Long-read sequencing of 111 rice genomes reveals significantly larger pan-genomes.

The concept of pan-genome, which is the collection of all genomes from a population, has shown a great potential in genomics study, especially for crop sciences. The rice pan-genome constructed from the second-generation sequencing (SGS) data is about 270 Mb larger than Nipponbare, the rice reference genome (NipRG), but it is still disadvantaged by incompleteness and loss of genomic contexts. The third-generation sequencing (TGS) with long reads can help to construct better pan-genomes. In this paper, we report a high-quality rice pan-genome construction method by introducing a series of new steps to deal with the long-read data, including unmapped sequence block filtering, redundancy removing, and sequence block elongating. Compared to NipRG, the long-read sequencing-based pan-genome constructed from 105 rice accessions, which contains 604 Mb novel sequences, is much more comprehensive than the one constructed from ∼3000 rice genomes sequenced with short reads. The repetitive sequences are the main components of novel sequences, which partially explain the differences between the pan-genomes based on TGS and SGS. Adding six wild rice accessions, there are about 879 Mb novel sequences and 19,000 novel genes in the rice pan-genome in total. In addition, we have created high-quality reference genomes for all representative rice populations, including five gapless reference genomes. This study has made significant progress in our understanding of the rice pan-genome, and this pan-genome construction method for long-read data can be applied to accelerate a broad range of genomics studies.

PPanG: a precision pangenome browser enabling nucleotide-level analysis of genomic variations in individual genomes and their graph-based pangenome.

Graph-based pangenome is gaining more popularity than linear pangenome because it stores more comprehensive information of variations. However, traditional linear genome browser has its own advantages, especially the tremendous resources accumulated historically. With the fast-growing number of individual genomes and their annotations available, the demand for a genome browser to visualize genome annotation for many individuals together with a graph-based pangenome is getting higher and higher. Here we report a new pangenome browser PPanG, a precise pangenome browser enabling nucleotide-level comparison of individual genome annotations together with a graph-based pangenome. Nine rice genomes with annotations were provided by default as potential references, and any individual genome can be selected as the reference. Our pangenome browser provides unprecedented insights on genome variations at different levels from base to gene, and reveals how the structures of a gene could differ for individuals. PPanG can be applied to any species with multiple individual genomes available and it is available at https://cgm.sjtu.edu.cn/PPanG .

All-trans retinoic acid plus low-dose rituximab vs low-dose rituximab in corticosteroid-resistant or relapsed ITP.

The study aimed to compare the efficacy and safety of all-trans retinoic acid (ATRA) plus low-dose rituximab (LD-RTX) with LD-RTX monotherapy in corticosteroid-resistant or relapsed immune thrombocytopenia (ITP) patients. Recruited patients were randomized at a ratio of 2:1 into 2 groups: 112 patients received LD-RTX plus ATRA, and 56 patients received LD-RTX monotherapy. Overall response (OR), defined as achieving a platelet count of ≥30 × 109/L confirmed on ≥2 separate occasions (≥7 days apart), at least a doubling of the baseline platelet count without any other ITP-specific treatment, and the absence of bleeding within 1 year after enrollment, was observed in more patients in the LD-RTX plus ATRA group (80%) than in the LD-RTX monotherapy group (59%) (between-group difference, 0.22; 95% CI, 0.07-0.36). Sustained response (SR), defined as maintenance of a platelet count >30 × 109/L, an absence of bleeding, and no requirement for any other ITP-specific treatment for 6 consecutive months after achievement of OR during 1 year following enrollment, was achieved by 68 (61%) patients in the combination group and 23 (41%) patients in the monotherapy group (between-group difference, 0.20; 95% CI, 0.04-0.35). The 2 most common adverse events (AEs) for the combination group were dry skin and headache or dizziness. Our findings demonstrated that ATRA plus LD-RTX significantly increased the overall and sustained response, indicating a promising treatment option for corticosteroid-resistant or relapsed adult ITP. This study is registered at www.clinicaltrials.gov as #NCT03304288.

Reciprocal adaptation of rice and Xanthomonas oryzae pv. oryzae: cross-species 2D GWAS reveals the underlying genetics.

