Modern Cultivars Research Articles

Characterizing the oligogenic architecture of plant growth phenotypes informs genomic selection approaches in a common wheat population

BackgroundGenetic variation in growth over the course of the season is a major source of grain yield variation in wheat, and for this reason variants controlling heading date and plant height are among the best-characterized in wheat genetics. While the major variants for these traits have been cloned, the importance of these variants in contributing to genetic variation for plant growth over time is not fully understood. Here we develop a biparental population segregating for major variants for both plant height and flowering time to characterize the genetic architecture of the traits and identify additional novel QTL.ResultsWe find that additive genetic variation for both traits is almost entirely associated with major and moderate-effect QTL, including four novel heading date QTL and four novel plant height QTL. FT2 and Vrn-A3 are proposed as candidate genes underlying QTL on chromosomes 3A and 7A, while Rht8 is mapped to chromosome 2D. These mapped QTL also underlie genetic variation in a longitudinal analysis of plant growth over time. The oligogenic architecture of these traits is further demonstrated by the superior trait prediction accuracy of QTL-based prediction models compared to polygenic genomic selection models.ConclusionsIn a population constructed from two modern wheat cultivars adapted to the southeast U.S., almost all additive genetic variation in plant growth traits is associated with known major variants or novel moderate-effect QTL. Major transgressive segregation was observed in this population despite the similar plant height and heading date characters of the parental lines. This segregation is being driven primarily by a small number of mapped QTL, instead of by many small-effect, undetected QTL. As most breeding populations in the southeast U.S. segregate for known QTL for these traits, genetic variation in plant height and heading date in these populations likely emerges from similar combinations of major and moderate effect QTL. We can make more accurate and cost-effective prediction models by targeted genotyping of key SNPs.

Field resistance to wheat stem rust in durum wheat accessions deposited at the USDA National Small Grains Collection.

Wheat stem rust, caused by Puccinia graminis f. sp. tritici, is a re‐emerging disease, posing a significant threat to durum wheat production worldwide. The limited number of stem rust resistance genes in modern cultivars compels us to identify and incorporate new effective genes in durum wheat breeding programs. We evaluated 8,245 spring durum wheat accessions deposited at the USDA National Small Grains Collection (NSGC) for resistance in field stem rust nurseries in Debre Zeit, Ethiopia and St. Paul, MN (USA). A higher level of disease development was observed at the Debre Zeit nursery compared with St. Paul, and the effective alleles of Sr13 in this nursery did not display the level of resistance observed at the St. Paul nursery. Four hundred and ninety‐one (∽6%) accessions exhibited resistant to moderately susceptible responses after three field evaluations at Debre Zeit and two at St. Paul. Nearly 70% of these accessions originated from Ethiopia, Mexico, Egypt, and USA. Eight additional countries, namely Portugal, Turkey, Italy, Canada, Chile, Australia, Syria, and Tunisia contributed to 19% of the resistant to moderately susceptible entries. Among the 491 resistant to moderately susceptible accessions, 53.8% (n = 265) were landraces, and 28.4% (n = 139) and 11.4% (n = 55) were breeding lines and cultivars, respectively. Breeding lines and cultivars displayed a higher level and frequency of resistance than the landraces. We concluded that a large number of durum wheat accessions from diverse origins deposited at the NSGC can be exploited for diversifying and improving stem rust resistance in wheat.

Stem rot management by nitrogen and potassium fertilization and effect on grain yield and quality of rice in Uruguay

Stem rot (Nakataea oryzae) limits rice (Oryza sativa) production in Uruguay when there are high inoculum levels in the soil. This disease is particularly damaging in potassium (K)-deficient soils that receive excessive nitrogen (N) fertilization. Nevertheless, no data exist for the response to stem rot in modern rice cultivars with respect to the interaction between balanced N and K fertilization. The aim of this work was to evaluate the combined effect of K and N fertilization and a foliar phosphite (Phi) in reducing stem rot severity in rice to prevent significant yield losses. A 3-year field study was conducted in a rice-producing region of Uruguay to investigate the effects of: (1) K fertilization rate, 0 or based on the Mg:K ratio; (2) N fertilization rate, 0 or 140 kg ha–1 N; and (3) Phi treatment, with or without foliar Phi (1.775 kg ha–1 of K Phi, 71%), at growth stage R2-R3. While the experiment was conducted in a soil with sufficient potassium, K fertilization reduced the severity and percentage of rice tillers that were severely affected by stem rot, resulting in a mean yield increment of 2% to 18% depending on the year (mean 7.5%). Nitrogen fertilization increased stem rot severity in only 1 year, but resulted in a mean yield increment of 10% over the 3 years of the experiment. Foliar Phi applied at the late boot to panicle exertion stage did not reduce disease incidence or severity and failed to increase the total rice grain and milling yield.

