N6-methyladenosine-modified CircPSMA7 enhances bladder cancer malignancy through the miR-128-3p/MAPK1 axis.

Several studies have indicated that circular RNAs (circRNAs) play vital roles in the progression of various diseases, including bladder cancer (BCa). However, the underlying mechanisms by which circRNAs drive BCa malignancy remain unclear. In this study, we identified a novel circRNA, circPSMA7 (circbaseID:has_circ_0003456), showing increased expression in BCa cell lines and tissues, by integrating the reported information with circRNA-seq and qRT-PCR. We revealed that circPSMA7 is associated with a higher tumor grade and stage in BCa. M6A modification was identified in circPSMA7, and IGF2BP3 recognized this modification and stabilized circPSMA7, subsequently increasing the circPSMA7 expression. In vitro and in vivo experiments showed that circPSMA7 promoted BCa proliferation and metastasis by regulating the cell cycle and EMT processes. CircPSMA7 acted as a sponge for miR-128-3p, which showed antitumor effects in BCa cell lines, increasing the expression of MAPK1. The tumor proliferation and metastasis suppression induced by silencing circPSMA7 could be partly reversed by miR-128-3p inhibition. Thus, the METTL3/IGF2BP3/circPSMA7/miR-128-3p/MAPK1 axis plays a critical role in BCa progression. Furthermore, circPSMA7 may be a potential diagnostic biomarker and novel therapeutic target for patients with BCa.

The influence of prostate volume on pathological outcomes after radical prostatectomy: A single-center retrospective study.

Currently, the association between prostate volume (PV) or prostate weight with pathological outcomes in patients with prostate cancer (PCa) is not well understood. This study aimed to explore whether PV can predict the adverse pathological outcomes of PCa patients after radical prostatectomy (RP). A total of 1063 men with confirmed localized PCa who underwent RP at the First Affiliated Hospital of Zhejiang University from January 2014 to April 2019 were retrospectively analyzed. Patients were assigned into small, medium and large groups based on the PV. The analysis of variance, χ2 test or Student t test was performed to compare differences among groups. Univariate and multivariate analyses were performed to identify significant predictors of pathological outcomes upgrading. Among the 1063 cases, approximately 35.0% had an upgrade of postoperative pathology. Compared with the small prostate group, more patients in the large prostate group achieved a Gleason score (GS) 6 and International Society of Urological Pathology (ISUP) grade 1 of postoperative pathological findings, clinical cT1c and cT2a stages and pathological pT2a and pT2b stages; the incidence of positive surgical margins and extraprostatic extension was relatively low (all P < .001). In multiple logistic regression, PV served as a significant predictor of any Gleason score upgrading (GSU) (odds ratio [OR] 0.988, 95% confidence interval [CI] 0.978-0.998), major GSU (OR 0.980, 95% CI 0.965-0.995) and any ISUP grade group upgrading (GGU) (OR 0.989, 95% CI 0.979-0.999). This study shows that PV can predict adverse pathological outcomes in PCa patients after radical prostatectomy. Pca patients with smaller prostate volume tend to have the high-grade disease at postoperative pathology as well as pathological outcome upgrading.

FTO promotes clear cell renal cell carcinoma progression via upregulation of PDK1 through an m6A dependent pathway.

FTO, as an m6A mRNA demethylase, is involved in various cancers. However, the role of FTO in clear cell renal cell carcinoma (ccRCC) remains unclear. In the present study, we discovered FTO is upregulated in ccRCC. Functionally, knockdown of FTO significantly impairs the proliferation and migration ability of ccRCC cells. Mechanistically, our data suggest FTO promotes the proliferation and migration of ccRCC through preventing degradation of PDK1 mRNA induced by YTHDF2 in an m6A-dependent mechanism. Overall, our results identify the protumorigenic role of FTO through the m6A/YTHDF2/PDK1 pathway, which could be a promising therapeutic target for ccRCC.

Whole-genome resequencing of the wheat A subgenome progenitor Triticum urartu provides insights into its demographic history and geographic adaptation.

