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Inference and prioritization of tissue-specific regulons in Arabidopsis and Oryza 拟南芥和旱生植物组织特异性调控子的推断和优先排序
IF 4.6 4区 农林科学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-07-16 DOI: 10.1007/s42994-024-00176-2
Honggang Dai, Yaxin Fan, Yichao Mei, Ling-Ling Chen, Junxiang Gao
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引用次数: 0
The acyl-CoA-binding protein VdAcb1 is essential for carbon starvation response and contributes to virulence in Verticillium dahliae 酰基-CoA 结合蛋白 VdAcb1 对于大丽轮枝菌的碳饥饿反应至关重要,并有助于提高其毒力
IF 4.6 4区 农林科学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-07-13 DOI: 10.1007/s42994-024-00175-3
Zhuang Jing, Ya-Duo Zhang, Wei-xia Sun, Juan Zong, Jun-Jiao Li, Xiao-Feng Dai, S. Klosterman, Jiemin Chen, Li Tian, K. Subbarao, Dan-Dan Zhang
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引用次数: 0
Genomic prediction and genome-wide association study using combined genotypic data from different genotyping systems: application to apple fruit quality traits. 利用来自不同基因分型系统的组合基因型数据进行基因组预测和全基因组关联研究:应用于苹果果实品质性状。
IF 7.6 Q1 GENETICS & HEREDITY Pub Date : 2024-07-08 eCollection Date: 2024-07-01 DOI: 10.1093/hr/uhae131
Mai F Minamikawa, Miyuki Kunihisa, Shigeki Moriya, Tokurou Shimizu, Minoru Inamori, Hiroyoshi Iwata

With advances in next-generation sequencing technologies, various marker genotyping systems have been developed for genomics-based approaches such as genomic selection (GS) and genome-wide association study (GWAS). As new genotyping platforms are developed, data from different genotyping platforms must be combined. However, the potential use of combined data for GS and GWAS has not yet been clarified. In this study, the accuracy of genomic prediction (GP) and the detection power of GWAS increased for most fruit quality traits of apples when using combined data from different genotyping systems, Illumina Infinium single-nucleotide polymorphism array and genotyping by random amplicon sequencing-direct (GRAS-Di) systems. In addition, the GP model, which considered the inbreeding effect, further improved the accuracy of the seven fruit traits. Runs of homozygosity (ROH) islands overlapped with the significantly associated regions detected by the GWAS for several fruit traits. Breeders may have exploited these regions to select promising apples by breeders, increasing homozygosity. These results suggest that combining genotypic data from different genotyping platforms benefits the GS and GWAS of fruit quality traits in apples. Information on inbreeding could be beneficial for improving the accuracy of GS for fruit traits of apples; however, further analysis is required to elucidate the relationship between the fruit traits and inbreeding depression (e.g. decreased vigor).

随着新一代测序技术的发展,各种标记基因分型系统已经开发出来,用于基因组学方法,如基因组选择(GS)和全基因组关联研究(GWAS)。随着新基因分型平台的开发,来自不同基因分型平台的数据必须结合起来。然而,合并数据在 GS 和 GWAS 中的潜在用途尚未明确。在这项研究中,当使用来自不同基因分型系统(Illumina Infinium 单核苷酸多态性阵列和随机扩增片段测序-直接基因分型(GRAS-Di)系统)的组合数据时,对于苹果的大多数果实品质性状,基因组预测(GP)的准确性和 GWAS 的检测能力都有所提高。此外,考虑了近交效应的 GP 模型进一步提高了七个果实性状的准确性。在几个水果性状中,同源染色体(ROH)岛与全球基因组分析系统检测到的显著相关区域重叠。育种者可能利用了这些区域,通过育种筛选出有潜力的苹果,从而提高了同源性。这些结果表明,将来自不同基因分型平台的基因分型数据结合起来,有利于苹果果实品质性状的GS和GWAS。近亲繁殖的信息有利于提高苹果果实性状基因组学分析的准确性;然而,要阐明果实性状与近亲繁殖抑制(如活力下降)之间的关系,还需要进一步的分析。
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引用次数: 0
Effects of functional defects in the NMD pathway on rice phenotype and transcriptome. NMD 通路功能缺陷对水稻表型和转录组的影响
Q3 Medicine Pub Date : 2024-07-01 DOI: 10.16288/j.yczz.24-063
Yue-Yang Wu, Xiao-Yan Zhou, Yu-Feng Wu, Ju Huang

Nonsense-mediated mRNA decay (NMD) is an important RNA quality control pathway. It aids in degrading harmful erroneous mRNA, thereby preserving a stable and healthy internal environment. In this study, we employed CRISPR/Cas9 and amiRNA technology to generate knock out or knock down mutants of realted genes in the rice NMD pathway. Through transcriptome sequencing and observing phenotype changes, the study explored the impact of NMD pathway defects on rice gene expression and alternative splicing. The results suggest that even partial defects will induce phenotypic changes such as plant height and pollen vitality to different degrees, showing necessity of NMD factors. Gene expression analysis reveals that most differentially expressed genes are upregulated in the mutants, with ko-upf1-like and kd-upf1 defects having a more significant impact than kd-upf2 and kd-upf3. Specifically, NMD pathway defects result in increased expression levels of rice defense response-related genes and decreased expression levels of secondary metabolism-related genes, with a wider range of affected genes observed in 60-day-old senescence mutants. Transcript analysis indicates that different NMD related genes defects alter hundreds of alternative splicing events, mostly enriched in genes involving alternative splicing regulatory pathways. Approximately half of these events are shared among different mutants, and a substantial number of affected transcripts show NMD target features. NMD could affect both the transcript abundance and their splicing subtypes to regulate the defense response and early-senescence associated pathways, which plays a vital role in rice growth and reproduction.