A 1D/2D genome-wide association study strategy was adopted to investigate the genetic systems underlying the reciprocal adaptation of rice (Oryza sativa) and its bacterial pathogen, Xanthomonas oryzae pv. oryzae (Xoo) using the whole-genome sequencing and large-scale phenotyping data of 701 rice accessions and 23 diverse Xoo strains. Forty-seven Xoo virulence-related genes and 318 rice quantitative resistance genes (QR-genes) mainly located in 41 genomic regions, and genome-wide interactions between the detected virulence-related genes and QR genes were identified, including well-known resistance genes/virulence genes plus many previously uncharacterized ones. The relationship between rice and Xoo was characterized by strong differentiation among Xoo races corresponding to the subspecific differentiation of rice, by strong shifts toward increased resistance/virulence of rice/Xoo populations and by rich genetic diversity at the detected rice QR-genes and Xoo virulence genes, and by genome-wide interactions between many rice QR-genes and Xoo virulence genes in a multiple-to-multiple manner, presumably resulting either from direct protein-protein interactions or from genetic epistasis. The observed complex genetic interaction system between rice and Xoo likely exists in other crop-pathogen systems that would maintain high levels of diversity at their QR-loci/virulence-loci, resulting in dynamic coevolutionary consequences during their reciprocal adaptation.

miR-206 alleviates LPS-induced inflammatory injury in cardiomyocytes via directly targeting USP33 to inhibit the JAK2/STAT3 signaling pathway.

Previous reports have confirmed that miR-206 participates in inflammatory cardiomyopathy, but its definite mechanism remains elusive. This study aims to elucidate the potential mechanism of miR-206 in septic cardiomyopathy (SCM). The primary mouse cardiomyocytes were isolated and exposed to lipopolysaccharides (LPS) to construct a septic injury model in vitro. Then, the gene transcripts and protein levels were detected by RT-qPCR and/or Western blot assay. Cell proliferation, apoptosis, and inflammatory responses were evaluated by CCK-8/EdU, flow cytometry, and ELISA assays, respectively. Dual luciferase assay, Co-IP, and ubiquitination experiments were carried out to validate the molecular interactions among miR-206, USP33, and JAK2/STAT3 signaling. miR-206 was significantly downregulated, but USP33 was upregulated in LPS-induced cardiomyocytes. Gain-of-function of miR-206 elevated the proliferation but suppressed the inflammatory responses and apoptosis in LPS-induced cardiomyocytes. USP33, as a member of the USP protein family, was confirmed to be a direct target of miR-206 and could catalyze deubiquitination of JAK2 to activate JAK2/STAT3 signaling. Rescue experiments presented that neither upregulation of USP33 nor JAK2/STAT3 signaling activation considerably reversed the protective effects of miR-206 upregulation in LPS-induced cardiomyocytes. The above data showed that miR-206 protected cardiomyocytes from LPS-induced inflammatory injuries by targeting the USP33/JAK2/STAT3 signaling pathway, which might be a novel target for SCM treatment.

Genomic variation in 3,010 diverse accessions of Asian cultivated rice.

Here we analyse genetic variation, population structure and diversity among 3,010 diverse Asian cultivated rice (Oryza sativa L.) genomes from the 3,000 Rice Genomes Project. Our results are consistent with the five major groups previously recognized, but also suggest several unreported subpopulations that correlate with geographic location. We identified 29 million single nucleotide polymorphisms, 2.4 million small indels and over 90,000 structural variations that contribute to within- and between-population variation. Using pan-genome analyses, we identified more than 10,000 novel full-length protein-coding genes and a high number of presence-absence variations. The complex patterns of introgression observed in domestication genes are consistent with multiple independent rice domestication events. The public availability of data from the 3,000 Rice Genomes Project provides a resource for rice genomics research and breeding.

Prediction of the bioaccessibility and accumulation of cadmium in the soil-rice-human system based on optimized DGT and BCR coupled models.

