High-throughput characterization, correlation, and mapping of leaf photosynthetic and functional traits in the soybean (Glycine max) nested association mapping population

Photosynthesis is a key target to improve crop production in many species including soybean [Glycine max (L.) Merr.]. A challenge is that phenotyping photosynthetic traits by traditional approaches is slow and destructive. There is proof-of-concept for leaf hyperspectral reflectance as a rapid method to model photosynthetic traits. However, the crucial step of demonstrating that hyperspectral approaches can be used to advance understanding of the genetic architecture of photosynthetic traits is untested. To address this challenge, we used full-range (500-2,400 nm) leaf reflectance spectroscopy to build partial least squares regression models to estimate leaf traits, including the rate-limiting processes of photosynthesis, maximum Rubisco carboxylation rate, and maximum electron transport. In total, 11 models were produced from a diverse population of soybean sampled over multiple field seasons to estimate photosynthetic parameters, chlorophyll content, leaf carbon and leaf nitrogen percentage, and specific leaf area (with R2 from 0.56 to 0.96 and root mean square error approximately \u3c10% of the range of calibration data). We explore the utility of these models by applying them to the soybean nested association mapping population, which showed variability in photosynthetic and leaf traits. Genetic mapping provided insights into the underlying genetic architecture of photosynthetic traits and potential improvement in soybean. Notably, the maximum Rubisco carboxylation rate mapped to a region of chromosome 19 containing genes encoding multiple small subunits of Rubisco. We also mapped the maximum electron transport rate to a region of chromosome 10 containing a fructose 1,6-bisphosphatase gene, encoding an important enzyme in the regeneration of ribulose 1,5-bisphosphate and the sucrose biosynthetic pathway. The estimated rate-limiting steps of photosynthesis were low or negatively correlated with yield suggesting that these traits are not influenced by the same genetic mechanisms and are not limiting yield in the soybean NAM population. Leaf carbon percentage, leaf nitrogen percentage, and specific leaf area showed strong correlations with yield and may be of interest in breeding programs as a proxy for yield. This work is among the first to use hyperspectral reflectance to model and map the genetic architecture of the rate-limiting steps of photosynthesis

Boosting predictive ability of tropical maize hybrids via genotype-by-environment interaction under multivariate GBLUP models.

Genomic selection has been implemented in several plant and animal breeding programs and it has proven to improve efficiency and maximize genetic gains. Phenotypic data of grain yield was measured in 147 maize (Zea mays L.) singlecross hybrids at 12 environments. Single-cross hybrids genotypes were inferred based on their parents (inbred lines) via single nucleotide polymorphism (SNP) markers obtained from genotyping-by-sequencing (GBS). Factor analytic multiplicative genomic best linear unbiased prediction (GBLUP) models, in the framework of multienvironment trials, were used to predict grain yield performance of unobserved tropical maize single-cross hybrids. Predictions were performed for two situations: untested hybrids (CV1), and hybrids evaluated in some environments but missing in others (CV2). Models that borrowed information across individuals through genomic relationships and within individuals across environments presented higher predictive accuracy than those models that ignored it. For these models, predictive accuracies were up to 0.4 until eight environments were considered as missing for the validation set, which represents 67% of missing data for a given hybrid. These results highlight the importance of including genotype-by-environment interactions and genomic relationship information for boosting predictions of tropical maize single-cross hybrids for grain yield

Biogeographic problem-solving reveals the Late Pleistocene translocation of a short-faced bear to the California Channel Islands

An accurate understanding of biodiversity of the past is critical for contextualizing biodiversity patterns and trends in the present. Emerging techniques are refining our ability to decipher otherwise cryptic human-mediated species translocations across the Quaternary, yet these techniques are often used in isolation, rather than part of an interdisciplinary hypothesis-testing toolkit, limiting their scope and application. Here we illustrate the use of such an integrative approach and report the occurrence of North America’s largest terrestrial mammalian carnivore, the short-faced bear, Arctodus simus, from Daisy Cave (CA-SMI-261), an important early human occupation site on the California Channel Islands. We identified the specimen by corroborating morphological, protein, and mitogenomic lines of evidence, and evaluated the potential natural and anthropogenic mechanisms of its transport and deposition. While representing just a single specimen, our combination of techniques opened a window into the behavior of an enigmatic species, suggesting that A. simus was a wide-ranging scavenger utilizing terrestrial and marine carcasses. This discovery highlights the utility of bridging archaeological and paleontological datasets to disentangle complex biogeographic scenarios and reveal unexpected biodiversity for island systems worldwide.Open Access fees paid for in whole or in part by the University of Oklahoma Libraries Radiocarbon and isotope laboratory work was supported in part by the NSF Archaeometry Program BCS-1460369 (to D.J.K. and B.J.C). M.B was supported by a Royal Society fellowship. Additional funding was provided by the University of Oklahoma, the University of Oregon, and the Smithsonian Institution.Ye

Report from Working Group 2: Higgs Physics at the HL-LHC and HE-LHC

The discovery of the Higgs boson in 2012, by the ATLAS and CMS experiments, was a success achieved with only a percent of the entire dataset foreseen for the LHC. It opened a landscape of possibilities in the study of Higgs boson properties, Electroweak Symmetry breaking and the Standard Model in general, as well as new avenues in probing new physics beyond the Standard Model. Six years after the discovery, with a conspicuously larger dataset collected during LHC Run 2 at a 13 TeV centre-of-mass energy, the theory and experimental particle physics communities have started a meticulous exploration of the potential for precision measurements of its properties. This includes studies of Higgs boson production and decays processes, the search for rare decays and production modes, high energy observables, and searches for an extended electroweak symmetry breaking sector. This report summarises the potential reach and opportunities in Higgs physics during the High Luminosity phase of the LHC, with an expected dataset of pp collisions at 14 TeV, corresponding to an integrated luminosity of 3~ab$^{-1}$. These studies are performed in light of the most recent analyses from LHC collaborations and the latest theoretical developments. The potential of an LHC upgrade, colliding protons at a centre-of-mass energy of 27 TeV and producing a dataset corresponding to an integrated luminosity of 15~ab$^{-1}$, is also discussed

Higgs Physics at the HL-LHC and HE-LHC

The discovery of the Higgs boson in 2012, by the ATLAS and CMS experiments, was a success achieved with only a percent of the entire dataset foreseen for the LHC. It opened a landscape of possibilities in the study of Higgs boson properties, Electroweak Symmetry breaking and the Standard Model in general, as well as new avenues in probing new physics beyond the Standard Model. Six years after the discovery, with a conspicuously larger dataset collected during LHC Run 2 at a 13 TeV centre-of-mass energy, the theory and experimental particle physics communities have started a meticulous exploration of the potential for precision measurements of its properties. This includes studies of Higgs boson production and decays processes, the search for rare decays and production modes, high energy observables, and searches for an extended electroweak symmetry breaking sector. This report summarises the potential reach and opportunities in Higgs physics during the High Luminosity phase of the LHC, with an expected dataset of pp collisions at 14 TeV, corresponding to an integrated luminosity of 3 ab$^{-1}$. These studies are performed in light of the most recent analyses from LHC collaborations and the latest theoretical developments. The potential of an LHC upgrade, colliding protons at a centre-of-mass energy of 27 TeV and producing a dataset corresponding to an integrated luminosity of 15 ab$^{-1}$, is also discussed