Historical Cultivars Research Articles

The cytosine methylation landscape of spring barley revealed by a new reduced representation bisulfite sequencing pipeline, WellMeth.

Patterns and level of cytosine methylation vary widely among plant species and are associated with genome size as well as the proportion of transposons and other repetitive elements in the genome. We explored epigenetic patterns and diversity in a representative proportion of the spring barley (Hordeum vulgare L.) genome across several commercial and historical cultivars. This study adapted a genotyping-by-sequencing (GBS) approach for the detection of methylated cytosines in genomic DNA. To analyze the data, we developed WellMeth, a complete pipeline for analysis of reduced representation bisulfite sequencing. WellMeth enabled quantification of context-specific DNA methylation at the single-base resolution as well as identification of differentially methylated sites (DMCs) and regions (DMRs). On average, DNA methylation levels were significantly higher than what is commonly observed in many plants species, reaching over 10-fold higher levels than those in Arabidopsis thaliana (L.) Heynh. in the CHH methylation. Preferential methylation was observed within and at the edges of long-terminal repeats (LTR) retrotransposons Gypsy and Copia. From a pairwise comparison of cultivars, numerous DMRs could be identified of which more than 5,000 were conserved within the analyzed set of barley cultivars. The subset of regions overlapping with genes showed enrichment in gene ontology (GO) categories associated with chromatin and cellular structure and organization. A significant correlation between genetic and epigenetic distances suggests that a considerable portion of methylated regions is under strict genetic control in barley. The data presented herein represents the first step in efforts toward a better understanding of genome-level structural and functional aspects of methylation in barley.

A compendium of genome-wide sequence reads from NBS (nucleotide binding site) domains of resistance genes in the common potato

SolariX is a compendium of DNA sequence tags from the nucleotide binding site (NBS) domain of disease resistance genes of the common potato, Solanum tuberosum Group Tuberosum. The sequences, which we call NBS tags, for nearly all NBS domains from 91 genomes—representing a wide range of historical and contemporary potato cultivars, 24 breeding programs and 200 years—were generated using just 16 amplification primers and high-throughput sequencing. The NBS tags were mapped to 587 NBS domains on the draft potato genome DM, where we detected an average, over all the samples, of 26 nucleotide polymorphisms on each locus. The total number of NBS domains observed, differed between potato cultivars. However, both modern and old cultivars possessed comparable levels of variability, and neither the individual breeder or country nor the generation or time appeared to correlate with the NBS domain frequencies. Our attempts to detect haplotypes (i.e., sets of linked nucleotide polymorphisms) frequently yielded more than the possible 4 alleles per domain indicating potential locus intermixing during the mapping of NBS tags to the DM reference genome. Mapping inaccuracies were likely a consequence of the differences of each cultivar to the reference genome used, coupled with high levels of NBS domain sequence similarity. We illustrate that the SolariX database is useful to search for polymorphism linked with NBS-LRR R gene alleles conferring specific disease resistance and to develop molecular markers for selection.

Genetic Diversity and Pedigree Analysis of Muscadine Grape Using SSR Markers

Muscadine grape (Vitis rotundifolia) is the first native North American grape to be domesticated. During the past century, breeding programs have created a large collection of muscadine cultivars. Muscadine cultivars are usually identified by evaluating morphological traits and checking breeding records, which can be ambiguous and unauthentic. During this study, simple sequence repeat (SSR) markers were used to generate DNA fingerprinting profiles to identify muscadine cultivars and verify their reported pedigrees. Eighty-nine Vitis accessions were genotyped using 20 SSRs from 13 linkage groups. From these, 81 unique subgenus Muscadinia accessions were identified, and a core set of five SSR markers was able to distinguish all of them. Eighteen misidentifications were found, and five previously unknown accessions were matched with cultivars in the dataset. The profiles of 12 cultivars were not consistent with their reported parentage–progeny relationships. Genetic diversity was analyzed at four levels: all V. rotundifolia cultivars (N = 67); current cultivars (N = 39); historical cultivars (N = 28); and wild V. rotundifolia accessions (N = 9). There was substantial genetic diversity in both wild and historically cultivated muscadines. The principle coordinate analysis (PCoA) showed clear separation among subgenus Vitis cultivars, wild muscadine accessions, and cultivated muscadines, with PCoA1 and PCoA2 explaining 11.0% and 9.3% of the total variation, respectively.

