Genome-wide development of insertion-deletion (InDel) markers for Cannabis and its uses in genetic structure analysis of Chinese germplasm and sex-linked marker identification

文献类型： 外文期刊

第一作者： Pan, Gen

作者： Pan, Gen;Li, Zheng;Huang, Siqi;Tao, Jie;Shi, Yaliang;Chen, Anguo;Li, Jianjun;Tang, Huijuan;Chang, Li;Deng, Yong;Li, Defang;Zhao, Lining;Pan, Gen;Huang, Siqi;Chen, Anguo;Li, Jianjun;Tang, Huijuan;Chang, Li;Deng, Yong;Li, Defang;Zhao, Lining

作者机构：

关键词： Cannabis; Insertion-deletion (InDel); Population structure; Sex identification

期刊名称：BMC GENOMICS （ 影响因子：3.969； 五年影响因子：4.478 ）

ISSN： 1471-2164

年卷期： 2021 年 22 卷 1 期

页码：

收录情况： SCI

摘要： BackgroundCannabis sativa L., a dioecious plant derived from China, demonstrates important medicinal properties and economic value worldwide. Cannabis properties have been usually harnessed depending on the sex of the plant. To analyse the genetic structure of Chinese Cannabis and identify sex-linked makers, genome-wide insertion-deletion (InDel) markers were designed and used.ResultsIn this study, a genome-wide analysis of insertion-deletion (InDel) polymorphisms was performed based on the recent genome sequences. In total, 47,558 InDels were detected between the two varieties, and the length of InDels ranged from 4bp to 87bp. The most common InDels were tetranucleotides, followed by pentanucleotides. Chromosome 5 exhibited the highest number of InDels among the Cannabis chromosomes, while chromosome 10 exhibited the lowest number. Additionally, 31,802 non-redundant InDel markers were designed, and 84 primers evenly distributed in the Cannabis genome were chosen for polymorphism analysis. A total of 38 primers exhibited polymorphisms among three accessions, and of the polymorphism primers, 14 biallelic primers were further used to analyse the genetic structure. A total of 39 fragments were detected, and the PIC value ranged from 0.1209 to 0.6351. According to the InDel markers and the flowering time, the 115 Chinese germplasms were divided into two subgroups, mainly composed of cultivars obtained from the northernmost and southernmost regions, respectively. Additional two markers, "Cs-I1-10" and "Cs-I1-15", were found to amplify two bands (398bp and 251bp; 293bp and 141bp) in the male plants, while 389-bp or 293-bp bands were amplified in female plants. Using the two markers, the feminized and dioecious varieties could also be distinguished.ConclusionBased on the findings obtained herein, we believe that this study will facilitate the genetic improvement and germplasm conservation of Cannabis in China, and the sex-linked InDel markers will provide accurate sex identification strategies for Cannabis breeding and production.

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