Understanding the genetics of superior dough performance is essential for improving wheat end-use quality. Here we present a de novo assembly of the genome of JM44, a Chinese wheat cultivar known for its exceptional end-use quality. The JM44 genome achieved reference-level quality (with a quality value of 66.74), depicting a complete picture of complex regions containing gluten genes. Our microsynteny analysis across the Triticum-Aegilops complex showed that high-molecular-weight glutenin subunit loci are highly conserved, while low-molecular-weight glutenin subunits and α-/β-gliadins exhibited greater structural variation. These variable loci appear to have been preferentially selected by humans and contributed substantially to the evolution of wheat quality traits. Moreover, we observed that epistatic interactions between gluten genes are strong in modern cultivars but markedly weaker in landraces, indicating the importance of epistatic selection during modern breeding. Our findings shed light on the genomics and evolution of wheat quality traits, providing valuable guidance for future breeding efforts.

Chlorophyll content is a pivotal agronomic trait that directly determines photosynthetic efficiency and visual quality in tomato (Solanum lycopersicum). While positive regulators of chlorophyll biosynthesis have been extensively characterized, the mechanisms of its transcriptional repression remain less understood. Here, we report that the GRAS family transcription factor SlGRAS17 functions as a key negative regulator of chlorophyll accumulation in tomato. We isolated a high-chlorophyll mutant, hcm1, from an ethyl methanesulfonate (EMS)-mutagenized population and identified the causative lesion as a premature stop codon in SlGRAS17. Both CRISPR/Cas9-generated slgras17 mutants and the original hcm1 allele exhibited dark-green leaves with significantly elevated chlorophyll content, whereas SlGRAS17-overexpressing plants displayed a pale-green phenotype with reduced chlorophyll levels. We demonstrated that SlGRAS17 localizes to the nucleus and directly binds to a distal region of the GOLDEN-like 1 (SlGLK1) promoter to repress its transcription. Genetic evidence from virus-induced gene silencing confirmed that the high-chlorophyll phenotype of slgras17 mutants is dependent on SlGLK1. Furthermore, we elucidated that SlGRAS17 physically interacts with the transcriptional co-repressor SEUSS (SlSEU3), which in turn bridges the interaction with LEUNIG (SlLUG) in a configuration that is proposed to form a complex with repressive function. Genetic analyses revealed that SlLUG is essential for SlGRAS17-mediated repression, as loss of SlLUG abolished the repressive effect of SlGRAS17 overexpression on chlorophyll accumulation. Our study unveils a previously unidentified transcriptional regulatory module in which SlGRAS17 recruits the SlSEU3-SlLUG co-repressor complex to suppress SlGLK1 expression, thereby fine-tuning chlorophyll biosynthesis in tomato.

The gut microbial is shaped by host genetics and the environment factor, and may be associated with growth-related traits. In this study, 108 adult Qinghai Bamei pigs reared under identical conditions were analyzed to evaluate associations among mitochondrial haplotypes, gut microbiota, and growth-related traits. Haplotype based on mitochondrial DNA (mtDNA) D-loop variation identified six haplotypes, with haplotype diversity (Hd) and nucleotide diversity (Pi) values of 0.553 and 0.199

Drastic karyotype changes are a major evolutionary force, potentially involving centromere position, number, distribution, or strength alterations. Yet, the genetic and epigenetic landscape of centromeres, especially in allopolyploid plants during subgenome reshuffling, remains poorly understood. Here, we present a near-complete chromosome-scale genome assembly of the allotetraploid Pennisetum purpureum 'Purple', resolving all 14 centromeres. We find that subgenome-biased expansion of six LTR retrotransposons drives architectural divergence between subgenomes. Centromeric satellite repeats (CentPs) show rapid sequence divergence across subgenomes and chromosomes, with CENH3 preferentially binding conserved higher order repeats. Intriguingly, centromeric retrotransposons in Pennisetum (CRPs) are evolutionarily younger compared to their noncentromeric counterparts, coupled with marked subgenome B-biased amplification. Notably, CRP insertions flanking CentP satellites correlate with elevated satellite DNA polymorphism, supporting a model wherein CentP homogenization processes actively purge retrotransposons from centromeric arrays. Despite rapid sequence diversification of centromeric repeats, the epigenetic landscapes remain evolutionarily conserved in the centromeres of two subgenomes. Additionally, comparative analyses across Pennisetum species demonstrate rapid species- and chromosome-level turnover of CentPs and CRPs. Overall, our study illuminates the genetic and epigenetic plasticity of centromeres in allopolyploids, revealing how centromeric repeats adapt post-subgenome reshuffling.

