Application of Genomics to Understand Salt Tolerance in Lentil

Abstract

Soil salinity is a major abiotic stress, limiting lentil productivity worldwide. Understanding the genetic basis of salt tolerance is vital to develop tolerant varieties. A diversity panel consisting of 276 lentil accessions was screened in a previous study through traditional and image-based approaches to quantify growth under salt stress. Genotyping was performed using two contrasting methods, targeted (tGBS) and transcriptome (GBS-t) genotyping-by-sequencing, to evaluate the most appropriate methodology. tGBS revealed the highest number of single-base variants (SNPs) (c. 56,349), and markers were more evenly distributed across the genome compared to GBS-t. A genome-wide association study (GWAS) was conducted using a mixed linear model. Significant marker-trait associations were observed on Chromosome 2 as well as Chromosome 4, and a range of candidate genes was identified from the reference genome, the most plausible being potassium transporters, which are known to be involved in salt tolerance in related species. Detailed mineral composition performed on salt-treated and control plant tissues revealed the salt tolerance mechanism in lentil, in which tolerant accessions do not transport Na+ ions around the plant instead localize within the root tissues. The pedigree analysis identified two parental accessions that could have been the key sources of tolerance in this dataset.

Targeted improvement of plant‐based protein: Genome‐wide association mapping of a lentil (Lens culinaris Medik.) diversity panel

“…Genome‐wide association studies (GWAS) have been extensively used in plant science to identify genetic markers and candidate genes associated with a range of traits (Tibbs Cortes et al, 2021). In lentil, GWAS has been used to identify markers associated with days to flower, seeds per pod, 100 seed weight, salinity tolerance, Aphanomyces root rot resistance, iron (Fe) and zinc (Zn) concentrations, prebiotic carbohydrate concentrations, and AA concentrations quantified by near‐infrared spectroscopy (Dissanayake et al, 2021; Hang, 2021; Hang et al, 2022; Johnson et al, 2021; Kumar et al, 2019; Ma et al, 2020; Rajendran et al, 2021). Protein‐quality traits have also been explored via GWAS in cereal crops (Chen et al, 2016) and legumes such as chickpea (Karaca et al, 2019) and common bean (Katuuramu et al, 2018).…”

Searching for Abiotic Tolerant and Biotic Stress Resistant Wild Lentils for Introgression Breeding Through Predictive Characterization

“…Wild relatives of lentil possess valuable genes conferring resistance and tolerance to biotic and abiotic stresses ( Gupta et al, 2011 ) and recent studies have reported promising results in the use of lentil wild relatives for breeding purposes (i.e., lentil rust, powdery mildew, or fusarium wilt resistance and drought and cold tolerance) ( Mohar et al, 2020 ; Asghar et al, 2021 ). Other works point to the identification of novel genes or alleles involved in overcoming salinity tolerance and incorporating them into commercial lentils, as the path to increase productivity ( Dissanayake et al, 2021 ), so the exploitation of genetic resources of lentil wild relatives gains special interest. The crossability among the different species of lentils has been widely studied, placing Lens culinaris ssp.…”

Conventional and new-breeding technologies for improving disease resistance in lentil (Lens culinaris Medik)

“…Genomewide association study (GWAS) was first demonstrated in lentil to reveal marker-trait association for Aphanomyces root rot resistance (Ma et al, 2020). Later, GWAS was used for identification of marker for improtant agronomic traits (Rajendran et al, 2021), prebiotic carbohydrates (Johnson et al, 2021) and salt tolerance (Dissanayake et al, 2021).…”

“…Ma et al (2020) used GBS strategy to genotype a RIL population and identified 19 QTLs for Aphanomyces root rot resistance in lentil. In parallel, genome wide association studies (GWAS) were also practiced in lentil for identification of marker-trait association for Aphanomyces root rot resistance (Ma et al, 2020), agronomic traits (Rajendran et al, 2021), prebiotic carbohydrates (Johnson et al, 2021) and salt tolerance (Dissanayake et al, 2021). All these above examples of detecting QTLs/associated SNPs for a targeted trait in lentil have shown promise to apply genomic selection to select genotypes with multiple disease resistance.…”