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Analysis of DNA methylation in different maize tissues

Journal of genetics and Genomics 2008年第1期35卷 41-48页

作者： yanli lu, tingzhao rong, moju cao maize research institute of sichuan agriculture university/key laboratory of crop genetic resource and improvement, ministry of education, ya’an, 625014, china maize research institute of sichuan agriculture university/key laboratory of crop genetic resource and improvement Ministry of Education Ya'an 625014 China

DNA methylation plays an important role in gene expression regulation during biological development and tissue differentiation in plants. This study adopted methylation-sensitive Amplified fragment length polymorphism (AFLP) to compare the levels of DNA cyto- sine methylation at CCGG sites in tassel, bracteal leaf, and ear leaf from maize inbred lines, 18 White and 18 Red, respectively, and also examined specific methylation patterns of the three tissues. Significant differences in cytosine methylation level among the three tissues and the same changing tendency in two inbred lines were detected. Both MSAP (methylation sensitive amplification polymorphism) ratio and full methylation level were the highest in bracteal leaf, and the lowest in tassel. Meanwhile, different methylation levels were ob- served in the same tissue from the inbred lines, 18 White and 18 Red. Full methylation of internal cytosine was the dominant type in the maize genome. The differential methylation patterns in the three tissues were observed. In addition, sequencing of nine differentially me- thylated fragments and the subsequent blast search revealed that the cytosine methylated 5′-CCGG-3′sequences were distributed in re- peating sequences, in the coding and noncoding regions. Southern hybridization was used to verify the methylation polymorphism. These results clearly demonstrated the power of the MSAP technique for large-scale DNA methylation detection in the maize genome, and the complexity of DNA methylation change during plant growth and development. The different methylation levels may be related to specific gene expression in various tissues.

关键词： DNA methylation MSAP isoschizomers

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The genetic Architecture of Flowering Time and Photoperiod Sensitivity in maize as Revealed by QTL Review and Meta Analysis

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Journal of Integrative Plant Biology 2012年第6期54卷 358-373页

作者： Jie Xu yaxi Liu Jian Liu moju cao Jing Wang Hai Lan Yunbi Xu yanli lu Guangtang Pan tingzhao rong maize research institute Sichuan Agricultural UniversityWenjiang 611130SichuanChina key laboratory of Biology and genetic improvement of maize in Southwest Region Ministry of AgricultureChina Triticeae research institute Sichuan Agricultural UniversityWenjiang 611130SichuanChina institute of crop Sciences National Key Facilities for Crop Genetic Resources and ImprovementChinese Academy of Agricultura SciencesBeijing 100081China International maize and Wheat improvement Center(CIMMYT) El Batan 56130TexcocoMexico

The control of flowering is not only important for reproduction, but also plays a key role in the processes of domestication and adaptation. To reveal the genetic architecture for flowering time and photoperiod sensitivity, a comprehensive evaluation of the relevant literature was performed and followed by meta analysis. A total of 25 synthetic con- sensus quantitative trait loci （QTL） and four hot-spot genomic regions were identified for photoperiod sensitivity including 11 genes related to photoperiod response or flower morphogenesis and development. Besides, a comparative analysis of the QTL for flowering time and photoperiod sensitivity highlighted the regions containing shared and unique QTL for the two traits. Candidate genes associated with maize flowering were identified through integrated analysis of the homologous genes for flowering time in plants and the consensus QTL regions for photoperiod sensitivity in maize （Zea mays L.）. Our results suggest that the combination of literature review, meta-analysis and homologous blast is an efficient approach to identify new candidate genes and create a global view of the genetic architecture for maize photoperiodic flowering. Sequences of candidate genes can be used to develop molecular markers for various models of marker-assisted selection, such as marker-assisted recurrent selection and genomic selection that can contribute significantly to crop environmental adaptation.

关键词： maize flowering time photoperiod sensitivity meta-analysis consensus quantitative trait loci (cQTL) molecular breeding.

