Abstract
BackgroundElymus nutans and E. sibiricus are two important forage grasses of the genus Elymus. But they are difficult to grow for commercial seed production due to serious seed shattering. We conducted a comparative transcriptome analysis of abscission zone to find possible transcription changes associated with seed shattering, explore candidate genes involved in seed shattering and identify candidate gene-based EST-SSR markers for germplasm evaluation.ResultscDNA libraries from abscission zone (AZ) and non-abscission zone (NAZ) tissues of E. nutans were constructed and sequenced. A total of 111,667 unigenes were annotated and 7644 differentially expressed transcripts (DETs) were predicted, corresponding to 6936 up-regulated in AZ and 708 down-regulated in NAZ. We identified 489 candidate genes related to transcription factor, cell wall hydrolysis or modification, hydrolase activity, phytohormone signaling and response, lignin biosynthesis, and signal transduction or protein turnover. Eleven similar candidate genes involved in polygalacturonase activity, hydrolase activity, and mitogen-activated protein kinase were up-regulated in the abscission zone of the two Elymus species, suggesting these genes may have specific function for abscission zone development and seed shattering. A total of 67 polymorphic EST-SSR markers were developed and characterized based on the sequences of these candidate genes. Fourteen polymorphic EST-SSR primers were finally used to study genetic diversity in 48 E. nutans genotypes with contrasting seed shattering habit. The dendrogram based on molecular data showed that most accessions with similar seed shattering degree tended to group together.ConclusionsThe expression data generated from this study provides an important resource for future molecular biological research. Many DETs were associated with abscission zone development, and EST-SSR loci related to candidate genes may have potential application in identifying trait-associated markers in E. nutans in the future.
Highlights
Elymus nutans and E. sibiricus are two important forage grasses of the genus Elymus
To identify candidate genes differentially expressed in the non-abscission zone (NAZ) and abscission zone (AZ) of E. nutans, six cDNA libraries were constructed from NAZ and AZ tissues RNA samples with three biological replicates, and sequenced using the Illumina HiSeqTM 4000 platform
In this study we described RNA-sequencing for abscission zone and non-abscission zone differentiation in E. nutans and AZ development of 21 and 28 days after heading in E. sibiricus
Summary
Elymus nutans and E. sibiricus are two important forage grasses of the genus Elymus They are difficult to grow for commercial seed production due to serious seed shattering. Seed Shattering is an important adaptive trait for seed dispersal in wild plants, but is a major cause of yield loss in many cereal crops and forage grasses during harvest [1]. As the two Elymus species have good forage yield and quality as well as excellent cold and drought tolerance, they have been widely used as forage crops in cultivated pastures and natural grassland Despite their economic importance, the two Elymus species are difficult to grow for commercial seed production due to serious seed shattering. Selection for seed retention and improvement of seed shattering for the two species could be important objectives in breeding programme
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