Triticum urartu is the progenitor of the A subgenome in tetraploid and hexaploid wheat. Uncovering the landscape of genetic variations in T. urartu will help us understand the evolutionary and polyploid characteristics of wheat. Here, we investigated the population genomics of T. urartu by genome-wide sequencing of 59 representative accessions collected around the world. A total of 42.2 million high-quality single-nucleotide polymorphisms and 3 million insertions and deletions were obtained by mapping reads to the reference genome. The ancient T. urartu population experienced a significant reduction in effective population size (Ne) from ∼3 000 000 to ∼140 000 and subsequently split into eastern Mediterranean coastal and Mesopotamian-Transcaucasian populations during the Younger Dryas period. A map of allelic drift paths displayed splits and mixtures between different geographic groups, and a strong genetic drift towards hexaploid wheat was also observed, indicating that the direct donor of the A subgenome originated from northwestern Syria. Genetic changes were revealed between the eastern Mediterranean coastal and Mesopotamian-Transcaucasian populations in genes orthologous to those regulating plant development and stress responses. A genome-wide association study identified two single-nucleotide polymorphisms in the exonic regions of the SEMI-DWARF 37 ortholog that corresponded to the different T. urartu ecotype groups. Our study provides novel insights into the origin and genetic legacy of the A subgenome in polyploid wheat and contributes a gene repertoire for genomics-enabled improvements in wheat breeding.

SMAD3 and FTO are involved in miR-5581-3p-mediated inhibition of cell migration and proliferation in bladder cancer.

Previous research evidence suggests that microRNAs (miRNAs) play an indispensable role in onset and progression of bladder cancer (BCa). Here, we explored the functions and mechanisms of miR-5581-3p in BCa. miR-5581-3p, as a tumor suppressor in BCa, was detected at a lower expression level in BCa tissue and cells in contrast with the non-malignant bladder tissue and cells. Over-expression of miR-5581-3p remarkably dampened the migration and proliferation of BCa in vitro and in vivo. SMAD3 and FTO were identified as the direct targets of miR-5581-3p by online databases prediction and mRNA-seq, which were further verified. SMAD3 as a star molecule in modulating EMT progress of BCa had been formulated in former studies. Meanwhile, FTO proved as an N6-methyladenosine (m6A) demethylase in decreasing m6A modification was confirmed to regulate the migration and proliferation in BCa. In addition, we conducted rescue experiments and confirmed overexpressing miR-5581-3p partially rescued the effects of the overexpressing SMAD3 and FTO in BCa cells. In conclusion, our studies exhibit that miR-5581-3p is a novel tumor inhibitor of BCa.

circKDM4C enhances bladder cancer invasion and metastasis through miR-200bc-3p/ZEB1 axis.

Circular RNAs (circRNAs) play essential roles in human bladder cancer (BCa) development, however, unusual expression patterns and functional dysfunction of circRNAs in BCa have not been evaluated. In this study, we validated that circKDM4C (hsa_circ_0001839), derived from the KDM4C gene, is elevated in BCa cell lines as well as tissues. Functionally, overexpression of circKDM4C significantly enhances, and silencing of circKDM4C suppresses migration and invasion capabilities of BCa cells. Mechanistically, circKDM4C can directly interact with miR-200b-3p and miR-200c-3p as a miRNA sponge, which enhances the expression of ZEB1 and promotes mesenchymal phenotype. Conclusively, our findings indicate that circKDM4C may act as a pro-oncogenic factor in BCa invasion and metastasis via the circKDM4C/miR-200bc-3p/ZEB1 axis, which is a potential biomarker or therapeutic target for bladder cancer.

Genome-wide identification of seed storage protein gene regulators in wheat through coexpression analysis.

Only a few transcriptional regulators of seed storage protein (SSP) genes have been identified in common wheat (Triticum aestivum L.). Coexpression analysis could be an efficient approach to characterize novel transcriptional regulators at the genome-scale considering the correlated expression between transcriptional regulators and target genes. As the A genome donor of common wheat, Triticum urartu is more suitable for coexpression analysis than common wheat considering the diploid genome and single gene copy. In this work, the transcriptome dynamics in endosperm of T. urartu throughout grain filling were revealed by RNA-Seq analysis. In the coexpression analysis, a total of 71 transcription factors (TFs) from 23 families were found to be coexpressed with SSP genes. Among these TFs, TuNAC77 enhanced the transcription of SSP genes by binding to cis-elements distributed in promoters. The homolog of TuNAC77 in common wheat, TaNAC77, shared an identical function, and the total SSPs were reduced by about 24% in common wheat when TaNAC77 was knocked down. This is the first genome-wide identification of transcriptional regulators of SSP genes in wheat, and the newly characterized transcriptional regulators will undoubtedly expand our knowledge of the transcriptional regulation of SSP synthesis.

