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The modification of seed shattering has been a recurring theme in rice evolution. The wild ancestor of cultivated rice disperses its seeds, but reduced shattering was selected during multiple domestication events to facilitate harvesting. Conversely, selection for increased shattering occurred during the evolution of weedy rice, a weed invading cultivated rice fields that has originated multiple times from domesticated ancestors. Shattering requires formation of a tissue known as the abscission zone (AZ), but how the AZ has been modified throughout rice evolution is unclear. We quantitatively characterized the AZ characteristics of relative length, discontinuity, and intensity in 86 cultivated and weedy rice accessions. We reconstructed AZ evolutionary trajectories and determined the degree of convergence among different cultivated varieties and among independent weedy rice populations. AZ relative length emerged as the best feature to distinguish high and low shattering rice. Cultivated varieties differed in average AZ morphology, revealing lack of convergence in how shattering reduction was achieved during domestication. In contrast, weedy rice populations typically converged on complete AZs, irrespective of origin. By examining AZ population-level morphology, our study reveals its evolutionary plasticity, and suggests that the genetic potential to modify the ecologically and agronomically important trait of shattering is plentiful in rice lineages. [ABSTRACT FROM AUTHOR]

Tibetan weedy barleys reside at the edges of qingke (hulless barley) fields in Tibet (Xizang). The spikes of these weedy barleys contain or lack a brittle rachis, with either two- or six-rowed spikes and either hulled or hulless grains at maturity. Although the brittle rachis trait of Tibetan weedy barleys is similar to that of wild barley (Hordeum vulgare ssp. spontaneum Thell.), these plants share genetic similarity with domesticated barley. The origin of Tibetan weedy barleys continues to be debated. Here, we show that most Tibetan weedy barleys originated from cross-pollinated hybridization of domesticated barleys, followed by hybrid self-pollination and recombination between Non-brittle rachis 1 (btr1) and 2 (btr2). We discovered the specific genetic ancestry of these weedy barleys in South Asian accessions. Tibetan weedy barleys exhibit lower genetic diversity than wild and Chinese landraces/cultivars and share a close relationship with qingke, genetically differing from typical eastern and western barley populations. We classified Tibetan weedy barleys into two groups, brittle rachis (BR) and non-brittle rachis (NBR); these traits align with the haplotypes of the btr1 and btr2 genes. Whereas wild barleys carry haplotype combinations of Btr1 and Btr2, each showing lower proportions in a population, the recombinant haplotype BTR2H8+BTR1H24 is predominant in the BR group. Haplotype block analysis based on whole-genome sequencing revealed two recombination breakpoints, which are present in 80.6% and 16.8% of BR accessions according to marker-assisted analysis. Hybridization events between wild and domesticated barley were rarely detected. These findings support the notion that Tibetan weedy barleys originated via recombination between Btr1 and Btr2 in domesticated barley.

Abstract Background Asian rice is one of the world’s most widely cultivated crops. Large-scale resequencing analyses have been undertaken to explore the domestication and de-domestication genomic history of Asian rice, but the evolution of rice is still under debate. Results Here, we construct a syntelog-based rice pan-genome by integrating and merging 74 high-accuracy genomes based on long-read sequencing, encompassing all ecotypes and taxa of Oryza sativa and Oryza rufipogon. Analyses of syntelog groups illustrate subspecies divergence in gene presence-and-absence and haplotype composition and identify massive genomic regions putatively introgressed from ancient Geng/japonica to ancient Xian/indica or its wild ancestor, including almost all well-known domestication genes and a 4.5-Mbp centromere-spanning block, supporting a single domestication event in main rice subspecies. Genomic comparisons between weedy and cultivated rice highlight the contribution from wild introgression to the emergence of de-domestication syndromes in weedy rice. Conclusions This work highlights the significance of inter-taxa introgression in shaping diversification and divergence in rice evolution and provides an exploratory attempt by utilizing the advantages of pan-genomes in evolutionary studies.

Control of weeds in cultivated crops is a pivotal component in successful crop production allowing higher yield and higher quality. In rice-growing regions worldwide, weedy rice (Oryza sativa f. spontanea Rosh.) is a weed related to cultivated rice which infests rice fields. With populations across the globe evolving a suite of phenotypic traits characteristic of weeds and of cultivated rice, varying hypotheses exist on the origin of weedy rice. Here, we investigated the genetic diversity and possible origin of weedy rice in California using 98 simple sequence repeat (SSR) markers and an Rc gene-specific marker. By employing phylogenetic clustering analysis, we show that four to five genetically distinct biotypes of weedy rice exist in California. Analysis of population structure and genetic distance among individuals reveals diverse evolutionary origins of California weedy rice biotypes, with ancestry derived from indica, aus, and japonica cultivated rice as well as possible contributions from weedy rice from the southern United States and wild rice. Because this diverse parentage primarily consists of weedy, wild, and cultivated rice not found in California, most existing weedy rice biotypes likely originated outside California.

