes and functional networks which ultimately facilitate the identification and cloning of functional genes. SNPs (single nucleotide polymorphisms), Indels (insertion/deletion) and CNVs (copy number variations)

Figure 2

Chromosome size distribution (y‐axis) and number of annotated genes (above each bar) of different Gossypium species. Differences in chromosome size and number of annotated genes (above each bar) by two independent studies between the sequenced genomes of (a) G. raimondii (Paterson et al., (blue); Wang et al., (red)); (b) At‐subgenome of G. hirsutum (Li et al., (blue); Zhang et al., (red)), and (c) Dt‐subgenome of G. hirsutum (Li et al., (blue); Zhang et al., (red)). These differences might be due to errors in their assemblies, which in turn also affects the various genome analyses among different cotton species. Currently, we need to devote more efforts in capturing, evaluating and fixing their misassemblies by developing quality control standards.

Figure 3

A venn diagram of the differentially expressed genes during fibre development, tissue and organ development, abiotic stress resistance and ovule development. The functional distribution of annotated genes from G. hirsutum (Zhang et al., 2015b) highlights that 52 854 differentially expressed genes were commonly identified during fibre, organ, tissue and ovule development and resistance against abiotic stress. However, more genes were differentially expressed during stress resistance than during fibre and organ development.