Biology subjects

Bett, K.

Publications and source records attributed to Bett, K..

15 recordsLinked to original sources

bioRxiv2026

Lens species genome assemblies reveal evolutionarily fragile chromosomes associated with pericentric inversions

The genus Lens is comprised of seven diploid species, including the cultivated crop Lentil, and six wild relatives often used in breeding programs for beneficial allele introgression. Lens species are proposed to exhibit considerable levels of genome structural variation both within and between species, which has implications for plant breeding and evolutionary genomics. Plant centromeres are key regions involved in chromosomal stability, where structural changes can be linked to meiotic abnormalities, resulting in inversions, translocations, and deletions of chromosomal segments. Fabeae centromeres are known to be diverse and do not fit the centromere drive model. The origins of this centromere diversity and the evolutionary trends remain unclear, but recent studies suggest that centromere structural variation plays a role in creating new sequence combinations that contribute to the unique centromere evolution patterns observed in legumes. We sequenced, assembled, and performed gene synteny analysis in the genomes of all seven Lens species using long-read sequencing technologies. We also located and characterized the centromeres in these genomes through ChIP-seq experiments to better understand their role in Lens chromosomal stability. Synteny analysis reveals that Lens genomes have undergone extensive rearrangements during evolution, with multiple translocations and inversions identified between species. Specific Lens chromosomes appear more susceptible to rearrangements over time. These same chromosomes also exhibit higher rates of rearrangement throughout Lens speciation. Fragile chromosomes are associated with the occurrence of pericentric inversions, likely disrupting stability. The diversity in satellite sequences in Lens centromeres likely results from structural changes accumulated throughout Lens evolution. These findings suggest that genome and centromere structure play significant roles in generating centromere diversity within this legume genus.

genomics↗

bioRxiv2026

SVPopEx: Population-Wide Visualization and Exploration of Structural Variants

Structural variants (SVs) are large-scale genomic variants, which can disrupt important functional and regulatory elements, leading to genomic disorders in humans and playing important roles in domestication, disease resistance, and traits in plants. SVs are generated across populations of individuals and used for association studies, consisting of large datasets with thousands of genomic loci. Visualization of these SVs aids in understanding their genomic distribution, identifying patterns across affected or phenotypic groups, and assessing their proximity to other genomic regions of interest. A variety of tools exist for visualizing SVs, including linear genome browsers and graph-based methods; however, many do not offer intuitive or scalable representations of SVs across large populations. To address this, we present SVPopEx, an interactive tool for population-wide visualization and exploration of SVs. SVPopEx provides a unique and intuitive representation for insertions, deletions, inversions, duplications, and translocations in a linear genome-style browser. Novel features were developed to support comparisons across genomes within user-defined regions, including rendering SVs based on one or more samples and visualizing haplotypes. Use of the tool is demonstrated with SV datasets from Schistosoma mansoni and Lens culinaris. A task-based evaluation was conducted using SVPopEx and two other linear genome browsers, which demonstrated that SVPopEx excelled in (1) providing a clear representation of the SVs present and (2) supporting comparisons across genomes.

bioinformatics↗

bioRxiv2025

Newly-identified lentil genotypes adapted to Mediterraneanagro-ecosystems

Lentil cultivation and consumption promote human health and sustainable agriculture, making a significant contribution to the transition toward a plant-based diet. In Europe, lentil yields are still unstable, and the lack of breeding efforts limits the choice of farmers to few varieties. Here, we characterized 46 lentil genotypes, including local cultivars and landraces from diverse geographic origins, in Mediterranean agro-environments for flowering, architectural and production traits in seven field trials, over 3 years (2019-2021), in two localities (central and southern Italy) and during two sowing seasons (autumn and spring). We estimated the genetic merit of each genotype and identified outperforming genotypes for all traits. Indian ILL 11557AGL and Argentinian IL 4605AGL domesticated varieties resulted superior for earliness. Italian landraces and French cultivars achieved the highest values for first pod height, while landraces and breeding materials from Ethiopia, Syria and Iran were the best-yielding. Data from all seven trials were available for 16 genotypes, so we analyzed the genotype, environment and genotype x environment interaction (GEI) to identify specific genotypic adaptations. European cultivars performed well for architectural traits, whereas the best-yielding genotypes were Middle Eastern and Ethiopian landraces. Environmental effect on yield related to sowing season and locality was detected, with an overall higher yield in autumn compared to spring sowing trials and in central rather than southern Italy. By dissecting the GEI structure using additive main effect and multiplicative interaction (AMMI) analysis and Weighted Average of Absolute Scores (WAASB) index, we identified a group of Iranian landraces (PI 431633 AGL and PI 432033 LSP AGL) adapted to both autumn and spring sowing and one Ethiopian landrace (IG 1959 AGL) showing high yield stability across all environmental conditions. These findings provide a foundation to unlock the full potential of lentil cultivation in European and Mediterranean systems by identifying adapted, high-performing genotypes.

