Genomic insight into the developmental history of southern highbush blueberry populations

ハイブッシュブルーベリーに暖地適応性をもたらした遺伝要因を解明 --ゲノムに刻まれたブルーベリーの育種履歴--. 京都大学プレスリリース. 2020-09-07.Interspecific hybridization is a common breeding approach for introducing novel traits and genetic diversity to breeding populations. Southern highbush blueberry (SHB) is a blueberry cultivar group that has been intensively bred over the last 60 years. Specifically, it was developed by multiple interspecific crosses between northern highbush blueberry [NHB, Vaccinium corymbosum L. (2n = 4x = 48)] and low-chill Vaccinium species to expand the geographic limits of highbush blueberry production. In this study, we genotyped polyploid blueberries, including 105 SHB, 17 NHB, and 10 rabbiteye blueberry (RE) (Vaccinium virgatum Aiton), from the accessions planted at Poplarville, Mississippi, and accessions distributed in Japan, based on the double-digest restriction site-associated DNA sequencing. The genome-wide SNP data clearly indicated that RE cultivars were genetically distinct from SHB and NHB cultivars, whereas NHB and SHB were genetically indistinguishable. The population structure results appeared to reflect the differences in the allele selection strategies that breeders used for developing germplasm adapted to local climates. The genotype data implied that there are no or very few genomic segments that were commonly introgressed from low-chill Vaccinium species to the SHB genome. Principal component analysis-based outlier detection analysis found a few loci associated with a variable that could partially differentiate NHB and SHB. These SNP loci were detected in Mb-scale haplotype blocks and may be close to the functional genes related to SHB development. Collectively, the data generated in this study suggest a polygenic adaptation of SHB to the southern climate, and may be relevant for future population-scale genome-wide analyses of blueberry

Genetic Diversity among Wheat Accessions from the USDA National Small Grains Collection

Accessions of common wheat (Triticum aestivum L. subsp. aestivum) from the USDA–ARS National Small Grains Collection (NSGC) are a resource for wheat scientists worldwide. The genetic diversity of the wheat core subset, representing approximately 10% of the collection’s 42,138 T. aestivum accessions, was examined using 390 diversity arrays technology (DArT) markers, 4941 single nucleotide polymorphisms (SNPs), and descriptor data. The marker profiles revealed duplicates, which were excluded to form an informative core (iCore) of 3230 accessions. The iCore population structure and diversity within various subgroups were examined with analysis of molecular variance, principal coordinate analysis, cluster analysis, and by ranking the contribution of individual accessions to overall diversity. Accession groups based on molecular marker data corresponded well to their geographic origin, and population structure was accounted for primarily by differences between Iranian landrace accessions and the rest of the accessions. Accessions classified as breeding lines were overrepresented among those ranked as most diverse based on SNP data, whereas Iranian landraces were underrepresented. Although less diverse as a group, Iranian landrace accessions had a higher frequency of resistance to bunt diseases and Russian wheat aphid compared with the iCore as a whole. The present study provides support for establishing core subsets based on geographic origin of accessions and will be a basis for further study of diversity among NSGC wheats

Population Genomics Related to Adaptation in Elite Oat Germplasm

Six hundred thirty five oat ( L.) lines and 4561 single-nucleotide polymorphism (SNP) loci were used to evaluate population structure, linkage disequilibrium (LD), and genotype–phenotype association with heading date. The first five principal components (PCs) accounted for 25.3% of genetic variation. Neither the eigenvalues of the first 25 PCs nor the cross-validation errors from = 1 to 20 model-based analyses suggested a structured population. However, the PC and = 2 model-based analyses supported clustering of lines on spring oat vs. southern United States origin, accounting for 16% of genetic variation ( < 0.0001). Single-locus -statistic () in the highest 1% of the distribution suggested linkage groups that may be differentiated between the two population subgroups. Population structure and kinship-corrected LD of = 0.10 was observed at an average pairwise distance of 0.44 cM (0.71 and 2.64 cM within spring and southern oat, respectively). On most linkage groups LD decay was slower within southern lines than within the spring lines. A notable exception was found on linkage group Mrg28, where LD decay was substantially slower in the spring subpopulation. It is speculated that this may be caused by a heterogeneous translocation event on this chromosome. Association with heading date was most consistent across location-years on linkage groups Mrg02, Mrg12, Mrg13, and Mrg24