Molecular Genetic Identification of Apple Cultivars Based on Microsatellite DNA Analysis. I.\xa0The Database of 600 Validated Profiles

Apple (Malus × domestica Borkh.) is the most widely grown permanent fruit crop of temperate climates. Although commercial apple growing is based on a small number of globally spread cultivars, its diversity is much larger and there are estimates about the existence of more than 10,000 documented varieties. The varietal diversity can be described and determined based on phenotypic characters of the external and internal traits of fruit, which, however, can be modulated by environmental factors. Consequently, molecular methods have become an important alternative means for the characterisation of apple cultivar diversity. In order to use multilocus microsatellite data for determination of unidentified or misidentified apple varieties, a database with molecular genetic fingerprints of well-determined reference cultivars needs to be available. The objective of the present work was to establish such a database that could be applied for the molecular genetic determination of a large number of historic and modern, diploid and triploid apple cultivars. Based on the analysis of more than 1600 accessions of apple trees sampled in 37 public and private cultivar collections in different European countries at 14 variable microsatellite loci, a database with 600 molecular genetic profiles was finally obtained. The key criterion for considering a molecular genetic profile as confirmed and for including it into the reference database was that at least two accessions of the same cultivar of different provenances generated an identical result, which was achieved for 98% of the apple cultivars present in the database. For the remaining genotypes, the cultivar assignment was supported by a parentage analysis or by comparison to molecular genetic profiles available in published works. The database is composed of 574 scion cultivars, 24 rootstock genotypes and two species of crab apples. Of the 574 scion cultivars, 61% were derived from historic or old cultivars, many of which were grown in Central Europe in the past. The remaining scion cultivars are currently grown or available in testing programmes and may gain importance in the future. In order to validate the genotyping data, parentage analysis was performed involving cultivars and rootstocks that arose after 1900, for which information about at least one parent cultivar was available from pomological and scientific literature and the molecular genetic profiles of the assumed parent(s) were also present in our database. This analysis revealed the presence of null alleles at locus COL, however, when excluding this locus, a mean genotyping error rate of only 0.28% per locus was revealed, which points to a high reliability of the dataset. The datasets with 14 and 13 loci (excluding locus COL) showed a high degree of discrimination power, with a combined non-exclusion probability of identity of 2.6 × 10−20 and 3.4 × 10−19. Five of the microsatellite loci analysed in the present study overlapped with another published dataset and after the application of conversion values, it was possible to align the allele lengths and compare the molecular genetic profiles of 20 randomly derived cultivars, which were analysed in both studies. This comparison evidenced an exact correspondence of the microsatellite profiles contained in the two datasets, further pointing to the accuracy of our database. Apart from its application to characterise genetic resources or to manage germplasm collections, the here presented database could serve as an important tool for quality control or as a useful instrument in breeding programmes.

A study of crown rust resistance in historical and modern oat cultivars representing 120 years of Polish oat breeding

