Genetic Diversity and Population Structure of the USDA Sweetpotato (Ipomoea batatas) Germplasm Collections Using GBSpoly

Sweetpotato (Ipomoea batatas) plays a critical role in food security and is the most important root crop worldwide following potatoes and cassava. In the United States (US), it is valued at over $700 million USD. There are two sweetpotato germplasm collections (Plant Genetic Resources Conservation Unit and US Vegetable Laboratory) maintained by the USDA, ARS for sweetpotato crop improvement. To date, no genome-wide assessment of genetic diversity within these collections has been reported in the published literature. In our study, population structure and genetic diversity of 417 USDA sweetpotato accessions originating from 8 broad geographical regions (Africa, Australia, Caribbean, Central America, Far East, North America, Pacific Islands, and South America) were determined using single nucleotide polymorphisms (SNPs) identified with a genotyping-by-sequencing (GBS) protocol, GBSpoly, optimized for highly heterozygous and polyploid species. Population structure using Bayesian clustering analyses (STRUCTURE) with 32,784 segregating SNPs grouped the accessions into four genetic groups and indicated a high degree of mixed ancestry. A neighbor-joining cladogram and principal components analysis based on a pairwise genetic distance matrix of the accessions supported the population structure analysis. Pairwise FST values between broad geographical regions based on the origin of accessions ranged from 0.017 (Far East – Pacific Islands) to 0.110 (Australia – South America) and supported the clustering of accessions based on genetic distance. The markers developed for use with this collection of accessions provide an important genomic resource for the sweetpotato community, and contribute to our understanding of the genetic diversity present within the US sweetpotato collection and the species

"Jumping Jack": Genomic Microsatellites Underscore the Distinctiveness of Closely Related Pseudoperonospora cubensis and Pseudoperonospora humuli and Provide New Insights Into Their Evolutionary Past

Downy mildews caused by obligate biotrophic oomycetes result in severe crop losses worldwide. Among these pathogens, Pseudoperonospora cubensis and P. humuli, two closely related oomycetes, adversely affect cucurbits and hop, respectively. Discordant hypotheses concerning their taxonomic relationships have been proposed based on host-pathogen interactions and specificity evidence and gene sequences of a few individuals, but population genetics evidence supporting these scenarios is missing. Furthermore, nuclear and mitochondrial regions of both pathogens have been analyzed using microsatellites and phylogenetically informative molecular markers, but extensive comparative population genetics research has not been done. Here, we genotyped 138 current and historical herbarium specimens of those two taxa using microsatellites (SSRs). Our goals were to assess genetic diversity and spatial distribution, to infer the evolutionary history of P. cubensis and P. humuli, and to visualize genome-scale organizational relationship between both pathogens. High genetic diversity, modest gene flow, and presence of population structure, particularly in P. cubensis, were observed. When tested for cross-amplification, 20 out of 27 P. cubensis-derived gSSRs cross-amplified DNA of P. humuli individuals, but few amplified DNA of downy mildew pathogens from related genera. Collectively, our analyses provided a definite argument for the hypothesis that both pathogens are distinct species, and suggested further speciation in the P. cubensis complex

Isolation and Characterization of Microsatellite Loci for <i>Cornus sanguinea</i> (Cornaceae)

Premise of the study: To facilitate genetic and conservation research of Cornus sanguinea, microsatellite loci were isolated and 29 individuals from 11 German populations were genotyped. Methods and Results: Sixteen microsatellite loci were characterized from an enriched small insert genomic library. The number of alleles detected ranged from five to 11 per locus, observed heterozygosity ranged from 0.00 to 1.00, expected heterozygosity ranged from 0.65 to 0.90, and polymorphic information content ranged from 0.59 to 0.88. Conclusions: The markers described in the study will allow further investigation of population dynamics and the degree of clonal reproduction within populations of C. sanguinea

Context-Specific Genomic Selection Strategies Outperform Phenotypic Selection for Soybean Quantitative Traits in the Progeny Row Stage