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A valine residue deletion in ZmSig2A, a sigma factor, accounts for a revertible leaf-color mutation in maize

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The crop Journal 2021年第6期9卷 1330-1343页

作者： Chuan Li Jingwen Wang Zhaoyong Hu Yuanyan Xia Qiang Huang Tao Yu Hongyang Yi yanli lu Jing Wang moju cao maize research institute Sichuan Agricultural UniversityChengdu 611130SichuanChina State key laboratory of crop Gene Exploration and Utilization in Southwest china Chengdu 611130SichuanChina

A nuclear-encoded sigma(σ) factor is essential for the transcriptional regulation of plant chloroplastencoded genes. Five putative maize r factors have been identified by database searches, but their functions are unknown. We report a maize leaf color mutant etiolated/albino leaf 1(eal1) that was derived from space mutation breeding. The eal1 mutant displays etiolated or albino leaves that then gradually turn to normal green at the seedling stage. The changes in eal1 leaf color are associated with changes in photosynthetic pigment content and chloroplast development. Map-based cloning revealed that a single amino-acid deletion changing Val_(480)-Val_(481)-Val_(482) to Val_(480)-Val_(481), in the C-terminal domain σ_(4) of the putative σ factor ZmSig2A, is responsible for the eal1 mutation. In comparison with the expression level of the wild-type(WT) allele ZmSig2A^(+) in WT plants, much higher expression of the mutant allele ZmSig2A^(⊿V) in eal1 plants was detected before the eal1 plants turned to normal green. ZmSig2A shows the highest similarity to rice OsSig2A and Arabidopsis SIG2. Ectopic expression of ZmSig2A^(+) or ZmSig2A^(⊿V) driven by the cauliflower mosaic virus 35 S promoter rescued the pale green leaf of the sig2 mutant, but ectopic expression of ZmSig2A^(⊿V) driven by the SIG2 promoter did not. We propose that the Val deletion generated a new weak allele of ZmSig2A that cannot completely abolish the ZmSig2A function. Some genes involved in chloroplast development and photosynthesis-associated nuclear genes showed significant expression differences between eal1 and WT plants. We conclude that ZmSig2A encoding a r factor is essential for maize chloroplast development. The eal1 mutant with a weak allele of ZmSig2A represents a valuable genetic resource for investigating the regulation of ZmSig2A-mediated chloroplast development in *** eal1 mutation may be useful as a marker for early identification and elimination of false hybrids or transgene transm

关键词： Leaf color mutant Map-based cloning Sigma factor Chloroplast development maize

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The Coix Genome Provides Insights into Panicoideae Evolution and Papery Hull Domestication

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Molecular Plant 2020年第2期13卷 309-320页

作者： Chao Guo yanan Wang Aiguo yang Jun He Chaowen Xiao Shanhua Lv Fengming Han Yibing Yuan Yuan Yuan Xiaolong Dong Juan Guo yawenyang-Hailan Liu Ningzhi Zuo yaxi Hu Kangxu Zhao Zhengbo Jiang Xing Wang Tingting Jiang yaou Sherf moju cao Yuan Wang Zhaobo Long tingzhao rong luqi Huang Shufeng Zhou State key laboratory of Exploration and Utilization of crop Gene resources in Southwest china Key Laboratory of Biology and Genetic Improvement of Maize in Southwest RegionMinistry of AgricultureMaize Research Institute of Sichuan Agricultural UniversityChengdu 611130China National resource Center for Chinese Materia Medica China Academy of Chinese Medical SciencesState Key Laboratory Breeding Base of Dao-di HerbsBeijing 100700China Tobacco research institute of Chinese Academy of Agricultural Sciences Qingdao 266101China key laboratory of Bio-resource and Eco-Environment of ministry of education College of Life SciencesSichuan UniversityChengdu 610064China College of Agronomy Liaocheng UniversityLiaocheng 252000China Biomarker Technologies Corporation Beijing 101300China

Coix is a grass crop domesticated as early as the Neolithic *** is still widely cultivated for both highly nutritional food and medicinal ***,the genetic study and breeding of this crop are hindered by the lack of a sequenced ***,we report de novo sequencing and assembly of the 1619-Mb genome of Coix,and annotation of 75.39%repeats and 39629 protein-coding *** genomics analysis showed that Coix is more closely related to sorghum than maize,but intriguingly only Coix and maize had a recent genome duplication event,which was not detected in *** further constructed a genetic map and mapped several important traits,especially the strength of *** of papery hull(thin:easy dehulling)from the stony hull(thick:difficult dehulling)in wild progenitors was a key step in Coix *** papery hull makes seed easier to process and *** and global transcriptome analysis revealed that the papery hull is a result of inhibition of cell division and wall *** also successfully demonstrated that seed hull pressure resistance is controlled by two major quantitative trait loci(QTLs),which are associated with hull thickness and color,*** two QTLs were further fine mapped within intervals of 250 kb and 146 kb,*** resources provide a platform for evolutionary studies and will facilitate molecular breeding of this important crop.

