Development of SSR Markers Based on Transcriptome Sequencing and Association Analysis with Drought Tolerance in Perennial Grass Miscanthus from China

Abstract

Drought has become a critical environmental stress affecting on plant in temperate area. As one of the promising bio-energy crops to sustainable biomass production, the genus Miscanthus has been widely studied around the world. However, the most widely used hybrid cultivar among this genus, Miscanthus × giganteus is proved poor drought tolerance compared to some parental species. Here we mainly focused on Miscanthus sinensis, which is one of the progenitors of M. × giganteus providing a comparable yield and well abiotic stress tolerance in some places. The main objectives were to characterize the physiological and photosynthetic respond to drought stress and to develop simple sequence repeats (SSRs) markers associated with drought tolerance by transcriptome sequencing within an originally collection of 44 Miscanthus genotypes from southwest China. Significant phenotypic differences were observed among genotypes, and the average of leaf relative water content (RWC) were severely affected by drought stress decreasing from 88.27 to 43.21%, which could well contribute to separating the drought resistant and drought sensitive genotype of Miscanthus. Furthermore, a total of 16,566 gene-associated SSRs markers were identified based on Illumina RNA sequencing under drought conditions, and 93 of them were randomly selected to validate. In total, 70 (75.3%) SSRs were successfully amplified and the generated loci from 30 polymorphic SSRs were used to estimate the genetic differentiation and population structure. Finally, two optimum subgroups of the population were determined by structure analysis and based on association analysis, seven significant associations were identified including two markers with leaf RWC and five markers with photosynthetic traits. With the rich sequencing resources annotation, such associations would serve an efficient tool for Miscanthus drought response mechanism study and facilitate genetic improvement of drought resistant for this species.

EST-SSR markers identification based on RNA-sequencing and application in Schisandra chinensis

“…Dinucleotides (37.83%) and trinucleotides (14.00%) were the main types of SSR in Schisandra; the two times higher frequency of the former compared to the latter is consistent with the trend observed in peanut [32], precocious trifoliate orange [37], and litchi [20], although there is also evidence that trinucleotides are the most common SSR type [20,23,26,28,31]. This difference may be related to the characteristics and quantity of EST-SSR and EST resources in plants.…”

“…This difference may be related to the characteristics and quantity of EST-SSR and EST resources in plants. TC/GA was the most common dinucleotide repeat unit in S. chinensis, which is the same as pigeonpea [34] but in contrast to barley, wheat, corn, sorghum, rice [28], eggplant [27], peanut [32], Miscanthus [26], thorn pear [35], and T. chinensis [30]. GAA/TTC was the most abundant trinucleotide repeat motif, as reported for pansy [38].…”

“…In order to facilitate comparisons with other species, we analyzed the results in two groups: one including and the other excluding mononucleotide repeats. In the former context, the SSR frequency in S. chinensis was 10.46%, which is higher than onion (5.57%) [23] and Phoebe nanmu (9.90%) [24] but lower than oil palm (11.26%) [25], Miscanthus (14.44%) [26], and eggplant (18.32%) [27]. Without considering mononucleotide repeats, the SSR distribution frequency was 5.79%, which is higher than corn (1.5%), barley (3.4%), rice (4.7%) [28], cucumber (4.03%) [29], Taxus chinensis (2.24%) [30], and Korean pine (4.…”

Development of EST-SSR Markers and Association Mapping with Floral Traits in Syringa Oblata

“…It is a long-term task for breeding workers to improve the oral traits of lilac and cultivate new varieties of lilac. Association mapping has been extensively used to determine associations between potential targeted loci and important traits [75][76][77]. Single-marker associations may be more powerful in this low LD tree species, comparing with the haplotype-based associations effecting from an individual signi cant marker [66].…”

Characteristics of Microsatellites Mined from Transcriptome Data and the Development of Novel Markers in Paeonia lactiflora

“…Microsatellites, also known as simple sequence repeats (SSRs), are widely used for plant fingerprinting, genetic diversity assessment and association analysis between target traits and Genes 2020, 11, 214 2 of 13 quantitative trait loci (QTLs) [3][4][5] due to their abundance in the genome, high polymorphism, codominant inheritance and good reproducibility [6,7]. SSRs can be developed from DNA or complementary DNA (cDNA) reverse transcribed from RNA [8].…”