Abstract
BackgroundSalinity severely limits wheat production in many parts of the world. Development of salt tolerant varieties represents the most practical option for enhancing wheat production from these areas. Application of marker assisted selection may assist in fast tracking development of salt tolerant wheat varieties. However, SSR markers available in the public domain are not specifically targeted to functional regions of wheat genome, therefore large numbers of these need to be analysed for identification of markers associated with traits of interest. With the availability of a fully annotated wheat genome assembly, it is possible to develop SSR markers specifically targeted to genic regions. We performed extensive analysis to identify candidate gene based SSRs and assessed their utility in characterizing molecular diversity in a panel of wheat genotypes.ResultsOur analysis revealed, 161 SSR motifs in 94 salt tolerance candidate genes of wheat. These SSR motifs were nearly equally distributed on the three wheat sub-genomes; 29.8% in A, 35.7% in B and 34.4% in D sub-genome. The maximum number of SSR motifs was present in exons (31.1%) followed by promoters (29.8%), 5’UTRs (21.1%), introns (14.3%) and 3’UTRs (3.7%). Out of the 65 candidate gene based SSR markers selected for validation, 30 were found polymorphic based on initial screening and employed for characterizing genetic diversity in a panel of wheat genotypes including salt tolerant and susceptible lines. These markers generated an average of 2.83 alleles/locus. Phylogenetic analysis revealed four clusters. Salt susceptible genotypes were mainly represented in clusters I and III, whereas high and moderate salt tolerant genotypes were distributed in the remaining two clusters. Population structure analysis revealed two sub-populations, sub-population 1 contained the majority of salt tolerant whereas sub-population 2 contained majority of susceptible genotypes. Moreover, we observed reasonably higher transferability of SSR markers to related wheat species.ConclusionWe have developed salt responsive gene based SSRs in wheat for the first time. These were highly useful in unravelling functional diversity among wheat genotypes with varying responses to salt stress. The identified gene based SSR markers will be valuable genomic resources for genetic/association mapping of salinity tolerance in wheat.
Highlights
Salinity severely limits wheat production in many parts of the world
Plant materials A diverse panel of 60 wheat genotypes including salt tolerant and susceptible genotypes were chosen for validation of identified candidate gene based simple sequence repeats (cg-simple sequence repeats (SSRs)) markers (Additional file 1: Table S1)
The majority of tri-nucleotide motifs were from exons (11.8%) followed by promoters (9.94%), whereas the majority of di-nucleotide repeat motifs were present in promoters (9.94%) followed by exons (9.32%) (Fig. 1b)
Summary
Development of salt tolerant varieties represents the most practical option for enhancing wheat production from these areas. With the availability of a fully annotated wheat genome assembly, it is possible to develop SSR markers targeted to genic regions. Salinity stress is the most damaging, affecting every stage of wheat plant development including germination, vegetative growth and grain filling resulting in lower than expected yield. Development of high salt tolerant wheat varieties presents an attractive and economical approach to enhancing wheat production from salt affected areas. This would require incorporation of modern genomics technologies for discovery of salt tolerant genes and their precise mobilization into salt sensitive wheat varieties that are otherwise agronomically superior
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