title: The ecological genomic basis of salinity adaptation in Tunisian Medicago truncatula.
abstract: BACKGROUND
  As our world becomes warmer, agriculture is increasingly impacted by rising soil salinity and understanding plant adaptation to salt stress can help enable effective crop breeding. Salt tolerance is a complex plant phenotype and we know little about the pathways utilized by naturally tolerant plants. Legumes are important species in agricultural and natural ecosystems, since they engage in symbiotic nitrogen-fixation, but are especially vulnerable to salinity stress.
  
  
  RESULTS
  Our studies of the model legume Medicago truncatula in field and greenhouse settings demonstrate that Tunisian populations are locally adapted to saline soils at the metapopulation level and that saline origin genotypes are less impacted by salt than non-saline origin genotypes; these populations thus likely contain adaptively diverged alleles. Whole genome resequencing of 39 wild accessions reveals ongoing migration and candidate genomic regions that assort non-randomly with soil salinity. Consistent with natural selection acting at these sites, saline alleles are typically rare in the range-wide species' gene pool and are also typically derived relative to the sister species M. littoralis. Candidate regions for adaptation contain genes that regulate physiological acclimation to salt stress, such as abscisic acid and jasmonic acid signaling, including a novel salt-tolerance candidate orthologous to the uncharacterized gene AtCIPK21. Unexpectedly, these regions also contain biotic stress genes and flowering time pathway genes. We show that flowering time is differentiated between saline and non-saline populations and may allow salt stress escape.
  
  
  CONCLUSIONS
  This work nominates multiple potential pathways of adaptation to naturally stressful environments in a model legume. These candidates point to the importance of both tolerance and avoidance in natural legume populations. We have uncovered several promising targets that could be used to breed for enhanced salt tolerance in crop legumes to enhance food security in an era of increasing soil salinization.
authors.affiliation: Section of Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA. mfriesen@msu.edu.
authors.forename: Maren L
authors.initials: ML
authors.lastname: Friesen
authors.forename: Eric J B
authors.initials: EJ
authors.lastname: von Wettberg
authors.forename: Mounawer
authors.initials: M
authors.lastname: Badri
authors.forename: Ken S
authors.initials: KS
authors.lastname: Moriuchi
authors.forename: Fathi
authors.initials: F
authors.lastname: Barhoumi
authors.forename: Peter L
authors.initials: PL
authors.lastname: Chang
authors.forename: Sonia
authors.initials: S
authors.lastname: Cuellar-Ortiz
authors.forename: Matilde A
authors.initials: MA
authors.lastname: Cordeiro
authors.forename: Wendy T
authors.initials: WT
authors.lastname: Vu
authors.forename: Soumaya
authors.initials: S
authors.lastname: Arraouadi
authors.forename: Naceur
authors.initials: N
authors.lastname: Djébali
authors.forename: Kais
authors.initials: K
authors.lastname: Zribi
authors.forename: Yazid
authors.initials: Y
authors.lastname: Badri
authors.forename: Stephanie S
authors.initials: SS
authors.lastname: Porter
authors.forename: Mohammed Elarbi
authors.initials: ME
authors.lastname: Aouani
authors.forename: Douglas R
authors.initials: DR
authors.lastname: Cook
authors.forename: Sharon Y
authors.initials: SY
authors.lastname: Strauss
authors.forename: Sergey V
authors.initials: SV
authors.lastname: Nuzhdin
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D055669:Ecological and Environmental Phenomena; D019143:Evolution, Molecular; D005787:Gene Frequency; D056426:Genetic Loci / Q000235:genetics; D023281:Genomics; D046913:Medicago truncatula / Q000235:genetics* / Q000502:physiology*; D058977:Molecular Sequence Annotation; D011995:Recombination, Genetic; D054712:Salinity; D012641:Selection, Genetic; D012987:Soil / Q000737:chemistry; D013045:Species Specificity
chemical_list: D012987:Soil