Biology subjects

Pillen, K.

Publications and source records attributed to Pillen, K..

14 recordsLinked to original sources

bioRxiv2026

Rate of meristem initiation driven by the MADS-WUS axis contributes to floral survival and inflorescence evolution in grasses

Crop domestication has repeatedly shaped inflorescence architecture to improve floral production, but mechanisms coordinating the rate of floral initiation, maturation and survival remain unclear. Combining morphometry, modelling and molecular genetic analyses, we show that floral production in the indeterminate barley (Hordeum vulgare L.) inflorescence follows an "initiate fast-die young" strategy orchestrated by a main MADS-box gene, SPIKELET INITIATION AND FERTILITY (SIF). SIF accomplishes this duality by coordinately terminating the inflorescence meristem via WUSCHEL and activating the floral meristem via APETALA1 (Vrn-H1). Hereby, the ancestral SIF "slow" allele promotes a timely commitment to floral maturation, whereas the derived "fast" allele permits more floral initiations. Postdomestication selection of SIF alleles thus enables diversified reproductive strategies in barley populations to maintain yield traits in the field. Finally, we show that a lineage-specific SIF duplication contributed to meristem fate transition and inflorescence evolution during Triticeae cold adaptation. Our results establish developmental rate as a key driver of architectural innovation and reproductive success.

plant biology↗

bioRxiv2024

Whole-Genome Sequencing of the Wild Barley Diversity Collection: A Resource for Identifying and Exploiting Genetic Variation for Cultivated Barley Improvement

To exploit allelic variation in Hordeum vulgare subsp. spontaneum, the Wild Barley Diversity Collection was evaluated for several agronomic traits and subjected to paired-end Illumina sequencing at [~]9X depth, generating 109.5 million single nucleotide polymorphisms after alignment to the Morex V3 assembly. A genome-wide association study of lemma color identified one marker-trait association (MTA) on chromosome 1HL close to HvBlp, the cloned gene controlling black lemma. Four MTAs were identified for stem rust resistance: one co-locating to the complex RMRL1-RMRL2 locus on 5HL, and three novel loci on 1HS, 1HL, and 5HL. Six MTAs for days to heading (DTH) on vernalized plants were identified on all chromosomes except 1H and 6H. Two MTAs for DTH on non-vernalized plants were identified on chromosomes 1HL and 2HS. All MTAs for DTH were novel. The whole genome sequence data described herein will facilitate the identification and utilization of new alleles for barley improvement.

genomics↗

bioRxiv2024

New loci and candidate genes in spring two-rowed barley detected through meta-analysis of a field trial European network

This study contributes new knowledge on quantitative trait loci (QTLs) and candidate genes for adaptive traits and yield in two-rowed spring barley. A meta-analysis of a network of field trials, varying in latitude and sowing date, with 151 cultivars across several European countries, increased QTL detection power compared to single-trial analyses. The traits analysed were heading date (HD), plant height (PH), thousand-grain weight (TGW), and grain yield (GY). Breaking down the analysis by the main genotype-by-environment trends revealed QTLs and candidate genes specific to conditions like sowing date and latitude. A historical look on the evolution of QTL frequencies revealed that early selection focused on PH and TGW, likely due to their high heritability. GY selection occurred later, facilitated by reduced variance in other traits. The study observed that favourable alleles for plant height were often fixed before those for grain yield and TGW. Some regions showed linkage in repulsion, suggesting targets for future breeding. Several candidate genes were identified, including known genes and new candidates based on orthology with rice. Remarkably, the deficiens allele of gene Vrs1, appears associated to higher GY. These findings provide valuable insights for barley breeders aiming to improve yield, and other agronomic traits. HighlightA dense genome-wide meta-analysis provides new QTLs, reveals breeding history trends and identifies new candidate genes for yield, plant height, grain weight and heading time of spring barley.

genetics↗

bioRxiv2024

Adaptive diversification through structural variation in barley

Pangenomes are collections of annotated genome sequences of multiple individuals of a species. The structural variants uncovered by these datasets are a major asset to genetic analysis in crop plants. Here, we report a pangenome of barley comprising long-read sequence assemblies of 76 wild and domesticated genomes and short-read sequence data of 1,315 genotypes. An expanded catalogue of sequence variation in the crop includes structurally complex loci that have become hot spots of gene copy number variation in evolutionarily recent times. To demonstrate the utility of the pangenome, we focus on four loci involved in disease resistance, plant architecture, nutrient release, and trichome development. Novel allelic variation at a powdery mildew resistance locus and population-specific copy number gains in a regulator of vegetative branching were found. Expansion of a family of starch-cleaving enzymes in elite malting barleys was linked to shifts in enzymatic activity in micro-malting trials. Deletion of an enhancer motif is likely to change the developmental trajectory of the hairy appendages on barley grains. Our findings indicate that rapid evolution at structurally complex loci may have helped crop plants adapt to new selective regimes in agricultural ecosystems.