Conditional survival of metastatic clear cell renal cell carcinoma: How prognosis evolves after cytoreductive surgery of primary tumor.

INTRODUCTION: Cytoreductive surgery is one of the recommended treatments for metastatic renal cell carcinoma, while the prognostic information of these patients treated with cytoreductive surgery is limited. In this study, we aimed to investigate the survival profiles based on conditional survival (CS) estimates in metastatic clear cell renal cell carcinoma (mccRCC) patients treated with cytoreductive surgery of primary tumor. METHODS AND MATERIALS: We identified and extracted mccRCC patients from the Surveillance, Epidemiology, and End Results database. We used Kaplan-Meier method to perform CS analyses. A multivariate Cox regression model was applied to explore the changes of well-known prognostic factors. RESULTS: Conditional overall survival (COS) and conditional cancer-specific survival (CCSS) improved increasingly at all periods of survivorships compared to survival estimates at baseline in overall population of mccRCC. The 36-month COS improved by 3.3%-6.4% given per 12 additional months of survivorships and the CCSS improved significantly from 45.1% (95% CI 42.8-47.3) at 12 months to 67.1% (95% CI 62.0-71.7) at 60 months. Much more survival gain was observed in patients with advanced disease. Furthermore, the prognostic significance of age and pathological factors diminished and even disappeared in a long-term survivorship. CONCLUSIONS: Conditional overall survival and CCSS improved with time dynamically in mccRCC patients treated with cytoreductive surgery of primary tumor. Patients with advanced disease achieved significant survival gain and even could harvest a better prognosis given that the time of survivorship exceeds a certain period. Our findings could provide valuable and practical data for patient counseling and surveillance strategy making.

Genetic Mapping of ms1s, a Recessive Gene for Male Sterility in Common Wheat.

The utilization of heterosis is an important way to improve wheat yield, and the production of wheat hybrid seeds mainly relies on male-sterile lines. Male sterility in line 15 Fan 03 derived from a cross of 72,180 and Xiaoyan 6 is controlled by a single recessive gene. The gene was mapped to the distal region of chromosome 4BS in a genetic interval of 1.4 cM and physical distance of 6.57 Mb between SSR markers Ms4BS42 and Ms4BS199 using an F2 population with 1205 individuals. Sterile individuals had a deletion of 4.57 Mb in the region presumed to carry the Ms1 locus. The allele for sterility was therefore named ms1s. Three CAPS markers were developed and verified from the region upstream of the deleted fragment and can be used for ms1s marker-assisted selection in wheat hybrid breeding. This work will enrich the utilization of male sterility genetic resources.

Characterization of the Mitochondrial Genome of a Wheat AL-Type Male Sterility Line and the Candidate CMS Gene.

Heterosis utilization is very important in hybrid seed production. An AL-type cytoplasmic male sterile (CMS) line has been used in wheat-hybrid seed production, but its sterility mechanism has not been explored. In the present study, we sequenced and verified the candidate CMS gene in the AL-type sterile line (AL18A) and its maintainer line (AL18B). In the late uni-nucleate stage, the tapetum cells of AL18A showed delayed programmed cell death (PCD) and termination of microspore at the bi-nucleate stage. As compared to AL18B, the AL18A line produced 100% aborted pollens. The mitochondrial genomes of AL18A and AL18B were sequenced using the next generation sequencing such as Hiseq and PacBio. It was found that the mitochondrial genome of AL18A had 99% similarity with that of Triticum timopheevii, AL18B was identical to that of Triticum aestivum cv. Chinese Yumai. Based on transmembrane structure prediction, 12 orfs were selected as candidate CMS genes, including a previously suggested orf256. Only the lines harboring orf279 showed sterility in the transgenic Arabidopsis system, indicating that orf279 is the CMS gene in the AL-type wheat CMS lines. These results provide a theoretical basis and data support to further analyze the mechanism of AL-type cytoplasmic male sterility in wheat.