Cadmium, as a typical heavy metal, has the potential to induce soil pollution and threaten human health through the soil-plant-human pathway. The conventional evaluation method based on the total content in soil cannot accurately represent the content migrated from the food chain to plants and the human body. Previous studies focused on the process of plant enrichment of heavy metals in soil, and very few studies directly predicted human exposure or risk through the labile state of Cd in soil. Hence, a relatively accurate and convenient prediction model of Cd release and translocation in the soil-rice-human system was developed. This model utilizes available Cd and soil parameters to predict the bioavailability of Cd in soil, as well as the in vitro bioaccessibility of Cd in cooked rice. The bioavailability of Cd was determined by the Diffusive Gradients in Thin-films technology and BCR sequential extraction procedure, offering in-situ quantification, which presents a significant advantage over traditional monitoring methods and aligns closely with the actual uptake of heavy metals by plants. The experimental results show that the prediction model based on the concentration of heavy metal forms measured by BCR sequential extraction procedure and diffusive gradients in thin-films technique can accurately predict the Cd uptake in rice grains, gastric and gastrointestinal phase (R2=0.712, 0.600 and 0.629). This model accurately predicts Cd bioavailability and bioaccessibility across the soil-rice-human pathway, informing actual human Cd intake, offering scientific support for developing more effective risk assessment methods.

Combined genome-wide association study and epistasis analysis reveal multifaceted genetic architectures of plant height in Asian cultivated rice.

Plant height (PH) in rice (Oryza sativa) is an important trait for its adaptation and agricultural performance. Discovery of the semi-dwarf1 (SD1) mutation initiated the Green Revolution, boosting rice yield and fitness, but the underlying genetic regulation of PH in rice remains largely unknown. Here, we performed genome-wide association study (GWAS) and identified 12 non-repetitive QTL/genes regulating PH variation in 619 Asian cultivated rice accessions. One of these was an SD1 structural variant, not normally detected in standard GWAS analyses. Given the strong effect of SD1 on PH, we also divided 619 accessions into subgroups harbouring distinct SD1 haplotypes, and found a further 85 QTL/genes for PH, revealing genetic heterogeneity that may be missed by analysing a broad, diverse population. Moreover, we uncovered two epistatic interaction networks of PH-associated QTL/genes in the japonica (Geng)-dominant SD1NIP subgroup. In one of them, the hub QTL/gene qphSN1.4/GAMYB interacted with qphSN3.1/OsINO80, qphSN3.4/HD16/EL1, qphSN6.2/LOC_Os06g11130, and qphSN10.2/MADS56. Sequence variations in GAMYB and MADS56 were associated with their expression levels and PH variations, and MADS56 was shown to physically interact with MADS57 to coregulate expression of gibberellin (GA) metabolic genes OsGA2ox3 and Elongated Uppermost Internode1 (EUI1). Our study uncovered the multifaceted genetic architectures of rice PH, and provided novel and abundant genetic resources for breeding semi-dwarf rice and new candidates for further mechanistic studies on regulation of PH in rice.

USF2 activates RhoB/ROCK pathway by transcriptional inhibition of miR-206 to promote pyroptosis in septic cardiomyocytes.

Septic cardiomyopathy (SCM) is one of the most serious complications of sepsis. The present study investigated the role and mechanism of upstream stimulatory factor 2 (USF2) in SCM. Serum samples were extracted from SCM patients and healthy individuals. A murine model of sepsis was induced by caecal ligation and puncture (CLP) surgery. Myocardial injury was examined by echocardiography and HE staining. ELISA assay evaluated myocardial markers (CK-MB, cTnI) and inflammatory cytokines (TNF-α, IL-1ß, IL-18). Primary mouse cardiomyocytes were treated with lipopolysaccharide (LPS) to simulate sepsis in vitro. RT-qPCR and Western blot were used for analyzing gene and protein levels. CCK-8 assay assessed cell viability. NLRP3 was detected by immunofluorescence. ChIP, RIP and dual luciferase reporter assays were conducted to validate the molecular associations. USF2 was increased in serum from SCM patients, septic mice and primary cardiomyocytes. USF2 silencing improved the survival of septic mice and attenuated sepsis-induced myocardial pyroptosis and inflammation in vitro and in vivo. Mechanistically, USF2 could directly bind to the promoter of miR-206 to transcriptionally inhibit its expression. Moreover, RhoB was confirmed as a target of miR-206 and could promote ROCK activation and NLRP3 inflammasome formation. Moreover, overexpression of RhoB remarkably reversed the protection against LPS-induced inflammation and pyroptosis mediated by USF2 deletion or miR-206 overexpression in cardiomyocytes. The above findings elucidated that USF2 knockdown exerted a cardioprotective effect on sepsis by decreasing pyroptosis and inflammation via miR-206/RhoB/ROCK pathway, suggesting that USF2 may be a novel drug target in SCM.

