Journal of Genetics and Genomics最新文献_第6页

Unlocking soybean potential: genetic resources and omics for breeding.

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-02-19 DOI: 10.1016/j.jgg.2025.02.004

Zongbiao Duan, Liangwei Xu, Guoan Zhou, Zhou Zhu, Xudong Wang, Yanting Shen, Xin Ma, Zhixi Tian, Chao Fang

{"title":"Unlocking soybean potential: genetic resources and omics for breeding.","authors":"Zongbiao Duan, Liangwei Xu, Guoan Zhou, Zhou Zhu, Xudong Wang, Yanting Shen, Xin Ma, Zhixi Tian, Chao Fang","doi":"10.1016/j.jgg.2025.02.004","DOIUrl":"10.1016/j.jgg.2025.02.004","url":null,"abstract":"Soybean (Glycine max) is a vital foundation of global food security, providing a primary source of high-quality protein and oil for human consumption and animal feed. The rising global population has significantly increased the demand for soybeans, emphasizing the urgency of developing high-yield, stress-tolerant, and nutritionally superior cultivars. The extensive collection of soybean germplasm resources-including wild relatives, landraces, and cultivars-represents a valuable reservoir of genetic diversity critical for breeding advancements. Recent breakthroughs in genomic technologies, particularly high-throughput sequencing and multi-omics approaches, have revolutionized the identification of key genes associated with essential agronomic traits within these resources. These innovations enable precise and strategic utilization of genetic diversity, empowering breeders to integrate traits that improve yield potential, resilience to biotic and abiotic stresses, and nutritional quality. This review highlights the critical role of genetic resources and omics-driven innovations in soybean breeding. It also offers insights into strategies for accelerating the development of elite soybean cultivars to meet the growing demands of global soybean production.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143473308","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Diverse functions of sex determination gene doublesex on sexually dimorphic neuronal development and behaviors.

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-02-19 DOI: 10.1016/j.jgg.2025.02.005

Jiangtao Chen, Wen Tu, Ziqi Li, Mingze Ma, Simei Jiang, Wenyue Guan, Rong Wang, Yufeng Pan, Qionglin Peng

{"title":"Diverse functions of sex determination gene doublesex on sexually dimorphic neuronal development and behaviors.","authors":"Jiangtao Chen, Wen Tu, Ziqi Li, Mingze Ma, Simei Jiang, Wenyue Guan, Rong Wang, Yufeng Pan, Qionglin Peng","doi":"10.1016/j.jgg.2025.02.005","DOIUrl":"10.1016/j.jgg.2025.02.005","url":null,"abstract":"Sex-specific neurons play pivotal roles in regulating sexually dimorphic behaviors. In insects, the sex determination gene doublesex (dsx) establishes major sexual dimorphism of the nervous system, in which male-specific dsxM promotes neuronal development, while female-specific dsxF inhibits neuronal development by promoting neuronal apoptosis. In this study, we find that dsx regulates the number of dsx-expressing central neurons in Drosophila in cell-specific manners. Although dsxM overall promotes an increase in the number of dsx neurons, it inhibits the emergence of specific pC1 neurons. dsxF reduces the number of different pC1/pC2 subtypes, but promotes the formation of pC1d. We also find that dsxM and dsxF barely affect the number of some pC2 neurons. Changes in the number of pC1/pC2 neuron numbers alter their roles in regulating different behaviors, including courtship, aggression, and locomotion. Our results illustrate the multifaceted functions of dsx in sexually dimorphic neuronal development and behaviors.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143473303","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Varying Bifidobacterium species in the maternal-infant gut microbiota correlate with distinct early neurodevelopmental outcomes.

