Transcriptome analysis of lentil (Lens culinaris Medikus) in response to seedling drought stress

Abstract

BackgroundDrought stress is one of the most harmful abiotic stresses in crop plants. As a moderately drought tolerant crop, lentil is a major crop in rainfed areas and a suitable candidate for drought stress tolerance research work. Screening for drought tolerance stress under hydroponic conditions at seedling stage with air exposure is an efficient technique to select genotypes with contrasting traits. Transcriptome analysis provides valuable resources, especially for lentil, as here the information on complete genome sequence is not available. Hence, the present studies were carried out.ResultsThis study was undertaken to understand the biochemical mechanisms and transcriptome changes involved in imparting adaptation to drought stress at seedling stage in drought-tolerant (PDL-2) and drought-sensitive (JL-3) cultivars. Among different physiological and biochemical parameters, a significant increase was recorded in proline, glycine betaine contents and activities of SOD, APX and GPX in PDL-2 compared to JL-3while chlorophyll, RWC and catalase activity decreased significantly in JL-3. Transcriptome changes between the PDL-2 and JL-3 under drought stress were evaluated using Illumina HiSeq 2500 platform. Total number of bases ranged from 5.1 to 6.7 Gb. Sequence analysis of control and drought treated cDNA libraries of PDL-2 and JL-3 produced 74032, 75500, 78328 and 81523 contigs, respectively with respective N50 value of 2011, 2008, 2000 and 1991. Differential gene expression of drought treated genotypes along with their controls revealed a total of 11,435 upregulated and 6,934 downregulated transcripts. For functional classification of DEGs, KEGG pathway annotation analysis extracted a total of 413 GO annotation terms where 176 were within molecular process, 128 in cellular and 109 in biological process groups.ConclusionThe transcriptional profiles provide a foundation for deciphering the underlying mechanism for drought tolerance in lentil. Transcriptional regulation, signal transduction and secondary metabolism in two genotypes revealed significant differences at seedling stage under severe drought. Our finding suggests role of candidate genes for improving drought tolerance in lentil.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3596-7) contains supplementary material, which is available to authorized users.

Legume genetic resources and transcriptome dynamics under abiotic stress conditions

“…For example, Illumina HiSeq was recently used to investigate transcriptome changes involved in the adaptation of drought‐tolerant PDL‐2 and drought‐sensitive JL‐3 lentil ( Lens culinaris Medikus) seedlings to drought stress (Singh et al, ). The transcriptome data revealed that genes involved in electron transport chains, oxidation–reduction processes, the tricarboxylic acid cycle, senescence, and reduction of stomatal conductance are all more highly up‐regulated in the drought‐tolerant lentil genotype than in the drought‐sensitive one, whereas genes associated with gamma‐aminobutyric acid synthesis, transcription binding, the synthesis of cell wall proteins, and the negative regulation of abscisic acid responses are all down‐regulated in the tolerant genotype compared with the susceptible genotype (Singh et al, ). Brasileiro et al () analyzed the gene expression profile of two wild peanuts ( Arachis duranensis and A rachis magna ) in response to progressive water deficit.…”

Widening the genetic base of cultivated gene pool following introgression from wild Lens taxa

“…(); Singh, Singh, Taunk, et al. (); Singh, Singh, Tomar, & Pal () have also reported similar variation for seed yield in lentil interspecific populations.…”

“…Other traits such as early seedling growth and vigour, rapid ground coverage, high biomass, early flowering and maturity were also considered useful for selecting drought‐tolerant germplasm (Hamdi & Eriskine, ). Singh, Singh, Taunk, and Tomar () studied genetic analysis and molecular mapping of seedling survival drought‐tolerance genes in lentil and also suggested introgression of drought tolerance into high yielding cultivars (Hamdi & Eriskine, ; Singh, Rana, et al., ; Singh, Singh, Taunk, et al., ; Singh, Singh, Tomar, & Pal, ). The following researchers have also identified tolerant sources against drought as Eston in Lens culinaris ssp.…”

“…Success of wide hybridization can be predicted based upon phenotypic similarity of species for pollen morphology and in vitro pollen length, pistil and style length (Fratini et al., ). Among few studies, comparative agronomic performance of lentil interspecific derivatives revealed high level of fruitful heterosis for seed yield and its important component traits (Singh, Rana, et al., ; Singh, Singh, Taunk, et al., ; Singh, Singh, Tomar, & Pal, ), which signifies the importance of inclusion of useful and unexplored gene reservoir from wild to cultivated species.…”

“…Recently, 1150 SNPs (distributed across the lentil genome) on a set of 138 cultivated lentil accessions from 34 countries with a wide range of variation for zinc (Zn) and iron (Fe) concentration in seeds were used, and two SNP markers tightly linked to Fe and one linked to Zn concentration were identified using marker–trait association analysis (Khazaei et al., ). Successful use of seven markers associated with two QTLs for seedling survival and pod set under heat stress for genotyping the intraspecific F 2 mapping population could potentially be further used to dissect candidate genes to develop heat‐tolerance molecular markers for improving lentil cultivars (Singh, Rana, et al., ; Singh, Singh, Taunk, et al., ; Singh, Singh, Tomar, & Pal, ). Despite these success reports of genomic maps and linked markers associated with the genomic region of genes of interest, there is no report on use of these markers in MAS of lentil breeding.…”