Nitrogen balance is a major challenge for herbivores when consuming a low-nitrogen diet. Gut microbiota-mediated urea nitrogen recycling facilitates protein homeostasis during times of nitrogen deficiency, yet its relevance to wild nonhibernating small mammals remains unclear. Here, through a combination of isotope tracing, metagenomics, targeted short-chain fatty acid analysis, and fecal microbiota transplantation, we investigated the effects of protein restriction in winter on urea nitrogen recycling in plateau pikas (Ochotona curzoniae) of the Qinghai-Tibetan Plateau. Hepatic urea-cycle metabolism was downregulated during winter protein restriction, accompanied by increases in beneficial bacteria with ureolytic capacity (such as the genus Alistipes), gut urease activity, and urea transporters, and acetate production, with a consequent increase in nitrogen reincorporation into the pika's protein pool. Critically, supplementing a low-protein diet with yak fecal microbiota enhanced the ureolytic capacity by increasing Alistipes abundance, revealing a critical mechanism whereby interspecies horizontal microbial transfer between sympatric species enhances host protein homeostasis. Our results reveal a functional role for the gut microbiota in urea nitrogen recycling to maintain protein balance in winter-active herbivorous small mammals and contribute to our understanding of species coexistence and mammalian adaptation to high-altitude environments. Our findings establish that microbiota-driven urea nitrogen recycling is a key adaptive strategy for protein homeostasis in winter-active herbivores. This work provides new insights into the mechanisms of mammalian adaptation to high-altitude environments and the dynamics of interspecies coexistence.

The plateau pika (pl-pika), a resilient mammal of the Qinghai-Tibet Plateau, exhibits remarkable adaptations to extreme conditions. This study delves into mutations within the Endothelial PAS Domain Protein 1 (EPAS1) gene, crucial for high-altitude survival. Surprisingly, a novel 6-bp insertion/deletion (indel) mutation in EPAS1’s Intron 13, along with an additional repeat unit downstream, was discovered during PCR amplification. Genetic analysis across altitude gradients revealed a correlation between this indel’s frequency and altitude, hinting at its role in altitude adaptation. Fluorescence enzyme assays unveiled enhancer activity within Intron 13, where the deletion of repeat units led to increased activity, indicating potential transcription factor binding. Notably, GCM1 emerged as a candidate transcription factor binding to the indel site, suggesting its involvement in EPAS1 regulation. These findings enrich our comprehension of high-altitude adaptation in plateau pikas, shedding light on the intricate interplay between genetic mutations, transcriptional regulation, and environmental pressures in evolutionary biology.

Most winter-active mammals experience protein restriction. Gut microbiota is a key regulator of host energy homeostasis during nutrient deficiency, yet cross talk between microbiota and factors (e.g., hormones, signaling molecules) that regulate host energy metabolism in a low-protein (LP) context has not been studied sufficiently. The LP diet triggered the hepatic FGF21 adaptive metabolic pathway, which increased thermogenesis and reduced body weight, and this adaptive response was dependent on the composition and function of gut microbiota. Specifically, the LP diet induced a reshaping of the gut microbiota, altering its metabolic profile to increase deoxycholic acid levels and thereby increasing UCP1-induced thermogenesis of brown adipose tissue in an FGF21-dependent manner. Fecal transplantation with LP-associated microbiota increased thermogenesis through activation of GCN2-eIF2α-FGF21 signaling. Supplementation of the LP diet with yak fecal bacteria in plateau pika reduced UCP1-associated thermogenesis by altering the gut microbiome, decreasing deoxycholic acid production, suppressing activation of GCN2-eIF2α-FGF21 signaling, and alleviating LP-induced weight loss. Our study reveals an association between the gut microbiota and LP diet-associated regulation of FGF21 signaling and thermogenesis and further demonstrates that this relationship is influenced by interspecies microbial transfer, indicating a critical mechanism whereby horizontal microbial exchange between sympatric species enhances host energy homeostasis. These findings provide novel insights into our understanding of the adaptations of mammals to high-elevation environments.