Upregulation of ARNTL2 is associated with poor survival and immune infiltration in clear cell renal cell carcinoma.

BACKGROUND: Aryl hydrocarbon receptor nuclear translocator like 2 (ARNTL2) is a member of the PAS superfamily. Previous studies explored the carcinogenic roles of transcription factor ARNTL2 in human malignancies. However, its roles in ccRCC have not been elucidated. This study sought to explore the roles of ARNTL2 in ccRCC and determine its correlations with tumor immunity. METHODS: The expression of ARNTL2 was analyzed using the GEO, TCGA and GTEx database, and verified in ccRCC tissue samples and cell lines by qRT-PCR and western blot analysis. Kaplan-Meier survival curve analysis, Cox regression analysis (including univariate and multivariate analysis) was utilized to evaluate the prognostic values of ARNTL2. Potential biological mechanisms of ARNTL2 were explored using GSEA method. Colony formation and wound healing assays were conducted to explore the oncogenic role of ARNTL2 in ccRCC. ssGSEA and xCell algorithm were used to explore the correlation between ARNTL2 expression and tumor immune microenvironment (TIME). RESULTS: ARNTL2 was significantly upregulated in ccRCC tissues and cell lines compared to normal kidney tissues and cell line. Enhanced expression of ARNTL2 was strongly linked to advanced clinical stage and unfavorable overall survival in ccRCC. ARNTL2 was determined as an independent prognostic marker through cox regression analysis. A prognostic nomogram was constructed to predict 1-, 3- and 5-year overall survival of ccRCC patients by integrating ARNTL2 expression with other clinicopathologic variables. GSEA analysis showed that focal adhesion, T cell receptor, cell cycle, and JAK-STAT signaling pathway were significantly enriched in high ARNTL2 samples. Silencing of ARNTL2 suppressed the colony formation ability and wound healing efficacy of ccRCC cell lines. xCell analysis showed that high expression level of ARNTL2 exhibited an immune infiltration status similar to CD8 + inflamed ccRCC subtype, which was characterized by high infiltration level of CD8 + T cell and high expression level of the immune escape biomarkers such as PD-L1, PD-L2, PD1 and CTLA4. CONCLUSION: ARNTL2 is an independent adverse predictor of ccRCC patient survival. High expression level of ARNTL2 is associated with immune infiltration, and may be a novel therapeutic target in ccRCC.

The MYB family transcription factor TuODORANT1 from Triticum urartu and the homolog TaODORANT1 from Triticum aestivum inhibit seed storage protein synthesis in wheat.

Seed storage proteins (SSPs) are determinants of wheat end-product quality. SSP synthesis is mainly regulated at the transcriptional level. Few transcriptional regulators of SSP synthesis have been identified in wheat and this study aims to identify novel SSP gene regulators. Here, the R2R3 MYB transcription factor TuODORANT1 from Triticum urartu was found to be preferentially expressed in the developing endosperm during grain filling. In common wheat (Triticum aestivum) overexpressing TuODORANT1, the transcription levels of all the SSP genes tested by RNA-Seq analysis were reduced by 49.71% throughout grain filling, which contributed to 13.38%-35.60% declines in the total SSP levels of mature grains. In in vitro assays, TuODORANT1 inhibited both the promoter activities and the transcription of SSP genes by 1- to 13-fold. The electrophoretic mobility shift assay (EMSA) and ChIP-qPCR analysis demonstrated that TuODORANT1 bound to the cis-elements 5'-T/CAACCA-3' and 5'-T/CAACT/AG-3' in SSP gene promoters both in vitro and in vivo. Similarly, the homolog TaODORANT1 in common wheat hindered both the promoter activities and the transcription of SSP genes by 1- to 112-fold in vitro. Knockdown of TaODORANT1 in common wheat led to 14.73%-232.78% increases in the transcription of the tested SSP genes, which contributed to 11.43%-19.35% elevation in the total SSP levels. Our data show that both TuODORANT1 and TaODORANT1 are repressors of SSP synthesis.