无义介导的 mRNA 衰变(NMD)是一种重要的 RNA 质量控制途径。它有助于降解有害的错误 mRNA,从而保持稳定健康的内环境。在这项研究中,我们利用 CRISPR/Cas9 和 amiRNA 技术生成了水稻 NMD 通路中相关基因的基因敲除或基因敲低突变体。通过转录组测序和观察表型变化,该研究探讨了 NMD 通路缺陷对水稻基因表达和替代剪接的影响。结果表明,即使是部分缺陷,也会在不同程度上引起植株高度和花粉活力等表型变化,显示了 NMD 因子的必要性。基因表达分析表明,大多数差异表达基因在突变体中上调,其中 ko-upf1-like 和 kd-upf1 缺陷的影响比 kd-upf2 和 kd-upf3 更为显著。具体来说,NMD 途径缺陷导致水稻防御反应相关基因的表达水平升高,次生代谢相关基因的表达水平降低,在 60 天衰老突变体中观察到的受影响基因范围更广。转录本分析表明,不同的 NMD 相关基因缺陷改变了数百个替代剪接事件,其中大部分富集在涉及替代剪接调控途径的基因中。这些事件中约有一半是不同突变体共有的,大量受影响的转录本显示出 NMD 的目标特征。NMD 可影响转录本的丰度及其剪接亚型,从而调控防御反应和早期衰老相关途径,这对水稻的生长和繁殖起着至关重要的作用。
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引用次数: 0
Integrated multi-omics reveals the relationship between growth performance, rumen microbes and metabolic status of Hu sheep with different residual feed intakes 综合多组学揭示不同剩余饲料摄入量下胡羊生长性能、瘤胃微生物和代谢状态之间的关系
IF 6.3 Pub Date : 2024-07-01 DOI: 10.1016/j.aninu.2024.04.021
Yanzhen Zhang, Xiaowei Zhang, Dingren Cao, Jinyong Yang, H. Mao, Lingling Sun, Chong Wang
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引用次数: 0
Body shape divergence of paradise thread fish (Polynemus paradiseus) collected from different coastal habitats of southern Bangladesh: A multivariate approach for population discrimination 从孟加拉国南部不同沿海生境采集的天堂线鱼(Polynemus paradiseus)的体形差异:种群鉴别的多元方法
Q1 Agricultural and Biological Sciences Pub Date : 2024-07-01 DOI: 10.1016/j.aaf.2024.05.001
Md Asaduzzaman, Mohammad Zafar Iqbal, Farjana Akter Chamily, Sumi Akter, Md Sadequr Rahman Khan, LiLian Wong, Sheikh Mustafizur Rahman, Md Moshiur Rahman
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引用次数: 0
Sheep-derived butyrate-producing Clostridium beijerinckii R8 alleviates diarrhea by shaping the gut microbiota of goat kids 绵羊源丁酸梭菌贝氏R8通过改造山羊幼崽的肠道微生物群缓解腹泻症状
IF 6.3 Pub Date : 2024-07-01 DOI: 10.1016/j.aninu.2024.06.004
Dingkun Fan, Yuze Fu, Jixian Zhang, Y. Bi, Tao Ma, Qiyu Diao, Naifeng Zhang
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引用次数: 0
Integrating mRNA transcripts and genomic information into genomic prediction. 将 mRNA 转录本和基因组信息整合到基因组预测中。
Q3 Medicine Pub Date : 2024-07-01 DOI: 10.16288/j.yczz.24-096
Yu-Long Hu, Fang Yang, Yan-Tong Chen, Shuo-Kai Shen, Yu-Bo Yan, Yue-Bo Zhang, Xiao-Lin Wu, Jia-Ming Wang, Jun He, Ning Gao

Genomic prediction has emerged as a pivotal technology for the genetic evaluation of livestock, crops, and for predicting human disease risks. However, classical genomic prediction methods face challenges in incorporating biological prior information such as the genetic regulation mechanisms of traits. This study introduces a novel approach that integrates mRNA transcript information to predict complex trait phenotypes. To evaluate the accuracy of the new method, we utilized a Drosophila population that is widely employed in quantitative genetics researches globally. Results indicate that integrating mRNA transcript data can significantly enhance the genomic prediction accuracy for certain traits, though it does not improve phenotype prediction accuracy for all traits. Compared with GBLUP, the prediction accuracy for olfactory response to dCarvone in male Drosophila increased from 0.256 to 0.274. Similarly, the accuracy for cafe in male Drosophila rose from 0.355 to 0.401. The prediction accuracy for survival_paraquat in male Drosophila is improved from 0.101 to 0.138. In female Drosophila, the accuracy of olfactory response to 1hexanol increased from 0.147 to 0.210. In conclusion, integrating mRNA transcripts can substantially improve genomic prediction accuracy of certain traits by up to 43%, with range of 7% to 43%. Furthermore, for some traits, considering interaction effects along with mRNA transcript integration can lead to even higher prediction accuracy.

