Subgenome-informed statistical modeling of transcriptomes in 25 common wheat accessions reveals cis- and trans- regulation architectures.

Common wheat is allohexaploid, where it is difficult to obtain homoeolog-distinguished transcriptome data. Lasy-Seq, a type of 3' RNA-seq, is a technology efficient at obtaining homoeolog-distinguished transcriptomes. Here we applied Lasy-Seq to obtain transcriptome data from the seedlings, second leaves, and root tips of 25 common wheat lines mainly from East Asia.

Reducing herbivory in mixed planting by genomic prediction of neighbor effects in the field.

Genetically diverse populations can increase plant resistance to natural enemies. Yet, beneficial genotype pairs remain elusive due to the occurrence of positive or negative effects of mixed planting on plant resistance, respectively called associational resistance or susceptibility. Here, we identify key genotype pairs responsible for associational resistance to herbivory using the genome-wide polymorphism data of the plant species Arabidopsis thaliana.

Bridging the gap: returning genetic results to indigenous communities in Latin America.

In response to inequality in access to genomics research, efforts are underway to include underrepresented minorities, but explicit (and enforcing) guidelines are mostly targeted toward the Global North. In this work, we elaborate on the need to return scientific results to indigenous communities, reporting the actions we have taken in a recent genomic study with Mapuche communities in Chile. Our approach acknowledged the social dynamics perpetuating colonial hierarchies.

Dominance in self-compatibility between subgenomes of allopolyploid Arabidopsis kamchatica shown by transgenic restoration of self-incompatibility.

The evolutionary transition to self-compatibility facilitates polyploid speciation. In Arabidopsis relatives, the self-incompatibility system is characterized by epigenetic dominance modifiers, among which small RNAs suppress the expression of a recessive SCR/SP11 haplogroup. Although the contribution of dominance to polyploid self-compatibility is speculated, little functional evidence has been reported.

Hyper-Cryptic radiation of a tropical montane plant lineage.

Species are seen as the fundamental unit of biotic diversity, and thus their delimitation is crucial for defining measures for diversity assessments and studying evolution. Differences between species have traditionally been associated with variation in morphology. And yet, the discovery of cryptic diversity suggests that the evolution of distinct lineages does not necessarily involve morphological differences.

Geographic Variation in Genomic Signals of Admixture Between Two Closely Related European Sepsid Fly Species.

Unlabelled: The extent of interspecific gene flow and its consequences for the initiation, maintenance, and breakdown of species barriers in natural systems remain poorly understood. Interspecific gene flow by hybridization may weaken adaptive divergence, but can be overcome by selection against hybrids, which may ultimately promote reinforcement. An informative step towards understanding the role of gene flow during speciation is to describe patterns of past gene flow among extant species.

UV RESISTANCE LOCUS 8-Mediated UV-B Response Is Required Alongside CRYPTOCHROME 1 for Plant Survival in Sunlight under Field Conditions.

As sessile, photoautotrophic organisms, plants are subjected to fluctuating sunlight that includes potentially detrimental ultraviolet-B (UV-B) radiation. Experiments under controlled conditions have shown that the UV-B photoreceptor UV RESISTANCE LOCUS 8 (UVR8) controls acclimation and tolerance to UV-B in Arabidopsis thaliana; however, its long-term impact on plant fitness under naturally fluctuating environments remain poorly understood. Here, we quantified the survival and reproduction of different Arabidopsis mutant genotypes under diverse field and laboratory conditions.

Seasonal pigment fluctuation in diploid and polyploid Arabidopsis revealed by machine learning-based phenotyping method PlantServation.

Long-term field monitoring of leaf pigment content is informative for understanding plant responses to environments distinct from regulated chambers but is impractical by conventional destructive measurements. We developed PlantServation, a method incorporating robust image-acquisition hardware and deep learning-based software that extracts leaf color by detecting plant individuals automatically. As a case study, we applied PlantServation to examine environmental and genotypic effects on the pigment anthocyanin content estimated from leaf color.

Genome-wide association study of aphid abundance highlights a locus affecting plant growth and flowering in .

Plant life-history traits, such as size and flowering, contribute to shaping variation in herbivore abundance. Although plant genes involved in physical and chemical traits have been well studied, less is known about the loci linking plant life-history traits and herbivore abundance. Here, we conducted a genome-wide association study (GWAS) of aphid abundance in a field population of .

A low-coverage 3' RNA-seq to detect homeolog expression in polyploid wheat.

Although allopolyploid species are common among natural and crop species, it is not easy to distinguish duplicated genes, known as homeologs, during their genomic analysis. Yet, cost-efficient RNA sequencing (RNA-seq) is to be developed for large-scale transcriptomic studies such as time-series analysis and genome-wide association studies in allopolyploids. In this study, we employed a 3' RNA-seq utilizing 3' untranslated regions (UTRs) containing frequent mutations among homeologous genes, compared to coding sequence.

Targeted single-cell gene induction by optimizing the dually regulated CRE/ system by a newly defined heat-shock promoter and the steroid hormone in .

