Genome-editing of a circadian clock gene TaPRR95 facilitates wheat peduncle growth and heading date.

Plant height and heading date are important agronomic traits in wheat (Triticum aestivum L.) that affect final grain yield. In wheat, knowledge of pseudo-response regulator (PRR) genes on agronomic traits is limited. Here, we identify a wheat TaPRR95 gene by genome-wide association study to be associated with plant height. Triple allele mutant plants produced by CRISPR/Cas9 show increased plant height, particularly the peduncle, with an earlier heading date. The longer peduncle is mainly caused by the increased cell elongation at its upper section, whilst the early heading date is accompanied by elevated expression of flowering genes, such as TaFT and TaCO1. A peduncle-specific transcriptome analysis reveals up-regulated photosynthesis genes and down-regulated IAA/Aux genes for auxin signaling in prr95aabbdd plants that may act as a regulatory mechanism to promote robust plant growth. A haplotype analysis identifies a TaPRR95-B haplotype (Hap2) to be closely associated with reduced plant height and increased thousand-grain weight. Moreover, the Hap2 frequency is higher in cultivars than that in landraces, suggesting the artificial selection on the allele during wheat breeding. These findings suggest that TaPRR95 is a regulator for plant height and heading date, thereby providing an important target for wheat yield improvement.

Comprehensive Comparative Analysis of the JAZ Gene Family in Common Wheat (Triticum aestivum) and Its D-Subgenome Donor Aegilops tauschii.

JASMONATE-ZIM DOMAIN (JAZ) repressor proteins work as co-receptors in the jasmonic acid (JA) signalling pathway and are essential for plant development and environmental adaptation. Despite wheat being one of the main staple food crops, until recently, comprehensive analysis of its JAZ gene family has been limited due to the lack of complete and high-quality reference genomes. Here, using the latest reference genome, we identified 17 JAZ genes in the wheat D-genome donor Aegilops tauschii. Then, 54 TaJAZs were identified in common wheat. A systematic examination of the gene structures, conserved protein domains, and phylogenetic relationships of this gene family was performed. Five new JAZ genes were identified as being derived from tandem duplication after wheat divergence from other species. We integrated RNA-seq data and yield QTL information and found that tandemly duplicated TaJAZ genes were prone to association with spike-related traits. Moreover, 12 TaJAZ genes were located within breeding selection sweeps, including 9 tandemly duplicated ones. Haplotype variation analysis of selected JAZ genes showed significant association of TaJAZ7A and TaJAZ13A with thousand-grain weight. Our work provides a clearer picture of wheat JAZ gene evolution and puts forward the possibility of using these genes for wheat yield improvement.

Grain yield improvement by genome editing of TaARF12 that decoupled peduncle and rachis development trajectories via differential regulation of gibberellin signalling in wheat.

Plant breeding is constrained by trade-offs among different agronomic traits by the pleiotropic nature of many genes. Genes that contribute to two or more favourable traits with no penalty on yield are rarely reported, especially in wheat. Here, we describe the editing of a wheat auxin response factor TaARF12 by using CRISPR/Cas9 that rendered shorter plant height with larger spikes. Changes in plant architecture enhanced grain number per spike up to 14.7% with significantly higher thousand-grain weight and up to 11.1% of yield increase under field trials. Weighted Gene Co-Expression Network Analysis (WGCNA) of spatial-temporal transcriptome profiles revealed two hub genes: RhtL1, a DELLA domain-free Rht-1 paralog, which was up-regulated in peduncle, and TaNGR5, an organ size regulator that was up-regulated in rachis, in taarf12 plants. The up-regulation of RhtL1 in peduncle suggested the repression of GA signalling, whereas up-regulation of TaNGR5 in spike may promote GA response, a working model supported by differential expression patterns of GA biogenesis genes in the two tissues. Thus, TaARF12 complemented plant height reduction with larger spikes that gave higher grain yield. Manipulation of TaARF12 may represent a new strategy in trait pyramiding for yield improvement in wheat.

Biodegradation of Aflatoxin B1 in the Baijiu Brewing Process by Bacillus cereus.

Aflatoxin is a potent mycotoxin and a common source of grain contamination that leads to great economic losses and health problems. Although distilled baijiu cannot be contaminated by aflatoxin, its presence in the brewing process affects the physiological activities of micro-organisms and reduces product quality. Bacillus cereus XSWW9 capable of degrading aflatoxin B1 (AFB1) was isolated from daqu using coumarin as the sole carbon source. XSWW9 degraded 86.7% of 1 mg/L AFB1 after incubation at 37 °C for 72 h and tolerated up to 1 mg/L AFB1 with no inhibitory effects. Enzymes in the cell-free supernatant of XSSW9 played a significant role in AFB1 degradation. The AFB1-degradation activity was sensitive to protease K and SDS treatment, which indicated that extracellular proteins were responsible for the degradation of AFB1. In order to investigate the AFB1-degradation ability of XSSW9 during the baijiu brewing process, AFB1 and XSWW9 were added to grain fermentation (FG-T) and normal grain fermentation without AFB1, while normal grain fermentation without AFB1 and XSWW9 was used as a control (FG-C). At the end of the fermentation, 99% AFB1 was degraded in the residue of fermented grains. The differences of microbial communities in the fermented grains showed that there were no significant differences between FG-T and FG-C in the relative abundance of dominant genera. The analysis of volatile compounds of their distillation showed that the contents of skeleton flavor components was similar between FG-T and FG-C. These results offer a basis for the development of effective strategies to reduce the effect of AFB1 on the brewing process and ensure that the production of baijiu is stable.

