作物学报 ›› 2018, Vol. 44 ›› Issue (7): 956-965.doi: 10.3724/SP.J.1006.2018.00956
赵仁欣1,李森业1,郭瑞星2,曾新华2,文静1,马朝芝1,沈金雄1,涂金星1,傅廷栋1,易斌1,*(
)
Ren-Xin ZHAO1,Sen-Ye LI1,Rui-Xing GUO2,Xin-Hua ZENG2,Jing WEN1,Chao-Zhi MA1,Jin-Xiong SHEN1,Jin-Xing TU1,Ting-Dong FU1,Bin YI1,*(
)
摘要:
以2016?2017年度187份国家油菜参试品种及2015?2016年度33份续试品种为材料, 利用油菜60K Illumina Infinium SNP (single nucleotide polymorphism)芯片进行基因分型, 得到52 157个SNP标记。按照分型为AA和BB频率不为0、最小基因型频率(minor freq)大于0.05、SNP得率(call freq)大于0.80、样品缺失率小于5%及分型明晰的要求筛选出5374个SNP标记。这些标记的PIC (polymorphism information content)均值为0.27, PIC值大于0.25的SNP标记占55.94%。其中有5143个SNP标记能对应到A1~A10、C1~C9连锁群上, 且比较全面地覆盖了油菜的基因组。用PowerMarker、MEGA等软件对224份样品的5374个标记分析, 结果显示: (1)设置8个品种重复2次点样对照, 得出Infinium芯片的技术误差为0.36%, 与Illumina公司公布的0.1%的技术误差十分接近。(2) NJ (Neighbor-joining)聚类分析中, 97.86%的区试品种的相似系数小于95%、87.88%的续试品种相似系数大于95%, 相似系数95%可作为品种特异性及一致性鉴定的阈值。这5374个SNP标记在油菜全基因组上分布均匀、多态性高、区分度好, 可用于甘蓝型油菜品种特异性和一致性的鉴定分析及甘蓝型油菜品种DNA指纹图谱构建的研究。
| [1] | 王美仙 . 国家冬油菜区试品种指纹鉴定及遗传多样性SSR分析. 华中农业大学硕士学位论文,湖北武汉, 2013 |
| Wang M X . Fingerprint Identification and SSR Based Genetic Diversity Analysis of Cultivars in National Winter Rapeseed Official Trials . MS Thesis of Huazhong Agricultural University, Wuhan, Hubei, China, 2013in Chinese with English abstract) | |
| [2] | 张志刚, 李瑞云, 马宾生, 郑启功, 王福建, 王迎杰, 魏民, 张硕 . 对《非主要农作物品种登记办法》的几点认识. 中国种业, 2017, ( 11):1-4 |
| Zhang Z G, Li R Y, Ma B S, Zheng Q G, Wang F J, Wang Y J, Wei M, Zhang S . Some understandings about the registration methods of non-main crop varieties. Chin Seed Ind, 2017, ( 11):1-4 (in Chinese) | |
| [3] | 刘可心 . 利用SNP芯片构建玉米DNA指纹技术的初步研究. 吉林农业大学硕士学位论文, 吉林长春, 2016 |
| Liu K X . A Preliminary Study on the Construction of Maize DNA Fingerprint Based on SNP Chip. MS Thesis of Jilin Agricultural University, Changchun, Jilin, China, 2016 (in Chinese with English abstract) | |
| [4] | 宁洽, 刘文国, 杨伟光, 路明 . SNP标记在玉米研究上的应用进展. 玉米科学, 2017,25(1):57-61 |
| Ning Q, Liu W G, Yang W G, Lu M . Progress and application of SNP markers in maize. J Maize Sci, 2017,25(1):57-61 (in Chinese with English abstract) | |
| [5] |
史亚兴, 卢柏山, 宋伟, 徐丽, 赵久然 . 基于SNP标记技术的糯玉米种质遗传多样性分析. 华北农学报, 2015,30(3):77-82
doi: 10.7668/hbnxb.2015.03.015 |
|
Shi Y X, Lu B S, Song W, Xu L, Zhao J R . Genetic diversity analysis of waxy corn inbred lines by single nucleotide polymorphism (SNP) markers. Acta Agric Boreali-Sin, 2015,30(3):77-82 (in Chinese with English abstract)
