Pub Date : 2024-11-08DOI: 10.1038/s41588-024-02008-x
Chiara Anania
{"title":"Single-cell 3D multi-omics during human brain development","authors":"Chiara Anania","doi":"10.1038/s41588-024-02008-x","DOIUrl":"10.1038/s41588-024-02008-x","url":null,"abstract":"","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"56 11","pages":"2296-2296"},"PeriodicalIF":31.7,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142596149","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-07DOI: 10.1038/s41588-024-01970-w
The calcium-dependent protein kinase ZmCPK39 is identified as a key immune component in maize infected with foliar pathogens. Its expression is lower in resistant maize lines than in susceptible lines, leading to stabilization of the transcription factor ZmDi19, elevated expression of the anti-microbial protein ZmPR10 and enhanced resistance to multiple foliar diseases.
{"title":"The kinase ZmCPK39 regulates foliar disease resistance in maize plants","authors":"","doi":"10.1038/s41588-024-01970-w","DOIUrl":"10.1038/s41588-024-01970-w","url":null,"abstract":"The calcium-dependent protein kinase ZmCPK39 is identified as a key immune component in maize infected with foliar pathogens. Its expression is lower in resistant maize lines than in susceptible lines, leading to stabilization of the transcription factor ZmDi19, elevated expression of the anti-microbial protein ZmPR10 and enhanced resistance to multiple foliar diseases.","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"56 12","pages":"2610-2611"},"PeriodicalIF":31.7,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142594376","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-05DOI: 10.1038/s41588-024-01960-y
Linda Ongaro, Emilia Huerta-Sanchez
The identification of a new hominin group in the Altai mountains called Denisovans was one of the most exciting discoveries in human evolution in the last decade. Unlike Neanderthal remains, the Denisovan fossil record consists of only a finger bone, jawbone, teeth and skull fragments. Leveraging the surviving Denisovan segments in modern human genomes has uncovered evidence of at least three introgression events from distinct Denisovan populations into modern humans in the past. Each of them presents different levels of relatedness to the sequenced Altai Denisovan, indicating a complex relationship between these sister lineages. Here we review the evidence suggesting that several Denisovan populations, who likely had an extensive geographical range, were adapted to distinct environments and introgressed into modern humans multiple times. We further discuss how archaic variants have been affected by demographic history, negative and positive selection and close by proposing possible new lines of future research. This review describes evidence of multiple Denisovan populations, each with varying relatedness to Altai Denisovans, that introgressed into modern humans and highlights how introgression influenced human adaptation to a range of environments.
{"title":"A history of multiple Denisovan introgression events in modern humans","authors":"Linda Ongaro, Emilia Huerta-Sanchez","doi":"10.1038/s41588-024-01960-y","DOIUrl":"10.1038/s41588-024-01960-y","url":null,"abstract":"The identification of a new hominin group in the Altai mountains called Denisovans was one of the most exciting discoveries in human evolution in the last decade. Unlike Neanderthal remains, the Denisovan fossil record consists of only a finger bone, jawbone, teeth and skull fragments. Leveraging the surviving Denisovan segments in