Transcript analysis in two alfalfa salt tolerance selected breeding populations relative to a non-tolerant population

Genome. 2017 Feb;60(2):104-127. doi: 10.1139/gen-2016-0111. Epub 2016 Oct 7.


With the growing limitations on arable land, alfalfa (a widely cultivated, low-input forage) is now being selected to extend cultivation into saline lands for low-cost biofeedstock purposes. Here, minerals and transcriptome profiles were compared between two new salinity-tolerant North American alfalfa breeding populations and a more salinity-sensitive western Canadian alfalfa population grown under hydroponic saline conditions. All three populations accumulated two-fold higher sodium in roots than shoots as a function of increased electrical conductivity. At least 50% of differentially expressed genes (p < 0.05) were down-regulated in the salt-sensitive population growing under high salinity, while expression remained unchanged in the saline-tolerant populations. In particular, most reduction in transcript levels in the salt-sensitive population was observed in genes specifying cell wall structural components, lipids, secondary metabolism, auxin and ethylene hormones, development, transport, signalling, heat shock, proteolysis, pathogenesis-response, abiotic stress, RNA processing, and protein metabolism. Transcript diversity for transcription factors, protein modification, and protein degradation genes was also more strongly affected in salt-tolerant CW064027 than in salt-tolerant Bridgeview and salt-sensitive Rangelander, while both saline-tolerant populations showed more substantial up-regulation in redox-related genes and B-ZIP transcripts. The report highlights the first use of bulked genotypes as replicated samples to compare the transcriptomes of obligate out-cross breeding populations in alfalfa.

Keywords: RNA-Seq; abiotic stress; alfalfa; luzerne; salinity; salinité; stress abiotique; transcriptome.

MeSH terms

  • Breeding*
  • Computational Biology / methods
  • Gene Expression Profiling*
  • Gene Expression Regulation, Plant
  • High-Throughput Nucleotide Sequencing
  • Ions / metabolism
  • Medicago sativa / genetics*
  • Medicago sativa / metabolism*
  • Minerals / metabolism
  • Molecular Sequence Annotation
  • Plant Growth Regulators / genetics
  • Salinity
  • Salt Tolerance / genetics*
  • Stress, Physiological / genetics
  • Transcriptome*


  • Ions
  • Minerals
  • Plant Growth Regulators