关键词： Coix genome Comparative genomics Panicoideae evolution hull domestication QTL mapping

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Cloning and characterizing of the fertility restoration associated DNA fragment for C-CMS in maize

Cloning and characterizing of the fertility restoration asso...

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第一届全国玉米生物学学术研讨会

作者：刘永明 moju cao maize research institute /key laboratory of crop genetic and improvement Ministry of Education/ Key Laboratory of Biology and Genetic Improvement of Maize in Southwest RegionMinistry of AgricultureP.R.ChinaSichuan Agricultural University

Compared with T/S-CMS,C-type cytoplasmic male sterility(C-CMS)is becoming the most widely applied form of CMS for the production of hybrid seeds in ***,its genetic basis of the system of fertility restoration is still unknown and *** our study,crosses were made with 6homocytoplasm-heterokaryotic C-CMS lines and 6 testers(diversiform fertility

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玉米雄性不育资源的发掘与利用

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遗传 2022年第2期44卷 134-152页

作者：时子文何青赵卓凡刘孝伟张鹏曹墨菊四川农业大学玉米研究所农业农村部西南玉米生物学与遗传育种重点实验室/西南作物基因资源发掘与利用国家重点实验室成都611130

植物雄性不育是指植物雄性生殖器官不能产生正常有功能花粉的现象。玉米(Zea mays L.)是重要的粮食作物之一,也是较早利用杂种优势的作物之一。当前,生产上广泛种植的玉米品种类型主要是单交种。我国玉米杂交种的播种面积常年稳定在6.2... 详细信息

植物雄性不育是指植物雄性生殖器官不能产生正常有功能花粉的现象。玉米(Zea mays L.)是重要的粮食作物之一,也是较早利用杂种优势的作物之一。当前,生产上广泛种植的玉米品种类型主要是单交种。我国玉米杂交种的播种面积常年稳定在6.2亿亩左右,年用种量10亿公斤以上,常年制种面积高达250多万亩。利用传统的人工去雄或机械去雄的制种方式进行杂交种子的生产,通常需要投入大量的人力、物力和财力。我国玉米制种基地具有明显的区域性,而玉米制种基地对劳动力的需求具有较强的季节性,当前伴随着大量农村劳动力的城市化转移,玉米制种基地出现了严重的用工慌,制种基地的租地费用和人工成本不断提高,使得种子生产成本不断升高。利用植物雄性不育系进行杂交种子的规模化生产,不仅能有效保证杂交种纯度,而且可以大大降低杂交种子的生产成本,同时还可避免极端天气条件下的人工去雄或机械去雄的田间操作困难等问题。因此利用雄性不育进行不育化制种是玉米种业发展的必然趋势。本文综述了我国玉米细胞质雄性不育以及包含光温敏雄性不育在内的细胞核雄性不育资源的发掘及创制进程、植物雄性不育资源从自然群体中获得到有目的性创制的发展过程及玉米雄性不育的研究进展,分析了玉米雄性不育的应用现状及存在的问题。基于我国玉米种业的发展趋势和雄性不育的研究及应用现状,提出了7个需要加强的方面,为玉米雄性不育的创制、研究和利用提供参考。

关键词：玉米雄性不育杂种优势应用现状

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玉米CMS-C同质异核、同核异质系叶绿体基因组比较分析

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四川农业大学学报 2019年第1期37卷 1-7页

作者：邱涛刘孝伟唐津张鹏易洪杨曹墨菊四川农业大学玉米研究所农业部西南玉米生物学及遗传育种重点实验室成都611130

【目的】基于玉米细胞质雄性不育材料粗制线粒体DNA高通量测序数据,对叶绿体基因组进行组装。【方法】应用Illumina Hiseq 2500平台进行线粒体DNA测序。利用软件Velvet对过滤后的clean reads进行拼接和叶绿体基因组的组装。采用在线注... 详细信息

