| 黄麻全基因组SSR鉴定与特征分析 |
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| 引用本文： | 姚嘉瑜,张立武,赵捷,徐益,祁建民,张列梅.黄麻全基因组SSR鉴定与特征分析[J].作物学报,2019,45(1):10-17. |
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| 作者姓名： | 姚嘉瑜 张立武 赵捷 徐益 祁建民 张列梅 |
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| 作者单位： | 福建农林大学作物遗传育种与综合利用教育部重点实验室/福建省作物设计育种重点实验室/作物科学学院;福建农林大学海峡联合研究院基因组与生物技术中心 |
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| 基金项目： | This study was supported by the National Natural Science Foundation of China(31771369);the China Agriculture Research System(CARS-19-E06);the Experiment Station of Jute and Kenaf in Southeast China (Nongkejiaofa 2011), and the Construction of Germplasm Resources Platform for Bast Fiber Crops in Fujian, China.(2010N2002) |
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| 摘 要： | 黄麻是世界上重要的天然韧皮部纤维作物之一。然而, SSR标记的缺乏限制了黄麻的遗传改良。本研究从圆果种黄麻测序品种CVL-1的基因组、基因、CDS和cDNA中挖掘SSR信息,利用SSR Primer软件查找SSR位点,并分析其分布特征。结果表明,基于基因组序列共开发了153,242个基因组SSR,平均密度为467.20个SSRMb~(–1);基于cDNA序列开发了10,747个SSR,平均密度为260.85 SSR Mb~(–1)。大部分重复基元为二至四核苷酸,占76.91%,其中cDNA序列SSR中三核苷酸重复基元数量较多而基因组SSR中二核苷酸重复基元数量较多。对于不同类型的SSR重复基元,随着重复单元数量的增加,其基因组和cDNA的SSR分布频率呈现逐步降低特征。黄麻全基因组SSR标记鉴定,不仅可以丰富黄麻分子标记的数量,而且为剖析黄麻重要农艺性状的遗传机制奠定基础。
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| 收稿时间： | 2018-05-18 |
Evaluation and characteristic analysis of SSRs from the whole genome of jute (Corchorus capsularis) |
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| Jia-Yu YAO,Li-Wu ZHANG,Jie ZHAO,Yi XU,Jian-Min QI,Lie-Mei ZHANG.Evaluation and characteristic analysis of SSRs from the whole genome of jute (Corchorus capsularis)[J].Acta Agronomica Sinica,2019,45(1):10-17. |
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| Authors: | Jia-Yu YAO Li-Wu ZHANG Jie ZHAO Yi XU Jian-Min QI Lie-Mei ZHANG |
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| Institution: | 1.Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops of Ministry of Education / Fujian Key Laboratory for Crop Breeding by Design / College of Crop Science, Fuzhou 350002, Fujian, China;2.Center for Genomics and Biotechnology of Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China |
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| Abstract: | Jute is one of the most important natural bast fiber crops worldwide. However, the lack of SSR markers limits the genetic improvement of jute. In this study, simple sequence repeats (SSRs) were identified from the genome, genes, CDS and cDNA of CVL-1, a sequenced variety in Corchorus capsularis. SSR loci was called using SSR Primer software and the characteristics of SSR loci were analyzed. The 153,242 genomic SSRs were called based on the genomic sequence with an average density of 467.20 SSRs Mb -1. Based on the cDNA sequence, we called 10,747 SSRs were developed with an average density of 260.85 SSRs Mb -1. The majority of repeat types were di- to tetra-nucleotides, accounting for 76.91%. Among them, the tri-nucleotide repeat types were the highest abundance repeat types in the cDNA_SSRs while the di-nucleotide repeat types were the highest abundance repeat types in the genomic SSRs. For different SSR repeat types, the genomic and cDNA-SSR frequency decreased dramatically as repeat times increased. Identification of SSR markers in the whole genome can not only enrich the number of molecular markers, but also lay a foundation for the analysis of genetic basis of important agronomic traits in jute. |
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| Keywords: | jute (Corchorus capsularis) genome cDNA SSRs |
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