Linking genome wide RNA sequencing with physio-biochemical and cytological responses to catalogue key genes and metabolic pathways for alkalinity stress tolerance in lentil (Lens culinaris Medikus)

Abstract

Background Alkaline soils cause low productivity in crop plants including lentil. Alkalinity adaptation strategies in lentil were revealed when morpho-anatomical and physio-biochemical observations were correlated with transcriptomics analysis in tolerant (PDL-1) and sensitive (L-4076) cultivars at seedling stage. Results PDL-1 had lesser salt injury and performed better as compared to L-4076. Latter showed severe wilting symptoms and higher accumulation of Na+ and lower K+ in roots and shoots. PDL-1 performed better under high alkalinity stress which can be attributed to its higher mitotic index, more accumulation of K+ in roots and shoots and less aberrantly dividing cells. Also, antioxidant enzyme activities, osmolytes’ accumulation, relative water content, membrane stability index and abscisic acid were higher in this cultivar. Differentially expressed genes (DEGs) related to these parameters were upregulated in tolerant genotypes compared to the sensitive one. Significantly up-regulated DEGs were found to be involved in abscisic acid (ABA) signalling and secondary metabolites synthesis. ABA responsive genes viz. dehydrin 1, 9-cis-epoxycarotenoid dioxygenase, ABA-responsive protein 18 and BEL1-like homeodomain protein 1 had log2fold change above 4.0. A total of 12,836 simple sequence repeats and 4,438 single nucleotide polymorphisms were identified which can be utilized in molecular studies. Conclusions Phyto-hormones biosynthesis—predominantly through ABA signalling, and secondary metabolism are the most potent pathways for alkalinity stress tolerance in lentil. Cultivar PDL-1 exhibited high tolerance towards alkalinity stress and can be used in breeding programmes for improving lentil production under alkalinity stress conditions.

Genome sequencing provides potential strategies for drug discovery and synthesis

“…Research on genome sequencing in medicinal plants has made considerable advancements, yielding crucial insights into the genomic characteristics, secondary metabolic pathways, and regulatory mechanisms [78][79][80] . Through the analysis of whole-genome expression characteristics, a very important intermediate in plants such as C. acuminata and C. roseus, known as strictosidine, was discovered.…”

Underlying Mechanisms of Action to Improve Plant Growth and Fruit Quality in Crops under Alkaline Stress

“…Initially, they promote an osmoregulatory system to reduce cellular Ψ [9] and maintain a high K + /Na + ratio [14]. Likewise, it promotes the activity of enzymatic and non-enzymatic antioxidant systems to combat oxidative stress [15,16] as well as the expression of hormones and a diversity of metabolites [17] derived from transcriptional modifications [18][19][20][21]. Alternatives in the management of crops developed in these environments include grafting [22], application of Ca 2+ -based fertilizers (to replace Na + ions) [23], micronutrients [24], nanotechnology [25], biochar [26], microorganisms [27], growth regulators [28], and genetic engineering [29,30].…”

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

“…To understand the adaptation strategies to alkalinity stress tolerance in lentil, the morphological, anatomical, biochemical and transcriptomics features were compared between a tolerant and sensitive cultivar to show that the secondary metabolism and ABA signaling contributed towards alkalinity stress tolerance in lentil ( Singh et al., 2022a ). The lentil variety PDL-1 shows significant alkalinity tolerance and has the potential to be used in genetic improvement programs of lentil ( Singh et al., 2022a ). Efforts have also been done to identify the genes for cold tolerance ( Hamdi et al., 1996 ) and salinity tolerance ( Singh et al., 2017b ) in L. culinaris ssp.…”

“…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 ).…”