The objective of this paper was to measure resistance to Puccinia coronata f.sp. avenae (Pca) in a set of 63 previously uncharacterised new and historical oat cultivars representing 120 years of Polish oat breeding. The distinctiveness of the obsolete and modern gene pools led to the expectation that the earlier cultivars could be a valuable source of useful resistance genes discarded during subsequent breeding. The plant material was tested at the seedling stage using 14 Pca pathotypes and at the adult plant stage under natural infection conditions in 3 years of field observations. In all, 23 genotypes displayed an immune response to at least one Pca pathotype in the test at the seedling stage, however, most of them were susceptible to crown rust infection in the field. The most resistant, presenting immunity to 9 out of 14 P. coronata isolates, was Celer. The infection profile of this cultivar corresponded to the pattern of reference line Pc39. An allelism test confirmed that the resistance of both the Pc39 line and Celer is conditioned by either the same locus or by tightly linked genes. The infection analysis also demonstrated that some of the newest cultivars (Elegant, Komfort and Harnaś) showed a relatively high level of resistance in each year of field trials, despite being completely susceptible at the seedling stage. Further research will be required to evaluate the source, durability and suitability of this resistance. The study did not find any novel resistance to crown rust in the historic cultivars. However, results provide a new insight into adult plant stage resistance in Polish modern cultivars. The resistance of these cultivars is the result of many years of selection in breeding programs and provides an excellent base for future work.

Yield Data from the Uniform Southern Soft Red Winter Wheat Nursery Emphasize Importance of Selection Location and Environment for Cultivar Development

Yield and agronomic data from a regional soft red winter wheat (Triticum aestivum L.) nursery—consisting of 604 advanced breeding lines (ABLs) and 36 testing locations over a 21‐yr period—were evaluated to understand recent genetic gains in wheat and determine the impact of selection location and environment on cultivar performance and adaptation. Relative mean yield improvement of ABLs with respect to historical cultivar AGS 2000 was 106 kg ha−1 yr−1 (1.58 bu acre−1 yr−1), equating to an annual genetic gain of 1.6%. Yield gains for wheat during this timespan were attributed to an increase in both yield potential and stability across environments. However, a strong tradeoff (r = −0.36, p < 2.2 × 10−16) was observed between yield potential and stability. Additionally, distance between selection and evaluation environments was significantly correlated with yield, with yield decreasing as distance between locations increased. Advanced breeding lines had a +221, +126, and −29.6 kg ha−1 yr−1 (+3.29, +1.88, and −0.44 bu acre−1) yield difference over the location mean when the selection location was within, adjacent, and nonadjacent to the trial location zone, respectively. Advanced breeding lines in general performed poorly in production environments west of their selection site. Based on data analyzed, elevation and latitude are significant geographic parameters to consider when determining optimal selection location for a production environment. Meanwhile, change in growing degree days between selection and evaluation location had a stronger influence on yield than precipitation. Findings demonstrate the importance and benefits of breeder collaborations and multienvironment testing on crop improvement, which will be needed to maximize yield gains in the 21st century.

Preservation via utilization: minor grape cultivars on-farm

Over the last 20 years, the reputation of minor grape cultivars has increased considerably. Grower magazines and wine journals have reported the renaissance of neglected and even threatened grape cultivars, raising awareness and promoting their cultivation by vine-growers. Minor cultivars represent huge value with respect to cultural heritage, adaptation to ecological conditions, diversification of products and marketing of specialities with a higher economic benefit. Recognizing the heritage and value of traditional crop genetic diversity maintained on farms, in 2017, the European Cooperative Program for Plant Genetic Resources (ECPGR) published a “Concept for on-farm conservation and management of plant genetic resources for food and agriculture”. ECPGR described a future strategy for the preservation of genetic resources. Priority actions defined are transmissible to grapevine. They encompass the development of descriptors, inventory of on-farm vineyards, definition of threat categories and overcoming of legal obstacles, ensuring that obsolete cultivars can be grown. Focus on these four issues took place under the scope of the ECPGR grant scheme activity “On-farm inventory of minor grape varieties in the European Vitis Database” in 2017. Twelve researchers from ten countries (Albania, Austria, Croatia, France, Germany, Italy, Montenegro, Portugal, Serbia, Spain) participated. Descriptors were selected for the grower (12 descriptors), cultivar preserved (17 descriptors), vineyard description (17 descriptors) and commitments (six descriptors). To date, 191 vineyards have been registered: in Spain (105), Albania (16), Montenegro (14), Croatia (13), Germany (13), France (17), Portugal (5), Serbia (5) and Austria (3). An on-farm database was developed (http://www.eu-vitis.de/on-farm/index.php). Criteria for four threat categories were defined and used to initiate a process for legal inclusion of rare historical cultivars in national cultivar catalogues. Preservation under practice conditions provides deeper knowledge of agronomic features and wine quality of traditional grape cultivars and relieves stress on grapevine collections.