Effects of fluorescent light cystoscopy in non-muscle-invasive bladder cancer: A systematic review and meta-analysis.

BACKGROUND: The benefits of fluorescent light (FL) cystoscopy with 5-aminolevulinic acid (5-ALA) or hexaminolevulinate (HAL) in non-muscle-invasive bladder cancer (NMIBC) have been mentioned in many trials. Meanwhile, several problems need to be addressed such as the rate of residual disease following these procedures. OBJECTIVE: To assess the effects of FL cystoscopy compared with white light (WL) cystoscopy on the rate of residual Ta, T1, and carcinoma in situ (CIS) tumors, recurrence-free survival (RFS) and progression-free survival (PFS). METHODS: A search in the databases PubMed, Embase, the Cochrane Library, China National Knowledge Infrastructure (CNKI) and China Biology Medicine (CBM) was undertaken. Studies were included if their outcomes included the residual tumor rate, PFS or RFS. The data was analyzed by REVMAN 5.3 and STATA 14.0. RESULTS: The residual tumor rate of the FL group was lower than that of the WL group (relative risk [RR] 0.42; 95 % confidence interval [CI] 0.26-0.80; P = 0.007), which was consistent with the residual Ta rate (RR 0.44; 95 % CI 0.28-0.69; P = 0.0004), the residual T1 rate (RR 0.42; 95 % CI 0.21-0.83; P = 0.01) and the residual CIS rate (RR 0.39; 95 % CI 0.19-0.80; P = 0.01). RFS at the 12-month follow-up (RR 1.15; 95 % CI 1.08-1.28; P = 0.0002) and 24-month follow-up (RR 1.26; 95 % CI 1.17-1.35; P < 0.00001) in the FL group was significantly higher than that in the WL group. However, no statistically significant differences were found in PFS at the 12-month follow-up (RR 1.01; 95 % CI 0.99-1.03; P = 0.17) or 24-month follow-up (RR 1.00; 95 % CI 0.97-1.03; P = 0.95). CONCLUSION: FL cystoscopy was related to a reduced residual tumor rate compared with WL cystoscopy in NMIBC, which was also consistent with the Ta, T1 and residual CIS rates. RFS was higher in patients with FL cystoscopy at the 12- to 24-month follow-up.

Combined Transcriptome and Proteome Analysis of Anthers of AL-type Cytoplasmic Male Sterile Line and Its Maintainer Line Reveals New Insights into Mechanism of Male Sterility in Common Wheat.

Cytoplasmic male sterility (CMS) plays an essential role in hybrid seeds production. In wheat, orf279 was reported as a CMS gene of AL-type male sterile line (AL18A), but its sterility mechanism is still unclear. Therefore, transcriptomic and proteomic analyses of the anthers of AL18A and its maintainer line (AL18B) were performed to interpret the sterility mechanism. Results showed that the electron transport chain and ROS scavenging enzyme expression levels changed in the early stages of the anther development. Biological processes, i.e., fatty acid synthesis, lipid transport, and polysaccharide metabolism, were abnormal, resulting in pollen abortion in AL18A. In addition, we identified several critical regulatory genes related to anther development through combined analysis of transcriptome and proteome. Most of the genes were enzymes or transcription factors, and 63 were partially homologous to the reported genic male sterile (GMS) genes. This study provides a new perspective of the sterility mechanism of AL18A and lays a foundation to study the functional genes of anther development.

A novel NAC family transcription factor SPR suppresses seed storage protein synthesis in wheat.

