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DNA methylation modification in heterosis initiation through analyzing rice hybrid contemporary seeds

The Crop Journal 2021年第5期9卷 1179-1190页

作者： Shirong Zhou Meiqing Xing Zhilong Zhao yincong gu Yunping Xiao Qiaoquan Liu Hongwei Xue State Key Laboratory of Crop Genetics and Germplasm Enhancement Jiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing 210095JiangsuChina Joint Center for Single Cell Biology School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghai 200240China National Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai 200032China Shanghai OEbiotech Shanghai 201210China Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province Key Laboratory of Plant Functional Genomics of the Ministry of EducationYangzhou UniversityYangzhou 225009JiangsuChina

Heterosis is an important biological phenomenon and widely applied in *** many studies have been performed by using vegetative organs of F_(1) hybrid plants,how heterosis (or hybrid vigor) is initiated and formed,particularly the underlying molecular mechanism,remain *** contemporary seeds of rice indica varieties 9311 and PA64 were innovatively used and analysis of DNA methylome of embryo and endosperm at early developing stages revealed the globally decreased DNA ***,especially those relate to hormones function and transcriptional regulation present non-additive *** identified heterosis-related superior genes are non-additively methylated in early developing hybrid contemporary seeds,suggesting that key genes/loci responsible for heterosis are epigenetically modified even in early developing hybrid seeds and hypomethylation of hybrid seeds after cross-pollination finally result in the long-term transcriptional change of F_(1) hybrid vegetative tissues after germination,demonstrating that altered DNA methylation in hybrid seeds is essential for initiation regulation and maintenance of heterosis exhibiting in F_(1) hybrid ***,a large number of genes show non-additive methylation in the endosperm of reciprocal hybrids,suggesting that endosperm might also contribute to heterosis.

关键词： DNA methylome Heterosis Rice Reciprocally hybrid seeds Embryo Endosperm

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Resequencing and genome-wide association studies of autotetraploid potato

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Molecular Horticulture 2022年第1期2卷 73-90页

作者： Feng Zhang Li Qu yincong gu Zhi-Hong Xu Hong-Wei Xue College of Agronomy Gansu Provincial Key Laboratory of Aridland Crop ScienceGansu Key Laboratory of Crop Improvement&Germplasm EnhancementGansu Agricultural UniversityLanzhou 730070China Shanghai Collaborative Innovation Center of Agri-Seeds Joint Center for Single Cell BiologySchool of Agriculture and BiologyShanghai Jiao Tong UniversityShanghai 200240China Shanghai OEbiotech Shanghai 201210China National Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai 200032China

Potato is the fourth most important food crop in the *** with a long history for breeding approaches,genomic information and association between genes and agronomic traits remain largely unknown particularly in autotetraploid potato cultivars,which limit the molecular breeding *** resequencing the genome of 108 main cultivar potato accessions with rich genetic diversity and population structure from International Potato Center,with approximate 20-fold coverage,we revealed more than 27 million Single Nucleotide Polymorphisms and~3 million Insertion and Deletions with high quality and *** analysis and genome-wide association studies(GWAS)identified candidate loci related to photoperiodic flowering time and temperature sensitivity as well as disease resistance,providing informative insights into the selection and domestication of cultivar *** addition,GWAS with GWASploy for 25 agronomic traits identified candidate loci by association signals,especially those related to tuber size,small-sized tuber weight and tuber thickness that was also validated by transcriptome *** study provides a valuable resource that facilitates the elucidation of domestication process as well as the genetic studies and agronomic improvement of autotetraploid potato.

关键词： Solanum tuberosum(potato) Autotetraploid cultivars Genome-wide association study(GWAS) Domestication Genome Resequencing

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Whole-genome sequencing reveals rare off-target mutations in CRISPR/Cas9-edited grapevine

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Horticulture Research 2021年第1期8卷 1352-1362页

作者： Xianhang Wang Mingxing Tu Ya Wang Wuchen Yin Yu Zhang Hongsong Wu yincong gu Zhi Li Zhumei Xi Xiping Wang State Key Laboratory of Crop Stress Biology in Arid Areas College of HorticultureNorthwest A&F University712100 YanglingShaanxiChina College of Enology Northwest A&F University712100 YanglingShaanxiChina Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China Ministry of AgricultureNorthwest A&F University712100 YanglingShaanxiChina Novogene Technologies Corporation 100000 BeijingChina OEbiotech Corporation 200000 ShanghaiChina

The CRISPR(clustered regularly interspaced short palindromic repeats)-associated protein 9(Cas9)system is a powerful tool for targeted genome editing,with applications that include plant biotechnology and functional genomics ***,the specificity of Cas9 targeting is poorly investigated in many plant species,including fruit *** assess the off-target mutation rate in grapevine(Vitis vinifera),we performed whole-genome sequencing(WGS)of seven Cas9-edited grapevine plants in which one of two genes was targeted by CRISPR/Cas9 and three wild-type(WT)*** total,we identified between 202,008 and 272,397 single nucleotide polymorphisms(SNPs)and between 26,391 and 55,414 insertions/deletions(indels)in the seven Cas9-edited grapevine plants compared with the three WT ***,3272 potential off-target sites were selected for further *** one off-target indel mutation was identified from the WGS data and validated by Sanger *** addition,we found 243 newly generated off-target sites caused by genetic variants between the Thompson Seedless cultivar and the grape reference genome(PN40024)but no true off-target *** conclusion,we observed high specificity of CRISPR/Cas9 for genome editing of grapevine.