genetics↗

bioRxiv2025

Development of a Nested Association Mapping (NAM) population for untangling complex traits in lentil (Lens culinaris Medik.)

Understanding the genetic basis of complex traits remains a key challenge in crop improvement. This study aimed to develop a structured, multi-parental mapping population to enhance the resolution of quantitative trait dissection, based on the hypothesis that a Nested Association Mapping (NAM) design would enable the detection of minor-effect loci often overlooked by traditional biparental or diversity panel-based approaches. A lentil (Lens culinaris Medik.) NAM population was developed by crossing the Canadian cultivar CDC Redberry with 32 diverse genotypes sourced globally from three major lentil-growing macro-environments: Northern temperate, Mediterranean, and South Asia. The resulting recombinant inbred lines were phenotyped for key phenological traits, days to emergence (DTE), flowering (DTF), and maturity (DTM), under field conditions, and genotyped using exome capture sequencing. Genome-wide association studies for DTF identified 14 significant loci across six chromosomes, including the known FTb locus and novel associations near AP3a, HUB2a, and PIF6 genes. These results demonstrate the utility of the NAM design in detecting both major and minor-effect loci that underlie complex trait variation. To our knowledge, this is the first publicly available NAM population in lentil. It provides a high-resolution, globally representative platform for trait discovery, pre-breeding, and collaborative genetic improvement of this nutritionally and agronomically important legume.

plant biology↗

bioRxiv2025

Oligo-FISH Validates Genome Assemblies and Delivers the Most Precise Karyotype for Lens Mill. Species

Chromosome structural rearrangements play a significant role in karyotype evolution and speciation. These rearrangements pose challenges for precise karyotyping, leading to asymmetric chromosomes and complicating the assembly of a genus pan-genome for crops and their wild relatives. Lens culinaris, an important cool-season legume primarily cultivated in India and Canada, is the cultivated species among six wild relatives. All seven species of Lens face significant challenges due to chromosomal rearrangements, ranging from introgression issues to difficulties in developing a precise karyotype and advancing genomic studies. Using the gene synteny analysis between the cultivated Lens species and six wild relatives, we developed cross-species oligo-FISH (Fluorescent in situ hybridization) probes aiming to further attest to the genome assembly and synteny analysis of Lens species. Roots of seven Lens spp. accessions were harvested and used for chromosome spread preparations. Those slides were then used for Oligo-FISH experiments, where the DNA present in the slides was denatured, and a set of red and green oligo probes was hybridized to the chromosomes. Pictures were taken using a fluorescence microscope. The combination of both oligo sets/probes resulted in a distinct pattern for each Lens spp. chromosome, allowing the inference of the most precise karyotype to date for six Lens species. The number of oligo probe signals reflects the species phylogenetic proximity, while the distribution of those signals changed drastically within the same gene pool. The karyotyping of Lens confirmed the proper assignment of chromosomes in the genome assemblies and validated the rearrangements detected in the synteny analysis. Differences in the assembly probe prediction and the oligo-FISH results were used to improve the assemblies. The results attest to a higher sequence-level similarity among the closest related species despite the occurrence of several structural changes among them. The oligo-FISH probes can be used in conjunction with plant genome assembly projects, supporting the delivery of a precise representation of their physical chromosomes.

genomics↗

bioRxiv2024

Variability in mineral composition of Canadian lentil cultivars

Lentils are a good source of essential minerals for the proper functioning of the human body. We evaluated 34 cultivars and elite lentil lines representing the breadth of the Canadian breeding program. Trials were established in 10 site-years across Saskatchewan Province. Concentrations of 27 minerals were quantified with an inductive coupled argon plasma emission spectrometer in whole and dehulled lentil seeds. Li, V, Cr, Co, As, Ag, Cd, Sn, La, Hg, and Pb had concentrations below the quantification limit and were excluded from further analysis. The effects of site year, tissue type (whole and dehulled), and lentil genotypes were analyzed using a mixed model. Mineral concentrations of Na, K, Ca, Mg, Cu, B, and Ba were stable across site years. Na, Zn, P, Cu, Se, and Mo had similar concentrations in whole and dehulled seeds. Ca, Fe, Mg, Mn, B, Al, and Ba were more concentrated in whole seeds, while K, S, and Ni were higher in dehulled seeds. Several lentil genotypes had outstanding concentrations of several minerals. Lentil genotypes with a higher composition of several minerals could be a starting point for enhancing mineral composition in lentils.

