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1. Estimating global genetic diversity loss

   https://doi.org/10.1126/science.add0007  

   Ruegg, Kristen; Turbek, Sheela (September 2022, Science)

   Preservation of genetic diversity is critical to the resilience of species in the face of global change. To meet international calls to preserve at least 90% of species’ genetic diversity, researchers and conservationists need a way to reliably predict genetic diversity loss resulting from human activities ( 1 ). On page 1431 of this issue, Exposito-Alonso et al. present a mathematical framework that elegantly bridges biodiversity and population genetics theory to model the relationship between genetic diversity and habitat loss ( 2 ). This approach builds on methods already used by biodiversity policy experts for predicting species extinctions based on habitat loss ( 3 ) and should be useful to those tasked with setting goals for preserving genetic diversity. 

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2. Patterns of genetic variation in a prairie wildflower, Silphium integrifolium , suggest a non‐prairie origin and locally adaptive variation

   https://doi.org/10.1002/ajb2.1603  

   Raduski, Andrew R.; Herman, Adam; Pogoda, Cloe; Dorn, Kevin M.; Van Tassel, David L.; Kane, Nolan; Brandvain, Yaniv (January 2021, American Journal of Botany)

   PREMISEUnderstanding the relationship between genetic structure and geography provides information about a species’ history and can be used for breeding and conservation goals. The North American prairie is interesting because of its recent origin and subsequent fragmentation.Silphium integrifolium, an iconic perennial American prairie wildflower, is targeted for domestication, having undergone a few generations of improvement. We present the first application of population genetic data in this species to address the following goals: (1) improve breeding by characterizing genetic structure and (2) identify the species geographic origin and potential targets and drivers of selection during range expansion. METHODSWe developed a reference transcriptome as a genotyping reference for samples from throughout the species range. Population genetic analyses were used to describe patterns of genetic variation, and demographic modeling was used to characterize potential processes that shaped variation. Outlier scans for selection and associations with environmental variables were used to identify loci linked to putative targets and drivers of selection. RESULTSGenetic variation partitioned samples into three geographic clusters. Patterns of variation and demographic modeling suggest that the species origin is in the American Southeast. Breeding program accessions are from the region with lowest observed genetic variation. CONCLUSIONSThis prairie species did not originate within the prairie. Breeding may be improved by including accessions from outside of the germplasm founding region. The geographic structuring and the identified targets and drivers of adaptation can guide collecting efforts toward populations with beneficial agronomic traits. 

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3. Genetic diversity and structure of the critically endangered Artocarpus annulatus, a crop wild relative of jackfruit ( A. heterophyllus )

   https://doi.org/10.7717/peerj.9897  

   Dickinson, Leta; Noble, Hilary; Gardner, Elliot; Puad, Aida Shafreena; Zakaria, Wan Nuur; Zerega, Nyree J.C. (January 2020, PeerJ)

   Limestone karsts of Southeast Asia can harbor high levels of endemism, but are highly fragmented, increasingly threatened, and their biodiversity is often poorly studied. This is true of the Padawan Limestone Area of Sarawak, Malaysia, home to the endemic Artocarpus annulatus, the closest known wild relative of two important and underutilized fruit tree crops, jackfruit ( A. heterophyllus ) and cempedak ( A. integer ). Identifying and conserving crop wild relatives is critical for the conservation of crop genetic diversity and breeding. In 2016 and 2017, five A. annulatus populations were located, and leaf material, locality information, and demographic data were collected. Microsatellite markers were used to assess genetic diversity and structure among populations, and to compare levels of genetic diversity to closely related congeneric species. Results indicate no evidence of inbreeding in A. annulatus , and there is no genetic structure among the five populations. However, diversity measures trended lower in seedlings compared to mature trees, suggesting allelic diversity may be under threat in the youngest generation of plants. Also, genetic diversity is lower in A. annulatus compared to closely related congeners. The present study provides a baseline estimate of A. annulatus genetic diversity that can be used for comparison in future studies and to other species in the unique limestone karst ecosystems. Considerations for in situ and ex situ conservation approaches are discussed. 

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4. Genomic population structure and local adaptation of the wild strawberry Fragaria nilgerrensis

   https://doi.org/10.1093/hr/uhab059  

   Hu, Yuxi; Feng, Chao; Yang, Lihua; Edger, Patrick P; Kang, Ming (January 2022, Horticulture Research)

   Abstract The crop wild relative Fragaria nilgerrensis is adapted to a variety of diverse habitats across its native range in China. Thus, discoveries made in this species could serve as a useful guide in the development of new superior strawberry cultivars that are resilient to new or variable environments. However, the genetic diversity and genetic architecture of traits in this species underlying important adaptive traits remain poorly understood. Here, we used whole-genome resequencing data from 193 F. nilgerrensis individuals spanning the distribution range in China to investigate the genetic diversity, population structure and genomic basis of local adaptation. We identified four genetic groups, with the western group located in Hengduan Mountains exhibiting the highest genetic diversity. Redundancy analysis suggested that both environment and geographic variables shaped a significant proportion of the genomic variation. Our analyses revealed that the environmental difference explains more of the observed genetic variation than geographic distance. This suggests that adaptation to distinct habitats, which present a unique combination of abiotic factors, likely drove genetic differentiation. Lastly, by implementing selective sweep scans and genome–environment association analysis throughout the genome, we identified the genetic variation associated with local adaptation and investigated the functions of putative candidate genes in F. nilgerrensis. 

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5. Engineered systems of inducible anti-repressors for the next generation of biological programming

   https://doi.org/10.1038/s41467-020-18302-1  

   Groseclose, Thomas M.; Rondon, Ronald E.; Herde, Zachary D.; Aldrete, Carlos A.; Wilson, Corey J. (September 2020, Nature Communications)

   Abstract Traditionally engineered genetic circuits have almost exclusively used naturally occurring transcriptional repressors. Recently, non-natural transcription factors (repressors) have been engineered and employed in synthetic biology with great success. However, transcriptional anti-repressors have largely been absent with regard to the regulation of genes in engineered genetic circuits. Here, we present a workflow for engineering systems of non-natural anti-repressors. In this study, we create 41 inducible anti-repressors. This collection of transcription factors respond to two distinct ligands, fructose (anti-FruR) or D-ribose (anti-RbsR); and were complemented by 14 additional engineered anti-repressors that respond to the ligand isopropyl β-d-1-thiogalactopyranoside (anti-LacI). In turn, we use this collection of anti-repressors and complementary genetic architectures to confer logical control over gene expression. Here, we achieved all NOT oriented logical controls (i.e., NOT, NOR, NAND, and XNOR). The engineered transcription factors and corresponding series, parallel, and series-parallel genetic architectures represent a nascent anti-repressor based transcriptional programming structure. 

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