Self-similar pulse compression in a tapered Pb-silicate photonic crystal fiber at 2 µm.

We report a 2-µm all-fiber nonlinear pulse compressor based on a tapered Pb-silicate photonic crystal fiber (PCF), which is capable of achieving large compression with low pedestal energy. A tapered Pb-silicate photonic crystal fiber with increased nonlinear coefficients is proposed for achieving self-similar pulse compression (SSPC) at 2 µm. The dynamic evolution of the fundamental order soliton is numerically analyzed based on the designed tapered fiber. After pulse compression in a tapered fiber with a length of 2.2 m, an initial 1.76 ps pulse can be compressed to 88 fs, increasing the peak power from 4.4 to 86 W with a compression factor of 20 and a quality factor of 98%. The results reveal that exponential variation yields superior compression performance and provides a promising solution for generating high-power femtosecond pulses at 2 µm.

Magnesium Ingot Stacking Segmentation Algorithm for Industrial Robot Based on the Correction of Image Overexposure Area.

This paper proposes an adaptive threshold segmentation algorithm for the magnesium ingot stack based on image overexposure area correction (ATSIOAC), which solves the problem of mirror reflection on the surface of magnesium alloy ingots caused by external ambient light and auxiliary light sources. Firstly, considering the brightness and chromaticity information of the mapped image, we divide the exposure probability threshold into weak exposure and strong exposure regions. Secondly, the saturation difference between the magnesium ingot region and the background region is used to obtain a mask for the magnesium ingot region to eliminate interference from the image background. Then, the RGB average of adjacent pixels in the overexposed area is used as a reference to correct the colors of the strongly exposed and weakly exposed areas, respectively. Furthermore, in order to smoothly fuse the two corrected images, pixel weighted average (WA) is applied. Finally, the magnesium ingot sorting experimental device was constructed and the corrected top surface image of the ingot pile was segmented through ATSIOAC. The experimental results show that the overexposed area detection and correction algorithm proposed in this paper can effectively correct the color information in the overexposed area, and when segmenting ingot images, complete segmentation results of the top surface of the ingot pile can be obtained, effectively improving the accuracy of magnesium alloy ingot segmentation. The segmentation algorithm achieves a segmentation accuracy of 94.38%.

The basic helix-loop-helix transcription factor gene, OsbHLH38, plays a key role in controlling rice salt tolerance.

The plant hormone abscisic acid (ABA) is crucial for plant seed germination and abiotic stress tolerance. However, the association between ABA sensitivity and plant abiotic stress tolerance remains largely unknown. In this study, 436 rice accessions were assessed for their sensitivity to ABA during seed germination. The considerable diversity in ABA sensitivity among rice germplasm accessions was primarily reflected by the differentiation between the Xian (indica) and Geng (japonica) subspecies and between the upland-Geng and lowland-Geng ecotypes. The upland-Geng accessions were most sensitive to ABA. Genome-wide association analyses identified four major quantitative trait loci containing 21 candidate genes associated with ABA sensitivity of which a basic helix-loop-helix transcription factor gene, OsbHLH38, was the most important for ABA sensitivity. Comprehensive functional analyses using knockout and overexpression transgenic lines revealed that OsbHLH38 expression was responsive to multiple abiotic stresses. Overexpression of OsbHLH38 increased seedling salt tolerance, while knockout of OsbHLH38 increased sensitivity to salt stress. A salt-responsive transcription factor, OsDREB2A, interacted with OsbHLH38 and was directly regulated by OsbHLH38. Moreover, OsbHLH38 affected rice abiotic stress tolerance by mediating the expression of a large set of transporter genes of phytohormones, transcription factor genes, and many downstream genes with diverse functions, including photosynthesis, redox homeostasis, and abiotic stress responsiveness. These results demonstrated that OsbHLH38 is a key regulator in plant abiotic stress tolerance.