doi: 10.7668/hbnxb.2015.03.015 |
|
| [6] |
Singh N, Jayaswal P K, Panda K, Mandal P, Kumar V, Singh B, Mishra S, Singh Y, Singh R, Rai V, Gupta A, Sharma T R, Singh N K . Single-copy gene based 50K SNP chip for genetic studies and molecular breeding in rice. Sci Rep, 2015,5:11600
doi: 10.1038/srep11600 pmid: 4481378 |
| [7] | Zhao K Y, Tung C W, Eizenga G C, Wright M H, Ali M L, Price A H, Norton G J, Islam M R, Reynolds A, Mezey J , McClung A M, Bustamante C D, McCouch S R. Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nat Commun, 2011,2:467 |
| [8] |
侯莉娟, 齐晓, 齐冬梅, 陈双燕, 刘公社 . 用于羊草基因分型的SNP分子标记技术研究. 草业学报, 2016,25:105-113
doi: 10.11686/cyxb2015466 |
|
Hou L J, Qi X, Qi D M, Chen S Y, Liu G S . A study of SNP molecular marker technology for Leymus chinensis genotyping. Acta Pratac Sin, 2016,25:105-113 (in Chinese with English abstract)
doi: 10.11686/cyxb2015466 |
|
| [9] |
赵久然, 王凤格, 易红梅, 田红丽, 杨扬 . 我国玉米品种标准DNA指纹库构建研究及应用进展. 作物杂志, 2015, ( 2):1-6
doi: 10.16035/j.issn.1001-7283.2015.02.001 |
|
Zhao J R, Wang F G, Yi H M, Tian H L, Yang Y . Progress of construction of Chinese maize varieties standard DNA fingerprint database. Crops, 2015, ( 2):1-6 (in Chinese with English abstract)
doi: 10.16035/j.issn.1001-7283.2015.02.001 |
|
| [10] |
Chen S, Yang Y, Shi W W, Ji Q, He F, Zhang Z D, Cheng Z K, Liu X N, Xu M L . Badh2, encoding betaine aldehyde dehydrogenase, inhibits the biosynthesis of 2-acetyl-1-pyrroline, a major component in rice fragrance. Plant Cell, 2008,20:1850-1861
doi: 10.1105/tpc.108.058917 |
| [11] |
Liu L Z, Qu C M, Wittkop B J, Yi B, Xiao Y, He Y J, Snowdon R J, Li J N . A high-density SNP map for accurate mapping of seed fibre QTL in Brassica napus L. PLoS One, 2013,8:e83052
doi: 10.1371/journal.pone.0083052 pmid: 3873396 |
| [12] | 邹喻苹, 葛颂 . 新一代分子标记-SNPs及其应用. 生物多样性, 2003,11:370-382 |
| Zou Y P, Ge S . A novel molecular marker-SNPs and its application. Biodiversity, 2003,11:370-382 (in Chinese with English abstract) | |
| [13] |
Yang X H, Xu Y B, Shah T, Li H H, Han Z H, Li J S, Yan J B . Comparison of SSRs and SNPs in assessment of genetic relatedness in maize. Genetica, 2011,139:1045-1054
doi: 10.1007/s10709-011-9606-9 pmid: 21904888 |
| [14] | 杨润婷, 吴波, 李翀, 曾培, 曾继吾, 钟云, 姜波, 周碧容, 钟广炎 . 两种SNP分型方法的比较及其在柚品种鉴定中的应用. 园艺学报, 2013,40:1061-1070 |