The synthesis of seed storage protein (SSP) is mainly regulated at the transcriptional level. However, few transcriptional regulators of SSP synthesis have been characterized in common wheat (Triticum aestivum) owing to the complex genome. As the A genome donor of common wheat, Triticum urartu could be an elite model in wheat research considering its simple genome. Here, a novel NAC family transcription factor TuSPR from T. urartu was found preferentially expressed in developing endosperm during grain-filling stages. In common wheat transgenically overexpressing TuSPR, the content of total SSPs was reduced by c. 15.97% attributed to the transcription declines of SSP genes. Both in vitro and in vivo assays showed that TuSPR bound to the cis-element 5'-CANNTG-3' distributed in SSP gene promoters and suppressed the transcription. The homolog in common wheat TaSPR shared a conserved function with TuSPR on SSP synthesis suppression. The knock-down of TaSPR in common wheat resulted in 7.07%-20.34% increases in the total SSPs. Both TuSPR and TaSPR could be superior targets in genetic engineering to manipulate SSP content in wheat, and this work undoubtedly expands our knowledge of SSP gene regulation.

TaCKX gene family, at large, is associated with thousand-grain weight and plant height in common wheat.

KEY MESSAGE: We used SMRT sequencing and explored the haplotypes of TaCKX genes, linked with thousand-grain weight and plant height, and developed the functionally validated markers, which can be used in the marker-assisted breeding program. Cytokinin oxidase/dehydrogenase (CKX) enzymes catalyze the permanent degradation of cytokinins. Identification of the TaCKX alleles associated with yield traits and the development of functional markers is the first step in using these alleles in marker-assisted breeding program. To identify the alleles, we sequenced the genome fragments, containing TaCKX genes from 48 wheat genotypes, by PacBio® sequencing. Six out of 22 TaCKX genes were found polymorphic, forming 14 distinct haplotypes. Functional markers were developed and validated for all the polymorphic TaCKX genes. Four specific haplotypes, i.e., TaCKX2A_2, TaCKX4A_2, TaCKX5A_3, and TaCKX9A_2, were found significantly associated with high thousand-grain weight (TGW) and short plant height (PH) in Chinese wheat micro-core collection (MCC) and GWAS open population (GWAS-OP), whereas TaCKX1B_2 in GWAS-OP and TaCKX11A_3 in MCC were significantly associated with high TGW and short PH. The mean values of TGW and PH for cumulative favorable haplotypes from chromosome 3A, i.e., TaCKX2A_2, TaCKX4A_2, and TaCKX5A_3, were significantly higher as compared to the cumulative unfavored haplotypes, and the change was additive in manner. Frequency distribution analysis revealed that since the 1960s, the frequency of the favorable haplotypes and TGW has gradually increased in Chinese wheat cultivars. Expression profiling in the seed tissue excised at 2, 4, 6, and 8 days after anthesis depicted that the favorable haplotypes are significantly less expressive as compared to the unfavored haplotypes. We conclude that the functional markers developed in this study can be used to select the favorable haplotypes of TaCKX genes in wheat marker-assisted breeding programs.

TubZIP28, a novel bZIP family transcription factor from Triticum urartu, and TabZIP28, its homologue from Triticum aestivum, enhance starch synthesis in wheat.

Starch in wheat grain provides humans with carbohydrates and influences the quality of wheaten food. However, no transcriptional regulator of starch synthesis has been identified first in common wheat (Triticum aestivum) due to the complex genome. Here, a novel basic leucine zipper (bZIP) family transcription factor TubZIP28 was found to be preferentially expressed in the endosperm throughout grain-filling stages in Triticum urartu, the A genome donor of common wheat. When TubZIP28 was overexpressed in common wheat, the total starch content increased by c. 4%, which contributed to c. 5% increase in the thousand kernel weight. The grain weight per plant of overexpression wheat was also elevated by c. 9%. Both in vitro and in vivo assays showed that TubZIP28 bound to the promoter of cytosolic AGPase and enhanced both the transcription and activity of the latter. Knockout of the homologue TabZIP28 in common wheat resulted in declines of both the transcription and activity of cytosolic AGPase in developing endosperms and c. 4% reduction of the total starch in mature grains. To the best of our knowledge, TubZIP28 and TabZIP28 are transcriptional activators of starch synthesis first identified in wheat, and they could be superior targets to improve the starch content and yield potential of wheat.

Natural variations in the promoter of Awn Length Inhibitor 1 (ALI-1) are associated with awn elongation and grain length in common wheat.

