Latent Dirichlet Allocation Uncovers Spectral Characteristics of Drought Stressed Plants

Understanding the adaptation process of plants to drought stress is essential in improving management practices, breeding strategies as well as engineering viable crops for a sustainable agriculture in the coming decades. Hyper-spectral imaging provides a particularly promising approach to gain such understanding since it allows to discover non-destructively spectral characteristics of plants governed primarily by scattering and absorption characteristics of the leaf internal structure and biochemical constituents. Several drought stress indices have been derived using hyper-spectral imaging. However, they are typically based on few hyper-spectral images only, rely on interpretations of experts, and consider few wavelengths only. In this study, we present the first data-driven approach to discovering spectral drought stress indices, treating it as an unsupervised labeling problem at massive scale. To make use of short range dependencies of spectral wavelengths, we develop an online variational Bayes algorithm for latent Dirichlet allocation with convolved Dirichlet regularizer. This approach scales to massive datasets and, hence, provides a more objective complement to plant physiological practices. The spectral topics found conform to plant physiological knowledge and can be computed in a fraction of the time compared to existing LDA approaches.Comment: Appears in Proceedings of the Twenty-Eighth Conference on Uncertainty in Artificial Intelligence (UAI2012

Potato late blight field resistance from QTL dPI09c is conferred by the NB-LRR gene R8

Following the often short-lived protection that major nucleotide binding, leucine-rich-repeat (NB-LRR) resistance genes offer against the potato pathogen Phytophthora infestans, field resistance was thought to provide a more durable alternative to prevent late blight disease. We previously identified the QTL dPI09c on potato chromosome 9 as a more durable field resistance source against late blight. Here, the resistance QTL was fine-mapped to a 186 kb region. The interval corresponds to a larger, 389 kb, genomic region in the potato reference genome of Solanum tuberosum Group Phureja doubled monoploid clone DM1-3 (DM) and from which functional NB-LRRs R8, R9a, Rpi-moc1, and Rpi-vnt1 have arisen independently in wild species. dRenSeq analysis of parental clones alongside resistant and susceptible bulks of the segregating population B3C1HP showed full sequence representation of R8. This was independently validated using long-range PCR and screening of a bespoke bacterial artificial chromosome library. The latter enabled a comparative analysis of the sequence variation in this locus in diverse Solanaceae. We reveal for the first time that broad spectrum and durable field resistance against P. infestans is conferred by the NB-LRR gene R8, which is thought to provide narrow spectrum race-specific resistance

Identification and rapid mapping of a gene conferring broad-spectrum late blight resistance in the diploid potato species <i>Solanum verrucosum</i> through DNA capture technologies

Key message: A broad-spectrum late blight disease-resistance gene from Solanum verrucosum has been mapped to potato chromosome 9. The gene is distinct from previously identified-resistance genes. Abstract: We have identified and characterised a broad-spectrum resistance to Phytophthora infestans from the wild Mexican species Solanum verrucosum. Diagnostic resistance gene enrichment (dRenSeq) revealed that the resistance is not conferred by previously identified nucleotide-binding, leucine-rich repeat genes. Utilising the sequenced potato genome as a reference, two complementary enrichment strategies that target resistance genes (RenSeq) and single/low-copy number genes (Generic-mapping enrichment Sequencing; GenSeq), respectively, were deployed for the rapid, SNP-based mapping of the resistance through bulked-segregant analysis. Both approaches independently positioned the resistance, referred to as Rpi-ver1, to the distal end of potato chromosome 9. Stringent post-enrichment read filtering identified a total of 64 informative SNPs that corresponded to the expected ratio for significant polymorphisms in the parents as well as the bulks. Of these, 61 SNPs are located on potato chromosome 9 and reside within 27 individual genes, which in the sequenced potato clone DM locate to positions 45.9 to 60.9 Mb. RenSeq- and GenSeq-derived SNPs within the target region were converted into allele-specific PCR-based KASP markers and further defined the position of the resistance to a 4.3 Mb interval at the bottom end of chromosome 9 between positions 52.62–56.98 Mb.</p

Experimental evolution in barley – 2 decades of natural adaptation to farming systems

Sustainable food production for a growing world population will pose a central challenge in the coming decades. Organic farming is among the most feasible approaches to achieving this goal if the yield gap to conventional farming can be decreased. However, uncertainties exist whether organic and conventional agro-ecosystems require different breeding strategies. A heterogeneous spring barley population was established between a wild barley and an elite cultivar to examine this question. The population was divided into two sets and sown into an organic and a conventional agro-ecosystem, without any artificial selection for two decades. A fraction of seeds harvested each year was sown in the following year. The parents and five generations from both environments up to the 23rd generation were whole-genome pool-sequenced to identify adaptation patterns towards ecosystem and climate conditions in the allele frequency shifts. Additionally, based on previously published QTLs in barley, a meta-data analysis was conducted to link genomic regions' increased fitness to agronomically related traits

