Caroline Callot

Since the beginning of the 20th century, the growth of the world's population and industrial development have led to increased soil pollution with metals, which poses a threat to the environment and human health. In this context, plants that are adapted to metalliferous soils and hyperaccumulate metals offer an opportunity to develop phytotechnologies for remediating metal-polluted soils. However, the molecular mechanisms by which plants tolerate and hyperaccumulate metals are not yet fully understood, which limits the improvement of these technologies. The metal hyperaccumulator species Noccaea caerulescens, belonging to the Brassicaceae family, is being developed as a genetic model to decipher these mechanisms. In this study, we have significantly improved the genome assembly of the N. caerulescens Cira accession and have produced high-quality assemblies for five additional accessions originating from different soil types and genetic groups. We used these high-quality assemblies to identify gene copy number variation associated with the metal hyperaccumulation trait in the Noccaea genus. Our analysis revealed that gene copy number variation affects a wide variety of biological functions in Noccaea, including genes that encode metal transporters belonging to the HMA, NRAMP and ZIP families. Notably, duplications affecting the magnesium transporter MGR2 suggest that the adaptation to ultramafic soils may be an ancestral trait in Noccaea. Finally, the association of transposable elements with gene duplications suggests that transposon activity may have played an important role in the evolution of metal hyperaccumulation in this genus.

Since the beginning of the 20th century, the growth of the world’s population and industrial development have led to increased soil pollution with metals, which poses a threat to the environment and human health. In this context, plants that are adapted to metalliferous soils and hyperaccumulate metals offer an opportunity to develop phytotechnologies for remediating metal-polluted soils. However, the molecular mechanisms by which plants tolerate and hyperaccumulate metals are not yet fully understood, which limits the improvement of these technologies. The metal hyperaccumulator species Noccaea caerulescens , belonging to the Brassicaceae family, is being developed as a genetic model to decipher these mechanisms. In this study, we have significantly improved the genome assembly of the N. caerulescens Cira accession and have produced high-quality assemblies for five additional accessions originating from different soil types and genetic groups. We used these high-quality assemblies to identify gene copy number variation associated with the metal hyperaccumulation trait in the Noccaea genus. Our analysis revealed that gene copy number variation affects a wide variety of biological functions in Noccaea , including genes that encode metal transporters belonging to the HMA, NRAMP and ZIP families. Notably, duplications affecting the magnesium transporter MGR2 suggest that the adaptation to ultramafic soils may be an ancestral trait in Noccaea . Finally, the association of transposable elements with gene duplications suggests that transposon activity may have played an important role in the evolution of metal hyperaccumulation in this genus.

The nitrogen-fixing root nodule symbiosis (RNS) is specifically formed by four orders of angiosperms. The largest of these four orders includes the legume family, the Fabaceae. Among legumes, historical model species have emerged, such as the RNS-forming Medicago truncatula and Lotus japonicus, or, more recently, Aeschynomene evenia. By contrast, legume species that have lost RNS have been largely ignored. Here, we describe the first near chromosome-level assembly for a non-RNS-forming legume, the tropical Papilionoideae Nissolia brasiliensis. We compared its genome to closely related legumes and identified genes associated with RNS. Finally, we developed a stable transformation protocol that can be deployed in the future to re-evolve RNS in legumes, a first step toward the goal of engineering RNS in non-legume crops.

Understanding the genetic basis of root architecture and its relevance for crop productivity can contribute to the sustainable intensification of agriculture. Leveraging the phenotypic and allelic diversity of an Austrian maize landrace, we dissected the genetic basis of lateral root (LR) length across developmental stages. LR length, a relevant trait for breeding resource-efficient varieties, showed high heritability in our experiments. We discovered eight quantitative trait loci (QTL) for LR length at the reproductive stage R2, overlapping with four QTL at stage R6 but not with QTL detected at vegetative stage V6, suggesting that the genetic regulation of LR length might differ in vegetative and reproductive stages. We fine-mapped qlr1, the most significant QTL for LR length, to a region of 2.3 Mb containing 46 annotated genes. Based on whole-genome sequence and comparative genomics analyses we suggest a candidate gene underlying qlr1. Additionally, we examined the impact of nitrogen, phosphorus, and irrigation treatments on root and shoot development, finding that LR length positively correlates with biomass accumulation under optimal nutrient supply but not under nitrogen stress. Our work provides insights into the genetic regulation of LR length in maize and its relevance for the adaptation to diverse growing environments.