A chromosome-level genome of a Kordofan melon illuminates the origin of domesticated watermelons

Wild relatives or progenitors of crops are important resources for breeding and for understanding domestication. Identifying them, however, is difficult because of extinction, hybridization, and the challenge of distinguishing them from feral forms. Here, we use collection-based systematics, iconography, and resequenced accessions of Citrullus lanatus and other species of Citrullus to search for the potential progenitor of the domesticated watermelon. A Sudanese form with nonbitter whitish pulp, known as the Kordofan melon (C. lanatus subsp. cordophanus), appears to be the closest relative of domesticated watermelons and a possible progenitor, consistent with newly interpreted Egyptian tomb paintings that suggest that the watermelon may have been consumed in the Nile Valley as a dessert by 4360 BP. To gain insights into the genetic changes that occurred from the progenitor to the domesticated watermelon, we assembled and annotated the genome of a Kordofan melon at the chromosome level, using a combination of Pacific Biosciences and Illumina sequencing as well as Hi-C mapping technologies. The genetic signature of bitterness loss is present in the Kordofan melon genome, but the red fruit flesh color only became fixed in the domesticated watermelon. We detected 15,824 genome structural variants (SVs) between the Kordofan melon and a typical modern cultivar, "97103," and mapping the SVs in over 400 Citrullus accessions revealed shifts in allelic frequencies, suggesting that fruit sweetness has gradually increased over the course of watermelon domestication. That a likely progenitor of the watermelon still exists in Sudan has implications for targeted modern breeding efforts.

Genome-wide association study for septoria tritici blotch resistance reveals the occurrence and distribution of Stb6 in a historic Swiss landrace collection

Septoria tritici blotch (STB), caused by the fungus Zymoseptoria tritici, is a major constraint in global wheat production. The lack of genetic diversity in modern elite wheat cultivars largely hinders the improvement of STB resistance. Wheat landraces are reservoirs of untapped genetic diversity, which can be exploited to find novel STB resistance genes or alleles. Here, we characterized 188 Swiss wheat landraces for resistance to STB using four Swiss Z. tritici isolates. We used a genome-wide association study (GWAS) to identify genetic variants associated with the amount of lesion and pycnidia production by the fungus. The majority of the landraces were highly resistant for both traits to the isolate 1E4, indicating a gene-for-gene relationship, while higher phenotypic variability was observed against other isolates. GWAS detected a significant SNP on chromosome 3A that was associated with both traits in the isolate 1E4. The resistance response against 1E4 was likely controlled by the Stb6 gene. Sanger sequencing revealed that the majority of these ~ 100-year-old landraces carry the Stb6 resistance allele. This indicates the importance of this gene in Switzerland during the early 1900s for disease control in the field. Our study demonstrates the importance of characterizing historic landrace collections for STB resistance to provide valuable information on resistance variability and contributing alleles. This will help breeders in the future to make decisions on integrating such germplasms in STB resistance breeding.

Fine mapping of hybrid necrosis gene Ne1 in common wheat (Triticum aestivum L.).

Hybrid necrosis gene Ne1 was delimited into an approximate 4.06 Mb region on chromosome arm 5BL and an InDel marker that co-segregated with Ne1 alleles was developed. Hybrid necrosis in wheat, characterized by progressive chlorosis and necrosis of plant leaves, tillers or whole plants in certain hybrids, is caused by complementary genes Ne1 and Ne2 located on chromosome arms 5BL and 2BS, respectively. Hybrid necrosis can be a barrier in combining desirable traits from various wheat genotypes. In this study, we fine mapped Ne1 on chromosome arm 5BL, and delimited it to a 4.06 Mb region using large segregating recombinant inbred line families from cross 'Zhengnong 17' × 'Yangbaimai'. Genetic characterization confirmed that the ne1 allele was closely associated with a 2.89 Mb deletion in Zhengnong 17. A tightly linked InDel marker, 5B-InDel385, for Ne1 was developed and was used to predict the presence of Ne1 in a diverse panel of 501 common wheat accessions. Among those accessions, 122 (61%) of 200 landraces were predicted to carry the Ne1 allele, whereas only 79 (26%) of 301 modern cultivars were predicted to carry Ne1. The significant decrease in Ne1 frequency in modern cultivars indicated that the Ne1 allele had been negatively selected in wheat breeding. This study provides a foundation for marker-assisted selection, gene cloning and functional studies of Ne1 in wheat.