Differentiating active from Inactive Sacroiliitis in ankylosing spondylitis by combination of DWI and Magnetization Transfer Imaging.

Objectives: To evaluate lesions of sacroiliac joint (SIJ) by combination of diffusion-weighted imaging (DWI) and magnetization transfer (MT). Methods: A retrospective study was used in this study. Forty-nine ankylosing spondylitis (AS) patients admitted to The China Academy of Chinese Medical Sciences Xiyuan Hospital from May 2020 to October 2020 were collected into active and inactive groups. Twenty-two healthy volunteers were recruited. Apparent diffusion coefficient (ADC) values for bone marrow edema (BME), sclerosis area, fat deposit area, and normal-appearing bone marrow (NABM) (both patients and healthy volunteers) and the magnetization transfer (MT) rate of the cartilage (MTRc) were analyzed in the groups. The above five parameters (ADC (NABM), ADC (BME) and ADC (fat deposit) and MTRc) between the active group and the inactive group were compared. The effectiveness of each parameter in diagnosing sacroiliac arthritis of ankylosing spondylitis were analyzed, and the predictive value of the parameters was compared. Result: ADC(BME), ADC(NABM) and MTRc showed statistically significant differences between the active and inactive groups (P <0.05). ADC (BME) and ADC (NABM) could predict the activity of AS sacroiliac arthritis (P <0.01). ADC (NABM) and MTRc were significantly different between healthy volunteers and the active group (P <0.01). The areas under the ROC curve (AUCs) of ADC (BME)_ADC(NABM), ADC(NABM)_MTR, and ADC(BME)_MTRc were 0.885 (cut-off value=0.69), 0.849 (cut-off value=0.56) and 0.864 (cut-off value=0.60), respectively. The predictive ability of the combined index ADC (BME)_MTRc and ADC(NABM)_MTRc was increased. Conclusion: The ability to diagnose and predict AS might be improved by the combination of diffusion-weighted imaging (DWI) and magnetization transfer (MT).

RGN1 controls grain number and shapes panicle architecture in rice.

Yield in rice is determined mainly by panicle architecture. Using map-based cloning, we identified an R2R3 MYB transcription factor REGULATOR OF GRAIN NUMBER1 (RGN1) affecting grain number and panicle architecture. Mutation of RGN1 caused an absence of lateral grains on secondary branches. We demonstrated that RGN1 controls lateral grain formation by regulation of LONELY GUY (LOG) expression, thus controlling grain number and shaping panicle architecture. A novel favourable allele, RGN1C , derived from the Or-I group in wild rice affected panicle architecture by means longer panicles. Identification of RGN1 provides a theoretical basis for understanding the molecular mechanism of lateral grain formation in rice; RGN1 will be an important gene resource for molecular breeding for higher yield.

The OsEIL1-OsERF115-target gene regulatory module controls grain size and weight in rice.

Grain size is one of the essential determinants of rice yield. Our previous studies revealed that ethylene plays an important role in grain-size control; however, the precise mechanism remains to be determined. Here, we report that the ethylene response factor OsERF115 functions as a key downstream regulator for ethylene-mediated grain development. OsERF115 encodes an AP2/ERF-type transcriptional factor that is specifically expressed in young spikelets and developing caryopses. Overexpression of OsERF115 significantly increases grain length, width, thickness and weight by promoting longitudinal elongation and transverse division of spikelet hull cells, as well as enhancing grain-filling activity, whereas its knockout mutations lead to the opposite effects, suggesting that OsERF115 positively regulates grain size and weight. OsERF115 transcription is strongly induced by ethylene, and OsEIL1 directly binds to the promoter to activate its expression. OsERF115 acts as a transcriptional repressor to directly or indirectly modulate a set of grain-size genes during spikelet growth and endosperm development. Importantly, haplotype analysis reveals that the SNP variations in the EIN3-binding sites of OsERF115 promoter are significantly associated with the OsERF115 expression levels and grain weight, suggesting that natural variations in the OsERF115 promoter contribute to grain-size diversity. In addition, the OsERF115 orthologues are identified only in grass species, implying a conserved and unique role in the grain development of cereal crops. Our results provide insights into the molecular mechanism of ethylene-mediated grain-size control and a potential strategy based on the OsEIL1-OsERF115-target gene regulatory module for genetic improvement of rice yield.

