数字农科院2.0

Sequencing 4.3 million mutations in wheat promoters to understand and modify gene expression

文献类型： 外文期刊

作者： Junli Zhang;Hongchun Xiong;Germán F. Burguener;Hans Vasquez-Gross;Qiujie Liu;Juan M. Debernardi;Alina Akhunova;Kimberly Garland-Campbell;Shahryar F. Kianian;Gina Brown-Guedira;Curtis Pozniak;Justin D. Faris;Eduard Akhunov;Jorge Dubcovsky

作者机构：

关键词： exome capture;functional genomics;promoter capture;VRN1;wheat

期刊名称： Proceedings of the National Academy of Sciences of the United States of America

ISSN： 1091-6490

年卷期： 2023 年 120 卷 38 期

页码：

收录情况： SCIE（2023版）

摘要： Wheat is an important contributor to global food security, and further improvements are required to feed a growing human population. Functional genetics and genomics tools can help us to understand the function of different genes and to engineer beneficial changes. In this study, we used a promoter capture assay to sequence 2-kb regions upstream of all high-confidence annotated genes from 1,513 mutagenized plants from the tetraploid wheat variety Kronos. We identified 4.3 million induced mutations with an accuracy of 99.8%, resulting in a mutation density of 41.9 mutations per kb. We also remapped Kronos exome capture reads to Chinese Spring RefSeq v1.1, identified 4.7 million mutations, and predicted their effects on annotated genes. Using these predictions, we identified 59% more nonsynonymous substitutions and 49% more truncation mutations than in the original study. To show the biological value of the promoter dataset, we selected two mutations within the promoter of the VRN-A1 vernalization gene. Both mutations, located within transcription factor binding sites, significantly altered VRN-A1 expression, and one reduced the number of spikelets per spike. These publicly available sequenced mutant datasets provide rapid and inexpensive access to induced variation in the promoters and coding regions of most wheat genes. These mutations can be used to understand and modulate gene expression and phenotypes for both basic and commercial applications, where limited governmental regulations can facilitate deployment. These mutant collections, together with gene editing, provide valuable tools to accelerate functional genetic studies in this economically important crop.

分类号：

  • 相关文献

[1]充分发掘保护利用生物多样性;促进农业可持续发展——《生物多样性与小麦改良》简评. 李祥洲. 1997

[2]Time-course transcriptome profiling revealed the specific expression patterns of MADS-box genes associated with the distinct developmental processes between winter and spring wheat. Yuchen Du,Chang Liu,Ninghui Li,Xiaoguang Lu,Rui Ge,Xin Liu,Lianshuang Fu,Lie Zhao,Jun Liu,Xiaonan Wang. 2022

[3]30个小麦新品系抗条锈病基因分析及成株期抗病性评价. 冯晶,蔺瑞明,林凤,徐世昌. 2013

[4]小麦抗菌蛋白编码基因BS108的克隆及其转基因抗病小麦的创制. 李钊,周淼平,张增艳,庄洪涛,徐惠君,杜丽璞,叶兴国. 2010

[5]渗透调节物质及有机附加物对小麦体细胞胚发生影响的研究(英文). 孙朝霞,侯思宇,王玉国. 2008

[6]普通小麦品种辐射敏感性模糊聚类分析<英文>. 冯志杰,王琳清. 1992

[7]基因枪转化小麦主要轰击参数的优化. 闵东红,何莎,张彦,夏兰琴. 2013

[8]小麦矮缩病毒分子群体遗传结构研究. 刘艳,王锡锋,周广和. 2008

[9]Genome-wide introgression lines and their use in genetic and molecular dissection of complex phenotypes in rice (Oryza sativa L.). Li, ZK,Fu, BY,Gao, YM,Xu, JL,Ali, J,Lafitte, HR,Jiang, YZ,Rey, JD,Vijayakumar, CHM,Maghirang, R,Zheng, TQ,Zhu, LH.

[10]Soybean Omics and Biotechnology in China. Guo, Yong,Wang, Xiao-Bo,He, Wei,Zhou, Guo-An,Guo, Bing-Fu,Zhang, Le,Liu, Zhang-Xiong,Luo, Zhong-Qin,Wang, Li-Hui,Qiu, Li-Juan. 2011

[11]Progress in Functional Genomics of Plant. Zhang, Shengli,Li, Dongfang,Zhou, Yan,Xu, Guifang,He, Jie,Lu, Hongwei. 2011

[12]High-throughput generation of an activation-tagged mutant library for functional genomic analyses in tobacco. Liu, Feng,Zhang, Qian,Zhang, Zhiguo,Wu, Jinxia,Gong, Daping,Wang, Dawei,Cui, Mengmeng,Liu, Guanshan,Wang, Yuanying.

[13]Large-scale production of enhancer trapping lines for rice functional genomics. Yang, YZ,Peng, H,Huang, HM,Wu, JX,Ha, SR,Huang, DF,Lu, TG.

[14]Chemical- and irradiation-induced mutants of indica rice IR64 for forward and reverse genetics. Wu, JL,Wu, CJ,Lei, CL,Baraoidan, M,Bordeos, A,Madamba, MRS,Ramos-Pamplona, M,Mauleon, R,Portugal, A,Ulat, VJ,Bruskiewich, R,Wang, GL,Leach, J,Khush, G,Leung, H.

[15]Recent Progress on Rice Genetics in China. Hua Jiang , Long-Biao Guo , Qian Qian *. 2007

[16]Developmental Sensitivity In Schistosoma Mansoni T.o Puromycin To Establish D rug Selection Of Transgenic Schistosomes. Yan, HB,Smout, MJ,Ju, C,Folley, AE,Skinner, DE,Mann, VH,Loukas, A,Hu, W,Brindley, PJ,Rinaldi, G. 2018

[17]Applications Of The Crispr/Cas9 System F.or Rice Grain Quality I mprovement: Perspectives And Opportunities. Fiaz, S, Ahmad, S, Noor, MA, Wang, XK, Younas, A, Riaz, A, Riaz, A, Ali, F. 2019

[18]Application of resequencing to rice genomics, functional genomics and evolutionary analysis. Longbiao Guo , Zhenyu Gao , Qian Qian *. 2014

[19]A large-scale whole-exome sequencing mutant resource for functional genomics in wheat. Xiong, Hongchun,Guo, Huijun,Fu, Meiyu,Xie, Yongdun,Zhao, Linshu,Gu, Jiayu,Zhao, Shirong,Ding, Yuping,Du, Qidi,Zhang, Jiazi,Qiu, Lin,Xie, Xiaomei,Zhou, Libin,Chen, Zhongxu,Liu, Luxiang. 2023

[20]Recent progression and future perspectives in cotton genomic breeding. Yang, Zhaoen,Gao, Chenxu,Zhang, Yihao,Yan, Qingdi,Hu, Wei,Yang, Lan,Wang, Zhi,Li, Fuguang. 2023

作者其他论文 更多>>