Diversity and sustainability of wheat landraces grown in Uzbekistan

Development of new wheat cultivars combining good local adaptation, disease resistance and grain quality represents an important strategy component for national food security. Uzbekistan was identified by N. Vavilov as important center of wheat diversity. An inventory of landraces was conducted in 2010–2013 in western Tien-Shan Mountains to survey, collect, and characterize old wheats still grown by farmers. Thirty landraces were collected from 17 villages in Jizzakh, Kashkadarya and Surkhandarya Regions. The material went through spike selection, head-rows, un-replicated trials in Tashkent, Uzbekistan (2012–2015), and replicated trials in Konya, Turkey (2018–2019). Landrace diversity was described using spike morphological traits and DNA profiles as reflected by single nucleotide polymorphism. A socioeconomic survey demonstrated that wheat landraces are grown in remote mountain communities by subsistence farmers despite having access to modern cultivars, and both are frequently grown together. The main reasons for the maintenance of landraces are: (1) large grain with excellent bread-making quality and suitability for home-baking; (2) specific adaptations allowing stable and reliable yield; and (3) straw yield and quality. Similar genomic profiles shared by some landraces from remote regions of Uzbekistan and neighboring Tajikistan demonstrated their common origin and are indicative of seed exchange between farmers. Agronomic characterization demonstrated the resilient nature of their adaptation based on spring and facultative growth habit and superiority of some landraces for grain yield and its components compared to local checks. Viable options for maintaining and expanding on-farm wheat diversity include their improvement through selection and breeding, market development, variable incentives, and capacity building. For the first time, this paper presents results of a unique 10-year study in Uzbekistan on social conditions in the areas where wheat landraces are grown, analyses the diversity of these landraces, evaluates agronomic characteristics, and discusses the sustainability options for on-farm wheat landraces use and conservation.

Physio-Morphological and Biochemical Trait-Based Evaluation of Ethiopian and Chinese Wheat Germplasm for Drought Tolerance at the Seedling Stage

For Ethiopia’s wheat production, drought is a major natural disaster. Exploration of drought-resistant varieties from a bulk of wheat germplasm conserved in the gene bank is of paramount importance for breeding climate change-resilient modern cultivars. The present study was aimed at identifying the best performing drought-resistant genotypes under non-stress and polyethylene glycol simulated (PEG) stress conditions in a growth chamber. Forty diverse Ethiopian bread and durum wheat cultivars along with three Chinese bread wheat cultivars possessing strong drought resistance and susceptibility were evaluated. After acclimation with the natural environment, the seedlings were imposed to severe drought stress (20% PEG6000), and 15 seedling traits including photosynthetic and free proline were investigated. Our findings indicated that drought stress caused a profound decline in plant water consumption (83.0%), shoot fresh weight (64.9%), stomatal conductance (61.6%), root dry weight (55.2%), and other investigated traits except root to shoot length ratio and proline content which showed a significant increase under drought stress. A significant and positive correlation was found between photosynthetic pigments in both growth conditions. Proline exhibited a negative correlation with most of the investigated traits except root to shoot length ratio and all photosynthetic pigments which showed a positive and non-significant association. Our result also showed a wide range of genetic variation (CV) ranging from 3.23% to 47.3%; the highest in shoot dry weight (SDW) (47.3%) followed by proline content (44.63%) and root dry weight (36.03%). Based on multivariate principal component biplot analysis and average sum of ranks (ASR), G12, G16 and G25 were identified as the best drought tolerant and G6, G42, G4, G11, and G9 as bottom five sensitive. The potential of these genotypes offers further investigation at a molecular and cellular level to identify the novel gene associated with the stress response.

The Gossypium stocksii genome as a novel resource for cotton improvement.