genetics↗

bioRxiv2024

Detecting color differences in lentil flour samples using an inexpensive, hand-held colorimeter.

Our lentil breeding program was interested in determining the effects of the red lentil genotype in processed food products colour intensity. This required a colorimeter that could accurately assess colour from the CIE L*a*b* colour space on a small sample of milled flour. Flour colour is commonly assessed with industry standard HunterLab colorimeters that require a large sample size ([~]6g flour/sample). In recent years a new spectrophotometer (Nix) has become available. It was designed to quickly and accurately obtain CIEL*a*b* values for everyday items and requires a small amount of sample for analysis (0.5 g flour/sample), but its use has not been tested in milled flour products. To test whether this instrument was appropriate for milled flour colour, eight red lentil genotypes were evaluated for red colour using both instruments. Mean colour scores with Nix (a* and b*) were comparable to those obtained with the HunterLab (r2 = 0.9-0.95), L* scores were less comparable (r2 = 0.58-0.61). Both instruments were able to differentiate and rank red colour intensity in milled flour from the different red lentil genotypes. Nix procedures are more repeatable and use less sample than HunterLab validating its use for assessing red colour intensity in lentil flour. Research HighlightsO_LICompanies making foods using red lentil flour seek red lentil genotypes that exhibit red colour intensity. C_LIO_LINix Spectro2 is an inexpensive photospectrometer made for small volume samples. It has not been tested on flour products. C_LIO_LIThe selected red lentil genotypes tested showed a range of red colour intensities. C_LIO_LINix Spectro2 performance was comparable to industry standard HunterLab colorimeter. C_LI

systems biology↗

bioRxiv2022

B vitamin quantification in lentil seed tissues using ultra-performance liquid chromatography-selected reaction monitoring mass spectrometry

Lentils are an important source of macronutrients, including protein and fiber, as well as micronutrients such as vitamins and minerals, especially in a plant-based diet. Quantifying variation among genotypes, including wild germplasm, is desirable to better understand the genetics of differential B vitamins content for breeding of this trait and to understand their potential contributions to the lentil crop. We analyzed thirty-four cultivated and three wild genotypes for vitamins B1, B2, B3, B5, B6, B7, and B9. Seeds were assayed whole, and separated into cotyledons only, or seed coats only. Variation for all B vitamins was observed across the cultivars. Overall, cotyledons had higher concentrations of B1 and B3, while seed coats had higher concentrations of B2, B5, B6, and B9. Wild accessions had the highest concentrations of vitamin B9 and were also among the highest for vitamin B2. These results demonstrate the differential distribution of B vitamins across seed tissues and lentil genotypes, and that dehulling prior to consumption results in the loss of B vitamins otherwise available in whole seeds. They also indicate there is genetic variability which could be used to increase B-vitamin levels in lentil via breeding.

plant biology↗

bioRxiv2022

CRISPR/Cas9-based repeat depletion for the high-throughput genotyping of complex plant genomes

High-throughput genotyping enables the large-scale analysis of genetic diversity in population genomics and genomewide association studies that combine the genotypic and phenotypic characterization of large collections of accessions. Sequencing-based approaches for genotyping are progressively replacing traditional genotyping methods due to the lower ascertainment bias. However, genome-wide genotyping based on sequencing becomes expensive in species with large genomes and a high proportion of repetitive DNA. Here we describe the use of CRISPR/Cas9 technology to deplete repetitive elements in the 3.76-Gb genome of lentil (Lens culinaris), 84% consisting of repeats, thus concentrating the sequencing data on coding and regulatory regions (single-copy regions). We designed a custom set of 566,766 gRNAs targeting 2.9 Gbp of repeats and excluding repetitive regions overlapping annotated genes and putative regulatory elements based on ATAC-Seq data. The novel depletion method removed [~]40% of reads mapping to repeats, increasing those mapping to single-copy regions by [~]2.6-fold. When analyzing 25 million fragments, this repeat-to-single-copy shift in the sequencing data increased the number of genotyped bases of [~]10-fold compared to non-depleted libraries. In the same condition, we were also able to identify [~]12-fold more genetic variants in the single-copy regions and increased the genotyping accuracy by rescuing thousands of heterozygous variants that otherwise would be missed due to low coverage. The method performed similarly regardless of the multiplexing level, type of library or genotypes, including different cultivars and a closely-related species (L. orientalis). Our results demonstrated that CRISPR/Cas9-driven repeat depletion focuses sequencing data on meaningful genomic regions, thus improving high-density and genome-wide genotyping in large and repetitive genomes.

