Biology subjects

Kreplak, J.

Publications and source records attributed to Kreplak, J..

5 recordsLinked to original sources

bioRxiv2023

afila, the origin and nature of a major innovation in the history of pea breeding

The afila (af) mutation of Pisum sativum L. (pea) is characterised by leaves that are composed of a basal pair of stipules, a petiole and a branched mass of tendrils. These are bipinnate leaves in which the leaflet primordia are replaced by midrib-like, or terminal tendril, primordia. The phenotype was first reported as a spontaneous mutation in 1953, and several reports of spontaneously occurring af mutants and induced mutations have been published since then. Despite its wide-scale introgression to improve standing ability in combine-harvested dry pea crops, the molecular basis of af has remained unknown. Here, we show that the deletion of two tandemly-arrayed Q-type Cys(2)His(2)-zinc finger transcription factors, viz. PsPALM1a and PsPALM1b, is responsible for the af phenotype. Based on molecular evidence for the presence/absence of seven consecutive pea genes, we identified eight haplotypes in the genomic region of chromosome 2 that harbours af. These haplotypes differ in the presence or absence of PsPALM1a-b and close genes and in the size of the deletion. Representative cultivars and spontaneous or induced mutants were assigned to the different haplotypes. The hitherto unrecognised diversity at the af locus reveals highly rich, unexplored, potential for pea improvement and sheds light on the breeding history of pea. This knowledge can also be used to breed innovative cultivars in related crops.

genetics↗

bioRxiv2022

Assembly of the 81.6 Mb centromere of pea chromosome 6 elucidates the structure and evolution of metapolycentric chromosomes

Centromeres in the legume genera Pisum and Lathyrus exhibit unique morphological characteristics, including extended primary constrictions and multiple separate domains of centromeric chromatin. These so-called metapolycentromeres resemble an intermediate form between monocentric and holocentric types, and therefore provide a great opportunity for studying the transitions between different types of centromere organizations. However, because of the exceedingly large and highly repetitive nature of metapolycentromeres, highly contiguous assemblies needed for these studies are lacking. Here, we report on the assembly and analysis of a 177.6 Mb region of pea (Pisum sativum) chromosome 6, including the 81.6 Mb centromere region (CEN6) and adjacent chromosome arms. Genes, DNA methylation profiles, and most of the repeats were uniformly distributed within the centromere, and their densities in CEN6 and chromosome arms were similar. The exception was an accumulation of satellite DNA in CEN6, where it formed multiple arrays up to 2 Mb in length. Centromeric chromatin, characterized by the presence of the CENH3 protein, was predominantly associated with arrays of three different satellite repeats; however, five other satellites present in CEN6 lacked CENH3. The presence of CENH3 chromatin was found to determine the spatial distribution of the respective satellites during the cell cycle. Finally, oligo-FISH painting experiments, performed using probes specifically designed to label the genomic regions corresponding to CEN6 in Pisum, Lathyrus, and Vicia species, revealed that metapolycentromeres evolved via the expansion of centromeric chromatin into neighboring chromosomal regions and the accumulation of novel satellite repeats. However, in some of these species, centromere evolution also involved chromosomal translocations and centromere repositioning. SignificanceDespite their conserved function, plant centromeres exhibit considerable variation in their morphology and sequence composition. For example, centromere activity is restricted to a single region in monocentric chromosomes, but is distributed along the entire chromosome length in holocentric chromosomes. The principles of centromere evolution that led to this variation are largely unknown, partly due to the lack of high-quality centromere assemblies. Here, we present an assembly of the pea metapolycentromere, a unique type of centromere that represents an intermediate stage between monocentric and holocentric organizations. This study not only provides a detailed insight into sequence organization, but also reveals possible mechanisms for the formation of the metapolycentromere through the spread of centromeric chromatin and the accumulation of satellite DNA.

