Noam Chayut

Understanding seed longevity in genebanks is fundamental for effective long-term conservation of plant genetic resources. Although storage environment, species biology, seed age, and oxygen exposure are known to influence viability, substantial variation in germination among accessions stored under identical conditions suggests the presence of additional genetic determinants. Here, we analysed 947 barley seed lots (686 hulled and 261 hulless) across nine harvest years (1975–2017) to assess the relationship between seed viability and a broad range of phenotypic traits, including plant phenology, inflorescence and seed morphology, and seed macronutrient composition. Each harvest year represented a distinct set of genebank accessions cultivated under uniform field conditions and stored for equal durations. Hulled barley consistently exhibited higher viability than hulless barley, and grain protein content was negatively associated with germination in five of the seven years studied. Additionally, year-specific but statistically significant associations were detected for ear emergence timing and lemma pigmentation. These results underscore the value of comprehensive genebank descriptors and phenotypic metadata for improving predictions of seed longevity and supporting strategic germplasm conservation.

Globally, 5.94 million accessions are conserved across 867 genebanks, of which 41.5% (2.47 million) are cereal crop accessions. Only a small portion of global germplasm diversity has been marker-genotyped or genome-sequenced. Accurate identification of genebank accessions is essential to improve the efficiency and effectiveness of global genebanking. It is crucial for preserving the legacy knowledge associated with the germplasm and for maintaining its value to current plant science and breeding efforts. Existing practices generally fall into two categories: either expensive and complex, or inefficient, labour-intensive, and inaccurate. The first relies on high-resolution genomic sequences or saturated markers, while the second relies on morphological comparisons of regenerated plants with historical records. We propose a genotyping method based on a minimal set of Single Nucleotide Polymorphism (SNP) markers and exemplify its use on a genebank scale. We identified a small, effective set of SNPs that can differentiate between the global diversity of genebank accessions of barley (Hordeum vulgare and Hordeum spontaneum) and tetraploid wheat collections (Triticum turgidum) maintained at the Germplasm Resources National Capability at the John Innes Centre, UK. This approach offers a straightforward, automatable, and inexpensive alternative to traditional genebank crop descriptors used during seed regeneration and distribution. By establishing the minimal genomic resolution needed to distinguish genetically distinct accessions, we show that as few as 24 and 25 carefully chosen SNP markers for barley and durum wheat, respectively, can effectively differentiate individual accessions. Unlike morphology-based identification, which can detect mislabelling or contamination but often cannot prevent or correct such errors, our SNP-based molecular labelling enables error correction and the retrieval of lost germplasm identity. This study highlights how accuracy and reliability in germplasm management can be improved without costly whole-genome sequencing or resource-intensive analysis. We discuss the impact of this method on enhancing quality assurance in genebanks and its broader usefulness for the user community.

Background: Fast Neutron induced mutants in the background of Pisum sativum (pea) JI2822 have been described in several studies. Here, we sought to organise this collection of mutagenized lineages to make them accessible, to investigate the type and frequency of mutations and to investigate their utility for systematic screening for mutants. Results: We investigated the use of Axiom markers to detect deletion mutations by screening for null alleles, and compared this method to low coverage sequencing, where variation in read mapping depth was used to detect deletions. These mutation screens identified many large deletions, but duplications were also found. The deletion mutations were not necessarily single contiguous spans. Some involved one or more nearby locations, implying that Fast Neutron induced mutations can be complex. We identified PsMYB32 as the Fuscopurpureus ( Cr ) gene and we propose candidate genes for other mutations affecting floral architecture and wax deposition. The identification of PsMYB32 as Cr suggested PsMYB37 as a candidate for the Roseus ( Ce ) gene and the evidence for this is discussed. Conclusions: Our analysis of 210 M2 derived families by the skim-sequencing method identified deletions that cover a little over 15% of the pea genome. This suggests that the population of approximately 5,000 families should contain deletions covering a substantial fraction of the pea genome. We detected hemizygous deletions, so mutants severely compromised in fertility or viability may be accessible for study in this population. The public availability of this resource should facilitate further gene identification in pea; this study provides the background data to support further characterisation of these lines by sequencing.

