Development of polymorphic EST-SSR markers and characterization of the autotetraploid genome of sainfoin (Onobrychis viciifolia)

Abstract

Background Sainfoin (Onobrychis viciifolia) is a highly nutritious, tannin-containing, and tetraploid forage legume. Due to the lack of detailed transcriptomic and genomic information on this species, genetic and breeding projects for sainfoin improvement have been significantly hindered. Methods In this study, a total of 24,630,711 clean reads were generated from 14 different sainfoin tissues using Illumina paired-end sequencing technology and deposited in the NCBI SRA database (SRX3763386). From these clean reads, 77,764 unigene sequences were obtained and 6,752 EST-SSRs were identified using de novo assembly. A total of 2,469 primer pairs were designed, and 200 primer pairs were randomly selected to analyze the polymorphism in five sainfoin wild accessions. Results Further analysis of 40 sainfoin individuals from the five wild populations using 61 EST-SSR loci showed that the number of alleles per locus ranged from 4 to 15, and the expected heterozygosity varied from 0.55 to 0.91. Additionally, by counting the EST-SSR band number and sequencing the three or four bands in one sainfoin individual, sainfoin was confirmed to be autotetraploid. This finding provides a high level of information about this plant. Discussion Through this study, 61 EST-SSR markers were successfully developed and shown to be useful for genetic studies and investigations of population genetic structures and variabilities among different sainfoin accessions.

Characterization and Development of Microsatellite Markers in Pseudotaxus chienii (Taxaceae) Based on Transcriptome Sequencing

“…Similarly, KEGG and KOG analysis indicated that SSRs-containing unigenes had a wide range of biological functions and were involved in various aspects of P. chienii growth and development. In addition, GO enrichment analysis showed that unigenes containing microsatellites were significantly enriched in terms related to "transcription, " similar to the reports in Onobrychis viciifolia (Shen et al, 2019) and Siberian wildrye (Zhou et al, 2016). Additionally, we found that some unigenes containing microsatellites were associated with transcription factors.…”

Genomic SSR and EST‐SSR markers for phylogenetic and pedigree reconstructions—A comparison in sea buckthorn

“…However, the amplification efficiency of EST‐SSRs is much higher than that of gSSRs, which may due to the relatively highly conserved transcribed regions in the primer sequences (Wu et al., 2014). EST‐SSR had a higher transferability than gSSRs in many species, such as Paeonia (Wu et al., 2014), Eucalyptus (Zhou et al., 2014) and sainfoin ( Onobrychis viciifolia ; Shen et al., 2019). It is worth noting that these studies all focussed on the characteristics of these two types of SSR markers, while studies are limited on the comparison of the application of these two types of SSRs in classification, species identification (e.g.…”

Genetic Relationship in Sainfoin (Onobrychis viciifolia) Landraces Cultivated East Anatolia by using RAPD and ISSR Markers

“…RAPD and ISSR primers are very useful in determining the relationship of the sainfoin and determining its genetic difference (Nosrati et al, 2012;Archer et al, 2013;Rasouli et al, 2013;Hejrankesh et al, 2014;Zarrabian and Majidi, 2015;Sharifi, 2016). Shen et al (2019) determined the genetic diversity of sainfoin collected from 5 different regions, using EST-SSR markers on 8 plants per region and reported a high level of genetic diversity among individuals. W ith this study, the aim was to facilitate the selection of parents for breeding programs by identifying the genetic diversity and the degree of relationship among cultivated sainfoin varieties before starting breeding.…”

“…Özkan and Bilgen (2018) reported that Nei's genetic diversity index obtained using 10 SSR markers was 0.210 for 5 different sainfoin populations. Shen et al (2019) reported that genetic diversity among sainfoin is high. The findings obtained from the study were in concordance with the findings of other researchers and it was determined that sainfoin has high genetic diversity.…”

“…The cultivated sainfoin is tetraploid genome (2n=4x=28) (Hesamzadeh Hejazi and Ziaei Nasab, 2010;Sepet et al, 2011;Kempf et al, 2016) and is a outcrossing species (Hayot-Carbonero et al, 2011). Sainfoin is known to have been originated from the Middle East and Central Asia (Shen et al, 2019). It is reported that it was first cultivated in settlements around the Rhine Valley at the end of the sixteenth century (Delgado et al, 2008).…”