Agricultural weeds descended from domesticated ancestors, directly from crops (endoferality) and/or from crop–wild hybridization (exoferality), may have evolutionary advantages by rapidly acquiring traits pre‐adapted to agricultural habitats. Understanding the role of crops on the origin and evolution of agricultural weeds is essential to develop more effective weed management programs, minimize crop losses due to weeds, and accurately assess the risks of cultivated genes escaping. In this review, we first describe relevant traits of weediness: shattering, seed dormancy, branching, early flowering and rapid growth, and their role in the feralization process. Furthermore, we discuss how the design of "super‐crops" can affect weed evolution. We then searched for literature documenting cases of agricultural weeds descended from well‐domesticated crops, and describe six case studies of feral weeds evolved from major crops: maize, radish, rapeseed, rice, sorghum, and sunflower. Further studies on the origin and evolution of feral weeds can improve our understanding of the physiological and genetic mechanisms underpinning the adaptation to agricultural habitats and may help to develop more effective weed‐control practices and breeding better crops. © 2022 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

The weedy rice (Oryza sativa f. spontanea) harbors large numbers of excellent traits and genetic diversities, which serves as a valuable germplasm resource and has been considered as a typical material for research about dedomestication. However, there are relatively few reference genomes on weedy rice that severely limit exploiting these genetic resources and revealing more details about de-domestication events. In this study, a highquality genome (~376.4 Mb) of weedy rice A02 was assembled based on Nanopore ultra-long platform with a coverage depth of about 79.3× and 35,423 genes were predicted. Compared to Nipponbare genome, 5,574 structural variations (SVs) were found in A02. Based on super pan-genome graph, population SVs of 238 weedy rice and cultivated rice accessions were identified using public resequencing data. Furthermore, the de-domestication sites of weedy rice and domestication sites of wild rice were analyzed and compared based on SVs and single-nucleotide polymorphisms (SNPs). Interestingly, an average of 2,198 genes about de-domestication could only be found by FST analysis based on SVs (SV-FST) while not by FST analysis based on SNPs (SNP-FST) in divergent region. Additionally, there was a low overlap between domestication and de-domestication intervals, which demonstrated that two different mechanisms existed in these events. Our finding could facilitate pinpointing of the evolutionary events that had shaped the genomic architecture of wild, cultivated, and weedy rice, and provide a good foundation for cloning of the superior alleles for breeding. [ABSTRACT FROM AUTHOR]

Culm color variation is an interesting phenomenon that contributes to the breeding of new varieties of ornamental plants during domestication. De-domesticated variation is considered ideal for identifying and interpreting the molecular mechanisms of plant mutations. However, the variation in culm color of bamboo remains unknown. In the present study, yellow and green culms generated from the same rhizome of Phyllostachys vivax cv. Aureocaulis (P. vivax) were used to elucidate the molecular mechanism of culm color formation. Phenotypic and physiological data showed that environmental suitability was higher in green culms than in yellow culms. High-throughput sequencing analysis showed 295 differentially expressed genes (DEGs) and 22 differentially expressed miRNAs (DEMs) in two different colored bamboo culms. There were 103 DEM-DEG interaction pairs, of which a representative “miRNA-mRNA” regulatory module involved in photosynthesis and pigment metabolism was formed by 14 DEM-DEG pairs. The interaction of the three key pairs was validated by qPCR and dual-luciferase assays. This study provides new insights into the molecular mechanism of miRNAs involved in P. vivax culm color formation, which provides evidence for plant de-domestication and is helpful for revealing the evolutionary mechanism of bamboo. [ABSTRACT FROM AUTHOR]

Hybridization between crops and their wild relatives may promote the evolution of de-domesticated (feral) weeds. Wild sunflower (Helianthus annuus L.) is typically found in ruderal environments, but crop–wild hybridization may facilitate the evolution of weedy populations. Using 1 crop-specific mitochondrial marker (CMS-PET1) and 14 nuclear SSR markers, we studied the origin and genetic diversity of a recently discovered weedy population of sunflower (named BRW). Then, using a resurrection approach, we tested for rapid evolution of weedy traits (seed dormancy, herbicide resistance, and competitive ability) by sampling weedy and wild populations 10 years apart (2007 and 2017). All the weedy plants present the CMS-PET1 cytotype, confirming their feral origin. At the nuclear markers, BRW showed higher genetic diversity than the cultivated lines and low differentiation with one wild population, suggesting that wild hybridization increased their genetic diversity. We found support for rapid evolution towards higher seed dormancy, but not for higher competitive ability or herbicide resistance. Our results highlight the importance of seed dormancy during the earliest stages of adaptation and show that crop–wild hybrids can evolve quickly in agricultural environments. [ABSTRACT FROM AUTHOR]