Trends in Soybean Trait Improvement over Generations of Selective Breeding

Improvement of agronomic and seed quality traits in soybean [Glycine max (L.) Merr.] occurs in breeding programs as a result of crossing elite soybean genotypes and selection of superior offspring in each cycle. The objective of this study was to evaluate changes in traits over 100 yr of selection in Ontario, Canada, in two soybean breeding programs at the University of Guelph: Guelph Campus (Maturity Group [MG] 0 and I) and Ridgetown Campus (MG II) programs. Fifty‐six Guelph cultivars (released between 1983 and 2016), 46 Ridgetown cultivars (released between 1987 and 2015), and 37 Guelph‐pedigree related historical cultivars (from 1913 to 1985) were grown in field trials over 3 yr (Guelph Campus) and 2 yr (Ridgetown Campus) at two locations per breeding program to measure 13 traits. Yield increased in the Guelph Campus cultivars by 17.1 kg ha−1 yr−1 and by 15.7 kg ha−1 yr−1 in the Ridgetown Campus cultivars, while yield per day of maturity per year of release significantly increased in elite cultivars. Protein in the Ridgetown Campus cultivars increased at 0.76 g kg−1 yr−1, whereas the Guelph Campus cultivars showed no trend. In Ridgetown Campus cultivars 100‐seed weight significantly increased at 0.1 g yr−1. Within the historical cultivars, 100‐seed weight was significantly correlated with both protein (r = 0.50) and oil (r = −0.42). Genotype × trait biplot analyses revealed differential patterns of trait relationships between the elite and historical cultivars. Oil and yield were associated within the Guelph Campus cultivars. The association of 100‐seed weight and protein was only found in the historical cultivars. Yield has increased in both breeding programs while seed traits have been altered over time.

Identification of powdery mildew resistance loci in wheat by integrating genome-wide association study (GWAS) and linkage mapping

Wheat powdery mildew (Blumeria graminis f. sp. tritici, Bgt) is a disease of increasing importance globally due to the adoption of high yielding varieties and modern sustainable farming technologies. Growing resistant cultivars is a preferred approach to managing this disease, and novel powdery mildew resistance genes are urgently needed for new cultivar development. A genome-wide association study was performed on a panel of 1292 wheat landraces and historical cultivars using 5011 single nucleotide polymorphism (SNP) markers. The association panel was evaluated for reactions to three Bgt inoculants, OKS(14)-B-3-1, OKS(14)-C-2-1, and Bgt15. Linkage disequilibrum (LD) analysis indicated that genome-wide LD decayed to 0.1 at 23 Mb, and population structure analysis revealed seven subgroups in the panel. Association analysis using a mixed linear model (MLM) identified three loci for powdery mildew resistance on chromosome 2B, designated QPm.stars-2BL1, QPm.stars-2BL2, and QPm.stars-2BL3. To evaluate the efficacy of GWAS in gene discovery, QPm.stars-2BL2 was validated using F2 and F2:3 populations derived from PI 420646 × OK1059060-126135-3. Linkage analysis delimited the powdery mildew resistance gene in PI 420646 to an interval where QPm.stars-2BL2 was located, lending credence to the GWAS results. QPm.stars-2BL1 and QPm.stars-2BL3, which were associated with four SNPs located at 457.7–461.7 Mb and two SNPs located at 696.6–715.9 Mb in the Chinese Spring reference IWGSC RefSeq v1.0, respectively, are likely novel loci for powdery mildew resistance and can be used in wheat breeding to improve powdery mildew resistance.

