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1. Plant conservation assessment at scale: Rapid triage of extinction risks

   https://doi.org/10.1002/ppp3.10355  

   AuBuchon‐Elder, Taylor ; Minx, Patrick ; Bookout, Bess ; Kellogg, Elizabeth A. ( January 2023 , PLANTS, PEOPLE, PLANET)

   The current rate of global biodiversity loss creates a pressing need to increase efficiency and throughput of extinction risk assessments in plants. We must assess as many plant species as possible, working with imperfect knowledge, to address the habitat loss and extinction threats of the Anthropocene. Using the biodiversity database, Botanical Information and Ecology Network (BIEN), and the Andropogoneae grass tribe as a case study, we demonstrate that large‐scale, preliminary conservation assessments can play a fundamental role in accelerating plant conservation pipelines and setting priorities for more in‐depth investigations.

   The International Union for the Conservation of Nature (IUCN) Red List criteria are widely used to determine extinction risks of plant and animal life. Here, we used The Red List's criterion B, Geographic Range Size, to provide preliminary conservation assessments of the members of a large tribe of grasses, the Andropogoneae, with ~1100 species, including maize, sorghum, and sugarcane and their wild relatives.

   We used georeferenced occurrence data from the Botanical Information and Ecology Network (BIEN) and automated individual species assessments using ConR to demonstrate efficacy and accuracy in using time‐saving tools for conservation research. We validated our results with those from the IUCN‐recommended assessment tool, GeoCAT.

   We discovered amore »remarkably large gap in digitized information, with slightly more than 50% of the Andropogoneae lacking sufficient information for assessment. ConR and GeoCAT largely agree on which taxa are of least concern (>90%) or possibly threatened (<10%), highlighting that automating assessments with ConR is a viable strategy for preliminary conservation assessments of large plant groups. Results for crop wild relatives are similar to those for the entire dataset.

   Increasing digitization and collection needs to be a high priority. Available rapid assessment tools can then be used to identify species that warrant more comprehensive investigation.

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2. The regulatory landscape of a core maize domestication module controlling bud dormancy and growth repression

   https://doi.org/10.1038/s41467-019-11774-w  

   Dong, Zhaobin ; Xiao, Yuguo ; Govindarajulu, Rajanikanth ; Feil, Regina ; Siddoway, Muriel L. ; Nielsen, Torrey ; Lunn, John E. ; Hawkins, Jennifer ; Whipple, Clinton ; Chuck, George ( August 2019 , Nature Communications)

   Many domesticated crop plants have been bred for increased apical dominance, displaying greatly reduced axillary branching compared to their wild ancestors. In maize, this was achieved through selection for a gain-of-function allele of the TCP transcription factorteosinte branched1(tb1). The mechanism for how a dominantTb1allele increased apical dominance, is unknown. Through ChIP seq, RNA seq, hormone and sugar measurements on 1 mm axillary bud tissue, we identify the genetic pathways putatively regulated by TB1. These include pathways regulating phytohormones such as gibberellins, abscisic acid and jasmonic acid, but surprisingly, not auxin. In addition, metabolites involved in sugar sensing such as trehalose 6-phosphate were increased. This suggests that TB1 induces bud suppression through the production of inhibitory phytohormones and by reducing sugar levels and energy balance. Interestingly, TB1 also putatively targets several other domestication loci, includingteosinte glume architecture1,prol1.1/grassy tillers1, as well as itself. This placestb1on top of the domestication hierarchy, demonstrating its critical importance during the domestication of maize from teosinte.
3. Domesticated tomatoes are more vulnerable to negative plant–soil feedbacks than their wild relatives

   https://doi.org/10.1111/1365-2745.13157  

   Carrillo, Juli ; Ingwell, Laura L. ; Li, Xiaohong ; Kaplan, Ian ; Pineda, ed., Ana ( March 2019 , Journal of Ecology)

   Domesticated plants can differ from their wild counterparts in the strength and outcome of species interactions, both above‐ and belowground. Plant–soil feedbacks influence plant success, and plant‐associated soil microbial communities can influence plant interactions with herbivores and their natural enemies, yet, it remains unclear if domestication has changed these relationships.