This article studies how the distribution of the work of punkah-pulling in European households and barracks of colonial India involved European masters making gradually multiplying claims on their servants' labouring time and how these claims fared in practice. The laborious task of punkah-pulling in such establishments was often resisted by native servants on counts of caste, custom or simply exhaustion. In the context of such conflicts, this article tries to understand how the colonial state and its legal and regulatory functions mediated the contested terrain of domestic and service work over the nineteenth century. Over the latter half of this century, punkah-pulling became a separate occupation, even as this occupation slid down the hierarchy of service work and became a more pronounced target of recurring racial violence. Against this background, the article also tries to grapple with the material limits encountered by the regimes of work involved in the cheap, day-and-night conduct of punkah-pulling that eventually led up to the acceptance of mechanised alternatives. [ABSTRACT FROM AUTHOR]

Weed seeds generally have stronger ageing resistance than crops, allowing them to maintain their persistence in the field. Weedy rice (Oryza sativa), de‐domesticated from cultivated rice (Oryza sativa L.), has become a pernicious weed in Chinese rice fields in recent years. Whether weedy rice rapidly evolved strong resistance to seed ageing in the process of de‐domestication, thereby contributing to its persistence in the paddy field, requires investigation. Accordingly, the seeds of weedy rice populations and their co‐existing rice varieties were collected from 61 regions of China and germinated after incubation at normal (25°C) and artificial accelerated ageing (50°C) conditions, for four consecutive years (2013–2016). The results showed that the seed‐ageing resistance of weedy rice was higher than that of its coexisting rice cultivars. The high temperature treatment and seed viability tests showed that weedy rice seeds had only weak dormancy in the first year (2013). Furthermore, a negative correlation was found between germination and latitude. At about 35° N, naturally selected weedy rice formed two distinct groups. This implies that indica–japonica differentiation might affect the ageing resistance of weedy rice and the coexisting cultivated rice. After dividing the weedy and cultivated rice into indica and japonica types, the germination percentage of the indica‐type was higher than that of the japonica type. These results indicate that weedy rice may have evolved new resistance to seed ageing that may be helpful in formulating prevention and control strategies for this problematic weed. [ABSTRACT FROM AUTHOR]

Abstract Control of weeds in cultivated crops is a pivotal component in successful crop production allowing higher yield and higher quality. In rice‐growing regions worldwide, weedy rice (Oryza sativa f. spontanea Rosh.) is a weed related to cultivated rice which infests rice fields. With populations across the globe evolving a suite of phenotypic traits characteristic of weeds and of cultivated rice, varying hypotheses exist on the origin of weedy rice. Here, we investigated the genetic diversity and possible origin of weedy rice in California using 98 simple sequence repeat (SSR) markers and an Rc gene‐specific marker. By employing phylogenetic clustering analysis, we show that four to five genetically distinct biotypes of weedy rice exist in California. Analysis of population structure and genetic distance among individuals reveals diverse evolutionary origins of California weedy rice biotypes, with ancestry derived from indica, aus, and japonica cultivated rice as well as possible contributions from weedy rice from the southern United States and wild rice. Because this diverse parentage primarily consists of weedy, wild, and cultivated rice not found in California, most existing weedy rice biotypes likely originated outside California.

De-domestication or feralization is an interesting phenomenon in crops and livestock. Previously, evidence for crop de-domestication was based mainly on studies using phenotypic and genotypic data from limited molecular markers or gene segments. Recent genomic studies in rice, barley, and wheat provide comprehensive landscapes of de-domestication on a whole-genome scale. Here, we summarize crop de-domestication processes, ecological roles of de-domesticates, mechanisms underlying crop de-domestication syndromes, and conditions potentially favoring de-domestication events. We further explain how recent de-domestication studies have expanded our understanding of the complexity of crop evolution, and highlight the genetic novelties of de-domesticates beneficial for modern crop breeding. De-domestication has recently been confirmed in several crop and livestock systems by genomic evidence and has been demonstrated to be not just a genetic reversal of domestication, despite reacquisition of wild-like phenotypes. Multiple pathways lead to the emergence of plant de-domestication, and de-domesticates have multiple roles in both wild and agricultural ecosystems. Under loosening artificial selection due to the wide application of non-intensive farming practices, crops, especially diploid ones, tend to be more likely to initiate de-domestication. Under natural selection, de-domesticates could provide valuable genetic resources for modern crop breeding. [ABSTRACT FROM AUTHOR]

