Biology subjects

Carlson, C. H.

Publications and source records attributed to Carlson, C. H..

10 recordsLinked to original sources

bioRxiv2026

CannSelect: A High-Quality Genotyping Platform for Cannabis sativa

The field of genomics has enabled extraordinary progress in horticultural crop research. However, there is still a need for cost-effective, high-resolution technologies flexible to the diversity found in emerging crops. To this end, we introduce CannSelect, a high-quality genotyping platform for Cannabis sativa. Designed for use in diversity analyses and trait mapping, probe targets were selected from four genotyped diversity panels and a curated gene list. This platform has been used to effectively map day-neutrality in a segregating population to the Autoflower1 locus with average capture efficiencies of 88.5%. With broad genome coverage, demonstrated target specificity, and reproducibility, CannSelect is expected to perform well across the diversity of C. sativa. We describe the methodology used to design CannSelect v1.0 and performance metrics for testing capture efficiency and target alignment in diverse genome assemblies. The CannSelect platform represents a robust and scalable, genome-wide genotyping tool for C. sativa researchers and breeders.

genomics↗

bioRxiv2024

A pangenome and pantranscriptome of hexaploid oat

Oat grain is a traditional human food rich in dietary fiber that contributes to improved human health. Interest in the crop has surged in recent years owing to its use as the basis for plant-based milk analogs. Oat is an allohexaploid with a large, repeat-rich genome that was shaped by subgenome exchanges over evolutionary timescales. In contrast to many other cereal species, genomic research in oat is still at an early stage, and surveys of structural genome diversity and gene expression variability are scarce. Here, we present annotated chromosome-scale sequence assemblies of 33 wild and domesticated oats along with an atlas of gene expression across six tissues of different developmental stages in 23 accessions. We describe the interplay of gene expression diversity across subgenomes, accessions and tissues. Gene loss in the hexaploid is accompanied by compensatory up-regulation of the remaining homeologs, but this process is constrained by subgenome divergence. Chromosomal rearrangements have significantly impacted recent oat breeding. A large pericentric inversion associated with early flowering explains distorted segregation on chromosome 7D and a homeologous sequence exchange between chromosomes 2A and 2C in a semidwarf mutant has risen to prominence in Australian elite varieties. The oat pangeome will promote the adoption of genomic approaches to understanding the evolution and adaptation of domesticated oats and will accelerate their improvement.

genomics↗

bioRxiv2022

Plant architecture is correlated with variation in cannabinoid concentration and biomass production in Cannabis sativa

Cannabis sativa is cultivated for multiple uses including the production of cannabinoids. In developing improved production systems for high-cannabinoid cultivars, scientists and cultivators must consider the optimization of complex and interacting sets of morphological, phenological, and biochemical traits, which have historically been shaped by natural and anthropogenic selection. Determining factors that modulate cannabinoid variation within and among genotypes is fundamental to developing efficient production systems and understanding the ecological significance of cannabinoids. Thirty-two high-cannabinoid hemp cultivars were characterized for traits including flowering date and shoot-tip cannabinoid concentration. Additionally, a set of plant architecture traits, as well as wet, dry, and stripped inflorescence biomass were measured at harvest. One plant per plot was partitioned post-harvest to quantify intra-plant variation in inflorescence biomass production and cannabinoid concentration. Some cultivars showed intra-plant variation in cannabinoid concentration, while many had a consistent concentration regardless of canopy position. There was both intra- and inter-cultivar variation in architecture that correlated with intra-plant distribution of inflorescence biomass, and concentration of cannabinoids sampled from various positions within a plant. These relationships among morphological and biochemical traits will inform future decisions by cultivators, regulators, and plant breeders as well as our broader understanding of intra-plant variation of specialized biochemicals. HighlightIn-season hemp plant architecture measurements can predict post-harvest traits related to the distribution of biomass and concentration of cannabinoids.

plant biology↗

bioRxiv2021

Mapping the sex determination region in the Salix F1 hybrid common parent population confirms a ZW system in six diverse species

