不同品种紫花苜蓿转录组分析及营养品质差异的探讨

doi:10.11686/cyxb2018721

草业学报 ›› 2019, Vol. 28 ›› Issue (10): 199-208.DOI: 10.11686/cyxb2018721

不同品种紫花苜蓿转录组分析及营养品质差异的探讨

成启明¹, 格根图¹, 撒多文², 王志军³, 范文强⁴, 卜振鲲¹, 司强¹, 李俊峰¹, 卢娟⁵, 贾玉山^1,*

1.内蒙古农业大学草原与资源环境学院,农业部饲草栽培、加工与高效利用重点试验室,草地资源教育部重点实验室,内蒙古呼和浩特 010011;
2.内蒙古自治区科技信息研究院,内蒙古呼和浩特 010010;
3.内蒙古自治区草原勘察规划院,内蒙古呼和浩特 010051;
4.内蒙古自治区农牧业科学院,内蒙古呼和浩特 010031;
5.四川省会东县农牧局,四川凉山 615000

收稿日期:2018-10-30 修回日期:2018-12-10 出版日期:2019-10-20 发布日期:2019-10-20
通讯作者: E-mail: jys_nm@sina.com
作者简介:成启明(1990-),男,四川广安人,在读博士。E-mail: 429845801@qq.com
基金资助:
国家自然基金面上项目(31572461)和国家重点研发项目(2016YFC0501308-3)资助

Transcriptome analyses provide insights into differences in nutritional quality among different alfalfa varieties

CHENG Qi-ming¹, GE Gen-tu¹, SA Duo-wen², WANG Zhi-jun³, FAN Wen-qiang⁴, BU Zhen-kun¹, SI Qiang¹, LI Jun-feng¹, LU Juan⁵, JIA Yu-shan^1,*

1.College of Grassland, Resources and Environment, Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization of the Ministry of Agriculture, and Key Laboratory of Grassland Resources of the Ministry of Education P.R of China, Inner Mongolia Agricultural University, Hohhot 010011, China;
2.Inner Mongolia Autonomous Region of institute of scientific & Technical information, Hohhot 010010, China;
3.Inner Mongolia Grassland and Planning Institute, Hohhot 010051, China;
4.Inner Mongolia Academy of Agriculture and Animal Husbandry Sciences, Hohhot 010031, China;
5.Huidong County Agriculture and Animal Husbandry Bureau, Liangshan 615000, China

Received:2018-10-30 Revised:2018-12-10 Online:2019-10-20 Published:2019-10-20
Contact: E-mail: jys_nm@sina.com

摘要/Abstract

摘要： 为了丰富紫花苜蓿转录组数据信息,找出不同品种紫花苜蓿的差异基因及代谢通路。通过Illumina HiSeq 4000平台对准格尔和WL319HQ的苜蓿叶片的RNA文库进行de novo组装。得到了约39G总的核苷酸,2亿多个reads,组装得到66734个Unigenes,平均长度为869 bp。将所得到的Unigenes与NCBI nonredundant protein(Nr),A manually annotated and reviewed protein sequence database(Swissprot),Clusters of eukaryotic orthologous groups(KOG)和Kyoto encyclopedia of genes and genomes(KEGG)数据库比对,分别获得44888(67.26%),29190(43.74%),24844(37.23%)和15647(23.45%)条序列的注释信息。在2个紫花苜蓿叶片中找到1098个差异表达基因 (DEGs) ,其中有706个上调,392个下调(准格尔-vs-WL319HQ)。对其差异基因做了Gene ontology(GO)功能分析和KEGG途径分析,初步分析了2个品种营养品质差异的内在原因。极大地丰富了紫花苜蓿转录组数据信息,为今后紫花苜蓿的转录组测序提供理论依据,同时为紫花苜蓿生产实践提供参考。

关键词: 紫花苜蓿, 转录组测序, 营养品质, de novo组装, 差异基因

Abstract: To enrich alfalfa (Medicago sativa) transcriptome data and clarify which genes and pathways are related to differences in nutritional quality among cultivars, two alfalfa varieties (Zhungeer and WL319HQ) were selected for de novo sequencing using the Illumina HiSeq 4000 platform. We obtained about 39 Gb total nucleotides and more than 200 million reads, and assembled 66734 unigenes with an average length of 869 bp. Then, 44888 (67.26%), 29190 (43.74%), 24844 (37.23%), and 15647 (23.45%) unigenes were annotated on the basis of information from the NCBI nonredundant protein (Nr), Swissprot (a manually annotated and reviewed protein sequence database), clusters of euKaryotic Orthologous Groups (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, respectively. We identified 1098 unigenes as differentially expressed genes (DEGs) in leaves between the two varieties of alfalfa (706 unigenes up-regulated and 392 unigenes down-regulated in Zhungeer vs. WL319HQ). The DEGs were subjected to Gene Ontology (GO) functional analysis and KEGG pathway enrichment analysis, the results of which preliminarily identified the intrinsic reasons for differences in nutritional quality between the two varieties. The data obtained in this study dramatically enrich the transcriptome data available for alfalfa. In addition, these data provide theoretical guidance for transcriptome sequencing of alfalfa in the future, as well as a reference for production practices.