A review on history, domestication and germplasm collections of quince (Cydonia oblonga Mill.) in the world

The areas between Dagestan to Talysh, in the Trans-Caucasia and north of Iran are the central regions of quince (Cydonia oblonga Mill.) origin. Historic documents present evidences of quince domestication in the Mesopotamia, between 5000 and 4000 BC that have been pursued to about 500 BC in the ancient Persian and Greek empires. By the end of nineteenth century, domesticated populations of this plant had been spread to the west and east Asia, Europe and America which in turn, created several centers of diversity along its distribution route in some regions such as plateau of Iran, Anatolia, Greece and southern Europe, north of the Black Sea and Russia. Gradually in the mentioned domestication routes, selected quinces such as, Isfahan, Smyrna, Ekmek, Esme, Vranja, Lescovatz and Champion have become commercialized as superior cultivars. Also genebank collections of the historic cultivars together with the promising genotypes of quince have been established in several countries including, Russia, Iran, Turkey, Greece, Italy, Bulgaria, Czech Republic, UK and USA. Investigations on morphological, molecular and horticultural characteristics of the germplasm have provided ample opportunities for application of advanced breeding programs especially to boost bearing potential, induce dwarfing, increase fruit quality and resistance to the main diseases such as fire blight. This review paper has attempted to give an account for quince historic origin, domestication, gene bank collections and breeding strategies.

How root traits would be affected by soybean yield improvement? An examination of historical cultivars grafted with record-yield cultivar scion

During historical yield improvement in soybean, breeders have seldom considered selection for root traits, generally focusing selection on yield traits. Yet, it is not known how root traits of historical cultivars would be altered if their shoot functions and grain yields were largely improved. Here we investigated the influence of record-yield soybean cultivars L14 and Z35 as scions on root traits of historical cultivars. A total of 11 cultivars, released in different decades, were used to graft with L14 or Z35 scions. Some morphological and physiological traits were measured in the pot-culture experiments. During grain-filling stage, the scions of L14 and Z35 had greater photosynthetic capacity, seed biomass and seed starch accumulation than those of other cultivars. Grafting of cultivars with L14 and Z35 scions resulted in significant decreases in root biomass, root-shoot ratio, root starch accumulation and root morphological traits compared with non-grafts or self-grafts. The genetic gain for these root traits of cultivars released from 1966 to 2006 increased by grafting record-yield cultivars scions, while that of grain yield and nutrient accumulation decreased. Our results revealed the uncoordinated improvement between roots and shoots during historical breeding in soybean.

Pathogenic variation of Pyrenophora teres f. teres in Australia

Pyrenophora teres f. teres (Ptt) is the causal agent of net form of net blotch (NFNB) – a major foliar disease of barley (Hordeum vulgare) crops worldwide. Deployment of genetic resistance in cultivars is the preferred method of control, but requires knowledge of the pathogenic variation of Ptt to be effective as spatial and temporal variation is common. In this study, 123 Ptt isolates collected from five states across Australia were examined for pathogenic variation using a set of 31 barley genotypes, composed of 11 international genotypes and 20 Australian cultivars. Barley seedlings were inoculated with spore suspensions from monoconidial isolate cultures and scored for infection response. Phenotypes were used to perform hierarchical cluster analysis for barley genotypes and Ptt isolates. Cluster analysis identified seven line groups, each containing barley genotypes that displayed similar responses to the Ptt isolates. Isolates clustered into four distinct isolate groups shown to harbour differential virulence to four key genotypes: Maritime, Prior, Skiff and Tallon. Isolates with virulence to any one of these genotypes accounted for 96.7% of the samples. Differential virulence was observed on a range of genotypes within each isolate group. The composition of isolate groups in eastern Australia was distinct from Western Australia, whereas all isolate groups were detected in southern Australia. Results suggest that cultivation of regionally adapted barley cultivars has led to regional evolution of Ptt, where the pathogen acquires virulence specific for resistance factors deployed in local cultivars. Detection of Ptt modern isolates that were highly virulent to historic cultivars indicates the long-term survival of virulence gene combinations in the pathogen population.