Tibetan weedy barleys reside at the edges of qingke (hulless barley) fields in Tibet (Xizang). The spikes of these weedy barleys contain or lack a brittle rachis, with either two- or six-rowed spikes and either hulled or hulless grains at maturity. Although the brittle rachis trait of Tibetan weedy barleys is similar to that of wild barley (Hordeum vulgare ssp. spontaneum Thell.), these plants share genetic similarity with domesticated barley. The origin of Tibetan weedy barleys continues to be debated. Here, we show that most Tibetan weedy barleys originated from cross-pollinated hybridization of domesticated barleys, followed by hybrid self-pollination and recombination between Non-brittle rachis 1 (btr1) and 2 (btr2). We discovered the specific genetic ancestry of these weedy barleys in South Asian accessions. Tibetan weedy barleys exhibit lower genetic diversity than wild and Chinese landraces/cultivars and share a close relationship with qingke, genetically differing from typical eastern and western barley populations. We classified Tibetan weedy barleys into two groups, brittle rachis (BR) and non-brittle rachis (NBR); these traits align with the haplotypes of the btr1 and btr2 genes. Whereas wild barleys carry haplotype combinations of Btr1 and Btr2, each showing lower proportions in a population, the recombinant haplotype BTR2H8+BTR1H24 is predominant in the BR group. Haplotype block analysis based on whole-genome sequencing revealed two recombination breakpoints, which are present in 80.6% and 16.8% of BR accessions according to marker-assisted analysis. Hybridization events between wild and domesticated barley were rarely detected. These findings support the notion that Tibetan weedy barleys originated via recombination between Btr1 and Btr2 in domesticated barley., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)

Agro-ecosystems are dominated by crop plants and the weedy species that thrive under agricultural conditions. Weedy crop relatives are some of the most difficult weeds to manage and can dramatically reduce crop yields when left unchecked. Weedy rice has resulted from multiple de-domestication events from crop rice in different rice growing regions. Interestingly, both South Korea and the United States harbor weedy rice populations that share ancestry with indica cultivars and temperate japonica cultivars. Here we compare weedy rice populations from South Korea and the United States on order to identify if they are the result of the same de-domestication events. We find that weedy rice populations in South Korea are genetically distinct from weedy rice found in the USA and are therefore the result of two unique de-domestication events. Low levels of genetic diversity among Korean weedy rice accessions (haplotype diversity = 0.0188 and 0.0324) indicate recent de-domestication events from crop relatives.

The evolution of problematic plants, both weeds and invasives, is a topic of increasing interest. Plants that have evolved from domesticated ancestors have certain advantages for study. Because of their economic importance, domesticated plants are generally well-characterized and readily available for ecogenetic comparison with their wild descendants. Thus, the evolutionary history of crop descendants has the potential to be reconstructed in some detail. Furthermore, growing crop progenitors with their problematic descendants in a common environment allows for the identification of significant evolutionary differences that correlate with weediness or invasiveness. We sought well-established examples of invasives and weeds for which genetic and/or ethnobotanical evidence has confirmed their evolution from domesticates. We found surprisingly few cases, only 13. We examine our list for generalizations and then some selected cases to reveal how plant pests have evolved from domesticates. Despite their potential utility, crop descendants remain underexploited for evolutionary study. Promising evolutionary research opportunities for these systems are abundant and worthy of pursuit.

Summary: De‐domestication is a unique evolutionary process during which crops re‐acquire wild‐like traits to survive and persist in agricultural fields without the need for human cultivation. The re‐acquisition of seed dispersal mechanisms is crucial for crop de‐domestication. Common wheat is an important cereal crop worldwide. Tibetan semi‐wild wheat is a potential de‐domesticated common wheat subspecies. However, the crucial genes responsible for its brittle rachis trait have not been identified.Genetic mapping, functional analyses and phylogenetic analyses were completed to identify the gene associated with Qbr.sau‐5A, which is a major locus for the brittle rachis trait of Tibetan semi‐wild wheat.The cloned Qbr.sau‐5A gene is a new Q allele (Qt) with a 161‐bp transposon insertion in exon 5. Although Qt is expressed normally, its encoded peptide lacks some key features of the APETALA2 family. The abnormal functions of Qt in developing wheat spikes result in brittle rachises. Phylogenetic and genotyping analyses confirmed that Qt originated from Q in common wheat and is naturally distributed only in Tibetan semi‐wild wheat populations.The identification of Qt provides new evidence regarding the origin of Tibetan semi‐wild wheat, and new insights into the re‐acquisition of wild traits during crop de‐domestication. See also the Commentary on this article by Ellstrand, 224: 550–551. [ABSTRACT FROM AUTHOR]

Agronomically critical weeds that have evolved alongside crop species are characterized by rapid adaptation and invasiveness, which can result in an enormous reduction in annual crop yield worldwide. We discuss here recent genome-based research studies on agricultural weeds and crop–weed interactions that reveal several major evolutionary innovations such as de-domestication, interactions mediated by allelochemical secondary metabolites, and parasitic genetic elements that play crucial roles in enhancing weed invasiveness in agricultural settings. We believe that these key studies will guide future research into the evolution of crop–weed interactions, and further the development of practical applications in agricultural weed control and crop breeding. Highlights Agricultural weeds can be generally classified into weedy crop relatives and non-crop relatives based on their genetic relationship to crops. They are not only economically important but are fascinating models for studying the adaptation and rapid evolution of plant species in human-mediated environments. Allelopathy by secondary metabolites is a central process underlying crop–weed interactions in agroecosystems. Biosynthetic gene clusters may be one important genomic mechanism governing these allelopathic interactions. Genetic exchanges occur frequently between crops and parasitic weeds, and can evidently have functional consequences. Recent genomic studies of weedy plants are providing in-depth insights into the evolution of weeds and the mechanisms of crop–weed interactions, and are likely to have a major impact on weed management and crop breeding. [ABSTRACT FROM AUTHOR]