Key words: Medicago sativa, transcriptome, nutritional quality, de novo, differentially expressed genes

成启明, 格根图, 撒多文, 王志军, 范文强, 卜振鲲, 司强, 李俊峰, 卢娟, 贾玉山. 不同品种紫花苜蓿转录组分析及营养品质差异的探讨[J]. 草业学报, 2019, 28(10): 199-208.

CHENG Qi-ming, GE Gen-tu, SA Duo-wen, WANG Zhi-jun, FAN Wen-qiang, BU Zhen-kun, SI Qiang, LI Jun-feng, LU Juan, JIA Yu-shan. Transcriptome analyses provide insights into differences in nutritional quality among different alfalfa varieties[J]. Acta Prataculturae Sinica, 2019, 28(10): 199-208.

参考文献

[1] Zhang X N.Study on drying mechanism and additives storage technology of alfalfa. Hohhot: Inner Mongolia Agricultural University, 2010.
张晓娜. 苜蓿助干机制及添加剂贮藏技术的研究. 呼和浩特: 内蒙古农业大学, 2010.
[2] Guo Z M.Effects of alfalfa hay supplementation on milk yield and milk fat of dairy. Journal of Animal Science and Veterinary Medicine, 2010, 29(3): 20-21, 23.
郭志明. 苜蓿干草不同添加量对奶牛产奶量和乳脂率的影响. 畜牧兽医杂志, 2010, 29(3): 20-21, 23.
[3] Zhao Y M, Zhong H, Cui Z W, et al. Nutritional properties of different varieties and harvest periods of alfalfa. Prataculturae & Animal Husbandry, 2015, (1): 17-22.
赵燕梅, 钟华, 崔志文, 等. 不同品种、刈割时期苜蓿的营养特性. 草业与畜牧, 2015, (1): 17-22.
[4] Yu H, Yao J H, Liu R, et al. Comprehensive evaluation on forage yield nutrition quality and winter surviving rate of different alfalfa varieties. Chinese Journal of Grassland, 2010, 32(3): 108-111.
于辉, 姚江华, 刘荣, 等. 四个紫花苜蓿品种草产量、营养品质及越冬率的综合评价. 中国草地学报, 2010, 32(3): 108-111.
[5] Kang J M, Yang Q C, Guo W S, et al. Yield evaluation of ten introduced alfalfa cultivars in Beijing area of China. Chinese Journal of Grassland, 2010, 32(6): 5-10.
康俊梅, 杨青川, 郭文山, 等. 北京地区10个紫花苜蓿引进品种的生产性能研究. 中国草地学报, 2010, 32(6): 5-10.
[6] Gao W W, Tong J M, Li Z, et al. Quantification of saponins in 45 different cultivars of alfalfa (Medicago sativa L.). Chinese Agricultural Science Bulletin, 2006, (2): 191-194.
高微微, 佟建明, 李展, 等. 不同品种紫花苜蓿中总皂苷含量的比较研究. 中国农学通报, 2006, (2): 191-194.
[7] Costo V, Angelini C, De F I, et al. Uncovering the complexity of transcriptomes with RNA-Seq. Biomed Biotechnol, 2010, 853-916.
[8] Lu T T, Lu G J, Fan D L, et al. Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq. Genome Research, 2010, 20: 1238-1249.
[9] Wang Z Y, Fang B P, Chen J Y, et al. De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweet potato (Ipomoea batatas). BMC genomics, 2010, 11(1): 726.
[10] Zhang J N, Liang S, Duan J L, et al. De novo assembly and characterization of the transcriptome during seed development, and generation of genic-SSR markers in peanut (Arachis hypogaea L.). BMC Genomics, 2012, 13(1): 90.
[11] Grabherr M G, Haas B J, Yassour M, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology, 2011, 29(7): 644-652.
[12] Mortazavi A, Williams B A, McCue K, et al. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods, 2008, 5(7): 621-628.
[13] Reiner A, Yekutieli D, Benjamini Y.Identifying differentially expressed genes using false discovery rate controlling procedures. Bioinformatics, 2003, 19(3): 368-375.
[14] Conesa A, Götz S, García-Gómez J M, et al. Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 2005, 21: 3674-3676.
[15] Ye J, Fang L, Zheng H K, et al. Wego: A web tool for plotting go annotations. Nucleic Acids Research, 2006, 34(2): 293-297.
[16] Yang S.Feed analysis and feed quality inspection technology. Beijing: China Agricultural University Press, 1999.
杨胜. 饲料分析及饲料质量检测技术. 北京: 北京农业大学出版社, 1999.
[17] Chen J.Comparison on agronomic traits and nutritional value of 20 alfalfa varieties in different soil conditions. Changchun: Northeast Normal University, 2017.
陈洁. 不同土壤条件下20个紫花苜蓿品种农艺性状及营养价值的比较. 长春: 东北师范大学, 2017.