Within the genus Salix, there are approximately 350 species native primarily to the northern hemisphere and adapted to a wide range of habitats. This diversity can be exploited to mine novel alleles conferring variation important for production as a bioenergy crop, but also to identify evolutionarily important genes, such as those involved in sex determination. To leverage this diversity, we created a mapping population by crossing six Salix species (S. viminalis, S. suchowensis, S. integra, S. koriyanagi, S. udensis, and S. alberti) to common male and female S. purpurea parents. Each family was genotyped via genotyping-by-sequencing and assessed for kinship and population structure as well as the construction of 16 backcross linkage maps to be used as a genetic resource for breeding and selection. Analyses of population structure resolved both the parents and F1 progeny to their respective phylogenetic section and indicated that the S. alberti parent was misidentified and was most likely S. suchowensis. Sex determining regions were identified on Salix chromosome 15 in the female-informative maps for seven of the eight families indicating that these species share a common female heterogametic ZW sex system. The eighth family, S. integra x S. purpurea, was entirely female and had a truncated chromosome 15. Beyond sex determination, the Salix F1 hybrid common parent population (Salix F1 HCP) introduced here will be useful in characterizing genetic factors underlying complex traits, aid in marker-assisted selection, and support genome assemblies for this promising bioenergy crop.

plant biology↗

bioRxiv2021

Nonadditive gene expression is correlated with nonadditive phenotypic expression in interspecific triploid hybrids of willow (Salix spp.)

Many studies have highlighted the complex and diverse basis for heterosis in inbred crops. Despite the lack of a consensus model, it is vital that we turn our attention to understanding heterosis in undomesticated, heterozygous, and polyploid species, such as willow (Salix spp.). Shrub willow is a dedicated energy crop bred to be fast-growing and high yielding on marginal land without competing with food crops. A trend in willow breeding is the consistent pattern of heterosis in triploids produced from crosses between diploid and tetraploid species. Here, we test whether differentially expressed genes are associated with heterosis in triploid families derived from diploid S. purpurea, diploid S. viminalis, and tetraploid S. miyabeana parents. Three biological replicates of shoot tips from all family progeny and parents were collected after 12 weeks in the greenhouse and RNA extracted for RNA-Seq analysis. This study provides evidence that nonadditive patterns of gene expression are correlated with nonadditive phenotypic expression in interspecific triploid hybrids of willow. Expression-level dominance was most correlated with heterosis for biomass yield traits and was highly enriched for processes involved in starch and sucrose metabolism. In addition, there was a global dosage effect of parent alleles in triploid hybrids, with expression proportional to copy number variation. Importantly, differentially expressed genes between family parents were most predictive of heterosis for both field and greenhouse collected traits. Altogether, these data will be used to progress models of heterosis to complement the growing genomic resources available for the improvement of heterozygous perennial bioenergy crops.

plant biology↗

bioRxiv2021

Morphometric relationships and their contribution to biomass and cannabinoid yield in hybrids of hemp (Cannabis sativa)

The breeding of hybrid cultivars of hemp (Cannabis sativa L.) is not well described, especially the segregation and inheritance of traits that are important for yield. A total of 23 families were produced from genetically diverse parents to investigate the inheritance of morphological traits and their association with biomass accumulation and cannabinoid yield. In addition, a novel classification method for canopy architecture was developed. The strong linear relationship between wet and dry biomass provided an accurate estimate of final dry stripped floral biomass. Of all field and aerial measurements, basal stem diameter was determined to be the single best selection criterion for final dry stripped floral biomass yield. Along with stem diameter, canopy architecture and stem growth predictors described the majority of the explainable variation of biomass yield. Within-family variance for morphological and cannabinoid measurements reflected the heterozygosity of the parents. While selfed populations suffered from inbreeding depression, hybrid development in hemp will require at least one inbred parent to achieve uniform growth and biomass yield. Nevertheless, floral phenology remains a confounding factor in selection because of its underlying influence on biomass production highlighting the need to understand the genetic basis for flowering time in the breeding of uniform cultivars. HighlightStem and canopy architecture traits are superior predictors of floral biomass yield and offer a good indication of hybrid uniformity in field plantings of genetically diverse cannabinoid hemp populations.

plant biology↗

bioRxiv2021

Integrative genomics reveals paths to sex dimorphism in Salix purpurea L.

Sex dimorphism and gene expression were studied in developing catkins in 159 F2 individuals from the bioenergy crop Salix purpurea, and potential mechanisms and pathways for regulating sex development were explored. Differential expression, eQTL, bisulfite sequencing, and network analysis were used to characterize sex dimorphism, detect candidate master regulator genes, and identify pathways through which the sex determination region (SDR) may mediate sex dimorphism. Eleven genes are presented as candidates for master regulators of sex, supported by gene expression and network analyses. These include genes putatively involved in hormone signaling, epigenetic modification, and regulation of transcription. eQTL analysis revealed a suite of transcription factors and genes involved in secondary metabolism and floral development that were predicted to be under direct control of the sex determination region. Furthermore, data from bisulfite sequencing and small RNA sequencing revealed strong differences in expression between males and females that would implicate both of these processes in sex dimorphism pathways. These data indicate that the mechanism of sex determination in Salix purpurea is likely different from that observed in the related genus Populus. This further demonstrates the dynamic nature of SDRs in plants, which involves a multitude of mechanisms of sex determination and a high rate of turnover.

genomics↗

bioRxiv2020

Sexual dimorphism and sex ratio bias in the dioecious willow Salix purpurea L.