genomics↗

bioRxiv2022

INCREASING DIVERSITY AMONG LENS SPECIES FOR IMPROVING BIOLOGICAL NITROGEN FIXATION IN LENTIL

Exotic germplasm is a key resource for reintroducing genetic variability into cultivars. We evaluated 36 accessions from cultivated lentil (Lens culinaris Medik.) and six related wild species, inoculated with a commercial strain of Rhizobium leguminosarum bv. viciae under greenhouse conditions. The objective was to explore Lens species and/or accessions that could contribute higher biological nitrogen fixation (BNF) ability to the lentil crop. A split plot design was used with either Rhizobium inoculation, added Nitrogen (N) or neither, as the main plots, and accessions in subplots randomized in blocks. Two repeats of the experiment were evaluated at flowering for N fixation and nodulation characters, and two subsequent experiments, with a subset of 14 accessions, were evaluated at maturity for seed production, seed quality and harvest index. Differences in phenotypic expression did not correspond to any particular Lens species. CDC Greenstar exhibited some of the highest N fixation values observed among the cultivars and also superior yield results compared to the added N treatment. Wild accessions, including IG 72643 (L. orientalis), displayed unique and multiple desirable characteristics compared to cultivars including indeterminate nodulation, higher N translocation, stable yield compared to added N treatment and exceptionally high protein concentration in seeds.

plant biology↗

bioRxiv2022

Focusing the GWAS Lens on days to flower using latent variable phenotypes derived from global multi-environment trials

Adaptation constraints within crop species have resulted in limited genetic diversity in some breeding programs and/or areas where new crops have been introduced, e.g., lentil (Lens culinaris Medik.) in North America. An improved understanding of the underlying genetics involved in phenology-related traits is valuable knowledge to aid breeders in overcoming limitations associated with unadapted germplasm and expanding their genetic diversity by introducing new, exotic material. We used a large, 18 site-year, multi-environment dataset, phenotyped for phenology-related traits across nine locations and over three years, along with accompanying latent variable phenotypes derived from a photothermal model and principal component analysis (PCA) of days from sowing to flower (DTF) data for a lentil diversity panel (324 accessions) which has also been genotyped with an exome capture array. Genomewide association studies (GWAS) on DTF across multiple environments helped confirm associations with known flowering time genes and identify new quantitative trait loci (QTL), which may contain previously unknown flowering time genes. Additionally, the use of latent variable phenotypes, which can incorporate environmental data such as temperature and photoperiod as both GWAS traits and as covariates, strengthened associations, revealed additional hidden associations, and alluded to potential roles of the associated QTL. Our approach can be replicated with other crop species, and the results from our GWAS serve as a resource for further exploration into the complex nature of phenology-related traits across the major growing environments for cultivated lentil.

genetics↗

bioRxiv2021

Genetic analysis of early phenology in lentil identifies distinct loci controlling component traits

Reproductive phenology is well known to be a key feature of crop adaptation to diverse ecogeographic variation and management practices. Lentil is one of the founder pulse crops of middle-eastern Neolithic agriculture, and the modern-day domesticated lentil germplasm is generally considered to form three broad adaptation groups: Mediterranean, South Asian and northern temperate, which correspond approximately to the major global production environments. Understanding the molecular basis of these adaptations is crucial to maximise efficiency of breeding programs. Here, we use a QTL approach to dissect the earliness that is characteristic of the South Asian pilosae ecotype, and that suits it to the typically short winter cropping season. We identified two loci, DTF6a and DTF6b, at which dominant alleles confer early flowering. We show that, although these loci can interact in an additive manner, DTF6a alone is sufficient to confer early flowering even in extremely short photoperiods. Comparisons with closely related legume species confirmed the presence of a conserved cluster of three FT orthologs among potential candidate genes in the region, and expression analysis in near-isogenic material showed that the early dtf6a allele is associated with a strong derepression of the FTa1 gene in particular. Analysis of sequence variation revealed the presence of a 7.4 kb deletion in the FTa1-FTa2 intergenic region in the pilosae parent, and a wide survey of over 400 accessions with diverse origin showed that the dtf6a allele is dominant in South Asia material. Collectively, these results contribute to understanding the molecular basis of global adaptation in lentil, and further emphasize the importance of this conserved genomic region for adaptation in temperate legumes generally.