Novel Sources of Leaf Rust Resistance in Winter Wheat

Leaf rust is one of the most widespread diseases of wheat (Titicum aestivum L.), causing significant yield losses. More than 70 leaf rust resistance genes have been identified, but most of them have lost their effectiveness in the southern Great Plains of the United States. The objectives of this study were to evaluate leaf rust resistance of newly released wheat breeding lines and to identify novel resistance sources from a worldwide collection of landraces and historical cultivars. Results showed that only 4 out of 183 cultivars and breeding lines recently developed in the United States were highly resistant in the seedling stage to Pt2013, a bulk of Puccinia triticina Eriks. (Pt) races collected from multiple fields in Oklahoma in 2013, indicating the urgency of finding new resistance genes. We screened a set of 2171 accessions using Pt2013 and identified 26 landraces and 61 historical cultivars exhibiting high resistance. In addition, 159 landraces and 309 historical cultivars showed moderate resistance to Pt2013. These highly or moderately resistant accessions were further evaluated for their responses to another two Pt races predominant in Oklahoma in 2015, Pt52‐2 and Pt54‐1, and 25 of them showed high resistance to these two races and to the race composite. Another 66 and 53 accessions showed high resistance to one and two Pt races, respectively. Genetic diversity analysis using 5011 single‐nucleotide polymorphism markers identified genetically diverse resistance sources. The resistance sources identified in this study may be valuable for breeding leaf rust resistance.

Genome-wide association study reveals genetic architecture of coleoptile length in wheat.

Eight QTL for coleoptile length were identified in a genome-wide association study on a set of 893 wheat accessions, four of which are novel loci. Wheat cultivars with long coleoptiles are preferred in wheat-growing regions where deep planting is practiced. However, the wide use of gibberellic acid (GA)-insensitive dwarfing genes, Rht-B1b and Rht-D1b, makes it challenging to breed dwarf wheat cultivars with long coleoptiles. To understand the genetic basis of coleoptile length, we performed a genome-wide association study on a set of 893 landraces and historical cultivars using 5011 single nucleotide polymorphism (SNP) markers. Structure analysis revealed four subgroups in the association panel. Association analysis results suggested that Rht-B1b and Rht-D1b genes significantly reduced coleoptile length, and eight additional quantitative trait loci (QTL) for coleoptile length were also identified. These QTL explained 1.45-3.18 and 1.36-3.11% of the phenotypic variation in 2015 and 2016, respectively, and their allelic substitution effects ranged from 0.31 to 1.75cm in 2015, and 0.63-1.55cm in 2016. Of the eight QTL, QCL.stars-1BS1, QCL.stars-2DS1, QCL.stars-4BS2, and QCL.stars-5BL1 are likely novel loci for coleoptile length. The favorable alleles in each accession ranged from two to eight with an average of 5.8 at eight loci in the panel, and more favorable alleles were significantly associated with longer coleoptile, suggesting that QTL pyramiding is an effective approach to increase wheat coleoptile length.

Phenotypic Plasticity of Winter Wheat Heading Date and Grain Yield across the US Great Plains