On the inference of complex phylogenetic networks by Markov Chain Monte-Carlo.

For various species, high quality sequences and complete genomes are nowadays available for many individuals. This makes data analysis challenging, as methods need not only to be accurate, but also time efficient given the tremendous amount of data to process. In this article, we introduce an efficient method to infer the evolutionary history of individuals under the multispecies coalescent model in networks (MSNC). Phylogenetic networks are an extension of phylogenetic trees that can contain reticulate nodes, which allow to model complex biological events such as horizontal gene transfer, hybridization and introgression. We present a novel way to compute the likelihood of biallelic markers sampled along genomes whose evolution involved such events. This likelihood computation is at the heart of a Bayesian network inference method called SnappNet, as it extends the Snapp method inferring evolutionary trees under the multispecies coalescent model, to networks. SnappNet is available as a package of the well-known beast 2 software. Recently, the MCMC_BiMarkers method, implemented in PhyloNet, also extended Snapp to networks. Both methods take biallelic markers as input, rely on the same model of evolution and sample networks in a Bayesian framework, though using different methods for computing priors. However, SnappNet relies on algorithms that are exponentially more time-efficient on non-trivial networks. Using simulations, we compare performances of SnappNet and MCMC_BiMarkers. We show that both methods enjoy similar abilities to recover simple networks, but SnappNet is more accurate than MCMC_BiMarkers on more complex network scenarios. Also, on complex networks, SnappNet is found to be extremely faster than MCMC_BiMarkers in terms of time required for the likelihood computation. We finally illustrate SnappNet performances on a rice data set. SnappNet infers a scenario that is consistent with previous results and provides additional understanding of rice evolution.

The role of hypoxia-inducible factor 1-alpha in inflammatory bowel disease.

Inflammatory bowel disease (IBD) develops as a result of a combination of genetic predisposition, dysbiosis of the gut microbiota, and environmental influences, which is mainly represented by ulcerative colitis (UC) and Crohn's disease (CD). IBDs can result in inflammatory hypoxia by causing intestinal inflammation and vascular damage. The hypoxia-inducible factor 1-alpha (HIF-1α), as a transcription factor, can regulate the cellular adaptation to low oxygen levels and support the development and function of the gut barrier. HIF-αplays its functions through translocating into the nucleus, dimerizing with HIF-1ß, and binding to hypoxia-responsive elements of HIF-1 target genes. So far, most studies have addressed the function of HIF-1α in murine models of IBD. In this review, we aim to outline the major roles of HIF-1α in the IBD.

Single-incision plus one-port laparoscopic gastrectomy versus conventional multi-port laparoscopy-assisted gastrectomy for gastric cancer: a retrospective study.

BACKGROUND: We compared short-term perioperative outcomes after single-incision plus one-port laparoscopic gastrectomy (SILG+1) and conventional multi-port laparoscopy-assisted gastrectomy (C-LAG) for gastric cancer. METHODS: The work was conducted between August 2017 and October 2019. A total of 90 patients with early or advanced gastric cancer were retrospectively analyzed: 43 patients of which underwent SILG+1, and 47 of which underwent C-LAG, respectively. These were divided into two groups: the total gastrectomy group (SILT+1 and C-LATG) and the distal gastrectomy group (SILD + 1 and C-LADG). The demographics, tumor characteristics, postoperative outcomes, and short-term complications of all enrolled patients were summarized and statistically analyzed. RESULTS: The mean incision length in SILT+1 group was 5.40 cm shorter than that in C-LATG group (3.15 ± 0.43 vs. 8.55 ± 2.72, P < 0.001). This comparison between the SILD + 1 and the C-LADG group produced comparable results. The SILT+1 group underwent a 56.32 min longer operation than the C-LATG group (273.03 ± 66.80 vs. 216.71 ± 82.61, P = 0.0205). SILG+1 group had better postoperative visual analog scale (VAS) and cosmetic score than those of the C-LATG group (P < 0.05). There were no significant differences in preoperative demographics or 30-day postoperative complication rates between the SILG+1 and C-LAG groups. Tumor-related index, including mass size, histological type, number of retrieved lymph nodes, pathological tumor-node-metastasis (TNM) stage, and proximal and distal edges were all equivalent between the SILG+1 and the C-LAG group. CONCLUSIONS: This retrospective study demonstrates the safety and feasibility of SILG+1 with D1+ or D2 lymphadenectomy for the treatment of early and advanced gastric cancers, compared with C-LAG.

