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Flow cytometry was used to characterize the genome sizes of 323 mulberry germplasm resources, comparing the results with those obtained for the internal standard reference genomes, which ranged from 0.36 to 3.08 Gb (Supplemental Table S1). In the analysis based on FCM, 320 (99%, 320/323) mulberry materials were identified with only one peak compared to the internal standard references, with genome sizes ranging from 0.36 to 3.08 Gb (Supplemental Table S1; Fig. 1). According to the genome size distribution range of the 320 mulberry germplasm resources, 32 representative mulberry materials were further selected for chromosome count (Supplemental Fig. S1; Fig. 1), which revealed that the 32 representative mulberry materials contained 20 mulberry diploids, five triploids, three tetraploids, two hexaploids, one nine-ploidy, and one 22-ploidy, with corresponding chromosome numbers of 2n = 14, 2n = 28, 2n = 42, 2n = 56, 2n = 84, 2n = 126, and 2n = 308, respectively (Fig. 1, Supplemental Fig. S1; Table 1). In these representative mulberry materials, genome size ranged from 0.36−0.44 Gb for diploid; 0.56−0.62 Gb for triploid; 0.71−0.83 Gb for tetraploid; 0.94−1.10 Gb for hexaploid. The genome size of the nine-ploidy was 1.44 Gb, and that of the 22-ploidy was 3.08 Gb (Table 1).
Figure 1.
FCM analysis and chromosome count of mulberry germplasm resources. This figure illustrates the results of FCM analysis and chromosome count of representative material of six different mulberry ploidies. The first column shows the FSC-SSC scatter plot of the sample cells, the horizontal axis is the FSC value, which represents the size of the cells, and the vertical axis is the SSC value, which represents the granularity of the cells. The second column of the graph shows the histograms of fluorescence signals FL2-H and cell counts; the horizontal axis represents the DNA fluorescence intensity, the vertical axis represents the number of cells, S denotes the sample material, and I denotes the internal standard reference material. The graphs in the third column are the chromosome count graphs of the corresponding materials, bar = 5 μm; (a) Shanyu1hao, diploid; (b) K34-1, triploid; (c) Ailaoshan5hao, tetraploid; (d) Huai30-2, hexaploid; (e) Pisang2hao, nine-ploidy; and (f) Yaosang, 22-ploidy.
Table 1. FCM analysis and chromosome count of 33 representative mulberry materials.
Material name Genome size (1C, Gb) Chromosome number Ploidy level Mixed ploids K27-1 0.38 28 2n = 2x no K41-1 0.38 28 2n = 2x no K47-1 0.38 28 2n = 2x no Aoyu 0.42 28 2n = 2x no Baiguo 0.37 28 2n = 2x no Chuansang 0.44 14 2n = 2x no Guihuami 0.37 28 2n = 2x no Huanglusang 0.36 28 2n = 2x no Xiang0hao 0.37 28 2n = 2x no Yichuanhong 0.37 28 2n = 2x no Guoxuan1hao 0.37 28 2n = 2x no Hongguo4hao 0.37 28 2n = 2x no Luban5hao 0.36 28 2n = 2x no Mengjian4hao 0.42 28 2n = 2x no Ribentiancheng 0.39 28 2n = 2x no Shanyu1hao 0.38 28 2n = 2x no Yanjian4hao 0.37 28 2n = 2x no Yuansang1hao 0.38 28 2n = 2x no Yuansang2hao 0.37 28 2n = 2x no Yunsang1hao 0.36 28 2n = 2x no K34-1 0.59 42 2n = 3x no K36-5 0.62 42 2n = 3x no Shidian6hao 0.59 42 2n = 3x no Yueshendashi 0.56 42 2n = 3x no Taiwanchangguosang 0.58 42 2n = 3x no Huasang 0.71 56 2n = 4x no Ailaoshan5hao 0.75 56 2n = 4x no Ailaoshan9hao 0.83 56 2n = 4x no Huai30_2 1.10 84 2n = 6x no Baojing7hao 0.94 84 2n = 6x no Pisang2hao 1.44 126 2n = 9x no Yaosang 3.08 308 2n = 22x no Jialing30hao 0.38 28 2n = 2x yes Jialing30hao 0.68 56 2n = 4x yes Among these 323 mulberry germplasm resources, three were also identified (1%, 3/323) that exhibited mixed-ploidy characteristics (Jialing30hao, Zhe7, Zhe12), with two distinct peaks in comparison with the internal standard references, corresponding to two different ploidy genomes of 0.38 and 0.68 Gb, 0.38 and 0.72 Gb, and 0.39 and 0.74 Gb, respectively, (Supplemental Table S1). Of those, Jialing30hao was selected to conduct a chromosome count. Based on the results, there were two sets of chromosomes in Jialing30hao, with chromosome numbers of 2n = 28 and 2n = 56 (Fig. 2), thus confirming that the material was a mixed ploidy consisting of diploid and tetraploid.
