Advances in genome sequencing and artificially induced mutation provides new avenues for cotton breeding

Abstract

Cotton production faces challenges in fluctuating environmental conditions due to limited genetic variation in cultivated cotton species. To enhance the genetic diversity crucial for this primary fiber crop, it is essential to augment current germplasm resources. High-throughput sequencing has significantly impacted cotton functional genomics, enabling the creation of diverse mutant libraries and the identification of mutant functional genes and new germplasm resources. Artificial mutation, established through physical or chemical methods, stands as a highly efficient strategy to enrich cotton germplasm resources, yielding stable and high-quality raw materials. In this paper, we discuss the good foundation laid by high-throughput sequencing of cotton genome for mutant identification and functional genome, and focus on the construction methods of mutant libraries and diverse sequencing strategies based on mutants. In addition, the important functional genes identified by the cotton mutant library have greatly enriched the germplasm resources and promoted the development of functional genomes. Finally, an innovative strategy for constructing a cotton CRISPR mutant library was proposed, and the possibility of high-throughput screening of cotton mutants based on a UAV phenotyping platform was discussed. The aim of this review was to expand cotton germplasm resources, mine functional genes, and develop adaptable materials in a variety of complex environments.

Keywords: cotton; diversity; germplasm resources; mutant library; sequencing.

Figure 1

Flowchart illustrating the process of establishing EMS-induced mutant libraries in cotton. The process starts with seed selection (Step 1), followed by the application of a suitable mutagenic treatment, such as EMS, X-ray, or γ-ray (Step 2). Mutated seed screening eliminates damaged and inviable seeds (Step 3), and germinated seeds are transplanted into small pots (Step 4). The selected seedlings are then transplanted to the field for phenotype observation (Step 5), while seeds from plants exhibiting desired traits are harvested (Step 6), forming the mutant population. This mutant population serves as the foundation for mutant sequencing and subsequent gene mapping (Steps 7 and 8, respectively), facilitating comprehensive genetic analysis and gene discovery.

Figure 2

Schematic diagram of different mutant sequencing methods. This figure outlines the steps involved in mutant sequencing methods, from constructing mutant populations to selecting materials and employing various techniques, including Whole Genome Sequencing (WGS), Bulk Segregant Analysis (BSA), Graded Pool-Seq, M2-Seq, Mutant Bulk Segregation (MBS), MMAPPR, MutMap, MutMap+, Mutmap-gap, QTG-Map, QTL-Seq, and Exome Sequencing. Each method serves distinct research purposes, from comprehensive genomic analysis (WGS) to the identification of mutations linked to specific traits (BSA), graded phenotyping (Graded Pool-Seq), or tracking M2 mutations (M2-Seq). These methods offer flexibility in characterizing mutant populations and uncovering genetic variations.

Figure 3

Adaptability of Mutant Plants in Diverse and Challenging Environments This figure highlights the adaptability of mutant plants in diverse and challenging environmental conditions, shedding light on their practical applications to complex scenarios. Mutant materials have proven invaluable in research and applications related to various environmental stressors, including drought, alkaline soil conditions, extreme temperature fluctuations (both high and low), flooding events, nutrient deficiencies, and light pollution. Additionally, these mutants have demonstrated resilience in coping with iron-related challenges. Mutant plants are crucial tools for exploring and enhancing crop adaptability to multiple environmental stresses.

Figure 4

Comparison of CRISPR and Mutagenesis Libraries. In this figure, a concise comparison is presented between CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and other mutagenesis libraries, outlining key differences implementation and utilization, offering insights into the distinct approaches employed in genetic research and manipulation.

Figure 5

Harnessing Mutation Breeding for Enhanced Stress Tolerance in Cotton Varieties. Mutation breeding offers a promising strategy for the development of cotton varieties resilient to abiotic stress while maintaining high yield potential. To achieve this, a diverse collection of cotton germplasm encompassing wild type, landrace, and cultivar varieties from different global regions is selected at the genus level. Mutations are induced in this germplasm pool through either space-based or x-ray-based mutagenic sources. Subsequently, unmanned aerial vehicle-based (UAV) phenotyping techniques are employed to screen the mutants for specific desired traits. Plants exhibiting the desired phenotypes undergo comprehensive whole-genome sequencing using both long-read and short-read technologies. Notably, emerging super pangenome strategies (Shang et al., 2022) can be employed for read mapping, enabling comprehensive analysis instead of relying on a single linear reference genome. This innovative approach facilitates the identification of novel insertions, deletions, inversions, and single nucleotide polymorphisms (SNPs) associated with stress tolerance, particularly in the context of drought stress induced by climate change.