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-02-07 DOI: 10.1016/j.jgg.2025.01.015

Cong Liu, Qun Lu, Qi Xi, Shuxin Xiao, Jiangbo Du, Rui Qin, Jinghan Wang, Bo Xu, Xiumei Han, Kun Zhou, Shiyao Tao, Hong Lv, Yangqian Jiang, Tao Jiang, Kan Ye, Guangfu Jin, Hongxia Ma, Yankai Xia, Hongbing Shen, Xingyin Liu, Yuan Lin, Zhibin Hu

{"title":"Varying Bifidobacterium species in the maternal-infant gut microbiota correlate with distinct early neurodevelopmental outcomes.","authors":"Cong Liu, Qun Lu, Qi Xi, Shuxin Xiao, Jiangbo Du, Rui Qin, Jinghan Wang, Bo Xu, Xiumei Han, Kun Zhou, Shiyao Tao, Hong Lv, Yangqian Jiang, Tao Jiang, Kan Ye, Guangfu Jin, Hongxia Ma, Yankai Xia, Hongbing Shen, Xingyin Liu, Yuan Lin, Zhibin Hu","doi":"10.1016/j.jgg.2025.01.015","DOIUrl":"10.1016/j.jgg.2025.01.015","url":null,"abstract":"The impact of mother-infant microbiota on neurodevelopment is an area of interest, but longitudinal studies are scarce. Using a cohort of 520 families from the Jiangsu birth cohort in China, we reveal that the maternal gut microbiota during early pregnancy play a substantial role, accounting for 3.34% of the variance in offspring neurodevelopmental scores. This contribution is notably higher than the 1.24% attributed to the infants' own microbiota at 1 year of age, underscoring the significant influence of maternal gut health on early child development. Remarkably, an elevation in maternal Bifidobacterium pseudocatenulatum is linked to decreased cognitive scores, whereas an enrichment of Bifidobacterium longum at 1 year of age is associated with higher cognitive scores. Furthermore, we find that maternal B. pseudocatenulatum is linked to the heterolactic fermentation metabolic pathway, while infant B. longum is associated with the Bifidobacterium shunt pathway. In summary, our analysis implies that maternal and infant gut microbiota play a distinct role in neurodevelopment, suggesting potential strategies for improving neurodevelopmental outcomes during early pregnancy or infant development by targeting gut microbiota composition.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143384136","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

PAMPHLET: PAM Prediction HomoLogous-Enhancement Toolkit for precise PAM prediction in CRISPR-Cas systems. PAMPHLET：PAM 预测同源逻辑增强工具包，用于在 CRISPR-Cas 系统中精确预测 PAM。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-02-01 Epub Date: 2024-11-08 DOI: 10.1016/j.jgg.2024.10.014

Chen Qi, Xuechun Shen, Baitao Li, Chuan Liu, Lei Huang, Hongxia Lan, Donglong Chen, Yuan Jiang, Dan Wang

{"title":"PAMPHLET: PAM Prediction HomoLogous-Enhancement Toolkit for precise PAM prediction in CRISPR-Cas systems.","authors":"Chen Qi, Xuechun Shen, Baitao Li, Chuan Liu, Lei Huang, Hongxia Lan, Donglong Chen, Yuan Jiang, Dan Wang","doi":"10.1016/j.jgg.2024.10.014","DOIUrl":"10.1016/j.jgg.2024.10.014","url":null,"abstract":"CRISPR-Cas technology has revolutionized our ability to understand and engineer organisms, evolving from a singular Cas9 model to a diverse CRISPR toolbox. A critical bottleneck in developing new Cas proteins is identifying protospacer adjacent motif (PAM) sequences. Due to the limitations of experimental methods, bioinformatics approaches have become essential. However, existing PAM prediction programs are limited by the small number of spacers in CRISPR-Cas systems, resulting in low accuracy. To address this, we develop PAMPHLET, a pipeline that uses homology searches to identify additional spacers, significantly increasing the number of spacers up to 18-fold. PAMPHLET is validated on 20 CRISPR-Cas systems and successfully predicts PAM sequences for 18 protospacers. These predictions are further validated using the DocMF platform, which characterizes protein-DNA recognition patterns via next-generation sequencing. The high consistency between PAMPHLET predictions and DocMF results for Cas proteins demonstrates the potential of PAMPHLET to enhance PAM sequence prediction accuracy, expedite the discovery process, and accelerate the development of CRISPR tools.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":"258-268"},"PeriodicalIF":6.6,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142632876","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Improved chromosome-level donkey (Equus asinus) genome provides insights into genome and chromosome evolution. 染色体级驴基因组的改进为了解基因组和染色体的进化提供了线索。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-02-01 Epub Date: 2024-11-13 DOI: 10.1016/j.jgg.2024.11.002