Phenotypic plasticity describes the range of phenotypes produced by a single genotype in different environments. We quantified the extent of phenotypic plasticity (evaluated as responsiveness to varying environmental conditions) of thermal time to heading and grain yield in 299 hard winter wheat (Triticum aestivum L.) genotypes from the US Great Plains. The genotypes, which included advanced breeding lines and recent and historic cultivars, were evaluated in 11 environments in 2011–2012 and 2012–2013. The average number of days from 1 January to heading across environments ranged from 109 to 150, and the cumulative growing degree days (GDD) from 1 January to heading ranged from 730 to 1112 GDD. Environmental mean grain yield varied from 1.3 to 5.3 Mg ha−1. Plasticity of GDD (GDDP) was strongly correlated with GDD (r = 0.81, P < 0.001), especially maximum GDD (r = 0.90, P < 0.001) across environments, indicating genotypes with greater plasticity developed later, especially within the earliest environments. Plasticity of GDD was negatively associated with yield (r = −0.58, P < 0.001) and therefore detrimental in the germplasm and environments evaluated. Yield plasticity of a genotype was positively correlated with its maximum (r = 0.80, P < 0.001) and minimum (r = 0.33, P < 0.001) grain yield across environments, indicating greater plasticity was favorable under optimal conditions, without a penalty under low‐yielding conditions. More than a century of wheat breeding in this region suggests GDDP has declined and yield plasticity has increased at similar rates. This is encouraging because it indicates the favorable plasticity traits (high yield plasticity, low GDDP) have been selected for indirectly and would respond to further selection.

Population Structure and Genotype-Phenotype Associations in a Collection of Oat Landraces and Historic Cultivars.

Population structure and genetic architecture of phenotypic traits in oat (Avena sativa L.) remain relatively under-researched compared to other small grain species. This study explores the historic context of current elite germplasm, including phenotypic and genetic characterization, with a particular focus on identifying under-utilized areas. A diverse panel of cultivated oat accessions was assembled from the USDA National Small Grains Collection to represent a gene pool relatively unaffected by twentieth century breeding activity and unlikely to have been included in recent molecular studies. The panel was genotyped using an oat iSelect 6K beadchip SNP array. The final dataset included 759 unique individuals and 2,715 polymorphic markers. Some population structure was apparent, with the first three principal components accounting for 38.8% of variation and 73% of individuals belonging to one of three clusters. One cluster with high genetic distinctness appears to have been largely overlooked in twentieth century breeding. Classification and phenotype data provided by the Germplasm Resources Information Network were evaluated for their relationship to population structure. Of the structuring variables evaluated, improvement status (cultivar or landrace) was relatively unimportant, indicating that landraces and cultivars included in the panel were all sampled from a similar underlying population. Instead, lemma color and region of origin showed the strongest explanatory power. An exploratory association mapping study of the panel using a subset of 2,588 mapped markers generated novel indications of genomic regions associated with awn frequency, kernels per spikelet, lemma color, and panicle type. Further results supported previous findings of loci associated with barley yellow dwarf virus tolerance, crown rust (caused by Puccinia coronata f. sp. avenae) resistance, days to anthesis, and growth habit (winter/spring). In addition, two novel loci were identified for crown rust resistance.

Historic American Apple Cultivars: Identification and Availability

Apples (Malus Mill.) have been economically and socially important throughout the centuries in North America. Apple cultivar (Malus ×domestica Borkh.) collections that include historic cultivars are valued for their unique diversity, historical significance, and also as a resource to identify unknown trees; however, not all of the historically significant apple cultivars are currently included in these collections. We used historic books, publications, and nursery catalogs to develop an inventory of apple cultivars that were propagated and grown in the United States before 1908. We collected synonym, introduction date, and original source country information for 891 historic apple cultivars. Most of the historic American cultivars originated as seedlings first planted in the United States. Some cultivars were brought to the United States from the United Kingdom, France, Russia, Germany, and other European countries. We classified historic apple cultivars based on their availability over time and popularity in nursery catalogs. Ninety percent of the most popular historic apple cultivars in the United States were available in 2015 in the U.S. and U.K. national collections and within several commercial and private collections. This work identified high priority historic cultivars that are not currently protected within genebanks that could be added to genebank collections in the future.