An RCT study showing few weeks of music lessons enhance audio-visual temporal processing.

Music involves different senses and is emotional in nature, and musicians show enhanced detection of audio-visual temporal discrepancies and emotion recognition compared to non-musicians. However, whether musical training produces these enhanced abilities or if they are innate within musicians remains unclear. Thirty-one adult participants were randomly assigned to a music training, music listening, or control group who all completed a one-hour session per week for 11 weeks. The music training group received piano training, the music listening group listened to the same music, and the control group did their homework. Measures of audio-visual temporal discrepancy, facial expression recognition, autistic traits, depression, anxiety, stress and mood were completed and compared from the beginning to end of training. ANOVA results revealed that only the music training group showed a significant improvement in detection of audio-visual temporal discrepancies compared to the other groups for both stimuli (flash-beep and face-voice). However, music training did not improve emotion recognition from facial expressions compared to the control group, while it did reduce the levels of depression, stress and anxiety compared to baseline. This RCT study provides the first evidence of a causal effect of music training on improved audio-visual perception that goes beyond the music domain.

InDels Identification and Association Analysis with Spike and Awn Length in Chinese Wheat Mini-Core Collection.

Diversity surveys of germplasm are important for gaining insight into the genomic basis for crop improvement; especially InDels, which are poorly understood in hexaploid common wheat. Here, we describe a map of 89,923 InDels from exome sequencing of 262 accessions of a Chinese wheat mini-core collection. Population structure analysis, principal component analysis and selective sweep analysis between landraces and cultivars were performed. Further genome-wide association study (GWAS) identified five QTL (Quantitative Trait Loci) that were associated with spike length, two of them, on chromosomes 2B and 6A, were detected in 10 phenotypic data sets. Assisted with RNA-seq data, we identified 14 and 21 genes, respectively that expressed in spike and rachis within the two QTL regions that can be further investigated for candidate genes discovery. Moreover, InDels were found to be associated with awn length on chromosomes 5A, 6B and 4A, which overlapped with previously reported genetic loci B1 (Tipped 1), B2 (Tipped 2) and Hd (Hooded). One of the genes TaAGL6 that was previously shown to affect floral organ development was found at the B2 locus to affect awn length development. Our study shows that trait-associated InDels may contribute to wheat improvement and may be valuable molecular markers for future wheat breeding.

A Multi-Omics Approach for Rapid Identification of Large Genomic Lesions at the Wheat Dense Spike (wds) Locus.

Optimal spike architecture provides a favorable structure for grain development and yield improvement. However, the number of genes cloned to underlie wheat spike architecture is extremely limited. Here, we obtained a wheat dense spike mutant (wds) induced by 60Co treatment of a common wheat landrace Huangfangzhu that exhibited significantly reduced spike and grain lengths. The shortened spike length was caused by longitudinal reduction in number and length of rachis cells. We adopted a multi-omics approach to identify the genomic locus underlying the wds mutant. We performed Exome Capture Sequencing (ECS) and identified two large deletion segments, named 6BL.1 at 334.8∼424.3 Mb and 6BL.2, 579.4∼717.8 Mb in the wds mutant. RNA-seq analysis confirmed that genes located in these regions lost their RNA expression. We then found that the 6BL.2 locus was overlapping with a known spike length QTL, qSL6B.2. Totally, 499 genes were located within the deleted region and two of them were found to be positively correlated with long spike accessions but not the ones with short spike. One of them, TraesCS6B01G334600, a well-matched homolog of the rice OsBUL1 gene that works in the Brassinosteroids (BR) pathway, was identified to be involved in cell size and number regulation. Further transcriptome analysis of young spikes showed that hormone-related genes were enriched among differentially expressed genes, supporting TraesCS6B01G334600 as a candidate gene. Our work provides a strategy to rapid locate genetic loci with large genomic lesions in wheat and useful resources for future wheat study.

Serum immune responses in common carp (Cyprinus carpio L.) to paraquat exposure: The traditional parameters and circulating microRNAs.

Paraquat (PQ) is a herbicide used worldwide, and it was shown to be a high-risk compound to aquatic organisms. This study was conducted to investigate the effects of PQ on traditional serum parameters and circulating microRNAs (miRNAs) in common carp to further elucidate the mechanism of PQ toxicity in fish. In the current study, a subacute toxicity test of common carp exposed to PQ at 1.596 and 3.192 mg/L for 7 d was conducted under laboratory conditions. The results showed that PQ exposure generally reduced the levels of T-AOC, SOD, CAT, and GST, but significantly increased MDA levels in the serum, indicating that PQ exposure induces oxidative stress and lipid peroxidation in the fish. The results of biochemical assays showed that PQ exposure not only significantly altered the activities of LDH, AST, ALT, ACP, AKP, and lysozyme and the contents of IgM and complement 3 but also promoted the expression of pro-inflammatory cytokines, including IFN-γ, IL-1ß, IL-6, IL-8, and TNF-α. Additionally, PQ inhibited the levels of the anti-inflammatory cytokines IL-10 and TGF-ß, suggesting that PQ exposure may cause fish tissue injury and promote immune inflammatory responses. Furthermore, we found that serum circulating miRNAs, such as ccr-mir-122, ccr-mir-125b, ccr-mir-146a, and ccr-mir-155, were generally promoted in fish following PQ exposure. Based on our results and reports on miRNA-based diagnosis of tissue damage and inflammatory responses in mammals, we suggest that serum ccr-mir-122, ccr-mir-125b, ccr-mir-146a, and ccr-mir-155 could be new biomarkers of PQ toxicity in fish.