A Consensus Map in Cultivated Hexaploid Oat Reveals Conserved Grass Synteny with Substantial Subgenome Rearrangement

Hexaploid oat ( L., 2 = 6 = 42) is a member of the Poaceae family and has a large genome (∼12.5 Gb) containing 21 chromosome pairs from three ancestral genomes. Physical rearrangements among parental genomes have hindered the development of linkage maps in this species. The objective of this work was to develop a single high-density consensus linkage map that is representative of the majority of commonly grown oat varieties. Data from a cDNA-derived single-nucleotide polymorphism (SNP) array and genotyping-by-sequencing (GBS) were collected from the progeny of 12 biparental recombinant inbred line populations derived from 19 parents representing oat germplasm cultivated primarily in North America. Linkage groups from all mapping populations were compared to identify 21 clusters of conserved collinearity. Linkage groups within each cluster were then merged into 21 consensus chromosomes, generating a framework consensus map of 7202 markers spanning 2843 cM. An additional 9678 markers were placed on this map with a lower degree of certainty. Assignment to physical chromosomes with high confidence was made for nine chromosomes. Comparison of homeologous regions among oat chromosomes and matches to orthologous regions of rice ( L.) reveal that the hexaploid oat genome has been highly rearranged relative to its ancestral diploid genomes as a result of frequent translocations among chromosomes. Heterogeneous chromosome rearrangements among populations were also evident, probably accounting for the failure of some linkage groups to match the consensus. This work contributes to a further understanding of the organization and evolution of hexaploid grass genomes

There and back again: historical perspective and future directions for Vaccinium breeding and research studies

The genus Vaccinium L. (Ericaceae) contains a wide diversity of culturally and economically important berry crop species. Consumer demand and scientific research in blueberry (Vaccinium spp.) and cranberry (Vaccinium macrocarpon) have increased worldwide over the crops' relatively short domestication history (~100&nbsp;years). Other species, including bilberry (Vaccinium myrtillus), lingonberry (Vaccinium vitis-idaea), and ohelo berry (Vaccinium reticulatum) are largely still harvested from the wild but with crop improvement efforts underway. Here, we present a review article on these Vaccinium berry crops on topics that span taxonomy to genetics and genomics to breeding. We highlight the accomplishments made thus far for each of these crops, along their journey from the wild, and propose research areas and questions that will require investments by the community over the coming decades to guide future crop improvement efforts. New tools and resources are needed to underpin the development of superior cultivars that are not only more resilient to various environmental stresses and higher yielding, but also produce fruit that continue to meet a variety of consumer preferences, including fruit quality and health related trait

INFLUENCE OF CROP VOLUNTEER AND GRASSY WEED GREENBRIDGE ON RHIZOCTONIA ROOT ROT OF CEREALS AND DISEASE RESISTANCE IN BRASSICA AND TRITICUM GERMPLASM

