Journal of Genetics and Genomics最新文献_第3页

3vGCIM: a compressed variance component mixed model for detecting QTL-by-environment interactions in RIL population. 3vGCIM：用于检测RIL群体中QTL-by-environment相互作用的压缩方差成分混合模型。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-06-10 DOI: 10.1016/j.jgg.2025.05.011

Mei Li, Yuan-Ming Zhang

{"title":"3vGCIM: a compressed variance component mixed model for detecting QTL-by-environment interactions in RIL population.","authors":"Mei Li, Yuan-Ming Zhang","doi":"10.1016/j.jgg.2025.05.011","DOIUrl":"10.1016/j.jgg.2025.05.011","url":null,"abstract":"Existing quantitative trait locus (QTL) mapping had low efficiency in identifying small-effect and closely linked QTL-by-environment interactions (QEIs) in recombinant inbred lines (RILs), especially in the era of global climate change. To address this challenge, here we integrate the compressed variance component mixed model with our GCIM to propose 3vGCIM for identifying QEIs in RILs, and extend 3vGCIM-random to 3vGCIM-fixed. 3vGCIM integrates genome-wide scanning with machine learning, significantly improving power. In the mixed full model, we consider all possible effects and control for all possible polygenic backgrounds. In simulation studies, 3vGCIM exhibits higher power (∼92.00%), higher accuracy of the estimates for QTL position (∼1.900 cM2) and effect (∼0.050), and lower false positive rate (∼0.48‰) and false negative rate (<8.10%) in three environments of 300 RILs each than ICIM (47.57%; 3.607 cM2, 0.583; 2.81‰; 52.43%) and MCIM (60.30%; 5.279 cM2, 0.274; 2.17‰; 39.70%). In the real data analysis of rice yield-related traits in 240 RILs, 3vGCIM mines more known genes (57-60) and known gene-by-environment interactions (GEIs) (14-19) and candidate GEIs (21-23) than ICIM (27, 2, and 7), and MCIM (21, 1, and 3), especially in small-effect and linked QTLs and QEIs. This makes 3vGCIM a powerful and sensitive tool for QTL mapping and molecular QTL mapping.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144287136","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

Harness the wild: progress and perspectives in wheat genetic improvement. 驾驭野生：小麦遗传改良的进展与展望。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-06-02 DOI: 10.1016/j.jgg.2025.05.010

Xiubin Tian, Ziyu Wang, Wenxuan Liu, Yusheng Zhao

引用次数: 0

Tensor decomposition reveals trans-regulated gene modules in maize drought response. 张量分解揭示玉米干旱响应中的跨调控基因模块

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-06-01 Epub Date: 2024-11-08 DOI: 10.1016/j.jgg.2024.10.011

Jiawen Lu, Yuxin Xie, Chunhui Li, Jinliang Yang, Junjie Fu

{"title":"Tensor decomposition reveals trans-regulated gene modules in maize drought response.","authors":"Jiawen Lu, Yuxin Xie, Chunhui Li, Jinliang Yang, Junjie Fu","doi":"10.1016/j.jgg.2024.10.011","DOIUrl":"10.1016/j.jgg.2024.10.011","url":null,"abstract":"When plants respond to drought stress, dynamic cellular changes occur, accompanied by alterations in gene expression, which often act through trans-regulation. However, the detection of trans-acting genetic variants and networks of genes is challenged by the large number of genes and markers. Using a tensor decomposition method, we identify trans-acting expression quantitative trait loci (trans-eQTLs) linked to gene modules, rather than individual genes, which were associated with maize drought response. Module-to-trait association analysis demonstrates that half of the modules are relevant to drought-related traits. Genome-wide association studies of the expression patterns of each module identify 286 trans-eQTLs linked to drought-responsive modules, the majority of which cannot be detected based on individual gene expression. Notably, the trans-eQTLs located in the regions selected during maize improvement tend towards relatively strong selection. We further prioritize the genes that affect the transcriptional regulation of multiple genes in trans, as exemplified by two transcription factor genes. Our analyses highlight that multidimensional reduction could facilitate the identification of trans-acting variations in gene expression in response to dynamic environments and serve as a promising technique for high-order data processing in future crop breeding.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":"786-798"},"PeriodicalIF":6.6,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142632883","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

Genomic insights into the absence of root nodule formation and nitrogen fixation in Zenia insignis. 荆芥根瘤形成和固氮缺失的基因组分析。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-06-01 Epub Date: 2024-12-09 DOI: 10.1016/j.jgg.2024.12.001

Hang Yu, Yongbin Lu, Chao Zhang, Wenyuan Yang, Hongjiang Xie, Huiru Liu, Haifeng Wang

引用次数: 0

High-quality genome of Firmiana hainanensis provides insights into the evolution of Malvaceae subfamilies and the mechanism of their wood density formation. 海南枫的高质量基因组为研究锦葵科亚科的进化及其木材密度形成机制提供了新的思路。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-06-01 Epub Date: 2024-12-19 DOI: 10.1016/j.jgg.2024.12.009

