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Development of Species-Specific InDel Markers in Citrus

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Abstract

Citrus taxonomy is complex owing to the existence of a wide range of species: Poncirus is used mainly for rootstock; Fortunella produces small fruit and edible pericarp; and Citrus comprises the most widespread fruit crop species worldwide. Rapidly increasing genome resources from different citrus species facilitate the development of convenient and genome-wide molecular markers that can be applied to both inter- and intra-species analyses. In this study, by comparing the genome sequences of four citrus species, a set of 1958 InDels were identified and 453 candidate InDels were converted into PCR-based markers. Among these candidate InDels, 268 (65%) exhibited length polymorphisms from 30 bp to 200 bp when applied to seven species from the genera Poncirus, Fortunella and Citrus. Seven InDel markers exhibited high intraspecific polymorphisms in a natural pummelo population. The results showed that the InDel markers are effective for both inter- and intra-specific variation and identification analyses. These InDel markers are expected to be applied to germplasm identification, phylogenetic analysis, genetic diversity evaluation and marker-assisted breeding in citrus.

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Acknowledgments

This work was funded by the National Natural Science Foundation of China (31572105 and 31330066) and the Fundamental Research Funds for the Central Universities.

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  1. Qiuying Fang and Lun Wang contributed equally to this work.

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  1. Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China

    Qiuying Fang, Lun Wang, Huiwen Yu, Yue Huang, Xiaolin Jiang, Xiuxin Deng & Qiang Xu

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  1. Qiuying Fang
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Correspondence to Qiang Xu.

Electronic supplementary material

Supplementary Table 1

The primer sequence of 268 InDel markers. (PDF 109 kb)

Supplementary Table 2

The polymorphism information of the 268 InDel markers in the eight citrus accessions. (PDF 523 kb)

Supplementary Table 3

The germplasm information of the pummelo population. (PDF 53 kb)

Supplementary Fig. 1

Statistical data of InDel fragment-length polymorphisms of 268 markers in the eight species. Black spots InDel polymorphisms in specific species with single spots representing the unique polymorphic InDels of one species and connected spots representing the polymorphic InDels shared by several species. Column chart on the vertical axis indicates the total number of polymorphic markers for each species. Column chart on the horizontal axis indicates the number of every type of polymorphisms. (PNG 129 kb)

High resolution image. (TIF 10494 kb)

Supplementary Fig. 2

The InDel length-polymorphisms of the marker HZAU-IND-chr2-149714A-cgr for the 128 pummelo accessions. Detailed information of the 128 accessions are available in Supplementary Table 3. The accessions with number 29, 42, 50 and 98 are grapefruits not used for analysis. M 100 bp DNA ladder. (PNG 2185 kb)

High resolution image (TIF 20566 kb)

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Fang, Q., Wang, L., Yu, H. et al. Development of Species-Specific InDel Markers in Citrus. Plant Mol Biol Rep 36, 653–662 (2018). https://doi.org/10.1007/s11105-018-1111-1

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