The rice production system in Japan is changing due to the aging of rice farmers, shortage of labor, mechanization, and increase of large-scale rice fields and increased application of direct sowing, all of which contribute to the lack of sophisticated weed management practices. Because the changing production system has not improved and likely worsened weed management practices, weedy rice (Oryza sativa L.) has become a serious threat to rice production in Japan. We analyzed weedy rice accessions from Nagano, the central part of Japan, and other rice accessions to elucidate the origin of this weedy rice using a whole-genome single nucleotide polymorphism (SNP) array. For developing sustainable weedy rice management practices, the elucidation of the origin of re-emerging weedy rice is crucial. Population genetic analysis indicated that weedy rice in Nagano was phylogenetically independent from the local red rice cultivar with low genetic diversity. Past and recently re-emerging weedy rice ecotypes in Nagano shared a similar genetic background which implies the evolution of weedy rice by severe natural selection. Window-based FST and selection sweep analysis revealed the divergence of some of the known key domestication-related genes, such as shattering gene sh4 and qsh1, of weedy rice from domesticated rice cultivars.

Many different crop species were selected for a common suite of 'domestication traits', which facilitates their use for studies of parallel evolution. Within domesticated rice ( Oryza sativa), there has also been independent evolution of weedy strains from different cultivated varieties. This makes it possible to examine the genetic basis of parallel weed evolution and the extent to which this process occurs through shared genetic mechanisms. We performed comparative QTL mapping of weediness traits using two recombinant inbred line populations derived from crosses between an indica crop variety and representatives of each of the two independently evolved weed strains found in US rice fields, strawhull (S) and blackhull awned (B). Genotyping-by-sequencing provided dense marker coverage for linkage map construction (average marker interval <0.25 cM), with 6016 and 13 730 SNPs mapped in F5 lines of the S and B populations, respectively. For some weediness traits (awn length, hull pigmentation and pericarp pigmentation), QTL mapping and sequencing of underlying candidate genes confirmed that trait variation was largely attributable to individual loci. However, for more complex quantitative traits (including heading date, panicle length and seed shattering), we found multiple QTL, with little evidence of shared genetic bases between the S and B populations or across previous studies of weedy rice. Candidate gene sequencing revealed causal genetic bases for 8 of 27 total mapped QTL. Together these findings suggest that despite the genetic bottleneck that occurred during rice domestication, there is ample genetic variation in this crop to allow agricultural weed evolution through multiple genetic mechanisms. [ABSTRACT FROM AUTHOR]

Domesticated animals that revert to a wild state can become invasive and significantly impact native biodiversity. Although dogs can be problematic locally, only the Australasian dingo is known to occur in isolation from humans. Western dogs have experienced more intense artificial selection, which potentially limits their invasiveness. However, feral dogs eradicated from Isabela Island, Galápagos in the 1980s could be the first-known exception. We used DNA and morphometric data from 92 of these dogs to test the hypotheses that (i) these dogs persisted independently of humans for up to a century and a half since descending from a handful of dogs introduced in the early 1800s, vs. (ii) similarly to other western feral dog populations, they reflected continuous recruitment of strays from human settlements on a portion of the Island. We detected one dominant maternal lineage and one dominant paternal lineage shared by the three subpopulations, along with low autosomal genetic diversity, consistent with the hypothesized common origins from a small founder population. Genetic diversity patterns among the three island subpopulations were consistent with stepping-stone founder effects, while morphometric differentiation suggested rapid phenotypic divergence, possibly due to drift and reinforced by selection corresponding to distinct microclimates and habitats on Isabela. Despite the continued presence of free-ranging dogs in the vicinity of settlements on Isabela and other Galápagos Islands, feral populations have not reestablished in remote areas since the 1980s, emphasizing the rarity of conditions necessary for feralization of modern western dogs. [ABSTRACT FROM AUTHOR]

