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Geographic patterns of genetic variation in wild species reflect the interplay of ecological and evolutionary processes. We assessed genetic variation in three genomes across four North American diploid strawberry taxa, with special emphasis on the gynodioecious Fragaria vesca subsp. bracteata (A.Heller) Staudt. Specifically, we sequenced one chloroplast (rpoC2) and two mitochondrial (atp8 and atp8-orf225) genes along with several nuclear microsatellite markers. In addition, we assessed indicators of breeding system (pollen viability and female frequency) for all taxa. The geographic perspective on the distribution of cytoplasmic and nuclear variation revealed the genetic affiliation of the restricted taxa (Fragaria vesca subsp. californica (Cham. & Schltdl.) Staudt and Fragaria mexicana Schltdl.) with the widespread F. vesca subsp. bracteata and identified a hotspot of hybridization within gynodioecious F. vesca subsp. bracteata. Higher pollen viability of hermaphrodites was found in the three hermaphroditic taxa relative to the gynodioecious one. Although theoretically predicted to be associated, the proportion of females within F. vesca subsp. bracteata populations was not correlated with population-level genetic variation, suggesting that the history of hybridization or population size variation is more influential on the distribution of genetic variation than sex ratio in this gynodioecious species. The documented patterns of genetic variation in this complex serve as an important point of reference for future ecological and evolutionary research in diploid Fragaria. Keywords: chloroplast, hybridization, genetic structure, gynodioecy, mitochondria, pollen viability. Les patrons geographiques de la variation genetique d'especes sauvages refletent l'interrelation entre les processus ecologiques et les evolutifs. Les auteurs ont evalue la variation de trois genomes a travers quatre taxons diploides de fraises en Amerique du Nord, en portant une attention particuliere a Fragaria vesca subsp. bracteata (A.Heller) Staudt gynodio'ique. Specifiquement, ils ont sequence un gene du chloroplaste (rpoC2) et deux genes mitochondriaux (atp8 et atp8-orf225) parallelement a plusieurs marqueurs microsatellites nucleaires. De plus, ils ont evalue des indicateurs du systeme de reproduction (viabilite du pollen et frequence des femelles) chez tous les taxons. La perspective geographique de la distribution de la variation cytoplasmique et nucleaire a revele l'affiliation genetique des taxons restreints (Fragaria vesca subsp. californica (Cham. & Schltdl.) Staudt et Fragaria mexicana Schltdl.) au taxon repandu F. vesca subsp. bracteata, et identifie un point chaud d'hybridation a l'interieur de F. vesca subsp. bracteata gynodio'ique. Une viabilite du pollen des hermaphrodites plus elevee a ete trouvee chez les trois taxons hermaphrodites comparativement au taxon gynodio'ique. Malgre les predictions theoriques d'une association, la proportion de femelles a l'interieur des populations de F. vesca subsp. bracteata n'etait pas correlee a la variation genetique au niveau de la population, suggerant que l'historique d'hybridation ou la variation de la taille de la population exerce une influence plus grande sur la distribution de la variation genetique que le ratio des sexes chez cette espece gynodio'ique. Les patrons documentes de variation genetique dans ce complexe servent de point de reference important pour la recherche future sur l'ecologie et l'evolution de Fragaria diploide. [Traduit par la Redaction] Mots-cles : chloroplaste, hybridation, structure genetique, gynodrecie, mitochondrie, viabilite du pollen., Introduction Patterns of phenotypic and genetic variation of wild species reflect their ecological and evolutionary history. Important questions that have emerged are: How is variation partitioned among and within populations [...]

With their extraordinary diversity in sexual systems, flowering plants offer unparalleled opportunities to understand sex determination and to reveal generalities in the evolution of sex chromosomes. Comparative genetic mapping of related taxa with good phylogenetic resolution can delineate the extent of sex chromosome diversity within plant groups, and lead the way to understanding the evolutionary drivers of such diversity. The North American octoploid wild strawberries provide such an opportunity. We performed linkage mapping using targeted sequence capture for the subdioecious western Fragaria virginiana ssp. platypetala and compared the location of its sexdetermining region (SDR) to those of 2 other (sub)dioecious species, the eastern subspecies, F. virginiana ssp. virginiana (whose SDR is at 0-5.5 Mb on chromosome VI of the B2 subgenome), and the sister species F. chiloensis (whose SDR is at 37 Mb on chromosome VI of the Av subgenome). Male sterility was dominant in F. virginiana ssp. platypetala and mapped to a chromosome also in homeologous group VI. Likewise, one major quantitative trait locus (QTL) for female fertility overlapped the male sterility region. However, the SDR mapped to yet another subgenome (B1), and to a different location (13 Mb), but similar to the location inferred in one population of the naturally occurring hybrid between F. chiloensis and F. virginiana (F. ×ananassa ssp. cuneifolia). Phylogenetic analysis of chromosomes across the octoploid taxa showed consistent subgenomic composition reflecting shared evolutionary history but also reinforced within-species variation in the SDR-carrying chromosome, suggesting either repeated evolution, or recent turnovers in SDR. [ABSTRACT FROM AUTHOR]