Ge Yang, Mian Gong, Qi-Meng Yang, Yi-Dan Li, Halima Jafari, Chu-Zhao Lei, Yu Jiang, Rui-Hua Dang

引用次数: 0

Genomic insights into demographic history, structural variation landscape, and complex traits from 514 Hu sheep genomes. 对514个湖羊基因组的人口历史、结构变异景观和复杂性状的基因组分析。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-02-01 Epub Date: 2024-12-04 DOI: 10.1016/j.jgg.2024.11.015

Kaiyu Chen, Yuelang Zhang, Yizhe Pan, Xin Xiang, Chen Peng, Jiayi He, Guiqing Huang, Zhengguang Wang, Pengju Zhao

{"title":"Genomic insights into demographic history, structural variation landscape, and complex traits from 514 Hu sheep genomes.","authors":"Kaiyu Chen, Yuelang Zhang, Yizhe Pan, Xin Xiang, Chen Peng, Jiayi He, Guiqing Huang, Zhengguang Wang, Pengju Zhao","doi":"10.1016/j.jgg.2024.11.015","DOIUrl":"10.1016/j.jgg.2024.11.015","url":null,"abstract":"Hu sheep is an indigenous breed from the Taihu Lake Plain in China, known for its high fertility. Although Hu sheep belong to the Mongolian group, their demographic history and genetic architecture remain inconclusive. Here, we analyze 697 sheep genomes from representatives of Mongolian sheep breeds. Our study suggests that the ancestral Hu sheep first separated from the Mongolian group approximately 3000 years ago. As Hu sheep migrated from the north and flourished in the Taihu Lake Plain around 1000 years ago, they developed a unique genetic foundation and phenotypic characteristics, which are evident in the genomic footprints of selective sweeps and structural variation landscape. Genes associated with reproductive traits (BMPR1B and TDRD10) and horn phenotype (RXFP2) exhibit notable selective sweeps in the genome of Hu sheep. A genome-wide association analysis reveals that structural variations at LOC101110773, MAST2, and ZNF385B may significantly impact polledness, teat number, and early growth in Hu sheep, respectively. Our study offers insights into the evolutionary history of Hu sheep and may serve as a valuable genetic resource to enhance the understanding of complex traits in Hu sheep.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":"245-257"},"PeriodicalIF":6.6,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142792709","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

OsbZIP27 coordinates with OsHUB1 and OsHUB2 to modulate drought tolerance in rice. OsbZIP27与OsHUB1和OsHUB2协同调节水稻抗旱性。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-02-01 Epub Date: 2024-12-04 DOI: 10.1016/j.jgg.2024.11.016

Zuntao Xu, Yachun Yang, Fei Zhang, Hao Li, Hui Ma, Wenge Wu, Yong Ding

引用次数: 0

Epigenetic control of plant abiotic stress responses. 植物非生物胁迫反应的表观遗传控制。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-02-01 Epub Date: 2024-09-23 DOI: 10.1016/j.jgg.2024.09.008

Lijun Ma, Lihe Xing, Zicong Li, Danhua Jiang

引用次数: 0

Activation of γ-globin expression by a common variant disrupting IKAROS-binding motif in β-thalassemia. 在β地中海贫血症中，一个破坏IKAROS结合基序的常见变体激活了γ-球蛋白的表达。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-02-01 Epub Date: 2024-11-08 DOI: 10.1016/j.jgg.2024.10.015

Hualei Luo, Jueheng Wang, Lang Qin, Xinhua Zhang, Hailiang Liu, Chao Niu, Mengyang Song, Congwen Shao, Peng Xu, Miao Yu, Haokun Zhang, Yuhua Ye, Xiangmin Xu