plant biology↗

bioRxiv2023

Investigating the genetic control of plant development under speed breeding conditions

Speed breeding is a powerful tool to accelerate breeding and research programmes by shortening generation time and has been widely adopted for a range of crop species. Despite its success and growing popularity with breeders the genetic basis of plant development under speed breeding remains unknown. In this study, we explored how genotypes respond in terms of developmental advancement under different photoperiod regimes in the context of speed breeding. A subset of the barley HEB-25 Nested Association Mapping population was evaluated for days to heading and maturity under two contrasting photoperiod conditions: 1) Speed Breeding (SB) consisting of 22 hours of light and 2 hours of darkness), and 2) Normal Breeding (NB) consisting of 16 hours of light and 8 hours of darkness. GWAS revealed that developmental responses under both conditions were largely controlled by two loci: PPDH-1 and ELF3. Allelic variants at these genes determine whether plants display early flowering and maturity under both NB and SB. At key QTL regions, domesticated alleles were associated with late flowering and maturity in NB and early flowering and maturity in SB, whereas wild alleles were associated with early flowering under both conditions. We hypothesise that this may be related to the dark dependent repression of PPD-H1 by ELF3 which might be more prominent in NB conditions. Furthermore, by comparing development under two contrasting photoperiod regimes, we were able to derive an estimate of plasticity for the two traits. Interestingly, plasticity in development was largely attributed to allelic variation at ELF3. Our results have important implications for our understanding and optimisation of speed breeding protocols particularly when incorporating genetics from wild relatives into breeding programmes and the design of breeding programmes to support the delivery of climate resilient crops.

plant biology↗

bioRxiv2023

Dynamic phytomeric growth contributes to local adaptation in barley

Vascular plants segment their body axis with iterative nodes of lateral branches and internodes. Appropriate node initiation and internode elongation are fundamental to plant fitness and crop yield formation; but how they are spatiotemporally coordinated remains elusive. We show that in barley (Hordeum vulgare L.), selections under domestication have extended the apical meristematic phase to promote node initiation, but constrained subsequent internode elongation. In both vegetative and reproductive axes, internode elongation displays a dynamic proximal - distal gradient, and among subpopulations of domesticated barleys at the global range, node initiation and proximal internode elongation are associated with latitudinal and longitudinal gradients, respectively. Genetic and functional analysis suggest that, in addition to their converging roles in node initiation, flowering time genes are repurposed to specify the dynamic internode elongation. Our study provides an integrated view of barley node initiation and internode elongation, and suggests that plant architecture has to be recognized as dynamic phytomeric units in the context of crop evolution.

plant biology↗

bioRxiv2022

An exotic allele of barley EARLY FLOWERING 3 contributes to developmental plasticity at elevated temperatures

Increase in ambient temperatures caused by climate change affects various morphological and developmental traits of plants, threatening crop yield stability. In the model plant Arabidopsis thaliana, EARLY FLOWERING 3 (ELF3) plays prominent roles in temperature sensing and thermomorphogenesis signal transduction. However, how crop species respond to elevated temperatures is poorly understood. Here, we show that the barley ortholog of AtELF3 interacts with high temperature to control growth and development. We used heterogeneous inbred family (HIF) pairs generated from a segregating mapping population and systematically studied the role of exotic ELF3 variants in barley temperature responses. An exotic ELF3 allele from Syrian origin promoted elongation growth in barley at elevated temperatures, whereas plant area and estimated biomass were drastically reduced, resulting in an open canopy architecture. The same allele accelerated inflorescence development at high temperature, which correlated with early transcriptional induction of MADS-box floral identity genes BM3 and BM8. Consequently, barley plants carrying the exotic ELF3 allele displayed stable total grain number and mitigated yield loss at elevated temperatures. Our findings therefore demonstrate that exotic ELF3 variants can contribute to phenotypic and developmental acclimation to elevated temperatures, providing a stimulus for breeding of climate resilient crops. HighlightWe demonstrate that an exotic allele of EARLY FLOWERING 3 (ELF3) contributes to plant architectural and developmental acclimation, and thereby improves yield stability at high ambient temperatures.

plant biology↗

bioRxiv2022

Exotic alleles of EARLY FLOWERING 3 determine plant development and grain yield in barley

