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Cotton breeding programs have focused on agronomically-desirable traits. Without targeted selection for tolerance to high temperature extremes, cotton will likely be more vulnerable to environment-induced yield loss. Recently-developed methods that couple chlorophyll fluorescence induction measurements with temperature response experiments could be used to identify genotypic variation in photosynthetic thermotolerance of specific photosynthetic processes for field-grown plants. It was hypothesized that diverse cotton genotypes would differ significantly in photosynthetic thermotolerance, specific thylakoid processes would exhibit differential sensitivities to high temperature, and that the most heat tolerant process would exhibit substantial genotypic variation in thermotolerance plasticity. A two-year field experiment was conducted at Tifton and Athens, Georgia, USA. Experiments included 10 genotypes in 2020 and 11 in 2021. Photosynthetic thermotolerance for field-collected leaf samples was assessed by determining the high temperature threshold resulting in a 15% decline in photosynthetic efficiency (T15) for energy trapping by photosystem II (ΦPo), intersystem electron transport (ΦEo), and photosystem I end electron acceptor reduction (ΦRo). Significant genotypic variation in photosynthetic thermotolerance was observed, but the response was dependent on location and photosynthetic parameter assessed. ΦEo was substantially more heat sensitive than ΦPo or ΦRo. Significant genotypic variation in thermotolerance plasticity of ΦEo was also observed. Identifying the weakest link in photosynthetic tolerance to high temperature will facilitate future selection efforts by focusing on the most heat-susceptible processes. Given the genotypic differences in environmental plasticity observed here, future research should evaluate genotypic variation in acclimation potential in controlled environments. 

Abstract Tailoring ultraconserved element (UCE) probe set design to focal taxa has been demonstrated to improve locus recovery and phylogenomic inference. However, beyond conducting expensive in vitro testing, it remains unclear how best to determine whether an existing UCE probe set is likely to suffice for phylogenomic inference or whether tailored probe design will be desirable. Here we investigate the utility of 8 different UCE probe sets for the in silico phylogenomic inference of scarabaeoid beetles. Probe sets tested differed in terms of (i) how phylogenetically distant from Scarabaeoidea taxa those used during probe design are, (ii) breadth of phylogenetic inference probe set was designed for, and (iii) method of probe design. As part of this study, 2 new UCE probe sets are produced for the beetle family Scarabaeidae and superfamily Hydrophiloidea. We confirm that probe set utility decreases with increasing phylogenetic distance from target taxa. In addition, narrowing the phylogenetic breadth of probe design decreases the phylogenetic capture range. We also confirm previous findings regarding ways to optimize UCE probe design. Finally, we make suggestions regarding assessment of need for de novo probe design.