The weedy rice ( Oryza sativa f. spontanea ) harbors large numbers of excellent traits and genetic diversities, which serves as a valuable germplasm resource and has been considered as a typical material for research about de-domestication. However, there are relatively few reference genomes on weedy rice that severely limit exploiting these genetic resources and revealing more details about de-domestication events. In this study, a high-quality genome (~376.4 Mb) of weedy rice A02 was assembled based on Nanopore ultra-long platform with a coverage depth of about 79.3× and 35,423 genes were predicted. Compared to Nipponbare genome, 5,574 structural variations (SVs) were found in A02. Based on super pan-genome graph, population SVs of 238 weedy rice and cultivated rice accessions were identified using public resequencing data. Furthermore, the de-domestication sites of weedy rice and domestication sites of wild rice were analyzed and compared based on SVs and single-nucleotide polymorphisms (SNPs). Interestingly, an average of 2,198 genes about de-domestication could only be found by F ST analysis based on SVs (SV- F ST ) in divergent region. Additionally, there was a low overlap between domestication and de-domestication intervals, which demonstrated that two different mechanisms existed in these events. Our finding could facilitate pinpointing of the evolutionary events that had shaped the genomic architecture of wild, cultivated, and weedy rice, and provide a good foundation for cloning of the superior alleles for breeding.F ST analysis based on SNPs (SNP- F ST ) in divergent region. Additionally, there was a low overlap between domestication and de-domestication intervals, which demonstrated that two different mechanisms existed in these events. Our finding could facilitate pinpointing of the evolutionary events that had shaped the genomic architecture of wild, cultivated, and weedy rice, and provide a good foundation for cloning of the superior alleles for breeding., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Ma, Wei, Yu, Lv, Zhang, Qian, Shang and Guo.)

The two independent domestication events in the genus Oryza that led to African and Asian rice offer an extremely useful system for studying the genetic basis of parallel evolution. This system is also characterized by parallel de-domestication events, with two genetically distinct weedy rice biotypes in the US derived from the Asian domesticate. One important trait that has been altered by rice domestication and de-domestication is hull colour. The wild progenitors of the two cultivated rice species have predominantly black-coloured hulls, as does one of the two U.S. weed biotypes; both cultivated species and one of the US weedy biotypes are characterized by straw-coloured hulls. Using Black hull 4 ( Bh4) as a hull colour candidate gene, we examined DNA sequence variation at this locus to study the parallel evolution of hull colour variation in the domesticated and weedy rice system. We find that independent Bh4-coding mutations have arisen in African and Asian rice that are correlated with the straw hull phenotype, suggesting that the same gene is responsible for parallel trait evolution. For the U.S. weeds, Bh4 haplotype sequences support current hypotheses on the phylogenetic relationship between the two biotypes and domesticated Asian rice; straw hull weeds are most similar to indica crops, and black hull weeds are most similar to aus crops. Tests for selection indicate that Asian crops and straw hull weeds deviate from neutrality at this gene, suggesting possible selection on Bh4 during both rice domestication and de-domestication. [ABSTRACT FROM AUTHOR]

The history of some invasive species is so complex that their origins can be difficult to determine. One example of such invasive species is the California invasive known as 'wild artichoke thistle' ( Cynara cardunculus var. sylvestris), found in natural and disturbed ecosystems. Wild artichoke thistle is a Mediterranean native and the progenitor of two domesticated horticultural taxa, artichoke and cardoon. Different hypotheses regarding the origins of California plants have included introductions by 19th century Italian immigrants and the de-domestication (evolutionary reversion to wild-type morphology) of feral (escaped, free-living) cultivars. Using microsatellite markers, we compared the genetic constitutions of 12 artichoke thistle populations in California with possible progenitor populations: 17 Spanish and Italian wild populations and eight different artichoke and cardoon cultivars. Each California population was compared with its putative progenitors using STRUCTURE analysis. Our results suggest that California's artichoke thistle populations are polyphyletic. Surprisingly, two-thirds of California's populations closely matched populations from the Iberian Peninsula. Three populations matched domesticated artichoke. One population appears to have wild and cultivar hybrid ancestry. Alleles specific to Italian populations were found at low frequencies in some California plants, suggesting that Italian wild plants may have been in California, but have left a trivial genetic legacy. Given that the de-domesticated plants in this study appear to be as invasive as the wild taxon, we conclude with a discussion of the role that ferality and de-domestication may have in plant invasions. [ABSTRACT FROM AUTHOR]

Culm color variation is an interesting phenomenon that contributes to the breeding of new varieties of ornamental plants during domestication. De-domesticated variation is considered ideal for identifying and interpreting the molecular mechanisms of plant mutations. However, the variation in culm color of bamboo remains unknown. In the present study, yellow and green culms generated from the same rhizome of Phyllostachys vivax cv. Aureocaulis ( P. vivax ) were used to elucidate the molecular mechanism of culm color formation. Phenotypic and physiological data showed that environmental suitability was higher in green culms than in yellow culms. High-throughput sequencing analysis showed 295 differentially expressed genes (DEGs) and 22 differentially expressed miRNAs (DEMs) in two different colored bamboo culms. There were 103 DEM-DEG interaction pairs, of which a representative "miRNA-mRNA" regulatory module involved in photosynthesis and pigment metabolism was formed by 14 DEM-DEG pairs. The interaction of the three key pairs was validated by qPCR and dual-luciferase assays. This study provides new insights into the molecular mechanism of miRNAs involved in P. vivax culm color formation, which provides evidence for plant de-domestication and is helpful for revealing the evolutionary mechanism of bamboo., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Zhu, Lou, Yang, Liu, Xiao, Li, Guo, Sun and Gao.)

