Prospects for Improving Alfalfa Yield Using Genomic- and Phenomic-Based Breeding

Alfalfa (Medicago sativa L.) is a perennial outcrossing legume that is cultivated as an important forage crop in many parts of the world. Yield is the most important trait for profitable alfalfa production, yet over the last 30 years yield improvement in California has stagnated. Current breeding methods focus on recurrent phenotypic selection; however, alternatives incorporating genomic- and phenomic-based information may enhance genetic gain and help to address the lack of yield improvement. Here we attempt to increase the yield potential of alfalfa using genomic selection (GS) in combination with high throughput phenotyping (HTP). A total of 193 families from two closely related elite populations were sown in the greenhouse and transplanted into mini sward plots at two locations near Davis, CA in May 2020. The trial was managed as a high-input system under full irrigation. Families were genotyped and phenotyped for biomass yield by mechanical harvest and a combination of drone and tower-based remote sensors across 12 harvests, 3 in the establishment year (2020), 7 in the first full year of production (2021) and 2 in 2022. Alfalfa yields ranged from 13-27 tonnes DM/hectare/year with a number of half-sib families outperforming popular cultivars in the first 2 years of production. Biomass volume predicted from the drone-based cameras had a moderate prediction accuracy with an overall R2 of 0.55. Some individual harvests reached accuracies as high as 0.85. Genotyping resulted in a dataset with 6,838 SNPs. Allele frequencies were used to generate a relationship matrix for GS. Narrow-sense heritability for dry matter yield was 0.31 and the predictive ability of the GS model was 0.15

Characterization of defect structures in nanocrystalline materials by X-ray line profile analysis

X-ray line profile analysis is a powerful alternative tool for determining dislocation densities, dislocation type, crystallite and subgrain size and size-distributions, and planar defects, especially the frequency of twin boundaries and stacking faults. The method is especially useful in the case of submicron grain size or nanocrystalline materials, where X-ray line broadening is a well pronounced effect, and the observation of defects with very large density is often not easy by transmission electron microscopy. The fundamentals of X-ray line broadening are summarized in terms of the different qualitative breadth methods, and the more sophisticated and more quantitative whole pattern fitting procedures. The efficiency and practical use of X-ray line profile analysis is shown by discussing its applications to metallic, ceramic, diamond-like and polymer nanomaterials

Nanocrystalline materials studied by powder diffraction line profile analysis

X-ray powder diffraction is a powerful tool for characterising the microstructure of crystalline materials in terms of size and strain. It is widely applied for nanocrystalline materials, especially since other methods, in particular electron microscopy is, on the one hand tedious and time consuming, on the other hand, due to the often metastable states of nanomaterials it might change their microstructures. It is attempted to overview the applications of microstructure characterization by powder diffraction on nanocrystalline metals, alloys, ceramics and carbon base materials. Whenever opportunity is given, the data provided by the X-ray method are compared and discussed together with results of electron microscopy. Since the topic is vast we do not try to cover the entire field

Cohesin mutations alter DNA damage repair and chromatin structure and create therapeutic vulnerabilities in MDS/AML

The cohesin complex plays an essential role in chromosome maintenance and transcriptional regulation. Recurrent somatic mutations in the cohesin complex are frequent genetic drivers in cancer including myelodysplatic syndromes (MDS) and acute myeloid leukemia (AML). Here, using genetic dependency screens of STAG2-mutant AML, we identified DNA damage repair and replication as genetic dependencies in cohesin-mutant cells. We demonstrated increased levels of DNA damage and sensitivity of cohesin-mutant cells to PARP inhibition. We developed a mouse model of MDS in which Stag2 mutations arise as clonal secondary lesions in the background of clonal hematopoiesis driven by Tet2 mutations, and demonstrated selective depletion of cohesin-mutant cells with PARP inhibition in vivo. Finally, we demonstrated a shift from STAG2- to STAG1-containing cohesin complexes in cohesin-mutant cells, which is associated with longer DNA loop extrusion, more intermixing of chromatin compartments, and increased interaction with PARP and RPA proteins. Our findings inform the biology and therapeutic opportunities for cohesin-mutant malignancies

STAG2 loss rewires oncogenic and developmental programs to promote metastasis in Ewing sarcoma

The core cohesin subunit STAG2 is recurrently mutated in Ewing sarcoma but its biological role is less clear. Here, we demonstrate that cohesin complexes containing STAG2 occupy enhancer and polycomb repressive complex (PRC2)-marked regulatory regions. Genetic suppression of STAG2 leads to a compensatory increase in cohesin-STAG1 complexes, but not in enhancer-rich regions, and results in reprogramming of cis-chromatin interactions. Strikingly, in STAG2 knockout cells the oncogenic genetic program driven by the fusion transcription factor EWS/FLI1 was highly perturbed, in part due to altered enhancer-promoter contacts. Moreover, loss of STAG2 also disrupted PRC2-mediated regulation of gene expression. Combined, these transcriptional changes converged to modulate EWS/FLI1, migratory, and neurodevelopmental programs. Finally, consistent with clinical observations, functional studies revealed that loss of STAG2 enhances the metastatic potential of Ewing sarcoma xenografts. Our findings demonstrate that STAG2 mutations can alter chromatin architecture and transcriptional programs to promote an aggressive cancer phenotype

Association and Linkage Analysis of Aluminum Tolerance Genes in Maize

Aluminum (Al) toxicity is a major worldwide constraint to crop productivity on acidic soils. Al becomes soluble at low pH, inhibiting root growth and severely reducing yields. Maize is an important staple food and commodity crop in acidic soil regions, especially in South America and Africa where these soils are very common. Al exclusion and intracellular tolerance have been suggested as two important mechanisms for Al tolerance in maize, but little is known about the underlying genetics. linkage populations with approximately 200 individuals each were used to study genetic variation in this complex trait. Al tolerance was measured as net root growth in nutrient solution under Al stress, which exhibited a wide range of variation between lines. Comparative and physiological genomics-based approaches were used to select 21 candidate genes for evaluation by association analysis.). These four candidate genes are high priority subjects for follow-up biochemical and physiological studies on the mechanisms of Al tolerance in maize. Immediately, elite haplotype-specific molecular markers can be developed for these four genes and used for efficient marker-assisted selection of superior alleles in Al tolerance maize breeding programs

Glial Hsp70 Protects K+ Homeostasis in the Drosophila Brain during Repetitive Anoxic Depolarization

Neural tissue is particularly vulnerable to metabolic stress and loss of ion homeostasis. Repetitive stress generally leads to more permanent dysfunction but the mechanisms underlying this progression are poorly understood. We investigated the effects of energetic compromise in Drosophila by targeting the Na+/K+-ATPase. Acute ouabain treatment of intact flies resulted in subsequent repetitive comas that led to death and were associated with transient loss of K+ homeostasis in the brain. Heat shock pre-conditioned flies were resistant to ouabain treatment. To control the timing of repeated loss of ion homeostasis we subjected flies to repetitive anoxia while recording extracellular [K+] in the brain. We show that targeted expression of the chaperone protein Hsp70 in glial cells delays a permanent loss of ion homeostasis associated with repetitive anoxic stress and suggest that this is a useful model for investigating molecular mechanisms of neuroprotection