Diet significantly influences gut microbiota composition. Grazing activities alter local vegetation communities, which in turn are related to changes in the availability of food resources for wildlife. However, the relationships between grazing and the dietary diversity and gut microbiota in subterranean rodents remain poorly understood. Using the plateau zokor (Eospalax baileyi) as a model species, chloroplast trnL and 16S rRNA gene sequencing were employed to characterize dietary composition and gastrointestinal microbial communities in zokors from grazing and non-grazing (control) areas. The analysis revealed significant differences in dietary diversity and composition of zokors between grazing and non-grazing areas. Meanwhile, the gastrointestinal microbial community diversity differed significantly between groups. Beneficial microbes (e.g., Lachnospiraceae and Christensenellaceae) showed higher abundance in the control group, while pathogenic Proteobacteria were enriched in the grazing groups. Notably, the complexity of stomach microbial co-occurrence networks increased in the grazing group, and functional differentiation of the gastrointestinal microbiota was observed between the control and grazing groups. Community assembly analysis displayed that stochastic processes dominated the assembly of stomach and gut microbiota, though these processes diminished in the grazing group, where divergent ecological processes emerged. Furthermore, we identified robust associations between zokor diets and stomach/gut microbiota, with specific microbial taxa significantly correlated with particular plants. Collectively, these findings highlight that grazing is associated with dietary changes and gut microbiota shifts in subterranean rodents, thereby advancing our understanding of the ecological impacts of grazing on terrestrial ecosystems.

Spike morphology is crucial for wheat (Triticum aestivum L.) yield and environmental adaptation. We developed a high-throughput phenotyping platform to dissect spike morphology traits based on 54 traits in 1,359 wheat accessions. These 54 spike morphology traits exhibited clear geographical differences among 306 worldwide accessions and breeding selection trend across different time windows for 1,053 accessions released from 1900 to 2020 in China. Based on geographical distribution and breeding selection of haplotypes, we attribute the differences in spike morphology to variable haplotype combinations. Wheat breeding breaks the trade-off between spike length and width/thickness, resulting in increased spike volume. A large proportion of genomic regions has been identified across wheat varieties and utilized as a fixed group to facilitate the targeted improvement and selection of desirable traits during wheat breeding programs. Overall, we provide a resource for the molecular design of spike morphology to facilitate future wheat breeding.

In eukaryotes, the mutation rate of the chloroplasts is lower than that of the nuclear genomes. Advances in Next-Generation Sequencing (NGS) and Third-Generation Sequencing (TGS) technologies, together with improvements in genome assembly algorithms, have substantially propelled research in chloroplast genomics. Although nearly 9,000 chloroplast genomes have been released, chloroplast population genetics for specific species remains unexplored. The chloroplast genome possesses a quadripartite structure consisting of a large single-copy (LSC) region, a small single-copy (SSC) region, and two inverted repeats (IRs). A longstanding question is why the maternally inherited chloroplast genome does not appear to suffer from the Muller’s ratchet effect. It has been hypothesized that intramolecular recombination within the chloroplast genome may counteract this effect; however, direct evidence for such recombination remains lacking. We conducted chloroplast population data analysis in hexaploid wheat and its ancestral relatives. One the basis of the pan-genome constructed and phylogeny analysis of chloroplast genomes of all samples, we calculated the chloroplast diversity of hexaploid wheat (π = 0.0001) is the lowest among the three ploidy types tested. Additionally, we found that during the formation of hexaploid wheat, only the chloroplasts from tetraploid wheat were inherited. Moreover, Aegilops tauschii contributed solely as the paternal provider of nuclear genome material. In the chloroplast genome assembly, we assembled IRa (inverted repeat A) and IRb (inverted repeat B), revealing multiple insertion/deletion sequence differences between them. Importantly, we discovered that recombination occurs between the IR regions of the chloroplast genome. Frequent recombination results in two structural configurations existing in nearly equal proportions within a single sample. This phenomenon has led to an increase in the nucleotide diversity of the chloroplast IR region within the wheat population, which was originally low among species in Poaceae. This study demonstrates the feasibility of assembling chloroplast genomes using low-depth whole-genome sequencing (WGS) and confirms that the chloroplast genome of hexaploid wheat originates from tetraploid wheat rather than Aegilops tauschii. Furthermore, we provide evidence of frequent intra-molecular recombination in the chloroplast IR regions, leading to the coexistence of two equimolar inversion isomers. Despite strong purifying selection, recombination increases genetic diversity within the IR regions, facilitating adaptation and maintaining the functional stability of essential genes. Our findings highlight the role of recombination in balancing genetic stability and flexibility in chloroplast genome evolution, offering new insights into nuclear-cytoplasmic interactions and polyploid adaptation.