Cotton is an important textile crop whose gains in production over the last century have been challenged by various diseases. Because many modern cultivars are susceptible to several pests and pathogens, breeding efforts have included attempts to introgress wild, naturally resistant germplasm into elite lines. Gossypium stocksii is a wild cotton species native to Africa, which is part of a clade of vastly understudied species. Most of what is known about this species comes from pest resistance surveys and/or breeding efforts, which suggests that G. stocksii could be a valuable reservoir of natural pest resistance. Here, we present a high-quality de novo genome sequence for G. stocksii. We compare the G. stocksii genome with resequencing data from a closely related, understudied species (Gossypium somalense) to generate insight into the relatedness of these cotton species. Finally, we discuss the utility of the G. stocksii genome for understanding pest resistance in cotton, particularly resistance to cotton leaf curl virus.

Grapes and vines of the Phoenicians: Morphometric analyses of pips from modern varieties and Iron Age archaeological sites in the Western Mediterranean

The present study aims to contribute to the investigation of the role of Phoenicians in the spreading and trade of the grapevine through the morphometric analysis of grape pips. Waterlogged and charred samples were selected from three Iron Age sites in the Western Mediterranean: Motya (Sicily, Italy), Nuraghe S’Urachi (Sardinia, Italy) and Huelva (Andalusia, Spain). While only Motya is a Phoenician foundation, all three were nevertheless associated with Phoenician expansion and cultural interaction. Ten cultivars from the “Vivaio Federico Paulsen” in Marsala (western Sicily) were chosen as modern reference material.The key challenge was the comparison of archaeological pips preserved through different fossilization processes, which was overcome using two reference datasets of the same modern cultivars, one uncharred and one charred.Statistical analyses of pip outlines show that archaeological remains from these sites is morphologically comparable to that of modern varieties, suggesting that the archaeological finds represent domesticated grapevines.PCA analyses allowed an inter-site comparison, showing that samples from the three sites are clearly distinguishable based on their morphology. This indicates the use of different varieties which may be due to different factors.Our analysis represents a first step towards a better understanding of diachronic and synchronic relationship between vines grown in the ancient West Mediterranean, which could be expanded by analysing grape pips from more contexts and more sites, compared against a wider selection of modern cultivars.

Long-term preservation of modern Russian potato cultivars in the VIR cryobank

Cryopreservation of shoot-tips (apexes) excised from in vitro plants is used for long-term preservation of potato cultivars. The most widely used method for creating potato cryo-collections is droplet-vitrification of shoot-tips which, together with its numerous modifications, is widely used in genebanks. A modified protocol of droplet vitrification method is used at VIR for cryopreservation of shoot tips from in vitro potato plants. This paper presents the results of cryopreservation of modern cultivars which were released by seven Russian breeding centers. In vitro clones used in the cryopreservation experiments were genetically identical to the cultivars’ nomenclatural standards and herbarium vouchers.The frequency of post-thaw regeneration in control experiments after short-term cryopreservation varied from 23.3 to 53.3%, depending on the genotype. Five out of 16 accessions (‘Varâg’, ‘Gusar’, ‘Evpatij’, ‘Solnečnyj’, ‘Tango’)* had low post-cryogenic regenerative capacity from 20 to 30%; the regeneration rate exceeded 30% in 11 accessions, and 8 cultivars (‘Grand’, ‘Zlatka’, ‘Lina’, ‘Safo’, ‘Siverskij’, ‘Signal’, ‘Utro’, ‘Ûna’) and ‘Аlyj Parus’ breeding clone had regeneration rate above 40%. The regeneration rate in the studied subset was genotype independent according to the ANOVA results (p=0.711). Viability and regeneration rate were significantly correlated (r=0.86). As a result of the experiments, explants of 14 modern cultivars and two breeding clones with the known post-thaw regeneration rate were successfully cryopreserved in the VIR cryobank. Four cultivars (‘Grand’, ‘Gusar’, ‘Signal’, ‘Utro’) were monitored for their regeneration capacity after the long-term (seven months) preservation in the VIR cryobank. On an average, these four cultivars demonstrated a post-thaw regeneration capacity of 41.8%. It can be concluded that the use of the modified method of droplet vitrification is relevant for increasing the VIR potato cryo-collection.