   To determine the effects of domestication on plant–soil interactions, we characterized soil microbial communities associated with various cultivars of domesticated tomato and some of its wild relatives. We measured the strength and direction of plant–soil feedbacks for domesticated and wild tomatoes, and the effects of soil on plant resistance to specialist herbivory byManduca sexta, and the attraction of a parasitoid wasp,Cotesia congregata.

   Domesticated tomatoes and their wild relatives had negative plant–soil feedbacks, as conspecifics cultivated soil that negatively impacted performance of subsequent plants (longer germination time, lower biomass) than if they grew in non‐tomato soils. Significant variation existed among domesticated and wild tomato varieties in the strength of these feedbacks, ranging from neutral to strongly negative. For above‐ground plant biomass, tomato wild relatives were unaffected by growing in tomato‐conditioned soil, whereas domesticated tomatoes grew smaller in tomato soil, indicating effects of plant domestication. Overall, increased microbial biomass within the rhizosphere resultedmore »in progressively less‐negative plant–soil feedbacks.

   Plant cultivars had different levels of resistance to herbivory byM. sexta, but this did not depend on plant domestication or soil type. The parasitoidC. congregatawas primarily attracted to herbivore damaged plants, independent of plant domestication status, and for these damaged plants, wasps preferred some cultivars over others, and wild plants grown in tomato soil over wild plants grown in non‐tomato soil.

   Synthesis.These results indicate that crop tomatoes are more likely to show negative plant–soil feedbacks than wild progenitors, which could partially explain their sensitivity to monocultures in agricultural soils. Furthermore, cultivar‐specific variation in the ability to generate soil microbial biomass, independent of domestication status, appears to buffer the negative consequences of sharing the same soil. Last, soil legacies were relatively absent for herbivores, but not for parasitoid wasps, suggesting trophic level specificity in soil feedbacks on plant–insect interactions.

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4. Genomes of cultivated and wild Capsicum species provide insights into pepper domestication and population differentiation

   https://doi.org/10.1038/s41467-023-41251-4  

   Liu, Feng ; Zhao, Jiantao ; Sun, Honghe ; Xiong, Cheng ; Sun, Xuepeng ; Wang, Xin ; Wang, Zhongyi ; Jarret, Robert ; Wang, Jin ; Tang, Bingqian ; et al ( September 2023 , Nature Communications)

   Pepper (Capsicumspp.) is one of the earliest cultivated crops and includes five domesticated species,C. annuumvar.annuum,C. chinense,C. frutescens,C. baccatumvar.pendulumandC. pubescens. Here, we report a pepper graph pan-genome and a genome variation map of 500 accessions from the five domesticatedCapsicumspecies and close wild relatives. We identify highly differentiated genomic regions among the domesticated peppers that underlie their natural variations in flowering time, characteristic flavors, and unique resistances to biotic and abiotic stresses. Domestication sweeps detected inC. annuumvar.annuumandC. baccatumvar.pendulumare mostly different, and the common domestication traits, including fruit size, shape and pungency, are achieved mainly through the selection of distinct genomic regions between these two cultivated species. Introgressions fromC. baccatumintoC. chinenseandC. frutescensare detected, including those providing genetic sources for various biotic and abiotic stress tolerances.
5. Salt tolerance mechanisms in the Lycopersicon clade and their trade-offs

   https://doi.org/10.1093/aobpla/plab072  

   Bonarota, Maria-Sole ; Kosma, Dylan K. ; Barrios-Masias, Felipe H. ; Wang, ed., Yizhou ( December 2021 , AoB PLANTS)

   Salt stress impairs growth and yield in tomato, which is mostly cultivated in arid and semi-arid areas of the world. A number of wild tomato relatives (Solanum pimpinellifolium, S. pennellii, S. cheesmaniae and S. peruvianum) are endemic to arid coastal areas and able to withstand higher concentration of soil salt concentrations, making them a good genetic resource for breeding efforts aimed at improving salt tolerance and overall crop improvement. However, the complexity of salt stress response makes it difficult to introgress tolerance traits from wild relatives that could effectively increase tomato productivity under high soil salt concentrations. Under commercial production, biomass accumulation is key for high fruit yields, and salt tolerance management strategies should aim to maintain a favourable plant water and nutrient status. In this review, we first compare the effects of salt stress on the physiology of the domesticated tomato and its wild relatives. We then discuss physiological and energetic trade-offs for the different salt tolerance mechanisms found within the Lycopersicon clade, with a focus on the importance of root traits to sustain crop productivity.