Wild horses are becoming dependent on transitional environments between domesticity and wildness. In Dutch new nature areas they are learning to perform roles as ecological surrogates for their extinct ancestors. In the U.S. wild horses are 'feral' and exist in numbers deemed to be in excess of the carrying capacity of semi-arid public range lands. The federal government is removing and relocating thousands to long-term holding pastures. The capabilities approach of Nussbaum (2006) allows us to evaluate this transitional environment against a threshold of opportunities to exercise capabilities judged to be central to their flourishing as wild horses. [ABSTRACT FROM AUTHOR]

Rapid range expansions are becoming more prevalent, especially as climate continues to change. The escape of ornamental plants within their native range represents a significant, but often overlooked component of this process. Few studies have focused on the role of ornamental plants in range expansions using molecular markers to identify the possibility of mixed native and cultivar populations. The purpose of the present study was to determine the genetic variation of a native woody plant with ornamental conspecifics at the edge of its distribution. We selected Ilex aquifolium L. (English holly) which grows naturally in Denmark but is spreading eastward in Scandinavia, possibly due to a combination of climate change and introduction of more frost-tolerant cultivars. We sampled 187 individuals from older and recently established populations, and cultivated I. aquifolium throughout Denmark, and compared them using nuclear SSR and AFLP. The overall results showed no structure or clustering of plants from the historical or the expanding range, or of wild or cultivated plants. The only clusters found were for a group of cultivated hybrid I. aquifolium. The samples represented four genetic groupings, indicating either hybridization between cultivated and wild I. aquifolium or replacement of the latter by cultivars. Thus, ornamental genotypes of I. aquifolium contribute to the northeastern range expansion of the species and eventual invasiveness within its native range. [ABSTRACT FROM AUTHOR]

Weedy rice has been becoming a notorious weed in the paddy field of China in recent decades due to its increasing damage to rice yield and rice quality. In this study, a microsatellite technique with 21 pairs of SSR markers was utilized to estimate the genetic structure of two biotypes of weedy rice with Japonica and Indica rice characteristics, collected from Liaoning and Guangdong provinces, respectively. The genetic diversity of the weedy rice in the two provinces was relatively low (Liaoning h = 0.086; Guangdong h = 0.160), and distinctly large genetic differences existed between these two provinces ( Gcs = 0.623). The genetic diversity was found primarily within populations, and genetic differentiation was relatively low within the same province. Both cluster analysis (UPGMA) and principle component analysis (PCA) showed that weedy rice had a closer relationship with the cultivated rice collected from the sample field than with other cultivated rice and common wild rice varieties in China. Thus, the results of this study on samples from the Liaoning and Guangdong provinces in China support the de-domestication hypothesis that weedy rice most probably originated from local cultivated rice. [ABSTRACT FROM AUTHOR]

Weedy forms of crop species infest agricultural fields worldwide and are a leading cause of crop losses, yet little is known about how these weeds evolve. Red rice ( Oryza sativa), a major weed of cultivated rice fields in the US, is recognized by the dark-pigmented grain that gives it its common name. Studies using neutral molecular markers have indicated a close relationship between US red rice and domesticated rice, suggesting that the weed may have originated through reversion of domesticated rice to a feral form. We have tested this reversion hypothesis by examining molecular variation at Rc, the regulatory gene responsible for grain pigmentation differences between domesticated and wild rice. Loss-of-function mutations at Rc account for the absence of proanthocyanidin pigments in cultivated rice grains, and the major rc domestication allele has been shown to be capable of spontaneous reversion to a functional form through additional mutations at the Rc locus. Using a diverse sample of 156 weedy, domesticated and wild Oryzas, we analysed DNA sequence variation at Rc and its surrounding 4 Mb genomic region. We find that reversion of domestication alleles does not account for the pigmented grains of weed accessions; moreover, we find that haplotypes characterizing the weed are either absent or very rare in cultivated rice. Sequences from genomic regions flanking Rc are consistent with a genomic footprint of the rc selective sweep in cultivated rice, and they are compatible with a close relationship of red rice to Asian Oryzas that have never been cultivated in the US. [ABSTRACT FROM AUTHOR]