[18] Mizrachi E, Hefer C A, Ranik M, et al. De novo assembled expressed gene catalog of a fast-growing eucalyptus tree produced by Illuminam RNA-Seq. BMC genomics, 2010, 11(1): 681.
[19] Wang Z, Fang B, Chen J, et al. De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweet potato (Ipomoea batatas). BMC genomics, 2010, 11: 726.
[20] Iorizzo M, Senalik D A, Grzebelus D, et al. De novo assembly and characterization of the carrot transcriptome reveals novel genes, new markers, and genetic diversit. BMC genomics, 2011, 12: 389.
[21] Gahlan P, Singh H R, Shankar R, et al. De novo sequencing and characterization of Picrorhiza kurrooa transcriptome at two temperatures showed major transcriptome adjustments. BMC genomics, 2012, 13: 126.
[22] Liu X Q, Zhang H, Gong P, et al. Transcriptome analysis of secondary cell wall synthesis regulation at different developmental stages in alfalfa (Medicago sativa L.). Scientia Agricultura Sinica, 2018, 51(11): 2049-2059.
刘希强, 张涵, 龚攀, 等. 紫花苜蓿不同发育时期次生壁合成调控的转录组分析. 中国农业科学, 2018, 51(11): 2049-2059.
[23] Zhang S H.De novo transcriptome sequencing and comparison of gene expression between fall dormant and non-fall dormant Medicago sativa L. Zhengzhou: Henan Agricultural University, 2013.
张森浩. 秋眠及非秋眠紫花苜蓿转录组测序及秋眠相关差异基因的筛选. 郑州: 河南农业大学, 2013.
[24] Yang Y, Xu M, Luo Q, et al. De novo transcriptome analysis of Liriodendron chinense petals and leaves by Illumina sequencing. Gene, 2014, 534(2): 155-162.
[25] Chen L, Li L N, Dai Y P, et al. De novo transcriptome sequencing and analysis of carotenoids biosynthesis related gene expression in Osmauthus serrulatus. Journal of Nanjing Forestry University (Natural Sciences Edition), 2016, 40(5): 21-28.
陈林, 李龙娜, 戴亚平, 等. 短丝木犀转录组测序及类胡萝卜素生物合成相关基因表达分析. 南京林业大学学报(自然科学版), 2016, 40(5): 21-28.
[26] Mu H N, Li H G, Wang L G, et al. Transcriptome sequencing and analysis of sweet osmanthus (Osmanthus fragrans Lour.). Genes genomics, 2014, 36(6): 777-788.
[27] Li Q Y, Zhong C L, Jiang Q B, et al. Sequencing and organization differentially expressed genes analysis of Michelia macclurei transcriptome. Molecular Plant Breeding, 2017, 15(11): 4396-4404.
李清莹, 仲崇禄, 姜清彬, 等. 火力楠转录组测序与组织差异表达基因分析. 分子植物育种, 2017, 15(11): 4396-4404.
[28] Wu X Y, Yan Y, Liu X L.Analysis of the transcriptome of Swertia mileensis based on high-throughput sequencing. Chinese Journal of Modern Applied Pharmacy, 2018, 35(3): 363-369.
吴昕怡, 严媛, 刘小莉. 基于高通量测序的青叶胆转录组研究. 中国现代应用药学, 2018, 35(3): 363-369.
[29] Qi X.The analysis of the differentially expressed genes in alfalfa under cold stress at transcriptome level. Beijing: Chinese Academy of Agricultural Science, 2017.
齐晓. 紫花苜蓿在转录组水平响应低温胁迫的差异表达基因研究. 北京: 中国农业科学院, 2017.
[30] Jiang C.Analysis of the alfalfa (Medicago sativa L.) transcriptome and physiological property in response to salinity stres. Tai’an: Shandong Agricultural University, 2014.
江超. 紫花苜蓿耐盐生理特性及转录组分析. 泰安: 山东农业大学, 2014.
[31] Deng M J, Dong Y P, Zhao Z L, et al. Illumina-based de novo sequencing and characterization of the transcriptome of Paulowuia plant. Scientia Silvae Sinicae, 2013, 49(6): 30-36.
邓敏捷, 董焱鹏, 赵振利, 等. 基于Illumina高通量测序的泡桐转录组研究. 林业科学, 2013, 49(6): 30-36.
[32] Zhang X S, Pei J J, Zhao L G, et al. Transcriptome analysis of different Osmanthus reveals insight into the difference of Osmanthus oil components. Natural Product Research and Development, 2016, 28(4): 529-535.
张雪松, 裴建军, 赵林果, 等. 不同品种桂花转录组分析及桂花精油成分差异的初步探讨. 天然产物研究与开发, 2016, 28(4): 529-535.
[33] Gao Y, Chen G H, Chen X J, et al. Regulation of cellulose biosynthesis in plant cell wall. Biotechnology Bulletin, 2014, (1): 1-7.
高艳, 陈光辉, 陈秀娟, 等. 植物细胞壁纤维素生物合成的调控. 生物技术通报, 2014, (1): 1-7.

