Identification of novel genes associated with herbicide tolerance in Lentil (Lens culinaris ssp. culinaris Medik.)

Abstract

Weeds pose a major constraint in lentil cultivation, leading to decrease farmers' revenues by reducing the yield and increasing the management costs. The development of herbicide tolerant cultivars is essential to increase lentil yield. Even though herbicide tolerant lines have been identified in lentils, breeding efforts are still limited and lack proper validation. Marker assisted selection (MAS) can increase selection accuracy at early generations. Total 292 lentil accessions were evaluated under different dosages of two herbicides, metribuzin and imazethapyr, during two seasons at Marchouch, Morocco and Terbol, Lebanon. Highly significant differences among accessions were observed for days to flowering (DF) and maturity (DM), plant height (PH), biological yield (BY), seed yield (SY), number of pods per plant (NP), as well as the reduction indices (RI) for PH, BY, SY and NP. A total of 10,271 SNPs markers uniformly distributed along the lentil genome were assayed using Multispecies Pulse SNP chip developed at Agriculture Victoria, Melbourne. Meta-GWAS analysis was used to detect marker-trait associations, which detected 125 SNPs markers associated with different traits and clustered in 85 unique quantitative trait loci. These findings provide valuable insights for initiating MAS programs aiming to enhance herbicide tolerance in lentil crop.

Figure 1

Distribution of lentil genotypes for herbicide damage scores (HDS1 and HDS2) under different dosages of imazethapyr and metribuzin during different locations and cropping seasons.

Figure 2

Phylogenetic tree of the studied lentil accessions using SNP genotyping data. The samples are color-coded based on their country of origin.

Figure 3

Manhattan plot and QQ plot of the highly significant associations existing between the SNP markers of the recorded traits. HDS2: second herbicide damage score, DF: days to flowering, RIDF: DF reduction index, RIDM: Days to maturity reduction index, BY: Biological yield per plant, NP: number of pods per plant, RINP: NP reduction index, NS: number of seeds per plant.

Figure 3

Manhattan plot and QQ plot of the highly significant associations existing between the SNP markers of the recorded traits. HDS2: second herbicide damage score, DF: days to flowering, RIDF: DF reduction index, RIDM: Days to maturity reduction index, BY: Biological yield per plant, NP: number of pods per plant, RINP: NP reduction index, NS: number of seeds per plant.

Figure 4

Physical map showing eighteen SNP markers (A to R) that are located on the genes. Green zones are the exomes (coded regions) interrupted by the black zones that are the introns (non-coding regions) and the yellow vertical line represents the location of SNP markers of interest.