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| 1 | Estimation of inbreeding and identification of regions under heavy selection based on runs of homozygosity in a Large White pig population显示文摘Background: Runs of homozygosity(ROHs) are homozygous segments of the genome where the two haplotypes inherited from the parents are identical. The current availability of genotypes for a very large number of single nucleotide polymorphisms(SNPs) is leading to more accurate characterization of ROHs in the whole genome. Here,we investigated the occurrence and distribution of ROHs in 3,692 Large White pigs and compared estimates of inbreeding coefficients calculated based on ROHs(FROH), homozygosity(FHOM), genomic relationship matrix(FGRM)and pedigree(FPED). Furthermore, we identified genomic regions with high ROH frequencies and annotated their candidate genes.Results: In total, 176,182 ROHs were identified from 3,569 animals, and all individuals displayed at least one ROH longer than 1 Mb. The ROHs identified were unevenly distributed on the autosomes. The highest and lowest coverages of Sus scrofa chromosomes(SSC) by ROH were on SSC14 and SSC13, respectively. The highest pairwise correlation among the different inbreeding coefficient estimates was 0.95 between FROH_totaland FHOM, while the lowest was-0.083 between FGRMand FPED. The correlations between FPEDand FROHusing four classes of ROH lengths ranged from 0.18 to 0.37 and increased with increasing ROH length, except for ROH > 10 Mb. Twelve ROH islands were located on four chromosomes(SSC1, 4, 6 and 14). These ROH islands harboured genes associated with reproduction, muscular development, fat deposition and adaptation, such as SIRT1, MYPN, SETDB1 and PSMD4.Conclusion: FROHcan be used to accurately assess individual inbreeding levels compared to other inbreeding coefficient estimators. In the absence of pedigree records, FROHcan provide an alternative to inbreeding estimates.Our findings can be used not only to effectively increase the response to selection by appropriately managing the rate of inbreeding and minimizing the negative effects of inbreeding depression but also to help detect genomic regions with an effect on traits under selection. | Liangyu Shi Ligang Wang Jiaxin Liu Tianyu Deng Hua Yan Longchao Zhang Xin Liu Hongmei Gao Xinhua Hou Lixian Wang Fuping Zhao | 2020 | Journal of Animal Science and Biotechnology2020，11，4： | 10 |
| 2 | A transceptor-channel complex couples nitrate sensing to calcium signaling in Ambidopsis显示文摘Nitrate-induced Ca^(2+) signaling is crucial for the primary nitrate response in plants.However,the molecular mechanism underlying the generation of the nitrate-specific calcium signature remains unknown.We report here that a cyclic nucleotide-gated channel(CNGC)protein,CNGC15,and the nitrate transceptor(NRT1.1)constitute a molecular switch that controls calcium influx depending on nitrate levels.The expression of CNGC15 is induced by nitrate,and its protein is localized at the plasma membrane after establishment of young seedlings.We found that disruption of CNGC15 results in the loss of the nitrate-induced Ca^(2+) signature(primary nitrate response)and retards root growth,reminiscent of the phenotype observed in the nrt1.1 mutant.We further showed that CNGC15 is an active Ca^(2+)-permeable channel that physically interacts with the NRT1.1 protein in the plasma membrane.Importantly,we discovered that CNGC15-NRT1.1 interaction silences the channel activity of the heterocomplex,which dissociates upon a rise in nitrate levels,leading to reactivation of the CNGC15 channel.The dynamic interactions between CNGC15 and NRT1.1 therefore control the channel activity and Ca^(2+) influx in a nitrate-dependent manner.Our study reveals a new nutrient-sensing mechanism that utilizes a nutrient transceptor-channel complex assembly to couple nutrient status to a specific Ca^(2+) signature. | Xiaohan Wang Changxin Feng LiLi Tian Congcong Hou Wang Tian Bin Hu Qian Zhang Zhijie Ren Qi Niu Jiali Song Dongdong Kong Liangyu Liu Yikun He Ligeng Ma Chengcai Chu Sheng Luan Legong Li | 2021 | Molecular Plant2021，14，5： | 5 |
| 3 | The interaction of CaM7 and CNGC14 regulates root hair growth in Arabidopsis显示文摘Oscillations in cytosolic free calcium determine the polarity of tip-growing root hairs.The Ca2+channel cyclic nucleotide gated channel 14(CNGC14)contributes to the dynamic changes in Ca^2+concentration gradient at the root hair tip.However,the mechanisms that regulate CNGC14 are unknown.In this study,we detected a direct interaction between calmodulin 7(CaM7)and CNGC14 through yeast two-hybrid and bimolecular fluorescence complementation assays.We demonstrated that the third EF-hand domain of CaM7 specifically interacts with the cytosolic C-terminal domain of CNGC14.A two-electrode voltage clamp assay showed that CaM7 completely inhibitsCNGC14-mediated Ca2+influx,suggesting that CaM7 neg-atively regulates CNGC14-mediated calcium signaling.Fur-thermore,CaM7 overexpressing lines phenocopy the short root hair phenotype of a cngc14 mutant and this phenotype is insensitive to changes in external Ca^2+concentrations.We,thus,identified CaM7-CNGC14 as a novel interacting module that regulates polar growth in root hairs by con-trolling the tip-focused Ca2+signal. | Qudsia Zeb Xiaohan Wang Congcong Hou Xiwen Zhang Mengqi Dong Sisi Zhang Qian Zhang Zhijie Ren Wang Tian Huifen Zhu Legong Li Liangyu Liu | 2020 | Journal of Integrative Plant Biology2020，62，7： | 3 |