Rhizoctonia root rot, caused by Rhizoctonia solani AG 8 and R. oryzae, is considered one of the main deterrents for farmers to adopt reduced tillage systems in the Pacific Northwest. Herbicide application before planting to eliminate weeds is the main management strategy for this disease. To determine the effect of timing of glyphosate applications on the severity of the disease, a 3-year experiment was conducted in a field naturally infested with R. solani and R. oryzae. Weeds were sprayed with glyphosate at 42, 28, 14, 7 and 2 days prior to planting with barley. As the herbicide application to planting interval increased, there were increases in shoot length and healthy roots rating and a decrease in disease severity, number of infected seminal roots and activity of R. solani AG 8.To investigate the impact of wild oat (Avena fatua L.), Italian ryegrass (Lolium multiflorum), and downy brome (Bromus tectorum L.) on incidence of the disease, the same three weed species were planted in soil infested with R. solani AG 8 and treated with glyphosate before planting with barley. Significant reductions in shoot length, root length and seedling fresh weight were observed in barley grown in wild oat and Italian ryegrass residue.Virulence of R. solani AG 2-1, AG 8, AG 10 and Ceratobasidium spp. on Brassica crops were tested. R. solani AG 2-1 appears to be the most aggressive pathogen followed by R. solani AG 8, Ceratobasidium spp. and R. solani AG 10, respectively. Three genotypes with moderate levels of resistance were identified. Regardless of the genotype, old seeds were more susceptible than newly harvested seeds.The tolerance of 7 synthetic wheat genotypes to R. solani and R. oryzae was studied in two soils. More disease was observed in sandy soil compared to the silty loam soil. R. solani AG 8 was found to be more virulent compared to R. oryzae. Two genotypes with moderate levels of resistance were identified. One QTL for shoot length reduction was located on chromosome 2B in the Louise x SPCB-3104 population. This QTL explained 29% of the phenotypic variation

Combining High-throughput Phenotyping and Multivariate Analysis to Assess Fruit Quality Traits in Southern Highbush Blueberry (Vaccinium corymbosum Interspecific Hybrids) Germplasm Collection

Breeding blueberry cultivars with enhanced fruit quality requires simple, accurate, and cost-effective assays to select individuals from segregating populations. In this study, berry diameter, berry weight, firmness, pH, total polyphenol, total acids, D-glucose, D-fructose, total glucose, and total sugar content were quantified in 188 southern highbush blueberry selections and cultivars over 2 years. Significant variation between years, genotype, and year × genotype interaction was detected for all traits. Glucose and fructose were the predominant sugars, and they were in a range of 32.14–64.72 and 28.61–69.63 mg/mL, respectively. Total sugars content ranged from 62.22 to 131.15 mg/mL. Correlation analysis showed a strong positive correlation between total sugar content measured with the discrete analyzer and total soluble solids assessed as Brix (r2 = 0.96). In addition, glucose, fructose, and total glucose showed high and positive correlation between them and with the total sugar content. The titratable acidity was positively correlated with total acids (r2 = 0.60) and strong positive correlation between berry diameter and berry weight (r2 = 0.94) was detected. Principal component analysis (PCA) showed that PC1 explained 44.9% of the variation and the major contributing traits for diversity were D-fructose, D-glucose, total glucose, and total sugars. PC2 accounted for 21.2% of the variation and was mainly attributed to berry weight and diameter. Cluster analysis showed that the blueberry genotypes fell into two major groups. Cluster-I comprised genotypes with the highest amounts of total acids, pH, polyphenol, D-glucose, D-fructose, total glucose, and total sugar, whereas Cluster-II has genotypes with distinctly lower amounts of tested compounds and larger berries. Information obtained from this study is critical to identify superior genotypes for future crosses and advance evaluation. In addition, the firmness tester and discrete analyzer used in this study were invaluable in improving the efficiency and precision of phenotyping

Draft genome assembly of \u3ci\u3ePassalora sequoiae\u3c/i\u3e a needle blight pathogen on Leyland cypress

Objective: Passalora sequoiae (family Mycosphaerellaceae) causes a twig blight on Leyland cypress that requires numerous fungicide applications annually to minimize economic losses for ornamental plant nursery and Christmas tree producers. The objective was to generate a high-quality draft assembly of the genome of P. sequoiae as a resource for primer development to investigate genotype diversity. Data description: We report here the genome sequence of P. sequoiae 9LC2 that was isolated from Leyland cypress ‘Leighton Green’ in 2017 in southern Mississippi, USA. The draft genome was obtained using Pacific Biosciences (PacBio) SMRT and Illumina HiSeq 2500 sequencing. Illumina reads were mapped to PacBio assembled contigs to determine base call consistency. Based on a total of 44 contigs with 722 kilobase (kb) average length (range 9.4 kb to 3.4 Mb), the whole genome size was estimated at 31,768,716 bp. Mapping of Illumina reads to PacBio contigs resulted in a 1000 × coverage and were used to confirm accuracy of the consensus sequences