Zeyu Dong, Shangkun Jin, Rui Fan, Pengcheng Sun, Lei Shao, Ting Zhao, Haojie Jiang, Zhiyuan Zhang, Haihong Shang, Xueying Guan, Yan Hu, Tianzhen Zhang, Fuyuan Zhu, Lei Fang

{"title":"High-quality genome of Firmiana hainanensis provides insights into the evolution of Malvaceae subfamilies and the mechanism of their wood density formation.","authors":"Zeyu Dong, Shangkun Jin, Rui Fan, Pengcheng Sun, Lei Shao, Ting Zhao, Haojie Jiang, Zhiyuan Zhang, Haihong Shang, Xueying Guan, Yan Hu, Tianzhen Zhang, Fuyuan Zhu, Lei Fang","doi":"10.1016/j.jgg.2024.12.009","DOIUrl":"10.1016/j.jgg.2024.12.009","url":null,"abstract":"The Malvaceae family, the most diverse family in the order Malvales, consists of nine subfamilies. Within the Firmiana genus of the Sterculioideae subfamily, most species are considered globally vulnerable, yet their genomes remain unexplored. Here, we present a chromosome-level genome assembly for a representative Firmiana species, F. hainanensis, 2n = 40, totaling 1536 Mb. Phylogenomic analysis shows that F. hainanensis and Durio zibethinus have the closest evolutionary relationship, with an estimated divergence time of approximately 21 millions of years ago (MYA) and distinct polyploidization events in their histories. Evolutionary trajectory analyses indicate that fissions and fusions may play a crucial role in chromosome number variation (2n = 14 to 2n = 96). Analysis of repetitive elements among Malvaceae reveals that the Tekay subfamily (belonging to the Gypsy group) contributes to variation in genome size (ranging from 324 Mb to 1620 Mb). Additionally, genes associated with P450, peroxidase, and microtubules, and thereby related to cell wall biosynthesis, are significantly contracted in F. hainanensis, potentially leading to its lower wood density relative to Hopea hainanensis. Overall, our study provides insights into the evolution of chromosome number, genome size, and the genetic basis of cell wall biosynthesis in Malvaceae species.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":"812-825"},"PeriodicalIF":6.6,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142873456","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

Near-complete de novo genome assemblies of tomato (Solanum lycopersicum) determinate cultivars Micro-Tom and M82. 番茄（Solanum lycopersicum）决定性栽培品种 Micro-Tom 和 M82 的近乎完整的全新基因组组装。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-06-01 Epub Date: 2024-06-17 DOI: 10.1016/j.jgg.2024.06.006

Shuangshuang Wang, Lei Lu, Min Xu, Jian Jiang, Xiaofeng Wang, Yao Zheng, Yitao Liang, Tianqi Zhang, Minghui Qin, Pinkuan Zhu, Ling Xu, Yina Jiang

引用次数: 0

Genetic interaction network of quantitative trait genes for heading date in rice. 水稻抽穗期数量性状基因的遗传互作网络。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-06-01 Epub Date: 2025-01-06 DOI: 10.1016/j.jgg.2024.12.019

Mengjiao Chen, Yifeng Hong, Jiongjiong Fan, Dengyi Cao, Chong Yin, Anjie Yu, Jie Qiu, Xuehui Huang, Xin Wei

{"title":"Genetic interaction network of quantitative trait genes for heading date in rice.","authors":"Mengjiao Chen, Yifeng Hong, Jiongjiong Fan, Dengyi Cao, Chong Yin, Anjie Yu, Jie Qiu, Xuehui Huang, Xin Wei","doi":"10.1016/j.jgg.2024.12.019","DOIUrl":"10.1016/j.jgg.2024.12.019","url":null,"abstract":"Several quantitative trait genes (QTGs) related to rice heading date, a key factor for crop development and yield, have been identified, along with complex interactions among genes. However, a comprehensive genetic interaction network for these QTGs has not yet been established. In this study, we use 18K-rice lines to identify QTGs and their epistatic interactions affecting rice heading date. We identify 264 pairs of interacting quantitative trait loci (QTL) and construct a comprehensive genetic network of these QTL. On average, the epistatic effects of QTL pairs are estimated to be approximately 12.5% of additive effects of identified QTL. Importantly, epistasis varies among different alleles of several heading date genes. Additionally, 57 pairs of interacting QTGs are also significant in their epistatic effects on 12 other agronomic traits. The identified QTL genetic interactions are further validated using near-isogenic lines, yeast two-hybrid, and split-luciferase complementation assays. Overall, this study provides a genetic network of rice heading date genes, which plays a crucial role in regulating rice heading date and influencing multiple related agronomic traits. This network serves as a foundation for understanding the genetic mechanisms of rice quantitative traits and for advancing rice molecular breeding.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":"747-760"},"PeriodicalIF":6.6,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142958986","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

