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Thinopyrum elongatum is an important gene pool for wheat genetic improvement. However, the origins of the Thinopyrum genomes and the nature of the genus' intraspecific relationships are still controversial. In this study, we used single-copy nuclear genes and non-denaturing fluorescence in situ hybridization (NDFISH) to characterize genome constitution and chromosome differentiation in Th. elongatum. According to phylogenetic analyses based on PepC and Pgk1 genes, there was an E genome with three versions ([E.sup.e],[E.sup.b],[E.sup.x])and St genomes in the polyploid Th. elongatum. The ND-FISH results of pSc119.2 and pAs1 revealed that the karyotypes of diploid Th. elongatum and Th. bessarabicum were different, and the chromosome differentiation occurred among accessions of the diploid Th. elongatum. In addition, the tetraploid Th. elongatum has two groups of ND-FISH karyotype, indicating that the tetraploid Th. elongatum might be a segmental allotetraploid. In summary, our results suggested that the diploid Th. elongatum, Th. Bessarabicum,andPseudoroegneria were the donors of the [E.sup.e],[E.sup.b], and St genomes to the polyploid Th. elongatum, respectively. Key words: Thinopyrum elongatum,phylogeny,PepC, Pgk1,ND-FISH. Le Thinopyrum elongatum constitue une importante ressource genetique pour l'amelioration du ble. Cependant, les origines et la nature des relations intraspecifiques des genomes presents au sein du genre Thinopyrum demeurent controversees. Dans ce travail, les auteurs ont employe l'hybridation in situ en fluorescence en conditions non-denaturantes (ND-FISH), en utilisant des genes nucleaires a simple copie comme sondes, pour etudier la composition genomique et la differenciation chromosomique chez le Th. elongatum. Sur la base d'analyses phylogenetiques realisees a l'aide des genes PepC et PgK1, trois versions d'un genome E ([E.sup.e],[E.sup.b] et [E.sup.x]) et des genomes St ont ete documentes chez le Th. elongatum polyploide. Les resultats des analyses ND-FISH a l'aide des sondes pSc119.2 et pAs1 ont revele que les caryotypes des Th. elongatum et Th. bessarabicum diploides etaient differents et qu'une differentiation chromosomique existait au sein des accessions diploides du Th. elongatum. De plus, le Th. elongatum tetraploidepresentedeux sortesde caryotypesND-FISH,cequi indique que le Th. elongatum tetraploide pourrait etre un allotetraploide segmentaire. En resume, les resultats obtenus suggerent que les especes diploides Th. elongatum, Th. bessarabicum et Pseudoroegneria seraient respectivement a l'origine des genomes [E.sup.e],[E.sup.b] et St presents chez les especes polyploides du Th. elongatum.[Traduit par la Redaction] Mots-cles : Thinopyrum elongatum, phylogenie, PepC, Pgk1, ND-FISH., Introduction The genus Thinopyrum is a perennial herb in the Triticeae, but the taxonomic status of this genus has been changed many times. The species in Thinopyrum were first classified [...]

Increasing yield is an important goal of barley breeding. In this study, 54 papers published from 2001–2022 on QTL mapping for yield and yield-related traits in barley were collected, which contained 1080 QTLs mapped to the barley high-density consensus map for QTL meta-analysis. These initial QTLs were integrated into 85 meta-QTLs (MQTL) with a mean confidence interval (CI) of 2.76 cM, which was 7.86-fold narrower than the CI of the initial QTL. Among these 85 MQTLs, 68 MQTLs were validated in GWAS studies, and 25 breeder's MQTLs were screened from them. Seventeen barley orthologs of yield-related genes in rice and maize were identified within the hcMQTL region based on comparative genomics strategy and were presumed to be reliable candidates for controlling yield-related traits. The results of this study provide useful information for molecular marker-assisted breeding and candidate gene mining of yield-related traits in barley. [ABSTRACT FROM AUTHOR]

The role of lncRNA and circRNA in wheat grain development is still unclear. The objectives of this study were to characterize the lncRNA and circRNA in the wheat grain development and to construct the interaction network among lncRNA, circRNA, and their target miRNA to propose a lncRNA–circRNA–miRNA module related to wheat grain development. Full transcriptome sequencing on two wheat varieties (Annong 0942 and Anke 2005) with significant differences in 1000-grain weight at 10 d (days after pollination), 20 d, and 30 d of grain development were conducted. We detected 650, 736, and 609 differentially expressed lncRNA genes, and 769, 1054, and 1062 differentially expressed circRNA genes in the grains of 10 days, 20 days and 30 days after pollination between Annong 0942 and Anke 2005, respectively. An analysis of the lncRNA–miRNA and circRNA–miRNA targeting networks reveals that circRNAs exhibit a more complex and extensive interaction network in the development of cereal grains and the formation of grain shape. Central to these interactions are tae-miR1177, tae-miR1128, and tae-miR1130b-3p. In contrast, lncRNA genes only form a singular network centered around tae-miR1133 and tae-miR5175-5p when comparing between varieties. Further analysis is conducted on the underlying genes of all target miRNAs, we identified TaNF-YB1 targeted by tae-miR1122a and TaTGW-7B targeted by miR1130a as two pivotal regulatory genes in the development of wheat grains. The quantitative real-time PCR (qRT-PCR) and dual-luciferase reporter assays confirmed the target regulatory relationships between miR1130a-TaTGW-7B and miR1122a-TaNF-YB1. We propose a network of circRNA and miRNA-mediated gene regulation in the development of wheat grains. [ABSTRACT FROM AUTHOR]