modern human genomes has uncovered evidence of at least three introgression events from distinct Denisovan populations into modern humans in the past. Each of them presents different levels of relatedness to the sequenced Altai Denisovan, indicating a complex relationship between these sister lineages. Here we review the evidence suggesting that several Denisovan populations, who likely had an extensive geographical range, were adapted to distinct environments and introgressed into modern humans multiple times. We further discuss how archaic variants have been affected by demographic history, negative and positive selection and close by proposing possible new lines of future research. This review describes evidence of multiple Denisovan populations, each with varying relatedness to Altai Denisovans, that introgressed into modern humans and highlights how introgression influenced human adaptation to a range of environments.","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"56 12","pages":"2612-2622"},"PeriodicalIF":31.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142580341","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-05DOI: 10.1038/s41588-024-01957-7
Yuanyuan Zhang, Zhiquan Yang, Yizhou He, Dongxu Liu, Yueying Liu, Congyuan Liang, Meili Xie, Yupeng Jia, Qinglin Ke, Yongming Zhou, Xiaohui Cheng, Junyan Huang, Lijiang Liu, Yang Xiang, Harsh Raman, Daniel J. Kliebenstein, Shengyi Liu, Qing-Yong Yang
Although individual genomic structural variants (SVs) are known to influence gene expression and trait variation, the extent and scale of SV impact across a species remain unknown. In the present study, we constructed a reference library of 334,461 SVs from genome assemblies of 16 representative morphotypes of neopolyploid Brassica napus accessions and detected 258,865 SVs in 2,105 resequenced genomes. Coupling with 5 tissue population transcriptomes, we uncovered 285,976 SV-expression quantitative trait loci (eQTLs) that associate with altered expression of 73,580 genes. We developed a pipeline for the high-throughput joint analyses of SV-genome-wide association studies (SV-GWASs) and transcriptome-wide association studies of phenomic data, eQTLs and eQTL-GWAS colocalization, and identified 726 SV–gene expression–trait variation associations, some of which were verified by transgenics. The pervasive SV impact on how SV reshapes trait variation was demonstrated with the glucosinolate biosynthesis and transport pathway. The study highlighting the impact of genome-wide and species-scale SVs provides a powerful methodological strategy and valuable resources for studying evolution, gene discovery and breeding. Multiomics joint analyses based on a structural variant (SV) map from 16 genome assemblies and 2,105 resequenced accession genomes shed light on the regulatory effect of SVs on gene expression and trait variation in Brassica napus.
{"title":"Structural variation reshapes population gene expression and trait variation in 2,105 Brassica napus accessions","authors":"Yuanyuan Zhang, Zhiquan Yang, Yizhou He, Dongxu Liu, Yueying Liu, Congyuan Liang, Meili Xie, Yupeng Jia, Qinglin Ke, Yongming Zhou, Xiaohui Cheng, Junyan Huang, Lijiang Liu, Yang Xiang, Harsh Raman, Daniel J. Kliebenstein, Shengyi Liu, Qing-Yong Yang","doi":"10.1038/s41588-024-01957-7","DOIUrl":"10.1038/s41588-024-01957-7","url":null,"abstract":"Although individual genomic structural variants (SVs) are known to influence gene expression and trait variation, the extent and scale of SV impact across a species remain unknown. In the