Novel resistance strategies to soybean cyst nematode (SCN) in wild soybean

Soybean cyst nematode (SCN, Heterodera glycine Ichinohe) is the most damaging soybean pest worldwide and management of SCN remains challenging. The current SCN resistant soybean cultivars, mainly developed from the cultivated soybean gene pool, are losing resistance due to SCN race shifts. The domestication process and modern breeding practices of soybean cultivars often involve strong selection for desired agronomic traits, and thus, decreased genetic variation in modern cultivars, which consequently resulted in limited sources of SCN resistance. Wild soybean (Glycine soja) is the wild ancestor of cultivated soybean (Glycine max) and it’s gene pool is indisputably more diverse than G. max. Our aim is to identify novel resistant genetic resources from wild soybean for the development of new SCN resistant cultivars. In this study, resistance response to HG type 2.5.7 (race 5) of SCN was investigated in a newly identified SCN resistant ecotype, NRS100. To understand the resistance mechanism in this ecotype, we compared RNA seq-based transcriptomes of NRS100 with two SCN-susceptible accessions of G. soja and G. max, as well as an extensively studied SCN resistant cultivar, Peking, under both control and nematode J2-treated conditions. The proposed mechanisms of resistance in NRS100 includes the suppression of the jasmonic acid (JA) signaling pathway in order to allow for salicylic acid (SA) signaling-activated resistance response and polyamine synthesis to promote structural integrity of root cell walls. Our study identifies a set of novel candidate genes and associated pathways involved in SCN resistance and the finding provides insight into the mechanism of SCN resistance in wild soybean, advancing the understanding of resistance and the use of wild soybean-sourced resistance for soybean improvement.

Developmental patterns and rates of organogenesis across modern and well-adapted wheat cultivars

Genetic gains in wheat yield are required to meet future demand. In order to design strategic crosses, it is essential to quantify the genetic variation among elite cultivars on traits responsible for the adaptation and the generation of yield components. We explored the degree of variation within well-adapted commercial cultivars on developmental phases (vegetative, early reproductive and late reproductive), final leaf number and phyllochron, leaf and spikelet plastochron, number of spikelets, florets, and dynamics of floret primordia development. Variation in flowering time among cultivars was minor but they differed in the partitioning of that time into particular phases. Main differences were found for the length of the late reproductive phase, partly linked to those in final leaf number. Variations on number of fertile florets at anthesis were mostly explained by floret survival, due to differential ability of labile florets to maintain normal development between cultivars. These differences were related to the duration of the floret development, but not to the synchrony of development among florets. These findings provide useful information for breeders when selecting genotypes for strategic crosses, as considering floret survival through duration of floret development in one of the parents (for which these processes shall be characterised in the elite germplasm) might increase the likelihood of transgressive segregation towards high-yielding offspring.

Grain yield, milling and breadmaking quality responses to foliar diseases in old and modern Argentinean wheat cultivars

Foliar diseases limit yield and modify the quality of the bread wheat. Due to genetic improvement reduced source:sink ratio, it is possible to speculate that the diseases infections penalize yield more in modern than in old cultivars, affecting differentially quality commercial and milling properties. The objective of this work was to analyze the changes in yield and quality of bread wheat due to the presence of foliar diseases in old and modern bread wheat cultivars artificially inoculated with Puccinia triticina, compared to a control plots protected with fungicide. Foliar diseases penalized yield due to reductions in the number of grains in all cultivars. Protein in grain-flour, wet-dry gluten and sedimentation were reduced when Pyrenophora tritici-repentis was the main pathogen, while Puccinia triticina only reduced the protein content in grain. Modern cultivars shower greater decreased proteins in grain-flour and gluten than old cultivars, probably associated with higher yield and lower source:sink ratio respect to the old cultivars. The changes in dough rheology and breadmaking quality, as a consequence of foliar diseases, were not as marked or as consistent as observed on milling quality, and the magnitude and direction of those effects were not as clear as those observed in milling quality.