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Over the past century, environmental changes have significantly impacted wheat spike morphology, crucial for adaptation and grain yield. However, the changes in wheat spike modifications during this period remain largely unknown. This study examines 16 spike morphology traits in 830 accessions released from 1900 to 2020. It finds that spike weight, grain number per spike (GN), and thousand kernel weight have significantly increased, while spike length has no significant change. The increase in fertile spikelets is due to fewer degenerated spikelets, resulting in a higher GN. Genome-wide association studies identified 49,994 significant SNPs, grouped into 293 genomic regions. The accumulation of favorable alleles in these genomic regions indicates the genetic basis for modification in spike morphology traits. Genetic network analysis of these genomic regions reveals the genetic basis for phenotypic correlations among spike morphology traits. The haplotypes of the identified genomic regions display obvious geographical differentiation in global accessions and environmental adaptation over the past 120 years. In summary, we reveal the genetic basis of adaptive evolution and the interactions of spike morphology, offering valuable resources for the genetic improvement of spike morphology to enhance environmental adaptation.

SUMMARYStructural variations (SVs) pervade plant genomes and contribute substantially to the phenotypic diversity. However, most SVs were ineffectively assayed due to their complex nature and the limitations of early genomic technologies. By applying the PacBio high‐fidelity (HiFi) sequencing for wheat genomes, we performed a comprehensive evaluation of mainstream long‐read aligners and SV callers in SV detection. The results indicated that the accuracy of deletion discovery is markedly influenced by callers, accounting for 87.73% of the variance, whereas both aligners (38.25%) and callers (49.32%) contributed substantially to the accuracy variance for insertions. Among the aligners, Winnowmap2 and NGMLR excelled in detecting deletions and insertions, respectively. For SV callers, SVIM achieved the best performance. We demonstrated that combining the aligners and callers mentioned above is optimal for SV detection. Furthermore, we evaluated the effect of sequencing depth on the accuracy of SV detection, revealing that low‐coverage HiFi sequencing is sufficiently robust for high‐quality SV discovery. This study thoroughly evaluated SV discovery approaches and established optimal workflows for investigating structural variations using low‐coverage HiFi sequencing in the wheat genome, which will advance SV discovery and decipher the biological functions of SVs in wheat and many other plants.

Plant height is a critical agronomic trait closely linked to yield, primarily regulated by Gibberellins (GA) and auxins, which interact in complex ways. However, the mechanism underlying their interactions remain incompletely understood. In this study, we identified a tomato mutant exhibiting significantly reduced plant height. Through gene cloning and bulked segregant analysis (BSA) sequencing, we found that the mutant gene corresponds to the tomato auxin response factor gene SlARF5/MP. Here, we show that overexpression of SlARF5/MP significantly enhances plant height. Additionally, treatment with GA3 restored the plant height of the mutant to wild-type (WT) levels, indicating that GA content is a key factor influencing plant height. We also observed significant upregulation of GA-biosynthesis genes, including GA2-oxidases GA20ox3 and GA20ox4, as well as the GA3 biosynthesis gene GA3ox1, in SlARF5-overexpressing plants. Furthermore, we demonstrated that SlARF5 directly binds to SlGA2ox3, which mediates the conversion of GA3 to inactive GA, therebyregulating its expression. Our findings suggest that SlARF5 modulates GA3 metabolism by regulating GA synthesis genes, ultimately leading to alterations in plant height.