present study, we constructed a reference library of 334,461 SVs from genome assemblies of 16 representative morphotypes of neopolyploid Brassica napus accessions and detected 258,865 SVs in 2,105 resequenced genomes. Coupling with 5 tissue population transcriptomes, we uncovered 285,976 SV-expression quantitative trait loci (eQTLs) that associate with altered expression of 73,580 genes. We developed a pipeline for the high-throughput joint analyses of SV-genome-wide association studies (SV-GWASs) and transcriptome-wide association studies of phenomic data, eQTLs and eQTL-GWAS colocalization, and identified 726 SV–gene expression–trait variation associations, some of which were verified by transgenics. The pervasive SV impact on how SV reshapes trait variation was demonstrated with the glucosinolate biosynthesis and transport pathway. The study highlighting the impact of genome-wide and species-scale SVs provides a powerful methodological strategy and valuable resources for studying evolution, gene discovery and breeding. Multiomics joint analyses based on a structural variant (SV) map from 16 genome assemblies and 2,105 resequenced accession genomes shed light on the regulatory effect of SVs on gene expression and trait variation in Brassica napus.","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"56 11","pages":"2538-2550"},"PeriodicalIF":31.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41588-024-01957-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142580333","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-05DOI: 10.1038/s41588-024-02017-w
Tanya J. Major, Riku Takei, Hirotaka Matsuo, Megan P. Leask, Nicholas A. Sumpter, Ruth K. Topless, Yuya Shirai, Wei Wang, Murray J. Cadzow, Amanda J. Phipps-Green, Zhiqiang Li, Aichang Ji, Marilyn E. Merriman, Emily Morice, Eric E. Kelley, Wen-Hua Wei, Sally P. A. McCormick, Matthew J. Bixley, Richard J. Reynolds, Kenneth G. Saag, Tayaza Fadason, Evgenia Golovina, Justin M. O’Sullivan, Lisa K. Stamp, Nicola Dalbeth, Abhishek Abhishek, Michael Doherty, Edward Roddy, Lennart T. H. Jacobsson, Meliha C. Kapetanovic, Olle Melander, Mariano Andrés, Fernando Pérez-Ruiz, Rosa J. Torres, Timothy Radstake, Timothy L. Jansen, Matthijs Janssen, Leo A. B. Joosten, Ruiqi Liu, Orsolya I. Gaal, Tania O. Crişan, Simona Rednic, Fina Kurreeman, Tom W. J. Huizinga, René Toes, Frédéric Lioté, Pascal Richette, Thomas Bardin, Hang Korng Ea, Tristan Pascart, Geraldine M. McCarthy, Laura Helbert, Blanka Stibůrková, Anne-K. Tausche, Till Uhlig, Véronique Vitart, Thibaud S. Boutin, Caroline Hayward, Philip L. Riches, Stuart H. Ralston, Archie Campbell, Thomas M. MacDonald, FAST Study Group, Akiyoshi Nakayama, Tappei Takada, Masahiro Nakatochi, Seiko Shimizu, Yusuke Kawamura, Yu Toyoda, Hirofumi Nakaoka, Ken Yamamoto, Keitaro Matsuo, Nariyoshi Shinomiya, Kimiyoshi Ichida, Japan Gout Genomics Consortium, Chaeyoung Lee, Asia Pacific Gout Consortium, Linda A. Bradbury, Matthew A. Brown, Philip C. Robinson, Russell R. C. Buchanan, Catherine L. Hill, Susan Lester, Malcolm D. Smith, Maureen Rischmueller, Hyon K. Choi, Eli A. Stahl, Jeff N. Miner, Daniel H. Solomon, Jing Cui, Kathleen M. Giacomini, Deanna J. Brackman, Eric M. Jorgenson, GlobalGout Genetics Consortium, Hongbo Liu, Katalin Susztak, 23andMe Research Team, Suyash Shringarpure, Alexander So, Yukinori Okada, Changgui Li, Yongyong Shi, Tony R. Merriman