PremiseSexual dimorphism in dioecious plant species is often not obvious or is absent. Dioecious species populations also often exhibit deviations from expected sex ratios. Previous studies on members of the Salicaceae family have shown strong, partial, and no sexual dimorphism. Some studies have shown sex-biased ratios in several Salix spp., however, S. purpurea has never been examined for evidence of sexual dimorphism or for the presence of sex-ratio bias, and therefore a comprehensive phenotypic study is needed to fill this knowledge gap. MethodsThis study examined a suite of morphological, phenological, physiological and wood composition traits from multi-environment and multi-year replicated field trials in a diversity panel of unrelated S. purpurea accessions and in full-sib F1 and F2 families produced through controlled cross pollinations to test for sexual dimorphism and sex ratio bias. Key ResultsSignificant evidence of sexual dimorphism was found in vegetative traits with greater means for many traits in male genotypes compared to females across three populations of S. purpurea, measured across multiple years that were highly predictive of biomass yield. Male plants exhibited greater nitrogen accumulation under fertilizer amendment as measured by SPAD in the diversity panel, and males showed greater susceptibility to fungal infection by Melampsora spp in the F2 family. There were also consistent female-biased sex ratios in both the F1 and F2 families. ConclusionsThese results provide the first evidence of sexual dimorphism in S. purpurea and also confirm the prevalence of female-biased sex ratios previously found in other Salix species.

plant biology↗

bioRxiv2020

Sex determination through X-Y heterogamety in Salix nigra

The development of non-recombining sex chromosomes has radical effects on the evolution of discrete sexes and sexual dimorphism. Although dioecy is rare in plants, sex chromosomes have evolved repeatedly throughout the diversification of angiosperms, and many of these sex chromosomes are relatively young compared to those found in vertebrates. In this study, we designed and used a sequence capture array to identify a novel sex-linked region (SLR) in Salix nigra, a basal species in the willow clade, and demonstrated that this species has XY heterogamety. We did not detect any genetic overlap with the previously characterized ZW SLRs in willows, which map to a different chromosome. The S. nigra SLR is characterized by strong recombination suppression across a 2 MB region and an excess of low frequency alleles, resulting in a low Tajimas D compared to the remainder of the genome. We speculate that either a recent bottleneck in population size or factors related to positive or background selection generated this differential pattern of Tajimas D on the X and autosomes. This discovery provides insights into factors that may influence the evolution of sex chromosomes in plants and contributes to a large number of recent observations that underscore their dynamic nature.

genomics↗

bioRxiv2019

A Willow Sex Chromosome Reveals Convergent Evolution of Complex Palindromic Repeats

BackgroundSex chromosomes in a wide variety of species share common characteristics, including the presence of suppressed recombination surrounding sex determination loci. They have arisen independently in numerous lineages, providing a conclusive example of convergent evolution. Mammalian sex chromosomes contain multiple palindromic repeats across the non-recombining region that facilitate sequence conservation through gene conversion, and contain genes that are crucial for sexual reproduction. Plant sex chromosomes are less well understood, and in particular it is not clear how coding sequence conservation is maintained in the absence of homologous recombination.\n\nResultsHere we present the first evidence of large palindromic structures in a plant sex chromosome, based on a highly contiguous assembly of the W chromosome of the dioecious shrub Salix purpurea. Two consecutive palindromes span over a region of 200 kb, with conspicuous 20 kb stretches of highly conserved sequences among the four arms. The closely-related species S. suchowensis also has two copies of a portion of the palindrome arm and provides strong evidence for gene conversion. Four genes in the palindrome are homologous to genes in the SDR of the closely-related genus Populus, which is located on a different chromosome. These genes show distinct, floral-biased expression patterns compared to paralogous copies on autosomes.\n\nConclusionThe presence of palindromic structures in sex chromosomes of mammals and plants highlights the intrinsic importance of these features in adaptive evolution in the absence of recombination. Convergent evolution is driving both the independent establishment of sex chromosomes as well as their fine-scale sequence structure.

genomics↗