Captivity is an important and efficient technique for rescuing endangered species. However, it induces infertility, and the underlying mechanism remains obscure. This study used the plateau pika (Ochotona curzoniae) as a model to integrate physiological, metagenomic, metabolomic, and transcriptome analyses and explore whether dysbiosis of the gut microbiota induced by artificial food exacerbates infertility in captive wild animals. Results revealed that captivity significantly decreased testosterone levels and the testicle weight/body weight ratio. RNA sequencing revealed abnormal gene expression profiles in the testicles of captive animals. The microbial α-diversity and Firmicutes/Bacteroidetes ratio were drastically decreased in the captivity group. Bacteroidetes and Muribaculaceae abundance notably increased in captive pikas. Metagenomic analysis revealed that the alteration of flora increased the capacity for carbohydrate degradation in captivity. The levels of microbe metabolites’ short-chain fatty acids (SCFAs) were significantly high in the captive group. Increasing SCFAs influenced the immune response of captivity plateau pikas; pro-inflammatory cytokines were upregulated in captivity. The inflammation ultimately contributed to male infertility. In addition, a positive correlation was observed between Gastranaerophilales family abundance and testosterone concentration. Our results provide evidence for the interactions between artificial food, the gut microbiota, and male infertility in pikas and benefit the application of gut microbiota interference in threatened and endangered species.

Dietary fiber (DF) is an important nutrient component in pig’s diet that remarkably influences their growth and slaughter performance. The ability of pigs to digest DF depends on the microbial composition of the intestinal tract, particularly in the hindgut. However, studies on how DF alters the growth and slaughter performance of pigs by shaping the gut microbial composition and metabolites are still limited. Therefore, this study aimed to investigate the effects of DF on microbial composition, functions, and metabolites, ultimately altering host growth and slaughter performance using Durco × Bamei crossbred pigs supplemented with 0%, 10%, 17%, and 24% broad bean silage in the basic diet. We found that the final weight, average daily gain, fat, and lean meat weight significantly decreased with increasing DF. Pigs with the lowest slaughter rate and fat weight were observed in the 24% fiber-supplemented group. Gut microbial communities with the highest alpha diversity were formed in the 17% fiber group. The relative abundance of fiber-degrading bacteria, bile acid, and succinate-producing bacteria, including Prevotella sp., Bacteroides sp., Ruminococcus sp., and Parabacteroides sp., and functional pathways, including the butanoate metabolism and the tricarboxylic acid [TCA] cycle, significantly increased in the high-fiber groups. The concentrations of several bile acids significantly decreased in the fiber-supplemented groups, whereas the concentrations of succinate and long-chain fatty acids increased. Our results indicate that a high-fiber diet may alter the growth and slaughter performance of Durco × Bamei crossbred pigs by modulating the composition of Prevotella sp., Bacteroides sp., Ruminococcus sp., Parabacteroides sp., and metabolite pathways of bile acids and succinate.

The RNA-Seq technology was used to screen the key genes that affect the early development of the testes of Duroc × Landrace × Yorkshire piglets, to determine the regulatory pathway and provide reference for subsequent reproductive performance research, breeding, and other production practices. This study selected 14-day-old Duroc × Landrace × Yorkshire piglets as the trial animals. Testes from piglets with similar weights and no pathological changes were divided into small testis (ST) and large testis (LT) groups, and the RNA-Seq screening of differentially expressed genes (DEGs) was performed to find candidate genes and regulatory pathways related to early testicular development. The results show that 570 DEGs were found in the ST and LT groups, with 281 upregulated and 289 downregulated. The DEGs were mainly enriched on 47 gene ontology (GO) functional items. The Kyoto encyclopedia of genes and genotypes (KEGG) enrichment analysis found that there were 44 significantly enriched KEGG signal pathways, and the regulation of testicular development mainly focused on the arachidonic acid metabolism, Wnt signaling pathway and GnRH secretion pathways. The PTGES, SFRP1, SPP1, PLA2G4E, KCNJ5, PTGS2, and HCN1 genes were found to be as closely related to the testicular development of these Duroc × Landrace × Yorkshire piglets, and the differential gene expression was consistent with the real-time quantitative reverse transcription PCR (real-time qRT-PCR) validation results. This study was validated by high-throughput sequencing analysis and real-time qRT-PCR, and showed that the PTGES, SFRP1, SPP1, PLA2G4E, KCNJ5, PTGS2, and HCN1 genes may be involved in the regulation of germ cell development, spermatogenesis and semen traits. These should be further studied as candidate genes for early testicular development and reproductive trait regulation in boars.