{"title":"Publisher Correction: A genome-wide association analysis reveals new pathogenic pathways in gout","authors":"Tanya J. Major, Riku Takei, Hirotaka Matsuo, Megan P. Leask, Nicholas A. Sumpter, Ruth K. Topless, Yuya Shirai, Wei Wang, Murray J. Cadzow, Amanda J. Phipps-Green, Zhiqiang Li, Aichang Ji, Marilyn E. Merriman, Emily Morice, Eric E. Kelley, Wen-Hua Wei, Sally P. A. McCormick, Matthew J. Bixley, Richard J. Reynolds, Kenneth G. Saag, Tayaza Fadason, Evgenia Golovina, Justin M. O’Sullivan, Lisa K. Stamp, Nicola Dalbeth, Abhishek Abhishek, Michael Doherty, Edward Roddy, Lennart T. H. Jacobsson, Meliha C. Kapetanovic, Olle Melander, Mariano Andrés, Fernando Pérez-Ruiz, Rosa J. Torres, Timothy Radstake, Timothy L. Jansen, Matthijs Janssen, Leo A. B. Joosten, Ruiqi Liu, Orsolya I. Gaal, Tania O. Crişan, Simona Rednic, Fina Kurreeman, Tom W. J. Huizinga, René Toes, Frédéric Lioté, Pascal Richette, Thomas Bardin, Hang Korng Ea, Tristan Pascart, Geraldine M. McCarthy, Laura Helbert, Blanka Stibůrková, Anne-K. Tausche, Till Uhlig, Véronique Vitart, Thibaud S. Boutin, Caroline Hayward, Philip L. Riches, Stuart H. Ralston, Archie Campbell, Thomas M. MacDonald, FAST Study Group, Akiyoshi Nakayama, Tappei Takada, Masahiro Nakatochi, Seiko Shimizu, Yusuke Kawamura, Yu Toyoda, Hirofumi Nakaoka, Ken Yamamoto, Keitaro Matsuo, Nariyoshi Shinomiya, Kimiyoshi Ichida, Japan Gout Genomics Consortium, Chaeyoung Lee, Asia Pacific Gout Consortium, Linda A. Bradbury, Matthew A. Brown, Philip C. Robinson, Russell R. C. Buchanan, Catherine L. Hill, Susan Lester, Malcolm D. Smith, Maureen Rischmueller, Hyon K. Choi, Eli A. Stahl, Jeff N. Miner, Daniel H. Solomon, Jing Cui, Kathleen M. Giacomini, Deanna J. Brackman, Eric M. Jorgenson, GlobalGout Genetics Consortium, Hongbo Liu, Katalin Susztak, 23andMe Research Team, Suyash Shringarpure, Alexander So, Yukinori Okada, Changgui Li, Yongyong Shi, Tony R. Merriman","doi":"10.1038/s41588-024-02017-w","DOIUrl":"10.1038/s41588-024-02017-w","url":null,"abstract":"","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"56 11","pages":"2577-2577"},"PeriodicalIF":31.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41588-024-02017-w.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142580519","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-04DOI: 10.1038/s41588-024-01968-4
Mang Zhu, Tao Zhong, Ling Xu, Chenyu Guo, Xiaohui Zhang, Yulin Liu, Yan Zhang, Yancong Li, Zhijian Xie, Tingting Liu, Fuyan Jiang, Xingming Fan, Peter Balint-Kurti, Mingliang Xu
Gray leaf spot, northern leaf blight and southern leaf blight are three of the most destructive foliar diseases affecting maize (Zea mays L.). Here we identified a gene, ZmCPK39, that encodes a calcium-dependent protein kinase and negatively regulates quantitative resistance to these three diseases. The ZmCPK39 allele in the resistant line displayed significantly lower pathogen-induced gene expression than that in the susceptible line. A marked decrease in ZmCPK39 abundance mitigated the phosphorylation and degradation of the transcription factor ZmDi19. This led to elevated expression of ZmPR10, a gene known to encode an antimicrobial protein, thereby enhancing maize resistance to foliar diseases. Moreover, the F1 hybrid with reduced ZmCPK39 expression favored disease resistance, thereby increasing yield. Hence, the discovery of the ZmCPK39–ZmDi19–ZmPR10 immune module provides insight into the mechanisms underlying broad-spectrum quantitative disease resistance and also offers a new avenue for the genetic control of maize foliar diseases. A calcium-dependent protein kinase ZmCPK39 regulates quantitative resistance to multiple foliar diseases in maize through the ZmCPK39–ZmDi19–ZmPR10 immune module.
