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.
Highlights
Soil salinity is identified as the second most significant abiotic stress after drought and in lentil (Lens culinaris Medik.), salt toxicity typically causes between 20% and 100%reduction in plant growth and seed yield [1,2]
The de novo approach was selected as the best pipeline for identifying genome-wide SNP markers for genome-wide association study (GWAS) analysis
Both marker systems pinpointed the major genomic region for salt tolerance on Chromosome 2, while tGBS identified an additional association on Chromosome 4, which was not detected by GBS-t approach
Summary
Soil salinity is identified as the second most significant abiotic stress after drought and in lentil (Lens culinaris Medik.), salt toxicity typically causes between 20% and 100%reduction in plant growth and seed yield [1,2]. Cl- ion-specific toxicity, creating an imbalance of ions (Ca2+ , K+ , Na+ ), thereby enforcing osmotic pressure, which interferes with soil water extraction. This results in severe distress to the plant’s morpho-physiological and biochemical features and significantly reduces crop yield [6]. Soil reclamation is one of the strategies used to improve the properties of sodic soils. Such methods may not be cost-effective for growers in these areas [2,8]
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