Abstract: The sunflower''s wild relative Helianthus annuus L. is a non-native invader in several regions of the world. It was introduced as an experimental forage plant in central Argentina six decades ago where it probably escaped and developed extended populations coexisting with the sunflower crop. If the invasive taxon was diffused without modifications, it would be expected to have phenotypic similarities with its parental sources. Nine populations representative of different geographic regions of central Argentina were compared with 17 populations from the USA (center of origin) in a common garden study at Bahía Blanca, Argentina using 47 phenotypic traits. The nine invasive wild populations were differentiated among themselves and from the native populations by plant form and life cycle traits, oil composition, inflorescence, and achene morphology. Populations from both continents shared traits related to domesticated sunflower, such as bract width over 0.8cm, but the frequency of this trait was higher in populations from Argentina. The high variability of wild H. annuus populations from Argentina did not reveal any founder effects. The diversity found in the invasive populations reflected about three-fourths of the phenotypic variability of those from the center of origin, even though the environmental conditions of the Argentine habitats represented only half of the variability present in the North American habitats. The current findings demonstrated that the invasive wild sunflower populations have developed within few decades a high degree of variability, which could be a source of a novel biodiversity useful as a genetic resource for sunflower crop improvement. [Copyright &y& Elsevier]

Red rice is an interfertile, weedy form of cultivated rice ( Oryza sativa L.) that competes aggressively with the crop in the southern US, reducing yields and contaminating harvests. No wild Oryza species occur in North America and the weed has been proposed to have evolved through multiple mechanisms, including “de-domestication” of US crop cultivars, accidental introduction of Asian weeds, and hybridization between US crops and Asian wild/weedy Oryza strains. The phenotype of US red rice ranges from “crop mimics”, which share some domestication traits with the crop, to strains closely resembling Asian wild Oryza species. Assessments of genetic diversity have indicated that many weed strains are closely related to Asian taxa (including indica and aus rice varieties, which have never been cultivated in the US, and the Asian crop progenitor O. rufipogon), whereas others show genetic similarity to the tropical japonica varieties cultivated in the southern US. Herein, we review what is known about the evolutionary origins and genetic diversity of US red rice and describe an ongoing research project to further characterize the evolutionary genomics of this aggressive weed. [ABSTRACT FROM AUTHOR]

• Accidental introduction of Peninsular Malaysian weedy rice has contributed partly to the weedy rice infestation in Sabah. • Population structure analysis revealed parallel evolution of Sabah wild-like weedy rice population. • Standing variations of local cultivars has facilitated de-domestication process, resulting in the occurrence of weedy rice. • Recent hybridization were detected in some weedy rice populations using genome wide single nucleotide polymorphisms. Weedy rice (Oryza spp.) is a major nuisance to rice farmers from all over the world. Although the emergence of weedy rice in East Malaysia on the island of Borneo is very recent, the threat to rice yield has reached an alarming stage. Using 47,027 genotyping-by-sequencing (GBS)-derived SNPs and candidate gene analysis of the plant architecture domestication gene TAC1 , we assessed the genetic variations and evolutionary origin of weedy rice in East Malaysia. Our findings revealed two major evolutionary paths for genetically distinct weedy rice types. Whilst the cultivar-like weedy rice are very likely to be the weedy descendant of local coexisting cultivars, the wild-like weedy rice appeared to have arisen through two possible routes: (i) accidental introduction from Peninsular Malaysia weedy rice populations, and (ii) weedy descendants of coexisting cultivars. The outcome of our genetic analyses supports the notion that Sabah cultivars and Peninsular Malaysia weedy rice are the potential progenitors of Sabah weedy rice. Similar TAC1 haplotypes were shared between Malaysian cultivated and weedy rice populations, which further supported the findings of our GBS-SNP analyses. These different strains of weedy rice have convergently evolved shared traits, such as seeds shattering and open tillers. A comparison with our previous simple-sequence repeat-based population genetic analyses highlights the strength of genome-wide SNPs, including detection of admixtures and low-level introgression events. These findings could inform better strategic management for controlling the spread of weedy rice in the region. [ABSTRACT FROM AUTHOR]

This article is a Commentary on Jiang et al., 224: 961–973. [ABSTRACT FROM AUTHOR]

The rice production system in Japan is changing due to the aging of rice farmers, shortage of labor, mechanization, and increase of large-scale rice fields and increased application of direct sowing, all of which contribute to the lack of sophisticated weed management practices. Because the changing production system has not improved and likely worsened weed management practices, weedy rice (Oryza sativa L.) has become a serious threat to rice production in Japan. We analyzed weedy rice accessions from Nagano, the central part of Japan, and other rice accessions to elucidate the origin of this weedy rice using a whole-genome single nucleotide polymorphism (SNP) array. For developing sustainable weedy rice management practices, the elucidation of the origin of re-emerging weedy rice is crucial. Population genetic analysis indicated that weedy rice in Nagano was phylogenetically independent from the local red rice cultivar with low genetic diversity. Past and recently re-emerging weedy rice ecotypes in Nagano shared a similar genetic background which implies the evolution of weedy rice by severe natural selection. Window-based FST and selection sweep analysis revealed the divergence of some of the known key domestication-related genes, such as shattering gene sh4 and qsh1, of weedy rice from domesticated rice cultivars. [ABSTRACT FROM AUTHOR]