| 4 | The landscape of chromatin accessibility in skeletal muscle during embryonic development in pigs显示文摘Background:The development of skeletal muscle in pigs during the embryonic stage is precisely regulated by transcriptional mechanisms,which depend on chromatin accessibility.However,how chromatin accessibility plays a regulatory role during embryonic skeletal muscle development in pigs has not been reported.To gain insight into the landscape of chromatin accessibility and the associated genome-wide transcriptome during embryonic muscle development,we performed ATAC-seq and RNA-seq analyses of skeletal muscle from pig embryos at 45,70 and 100 days post coitus(dpc).Results:In total,21,638,35,447 and 60,181 unique regions(or peaks)were found across the embryos at 45 dpc(LW45),70 dpc(LW70)and 100 dpc(LW100),respectively.More than 91%of the peaks were annotated within−1 kb to 100 bp of transcription start sites(TSSs).First,widespread increases in specific accessible chromatin regions(ACRs)from embryos at 45 to 100 dpc suggested that the regulatory mechanisms became increasingly complicated during embryonic development.Second,the findings from integrated ATAC-seq and RNA-seq analyses showed that not only the numbers but also the intensities of ACRs could control the expression of associated genes.Moreover,the motif screening of stage-specific ACRs revealed some transcription factors that regulate muscle developmentrelated genes,such as MyoG,Mef2c,and Mef2d.Several potential transcriptional repressors,including E2F6,OTX2 and CTCF,were identified among the genes that exhibited different regulation trends between the ATAC-seq and RNA-seq data.Conclusions:This work indicates that chromatin accessibility plays an important regulatory role in the embryonic muscle development of pigs and regulates the temporal and spatial expression patterns of key genes in muscle development by influencing the binding of transcription factors.Our results contribute to a better understanding of the regulatory dynamics of genes involved in pig embryonic skeletal muscle development. | Jingwei Yue Xinhua Hou Xin Liu Ligang Wang Hongmei Gao Fuping Zhao Lijun Shi Liangyu Shi Hua Yan Tianyu Deng Jianfei Gong Lixian Wang Longchao Zhang | 2021 | Journal of Animal Science and Biotechnology2021，12，4： | 2 |
| 5 | In-field harvest loss of mechanically-harvested maize grain and affecting factors in China显示文摘Field harvest loss is a common problem of maize grain mechanical harvesting in China and abroad.From 2012 to 2019,2987 groups of samples for the quality of mechanical grain harvesting in field were obtained in 21 major maize-producing provinces,cities,and regions of China.The analysis performed in this study showed that the average harvest loss of fallen ears was equivalent to 76.5%of the total harvest loss,indicating that the harvest loss in the mechanical harvesting of maize grain mainly came from the loss of fallen ears.Meanwhile,statistical analysis of the harvest loss in different ranges of grain moisture contents showed that,when the grain moisture content fell below 20%,the harvest loss rate of fallen ears and the total harvest loss rate both increased sharply,and the harvest loss of fallen ears increased faster than the harvest loss of fallen grain with a decreasing grain moisture content.Moreover,the results of multi-point experiments and harvest experiments in different periods showed that,during harvesting time,the harvest loss of fallen ears caused by lodging was the main reason for in-field harvest losses in the mechanical harvesting of maize grain.Apart from the above mentioned,the test results of 35 groups of harvesters for the in-field mechanical harvesting of maize grain showed that the harvester types and their operating parameters were important factors affecting the harvest loss in the mechanical harvesting of maize grain.Therefore,the principal paths to reduce harvest loss in the mechanical harvesting of maize grain are to breed lodging-resistant maize varieties,adopt reasonable planting densities,cultivate healthy plants,develop harvesters with low harvesting loss,intensify the training of operators,and harvest at an appropriate time. | Liangyu Hou Keru Wang Yizhou Wang Lulu Li Bo Ming Ruizhi Xie Shaokun Li | 2021 | International Journal of Agricultural and Biological Engineering2021，14，1： | 1 |