The Monochoria genome provides insights into the molecular mechanisms underlying floral heteranthery. 单孢菌基因组提供了深入了解花异花异种的分子机制。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-06-01 Epub Date: 2025-02-26 DOI: 10.1016/j.jgg.2025.02.008

Jingshan Yang, Jinming Chen, Xiangyan He, Guangxi Wang, Spencer C H Barrett, Zhizhong Li

{"title":"The Monochoria genome provides insights into the molecular mechanisms underlying floral heteranthery.","authors":"Jingshan Yang, Jinming Chen, Xiangyan He, Guangxi Wang, Spencer C H Barrett, Zhizhong Li","doi":"10.1016/j.jgg.2025.02.008","DOIUrl":"10.1016/j.jgg.2025.02.008","url":null,"abstract":"Heteranthery, the occurrence of functionally and structurally distinct stamens within a flower, represents a striking example of convergent evolution among diverse animal-pollinated lineages. Although the ecological basis of this somatic polymorphism is understood, the developmental and molecular mechanisms are largely unknown. To address this knowledge gap, we selected Monochoria elata (Pontederiaceae) as our study system due to its typical heterantherous floral structure. We constructed a chromosome-level genome assembly of M. elata, conducted transcriptomic analyses and target phytohormone metabolome analysis to explore gene networks and hormones associated with heteranthery. We focused on three key stamen characteristics-colour, spatial patterning, and filament elongation-selected for their significant roles in stamen differentiation and their relevance to the functional diversity observed in heterantherous species. Our analyses suggest that gene networks involving MelLEAFY3, MADS-box, and TCP genes regulate stamen identity, with anthocyanin influencing colour, and lignin contributing to filament elongation. Additionally, variation in jasmonic acid and abscisic acid concentration between feeding and pollinating anthers appears to contribute to their morphological divergence. Our findings highlight gene networks and hormones associated with intra-floral stamen differentiation and indicate that whole genome duplications have likely facilitated the evolution of heteranthery during divergence from other Pontederiaceae without heteranthery.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":"826-838"},"PeriodicalIF":6.6,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143532227","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

Structural variation-based and gene-based pangenome construction reveals untapped diversity of hexaploid wheat. 基于结构变异和基因的全基因组构建揭示了六倍体小麦未开发的多样性。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-06-01 Epub Date: 2025-04-04 DOI: 10.1016/j.jgg.2025.03.015

Hong Cheng, Lingpeng Kong, Kun Zhu, Hang Zhao, Xiuli Li, Yanwen Zhang, Weidong Ning, Mei Jiang, Bo Song, Shifeng Cheng

{"title":"Structural variation-based and gene-based pangenome construction reveals untapped diversity of hexaploid wheat.","authors":"Hong Cheng, Lingpeng Kong, Kun Zhu, Hang Zhao, Xiuli Li, Yanwen Zhang, Weidong Ning, Mei Jiang, Bo Song, Shifeng Cheng","doi":"10.1016/j.jgg.2025.03.015","DOIUrl":"10.1016/j.jgg.2025.03.015","url":null,"abstract":"Increasing number of structural variations (SVs) have been identified as causative mutations for diverse agronomic traits. However, the systematic exploration of SVs quantity, distribution, and contribution in wheat was lacking. Here, we report high-quality gene-based and SV-based pangenomes comprising 22 hexaploid wheat assemblies showing a wide range of chromosome size, gene number, and TE component, which indicates their representativeness of wheat genetic diversity. Pan-gene analyses uncover 140,261 distinct gene families, of which only 23.2 % are shared in all accessions. Moreover, we build a ∼16.15 Gb graph pangenome containing 695,897 bubbles, intersecting 5132 genes and 230,307 cis-regulatory regions. Pairwise genome comparisons identify ∼1,978,221 non-redundant SVs and 497 SV hotspots. Notably, the density of bubbles as well as SVs show remarkable aggregation in centromeres, which probably play an important role in chromosome plasticity and stability. As for functional SVs exploration, we identify 2769 SVs with absolute relative frequency differences exceeding 0.7 between spring and winter growth habit groups. Additionally, several reported functional genes in wheat display complex structural graphs, for example, PPD-A1, VRT-A2, and TaNAAT2-A. These findings deepen our understanding of wheat genetic diversity, providing valuable graphical pangenome and variation resources to improve the efficiency of genome-wide association mapping in wheat.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":"774-785"},"PeriodicalIF":6.6,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143797166","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

Unravelling sorghum functional genomics and molecular breeding: past achievements and future prospects. 揭示高粱功能基因组学和分子育种：过去的成就和未来的前景。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-06-01 Epub Date: 2024-07-23 DOI: 10.1016/j.jgg.2024.07.016

Fangyuan Liu, Baye Wodajo, Kangxu Zhao, Sanyuan Tang, Qi Xie, Peng Xie

引用次数: 0