EARLY FLOWERING 3 (ELF3) is an important regulator of various physiological and developmental processes and hence may serve to improve plant adaptation which will be substantial for future plant breeding. To expand the limited knowledge on barley ELF3 in determining agronomic traits, we conducted field studies with heterogeneous inbred families (HIFs) derived from selected lines of the wild barley nested association mapping population HEB-25. During two growing seasons, phenotypes of nearly isogenic HIF sister lines, segregating for exotic and cultivated alleles at the ELF3 locus, were compared for ten developmental and yield-related traits. We determine novel exotic ELF3 alleles and show that HIF lines, carrying the exotic ELF3 allele, accelerated plant development compared to the cultivated ELF3 allele, depending on the genetic background. Remarkably, the most extreme phenotypic effects could be attributed to one exotic ELF3 allele, differing in only one SNP from the cultivated Barke ELF3 allele. This SNP causes an amino acid change, which predictively has an impact on the protein structure of ELF3, thereby possibly affecting phase separation behaviour and nano-compartment formation of ELF3 and, potentially, also affecting its local cellular interactions causing significant trait differences between HIF sister lines.

genetics↗

bioRxiv2021

IDENTIFYING PLANT GENES SHAPING MICROBIOTA COMPOSITION IN THE BARLEY RHIZOSPHERE

A prerequisite to exploiting soil microbes for sustainable crop production is the identification of the plant genes shaping microbiota composition in the rhizosphere, the interface between roots and soil. Here we use metagenomics information as an external quantitative phenotype to map the host genetic determinants of the rhizosphere microbiota in wild and domesticated genotypes of barley, the fourth most cultivated cereal globally. We identify a small number of loci with a major effect on the composition of rhizosphere communities. One of those, designated the QRMC-3HS, emerges as a major determinant of microbiota composition. We subject soil-grown sibling lines harbouring contrasting alleles at QRMC-3HS and hosting contrasting microbiotas to comparative root RNA-seq profiling. This allows us to identify three primary candidate genes, including a Nucleotide-Binding-Leucine-Rich-Repeat (NLR) gene in a region of structural variation of the barley genome. Our results provide insights into the footprint of crop improvement on the plants capacity of shaping rhizosphere microbes.

plant biology↗

bioRxiv2021

The genetic diversity of Ethiopian barley genotypes in relation to their geographical origin

Ethiopia is recognized as a center of diversity for barley, and its landraces are known for the distinct genetic features compared to other barley collections. The genetic diversity of Ethiopian barley likely results from the highly diverse topography, altitude, climate conditions, soil types, and farming systems. To get detailed information on the genetic diversity a panel of 260 accessions, comprising 239 landraces and 21 barley breeding lines, obtained from the Ethiopian biodiversity institute (EBI) and the national barley improvement program, respectively were studied for their genetic diversity using the 50k iSelect single nucleotide polymorphism (SNP) array. A total of 983 highly informative SNP markers were used for structure and diversity analysis. Three genetically distinct clusters were obtained from the structure analysis comprising 80, 71, and 109 accessions, respectively. Analysis of molecular variance (AMOVA) revealed the presence of higher genetic variation (89%) within the clusters than between the clusters (11%), with moderate genetic differentiation (PhiPT=0.11) and adequate gene flow (Nm=2.02). The Mantel test revealed that the genetic distance between accessions is poorly associated with their geographical distance. Despite the observed weak correlation between geographic distance and genetic differentiation, for some regions like Gonder, Jimma, Gamo-Gofa, Shewa, and Welo, more than 50% of the landraces derived from these regions are assigned to one of the three clusters.

genetics↗

bioRxiv2020

On the origin of photoperiod non-responsiveness in barley

In barley, the transition from the vegetative to reproductive phase is complex and under the control of photoperiodic and temperature conditions. One major gene involved is PPD-H1, a PSEUDO-RESPONSE REGULATOR 7 (PRR7) that encodes a component of the circadian clock. Mutation at PPD-H1 resulted in the photoperiod non-responsive ppd-H1 alleles that are beneficial under high latitudinal environments as they allow vegetative growth during the long-day summer conditions whereby higher yields are harvested by farmers. Utilizing a diverse GWAS panel of world-wide origin and a genome-wide gene-based set of 50K SNP markers, a strong association of days to heading with the PPD-H1 gene was detected in multi-location field trials. Re-sequencing of the gene spanning putative causative SNPs, SNP22 (Turner et al. 2005) and SNP48 (Jones et al. 2008), detected recombination between the two, previously reported to be in complete LD. Phenotyping of the recombinants and phylogenetic relationships among haplotypes supported the original conclusion of Turner et al. (2005) that SNP22, present in the CCT domain, is the most likely causative SNP. To infer the origin of non-responsiveness, the PPD-H1 gene was re-sequenced in a geo-referenced collection of 2057 wild and domesticated barleys and compared with the allelic status of the 6000-year-old barley sample from the Yoram cave in the Masada cliff. A monophyletic and post-domestication origin in the Fertile Crescent was found in contrast to the pre-domestication origin proposed by Jones et al. (2008). We show that the photoperiod non-responsiveness originated from Desert type wild barley in the Southern Levant.Competing Interest StatementThe authors have declared no competing interest.View Full Text

plant biology↗

bioRxiv2020

Loss of Photosynthetic Rhythm Thermal Plasticity Under Domestication and RepurposingDrivers of Circadian Clock (DOC) Loci for Adaptive Breeding in Barley