| 6 | A chloride efflux transporter,BIG RICE GRAIN 1,is involved in mediating grain size and salt tolerance in rice显示文摘Grain size is determined by the size and number of cells in the grain.The regulation of grain size is crucial for improving crop yield;however,the genes and molecular mechanisms that control grain size remain elusive.Here,we report that a member of the detoxification efflux carrier/Multidrug and Toxic Compound Extrusion(DTX/MATE)family transporters,BIG RICE GRAIN 1(BIRG1),negatively influences grain size in rice(Oryza sativa L.).BIRG1 is highly expressed in reproductive organs and roots.In birg1 grain,the outer parenchyma layer cells of spikelet hulls are larger than in wild-type(WT)grains,but the cell number is unaltered.When expressed in Xenopus laevis oocytes,BIRG1 exhibits chloride efflux activity.Consistent with this role of BIRG1,the birg1 mutant shows reduced tolerance to salt stress at a toxic chloride level.Moreover,grains from birg1 plants contain a higher level of chloride than those of WT plants when grown under normal paddy field conditions,and the roots of birg1 accumulate more chloride than those of WT under saline conditions.Collectively,the data suggest that BIRG1 in rice functions as a chloride efflux transporter that is involved in mediating grain size and salt tolerance by controlling chloride homeostasis. | Zhijie Ren Fenglin Bai Jingwen Xu Li Wang Xiaohan Wang Qian Zhang Changxin Feng Qi Niu Liying Zhang Jiali Song Fang Bao Liangyu Liu Yikun He Ligeng Ma Wang Tian Congcong Hou Legong Li | 2021 | Journal of Integrative Plant Biology2021，63，12： | 1 |
| 7 | Improving harvest efficiency of maize varieties via accumulated temperature in a certain planting area显示文摘The ripening and drying of maize(Zea mays L.)grain are closely related to temperature.In accordance with maize grain drying characteristics,regional accumulated temperature(AT0≥0℃)distribution is of great significance for a rational allocation of maize varieties,thus reducing grain moisture content(MC)to improve maize harvest efficiency.From 2016 to 2018,a multi-site trial was carried out in the spring maize production area of Northeastern China.In this study,under a guaranteed rate of 80%for AT0,this area was divided into 15 accumulated temperature zones(ATZs)with an interval of 100℃ based on climatic data of 78 local weather stations.Then the AT0 demand of different maize varieties during different growth stages was calculated by combining experimental records with the established prediction model of MC,and then,the spatial partition for different types of maize varieties under different MCs was analyzed.The results showed that all the tested varieties could not reach physiological maturity(PM)at ATZs 13-15,hence,where maize planting is risky.With the increasing accumulated temperature demand of different types of maize varieties from planting to PM,to the MC of 25%and to the MC of 20%,the unplantable areas were gradually expanded from south to north while the region where the maize varieties could be harvested under different MCs was also moved southwardly.Additionally,at 1-2 ATZs,it is entirely possible to achieve mechanical kernel harvesting under the MC of 20%,even though the AT0 requirements of the varieties are relatively high.Conclusively,on the grounds of AT0 demand law of maize varieties and heat resource distribution in Northeastern China,the layout optimization for achieving different harvesting scenarios is conducive to providing a basis not only for selecting suitable varieties but also for promoting mechanical kernel harvesting in the spring maize production area of this region. | Zhaofu Huang Liangyu Hou Jun Xue Keru Wang Ruizhi Xie Peng Hou Bo Ming Shaokun Li | 2021 | International Journal of Agricultural and Biological Engineering2021，14，4： | 1 |
| 8 | Comprehensive and deep profiling of the plasma proteome with protein corona on zeolite NaY显示文摘Proteomic characterization of plasma is critical for the development of novel pharmacodynamic biomarkers.However,the vast dynamic range renders the profiling of proteomes extremely challenging.Here,we synthesized zeolite NaY and developed a simple and rapid method to achieve comprehensive and deep profiling of the plasma proteome using the plasma protein corona formed on zeolite NaY.Specifically,zeolite NaY and plasma were co-incubated to form plasma protein corona on zeolite NaY(NaY-PPC),followed by conventional protein identification using liquid chromatography-tandem mass spectrometry.NaY was able to significantly enhance the detection of low-abundance plasma proteins,minimizing the“masking”effect caused by high-abundance proteins.The relative abundance of middleand low-abundance proteins increased substantially from 2.54%to 54.41%,and the top 20 highabundance proteins decreased from 83.63%to 25.77%.Notably,our method can quantify approximately 4000 plasma proteins with sensitivity up to pg/mL,compared to only about 600 proteins identified from untreated plasma samples.A pilot study based on plasma samples from 30 lung adenocarcinoma patients and 15 healthy subjects demonstrated that our method could successfully distinguish between healthy and disease states.In summary,this work provides an advantageous tool for the exploration of plasma proteomics and its translational applications. | Congcong Ma Yanwei Li Jie Li Lei Song Liangyu Chen Na Zhao Xueping Li Ning Chen Lixia Long Jin Zhao Xin Hou Li Ren Xubo Yuan | 2023 | Journal of Pharmaceutical Analysis2023，13，5： | 0 |
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