{"title":"The ZmCPK39–ZmDi19–ZmPR10 immune module regulates quantitative resistance to multiple foliar diseases in maize","authors":"Mang Zhu, Tao Zhong, Ling Xu, Chenyu Guo, Xiaohui Zhang, Yulin Liu, Yan Zhang, Yancong Li, Zhijian Xie, Tingting Liu, Fuyan Jiang, Xingming Fan, Peter Balint-Kurti, Mingliang Xu","doi":"10.1038/s41588-024-01968-4","DOIUrl":"10.1038/s41588-024-01968-4","url":null,"abstract":"Gray leaf spot, northern leaf blight and southern leaf blight are three of the most destructive foliar diseases affecting maize (Zea mays L.). Here we identified a gene, ZmCPK39, that encodes a calcium-dependent protein kinase and negatively regulates quantitative resistance to these three diseases. The ZmCPK39 allele in the resistant line displayed significantly lower pathogen-induced gene expression than that in the susceptible line. A marked decrease in ZmCPK39 abundance mitigated the phosphorylation and degradation of the transcription factor ZmDi19. This led to elevated expression of ZmPR10, a gene known to encode an antimicrobial protein, thereby enhancing maize resistance to foliar diseases. Moreover, the F1 hybrid with reduced ZmCPK39 expression favored disease resistance, thereby increasing yield. Hence, the discovery of the ZmCPK39–ZmDi19–ZmPR10 immune module provides insight into the mechanisms underlying broad-spectrum quantitative disease resistance and also offers a new avenue for the genetic control of maize foliar diseases. A calcium-dependent protein kinase ZmCPK39 regulates quantitative resistance to multiple foliar diseases in maize through the ZmCPK39–ZmDi19–ZmPR10 immune module.","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"56 12","pages":"2815-2826"},"PeriodicalIF":31.7,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41588-024-01968-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142574512","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-04DOI: 10.1038/s41588-024-01963-9
Yuchang Wu, Zhongxuan Sun, Qinwen Zheng, Jiacheng Miao, Stephen Dorn, Shubhabrata Mukherjee, Jason M. Fletcher, Qiongshi Lu
Almost every recent Alzheimer’s disease (AD) genome-wide association study (GWAS) has performed meta-analysis to combine studies with clinical diagnosis of AD with studies that use proxy phenotypes based on parental disease history. Here, we report major limitations in current GWAS-by-proxy (GWAX) practices due to uncorrected survival bias and nonrandom participation in parental illness surveys, which cause substantial discrepancies between AD GWAS and GWAX results. We demonstrate that the current AD GWAX provide highly misleading genetic correlations between AD risk and higher education, which subsequently affects a variety of genetic epidemiological applications involving AD and cognition. Our study sheds light on potential issues in the design and analysis of middle-aged biobank cohorts and underscores the need for caution when interpreting genetic association results based on proxy-reported parental disease history. Genetic associations based on parental history of Alzheimer’s disease are shown to be impacted by uncorrected survival bias and nonrandom survey participation, underscoring the need for caution when interpreting results based on this study design.
几乎所有最新的阿尔茨海默病（AD）全基因组关联研究（GWAS）都进行了荟萃分析，将临床诊断为AD的研究与使用基于父母疾病史的替代表型的研究结合起来。在此，我们报告了目前通过代理进行 GWAS（GWAX）研究的主要局限性，这些局限性是由于未校正的生存偏倚和非随机参与的父母疾病调查造成的，它们导致了 AD GWAS 和 GWAX 结果之间的巨大差异。我们证明，目前的 AD GWAX 在 AD 风险与高等教育之间提供了极具误导性的遗传相关性，进而影响了涉及 AD 和认知的各种遗传流行病学应用。我们的研究揭示了中年生物库队列的设计和分析中可能存在的问题，并强调在解释基于近亲报告的父母疾病史的遗传关联结果时需要谨慎。
{"title":"Pervasive biases in proxy genome-wide association studies based on parental history of Alzheimer’s disease","authors":"Yuchang Wu, Zhongxuan Sun, Qinwen Zheng, Jiacheng Miao, Stephen Dorn, Shubhabrata Mukherjee, Jason M. Fletcher, Qiongshi Lu","doi":"10.1038/s41588-024-01963-9","DOIUrl":"10.1038/s41588-024-01963-9","url":null,"abstract":"Almost every recent Alzheimer’s disease (AD) genome-wide association study (GWAS) has performed meta-analysis to combine studies with clinical diagnosis of AD with studies that use proxy phenotypes based on parental disease history. Here, we report major limitations in current GWAS-by-proxy (GWAX) practices due to uncorrected survival bias and nonrandom participation in parental illness surveys, which cause substantial discrepancies between AD GWAS and GWAX results. We demonstrate that the current AD GWAX provide highly misleading genetic correlations between AD risk and higher education, which subsequently affects a variety of genetic