Omics Path to Increasing Productivity in Less-Studied Crops Under Changing Climate—Lentil a Case Study

Abstract

Conventional breeding techniques for crop improvement have reached their full potential, and hence, alternative routes are required to ensure a sustained genetic gain in lentils. Although high-throughput omics technologies have been effectively employed in major crops, less-studied crops such as lentils have primarily relied on conventional breeding. Application of genomics and transcriptomics in lentils has resulted in linkage maps and identification of QTLs and candidate genes related to agronomically relevant traits and biotic and abiotic stress tolerance. Next-generation sequencing (NGS) complemented with high-throughput phenotyping (HTP) technologies is shown to provide new opportunities to identify genomic regions and marker-trait associations to increase lentil breeding efficiency. Recent introduction of image-based phenotyping has facilitated to discern lentil responses undergoing biotic and abiotic stresses. In lentil, proteomics has been performed using conventional methods such as 2-D gel electrophoresis, leading to the identification of seed-specific proteome. Metabolomic studies have led to identifying key metabolites that help differentiate genotypic responses to drought and salinity stresses. Independent analysis of differentially expressed genes from publicly available transcriptomic studies in lentils identified 329 common transcripts between heat and biotic stresses. Similarly, 19 metabolites were common across legumes, while 31 were common in genotypes exposed to drought and salinity stress. These common but differentially expressed genes/proteins/metabolites provide the starting point for developing high-yielding multi-stress-tolerant lentils. Finally, the review summarizes the current findings from omic studies in lentils and provides directions for integrating these findings into a systems approach to increase lentil productivity and enhance resilience to biotic and abiotic stresses under changing climate.

The Prospects of gene introgression from crop wild relatives into cultivated lentil for climate change mitigation

“…The integration of traditional breeding methods with a new era of molecular breeding can tackle the challenges of changing global climate and sustain the crop productivity for future food and nutritional security ( Huang et al., 2022 ; Yaqoob et al., 2023 ). Although, limited efforts have gone into the genomics-assisted breeding of lentil so far ( Tiwari et al., 2022 ; Zeroual et al., 2023 ), an accelerated development of genomic resources during the last decade raises many hopes ( Kumar et al., 2015 ; Kumar et al., 2021 ).…”

“…Transcriptomic studies provide information about functionality and regulation of genes and show how reprogramming at transcriptional level can modulate innate physiological parameters in plants to withstand external stresses. Transcriptomic studies in lentil have resulted in identification of many candidate genes/loci linked to useful agronomic traits ( Kaur et al., 2011 ; Sudheesh et al., 2016 ; Cao et al., 2019 ; García-García et al., 2019 ; Morgil et al., 2019 ; Singh et al., 2019 ; Wang et al., 2020 ; Dadu et al., 2021 ; Kumar et al., 2021 ; Tiwari et al., 2022 ). ESTs-based methods coupled with NGS are widely used for transcriptome studies.…”

“…The biotic stresses in the form of Ascochyta and Stemphylium blights, anthracnose and rust contribute to major losses ranging upto 70% in lentil production across the world ( Singh et al., 2017a ; Cao et al., 2019 ). The transcriptomic studies ( Cao et al., 2019 ; Singh et al., 2019 ; Mishra et al., 2021 ; Tiwari et al., 2022 ) have largely focussed on foliar diseases caused by the two most potent lentil pathogens A. lentils and S. botryosum . The transcriptome profile was studied in two L. ervoides cultivars ‘LR-66-637’ (resistant) and ‘LR-66-577’ (susceptible) to S. botryosum .…”

“…(2019) , studied the transcriptome profiling of ‘ILL7537’ (resistant) and ‘ILL6002’ (susceptible) lentil cultivars infected with A. lenti , after 2, 6 and 24 hours after the infection to reveal upregulation of two genes involved in defense-related functions namely calmodulin domain protein kinase-like ( CDPK ) genes, and LRR-receptor like kinase ( LRR-RLKs ) ( Khorramdelazad et al., 2019 ). Interestingly, some common DEGs expressed during infection with both the above pathogens correlated with genes associated with phytohormones, E3 ubiquitin protein, LRR-RLKs, CDPK indicate the prevalence of a common defence mechanism against both these lentil pathogens ( Tiwari et al., 2022 ).…”

“…Recent advances in large-scale genome analyses, such as next generation sequencing (NGS), high throughput genotyping (HTG) and high throughput phenotyping (HTP) have added to the breadth of genetic diversity, development of genomic resources databases and knowledge on phylogenetics in the genus Lens. This information can be used for precise and efficient molecular genetic improvement and enhancement programs of lentils ( Kumar et al., 2021 ; Pratap et al., 2021 ; Hussain et al., 2022 ; Salaria et al., 2022 ; Salgotra and Stewart, 2022 ; Singh et al., 2022a ; Tiwari et al., 2022 ; Civantos-Go´ mez et al., 2022 ; Roy et al., 2023 ; Zeroual et al., 2023 ) similar to what has been achieved in major crops such as rice, wheat and maize ( Yoshino et al., 2019 ; Mishra et al., 2021 ).…”