Integrierte Pflanzenschutz und erhöhte Biodiversität durch organisch heterogenes Material? Eine Langzeitstudie in drei Kulturen

Seit Anfang 2022 können heterogene Populationen, die unter ökologischer / biologischer Bewirtschaftung erzeugt wurden, beim Bundessortenamt notifiziert. Nach erfolgter Notifizierung ist das Material dieser Populationen unter dem Begriff Ökologisch Heterogenes Material (ÖHM) als Saatgut verkehrsfähig – kann also verkauft und von anderen angebaut werden. Ersten Studien zufolge weisen sie eine erhöhte Ertragsstabilität und ein ausgeprägteres Wurzelsystem auf. Darüber hinaus gibt es aber noch viele Unbekannte Aspekte dieser Anbauform. Darunter fallen beispielsweise die Fragestellungen − Sind ÖHM auch im konventionellen Anbau sinnvoll? − Hat die Befruchtungsform einen Einfluss auf die Anpassung und Resilienz? − Wie ändert sich die populationsinterne Diversität im Verlauf der Generationen? − Thema biotische Resistenzen – werden die Populationen mit den Generationen gesünder? Speziell im ökologischen Anbau

Multiple QTLs linked to agro-morphological and physiological traits related to drought tolerance in potato.

Dissection of the genetic architecture of adaptation and abiotic stress-related traits is highly desirable for developing drought-tolerant potatoes and enhancing the resilience of existing cultivars, particularly as agricultural production in rain-fed areas may be reduced by up to 50 % by 2020. The “DMDD” potato progeny was developed at International Potato Center (CIP) by crossing the sequenced double monoploid line DM and a diploid cultivar of the Solanum tuberosum diploid Andigenum Goniocalyx group. Recently, a high-density integrated genetic map based on single nucleotide polymorphism (SNP), diversity array technology (DArT), simple sequence repeats (SSRs), and amplified fragment length polymorphism (AFLP) markers was also made available for this population. Two trials were conducted, in greenhouse and field, for drought tolerance with two treatments each, well-watered and terminal drought, in which watering was suspended 60 days after planting. The DMDD population was evaluated for agro-morphological and physiological traits before and after initiation of stress, at multiple time points. Two dense parental genetic maps were constructed using published genotypic data, and quantitative trait locus (QTL) analysis identified 45 genomic regions associated with nine traits in well-watered and terminal drought treatments and 26 potentially associated with drought stress. In this study, the strong influence of environmental factors besides water shortage on the expression of traits and QTLs reflects the multigenic control of traits related to drought tolerance. This is the first study to our knowledge in potato identifying QTLs for drought-related traits in field and greenhouse trials, giving new insights into genetic architecture of drought-related traits. Many of the QTLs identified have the potential to be used in potato breeding programs for enhanced drought tolerance

Lr21 diversity unveils footprints of wheat evolution and its new role in broad-spectrum leaf rust resistance

Aegilops tauschii, the progenitor of the wheat D genome, contains extensive diversity for biotic and abiotic resistance. Lr21 is a leaf rust resistance gene which did not enter the initial gene flow from Ae. tauschii into hexaploid wheat due to restrictive hybridization events. Here, we employed population genetics and high-resolution comparative genomics to study evolutionary and functional divergence of Lr21 in diploid and hexaploid wheats. Population genetics identified the original Lr21, lr21-1 and lr21-2 alleles and their evolutionary history among Ae. tauschii accessions. Comparative genetics of Lr21 variants between Ae. tauschii and cultivated genotypes suggested at least two independent polyploidization events in bread wheat evolution. Further, a recent re-birth of a unique Lr21-tbk allele and its neofunctionalization was discovered in the hexaploid wheat cv. Tobak. Altogether, four independent alleles were investigated and validated for leaf rust resistance in diploid, synthetic hexaploid and cultivated wheat backgrounds. Besides seedling resistance, we uncover a new role of the Lr21 gene in conferring an adult plant field resistance. Seedling and adult plant resistances turned out to be correlated with developmentally dependent variation in Lr21 expression. Our results contribute to understand Lr21 evolution and its role in establishing a broad-spectrum leaf rust resistance in wheat