Identification of Candidate Genes for Salinity Tolerance and Their Application in Alfalfa Breeding


Biligetu B, Bhattarai S, Fu YB, Wang H. Identification of Candidate Genes for Salinity Tolerance and Their Application in Alfalfa Breeding. Plant and Animal Genome 30 Conference (PAG30), San Diego, CA, January 13-18, 2023

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This study applied the new technology called RNA-Seq to identify differently expressed genes in salt tolerant "Halo" and sensitive "Vernal" alfalfa cultivars for a marker-assisted breeding. The study found 237 differentially expressed genes and developed several useful genetic markers to identify salt-tolerant alfalfa lines. This research finding is significant for the Canadian alfalfa breeding.


Salt tolerance in alfalfa (Medicago sativa L.) is a complex trait controlled by multiple genes, involving different signaling pathways. Although recurrent selection under salt stress is an effective method for improving salt tolerance, molecular markers may be critical for detecting major genes involved in salt tolerance in alfalfa. We identified a total of 237 differentially expressed genes (DEGs) in leaves of the salt tolerant ‘Halo’ alfalfa and salt sensitive ‘ Vernal’ using an RNA-Seq analysis. Of these, 28 salt responsive candidate genes were highly expressed in ‘Halo’ under salt stress. We developed Kompetitive allele-specific Polymerase Chain Reaction (KASP) assay for the SNPs linked to the highly expressed genes. Then we genotyped four salt tolerant alfalfa breeding lines, in addition to ‘Halo’ and salt susceptible cultivar ‘Rangelander’. Our results showed that four cycles of recurrent selection have accumulated certain salt resistant related favorable alleles in the alfalfa breeding lines. Certain KASP markers were able to differentiate the six alfalfa populations used in the study. This indicates that these KASP markers can be used for detecting important alleles frequency associated with alfalfa salt tolerance.

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