Advancing Grain Legumes Domestication and Evolution Studies with Genomics

Unraveling Mendel's final mysteries: A genomic retelling of pea genetics

Using modern genomic tools, Feng et al. revisited Mendel's seven pea traits in a recent Nature study, uncovering the molecular genetic basis of all of them, including the three unresolved ones: pod color, pod shape, and flower position. Their work highlights the level of complexity provided by structural variation that could impact genes and their regulatory regions and thus influence the expression of plant traits. The authors demonstrate how revisiting foundational experiments with contemporary tools can manifest novel biological insights and also guide future crop improvement.

Genomic structure of yellow lupin (Lupinus luteus): genome organization, evolution, gene family expansion, metabolites and protein synthesis

Yellow lupin (Lupinus luteus) gives valuable high-quality protein and has good sustainability due to its ability in nitrogen fixation and exudation of organic acids, which reduces the need for chemical-based phosphate fertilization in acid soils. However, the crop needs further improvements to contribute in a major way to sustainable agriculture and food security.In this study, we present the first chromosome-level genome assembly of L. luteus. The results provide insights into its genomic organization, evolution, and functional attributes. Using integrated genomic approaches, we unveil the genetic bases governing its adaptive responses to environmental stress, delineating the intricate interplay among alkaloid biosynthesis, mechanisms of pathogen resistance, and secondary metabolite transporters. Our comparative genomic analysis of closely related species highlights recent speciation events within the Lupinus genus, exposing extensive synteny preservation alongside notable structural alterations, particularly chromosome translocations. Remarkable expansions of gene families implicated in terpene metabolism, stress responses, and conglutin proteins were identified, elucidating the genetic basis of L. luteus' superior nutritional profile and defensive capabilities. Additionally, a diverse array of disease resistance-related (R) genes was uncovered, alongside the characterization of pivotal enzymes governing quinolizidine alkaloid biosynthesis, thus shedding light on the molecular mechanisms underlying "bitterness" in lupin seeds.This comprehensive genomic analysis serves as a valuable resource to improve this species in terms of resilience, yield, and seed protein levels to contribute to food and feed to face the worldwide challenge of sustainable agriculture and food security.

What Are We Learning from Plant Pangenomes?

A single reference genome does not fully capture species diversity. By contrast, a pangenome incorporates multiple genomes to capture the entire set of nonredundant genes in a given species, along with its genome diversity. New sequencing technologies enable researchers to produce multiple high-quality genome sequences and catalog diverse genetic variations with better precision. Pangenomic studies have detected structural variants in plant genomes, dissected the genetic architecture of agronomic traits, and helped unravel molecular underpinnings and evolutionary origins of plant phenotypes. The pangenome concept has further evolved into a so-called super-pangenome that includes wild relatives within a genus or clade and shifted to graph-based reference systems. Nevertheless, building pangenomes and representing complex structural variants remain challenging in many crops. Standardized computing pipelines and common data structures are needed to compare and interpret pangenomes. The growing body of plant pangenomics data requires new algorithms, huge data storage capacity, and training to help researchers and breeders take advantage of newly discovered genes and genetic variants.

Deciphering PDH1's role in mung bean domestication: a genomic perspective on pod dehiscence

Mung bean (Vigna radiata) stands as a crucial legume crop in Asia, contributing to food security. However, our understanding of the underlying genetic foundation governing domesticated agronomic traits, especially those linked to pod architecture, remains largely unexplored. In this study, we delved into the genomic divergence between wild and domesticated mung bean varieties, leveraging germplasm obtained from diverse sources. Our findings unveiled pronounced variation in promoter regions (35%) between the two mung bean subpopulations, suggesting substantial changes in gene expression patterns during domestication. Leveraging transcriptome analysis using distinct reproductive stage pods and subpopulations, we identified candidate genes responsible for pod and seed architecture development, along with Genome-Wide Association Studies (GWAS) and Quantitative Trait Locus (QTL) analysis. Notably, our research conclusively confirmed PDH1 as a parallel domesticated gene governing pod dehiscence in legumes. This study imparts valuable insights into the genetic underpinnings of domesticated agronomic traits in mung bean, and simultaneously highlighting the parallel domestication of pivotal traits within the realm of legume crops.

Cell Mutagenic Autopolyploidy Enhances Salinity Stress Tolerance in Leguminous Crops

Salinity stress affects plant growth and development by causing osmotic stress and nutrient imbalances through excess Na+, K+, and Cl- ion accumulations that induce toxic effects during germination, seedling development, vegetative growth, flowering, and fruit set. However, the effects of salt stress on growth and development processes, especially in polyploidized leguminous plants, remain unexplored and scantly reported compared to their diploid counterparts. This paper discusses the physiological and molecular response of legumes towards salinity stress-based osmotic and ionic imbalances in plant cells. A multigenic response involving various compatible solutes, osmolytes, ROS, polyamines, and antioxidant activity, together with genes encoding proteins involved in the signal transduction, regulation, and response mechanisms to this stress, were identified and discussed. This discussion reaffirms polyploidization as the driving force in plant evolution and adaptation to environmental stress constraints such as drought, feverish temperatures, and, in particular, salt stress. As a result, thorough physiological and molecular elucidation of the role of gene duplication through induced autopolyploidization and possible mechanisms regulating salinity stress tolerance in grain legumes must be further studied.