The evaluation of the intrinsic and extrinsic forces that determine geographical range sizes and niche breadth is key to the understanding of species distributions and for informing the conservation of biodiversity. Fragaria ( Rosaceae) contains the economically important cultivated strawberry ( Fragaria × ananassa subsp. ananassa) and numerous wild species. Using georeferenced species records and global bioclimatic data, we describe the bioclimatic niches for 21 Fragaria spp. and investigate the relationship between their niches and geographical range size, breeding system, ploidy and time since divergence. We found no evidence of phylogenetic signal for bioclimatic niches. There was also no relationship between ploidy and geographical or bioclimatic range area, but geographical range area was significantly greater for species that were capable of self-fertilization. In addition, we found a significant decelerating relationship between species age and geographical range area. Overall, our results suggest that Fragaria spp., although similar in morphology and life history, show high levels of divergence in bioclimatic niches and significant over-dispersion along some bioclimatic gradients, suggesting evolutionary lability in physiology and climate tolerance. As a consequence, wild species will remain a valuable resource for cultivated strawberry sustainability, especially under changing future climate. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 176, 99-114. [ABSTRACT FROM AUTHOR]

Phenotypes such as branching, photoperiod sensitivity, and height were modified during plant domestication and crop improvement. Here, we perform quantitative trait locus (QTL) mapping of these and other agronomic traits in a recombinant inbred line (RIL) population derived from an interspecific cross between Sorghum propinquum and Sorghum bicolor inbred Tx7000. Using low-coverage Illumina sequencing and a bin-mapping approach, we generated ∼1920 bin markers spanning ∼875 cM. Phenotyping data were collected and analyzed from two field locations and one greenhouse experiment for six agronomic traits, thereby identifying a total of 30 QTL. Many of these QTL were penetrant across environments and co-mapped with major QTL identified in other studies. Other QTL uncovered new genomic regions associated with these traits, and some of these were environment-specific in their action. To further dissect the genetic underpinnings of tillering, we complemented QTL analysis with transcriptomics, identifying 6189 genes that were differentially expressed during tiller bud elongation. We identified genes such as Dormancy Associated Protein 1 (DRM1) in addition to various transcription factors that are differentially expressed in comparisons of dormant to elongating tiller buds and lie within tillering QTL, suggesting that these genes are key regulators of tiller elongation in sorghum. Our study demonstrates the usefulness of this RIL population in detecting domestication and improvement-associated genes in sorghum, thus providing a valuable resource for genetic investigation and improvement to the sorghum community., (© The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America.)

Forward genetics remains a powerful method for revealing the genes underpinning organismal form and function, and for revealing how these genes are tied together in gene networks. In maize, forward genetics has been tremendously successful, but the size and complexity of the maize genome made identifying mutant genes an often arduous process with traditional methods. The next generation sequencing revolution has allowed for the gene cloning process to be significantly accelerated in many organisms, even when genomes are large and complex. Here, we describe a bulked-segregant analysis sequencing (BSA-Seq) protocol for cloning mutant genes in maize. Our simple strategy can be used to quickly identify a mapping interval and candidate single nucleotide polymorphisms (SNPs) from whole genome sequencing of pooled F2 individuals. We employed this strategy to identify narrow odd dwarf as an enhancer of teosinte branched1 , and to identify a new allele of defective kernel1 Our method provides a quick, simple way to clone genes in maize., (Copyright © 2018 Klein et al.)

Gynodioecy, the coexistence of females and hermaphrodites, occurs in 20% of angiosperm families and often enables transitions between hermaphroditism and dioecy. Clarifying mechanisms of sex determination in gynodioecious species can thus illuminate sexual system evolution. Genetic determination of gynodioecy, however, can be complex and is not fully characterized in any wild species. We used targeted sequence capture to genetically map a novel nuclear contributor to male sterility in a self-pollinated hermaphrodite of Fragaria vesca subsp. bracteata from the southern portion of its range. To understand its interaction with another identified locus and possibly additional loci, we performed crosses within and between two populations separated by 2000 km, phenotyped the progeny and sequenced candidate markers at both sex-determining loci. The newly mapped locus contains a high density of pentatricopeptide repeat genes, a class commonly involved in restoration of fertility caused by cytoplasmic male sterility. Examination of all crosses revealed three unlinked epistatically interacting loci that determine sexual phenotype and vary in frequency between populations. Fragaria vesca subsp. bracteata represents the first wild gynodioecious species with genomic evidence of both cytoplasmic and nuclear genes in sex determination. We propose a model for the interactions between these loci and new hypotheses for the evolution of sex determining chromosomes in the subdioecious and dioecious Fragaria., (Copyright © 2015 Ashman et al.)

Gynodioecy is a sexual system wherein females coexist with hermaphrodites. It is of interest not only because male-sterile plants are advantageous in plant breeding but also because it can be a crucial step in the evolutionary transition to entirely separate sexes (dioecy) from a hermaphroditic ancestor. The gynodioecious diploid wild strawberry, Fragaria vesca ssp. bracteata (Rosaceae), is a member of a clade with both dioecious and cultivated species, making it an ideal model in which to study the genetics of male sterility. To create a genetic map of F. v. ssp. bracteata, we identified informative polymorphisms from genomic sequencing (3-5x coverage) of two outbred plants from the same population. Using targeted enrichment, we sequenced 200 bp surrounding each of 6575 polymorphisms in 48 F1 offspring, yielding genotypes at 98% of targeted sites with mean coverage >100x, plus more than 600-kb high-coverage nontargeted sequence. With the resulting linkage map of 7802 stringently filtered markers (5417 targeted), we assessed recombination rates and genomic incongruities. Consistent with past work in strawberries, male sterility is dominant, segregates 1:1, and maps to a single location in the female. Further mapping an additional 55 offspring places male sterility in a gene-dense, 338-kb region of chromosome 4. The region is not syntenic with the sex-determining regions in the closely related octoploids, F. chiloensis and F. virginiana, suggesting either independent origins or translocation. The 57 genes in this region do not include protein families known to control male sterility and thus suggest alternate mechanisms for the suppression of male function.