Circadian clock rhythms are critical to control physiological and development traits, allowing, plants to adapt to changing environments. Here we show that the circadian rhythms of cultivated barley (Hordeum vulgare) have slowed and amplitude increased under domestication by comparing with its wild ancestor (H. spontaneum). Moreover, we show a significant loss of thermal plasticity during barley evolution for the period and more extensively for amplitude. Our genetic analysis indicates that wild allele at epistatic loci, which mutually condition clock variation and its thermal plasticity in interspecific crosses, are absent in a contemporary barley breeding panel. These epistatic interactions include conditioned effects of Drivers of Circadian (DOC) clock loci on chromosome 3 and 5, which mediate amplitude decrease and period lengthening, respectively, under domestication. Notably, two significant loci, DOC3.1 and DOC5.1, which are not associated with clock diversity in cultivated breeding material, do show pleiotropic effects on flowering time and grain yield at multiple experimental sites across the U.S. in a temperature-dependent manner. We suggest that transition from winter growth of wild barley (H. spontaneum) to spring growth of modern cultivars included the loss and repurposing of circadian clock regulators to yield adaptation by mechanisms yet to be clarified. Significance statementCircadian clock rhythms are crucial factors affecting crop adaptation to changing environments. If faced with increased temperature plants could respond with temperature compensation adaptation and maintain clock rhythms, or they can change period and/or amplitude to adapt. We used a combination of approaches: high-throughput clock analysis under optimal and elevated heat conditions, genome-wide association study (GWAS) with cultivated and wild diversity panels to identify changes under domestication and quantitative trait loci (QTL) that control the clock and its responses, and QTL-environment association for testing environmentally-conditioned effects of these QTLongrain yield and flowering timingacross US. Our findings provide insights into changes of circadian rhythms under domestication and genetic tools for plant breeders to develop better-adapted cultivars to changing environments.

genetics↗

bioRxiv2018

Barley yield formation under abiotic stress depends on the interplay between flowering time genes and environmental cues

Since the dawn of agriculture, crop yield has always been impaired through abiotic stresses. In a field trial across five locations worldwide, we tested three abiotic stresses, nitrogen deficiency, drought and salinity, using HEB-YIELD, a selected subset of the wild barley nested association mapping population HEB-25. We show that barley flowering time genes Ppd-H1, Sdw1, Vrn-H1 and Vrn-H3 exert pleiotropic effects on plant development and grain yield. Under field conditions, these effects are strongly influenced by environmental cues like day length and temperature. For example, in Al-Karak, Jordan, the day length-sensitive wild barley allele of Ppd-H1 was associated with an increase of grain yield by up to 30% compared to the insensitive elite barley allele. The observed yield increase is accompanied by pleiotropic effects of Ppd-H1 resulting in shorter life cycle, extended grain filling period and increased grain size. Our study indicates that the adequate timing of plant development is crucial to maximize yield formation under harsh environmental conditions. We provide evidence that wild barley germplasm, introgressed into elite barley cultivars, can be utilized to improve grain yield. The presented knowledge may be transferred to related crop species like wheat and rice securing the rising global food demand for cereals.

genetics↗

bioRxiv2017

Genome scan identifies flowering-independent effects of barley HsDry2.2 locus on yield traits under water deficit

Increasing crop productivity under climate change requires the identification, selection and utilization of novel alleles for breeding. We analyzed the genotype and field phenotype of the barley HEB-25 multi-parent mapping population under well-watered and water-limited (WW and WL) environments for two years. A genome-wide association study (GWAS) for genotype by-environment interactions was performed for ten traits including flowering time (HEA), plant grain yield (PGY). Comparison of the GWAS for traits per-se to that for QTL-by-environment interactions (QxE), indicates the prevalence of QxE mostly for reproductive traits. One QxE locus on chromosome 2, Hordeum spontaneum Dry2.2 (HsDry2.2), showed a positive and conditional effect on PGY and grain number (GN). The wild allele significantly reduced HEA, however this earliness was not conditioned by water deficit. Furthermore, BC2F1 lines segregating for the HsDry2.2 showed the wild allele confers an advantage over the cultivated in PGY, GN and harvest index as well as modified shoot morphology, longer grain filling period and reduced senescence (only under drought), therefore suggesting adaptation mechanism against water deficit other than escape. This study highlights the value of evaluating wild relatives in search of novel alleles and clues to resilience mechanism underlying crop adaptation to abiotic stress.\n\nHighlightA flowering-time independent reproductive advantage of wild over cultivated allele under drought identified in a barley GWAS for genotype-by-environment interactions, with modified shoot morphology, reduced senescence and longer grain filling

genetics↗