Large-scale SNP discovery and dense genetic mapping in a lentil intraspecific cross permitted identification of a single chromosomal region controlling tolerance to boron toxicity, an important breeding objective. Lentil (Lens culinaris Medik.) is a highly nutritious food legume crop that is cultivated world-wide. Until recently, lentil has been considered a genomic 'orphan' crop, limiting the feasibility of marker-assisted selection strategies in breeding programs. The present study reports on the identification of single-nucleotide polymorphisms (SNPs) from transcriptome sequencing data, utilisation of expressed sequence tag (EST)-derived simple sequence repeat (SSR) and SNP markers for construction of a gene-based genetic linkage map, and identification of markers in close linkage to major QTLs for tolerance to boron (B) toxicity. A total of 2,956 high-quality SNP markers were identified from a lentil EST database. Sub-sets of 546 SSRs and 768 SNPs were further used for genetic mapping of an intraspecific mapping population (Cassab × ILL2024) that exhibits segregation for B tolerance. Comparative analysis of the lentil linkage map with the sequenced genomes of Medicago truncatula Gaertn., soybean (Glycine max [L.] Merr.) and Lotus japonicus L. indicated blocks of conserved macrosynteny, as well as a number of rearrangements. A single genomic region was found to be associated with variation for B tolerance in lentil, based on evaluation performed over 2 years. Comparison of flanking markers to genome sequences of model species (M. truncatula, soybean and Arabidopsis thaliana) identified candidate genes that are functionally associated with B tolerance, and could potentially be used for diagnostic marker development in lentil.

Soil salinity is a major abiotic stress in Australian lentil-producing areas. It is therefore imperative to identify genetic variation for salt tolerance in order to develop lentil varieties suitable for saline soils. Conventional screening methods include the manual assessment of stress symptoms, which can be very laborious, time-consuming, and error-prone. Recent advances in image-based high-throughput phenotyping (HTP) technologies have provided unparalleled opportunities to screen plants for a range of stresses, such as salt toxicity. The current study describes the development and application of an HTP method for salt toxicity screening in lentils. In a pilot study, six lentil genotypes were evaluated to determine the optimal salt level and the growth stage for distinguishing lentil genotypes using red–green–blue (RGB) images on a LemnaTec Scanalyzer 3D phenomics platform. The optimized protocol was then applied to screen 276 accessions that were also assessed earlier in a conventional phenotypic screen. Detailed phenotypic trait assessments, including plant growth and green/non-green color pixels, were made and correlated to the conventional screen (r = 0.55; p < 0.0001). These findings demonstrated the improved efficacy of an image-based phenotyping approach that is high-throughput, efficient, and better suited to modern breeding programs.

Grain growers in south-eastern Australia have reported unexpected crop failures with theoretically safe recropping periods for acetolactate synthase herbicides in alkaline soils. This experience has led to the concern that these herbicides may degrade very slowly in alkaline soils, and herbicide residues have at times been blamed for unexplained crop losses. To address this issue, we established 5 recropping trials across Victoria and South Australia with 5 acetolactate synthase herbicides (chlorsulfuron, triasulfuron, metsulfuron-methyl, imazethapyr, and flumetsulam). The herbicides were applied to separate plots in years 1, 2 or 3, and sensitive crop species were sown in year 4 to measure the impact of herbicide residues. We observed that the persistence of the sulfonylureas (chlorsulfuron, triasulfuron, metsulfuron-methyl) varied between herbicides, but all persisted longer in alkaline soils than in acid soils, and were, therefore, more likely to damage crops in alkaline soil. Imazethapyr persisted longer in clay soils than in sandy soils and was, therefore, more likely to damage crops in clay soils. All herbicides persisted longer when rainfall was below average. Canola was more sensitive to imazethapyr than either pea, lentil or medic, but was less sensitive to the sulfonylureas. In contrast, lentil and medic were the most sensitive to sulfonylureas. Despite some damage, we found that safe recropping periods could be predicted from the product labels in all but one situation. The sole exception was that metsulfuron-methyl reduced dry matter and yield of lentil and medic sown 10 months after application in a soil with pH 8.5. We hypothesise that the real cause of crop failure in many situations is not unusual herbicide persistence, but failure to take full account of soil type (pH and clay content including variation in the paddock) and rainfall when deciding to recrop after using acetolactate synthase herbicides.

The sulfonylurea herbicides are commonly used in the cereal belt of south-eastern Australia and there is concern that their persistence in alkaline soils is long enough to damage subsequent rotational crops such as legumes and oilseeds. In this study, we investigated leaching and persistence of 3 commonly used herbicides (chlorsulfuron, triasulfuron and metsulfuron-methyl) in alkaline soils of south-eastern Australia (pH range 7.4–8.6) for at least 4 years after treatment. In general, chlorsulfuron was predicted to persist for 3–5 years [time to degrade to 1% (DT99) of 33–63 months after treatment depending on the field site], triasulfuron for 1–3 years (DT99 of 13–37 months after treatment), and metsulfuron-methyl for less than 1 year (although data were insufficient for degradation estimates) after its application. However, this varied between sites and years of application. Although, the majority of residues remained in the top 20 cm of the soil profile throughout the study, leaching of a small fraction of the residue to deeper layers of the profiles (up to 1 m) was observed. Despite their slow rate of degradation, the herbicides did eventually dissipate, even in soils with very high pH (8.5). In most cases, the current product labels provide an adequate safety period to protect sensitive rotational crops from potential damage due to excessive persistence. However, in particular years at 3 of the 5 field sites, metsulfuron-methyl and triasulfuron persisted beyond the recommended recropping period (9 months for metsulfuron-methyl and 22 months for triasulfuron in soils up to pH 7.5 or 24 months in soils pH 7.6 and above). An accurate measurement of soil pH and its variability within the paddock is essential to minimise any subsequent crop damage by these herbicides.

Imazethapyr and flumetsulam are acetolactate synthase herbicides commonly used in the cereal belt of south-eastern Australia. As their labels recommend recropping periods of up to 34 months for imazethapyr and 24 months for flumetsulam, there are concerns that in some cases their persistence may damage subsequent rotation crops. This is the first major study in south-eastern Australia to investigate their leaching and persistence for up to 4 years after treatment. Imazethapyr persisted for more than 3 years at 2 sites and flumetsulam for more than 2 years at 3 sites. For imazethapyr, soil type (clay content) rather than soil pH seemed to be most important in determining persistence, with residues of 10% of applied imazethapyr predicted to persist for 24 months after treatment in clay soil and 5 months after treatment in sandy soil. The potential for leaching below our studied soil depth of 40 cm is of concern for imazethapyr but not for flumetsulam. The current labels appear to provide adequate information for safe recropping periods, but may be conservative for imazethapyr in sandy soils.