| Yang R T, Wu B, Li C, Zeng P, Zeng J W, Zhong Y, Jiang B, Zhou B R, Zhong G Y . Comparison of allele-specific PCR and high resolution melting analysis in SNP genotyping and their application in pummelo cultivar identification. Acta Hortic Sin, 2013,40:1061-1070 (in Chinese with English abstract) | |
| [15] | 徐群 . 我国籼稻品种遗传结构与多样性的SNP分析. 中国农业科学院博士学位论文, 浙江杭州, 2016 |
| Xu Q . The Genetic Diversity and Structure of Indica Rice in China as Detected by Single Nucleotide Polymorphism Analysis . PhD Dissertation of Chinese Academy of Agricultural Sciences, Hangzhou, Zhejiang, China, 2016 (in Chinese with English abstract) | |
| [16] |
Blair M W, Cortes A J, Penmetsa R V, Farmer A, Carrasquilla- Garcia N, Cook D R . A high-throughput SNP marker system for parental polymorphism screening, and diversity analysis in common bean (Phaseolus vulgaris L.). Theor Appl Genet, 2013,126:535-548
doi: 10.1007/s00122-012-1999-z pmid: 23124389 |
| [17] | 吴金锋 . 甘蓝型油菜SNP与SSR分析及耐旱性状的全基因组关联分析. 中国农业科学院硕士学位论文, 湖北武汉, 2014 |
| Wu J F . SNP and SSR Analysis and Genome-Wide Association Mapping of Drought Tolerance Trait in Brassica napus. MS Thesis of Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China, 2014 (in Chinese with English abstract) | |
| [18] | 张昆鹏 . 利用SNP标记构建油菜品种指纹图谱及定位下卷叶性状基因的研究. 南京农业大学硕士学位论文, 江苏南京, 2013 |
| Zhang K P . Studies on Rapeseed Variety Fingerprints and Mapping of Gene of the Down-Curly Leaf by Use of SNP Markers in Brassica napus L. MS Thesis of Nanjing Agricultural University, Nanjing, Jiangsu, China, 2013 (in Chinese with English abstract) | |
| [19] |
Wu X, Li Y X, Shi Y S, Song Y C, Wang T Y, Huang Y B, Li Y . Fine genetic characterization of elite maize germplasm using high-throughput SNP genotyping. Theor Appl Genet, 2014,127:621-631
doi: 10.1007/s00122-013-2246-y pmid: 24343198 |
| [20] |
Delourme R, Falentin C, Fomeju B F, Boillot M, Lassalle G, André I, Duarte J, Gauthier V, Lucante N, Marty A, Pauchon M, Pichon J P, RibIère N, Trotoux G, Blanchard P, Rivière N, Martinant J P, Pauquet J , High-density SNP-based genetic map development and linkage disequilibrium assessment in Brassica napus L. BMC Genomics, 2013,14:120
doi: 10.1186/1471-2164-14-120 pmid: 3600037 |
| [21] | 喻辉辉, 张启发, 周发松 . 水稻基因组育种芯片及其应用. 生命科学, 2016,28:1258-1267 |
| Yu H H, Zhang Q F, Zhou F S . Rice genomic breeding chips and its applications. Chin Bull Life Sci, 2016,28:1258-1267 (in Chinese with English abstract) | |
| [22] |
王凤格, 赵久然, 田红丽, 杨扬, 易红梅 . 农作物品种DNA指纹库构建研究进展. 分子植物育种, 2015,13:2118-2126