Mendel¹ studied in detail seven pairs of contrasting traits in pea (Pisum sativum), establishing the foundational principles of genetic inheritance. Here we investigate the genetic architecture that underlies these traits and uncover previously undescribed alleles for the four characterized Mendelian genes^2,3,4,5,6,7, including a rare revertant of Mendel’s white-flowered a allele. Primarily, we focus on the three remaining uncharacterized traits and find that (1) an approximately 100-kb genomic deletion upstream of the Chlorophyll synthase (ChlG) gene disrupts chlorophyll biosynthesis through the generation of intergenic transcriptional fusion products, conferring the yellow pod phenotype of gp mutants; (2) a MYB gene with an upstream Ogre element insertion and a CLE peptide-encoding gene with an in-frame premature stop codon explain the v and p alleles, which disrupt secondary cell wall thickening and lignification, resulting in the parchmentless, edible-pod phenotype; and (3) a 5-bp exonic deletion in a CIK-like co-receptor kinase gene, in combination with a genetic modifier locus, is associated with the fasciated stem (fa) phenotype. Furthermore, we characterize genes and alleles associated with diverse agronomic traits, such as axil ring anthocyanin pigmentation, seed size and the ‘semi-leafless’ form. This study establishes a foundation for fundamental research, education in biology and genetics, and pea breeding practices.

The taxonomy of the tribe Fabeae (Vicieae) has long been problematic, but an analysis by Schaefer et al. in 2012 gave an exceptionally clear view of the tribe and noted the possibility that some nomenclatural adjustments may be required at some future date. These authors suggested several options, expressing some preferences. However, there has been a recent change to formally accepted names, implementing one of these possibilities, but without any additional relevant information. This change seems unjustified and unhelpful. We therefore present an argument for the retention, or re-instatement, of the genera Pisum, Vavilovia, and Lens until such time as new data support this requirement and there is no nomenclatural solution that is both accurate and convenient.

The taxonomy of the Fabeae (Vicieae) has long been problematic, but an analysis by Schaefer et al in 2012 gave an exceptionally clear view of the tribe and noted the possibility that some nomenclatural adjustments may be required at some future date. These authors suggested several options, expressing some preferences. However, there has been a recent change to formally accepted names implementing one of these possibilities, but without any additional relevant information. This change seems unjustified and unhelpful. We therefore present an argument for the retention, or re-instatement, of the genera Pisum, Vavilovia and Lens until such time as new data supports this requirement and there is no nomenclatural solution that is both accurate and convenient.

Pea, Pisum sativum , is an excellent model system through which Gregor Mendel established the foundational principles of inheritance. Surprisingly, till today, the molecular nature of the genetic differences underlying the seven pairs of contrasting traits that Mendel studied in detail remains partially understood. Here, we present a genomic and phenotypic variation map, coupled with haplotype-phenotype association analyses across a wide range of traits in a global Pisum diversity panel. We focus on a genomics-enabled genetic dissection of each of the seven traits Mendel studied, revealing many previously undescribed alleles for the four characterized genes, R , Le , I and A , and elucidating the gene identities and mutations for the remaining three uncharacterized traits. Notably, we identify: (1) a ca. 100kb deletion upstream of the Chlorophyll synthase ( ChlG ) gene, which generates aberrant transcripts and confers the yellow pod phenotype of gp mutants; (2) an in-frame premature stop codon mutation in a Dodeca-CLE41/44 signalling peptide which explains the parchmentless mutant phenotype corresponding to p ; and (3) a 5bp in-frame deletion in a CIK-like receptor kinase gene corresponding to the fasciated stem phenotype fa , which Mendel described in terms of flower position, and we postulate the existence of a Modifier of fa ( Mfa ) locus that masks this meristem defect. Mendel noted the pleiotropy of the a mutation, including inhibition of axil ring anthocyanin pigmentation, a trait we found to be controlled by allelic variants of the gene D within an R2R3-MYB gene cluster. Furthermore, we characterize and validate natural variation of a quantitative genetic locus governing both pod width and seed weight, characters that Mendel deemed were not sufficiently demarcated for his analyses. This study establishes a cornerstone for fundamental research, education in biology and genetics, and pea breeding practices.

