Polypoid species play significant roles in agriculture and food production. Many crop species are polyploid, such as potato, wheat, strawberry, and sugarcane. Genotyping has been a daunting task for genetic studies of polyploid crops, which lags far behind the diploid crop species. Single nucleotide polymorphism (SNP) array is considered to be one of, high-throughput, relatively cost-efficient and automated genotyping approaches. However, there are significant challenges for SNP identification in complex, polyploid genomes, which has seriously slowed SNP discovery and array development in polyploid species. Ploidy is a significant factor impacting SNP qualities and validation rates of SNP markers in SNP arrays, which has been proven to be a very important tool for genetic studies and molecular breeding. In this review, we (1) discussed the pros and cons of SNP array in general for high throughput genotyping, (2) presented the challenges of and solutions to SNP calling in polyploid species, (3) summarized the SNP selection criteria and considerations of SNP array design for polyploid species, (4) illustrated SNP array applications in several different polyploid crop species, then (5) discussed challenges, available software, and their accuracy comparisons for genotype calling based on SNP array data in polyploids, and finally (6) provided a series of SNP array design and genotype calling recommendations. This review presents a complete overview of SNP array development and applications in polypoid crops, which will benefit the research in molecular breeding and genetics of crops with complex genomes.

/pdf/development-and-applications-of-a-high-throughput-genotyping-4iicjid0m3.pdf

Development and Applications of a High Throughput Genotyping Tool for Polyploid Crops: Single Nucleotide Polymorphism (SNP) Array.

The draft genome sequence of a wild rose (Rosa multiflora Thunb.) was determined using Illumina MiSeq and HiSeq platforms. The total length of the scaffolds was 739,637,845 bp, consisting of 83,189 scaffolds, which was close to the 711 Mbp length estimated by k-mer analysis. N50 length of the scaffolds was 90,830 bp, and extent of the longest was 1,133,259 bp. The average GC content of the scaffolds was 38.9%. After gene prediction, 67,380 candidates exhibiting sequence homology to known genes and domains were extracted, which included complete and partial gene structures. This large number of genes for a diploid plant may reflect heterogeneity of the genome originating from self-incompatibility in R. multiflora. According to CEGMA analysis, 91.9% and 98.0% of the core eukaryotic genes were completely and partially conserved in the scaffolds, respectively. Genes presumably involved in flower color, scent and flowering are assigned. The results of this study will serve as a valuable resource for fundamental and applied research in the rose, including breeding and phylogenetic study of cultivated roses.

/pdf/genome-structure-of-rosa-multiflora-a-wild-ancestor-of-2qgvj561d4.pdf

Genome structure of Rosa multiflora, a wild ancestor of cultivated roses.

The recent completion of the rose genome sequence is not the end of a process, but rather a starting point that opens up a whole set of new and exciting activities. Next to a high-quality genome sequence other genomic tools have also become available for rose, including transcriptomics data, a high-density single-nucleotide polymorphism array and software to perform linkage and quantitative trait locus mapping in polyploids. Rose cultivars are highly heterogeneous and diverse. This vast diversity in cultivated roses can be explained through the genetic potential of the genus, introgressions from wild species into commercial tetraploid germplasm and the inimitable efforts of historical breeders. We can now investigate how this diversity can best be exploited and refined in future breeding work, given the rich molecular toolbox now available to the rose breeding community. This paper presents possible lines of research now that rose has entered the genomics era, and attempts to partially answer the question that arises after the completion of any draft genome sequence: ‘Now that we have “the” genome, what’s next?’. Having access to a genome sequence will allow both (fundamental) scientific and (applied) breeding-orientated questions to be addressed. We outline possible approaches for a number of these questions.

/pdf/in-the-name-of-the-rose-a-roadmap-for-rose-research-in-the-1rj1zb0wms.pdf

In the name of the rose: a roadmap for rose research in the genome era

Cultivated chrysanthemum is an outcrossing hexaploid (2n = 6× = 54) with a disputed mode of inheritance. In this paper, we present a single nucleotide polymorphism (SNP) selection pipeline that was used to design an Affymetrix Axiom array with 183 k SNPs from RNA sequencing data (1). With this array, we genotyped four bi-parental populations (with sizes of 405, 53, 76 and 37 offspring plants respectively), and a cultivar panel of 63 genotypes. Further, we present a method for dosage scoring in hexaploids from signal intensities of the array based on mixture models (2) and validation of selection steps in the SNP selection pipeline (3). The resulting genotypic data is used to draw conclusions on the mode of inheritance in chrysanthemum (4), and to make an inference on allelic expression bias (5). With use of the mixture model approach, we successfully called the dosage of 73,936 out of 183,130 SNPs (40.4%) that segregated in any of the bi-parental populations. To investigate the mode of inheritance, we analysed markers that segregated in the large bi-parental population (n = 405). Analysis of segregation of duplex x nulliplex SNPs resulted in evidence for genome-wide hexasomic inheritance. This evidence was substantiated by the absence of strong linkage between markers in repulsion, which indicated absence of full disomic inheritance. We present the success rate of SNP discovery out of RNA sequencing data as affected by different selection steps, among which SNP coverage over genotypes and use of different types of sequence read mapping software. Genomic dosage highly correlated with relative allele coverage from the RNA sequencing data, indicating that most alleles are expressed according to their genomic dosage. The large population, genotyped with a very large number of markers, is a unique framework for extensive genetic analyses in hexaploid chrysanthemum. As starting point, we show conclusive evidence for genome-wide hexasomic inheritance.

