基于全长转录组信息的枸杞SSR标记开发
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作者单位:

1. 北京林业大学生物科学与技术学院 / 林木、花卉育种生物工程国家林业和草原局重点实验室; 2 宁夏农林科学院枸杞科学研究所

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基金项目:

国家林业和草原局林业行业标准制定(2020-LY-063);宁夏回族自治区农业育种专项项目(2018NYYZ01-05);宁夏回族自治区重点研发技术项目(2021BEF02005)


SSR Marker Development of Lycium Germplasm Based on Full-length Transcriptome Information
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Affiliation:

1. College of Biological Sciences and Technology,Beijing Forestry University/Key Laboratory of Forest and Flower Breeding Biological Engineering,National Forestry and Grassland Administration;2.The Wolfberry Sciences Research Institute,Ningxia Academy of Agriculture and Forestry Science

Fund Project:

National Forestry and Grassland Administration Forestry Industry Standards Formulation(2020-LY-063);Special Project of Agricultural Breeding in Ningxia Hui Autonomous Region(2018NYYZ01-05);Key Research and Development Technology Project of Ningxia Hui Autonomous Region(2021BEF02005)

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    摘要:

    枸杞茄科枸杞属的重要经济植物,广泛分布于我国西北地区,环境适应性强。本研究分析了枸杞基因组中SSR的分布特征,并基于‘宁杞1号’全长转录组开发SSR分子标记,对28个枸杞种质进行遗传多样性分析和亲缘关系分析。用MISA软件搜索全长转录组中SSR位点,设计并筛选多态性好的SSR引物,对206对引物经过毛细管电泳筛选后最终选出23对引物对28个不同分布区的枸杞种质进行遗传多样性分析,遗传系数用非加权组平均法(UPGMA)聚类。23对引物共扩增得到240个等位基因,每个位点的等位基因数范围为4~17,Shannon信息指数最大值为1.177~2.487。期望杂合度和观测杂合度的范围分别为0.635~0.909和0.250~0.964。PIC的范围是0.58~0.902。 遗传距离聚类分析显示28份枸杞种质在相似系数为0.71时被分为四类,宁杞系列种质为Ⅰ类,天精系列和广东种质为Ⅱ类,黑果枸杞种质为Ⅲ类,Ⅳ类中只有枸杞岛种质。利用全长转录组序列可以高质量实现枸杞SSR标记开发,新开发的23对引物后续可用于枸杞种质遗传多样性分析和分子标记辅助育种工作。

    Abstract:

    Lycium is an important economic genus belonging to solanaceae. It is widely distributed in Northwest China and highly adaptable to the environment. In this study, SSR markers were developed based on the full-length transcriptome of Lycium variety ‘Ningqi 1’, followed by genotyping of 28 Lycium germplasm using a subset of polymorphic SSR markers. SSR loci were in silico identified using MISA software and subjected for primer pickup. Twenty-three SSR markers selected from 206 pairs of primers were used for genotyping and analyzing the genetic diversity of Lycium barbarum germplasm from 28 different distribution regions. Genetic coefficients were clustered by unweighted group average (UPGMA) method. A total of 240 alleles were amplified using 23 SSR markers with 4 to 17 alleles at each locus. The maximum Shannon information index was 1.177 to 2.487. The expected and observed heterozygosity ranged from 0.635 to 0.909 and 0.250 to 0.964, respectively. PIC ranged from 0.58 to 0.902. The genetic distance clustering analysis suggested four groups in 28 Lycium germplasm (similarity coefficient = 0.71). The Ningqi series germplasm belonged to group Ⅰ, the Tianjing series and Guangdong germplasm belonged to group Ⅱ, the Lycium ruthenicum germplasm belonged to group Ⅲ, and only Gouqi Island germplasm belonged to group Ⅳ. The total length transcriptomic sequence of Ningqi 1 could be used to develop SSR markers. Collectively, the full-length transcriptome sequences of Lycium are of interest to develop SSR markers, and these newly-developed SSR markers can be used for genetic diversity analysis of Lycium germplasm and molecular marker assisted breeding.

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秦英之,车佳航,尹 跃,等.基于全长转录组信息的枸杞SSR标记开发[J].植物遗传资源学报,2022,23(6):1816-1827.

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  • 收稿日期:2022-03-30
  • 最后修改日期:2022-05-05
  • 录用日期:2022-05-13
  • 在线发布日期: 2022-11-16
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