关键词： Whole Sanger rare

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基于454测序的油茶DNA序列微卫星观察与分析

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林业科学 2013年第8期49卷 43-50页

作者：温强徐林初江香梅李江顾胤聪徐立安黄敏仁南京林业大学林木遗传与生物技术省部共建教育部重点实验室南京210037 江西省林业科学院南昌330032

采用MISA软件挖掘比较各1/4个454高通量测序反应获得的普通油茶、浙江红山茶和短柱茶EST序列及普通油茶基因组序列中的微卫星信息。结果显示:3个种的EST序列微卫星出现频率大小相近,普通油茶EST序列的微卫星出现频率高于其基因组序列的... 详细信息

采用MISA软件挖掘比较各1/4个454高通量测序反应获得的普通油茶、浙江红山茶和短柱茶EST序列及普通油茶基因组序列中的微卫星信息。结果显示:3个种的EST序列微卫星出现频率大小相近,普通油茶EST序列的微卫星出现频率高于其基因组序列的;在所有被检索序列的二至六碱基微卫星中,均以二碱基微卫星最多(>55%),并以(AG)n类型为主,但三碱基微卫星在所有EST序列中以(AAG)n类型最多,而在普通油茶基因组序列中则以(AAT)n最多;除六碱基微卫星外,二至五碱基微卫星均表现为不同微卫星重复单元的丰度随着微卫星碱基长度增加而减少。在转录组序列中,除六碱基微卫星之外,不同微卫星单元重复数的变异与重复单元长度呈负相关,推测二碱基微卫星理论多态性最高,而五碱基微卫星理论多态性最低;对在无冗余独立基因各区域中的微卫星进行统计,显示分布比例依次为3'UTR>CDS>5'UTR,在相同区域内比较,UTR区域中二碱基微卫星占总数量比例最大,CDS区域内三碱基微卫星的比例最高,此外5'UTR区域的三碱基微卫星的分布比例均高于3'UTR,初步推断5'UTR区域的微卫星相对3'UTR要保守些。

关键词：山茶属 454高通量测序微卫星

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壳聚糖的血液相容性及其改善方法的研究进展

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化工新型材料 2016年第1期44卷 238-240页

作者：谷春秀李若慧鲍尹聪北京联合大学生物化学工程学院北京100023

综述了近年来改善壳聚糖血液相容性的方法,包括化学修饰改性壳聚糖,在壳聚糖大分子上接枝亲水性高分子链,对壳聚糖进行特殊生物活化,与血液相容性良好的物质相复合等。从改善壳聚糖结构的角度,对今后进一步改善壳聚糖血液相容性的研究... 详细信息

综述了近年来改善壳聚糖血液相容性的方法,包括化学修饰改性壳聚糖,在壳聚糖大分子上接枝亲水性高分子链,对壳聚糖进行特殊生物活化,与血液相容性良好的物质相复合等。从改善壳聚糖结构的角度,对今后进一步改善壳聚糖血液相容性的研究方向进行了展望。

关键词：壳聚糖血液相容性抗凝血化学改性

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手性高效液相色谱法测定左卡尼汀片中右旋卡尼汀的含量

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生命科学仪器 2015年第2期13卷 42-47页

作者：谷春秀程梦威刘露于亚萌张童鲍尹聪北京联合大学生物化学工程学院北京100023

目的：建立以高效液相色谱法测定左卡尼汀片中右旋卡尼汀含量的测定方法。方法：采用phenomenex LUX Cellulose-1（250mm×4.6mm,5μm）色谱柱,流动相为乙腈-0.5mol/L高氯酸钠溶液,梯度洗脱,流速：0.4ml·min^-1,检测波长235 nm,柱温：2... 详细信息

目的：建立以高效液相色谱法测定左卡尼汀片中右旋卡尼汀含量的测定方法。方法：采用phenomenex LUX Cellulose-1（250mm×4.6mm,5μm）色谱柱,流动相为乙腈-0.5mol/L高氯酸钠溶液,梯度洗脱,流速：0.4ml·min^-1,检测波长235 nm,柱温：28℃。结果：在本色谱条件下进样量：10μl;右卡尼汀在浓度1.978μg·ml-1~23.741μg·ml-1范围内线性关系良好,加样回收率（n=9）均在80%~120%之间,RSD值均小于5.0%。结论：本方法快速、准确,重复性好。可以满足左卡尼汀片中右旋卡尼汀含量的测定要求。

关键词：手性高效液相色谱法左卡尼汀片右旋卡尼汀含量测定

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