Genetic control of salt tolerance traits in seashore paspalum (Paspalum vaginatum Sw.)
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Seashore paspalum (Paspalum vaginatum Swartz) is an exceptionally salt tolerant grass species which inhabits warm, coastal areas around the world. Due to its growth habit and its ability to tolerate high levels of salt, it has been used as a turfgrass in locations near the sea and in other areas with water quality issues. Seashore paspalum’s ability to thrive in saline environments makes it an important resource that could contribute as a model to the study of salt tolerance in the grasses, but also as a potential source of salt tolerance genes that could be used for increasing the salt tolerance of other species. In general, the germplasm resources of crop species, including their wild-relatives, lack significant salt tolerance. For this reason, it has been difficult to develop salt tolerant cultivars in most crops. Despite this limitation, salinity is an increasingly important contributor to yield-limiting stress worldwide and the amount of arable land which is salt-affected is increasing annually. If the salt tolerance genes of seashore paspalum could be leveraged to increase salt tolerance in other crops, that could have broad implications for agriculture. With this in mind, we conducted a series of studies on seashore paspalum with the goal of identifying the genes which condition its high level of salt tolerance. In general, we elected to employ a genetic mapping approach. To identify a pair of paspalum lines for use as parents for a mapping population, we developed microsatellite markers and used them to complete a genetic diversity study on a panel of 90 diploid accessions. Two genetically diverse parents which were also identified as differing in salt tolerance were used to create an F1 mapping population. Using a genotyping-by-sequencing approach, we developed several thousand single nucleotide polymorphism markers and used them to construct a pair of genetic maps which were compared to the Sorghum bicolor and Setaria italica reference genomes. We screened the mapping population for a number of salt tolerance traits including sodium ion and potassium ion accumulation in leaves and the maintenance of high K+/Na+ ratios in leaves. We consistently identified QTL for each of these traits and used our comparative genomic analysis to identify seven total candidate genes in the two orthologous regions of sorghum. A survey of the reported functions of the closest characterized homologs of these candidates in Swiss-Prot suggested a possible role in the potassium accumulation and ion ratio traits for a high-affinity potassium transporter (HKT), while each of the positional candidates in the region associated with sodium accumulation seemed unlikely to confer the trait. A preliminary analysis of an RNA-Seq dataset generated from the parental lines confirmed expression of the HKT gene in leaves but not roots and also identified a metallothionein gene as a strong candidate for the sodium accumulation trait. Metallothionein transcripts are among the most highly expressed in both roots and leaves, show increased expression under salt, and exhibits higher expression in the paternal than maternal parent. Finally, in sorghum, a fragment with homology to the gene localizes to the region in paspalum which contains the sodium abundance QTL.