Identification, analysis and development of salt responsive candidate gene based SSR markers in wheat

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.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1476-1) contains supplementary material, which is available to authorized users.

Morphological and Genetic Diversity within Salt Tolerance Detection in Eighteen Wheat Genotypes

“…Almanza-Pinzon et al [30] found that the tested primers were highly informative and capable of distinguishing between wheat genotypes for salt tolerance, as they complied with those obtained using different SSR primers [29,31,32]. The identification of Nax1 gene was performed using the SSR markers Xgwm312 and Xwmc170, contributing to the detection of the tolerance genes, as a result of their association with specific DNA fragments that are closely linked to specific genes affecting the salt tolerance of wheat located on the long arm of chromosome 2A [33,34].…”

“…SSRs are powerful markers used in assessing polymorphisms and the degree of genetic variation of many plant species, including wheat [70]. In this study, 43 different SSR markers were tested and selected for their association with salt tolerance genes in wheat [29,32,44]. Here, we evaluated 23 SSR markers that generated polymorphisms to decipher their discriminating capacity between the salt-tolerant genotypes through identifying allele markers that are associated with each genotype.…”

“…SSR markers occur with a high relative abundance and locus specificity and are less time-consuming than other markers. They are distributed widely across the genome, are repeatable across environments, and above all, they are co-dominant and high-throughput in nature [27][28][29]. This all makes SSR markers a good option for genetic diversity studies concerning cultivars and lines of wheat, due to their importance and high yield demand.…”

Genome-Wide Association Study Reveals Genomic Regions Associated With Ten Agronomical Traits in Wheat Under Late-Sown Conditions

“…The significantly high proportion of admixture in the three subpopulations based on STRUCTURE analysis confirms extensive intermixing of the genomes among the AM panel genotypes. An earlier study (Singh et al, 2018) has also reported high percentage of admixtures in the Indian germplasm lines. Nevertheless, we did observe that advance breeding lines of two different crosses were grouped as expected.…”

Characterization and novel Est-SSR marker development of an important Chinese medicinal plant, Morinda officinalis How (Rubiaceae)

“…These researches also showed that the wild resources of M. officinalis may contain ample useful chemical compounds, which calls for urgent protection of its natural populations and scientific researches on its genetic resources. Therefore, by utilizing the high-throughput sequencing technology, we sequenced the transcriptome of M. officinalis, producing tens of thousands of genetic sequences, which could be helpful for studies on gene functions [29]. These novel SSR markers could be greatly useful in further studies on the genetic diversity of M. officinalis to lay out plans for the protection of the species.…”