/pdf/conclusive-evidence-for-hexasomic-inheritance-in-2vqosg3ub5.pdf

Conclusive evidence for hexasomic inheritance in chrysanthemum based on analysis of a 183 k SNP array

The rose is one of the most important ornamental woody plants because of its extensive use and high economic value. Herein, we sequenced a complete chloroplast genome of the miniature rose variety Rosa ‘Margo Koster’ and performed comparative analyses with sequences previously published for other species in the Rosaceae family. The chloroplast genome of Rosa ‘Margo Koster’, with a size of 157,395 bp, has a circular quadripartite structure typical of angiosperm chloroplast genomes and contains a total of 81 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Conjunction regions in the chloroplast genome of Rosa ‘Margo Koster’ were verified and manually corrected by Sanger sequencing. Comparative genome analysis showed that the IR contraction and expansion events resulted in rps19 and ycf1 pseudogenes. The phylogenetic analysis within the Rosa genus showed that Rosa ‘Margo Koster’ is closer to Rosa odorata than to other Rosa species. Additionally, we identified and screened highly divergent sequences and cpSSRs and compared their power to discriminate rose varieties by Sanger sequencing and capillary electrophoresis. The results showed that 15 cpSSRs are polymorphic, but their discriminating power is only moderate among a set of rose varieties. However, more than 150 single nucleotide variations (SNVs) were discovered in the flanking region of cpSSRs, and the results indicated that these SNVs have a higher divergence and stronger power for profiling rose varieties. These findings suggest that nucleotide mutations in the chloroplast genome may be an effective and powerful tool for rose variety discrimination and DNA profiling. These molecular markers in the chloroplast genome sequence of Rosa spp. will facilitate population and phylogenetic studies and other related studies of this species.

Molecular markers from the chloroplast genome of rose provide a complementary tool for variety discrimination and profiling.

Dense genetic maps create a base for QTL analysis of important traits and future implementation of marker-assisted breeding In tetraploid rose, the existing linkage maps include <300 markers to cover 28 linkage groups (4 homologous sets of 7 chromosomes) Here we used the 68k WagRhSNP Axiom single-nucleotide polymorphism (SNP) array for rose, in combination with SNP dosage calling at the tetraploid level, to genotype offspring from the garden rose cultivar ‘Red New Dawn’ The offspring proved to be not from a single bi-parental cross In rose breeding, crosses with unintended parents occur regularly We developed a strategy to separate progeny into putative populations, even while one of the parents was unknown, using principle component analysis on pairwise genetic distances based on sets of selected SNP markers that were homozygous, and therefore uninformative for one parent One of the inferred populations was consistent with self-fertilization of ‘Red New Dawn’ Subsequently, linkage maps were generated for a bi-parental and a self-pollinated population with ‘Red New Dawn’ as the common maternal parent The densest map, for the selfed parent, had 1929 SNP markers on 25 linkage groups, covering 17655 cM at an average marker distance of 09 cM Synteny with the strawberry (Fragaria vesca) genome was extensive Rose ICM1 corresponded to F vesca pseudochromosome 7 (Fv7), ICM4 to Fv4, ICM5 to Fv3, ICM6 to Fv2 and ICM7 to Fv5 Rose ICM2 corresponded to parts of F vesca pseudochromosomes 1 and 6, whereas ICM3 is syntenic to the remainder of Fv6 The rose genome has been mapped in greater detail than ever, and a new method to determine hybrid plants' parentage developed A Dutch team, led by Rene Smulders of Wageningen University, planned to cross two roses, 'Morden Centennial' and 'Red New Dawn,' and map the resulting hybrid's genome However, the crossed population displayed unexpected traits Using genetic differences at DNA sites known as 'single nucleotide polymorphisms,' the team determined the heritage of this population They found not only crosses of 'Morden Centennial' and 'Red New Dawn', but also 'Red New Dawn' with an unknown parent, and self-fertilized 'Red New Dawn' This evidence for self-fertilization in roses presents both challenges and opportunities for breeders The team generated three genetic maps, the most detailed for the self-fertilized plants, supporting further genomic analysis and cultivar development in roses

/pdf/high-density-snp-based-genetic-maps-for-the-parents-of-an-1crsh8us7k.pdf

High-density SNP-based genetic maps for the parents of an outcrossed and a selfed tetraploid garden rose cross, inferred from admixed progeny using the 68k rose SNP array.

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High-density SNP-based genetic maps for the parents of an outcrossed and a selfed tetraploid garden rose cross, inferred from admixed progeny using the 68k rose SNP array.