Landscape complexity benefits bumble bee visitation in faba bean (Vicia faba minor L.) but crop productivity is not pollinator-dependent

Faba bean (Vicia faba minor L.) is partially dependent on insects for pollination, but the degree of pollinator-dependency and whether crop productivity is limited by insufficient insect pollination remain unknown. We monitored insect pollinators and their foraging behaviors (i. e., legitimate flower visitation, nectar robbing and extra-floral nectary visitation) in a total of 20 faba bean fields of a single cultivar (Tiffany) 2018–2019. Focal fields were situated along a gradient of landscape complexity. In each field, a pollination experiment was established, where plants were either bagged to exclude pollination by insects or remained open for pollinator visits. In addition, all flowers on half of the bagged and open-pollinated plants were pollinated by hand to measure the degree of pollen limitation. We found that bumble bee abundance was higher, and legitimate flower visitor abundance tended to be higher, in complex landscapes with more semi-natural habitat, indicating that the faba bean pollination potential is higher in complex landscapes. The pollination experiment showed that the number of beans per pod was lower in bagged plants compared with other treatments in one of the years, but the lower number of beans per pod was compensated for by a higher individual bean weight, such that there was no pollinator-dependency or effect of hand pollination on total bean mass per plant. We conclude that to be able to characterize the value of insect pollination services in faba bean we need an improved understanding of how pollinator-dependency varies across modern cultivars, and how environmental conditions can increase or, as in our case, cancel this pollinator-dependency.

Social network analysis of the genealogy of strawberry: retracing the wild roots of heirloom and modern cultivars.

The widely recounted story of the origin of cultivated strawberry (Fragaria × ananassa) oversimplifies the complex interspecific hybrid ancestry of the highly admixed populations from which heirloom and modern cultivars have emerged. To develop deeper insights into the three-century-long domestication history of strawberry, we reconstructed the genealogy as deeply as possible—pedigree records were assembled for 8,851 individuals, including 2,656 cultivars developed since 1775. The parents of individuals with unverified or missing pedigree records were accurately identified by applying an exclusion analysis to array-genotyped single-nucleotide polymorphisms. We identified 187 wild octoploid and 1,171 F. × ananassa founders in the genealogy, from the earliest hybrids to modern cultivars. The pedigree networks for cultivated strawberry are exceedingly complex labyrinths of ancestral interconnections formed by diverse hybrid ancestry, directional selection, migration, admixture, bottlenecks, overlapping generations, and recurrent hybridization with common ancestors that have unequally contributed allelic diversity to heirloom and modern cultivars. Fifteen to 333 ancestors were predicted to have transmitted 90% of the alleles found in country-, region-, and continent-specific populations. Using parent–offspring edges in the global pedigree network, we found that selection cycle lengths over the past 200 years of breeding have been extraordinarily long (16.0-16.9 years/generation), but decreased to a present-day range of 6.0-10.0 years/generation. Our analyses uncovered conspicuous differences in the ancestry and structure of North American and European populations, and shed light on forces that have shaped phenotypic diversity in F. × ananassa.

Unlocking the Patterns of the Tunisian Durum Wheat Landraces Genetic Structure Based on Phenotypic Characterization in Relation to Farmer’s Vernacular Name

During the 1970s, Tunisian durum wheat landraces were replaced progressively by modern cultivars. These landraces are nowadays maintained by smallholder farmers in some ecological niches and are threatened gradually by extinction resulting in the narrowing of the genetic diversity. This study aims to investigate patterns of phenotypic variability using twelve quantitative traits in a panel of 189 durum wheat landraces and seven checks, based on farmer’s population name attribution and genetic structure. Our results showed high phenotypic variability among and within landraces and checks for ten out of twelve studied traits. The principal components analysis showed similar grouping using farmers name attribution and genetic structure using K = 6. These results confirmed the identification of a new gene pool in the oases of Tunisia, represented by the sub-population Jenah Zarzoura and the robustness and high relationships between phenotypic and genome-wide genetic structure using DArTseq method. These findings will enhance the conservation efforts of these landraces and their use in breeding efforts at national and international levels to adapt to dry conditions.

Population genomics of Mediterranean oat (A. sativa) reveals high genetic diversity and three loci for heading date