不同品种紫花苜蓿转录组分析及营养品质差异的探讨

Transcriptome analyses provide insights into differences in nutritional quality among different alfalfa varieties

RichHTML

PDF (PC)

可视化

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 15

编辑推荐

Metrics

[1]	吴勇, 刘晓静, 蔺芳, 童长春. 河西荒漠灌区紫花苜蓿施肥效应及其基于数据包络分析法的经济效益研究[J]. 草业学报, 2020, 29(9): 94-105.
[2]	邢易梅, 蕫理, 战力峰, 才华, 杨圣秋, 孙娜. 混合接种摩西球囊霉和根瘤菌对紫花苜蓿耐碱能力的影响[J]. 草业学报, 2020, 29(9): 136-145.
[3]	覃凤飞, 李志华, 刘信宝, 渠晖, 平措卓玛, 洛松群措, 苏梦涵. 外源2,4表油菜素内酯对越夏期高温与弱光胁迫下紫花苜蓿生长和光合性能的影响[J]. 草业学报, 2020, 29(9): 146-160.
[4]	童长春, 刘晓静, 蔺芳, 于铁峰. 基于平衡施肥的紫花苜蓿光合特性及光合因子的产量效应研究[J]. 草业学报, 2020, 29(8): 70-80.
[5]	何国兴, 宋建超, 温雅洁, 刘彩婷, 祁娟. 不同根瘤菌肥对紫花苜蓿生产力及土壤肥力的综合影响[J]. 草业学报, 2020, 29(5): 109-120.
[6]	于浩然, 格根图, 王志军, 贾玉山, 连植, 贾鹏飞. 甲酸添加剂及青贮时间对紫花苜蓿青贮品质的影响[J]. 草业学报, 2020, 29(3): 89-95.
[7]	高丽敏, 苏晶, 田倩, 沈益新. 施氮对不同水分条件下紫花苜蓿氮素吸收及根系固氮酶活性的影响[J]. 草业学报, 2020, 29(3): 130-136.
[8]	游永亮, 李源, 赵海明, 武瑞鑫, 刘贵波. 海河平原区施氮磷肥对饲用小黑麦生产性能及营养品质的影响[J]. 草业学报, 2020, 29(3): 137-146.
[9]	钱志豪, 韩丙芳, 刘自婷, 蔡伟, 伏兵哲, 马红彬. 渗灌对宁夏引黄灌区苜蓿生长性状及水分利用率的影响[J]. 草业学报, 2020, 29(3): 147-156.
[10]	张永亮, 于铁峰, 郝凤, 高凯. 施肥与混播比例对豆禾混播牧草产量及氮磷钾利用效率的影响[J]. 草业学报, 2020, 29(11): 91-101.
[11]	孙林, 刘广华, 张欣昕, 薛艳林, 吴晓光, 肖燕子, 殷国梅, 刘思博, 张福金. 蒙药黄芩与制粒对紫花苜蓿维生素和化学成分的影响[J]. 草业学报, 2020, 29(10): 99-108.
[12]	赵雅姣, 刘晓静, 童长春, 吴勇. 紫花苜蓿/玉米间作对紫花苜蓿结瘤固氮特性的影响[J]. 草业学报, 2020, 29(1): 95-105.
[13]	徐洪雨, 李向林. 控水处理对紫花苜蓿抗寒性影响的代谢组学分析[J]. 草业学报, 2020, 29(1): 106-116.
[14]	李应德, 丁婷婷, 段廷玉. AM真菌对紫花苜蓿应答蚜虫胁迫的影响[J]. 草业学报, 2020, 29(1): 155-162.
[15]	苗晓茸, 孙艳梅, 于磊, 马春晖, 张前兵. 氮磷互作对不同茬次滴灌苜蓿生产性能及营养品质的影响[J]. 草业学报, 2019, 28(9): 55-66.