Integrated omics approaches for flax improvement under abiotic and biotic stress: Current status and future prospects

Abstract

Flax (Linum usitatissimum L.) or linseed is one of the important industrial crops grown all over the world for seed oil and fiber. Besides oil and fiber, flax offers a wide range of nutritional and therapeutic applications as a feed and food source owing to high amount of α-linolenic acid (omega-3 fatty acid), lignans, protein, minerals, and vitamins. Periodic losses caused by unpredictable environmental stresses such as drought, heat, salinity-alkalinity, and diseases pose a threat to meet the rising market demand. Furthermore, these abiotic and biotic stressors have a negative impact on biological diversity and quality of oil/fiber. Therefore, understanding the interaction of genetic and environmental factors in stress tolerance mechanism and identification of underlying genes for economically important traits is critical for flax improvement and sustainability. In recent technological era, numerous omics techniques such as genomics, transcriptomics, metabolomics, proteomics, phenomics, and ionomics have evolved. The advancements in sequencing technologies accelerated development of genomic resources which facilitated finer genetic mapping, quantitative trait loci (QTL) mapping, genome-wide association studies (GWAS), and genomic selection in major cereal and oilseed crops including flax. Extensive studies in the area of genomics and transcriptomics have been conducted post flax genome sequencing. Interestingly, research has been focused more for abiotic stresses tolerance compared to disease resistance in flax through transcriptomics, while the other areas of omics such as metabolomics, proteomics, ionomics, and phenomics are in the initial stages in flax and several key questions remain unanswered. Little has been explored in the integration of omic-scale data to explain complex genetic, physiological and biochemical basis of stress tolerance in flax. In this review, the current status of various omics approaches for elucidation of molecular pathways underlying abiotic and biotic stress tolerance in flax have been presented and the importance of integrated omics technologies in future research and breeding have been emphasized to ensure sustainable yield in challenging environments.

The ÓMICAS alliance, an international research program on multi-omics for crop breeding optimization

“…The application of omics technologies for the improvement of plant traits has enabled significant advances in recent years, as summarized in different reviews; (Großkinsky et al, 2017;Zander et al, 2020;Jamil et al, 2020;Yang et al, 2021) which describe, for the most part, partial integrative approaches, the application of different omics levels to address specific plant models and traits (Rasheed et al, 2013;Singh et al, 2020;Yadav et al, 2022), or the use of modeling and simulation to drive discovery and optimization (Matthews and Marshall-Coloń, 2021;Marshall-Colon, 2022). The creation of global networks, such as the International Plant Phenotyping Network (IPPN), (IPPN, 2022) is also contributing to the visibility, information sharing, and application of omics science and technology in agriculture.…”

Overview and Management of the Most Common Eukaryotic Diseases of Flax (Linum usitatissimum)

“…The causative pathogens, their lifestyle and affected flax organs are detailed in Table 2. There is no general survey or data on flax yield losses due to the different diseases, but the most damaging effects are due to wilts, rust and pasmo [9]. Managing this broad range of diseases can be challenging because each pathogen has its own characteristics, such as its mode of transmission, the affected plant organ and the developmental stage of the plant when infection occurs.…”

Diversity of Linum genetic resources in global genebanks: from agro-morphological characterisation to novel genomic technologies – a review

“…Interestingly, 45 of the identified QTLs spanned 85 resistance gene analogs including a large toll interleukin receptor, nucleotide-binding site, and leucine-rich repeat (TNL) type gene cluster (213). In a similar fashion, GWAS have been deployed in the genetic dissection of other complex traits in linseed including fiber-related traits, fatty acid biosynthesis, mucilage and seed hull content, capsule numbers, branch numbers, and other important agronomic traits (21,214,(226)(227)(228). Detailed information on GWAS in linseed has been presented (Supplementary Table 3).…”

“…Renewed interest has led to an increase in consumer demand for linseed-based products not only for culinary use but also for novel industrial applications, such as geotextiles, biopolymers, and biofuels. However, unpredictable environmental stresses, such as drought, salinity, heat, diseases, and pest pressure, result in huge losses in yield and quality of oil/fiber (20)(21)(22)(23). Hence, in the near future, climate change may exert strong pressure on flax breeding programs to adapt cultivars to changing conditions at an accelerating rate.…”