epidemiological applications involving AD and cognition. Our study sheds light on potential issues in the design and analysis of middle-aged biobank cohorts and underscores the need for caution when interpreting genetic association results based on proxy-reported parental disease history. Genetic associations based on parental history of Alzheimer’s disease are shown to be impacted by uncorrected survival bias and nonrandom survey participation, underscoring the need for caution when interpreting results based on this study design.","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"56 12","pages":"2696-2703"},"PeriodicalIF":31.7,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142574513","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Grapevine breeding is hindered by a limited understanding of the genetic basis of complex agronomic traits. This study constructs a graph-based pangenome reference (Grapepan v.1.0) from 18 newly generated phased telomere-to-telomere assemblies and 11 published assemblies. Using Grapepan v.1.0, we build a variation map with 9,105,787 short variations and 236,449 structural variations (SVs) from the resequencing data of 466 grapevine cultivars. Integrating SVs into a genome-wide association study, we map 148 quantitative trait loci for 29 agronomic traits (50.7% newly identified), with 12 traits significantly contributed by SVs. The estimated heritability improves by 22.78% on average when including SVs. We discovered quantitative trait locus regions under divergent artificial selection in metabolism and berry development between wine and table grapes, respectively. Moreover, significant genetic correlations were detected among the 29 traits. Under a polygenic model, we conducted genomic predictions for each trait. In general, our study facilitates the breeding of superior cultivars via the genomic selection of multiple traits. By constructing a graph-based grapevine pangenome reference (Grapepan v.1.0) and incorporating structural variations and phenotypic maps, the study investigates the genetic basis of agronomic traits, empowering grapevine genomic breeding.
{"title":"Grapevine pangenome facilitates trait genetics and genomic breeding","authors":"Zhongjie Liu, Nan Wang, Ying Su, Qiming Long, Yanling Peng, Lingfei Shangguan, Fan Zhang, Shuo Cao, Xu Wang, Mengqing Ge, Hui Xue, Zhiyao Ma, Wenwen Liu, Xiaodong Xu, Chaochao Li, Xuejing Cao, Bilal Ahmad, Xiangnian Su, Yuting Liu, Guizhou Huang, Mengrui Du, Zhenya Liu, Yu Gan, Lei Sun, Xiucai Fan, Chuan Zhang, Haixia Zhong, Xiangpeng Leng, Yanhua Ren, Tianyu Dong, Dan Pei, Xinyu Wu, Zhongxin Jin, Yiwen Wang, Chonghuai Liu, Jinfeng Chen, Brandon Gaut, Sanwen Huang, Jinggui Fang, Hua Xiao, Yongfeng Zhou","doi":"10.1038/s41588-024-01967-5","DOIUrl":"10.1038/s41588-024-01967-5","url":null,"abstract":"Grapevine breeding is hindered by a limited understanding of the genetic basis of complex agronomic traits. This study constructs a graph-based pangenome reference (Grapepan v.1.0) from 18 newly generated phased telomere-to-telomere assemblies and 11 published assemblies. Using Grapepan v.1.0, we build a variation map with 9,105,787 short variations and 236,449 structural variations (SVs) from the resequencing data of 466 grapevine cultivars. Integrating SVs into a genome-wide association study, we map 148 quantitative trait loci for 29 agronomic traits (50.7% newly identified), with 12 traits significantly contributed by SVs. The estimated heritability improves by 22.78% on average when including SVs. We discovered quantitative trait locus regions under divergent artificial selection in metabolism and berry development between wine and table grapes, respectively. Moreover, significant genetic correlations were detected among the 29 traits. Under a polygenic model, we conducted genomic predictions for each trait. In general, our study facilitates the breeding of superior cultivars via the genomic selection of multiple traits. By constructing a graph-based grapevine pangenome reference (Grapepan v.1.0) and incorporating structural variations and phenotypic maps, the study investigates the genetic basis of agronomic traits, empowering grapevine genomic breeding.","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"56 12","pages":"2804-2814"},"PeriodicalIF":31.7,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41588-024-01967-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142574511","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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