Key messageGenomic analysis of Mediterranean oats reveals high genetic diversity and three loci for adaptation to this environment. This information together with phenotyping and passport data, gathered in an interactive map, will be a vital resource for oat genetic improvement.During the twentieth century, oat landraces have increasingly been replaced by modern cultivars, resulting in loss of genetic diversity. However, landraces have considerable potential to improve disease and abiotic stress tolerance and may outperform cultivars under low input systems. In this work, we assembled a panel of 669 oat landraces from Mediterranean rim and 40 cultivated oat varieties and performed the first large-scale population genetic analysis of both red and white oat types of Mediterranean origin. We created a public database associated with an interactive map to visualize information for each accession. The oat collection was genotyped with 17,288 single-nucleotide polymorphism (SNP) loci to evaluate population structure and linkage disequilibrium (LD); to perform a genome-wide association study (GWAs) for heading date, a key character closely correlated with performance in this drought-prone area. Population genetic analysis using both structure and PCA distinguished two main groups composed of the red and white oats, respectively. The white oat group was further divided into two subgroups. LD decay was slower within white lines in linkage groups Mrg01, 02, 04, 12, 13, 15, 23, 33, whereas it was slower within red lines in Mrg03, 05, 06, 11, 21, 24, and 28. Association analysis showed several significant markers associated with heading date on linkage group Mrg13 in white oats and on Mrg01 and Mrg08 in red oats.

Tracing the origins of hybrids through history: monstrous cultivars and Napoléon Bonaparte’s exiled paper daisies (Asteraceae; Gnaphalieae)

Abstract Golden everlasting paper daisies (Xerochrysum, Gnaphalieae, Asteraceae) were some of the earliest Australian native plants to be cultivated in Europe. Reputedly a favourite of Napoléon Bonaparte and Empress Joséphine, X. bracteatum is thought to have been introduced to the island of St Helena in the South Atlantic during Napoléon’s exile there. Colourful cultivars were developed in the 1850s, and there is a widely held view that these were produced by crossing Xerochrysum with African or Asian Helichrysum spp. Recent molecular phylogenetic analyses and subtribal classification of Gnaphalieae cast doubt on this idea. Using single-nucleotide polymorphism (SNP) data, we looked for evidence of gene flow between modern cultivars, naturalized paper daisies from St Helena and four Xerochrysum spp. recorded in Europe in the 1800s. There was strong support for gene flow between cultivars and X. macranthum. Paper daisies from St Helena were genotypically congruent with X. bracteatum and showed no indications of ancestry from other species or from the cultivars, consistent with the continuous occurrence of naturalized paper daisies introduced by Joséphine and Napoléon. We also present new evidence for the origin of colourful Xerochrysum cultivars and hybridization of congeners in Europe from Australian collections.

Labelling Selective Sweeps Used in Durum Wheat Breeding from a Diverse and Structured Panel of Landraces and Cultivars.

Simple SummaryEvaluation of the genetic diversity of a crop species is a critical step for breeding. Landraces are essential to avoid genetic erosion, and Mediterranean landraces are an important group of genetic resources due to their high genetic variability, adaptation to local conditions in rainfed environments, and their resilience to pests and pathogens. This study uses a genome-wide association approach employing eigenvectors to identify selective sweeps among Mediterranean durum wheat landraces and a world panel of modern cultivars.A panel of 387 durum wheat genotypes including Mediterranean landraces and modern cultivars was characterized with 46,161 diversity arrays technology (DArTseq) markers. Analysis of population structure uncovered the existence of five subpopulations (SP) related to the pattern of migration of durum wheat from the domestication area to the west of the Mediterranean basin (SPs 1, 2, and 3) and further improved germplasm (SPs 4 and 5). The total genetic diversity (HT) was 0.40 with a genetic differentiation (GST) of 0.08 and a mean gene flow among SPs of 6.02. The lowest gene flow was detected between SP 1 (presumably the ancient genetic pool of the panel) and SPs 4 and 5. However, gene flow from SP 2 to modern cultivars was much higher. The highest gene flow was detected between SP 3 (western Mediterranean germplasm) and SP 5 (North American and European cultivars). A genome wide association study (GWAS) approach using the top ten eigenvectors as phenotypic data revealed the presence of 89 selective sweeps, represented as quantitative trait loci (QTL) hotspots, widely distributed across the durum wheat genome. A principal component analysis (PCoA) using 147 markers with −log10 p > 5 identified three regions located on chromosomes 2A, 2B and 3A as the main drivers for differentiation of Mediterranean landraces. Gene flow between SPs offers clues regarding the putative use of Mediterranean old durum germplasm by the breeding programs represented in the structure analysis. EigenGWAS identified selective sweeps among landraces and modern cultivars. The analysis of the corresponding genomic regions in the ‘Zavitan’, ‘Svevo’ and ‘Chinese Spring’ genomes discovered the presence of important functional genes including Ppd, Vrn, Rht, and gene models involved in important biological processes including LRR-RLK, MADS-box, NAC, and F-box.