Genetic basis underlying tiller angle in rice (Oryza sativa L.) by genome-wide association study.

KEY MESSAGE: Novel alleles of two reported tiller angle genes and eleven candidate genes for rice tiller angle were identified by combining GWAS with transcriptomic, qRT-PCR and haplotype analysis. Rice tiller angle is a key agronomic trait determining rice grain yield. Several quantitative trait loci (QTLs) affecting rice tiller angle have been mapped in the past decades. Little is known about the genetic base of tiller angle in rice, because rice tiller angle is a complex polygenic trait. In this study, we performed genome-wide association study (GWAS) on tiller angle in rice using a population of 164 japonica varieties derived from the 3 K Rice Genomes Project (3 K RGP). We detected a total of 18 QTLs using 1135519 single-nucleotide polymorphisms (SNP) based on three GWAS models (GLM, FastLMM and FarmCPU). Among them, two identified QTLs, qTA8.3 and qTA8.4, overlapped with PAY1 and TIG1, respectively, and additional 16 QTLs were identified for the first time. Combined with haplotype and expression analyses, we further revealed that PAY1 harbors one non-synonymous variation at its coding region, likely leading to variable tiller angle in the population, and that nature variations in the promoter of TIG1 significantly affect its expression, closely correlating with tiller angle phenotypes observed. Similarly, using qRT-PCR and haplotype analysis, we identified 1 and 7 candidate genes in qTA6.1 and qTA8.1 that were commonly detected by two GWAS models, respectively. In addition, we identified 3 more candidate genes in the remaining 14 novel QTLs after filtering by transcriptome analysis and qRT-PCR. In summary, this study provides new insights into the genetic architecture of rice tiller angle and candidate genes for rice breeding.

Evaluation of environmental and physiological indicators in lactating dairy cows exposed to heat stress.

This study aimed to better understand environmental heat stress and physiological heat strain indicators in lactating dairy cows. Sixteen heat stress indicators were derived using microenvironmental parameters that were measured at the surrounding of cows and at usual fixed locations in the barn by using handheld and fixed subarea sensors, respectively. Twenty high-producing Holstein-Friesian dairy cows (> 30.0 kg/day) from an intensive dairy farm were chosen to measure respiration rate (RR), vaginal temperature (VT), and body surface temperature of forehead (FT), eye (ET), and muzzle (MT). Our results show that microenvironments measured by the handheld sensor were slightly warmer and drier than those measured by the fixed subarea sensor; however, their derived heat stress indicators correlated equally well with physiological indicators. Interestingly, ambient temperature (Ta) had the highest correlations with physiological indicators and the best classification performance in recognizing actual heat strain state. Using segmented mixed models, the determined Ta thresholds for maximum FT, mean FT, RR, maximum ET, mean ET, VT, mean MT, and maximum MT were 24.1 °C, 24.2 °C, 24.4 °C, 24.6 °C, 24.6 °C, 25.3 °C, 25.4 °C, and 25.4 °C, respectively. Thus, we concluded that the fixed subarea sensor is a reliable tool for measuring cows' microenvironments; Ta is an appropriate heat stress indicator; FT, RR, and ET are good early heat strain indicators. The results of this study could be helpful for dairy practitioners in a similar intensive setting to detect and respond to heat strain with more appropriate indicators.