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Genetic diversity and phylogenetic relationships of citron (Citrus medica L.) and its relatives in southwest China

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Abstract

Understanding the genetic diversity and phylogenetic relationship of citron (Citrus medica L.) is of great importance for making conservation and utilization strategies. Southeast Asia and its vicinity are usually regarded as one of the centers of origin for Citrus. The principal aims of this work were to evaluate the genetic diversity of 56 accessions of citron and its relatives mainly from southwest China, to investigate the genetic structures of citron populations, and to construct a phylogenetic tree to understand the evolution of some hybrids among citrons and other citrus types. SSR analysis detected a total of 387 alleles ranging from 2 to 12 alleles per locus, and nearly all accessions identified could be unequivocally distinguished. The observed and expected heterozygosities averaged 0.36 and 0.49, respectively. From a Bayesian cluster analysis, citrons were characterized by two distinguished genetic structures, which corresponded to the geographical distribution in southwest China. Citron and fingered citron might derive from a common ancestor. Based on the chloroplast sequences, the phylogenetic trees were constructed with congruent topologies and similar levels of statistical support for relationships among citron and its relatives using both maximum parsimony and Bayesian inference methods. Citron formed a monophyletic clade, which was completely different from mandarin (C. reticulata) and pummelo (C. grandis). The genetic contributors of some hybrid species, such as C. limonia, C. aurantifolia, and C. limon, were also discussed, and citron appeared to be a primary contributor to the speciation of these secondary citrus species.

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Acknowledgments

This work was funded by the National Natural Science Foundation of China (31330066 and 31221062), the Special Fund for Agro-scientific Research in the Public Interest (201303093), and the Ministry of Agriculture (CARS-27). The authors are grateful to Dr. Xiuli Zeng for collecting plant materials.

Data archiving statement

We follow standard Tree Genetics and Genomes policy. All the chloroplast gene sequences will be submitted to GenBank, and accession numbers will be provided once available.

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

    Xiaoming Yang, Hang Li, Mei Liang, Qiang Xu, Lijun Chai & Xiuxin Deng

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  1. Xiaoming Yang
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  2. Hang Li
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Communicated by W.-W. Guo

This article is part of the Topical Collection on Germplasm Diversity

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Supplementary Fig. 1

Plot of Delta K (filled circles, solid line) calculated as the mean of the second-order rate of change in likelihood of K divided by the standard deviation of the likelihood of K, m(|L"(K)|)/s [L(K)] (GIF 73 kb)

High Resolution Image (TIF 54 kb)

Supplementary Fig. 2

Inferred clusters based on Bayesian analysis for K = 2 among 36 citron and fingered citron accessions. Each vertical line represents an individual genotype. Different colors stand for the most likely ancestry of the cluster. Individuals with multiple colors have admixed genotypes. The height of each bar represents the probability of a variety belonging to a different subgroup. The identified abbreviated accession names of corresponding samples are listed in Supplementary Table S1 (GIF 28 kb)

High Resolution Image (TIF 250 kb)

Supplementary Fig. 3

The 50 % majority rule consensus tree of 1502 trees obtained from four rounds of Bayesian analysis of the combined data set (matk, trnS-trnG, rps16, rpl16, atpB-rbcL, and accD-psaI chloroplast DNA regions), implementing the GTR model from 39 Citrus taxa. Branch lengths reflect changes per site. Posterior probabilities are given above branches. Clades defined as I, II, III, and IV represent different groups (GIF 54 kb)

High Resolution Image (TIF 2060 kb)

Supplementary Table S1

Classification, origin, group, and list of studied accessions (DOCX 27 kb)

Supplementary Table S2

Summary information of the 77 nSSR primer pairs and the value of annealing temperature (T) (DOCX 20 kb)

Supplementary Table S3

The six chloroplast DNA regions used in the phylogenetic analysis, the marker names and sequences used to amplify them, the type of DNA each region contains and their annealing temperature (T) (DOCX 17 kb)

Supplementary Table S4

Heterozygosity observed in all the analyzed accessions by the 77 nSSR markers (DOCX 17 kb)

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Yang, X., Li, H., Liang, M. et al. Genetic diversity and phylogenetic relationships of citron (Citrus medica L.) and its relatives in southwest China. Tree Genetics & Genomes 11, 129 (2015). https://doi.org/10.1007/s11295-015-0955-x

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