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Wild species in the genus Vigna are a great resource of tolerance to various stresses including salinity. We have previously screened the genetic resources of the genus Vigna and identified several accessions that have independently evolved salt tolerance. However, many aspects of such tolerance have remained unknown. Thus, we used autoradiography with radioactive sodium (22Na+) and Inductively Coupled Plasma Mass Spectrometry (ICP-MS) to visualize and compare Na+ allocation in Vigna angularis (Willd.) Ohwi & H.Ohashi (azuki bean), Vigna nakashimae (Ohwi) Ohwi & H.Ohashi, Vigna riukiuensis (Ohwi) Ohwi & H.Ohashi, Vigna luteola (Jacq.) Benth. and Vigna marina (Burm.) Merr.. The results indicated: 1) Tolerant accessions suppress Na+ accumulation compared to azuki bean. 2) V. nakashimae and V. marina does so by accumulating higher amount of K+, whereas V. riukiuensis and V. luteola does so by other mechanisms. 3) V. luteola avoids salt-shedding by allocating excess Na+ to newly expanded leaves. As the mechanisms of the tolerant species were different, they could be piled up in a single crop via classical breeding or by genetic engineering or genome editing. [ABSTRACT FROM AUTHOR]

Salt tolerance has been an important issue as a solution for soil salinization and groundwater depletion. To challenge this issue, genetic diversity of wild plants must be harnessed. Here we report a discovery of a candidate gene for salt tolerance in Vigna nakashimae, one of the coastal species in the genus Vigna. Using intraspecific variation, we performed a forward genetic analysis and identified a strong QTL region harboring ~200 genes. To further narrow down the candidate genes, we performed a comparative transcriptome analysis, using the genome sequence of azuki bean (V. angularis) as a reference. However the detected differentially-expressed genes (DEGs) did not include those related to salt tolerance. As we suspected that the target gene in V. nakashimae is missing in V. angularis, we sequenced the whole genome sequence of V. nakashimae with long-reads. By re-analyzing the transcriptome data with the new reference genome, we successfully identified POCO1 as a candidate gene, which was missing not only in V. angularis but also in the salt-sensitive accession of V. nakashimae. Further comparative analysis revealed that the tolerant genotypes conserved the ancestral form of the locus, while the sensitive genotypes did not. We also emphasize the pitfalls in our study, such as position effect in a growth chamber, missing important genes in the reference genome, and limited reproducibility of RNA-seq experiments. [ABSTRACT FROM AUTHOR]

Salt tolerance has been an important issue as a solution for soil salinization and groundwater depletion. To challenge this issue, genetic diversity of wild plants must be harnessed. Here we report a discovery of a can‐ didate gene for salt tolerance in Vigna nakashimae, one of the coastal species in the genus Vigna. Using in‐ traspecific variation, we performed a forward genetic analysis and identified a strong QTL region harboring ~200 genes. To further narrow down the candidate genes, we performed a comparative transcriptome analy‐ sis, using the genome sequence of azuki bean (V. angularis) as a reference. However the detected differen‐ tially-expressed genes (DEGs) did not include those related to salt tolerance. As we suspected that the target gene in V. nakashimae is missing in V. angularis, we sequenced the whole genome sequence of V. nakashimae with long-reads. By re-analyzing the transcriptome data with the new reference genome, we successfully identified POCO1 as a candidate gene, which was missing not only in V. angularis but also in the salt-sensi‐ tive accession of V. nakashimae. Further comparative analysis revealed that the tolerant genotypes conserved the ancestral form of the locus, while the sensitive genotypes did not. We also emphasize the pitfalls in our study, such as position effect in a growth chamber, missing important genes in the reference genome, and limited reproducibility of RNA-seq experiments. [ABSTRACT FROM AUTHOR]