ABSTRACT Differentiation of the gut microbiota between individuals within a species can be identified by enterotypes. However, whether different enterotypes are associated with host-related physiological status and adaptation to specific habitats is still poorly understood. In this study, we collected 308 cecal samples from plateau pikas during varying seasons and altitudes. We identified three bacterial and two fungal enterotypes. The proportion of Rikenellaceae_RC9_gut_group- and Prevotella-predominated enterotype 3 was higher than that of the other two enterotypes in all samples. Enterotype 1, distinguished by norank Muribaculaceae, was mainly detected during the warm season and at high altitudes, whereas enterotype 2, which is unclassified Lachnospiraceae, was mainly detected during the cold season. Plateau pikas with bacterial enterotypes 2 and 3 showed significantly higher alpha diversity than those with enterotype 1, while pikas with fungal enterotype 1 displayed higher diversity than those with enterotype 2. Functional pathways of lipid metabolism were enriched in bacterial enterotype 1, carbohydrate and amino acid metabolism were enriched in enterotype 2, and energy metabolism was enriched in enterotype 3. The neutral process was more important in bacterial enterotype 3 than in enterotypes 1 and 2. The body temperature and resting metabolic rate of pikas with bacterial enterotypes 1 and 3 were significantly higher than those with enterotype 2. Pikas with unclassified Sporormiaceae- and Sporormiella-dominated fungal enterotypes may engage more frequently in coprophagy. Overall, this study revealed that both gut bacterial and fungal communities in pikas can be clustered into enterotypes, and individuals with different enterotypes showed significant differences in thermogenesis. IMPORTANCE The gut microbiotas of small mammals play an important role in host energy homeostasis. However, it is still unknown whether small mammals with different enterotypes show differences in thermogenesis characteristics. Our study confirmed that plateau pikas with different bacterial enterotypes harbored distinct thermogenesis capabilities and employed various strategies against cold environments. Additionally, we also found that pikas with different fungal enterotypes may display differences in coprophagy.

Deep knowledge of crop biodiversity is essential to improving global food security. Despite bread wheat serving as a keystone crop worldwide, the population history of bread wheat and its relatives, both cultivated and wild, remains elusive. By analysing whole-genome sequences of 795 wheat accessions, we found that bread wheat originated from the southwest coast of the Caspian Sea and underwent a slow speciation process, lasting ~3,300 yr owing to persistent gene flow from its relatives. Soon after, bread wheat spread across Eurasia and reached Europe, South Asia and East Asia ~7,000 to ~5,000 yr ago, shaping a diversified but occasionally convergent adaptive landscape in novel environments. By contrast, the cultivated relatives of bread wheat experienced a population decline by ~82% over the past ~2,000 yr due to the food choice shift of humans. Further biogeographical modelling predicted a continued population shrinking of many bread wheat relatives in the coming decades because of their vulnerability to the changing climate. These findings will guide future efforts in protecting and utilizing wheat biodiversity to enhance global wheat production.

Roots are the main organs through which plants absorb water and nutrients. As the key phytohormone involved in root growth, auxin functions in plant environmental responses by modulating auxin synthesis, distribution and polar transport. The Arabidopsis thaliana trehalose-6-phosphate phosphatase gene AtTPPI can improve root architecture, and tppi1 mutants have significantly shortened primary roots. However, the mechanism underlying the short roots of the tppi1 mutant and the upstream signaling pathway and downstream genes regulated by AtTPPI are unclear. Here, we demonstrated that the AtTPPI gene could promote auxin accumulation in AtTPPI-overexpressing plants. By comparing the transcriptomic data of tppi1 and wild-type roots, we found several upregulations of auxin-related genes, including GH3.3, GH3.9 and GH3.12, may play an important role in the AtTPPI gene-mediated auxin transport signaling pathway, ultimately leading to changes in auxin content and primary root length. Moreover, increased AtTPPI expression can regulate primary root growth and lateral root elongation under different concentration of nitrate conditions. Overall, constitutive expression of AtTPPI increased auxin contents and improved lateral root elongation, constituting a new method for improving the nitrogen utilization efficiency of plants.