{"title":"Activation of γ-globin expression by a common variant disrupting IKAROS-binding motif in β-thalassemia.","authors":"Hualei Luo, Jueheng Wang, Lang Qin, Xinhua Zhang, Hailiang Liu, Chao Niu, Mengyang Song, Congwen Shao, Peng Xu, Miao Yu, Haokun Zhang, Yuhua Ye, Xiangmin Xu","doi":"10.1016/j.jgg.2024.10.015","DOIUrl":"10.1016/j.jgg.2024.10.015","url":null,"abstract":"Programmed silencing of γ-globin genes in adult erythropoiesis is mediated by several chromatin remodeling complexes, which determine the stage-specific genome architecture in this region. Identification of cis- or trans-acting mutations contributing to the diverse extent of fetal hemoglobin (Hb F) might illustrate the underlying mechanism of γ-β-globin switching. Here, we recruit a cohort of 1142 β-thalassemia patients and dissect the natural variants in the whole β-globin gene cluster through a targeted next-generation sequencing panel. A previously unreported SNP rs7948668, predicted to disrupt the binding motif of IKAROS as a key component of chromatin remodeling complexes, is identified to be significantly associated with higher levels of Hb F and age at onset. Gene-editing on this SNP leads to the elevation of Hb F in both HUDEP-2 and primary CD34+ cells while the extent of elevation is amplified in the context of β-thalassemia mutations, indicating epistasis effects of the SNP in the regulation of Hb F. Finally, we perform ChIP-qPCR and 4C assays to prove that this variant disrupts the binding motif of IKAROS, leading to enhanced competitiveness of HBG promoters to locus control regions. This study highlights the significance of common regulatory SNPs and provides potential targets for treating β-hemoglobinopathy.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":"157-167"},"PeriodicalIF":6.6,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142632860","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genome-wide association analysis reveals regulatory genes for the metabolite synthesis of 2-acetyl-1-pyrroline in aromatic coconut (Cocos nucifera L.). 全基因组关联分析揭示了芳香椰子（Cocos nucifera L.）代谢产物2-乙酰基-1-吡咯啉合成的调控基因。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-02-01 Epub Date: 2024-12-13 DOI: 10.1016/j.jgg.2024.12.002

Hao Ding, Xiang Lv, Guangzhen Zhou, Xiaomei Liu, Xiwei Sun, Jing Li, Amjad Iqbal, Yaodong Yang

{"title":"Genome-wide association analysis reveals regulatory genes for the metabolite synthesis of 2-acetyl-1-pyrroline in aromatic coconut (Cocos nucifera L.).","authors":"Hao Ding, Xiang Lv, Guangzhen Zhou, Xiaomei Liu, Xiwei Sun, Jing Li, Amjad Iqbal, Yaodong Yang","doi":"10.1016/j.jgg.2024.12.002","DOIUrl":"10.1016/j.jgg.2024.12.002","url":null,"abstract":"Coconut (Cocos nucifera L.) is a key tropical economic tree valued for its fruit flavor, particularly 2-acetyl-1-pyrroline (2AP), a vital aroma metabolite. To enhance high-aromatic coconut breeding efforts, it is essential to deeply understand the hereditary factors governing the production of 2AP. In this study, a genome-wide association analysis identifies 32 loci that exhibit significant associations with 2AP content based on single nucleotide polymorphism (SNP) variations from 168 aromatic coconut germplasm resources. Transcriptome analysis then pinpoints 22 candidate genes near significant loci involved in 2AP metabolism. Proteins encoded by these genes are involved in amino acid metabolism, glycolysis, and secondary metabolism. Among these, Asparagine synthetase coding gene ASN1, Gamma-glutamylcysteine synthetase coding gene GSH1, and UbiA prenyltransferase coding gene UBIA are enriched in the linkage region constructed by significant locus Chr04_61490504. In particular, the SNP mutation of CnASN1 leads to amino acid changes in the functional region of the coding protein, potentially resulting in differences in 2AP content among haplotype populations. Identifying variations in related candidate genes, particularly the gene CnASN1, provides molecular markers closely associated with 2AP synthesis for coconut breeding and offers further insights into the metabolic mechanisms of 2AP.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":"179-188"},"PeriodicalIF":6.6,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142829978","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0