Characterization of novel SSR markers in diverse sainfoin (Onobrychis viciifolia) germplasm

Abstract

BackgroundSainfoin is a perennial forage legume with beneficial properties for animal husbandry due to the presence of secondary metabolites. However, worldwide cultivation of sainfoin is marginal due to the lack of varieties with good agronomic performance, adapted to a broad range of environmental conditions. Little is known about the genetics of sainfoin and only few genetic markers are available to assist breeding and genetic investigations. The objective of this study was to develop a set of SSR markers useful for genetic studies in sainfoin and their characterization in diverse germplasm.ResultsA set of 400 SSR primer combinations were tested for amplification and their ability to detect polymorphisms in a set of 32 sainfoin individuals, representing distinct varieties or landraces. Alleles were scored for presence or absence and polymorphism information content of each SSR locus was calculated with an adapted formula taking into account the tetraploid character of sainfoin. Relationships among individuals were visualized using cluster and principle components analysis. Of the 400 primer combinations tested, 101 reliably detected polymorphisms among the 32 sainfoin individuals. Among the 1154 alleles amplified 250 private alleles were observed. The number of alleles per locus ranged from 2 to 24 with an average of 11.4 alleles. The average polymorphism information content reached values of 0.14 to 0.36. The clustering of the 32 individuals suggested a separation into two groups depending on the origin of the accessions.ConclusionsThe SSR markers characterized and tested in this study provide a valuable tool to detect polymorphisms in sainfoin for future genetic studies and breeding programs. As a proof of concept, we showed that these markers can be used to separate sainfoin individuals based on their origin.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-016-0431-0) contains supplementary material, which is available to authorized users.

Benefits of Condensed Tannins in Forage Legumes Fed to Ruminants: Importance of Structure, Concentration, and Diet Composition

“…Some of the SSR markers were used to assess the genetic diversity of European sainfoin accessions representing cultivars and noncultivars (ecotypes, landraces) (Kempf et al, 2016). Next-generation sequencing technology is facilitating the identification and use of molecular markers in plant genetics and breeding.…”

“…Next-generation sequencing technology is facilitating the identification and use of molecular markers in plant genetics and breeding. We anticipate that the sequence and molecular marker information now available (Kempf et al, 2016; can be used to assist breeding of novel sainfoin cultivars with CT traits that are optimized for animal nutrition and health. The first such library of expressed genes in sainfoin was obtained from five accessions using this technology .…”

“…Research on CT-containing feeds has the potential to improve ruminant health by preventing bloat and mitigating effects of parasitism, as well as lowering environmental footprints and improving the sustainability of food quality and production for consumers (Tedeschi et al, 2014). Apart from research by Mosjidis and colleagues, who selected for low CT concentration and grazing-tolerant sericea lespedeza for cattle production (Mosjidis, 2001), there has been hardly any plant breeding for enhanced CT composition; however, progress is becoming feasible, as new genomic data and molecular markers for CTs have been obtained (Kempf et al, 2016;. Apart from research by Mosjidis and colleagues, who selected for low CT concentration and grazing-tolerant sericea lespedeza for cattle production (Mosjidis, 2001), there has been hardly any plant breeding for enhanced CT composition; however, progress is becoming feasible, as new genomic data and molecular markers for CTs have been obtained (Kempf et al, 2016;.…”

Marker-trait association analysis for agronomic and compositional traits in sainfoin (Onobrychis viciifolia)

“…Table S1. Forward and reverse primers for SSR (Kempf et al, 2016) and SRAP (Li and Quiros, 2001) markers used to test for marker trait associations. Table S2.…”

“…Sequence-related amplified polymorphism (SRAP), which preferentially amplify in gene rich regions (Li and Quiros, 2001), have been successfully used for the molecular investigation of allogamy and autogamy in sainfoin (Kempf et al, 2015). Recently, RNA transcriptome sequencing, using next-generation sequencing, has been successfully used to develop comprehensive simple sequence repeats (SSR) marker resources that can be applied to assess genetic diversity in sainfoin (Kempf et al, 2016;Mora-Ortiz et al, 2016). In order to use these newly developed marker resources to identify possible marker trait associations in sainfoin, the objectives of the present study were to i) phenotype a biparental F 1 population of sainfoin for a wide range of traits under field conditions, ii) investigate correlations among agronomic and compositional traits, and iii) identify dominant SRAP and co-dominant SSR markers associated with phenotypic traits.…”