基因组预测已成为牲畜、农作物遗传评估和人类疾病风险预测的关键技术。然而,传统的基因组预测方法在整合生物先验信息(如性状的遗传调控机制)方面面临挑战。本研究介绍了一种整合 mRNA 转录本信息来预测复杂性状表型的新方法。为了评估新方法的准确性,我们利用了全球数量遗传学研究中广泛使用的果蝇种群。结果表明,整合 mRNA 转录本数据可显著提高某些性状的基因组预测准确性,但并不能提高所有性状的表型预测准确性。与 GBLUP 相比,雄果蝇对 dCarvone 的嗅觉反应的预测准确率从 0.256 提高到 0.274。同样,雄果蝇对咖啡的预测准确率也从 0.355 提高到了 0.401。雄果蝇的生存_百草枯预测准确率从 0.101 提高到 0.138。雌果蝇对 1hexanol 的嗅觉反应的预测准确率从 0.147 提高到 0.210。总之,整合 mRNA 转录本可以大幅提高某些性状的基因组预测准确率,最高可达 43%,范围在 7% 至 43% 之间。此外,对于某些性状,在整合 mRNA 转录本的同时考虑互作效应可以提高预测准确率。
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引用次数: 0
Influences of lauric acid addition on performance, nutrient digestibility and proteins related to mammary gland development in dairy cows 添加月桂酸对奶牛生产性能、营养消化率和乳腺发育相关蛋白质的影响
IF 6.3 Pub Date : 2024-07-01 DOI: 10.1016/j.aninu.2024.06.002
Jing Zhang, Lijun Bu, Yapeng Liu, Wenjie Huo, Chengqiang Xia, C. Pei, Qiang Liu
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引用次数: 0
Marine red yeast supplementation improves laying performance by regulating small intestinal homeostasis in aging chickens 补充海洋红酵母,通过调节老龄鸡的小肠平衡改善产蛋性能
IF 6.3 Pub Date : 2024-07-01 DOI: 10.1016/j.aninu.2024.04.022
Yudian Zhao, Sujin Si, Y. Ren, Xing Wu, Zihao Zhang, Yixiang Tian, Jing Li, Yijie Li, Meng Hou, Xueyang Yao, Zhaoheng Xu, Ruirui Jiang, Xiangtao Kang, Yujie Gong, Qiang Li, Yadong Tian
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引用次数: 0
期刊
全部 Acta Ecologica Sinica Acta Agronomica Sinica Animal Husbandry and Feed Science 中国农学通报 China Cucurbits and Vegetables 中国畜牧杂志 生态学杂志 Chinese Journal of Eco-agriculture 中国比较医学杂志 中国畜牧兽医 Chinese Journal of Rice Science Chinese Tobacco Science 农药学学报 Cotton Science Crop research Edible Fungi of China Fujian Science and Technology of Rice and Wheat 福建农业学报 广东农业科学 湖北农业科学 Journal of Agriculture 农业资源与环境学报 Journal of Beijing University of Agriculture 中国农业大学学报 Journal of Fisheries of China Journal of fishery sciences of China Journal of Fruit Science 南京农业大学学报 Journal of Nuclear Agricultural Sciences 植物遗传资源学报 Journal of Plant Resources and Environment Journal of Plant Protection Journal of Shanxi Agricultural Sciences Journal of Shenyang Agricultural University 南方农业学报 Modern Agrochemicals Modern Agricultural Science and Technology Progress in Veterinary Medicine 西南农业学报 Tobacco Science & Technology Oil Crop Science Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji Aquaculture and Fisheries 中国农业气象 Hupo Kexue/Journal of Lake Sciences 中国农业科学 Journal of Agricultural Sciences aBIOTECH Journal of Resources and Ecology Information Processing in Agriculture 美国植物学期刊(英文) 土壤科学期刊(英文) 园艺研究(英文) 耕作与栽培 湖北农学院学报 昆虫学(英文) 海洋渔业 J Immune Based Ther Vaccines Antimicrob 海岸生命医学杂志(英文版) Life Res (Auckl) 兽医学(英文) Anim. Nutr. Plant Diseases and Pests(植物病虫害研究:英文版) 动物科学期刊(英文) 农业科学 Zhi Wu Sheng Li Yu Fen Zi Sheng Wu Xue Xue Bao 水产研究 湿地科学 湖南农业大学学报(自然科学版) 亚洲兽医病例研究 农业化学和环境(英文) 生态科学 土壤科学 经济动物学报 福建畜牧兽医
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