Bread wheat ( Triticum aestivum ) is a globally dominant crop and major source of calories and proteins for the human diet. Compared to its wild ancestors, modern bread wheat shows lower genetic diversity caused by polyploidisation, domestication, and breeding bottlenecks ^1,2 . Wild wheat relatives represent genetic reservoirs, harbouring diversity and beneficial alleles that have not been incorporated into bread wheat. Here, we establish and analyse pangenome resources for Tausch’s goatgrass, Aegilops tauschii , the donor of the bread wheat D genome. This new pangenome facilitated the cloning of a disease resistance gene and haplotype analysis across a complex disease resistance locus, allowing us to discern alleles from paralogous gene copies. We also reveal the complex genetic composition and history of the bread wheat D genome, involving previously unreported contributions from genetically and geographically discrete Ae. tauschii subpopulations. Together, our results reveal the complex history of the bread wheat D genome and demonstrate the potential of wild relatives in crop improvement.

Genomic resources are becoming available for Pisum but to link these to phenotypic diversity requires well marked populations segregating for relevant traits. Here we describe two such resources. Two recombinant inbred populations, derived from wide crosses in Pisum are described. One high resolution mapping population involves cv Caméor, for which the first pea whole genome assembly was obtained, crossed to JI0281, a basally divergent P. sativum sativum landrace from Ethiopia. The other is an inter sub-specific cross between P. s. sativum and the independently domesticated P. s. abyssinicum. The corresponding genetic maps provide information on chromosome level sequence assemblies and identify structural differences between the genomes of these two Pisum subspecies. In order to visualise chromosomal translocations that distinguish the mapping parents, we created a simplified version of Threadmapper to optimise it for interactive 3-dimensional display of multiple linkage groups. The genetic mapping of traits affecting seed coat roughness and colour, plant height, axil ring pigmentation, leaflet number and leaflet indentation enabled the definition of their corresponding genomic regions. The consequence of structural rearrangement for trait analysis is illustrated by leaf serration. These analyses pave the way for identification of the underlying genes and illustrate the utility of these publicly available resources. Segregating inbred populations derived from wide crosses in Pisum, together with the associated marker data, are made publicly available for trait dissection. Genetic analysis of these populations is informative about chromosome scale assemblies, structural diversity in the pea genome and has been useful for the fine mapping of several discrete and quantitative traits.

Breeding crops resilient to climate change is urgently needed to help ensure food security. A key challenge is to harness genetic diversity to optimise adaptation, yield, stress resilience and nutrition. We examined the genetic and phenotypic diversity of the A.E. Watkins landrace collection of bread wheat ( Triticum aestivum ), a major global cereal, through whole-genome re-sequencing (827 Watkins landraces and 208 modern cultivars) and in-depth field evaluation spanning a decade. We discovered that modern cultivars are derived from just two of the seven ancestral groups of wheat, leaving five groups as previously untapped sources for breeding. This provides access to landrace-specific functional variations using structured germplasm, genotyping and informatics resources. Employing complementary genetic populations and approaches, we identified thousands of high-resolution quantitative trait loci (QTL) and significant marker–trait associations for major traits, revealing many Watkins-unique loci that can confer superior traits in modern wheat. Furthermore, we identified and functionally verified causative genes for climate-change adaptation, nutritional enhancement and resistance to wheat blast. Finally, we assessed the phenotypic effects of 44,338 Watkins-unique haplotypes, introgressed from 143 prioritised QTL in the context of modern cultivars, bridging the gap between landrace diversity and current breeding. This study establishes a framework for systematically utilising genetic diversity in crop improvement to achieve sustainable food security.