The crop rhizosphere is the main site of soil microbial activities. Understanding the structure and diversity of microbial communities in the crop rhizosphere will help us reveal interactions between rhizosphere microorganisms and plant growth. In this study, the rhizosphere soil was collected from 35 cultivated barley varieties at the mature stage. To investigate the structure and diversity of bacterial communities in the rhizosphere of different barley varieties, the 16S rDNA gene of microorganisms from the soil was sequenced using Illumina MiSeq next-generation high-throughput sequencing technology. The results showed that 13, 25, 49, and 59 bacterial flora with relative abundance >1% were detected from 35 barley rhizosphere samples at the phylum, class, order, and family levels, respectively. The abundance of bacteria among varieties differed relatively little, but the abundance of the same bacteria in rhizospheres of different varieties was different. In addition, both the cluster analysis and principal component analysis (PCA) divided the 35 samples into three clusters at the phylum level. Groups III and IV showed significantly higher abundance than group II in Proteobacteria, while group II exhibited significantly higher abundance of Chloroflexi than groups III and IV. This finding provides a realistic basis for further using the relationship between barley rhizosphere microorganisms and barley growth to improve the resistance and quality of barley. [ABSTRACT FROM AUTHOR]

Abstract: Two single-copy nuclear genes, the second largest subunit of RNA polymerase II (RPB2) and thioredoxin-like gene (HTL), were used to explore the phylogeny and origin of polyploid species in [...]

Wheat grain development is an important biological process to determine grain yield and quality, which is controlled by the interplay of genetic, epigenetic, and environmental factors. Wheat grain development has been extensively characterized at the phenotypic and genetic levels. The advent of innovative molecular technologies allows us to characterize genes, proteins, and regulatory factors involved in wheat grain development, which have enhanced our understanding of the wheat seed development process. However, wheat is an allohexaploid with a large genome size, the molecular mechanisms underlying the wheat grain development have not been well understood as those in diploids. Understanding grain development, and how it is regulated, is of fundamental importance for improving grain yield and quality through conventional breeding or genetic engineering. Herein, we review the current discoveries on the molecular mechanisms underlying wheat grain development. Notably, only a handful of genes that control wheat grain development have, thus far, been well characterized, their interplay underlying the grain development remains elusive. The synergistic network-integrated genomics and epigenetics underlying wheat grain development and how the subgenome divergence dynamically and precisely regulates wheat grain development are unknown. [ABSTRACT FROM AUTHOR]

Polyploid species have played an essential role in plant evolution, exemplified by adaptive advantages to abiotic stress. N6-Methyladenosine (m6A) is suggested to play an important role in stress response. However, whether genome doubling affects m6A to increase autopolyploids stress tolerance is still unclear. This study aims to compare physiological (maintaining osmoregulatory homeostasis) and m6A changes between autotetraploid and diploid wild barley (Hordeum bulbosum) in response to salt (NaCl) stress. Results showed that autotetraploids physiologically had enhanced stress tolerance based on the measured parameters of relative water content, water loss, proline, H2O2, and chlorophyll. Diploid H. bulbosum experienced an excessive abundance of proline following salt stress where tetraploids had beneficial proline accumulation and thus enhanced osmoregulation. The significantly higher level of proline and H2O2 in diploid than in autotetraploid implies that diploids suffered higher osmotic stress than autotetraploid. Autotetraploid produced enough proline to protect stress, but not so much to cause toxicity. m6A in total RNA showed no significant difference between ploidies in controls, but was significantly higher in autotetraploids than in diploids during stress and recovery. These results suggest that increased m6A might be one of molecular mechanisms that increases salt tolerance in autotetraploid H. bulbosum compared to diploids, which enhances the adaptation of autopolyploids. [ABSTRACT FROM AUTHOR]

