Genetic diversity and population structure of the sweet leaf herb, Stevia rebaudiana B., cultivated and landraces germplasm assessed by EST-SSRs genotyping and steviol glycosides phenotyping

Abstract

BackgroundStevia rebaudiana (Asteraceae), native from Paraguay, accumulates steviol glycosides (SGs) into its leaves. These compounds exhibit acaloric intense sweet taste which answers to consumer demands for reducing daily sugar intake. Despite the developpement of S. rebaudiana cultivation all over the world, the development of new cultivars is very recent, in particular due to a colossal lack of (1) germplasm collection and breeding, (2) studies on genetic diversity and its structuring, (3) genomic tools.ResultsIn this study, we developped 18 EST-SSR from 150,258 EST from The Compositae Genome Project of UC Davis (http://compgenomics.ucdavis.edu/data/). We genotyped 145 S. rebaudiana individuals, issued from thirty-one cultivars and thirty-one landraces of various origins worldwide. Markers polymorphic information content (PIC) ranged between 0.60 and 0.84. An average of 12 alleles per locus and a high observed heterozygoty of 0.69 could be observed. The landraces revealed twice as many private alleles as cultivars. The genotypes could be clustered into 3 genetic populations. The landraces were grouped in the same cluster in which the oldest cultivars “Eirete” and “MoritaIII” type are also found. The other two clusters only include cultivated genotypes. One of them revealed an original genetic variability. SG phenotypes could not discriminate the three genetic clusters but phenotyping showed a wide range of composition in terms of bitter to sweet SGs.ConclusionThis is the first study of genetic diversity in Stevia rebaudiana involving 145 genotypes, including known cultivars as well as landrace populations of different origin. This study pointed out the structuration of S. rebaudiana germplasm and the resource of the landrace populations for genetic improvement, even on the trait of SG’s composition.

ISSR markers to assess genetic diversity of cultivated populations from artificial selection of <i>Stevia rebaudiana</i> (Bert.) Bertoni

“…Likewise, as was observed in our study with ISSR markers, the selection pressure adopted by Carvalho et al (2011) to form crops with characteristics of interest resulted in genetically structured. EST-SSR also revealed higher genetic diversity in landraces than in the cultivated populations ( Cosson et al 2019 ).…”

“…Genetic diversity within each accession or collection has not been revealed by ISSR markers. Molecular polymorphism within landraces and cultivated populations of stevia have been investigated by esterase isozymes and expressed sequence tags (EST) in simple sequence repeats (SSRs) as markers ( Carvalho et al 2011 , Cosson et al 2019 ). Genetic diversity in esterase loci within of S. rebaudiana cultivated populations which were subjected to artificial selection pressure of characteristics such as greater height or early flowering, demonstrated that this procedure leads towards the fixation of different alleles and different esterase phenotype patterns ( Carvalho et al 2011 ).…”

“…Isozymes analysis showed high genetic diversity in stevia cultivars ( Carvalho et al 2011 ). DNA sequences amplified by polymerase chain reaction (PCR) such as RAPD, EST-SSR and ISSR markers also have showed high polymorphism in collections ( Dyduch-Siemińska et al 2020 , Sharma et al 2016 ), accessions ( Chester et al 2013 ) and cultivars ( Cosson et al 2019 ) of stevia. Inter Simples Sequences Repeats of DNA (ISSR markers) are DNA sequences of 100–3000 bp, amplified by PCR, using a single primer (16–20 bp) constructed from microsatellite sequences ( Zietkiewicz et al 1994 ).…”

Phenological growth stages of stevia (Stevia rebaudiana Bertoni) according to the Biologische Bundesanstalt Bundessortenamt and Chemical Industry (BBCH) scale

“…In the Liposthey field, four genetic resources (Table 1) of different origins studied in Hastoy, Cosson, et al (2019) were chosen. In the Blagon field, four populations from crosses between genetic resources presented in Cosson et al (2019), namely Cult76_GER × Cult35_FRA, Cult102_SPA × Cult35_FRA, Cult36_FRA × Cult103_SPA and Cult34_FRA × Cult36_FRA, were analysed (Table 2).…”

Stevia rebaudiana germplasm characterization using microsatellite markers and steviol glycosides quantification by HPLC

“…These markers can competently be used in the genotyping process with a good genome sampling, which makes them suitable to estimate genotypes relatedness that requires multilocus genotype identification [ 28 ]. Kaur et al [ 29 ] and Bhandawat et al [ 30 ] were the pioneers in microsatellite markers development and use in S. rebaudiana and, recently, from freely available expressed sequence data (ESTs), and Cosson et al [ 31 ] also developed molecular markers (EST-SSRs) for population genetic and germplasm characterization studies. Recently, also a group of S. rebaudiana genotypes from Paraguay were studied with SSR and ISSR [ 32 ], and analysed as dominant markers.…”