genetics↗

bioRxiv2021

Identification of anthracnose (Colletotrichum lentis) race 1 resistance loci in lentil by integrating linkage mapping and a genome-wide association study

Anthracnose, caused by Colletotrichum lentis, is a devastating disease of lentil in Western Canada. Growing resistant lentil cultivars is the most cost-effective and environmentally friendly approach to prevent seed yield losses that can exceed 70%. To identify loci conferring resistance to anthracnose race 1 in lentil, biparental quantitative trait loci (QTL) mapping of two recombinant inbred line (RIL) populations was integrated with a genome-wide association study (GWAS) using 200 diverse lentil accessions from a lentil diversity panel (LDP). A major-effect QTL (qAnt1.Lc-3) conferring resistance to race 1 was mapped to lentil chromosome 3 and co-located on the lentil physical map for both RIL populations. Clusters of candidate nucleotide binding-leucine-rich repeats (NB-LRR) and other defense-related genes were uncovered within the QTL region. A GWAS detected 14 significant SNP markers associated with race 1 resistance on chromosomes 3, 4, 5, and 6. The most significant GWAS SNPs on chromosome 3 supported qAnt1.Lc-3 and delineated a region of 1.6 Mb containing candidate resistance genes. The identified SNP markers can be directly applied in marker-assisted selection to accelerate the introgression of race 1 resistance in lentil breeding.

genomics↗

bioRxiv2020

Understanding photothermal interactions will help expand production range and increase genetic diversity of lentil (Lens culinaris Medik.)

O_LILentil (Lens culinaris Medik.) is cultivated under a wide range of environmental conditions, which led to diverse phenological adaptations and resulted in a decrease in genetic variability within breeding programs due to reluctance in using genotypes from other environments. C_LIO_LIWe phenotyped 324 genotypes across nine locations over three years to assess their phenological response to the environment of major lentil production regions and to predict days from sowing to flowering (DTF) using a photothermal model. C_LIO_LIDTF was highly influenced by the environment and is sufficient to explain adaptation. We were able to predict DTF reliably in most environments using a simple photothermal model, however, in certain site-years, results suggest there may be additional environmental factors at play. Hierarchical clustering of principal components revealed the presence of eight groups based on the responses of DTF to contrasting environments. These groups are associated with the coefficients of the photothermal model and revealed differences in temperature and photoperiod sensitivity. C_LIO_LIExpanding genetic diversity is critical to the success of a breeding program; understanding adaptation will facilitate the use of exotic germplasm. Future climate change scenarios will result in increase temperature and/or shifts in production areas, we can use the photothermal model to identify genotypes most likely to succeed in these new environments. C_LI

plant biology↗

bioRxiv2019

The BELT and phenoSEED platforms: shape andcolour phenotyping of seed samples

BackgroundSeed analysis is currently a bottleneck in phenotypic analysis of seeds. Measurements are slow and imprecise with potential for bias to be introduced when gathered manually. New acquisition tools were requested to improve phenotyping efficacy with an emphasis on obtaining colour information.\n\nResultsA portable imaging system (BELT) supported by image acquisition and analysis software (phenoSEED) was created for small-seed optical analysis. Lentil (Lens culinaris L.) phenotyping was used as the primary test case. Seeds were loaded into the system and all seeds in a sample were automatically and individually imaged to acquire top and side views as they passed through an imaging chamber. A Python analysis script applied a colour calibration and extracted quantifiable traits of seed colour, size and shape. Extraction of lentil seed coat patterning was implemented to further describe the seed coat. The use of this device was forecasted to eliminate operator biases, increase the rate of acquisition of traits, and capture qualitative information about traits that have been historically analyzed by eye.\n\nConclusionsIncreased precision and higher rates of data acquisition compared to traditional techniques will help breeders to develop more productive cultivars. The system presented is available as an open-source project for academic and non-commercial use.

plant biology↗