Multicellular organisms rely on intercellular communication systems to organize their cellular functions. In studies focusing on intercellular communication, the key experimental techniques include the generation of chimeric tissue using transgenic DNA recombination systems represented by the CRE/ system. If an experimental system enables the induction of chimeras at highly targeted cell(s), it will facilitate the reproducibility and precision of experiments.

The genetic history of the Southern Andes from present-day Mapuche ancestry.

The southernmost regions of South America harbor some of the earliest evidence of human presence in the Americas. However, connections with the rest of the continent and the contextualization of present-day indigenous ancestries remain poorly resolved. In this study, we analyze the genetic ancestry of one of the largest indigenous groups in South America: the Mapuche.

Detecting frequency-dependent selection through the effects of genotype similarity on fitness components.

Frequency-dependent selection (FDS) is an evolutionary regime that can maintain or reduce polymorphisms. Despite the increasing availability of polymorphism data, few effective methods are available for estimating the gradient of FDS from the observed fitness components. We modeled the effects of genotype similarity on individual fitness to develop a selection gradient analysis of FDS.

Phenotypic variation of a new synthetic allotetraploid enhanced in natural environment.

The phenotypic variation of vegetative organs and reproductive organs of newly synthesized and natural genotypes was investigated in both a controlled environment and a natural environment in an experimental garden. When we compared the variation of their leaf shape as a vegetative organ, the synthetic individuals grown in the garden showed larger variation compared with the individuals incubated in a growth chamber, suggesting enhanced phenotypic variation in a natural fluctuating environment. In contrast, the natural genotypes did not show significant change in variation by growth condition.

A global analysis of matches and mismatches between human genetic and linguistic histories.

Human history is written in both our genes and our languages. The extent to which our biological and linguistic histories are congruent has been the subject of considerable debate, with clear examples of both matches and mismatches. To disentangle the patterns of demographic and cultural transmission, we need a global systematic assessment of matches and mismatches.

Robustness and the generalist niche of polyploid species: Genome shock or gradual evolution?

The prevalence of polyploidy in wild and crop species has stimulated debate over its evolutionary advantages and disadvantages. Previous studies have focused on changes occurring at the polyploidization events, including genome-wide changes termed "genome shock," as well as ancient polyploidy. Recent bioinformatics advances and empirical studies of Arabidopsis and wheat relatives are filling a research gap: the functional evolutionary study of polyploid species using RNA-seq, DNA polymorphism, and epigenomics.

Development of a high-throughput field phenotyping rover optimized for size-limited breeding fields as open-source hardware.

Phenotyping is a critical process in plant breeding, especially when there is an increasing demand for streamlining a selection process in a breeding program. Since manual phenotyping has limited efficiency, high-throughput phenotyping methods are recently popularized owing to progress in sensor and image processing technologies. However, in a size-limited breeding field, which is common in Japan and other Asian countries, it is challenging to introduce large machinery in the field or fly unmanned aerial vehicles over the field.

Global genomic analyses of wheat powdery mildew reveal association of pathogen spread with historical human migration and trade.

The fungus Blumeria graminis f. sp. tritici causes wheat powdery mildew disease.

Polyploidy before and after domestication of crop species.

Recent advances in the genomics of polyploid species answer some of the long-standing questions about the role of polyploidy in crop species. Here, we summarize the current literature to reexamine scenarios in which polyploidy played a role both before and after domestication. The prevalence of polyploidy can help to explain environmental robustness in agroecosystems.

, an Atypical Rhomboid-Related Gene, Is Required for Callose Accumulation and Pollen Wall Development.

Fertilization is a key event for sexually reproducing plants. Pollen-stigma adhesion, which is the first step in male-female interaction during fertilization, requires proper pollen wall patterning. Callose, which is a β-1.

A Natural Low Phytic Acid Finger Millet Accession Significantly Improves Iron Bioavailability in Indian Women.

Iron deficiency and anemia are common in low- and middle-income countries. This is due to a poor dietary iron density and low iron absorption resulting from the high inhibitory phytic acid content in cereal and millet-based diets. Here, we report that a naturally occurring low phytic acid finger millet accession (571 mg 100 g), stable across three growing seasons with normal iron content (3.

Pollen Number and Ribosome Gene Expression Altered in a Genome-Editing Mutant of Gene.

The number of pollen grains varies within and between species. However, little is known about the molecular basis of this quantitative trait, in contrast with the many studies available on cell differentiation in the stamen. Recently, the first gene responsible for pollen number variation, (), was isolated by genome-wide association studies of and exhibited the signature of natural selection.

Demography and selection analysis of the incipient adaptive radiation of a Hawaiian woody species.

Ecological divergence in a species provides a valuable opportunity to study the early stages of speciation. We focused on Metrosideros polymorpha, a unique example of the incipient radiation of woody species, to examine how an ecological divergence continues in the face of gene flow. We analyzed the whole genomes of 70 plants collected throughout the island of Hawaii, which is the youngest island with the highest altitude in the archipelago and encompasses a wide range of environments.

Corrigendum: An Affordable Image-Analysis Platform to Accelerate Stomatal Phenotyping During Microscopic Observation.

[This corrects the article DOI: 10.3389/fpls.2021.