Wheat awn plays a vital role in photosynthesis, grain production, and drought tolerance. However, the systematic identification or cloning of genes controlling wheat awn development is seldom reported. Here, we conducted a genome-wide association study (GWAS) with 364 wheat accessions and identified 26 loci involved in awn length development, including previously characterized B1, B2, Hd, and several rice homologs. The dominant awn suppressor B1 was fine mapped to a 125-kb physical interval, and a C2 H2 zinc finger protein Awn Length Inhibitor 1 (ALI-1) was confirmed to be the underlying gene of the B1 locus through the functional complimentary test with native awnless allele. ALI-1 expresses predominantly in the developing spike of awnless individuals, transcriptionally suppressing downstream genes. ALI-1 reduces cytokinin content and simultaneously restrains cytokinin signal transduction, leading to a stagnation of cell proliferation and reduction of cell numbers during awn development. Polymorphisms of four single nucleotide polymorphisms (SNPs) located in ALI-1 promoter region are diagnostic for the B1/b1 genotypes, and these SNPs are associated with awn length (AL), grain length (GL) and thousand-grain weight (TGW). More importantly, ali-1 was observed to increase grain length in wheat, which is a valuable attribute of awn on grain weight, aside from photosynthesis. Therefore, ALI-1 pleiotropically regulates awn and grain development, providing an alternative for grain yield improvement and addressing future climate changes.

Unraveling the genetic architecture of grain size in einkorn wheat through linkage and homology mapping and transcriptomic profiling.

Understanding the genetic architecture of grain size is a prerequisite to manipulating grain development and improving the potential crop yield. In this study, we conducted a whole genome-wide quantitative trait locus (QTL) mapping of grain-size-related traits by constructing a high-density genetic map using 109 recombinant inbred lines of einkorn wheat. We explored the candidate genes underlying QTLs through homologous analysis and RNA sequencing. The high-density genetic map spanned 1873 cM and contained 9937 single nucleotide polymorphism markers assigned to 1551 bins on seven chromosomes. Strong collinearity and high genome coverage of this map were revealed by comparison with physical maps of wheat and barley. Six grain size-related traits were surveyed in five environments. In total, 42 QTLs were identified; these were assigned to 17 genomic regions on six chromosomes and accounted for 52.3-66.7% of the phenotypic variation. Thirty homologous genes involved in grain development were located in 12 regions. RNA sequencing identified 4959 genes differentially expressed between the two parental lines. Twenty differentially expressed genes involved in grain size development and starch biosynthesis were mapped to nine regions that contained 26 QTLs, indicating that the starch biosynthesis pathway plays a vital role in grain development in einkorn wheat. This study provides new insights into the genetic architecture of grain size in einkorn wheat; identification of the underlying genes enables understanding of grain development and wheat genetic improvement. Furthermore, the map facilitates quantitative trait mapping, map-based cloning, genome assembly, and comparative genomics in wheat taxa.

A wheat dominant dwarfing line with Rht12, which reduces stem cell length and affects gibberellic acid synthesis, is a 5AL terminal deletion line.

Dwarfing and semi-dwarfing are important agronomic traits that have great potential for the improvement of wheat yields. Rht12, a dominant gibberellic acid (GA)-responsive dwarfing gene from the gamma-ray-induced wheat mutant Karcagi 522M7K, is located in the long arm of chromosome 5A, which is closely linked with the locus Xwmc410. Rht12 is likely an ideal gene for GA biosynthesis and deactivation research in common wheat. However, information on the Rht12 locus and sequence is lacking. In this study, Rht12 significantly shortened stem cell length and decreased GA biosynthetic components. Using bulked segregant RNA-Seq, wheat 660k single nucleotide polymorphism chip detection, and newly developed simple sequence repeat markers, Rht12 was mapped to a 11.21-Mb region at the terminal end of chromosome 5AL, and was found to be closely linked with the Xw5ac207SSR marker with a 10.73-Mb fragment deletion in all of the homologous dwarfing plants. Transcriptome analyses of the remaining 483-kb region showed significantly higher expression of the TraesCS5A01G543100 gene encoding the GA metabolic enzyme GA 2-ß-dioxygenase in dwarfing plants than in high stalk plants, suggesting that Rht12 reduces plant height by activating TaGA2ox-A14. Taken together, our findings will promote cloning and functional studies of Rht12 in common wheat.