Evaluating different breeding selection strategies for relative utility is necessary to choose those that maximize efficiency. Soybean [Glycine max (L.) Merr.] seed yield and fatty acid, protein, and oil contents are all commercially important traits that display complex quantitative inheritance. A soybean population consisting of 860 F5–derived recombinant inbred lines (RILs), genotyped with 4867 polymorphic single nucleotide polymorphism (SNPs) was used to compare phenotypic and context specific genomic selection (GS) strategies. To simulate progeny rows, each RIL was grown in a single plot in 2010 in Knoxville, TN, and phenotype was recorded. A subset of 276 RILs with similar maturity was then grown in multilocation, replicated field trials in 2013 to compare the performance of each selection method in field conditions. Notably, the preferred method for each trait was GS. Of the GS approaches evaluated, Epistacy performed best for yield, and BayesB and/or genomic best linear unbiased prediction (G-BLUP) were preferred for each of the other traits. Yield was the only trait for which the predictions had a large change when the number of SNPs and the number of RILs were randomly reduced for the G-BLUP model, with the best predictions occurring when RILs with different maturity that were not grown in 2013 were removed from the training set. These findings provide important information on how soybean breeders can maximize selections from the progeny row stage for yield and fatty acid, protein, and oil contents by using appropriate selection strategies

Population Structure and Genetic Diversity Within the Endangered Species Pityopsis ruthii (Asteraceae)

Pityopsis ruthii (Ruth’s golden aster) is a federally endangered herbaceous perennial endemic to the Hiwassee and Ocoee Rivers in southeastern Tennessee, United States. Comprehensive genetic studies providing novel information to conservationists for preservation of the species are lacking. Genetic variation and gene flow were evaluated for 814 individuals from 33 discrete locations using polymorphic microsatellites: seven chloroplast and twelve nuclear. A total of 198 alleles were detected with the nuclear loci and 79 alleles with the chloroplast loci. Gene flow was estimated, with the Hiwassee River (Nm = 2.16; FST = 0.15) showing higher levels of gene flow and lower levels of population differentiation than the Ocoee River (Nm = 1.28; FST = 0.19). Population structure was examined using Bayesian cluster analyses. Nuclear and chloroplast analyses were incongruent. From the chloroplast microsatellites, three clusters were identified; all were present in sampling sites at both rivers, indicating a lack of allele fixation along rivers. Nuclear markers revealed two clusters and separated by river. When the Hiwassee River locations were analyzed, four clusters were identified for both the chloroplast and nuclear microsatellites, though the individuals clustered differently. Analysis of the Ocoee River revealed two clusters for the chloroplast microsatellites and three for the nuclear microsatellites. We recommend P. ruthii be managed as four populations for the Hiwassee River and three populations for the Ocoee River. Our results provide critical genetic information for P. ruthii that can be used for species management decisions to drive future population augmentation/reintroduction and ex situ conservation efforts

Complete chloroplast genome comparisons for Pityopsis (Asteraceae).

Pityopsis includes several regionally and one federally endangered species of herbaceous perennials. Four species are highly localized, including the federally endangered P. ruthii. The genus includes several ploidy levels and interesting ecological traits such as drought tolerance and fire-dependent flowering. Results from previous cladistic analyses of morphology and from initial DNA sequence studies did not agree with one another or with the infrageneric taxonomic classification, with the result that infrageneric relationships remain unresolved. We sequenced, assembled, and compared the chloroplast (cp) genomes of 12 species or varieties of Pityopsis to better understand generic evolution. A reference cp genome 152,569 bp in length was assembled de novo from P. falcata. Reads from other sampled species were then aligned to the P. falcata reference and individual chloroplast genomes were assembled for each, with manual gapfilling and polishing. After removing the duplicated second inverted region, a multiple sequence alignment of the cp genomes was used to construct a maximum likelihood (ML) phylogeny for the twelve cp genomes. Additionally, we constructed a ML phylogeny from the nuclear ribosomal repeat region after mapping reads to the Helianthus annuus region. The chloroplast phylogeny supported two clades. Previously proposed clades and taxonomic sections within the genus were largely unsupported by both nuclear and chloroplast phylogenies. Our results provide tools for exploring hybridity and examining the physiological and genetic basis for drought tolerance and fire-dependent flowering. This study will inform breeding and conservation practices, and general knowledge of evolutionary history, hybridization, and speciation within Pityopsis