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1. Genetic control of photoprotection and photosystem II operating efficiency in plants

   https://doi.org/10.1111/nph.18980  

   Sahay, Seema; Grzybowski, Marcin; Schnable, James C.; Głowacka, Katarzyna (May 2023, New Phytologist)

   Summary Photoprotection against excess light via nonphotochemical quenching (NPQ) is indispensable for plant survival. However, slow NPQ relaxation under low light conditions can decrease yield of field‐grown crops up to 40%.Using semi‐high‐throughput assay, we quantified the kinetics of NPQ and photosystem II operating efficiency (ΦPSII) in a replicated field trial of more than 700 maize (Zea mays) genotypes across 2 yr. Parametrized kinetics data were used to conduct genome‐wide association studies.For six candidate genes involved in NPQ and ΦPSII kinetics in maize the loss of function alleles of orthologous genes in Arabidopsis (Arabidopsis thaliana) were characterized: two thioredoxin genes, and genes encoding a transporter in the chloroplast envelope, an initiator of chloroplast movement, a putative regulator of cell elongation and stomatal patterning, and a protein involved in plant energy homeostasis.Since maize and Arabidopsis are distantly related, we propose that genes involved in photoprotection and PSII function are conserved across vascular plants. The genes and naturally occurring functional alleles identified here considerably expand the toolbox to achieving a sustainable increase in crop productivity. 

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2. PacBio high‐throughput multi‐locus sequencing reveals high genetic diversity in mushroom‐forming fungi

   https://doi.org/10.1111/1755-0998.13885  

   Swenie, Rachel A.; Looney, Brian P.; Ke, Yi‐Hong; Alejandro Rojas, J.; Cubeta, Marc A.; Langer, Gitta J.; Vilgalys, Rytas; Brandon Matheny, P. (October 2023, Molecular Ecology Resources)

   Abstract Multi‐locus sequence data are widely used in fungal systematic and taxonomic studies to delimit species and infer evolutionary relationships. We developed and assessed the efficacy of a multi‐locus pooled sequencing method using PacBio long‐read high‐throughput sequencing. Samples included fresh and dried voucher specimens, cultures and archival DNA extracts of Agaricomycetes with an emphasis on the order Cantharellales. Of the 283 specimens sequenced, 93.6% successfully amplified at one or more loci with a mean of 3.3 loci amplified. Our method recovered multiple sequence variants representing alleles of rDNA loci and single copy protein‐coding genesrpb1,rpb2 andtef1. Within‐sample genetic variation differed by locus and taxonomic group, with the greatest genetic divergence observed among sequence variants ofrpb2 andtef1 from corticioid Cantharellales. Our method is a cost‐effective approach for generating accurate multi‐locus sequence data coupled with recovery of alleles from polymorphic samples and multi‐organism specimens. These results have important implications for understanding intra‐individual genomic variation among genetic loci commonly used in species delimitation of fungi. 

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3. The Genome of Lolium multiflorum Reveals the Genetic Architecture of Paraquat Resistance

   https://doi.org/10.1111/mec.17775  

   Brunharo, Caio A; Short, Aidan W; Bobadilla, Lucas K; Streisfeld, Matthew A (May 2025, Molecular Ecology)

   ABSTRACT Herbicide resistance in agricultural weeds has become one of the greatest challenges for sustainable crop production. The repeated evolution of herbicide resistance provides an excellent opportunity to study the genetic and physiological basis of the resistance phenotype and the evolutionary responses to human‐mediated selection pressures.Lolium multiflorumis a ubiquitous weed that has evolved herbicide resistance repeatedly around the world in various cropping systems. We assembled and annotated a chromosome‐scale genome forL. multiflorumand elucidated the genetic architecture of paraquat resistance by performing quantitative trait locus analysis, genome‐wide association studies, genetic divergence analysis and transcriptome analyses from paraquat‐resistant and ‐susceptibleL. multiflorumplants. We identified two regions on chromosome 5 that were associated with paraquat resistance. These regions both showed evidence for positive selection among the resistant populations we sampled, but the effects of this selection on the genome differed, implying a complex evolutionary history. In addition, these regions contained candidate genes that encoded cellular transport functions, including a novel multidrug and toxin extrusion (MATE) protein and a cation transporter previously shown to interact with polyamines. Given thatL. multiflorumis a weed and a cultivated crop species, the genomic resources generated will prove valuable to a wide spectrum of the plant science community. Our work contributes to a growing body of knowledge on the underlying evolutionary and ecological dynamics of rapid adaptation to strong anthropogenic selection pressure that could help initiate efforts to improve weed management practices in the long term for a more sustainable agriculture. 

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4. P ool P arty 2: An integrated pipeline for analysing pooled or indexed low‐coverage whole‐genome sequencing data to discover the genetic basis of diversity

   https://doi.org/10.1111/1755-0998.13888  

   Willis, Stuart; Micheletti, Steven; Andrews, Kimberly R.; Narum, Shawn (November 2023, Molecular Ecology Resources)

   Abstract Whole‐genome sequencing data allow survey of variation from across the genome, reducing the constraint of balancing genome sub‐sampling with estimating recombination rates and linkage between sampled markers and target loci. As sequencing costs decrease, low‐coverage whole‐genome sequencing of pooled or indexed‐individual samples is commonly utilized to identify loci associated with phenotypes or environmental axes in non‐model organisms. There are, however, relatively few publicly available bioinformatic pipelines designed explicitly to analyse these types of data, and fewer still that process the raw sequencing data, provide useful metrics of quality control and then execute analyses. Here, we present an updated version of a bioinformatics pipeline calledPoolParty2that can effectively handle either pooled or indexed DNA samples and includes new features to improve computational efficiency. Using simulated data, we demonstrate the ability of our pipeline to recover segregating variants, estimate their allele frequencies accurately, and identify genomic regions harbouring loci under selection. Based on the simulated data set, we benchmark the efficacy of our pipeline with another bioinformatic suite,angsd, and illustrate the compatibility and complementarity of these suites usingangsdto generate genotype likelihoods as input for identifying linkage outlier regions using alignment files and variants provided byPoolParty2. Finally, we apply our updated pipeline to an empirical dataset of low‐coverage whole genomic data from population samples of Columbia River steelhead trout (Oncorhynchus mykiss), results from which demonstrate the genomic impacts of decades of artificial selection in a prominent hatchery stock. Thus, we not only demonstrate the utility ofPoolParty2for genomic studies that combine sequencing data from multiple individuals, but also illustrate how it compliments other bioinformatics resources such asangsd. 

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5. Genetic diversity, population structure, and ancestry estimation in the Antennaria rosea (Asteraceae: Gnaphalieae) polyploid agamic complex

   https://doi.org/10.1002/tax.12420  

   Thapa, Ramhari; Bayer, Randall J.; Mandel, Jennifer R. (February 2021, TAXON)