PI: Sergey Nuzhdin, University of Southern California Co-PI: Eric von Wettberg, University of California, Davis
Legume plants, including the agriculturally important species soybean, alfalfa, pea, and bean, collaborate with rhizobium bacteria to convert atmospheric nitrogen to biologically available ammonia. This property has enabled legumes to colonize marginal habitats and provides an ideal system to study how coevolution promotes adaptation to stressful environments. The model legume Medicago truncatula is a close relative of alfalfa and grows naturally in both highly saline soils across North Africa as well as on normal soils. In collaboration with Tunisian and French researchers, this research project will use genomic resources to understand how Medicago and its partner Sinorhizobium have adapted to saline soil. The main goal of this research is to identify both the genes and the genetic and biochemcial networks that underlie ecological differences between saline-adapted and non-adapted populations. By measuring the effects of these genes and networks under the natural conditions that plants experience, this research has the unique potential to bridge genetics, ecology, and evolution.
Statement broader impacts Soil salinisation is a growing problem with the potential to impact up to one third of agricultural land world-wide. Thus, understanding how abiotic factors, including salinity, impact symbiotic efficiency represents an important challenge for agriculture both in the developed and developing world. Since Medicago truncatula is a model species, the genes and pathways identified in this research will be directly applicable to breeding efforts to improve many agriculturally important legumes and more broadly to plant biology as a whole. The interdisciplinary and inter-continental nature of this project further provides an exceptional training opportunity. This project will integrate Tunisian and American teams-facilitated by generous matching funds from public (UC Davis) and private (USC) institutions-by cooperatively performing field experiments in Tunisia and through the exchange of personnel. Tunisian students and scholars will be hosted at the US institutions where they will engage in research, undertake individually-tailored coursework, and make contacts that will spur their professional growth. American undergraduate and graduate students will benefit via hands-on research experience, individual mentored projects, and the opportunity to participate in workshops and conferences in North Africa.
All data generated by this research will be made publicly available at http://nlab.usc.edu. The project website will be publicly accessible with released data and project updates. The genotyping array, and the genotype and phenotype data collected will serve as a community resource enabling future work on Medicago. The results of this research will be published in peer-reviewed open-access journals, made accessible to the American and African media, and presented by junior members of the team at international meetings across the globe.
The current NSF PGRP (#0703316 to Nuzhdin, von Wettberg, Cook, and Strauss) activities have been global in scope – including collaborators from Tunisia, Australia and Portugal – and fostered undergraduate, graduate, and post-doctoral level trainees. Several key outcomes have been obtained: 1): Replicate saline and non-saline populations of Mtr in Tunisia are locally adapted to salt stress: In a reciprocal transplant experiment of 40 genotypes in field-collected soils from the four sites where these genotypes originated, , and in soils with artificially manipulated salininy, saline origin genotypes tended to outperform non-saline origin genotypes on saline field soils but were outperformed on non-saline field soils. 2) Whole-genome Illumina re-sequencing of 40 of our Tunisian Mtr genotypes: We identified genomic regions that may contribute to performance differences among saline- and non-saline-origin genotypes. We identified 16 genomic regions, containing 57 candidate genes with non-synonymous soil-assorting SNPs and including Constans (CO), a zinc-finger transcription activator that controls the expression of floralinductive genes 3) New germplasm resources to enable model legume biology: We undertook the development of a novel germplasm resource for the Mtr research community to have many accessions from a each of two populations for GWAS. 4) Nodulation RNAseq reveals crosstalk between nodulation, root development and possibly flowering time. 5) Transgenerational epigenetic inheritance modifies salinity tolerance and patterns of selection: Parental environments (PEs) influence phenotypes, and we quantified the influences of soil salinity of parents on offspring phenotypes using 40 Mtr genotypes. For many traits, including biomass production and flowering time , plant genotypes had distinct responses to PE. Four Mtr genotypes were analysed for PE contributions to maternally-derived transcripts in mature seed. Among 4,358 expressed genes, GO analysis pointed to stress response, epigenetics, postembryonic development, protein and lipid and carbohydrate metabolism, catabolic and biosynthetic processes, DNA and protein precursors and translation. 6) Mtr-Rhizobium epistasis for salinity response: To investigate the role of rhizobial symbionts on salt tolerance, we grew six Mtr genotypes factorially with fully sequenced strains Sinorhizobium melioti Rm1021 and Sinorhizobium medicae WSM419 at three salt concentrations in aseptic nutrient agar; finding a Mtr x strain x salt interaction for shoot length. 7) The core and pan-genomes of legume symbiont populations: To study legume-rhizobium coadaptation, we characterized the draft genomes of a collection of wild symbiotic Mesorhizobium isolates with known nickel tolerance profiles. 8) Transcriptome analysis of the Medicago relatives Melilotus siculus (Mes) and Melilotus albus (Mea): To gain insight on highly salt tolerant relative of Mtr, Mes, we took a transcriptome approach. Water-logging treatment causes massive shifts in the transcriptome in Mea, including upregulation of central metabolism. 9) Mtr-M. littoralis (Mli) hybrid zone in Portugal: Mli occurs in sandy shores and Mtr in moderate to heavy soils, overlapping with intermediate hybrid forms. These hybrids may reveal novel sources of adaptation to soil salinity/texture. We found a species by treatment interactions where hybrids had a lower decrease on root growth rate with increasing salt concentration and where roots tend to get thicker at a higher rate than the "pure" parent species. 10) Development of a Generic Model Organism Database phenotype schema and prototype web interface: To facilitate our research while simultaneously contributing synergistically to the broader community of biologists working to develop interoperable databases for phenotype data, we co-developed the Chado "Natural Diversity" module. 11) Broader Impacts. We have fulfilled an ambitious training program to bring together scientists from the US, Tunisia, Mexico, France, Australia, and Portugal. Foreign scholars have been hosted at USC, UCD, and FIU, where they have participated in cutting-edge research, trained in new genomic tools, and made contacts to enhance their professional growth. These exchanges, which include joint field and lab work in Tunisia, have opened new doors in terms of access to technology and knowledge. Similarly, Undergraduate and Graduate Fellows from the US have benefited from project sponsored seminars, hands-on research experience, mentored individual projects, and interactions with scholars and agronomists from around the world. Both postdocs co-leading this project have secured independent positions: E. von Wettberg is an Assistant Professor at FIU; and M. Friesen is starting tenure-track Assistant Professor in Michigan State Univerisity.