genomics↗

bioRxiv2022

The giant diploid faba genome unlocks variation in a global protein crop

Increasing the proportion of locally produced plant protein in currently meat-rich diets could substantially reduce greenhouse gas emission and loss of biodiversity. However, plant protein production is hampered by the lack of a cool-season legume equivalent to soybean in agronomic value. Faba bean (Vicia faba L.) has a high yield potential and is well-suited for cultivation in temperate regions, but genomic resources are scarce. Here, we report a high-quality chromosome-scale assembly of the faba bean genome and show that it has grown to a massive 13 Gb in size through an imbalance between the rates of amplification and elimination of retrotransposons and satellite repeats. Genes and recombination events are evenly dispersed across chromosomes and the gene space is remarkably compact considering the genome size, though with significant copy number variation driven by tandem duplication. Demonstrating practical application of the genome sequence, we develop a targeted genotyping assay and use high-resolution genome-wide association (GWA) analysis to dissect the genetic basis of hilum colour. The resources presented constitute a genomics-based breeding platform for faba bean, enabling breeders and geneticists to accelerate improvement of sustainable protein production across Mediterranean, subtropical, and northern temperate agro-ecological zones.

plant biology↗

bioRxiv2022

SNP discovery by exome capture and resequencing in a pea genetic resource collection

Background & SummaryIn addition to being the model plant used by Mendel1 to establish genetic laws, pea (Pisum sativum L., 2n=14) is a major pulse crop cultivated in many temperate regions of the world. In order to face new challenges imposed particularly by global climate change and new regulations targeted at reducing chemical inputs, pea breeders have to take advantage of the genetic diversity present in the Pisum genepool to develop improved, resilient varieties. The aim of this study was to assess the genetic diversity of a pea germplasm collection and allow genome-wide association studies using this collection. To be able to perform genome-wide association approaches with high resolution, genotyping with a large set of genetic markers such as Single Nucleotide Polymorphism (SNP) markers well-spread over the genome is required. Rapid advances in second-generation sequencing technologies and the development of bioinformatic tools have revolutionized the access to and the characterization of available genetic diversity. High-density, high-throughput genotyping has been possible for a large number of species, including those with large and complex genomes2 such as pea (2n=14) which genome size is estimated to be 4.45 Gb3. In this study, which is part of the PeaMUST project4, we used a target capture technology based on pea transcriptome sequences to generate exome-enriched genomic libraries that were further subjected to Illumina sequencing in paired-end mode. This methodology was chosen because whole-genome resequencing is relatively expensive for species with large genomes and because capturing genetic variations in repeated non-coding regions is difficult to achieve or to interpret5. Whole-exome sequencing represented an interesting alternative that focused on coding regions only6,7. Mapping the obtained reads on the reference pea genome sequence enabled the discovery of an abundant set of SNPs. The development of this resource is a crucial cornerstone in research and breeding projects towards boosting the improvement of pea production and quality.

genomics↗

bioRxiv2022

Genetic analysis of global faba bean germplasm maps agronomic traits and identifies strong selection signatures for geographical origin

Faba bean (Vicia faba L.) is a high-protein grain legume crop with great potential for further cultivation. However, little is known about the genetics underlying trait diversity. In this study, we use 21,345 high-quality SNP markers to genetically characterise 2,678 faba bean genotypes. We perform genome-wide association studies of key agronomic traits using a Seven-parent-MAGIC population and detect 238 significant marker-trait associations linked to 12 traits of agronomic importance, with 65 of these being stable across multiple environments. Using a non-redundant diversity panel of 685 accessions from 52 countries, we identify 3 subpopulations differentiated by geographical origin and 33 genomic regions subject to strong diversifying selection between subpopulations. We find that SNP markers associated with the differentiation of northern and southern accessions were able to explain a significant proportion of agronomic trait variance in the Seven-parent-MAGIC population, suggesting that some of these traits have played an important role in breeding. Altogether, our findings point to genomic regions associated with important agronomic traits and selection in faba bean, which can be used for breeding purposes. Key MessageWe identified marker-trait associations for key faba bean agronomic traits and genomic signatures of selection within a global germplasm collection.

genetics↗