doi: 10.13271/j.mpb.013.002118 |
|
Wang F G, Zhao J R, Tian H L, Yang Y, Yi H M . The progress of the crop varieties DNA fingerprint database construction. Mol Plant Breed, 2015,13:2118-2126 (in Chinese with English abstract)
doi: 10.13271/j.mpb.013.002118 |
|
| [23] |
王凤格, 杨扬, 易红梅, 赵久然, 任洁, 王璐, 葛建镕, 江彬, 张宪晨, 田红丽, 侯振华 . 中国玉米审定品种标准SSR指纹库的构建. 中国农业科学, 2017,50:1-14
doi: 10.3864/j.issn.0578-1752.2017.01.001 |
|
Wang F G, Yang Y, Yi H M, Zhao J R, Ren J, Wang L, Ge J R, Jiang B, Zhang X C, Tian H L, Hou Z H . Construction of an SSR-based standard fingerprint database for corn variety authorized in China. Sci Agric Sin, 2017,50:1-14 (in Chinese with English abstract)
doi: 10.3864/j.issn.0578-1752.2017.01.001 |
| [1] | 田红丽, 杨扬, 范亚明, 易红梅, 郭丹丹, 王凤格, 赵久然. 适于玉米品种鉴定的一套三等位变异SNP新型标记组合[J]. 作物学报, 2026, 52(4): 993-1005. |
| [2] | 马毅娜, 吴晓明玉, 李藕琪, 王圆, 陈丽, 张盈川, 赵伦, 文静, 傅廷栋, 沈金雄. Bna-miR1040-EIF3A模块调控油菜开花时间的功能研究[J]. 作物学报, 2026, 52(2): 349-362. |
| [3] | 李云香, 郭千纤, 侯万伟, 张小娟. 引进ICARDA小麦苗期根系抗旱性状的全基因组关联分析[J]. 作物学报, 2025, 51(9): 2387-2398. |
| [4] | 王彬, 蒙姜宇, 邱浩良, 贺亚军, 钱伟. 甘蓝型油菜BnaDUF579基因家族的鉴定与表达模式分析[J]. 作物学报, 2025, 51(8): 2100-2110. |
| [5] | 王琼, 邹丹霞, 陈兴运, 张威, 张红梅, 刘晓庆, 贾倩茹, 魏利斌, 崔晓艳, 陈新, 王学军, 陈华涛. 大豆开花时间和成熟期性状全基因组关联分析与候选基因预测[J]. 作物学报, 2025, 51(6): 1558-1568. |
| [6] | 孟祥宇, 刁邓超, 刘雅睿, 李云丽, 孙玉晨, 吴玮, 赵雯, 汪妤, 吴建辉, 李春莲, 曾庆东, 韩德俊, 郑炜君. 小麦新品种西农877高产稳产的遗传特性解析[J]. 作物学报, 2025, 51(5): 1261-1276. |
| [7] | 夏琦, 郭滢, 王坤美, 王思忆, 巨建业, 彭雅雯, 刘忠松, 夏石头. 甘蓝型油菜种子和种皮中水杨酸含量与原花色素积累的关系研究[J]. 作物学报, 2025, 51(5): 1189-1197. |
| [8] | 王亚雯, 戚正阳, 尤佳琦, 聂新辉, 曹娟, 杨细燕, 涂礼莉, 张献龙, 王茂军. 棉花60K功能位点基因芯片的制备及应用[J]. 作物学报, 2025, 51(5): 1178-1188. |
| [9] | 王晓琳, 刘忠松, 康雷, 杨柳. 甘蓝型油菜角果长度和每角粒数基因定位以及角果皮转录组动态分析[J]. 作物学报, 2025, 51(4): 888-899. |
| [10] | 张琴, 戴成, 马朝芝. 生长素响应报告基因转化甘蓝型油菜及各组织GUS动态信号分析[J]. 作物学报, 2025, 51(3): 667-675. |
| [11] | 孙程明, 周晓婴, 陈锋, 张维, 王晓东, 彭琦, 郭月, 高建芹, 胡茂龙, 付三雄, 张洁夫. 长链非编码RNA (lncRNA)在甘蓝型油菜分枝角度调控中的功能分析与预测[J]. 作物学报, 2025, 51(3): 559-567. |
| [12] | 黄绒, 周渠晨, 陈楚铭, 罗倩, 易东, 杜常欢, 黄祥宇, 盛锋, 杜雪竹. 过表达BnNRT2.3-like对油菜氮素吸收利用及产量的影响[J]. 作物学报, 2025, 51(12): 3184-3197. |
| [13] | 巨建业, 杨柳, 陈浩, 康雷, 夏石头, 刘忠松. 单细胞核转录组分析揭示油菜种皮分化过程和种子颜色差异原因[J]. 作物学报, 2025, 51(11): 2860-2874. |
| [14] | 张雯, 李玉, 王创, 石磊, 丁广大. 甘蓝型油菜磷转运蛋白BnaPT48的功能研究[J]. 作物学报, 2025, 51(11): 2983-2995. |
| [15] | 胡志康, 舒雨, 王会, 杨莹莹, 廖俊宇, 刘佳, 成洪涛, 郭晨, 张园园, 刘胜毅, 胡琼, 梅德圣, 李超. 甘蓝型油菜苗期耐碱性种质综合鉴定与评价[J]. 作物学报, 2025, 51(10): 2681-2692. |
|
||