Genome-wide characterization of genetic diversity and population structure in Secale

Abstract

BackgroundNumerous rye accessions are stored in ex situ genebanks worldwide. Little is known about the extent of genetic diversity contained in any of them and its relation to contemporary varieties, since to date rye genetic diversity studies had a very limited scope, analyzing few loci and/ or few accessions. Development of high throughput genotyping methods for rye opened the possibility for genome wide characterizations of large accessions sets. In this study we used 1054 Diversity Array Technology (DArT) markers with defined chromosomal location to characterize genetic diversity and population structure in a collection of 379 rye accessions including wild species, landraces, cultivated materials, historical and contemporary rye varieties.ResultsAverage genetic similarity (GS) coefficients and average polymorphic information content (PIC) values varied among chromosomes. Comparison of chromosome specific average GS within and between germplasm sub-groups indicated regions of chromosomes 1R and 4R as being targeted by selection in current breeding programs. Bayesian clustering, principal coordinate analysis and Neighbor Joining clustering demonstrated that source and improvement status contributed significantly to the structure observed in the analyzed set of Secale germplasm. We revealed a relatively limited diversity in improved rye accessions, both historical and contemporary, as well as lack of correlation between clustering of improved accessions and geographic origin, suggesting common genetic background of rye accessions from diverse geographic regions and extensive germplasm exchange. Moreover, contemporary varieties were distinct from the remaining accessions.ConclusionsOur results point to an influence of reproduction methods on the observed diversity patterns and indicate potential of ex situ collections for broadening the genetic diversity in rye breeding programs. Obtained data show that DArT markers provide a realistic picture of the genetic diversity and population structure present in the collection of 379 rye accessions and are an effective platform for rye germplasm characterization and association mapping studies.

DArT Markers Effectively Target Gene Space in the Rye Genome

“…The putatively disease resistance-related sequences were preferentially located in the long arms of chromosomes 4R and 6R. Interestingly, both these chromosomes were indicated as containing regions targeted by selection in current breeding programs (4R) and during domestication (6R; Bolibok-Bragoszewska et al, 2014). While disease resistance is one of the major objectives in cereal breeding, it is not one of the primary traits typically associated with domestication (Fuller, 2007; Purugganan and Fuller, 2009).…”

“…For sequencing we selected DArT clones which fulfilled at least one of the following criteria: They were genetically mapped (Milczarski et al, 2011), they differentiated diverse rye accessions (Bolibok-Bragoszewska et al, 2014), they were located in the vicinity of QTLs for powdery mildew or leaf rust (Ciszkowicz et al, in preparation), or they were addressed to BAC clones following DArT based BAC library screening (Bolibok-Bragoszewska et al, 2015). The inserts of selected clones were amplified using the primers: ‘M13r nested improved’ (5’-TCACGACGTTGTAAAACGAC-3’) and ‘PCR2.1 fwd’ (5’-CAGGAAACAGCTATGACCATGATT-3’) and sent for sequencing by commercial Sanger sequencing service providers.…”

“…The first high-throughput genotyping technology was established for rye in 2009 with the development of a 1520-clone DArT genotyping panel (Bolibok-Bragoszewska et al, 2009). Since then, it was successfully applied for high density genetic map construction, both in rye and triticale (Bolibok-Bragoszewska et al, 2009; Milczarski et al, 2011; Tyrka et al, 2011, 2015), genome-wide germplasm characterization (Bolibok-Bragoszewska et al, 2014), QTL/gene mapping (Stojałowski et al, 2011; Miedaner et al, 2012; Myśków et al, 2012; Milczarski et al, 2016), and genomic selection (Wang et al, 2014, 2015; Schulthess et al, 2015). Following transcriptome sequencing a Rye5K SNP genotyping panel was developed and used for construction of high density transcript map (Haseneyer et al, 2011; Martis et al, 2013).…”

Genetic diversity and population structure of Chinese natural bermudagrass [Cynodon dactylon (L.) Pers.] germplasm based on SRAP markers

“…Pairwise PhiPT value, an analogue of F ST [44] to estimate of population genetic differentiation was also performed using GenAlEx with 999 permutations. Principal coordinates analysis (PCoA) was performed using GenAlEx based on genetic distance, and the first two principal coordinates were plotted in two-dimensional space.…”

Application of RAD Sequencing for Evaluating the Genetic Diversity of Domesticated Panax notoginseng (Araliaceae)

“…The wild individuals were probably driven to extinction by over harvesting in the past years. On the other hand, the cultivated Sanqi probably originated from the hybrid events of wild relative species, which could be deduced by its owning of admixed ancestry as revealed by structure analysis [74–79]. Fortunately, wild populations of several generic species such as P .…”