【目的】基于玉米细胞质雄性不育材料粗制线粒体DNA高通量测序数据,对叶绿体基因组进行组装。【方法】应用Illumina Hiseq 2500平台进行线粒体DNA测序。利用软件Velvet对过滤后的clean reads进行拼接和叶绿体基因组的组装。采用在线注释软件DOGMA(http://***/)对叶绿体基因组完整序列进行基因预测和基因功能分析。【结果】成功组装出C48-2和C黄早四2个不育系及48-2和黄早四2个保持系的叶绿体基因组,大小分别为140 473 bp(C48-2)、140 478 bp(C黄早四)、140 458 bp(48-2)、140 448 bp(黄早四),均包含84种编码基因,30种tRNA基因,4种r RNA基因。新组装的4个叶绿体基因组,在基因组大小及所包含的基因种类及数量方面都与叶绿体参考基因组具有较高的相似性,说明粗制线粒体的高通量测序数据可以用来组装叶绿体基因组。叶绿体基因组高度保守,但也存在SNP及InDel,基于不育系与保持系叶绿体DNA(cpDNA)的SNP位点设计特异引物,可用来鉴定区分CMS-C不育胞质与正常胞质。【结论】利用粗制线粒体DNA的高通量测序数据可以完成叶绿体基因组的组装,玉米CMS-C不育系与保持系的叶绿体基因组具有高度的一致性,但也存在一些多态性位点,基于多态性位点成功开发出可区分CMS-C不育胞质与正常胞质的特异标记。

关键词：玉米细胞质雄性不育线粒体DNA 叶绿体基因组高通量测序

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玉米CMS-C同质异核不育系育性恢复的遗传研究

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遗传 2018年第5期40卷 402-414页

作者：赵卓凡黄玲刘永明张鹏魏桂曹墨菊四川农业大学玉米研究所教育部作物基因资源与遗传改良重点实验室农业部西南玉米生物学及遗传育种重点实验室成都611130 四川省农业科学院经济作物育种栽培研究所成都610300

玉米是最早利用细胞质雄性不育系生产杂交种的作物之一,C型细胞质雄性不育系(C-type cytoplasmic male sterile,CMS-C)在杂交种生产中具有重要的作用,育性恢复的稳定性直接影响其应用价值。然而,玉米CMS-C的育性恢复机理复杂,且至今仍... 详细信息

玉米是最早利用细胞质雄性不育系生产杂交种的作物之一,C型细胞质雄性不育系(C-type cytoplasmic male sterile,CMS-C)在杂交种生产中具有重要的作用,育性恢复的稳定性直接影响其应用价值。然而,玉米CMS-C的育性恢复机理复杂,且至今仍不明确。为进一步探究玉米CMS-C育性恢复的影响因素,本研究以玉米CMS-C同质异核不育系C48-2、C黄早四和C478为母本,分别与测验系18白、自330、5022以及恢复系A619组配杂交获得F1。其中育性恢复F1通过自交获得F2,并以育性恢复F1为父本分别给育性保持F1授粉,组配双交群体,共获得4个F2群体,6个双交群体。同时以不育系C48-2、C黄早四和C478为母本,各自的保持系48-2、黄早四和478为父本杂交组配不完全双列杂交F1。将所有杂交组合的F1、F2以及双交组合群体分别在不同年份不同地点种植观察,通过植株田间育性调查并结合室内花粉镜检鉴定育性表现。结果表明:1)同一测验系对玉米CMS-C同质异核不育系的恢保关系不同,暗示不育系的核背景参与调控育性恢复表现;2)在不同年份不同地点对(C48-2×A619)F2群体进行种植观察,发现不同环境下F2群体可育株与不育株的分离比均符合15∶1,但在云南种植的可育株的育性级别主要为Ⅲ和Ⅳ级,而在四川种植的可育株的育性级别主要为Ⅴ级,表明环境对恢复系A619恢复后代的育性表现有影响;3)通过恢保关系测定发现18白不能恢复C478,48-2也不能恢复C478,但双交群体[(C478×18白)F1S×(C48-2×18白)F1F]后代却出现了可育株与不育株的分离;同理,双交群体[(C48-2×自330)F1S×(C478×自330)F1F]的后代也出现了可育株与不育株的分离。因此,本文推测C48-2、C478核背景中存在微效恢复基因,这些微效基因与18白、自330中的微效恢复基因通过杂交聚合后能使C478、C48-2的育性恢复,暗示玉米CMS-C的育性恢复呈现一定的剂量效应。这些结果为进一步认识玉米CMS-C育性恢复的复杂性和多样性奠定了基础,为深入研究玉米CMS-C育性恢复机理以及加快CMS-C在不育化制种中的应用提供重要参考。

关键词：玉米 CMS-C 育性恢复双交群体

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