Spike morphology is a key characteristic in the study of barley genetics, breeding, and domestication. Variation at the six-rowed spike 1 (vrs1) locus is sufficient to control the development and fertility of the lateral spikelet of barley. To study the genetic variation of vrs1 in wild barley (Hordeum vulgare subsp. spontaneum) and cultivated barley (Hordeum vulgare subsp. vulgare), nucleotide sequences of vrs1 were examined in 84 wild barleys (including 10 six-rowed) and 20 cultivated barleys (including 10 six-rowed) from four populations. The length of the vrs1 sequence amplified was 1536 bp. A total of 40 haplotypes were identified in the four populations. The highest nucleotide diversity, haplotype diversity, and per-site nucleotide diversity were observed in the Southwest Asian wild barley population. The nucleotide diversity, number of haplotypes, haplotype diversity, and per-site nucleotide diversity in two-rowed barley were higher than those in six-rowed barley. The phylogenetic analysis of the vrs1 sequences partially separated the six-rowed and the two-rowed barley. The six-rowed barleys were divided into four groups. Key words: vrs1, nucleotide diversity, Hordeum vulgare. L'architecture de l'epi est un caractere cle pour l'etude de la genetique, de la selection et de la domestication chez l'orge. Les alleles au locus vrs1 controlent le developpement et la fecondite des epillets lateraux chez l'orge. Pour etudier la variation genetique au locus vrs1 chez l'orge sauvage (Hordeum vulgare subsp. spontaneum) et cultive (Hordeum vulgare subsp. vulgare), les sequences nucleotidiques de vrs1 ont ete determinees chez 84 orges sauvages (incluant 10 a six rangs) et 20 orges cultivees (dont 10 a six rangs) provenant de quatre populations. La sequence vrs1 amplifiee totalisait 1536 pb. Au total, 40 haplotypes ont ete identifies au sein des quatre populations. La plus grande diversite nucleotidique, haplotypique et nucleotidique par site a ete observee au sein des orges sauvages de l'Asie du Sud-Est. La diversite nucleotidique, le nombre d'haplotypes, la diversite haplotypique et la diversite nucleotidique par site etaient tous superieurs au sein des orges a deux rangs que parmi les orges a six rangs. Une analyse phylogenetique des sequences vrs1 a permis de separer partiellement les orges a six rangs des orges a deux rangs. Les orges a six rangs etaient subdivisees en quatre groupes. [Traduit par la Redaction] Mots-cles: vrs1, diversite nucleotidique, Hordeum vulgare., Introduction The barley spike is characterized by a triple spikelet meristem (one central and two lateral spikelets) at each rachis node (von Bothmer et al. 1985). Based on the central [...]

Evidence accumulated over the last decade has shown that allopolyploid genomes may undergo complex reticulate evolution. In this study, 13 accessions of tetraploid Elymus pendulinus were analyzed using two low-copy nuclear genes (RPB2 and PepC) and two regions of chloroplast genome (Rps16 and trnD-trnT). Previous studies suggested that Pseudoroegneria (St) and an unknown diploid (Y) were genome donors to E. pendulinus, and that Pseudoroegneria was the maternal donor. Our results revealed an extreme reticulate pattern, with at least four distinct gene lineages coexisting within this species that might be acquired through a possible combination of allotetraploidization and introgression from both within and outside the tribe Hordeeae. Chloroplast DNA data identified two potential maternal genome donors (Pseudoroegneria and an unknown species outside Hordeeae) to E. pendulinus. Nuclear gene data indicated that both Pseudoroegneria and an unknown Y diploid have contributed to the nuclear genome of E. pendulinus, in agreement with cytogenetic data. However, unexpected contributions from Hordeum and unknown aliens from within or outside Hordeeae to E. pendulinus without genome duplication were observed. Elymus pendulinus provides a remarkable instance of the previously unsuspected chimerical nature of some plant genomes and the resulting phylogenetic complexity produced by multiple historical reticulation events. Key words: Elymus pendulinus, allopolyploid, reticulate evolution, introgression, nuclear DNA, chloroplast DNA. Les evidences obtenues au fil de la derniere decennie ont montre que les genomes allopolyploides peuvent connaitre une evolution reticulee complexe. Dans ce travail, 13 accessions de l'Elymus pendulinus tetraploide ont ete etudiees en examinant deux genes nucleaires a faible nombre de copies (RPB2 et PepC) ainsi que deux regions du genome chloroplastique (Rps16 et trnD-trnT). Des etudes anterieures avaient suggere que les especes diploides sources des genomes chez l'E. pendulinus etaient Pseudoroegneria (genome St) et une autre espece inconnue (genome Y), et que le Pseudoroegneria avait ete le parent maternel. Les resultats de ce travail revelent une reticulation extreme avec au moins quatre lignages genetiques distincts coexistant au sein de cette espece, lesquels auraient pu survenir via une possible combinaison d allotetraploidisation et d introgression provenant de l'interieur et de l'exterieur des hordees. Les donnees chloroplastiques ont mis en evidence deux sources potentielles du genome maternel, soit le Pseudoroegneria et une espece inconnue hors des hordees. Les donnees nucleaires ont indique que deux especes, Pseudoroegneria et l espece diploide source du genome Y, auraient contribue au genome nucleaire de l E. pendulinus, conformement aux donnees cytogenetiques. Cependant, des contributions inattendues, sans duplication genomique, ont ete notees en provenance du genre Hordeum et d'especes additionnelles parmi les hordees et au-dela. L'E. pendulinus fournit ainsi un cas remarquable de la nature chimerique, jusque la insoupconnee, de certains genomes de plantes et de la complexite phylogenetique qui resulte de plusieurs evenements de reticulation. Mots-cles : Elymus pendulinus, allopolyploide, evolution reticulee, introgression, ADN nucleaire, ADN chloroplastique., Introduction Hybridization and polyploidization have contributed greatly to speciation (Cui et al. 2006). Numerous studies have indicated that almost all angiosperm species are of polyploid origin or have been affected [...]