Investigation of Mal d 1 Allelic Variants and Phylogenetic Diversity in Contemporary and Historical Polish Apple Cultivars

Allergy is considered as the most common health problem of XXI century. Apple allergenicity is of great importance and at present the only therapy for food allergy is avoidance. Fruits are important components of a healthy diet, and therefore complete avoidance of apple and related fruits like pear, peach, and cherry can have a significant negative impact since deprives the patient’s diet from important sources of vitamins, minerals and fibers. In order to provide a contribution towards a better understanding of the genetics of the family of Mal d 1 gene, the major apple allergen, and to establish the basis for further research on allelic diversity among cultivars in relation to variation in allergenicity we evaluated Mal d 1 gene variability in contemporary and historical Polish apple cultivars (Malus × domestica Borkh.). We identified new Mal d 1 alleles and further assessed phylogenetic distance between Mal d 1 variants and antigens derived from other food sources. We also predicted possible cross-reactions between allergens originated from Malus x domestica and other plant taxa as well as showed potential binding sites of apple allergens to the antibody. Thanks to multiple sequence alignment of the amino acid sequences limited to residues which serve as interaction partners for the antibody we were able to more precisely establish phylogenetic distance between analyzed antigens in regards to the antigen epitope residues.

Development and analysis of a 20K SNP array for potato (Solanum tuberosum): an insight into the breeding history.

Key messageA 20K SNP array was developed and a comprehensive set of tetraploid cultivar was genotyped. This allowed us to identify footprints of the breeding history in contemporary breeding material such as identification of introgression segments, selection and founder signatures.A non-redundant subset of 15,138 previously identified SNPs and 4454 SNPs originating from the SolCAP project were combined into a 20k Infinium SNP array for genotyping a total of 569 potato genotypes. In this study we describe how this SNP array (encoded SolSTW array) was designed and analysed with fitTetra, software designed for autotetraploids. Genotypes from different countries and market segments, complemented with historic cultivars and important progenitors, were genotyped. This comprehensive set of genotypes combined with the deliberate inclusion of a large proportion of SNPs with a low minor allele frequency allowed us to distinguish genetic variation contributed by introgression breeding. This “new” (post 1945) genetic variation is located on specific chromosomal regions and enables the identification of SNP markers linked to R-genes. In addition, when the genetic composition of modern cultivars was compared with cultivars released before 1945, it appears that 96 % of the genetic variants present in those ancestral cultivars remains polymorphic in modern cultivars. Hence, genetic erosion is almost absent in potato. Finally, we studied population genetic processes shaping the genetic composition of the modern European potato including drift, selection and founder effects. This resulted in the identification of major founders contributing to contemporary germplasm.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-015-2593-y) contains supplementary material, which is available to authorized users.

Yield gap simulations using ten maize cultivars commonly planted in Northeast China during the past five decades

Northeast China (NEC) is one of the most important agricultural production areas in China and is one of the most sensitive areas in the country to climate change, particularly during the last five decades when strong climate warming occurred. Thus, a better understanding of the potential, attainable, and farm yields and yield gaps of spring maize under climate change is necessary with respect to historical cultivars improvements. Ten spring maize cultivars commonly planted from the 1960s to the 2000s were selected for a two-year field experiment in Lishu, NEC. The APSIM-maize model was used to simulate the potential and attainable yields of spring maize from 1961 to 2009 using real-time cultivar calibration and validation during the past five decades. Our results indicated that the yield gap between the potential and farm yields was 9.7tha−1, or 66.2% of the potential yield; the yield gap between the attainable and farm yields was 5.6tha−1, or approximately 54% of the attainable yield. Climate change from 1961 to 2009 led to a reduction in the potential yield by 2.1% and a reduction in the attainable yield by 8.0%. Improved cultivars and agricultural practices have led to an increase of 62.2% and 80.5% in potential and attainable yields, respectively. Therefore, the combined impact of climate change and improvements in cultivars and agricultural practices increased potential and attainable yields 53.3% and 70.3%, respectively, for the period 1961–2009 relative to the yields of the cultivar planted in the 1960s. In conclusion, improvements in cultivars and agricultural practices for spring maize in NEC played a dominate role for the increase of yield, and the persistent large yield gap between farm and attainable or potential yields provides farmers an opportunity to increase their agricultural production.