Figure 2.
FCM analysis and chromosome count of the haploid mulberry germplasm resource Jialing30hao. The first graph, from left to right, showed the FSC-SSC scatter plot of the sample cells. The horizontal axis is the FSC value, which represents the size of the cells, and the vertical axis is the SSC value, which means the granularity of the cells. The second graph is the histogram of fluorescence signal FL2-H and cell counts. The horizontal axis represents the DNA fluorescence intensity, the vertical axis represents the number of cells, the S of the first peak indicates the sample diploid of Jialing30hao, the second peak of S indicates the tetraploid of sample Jialing30hao, and I indicates the internal standard references Z. mays. The third graph shows the results of the chromosome count of the diploid of Jialing30hao; and the fourth graph shows the chromosome count results of the tetraploid Jialing30hao, bar = 5 μm.
Positive correlation between genome size and chromosome number in mulberry
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Thirty three representative mulberry materials were selected for chromosome count and the chromosome number and ploidy of these materials were confirmed. These 33 representative mulberry materials contained seven different ploidies (2n = 2x, 3x, 4x, 6x, 9x, 22x, and 2x/4x) with chromosome numbers ranging from 28 to 308 and genome sizes ranging from 0.36 to 3.08 Gb. A linear regression analysis of chromosome number and genome size was further performed (Fig. 3), which revealed a correlation coefficient R2 = 0.9853, indicating that these two factors are directly correlated. For example, in Shanyu1hao, the chromosome number was 2n = 28, with a genome size of 0.38 Gb. K34-1, chromosome number was 2n = 42, with a genome size of 0.59 Gb.
Figure 3.
Linear regression analysis between genome size and chromosome number for 33 representative mulberry samples. The horizontal axis is the genome size, and the vertical axis is the chromosome number.
Mulberry genome size, chromosome number, and ploidy database MGCPdb (https://mgcpdb.biodb.org)
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For more convenience, the genome size, chromosome number, and ploidy database MGCPdb were constructed for mulberry by summarizing the information of all materials investigated in this study (Fig. 4a). This database offers both global and targeted search options (Supplemental Fig. S2), allowing researchers to quickly search (Fig. 4b) and browse (Fig. 4c) detailed information on the material of interest, including information on genome size, chromosome number, ploidy, chromosome diagram (Fig. 4d), and flow cytometry analysis results (Fig. 4e). In addition, there is the option to directly copy or download data in CSV, XLSX, and PDF formats (Supplemental Fig. S2). Raw flow cytometry results for all materials are available for download in MGCPdb, making it easy for users to analyze the data locally (Fig. 4c).
Figure 4.
The process of retrieving relevant information in MGCPdb. (a) The menu navigates the MGCPdb database at the top of the page, which contains four main sections: Home, Browse, Help, Contact, and a global search tool in the upper right. (b) The browsing interface for the MGCPdb database, clicking on the four functional areas in the upper left, allows you to directly copy or download the data in CSV, XLSX, and PDF formats, with a personalized search function on top of each column of data. (c) The MGCPdb database provides detailed data tables on genome size, chromosome number, ploidy, and other related information of every sample. (d) and (e) correspond to the sample analysis graph's chromosome count and FCM results.
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All data generated or analyzed during this study are included in this published article and its supplementary information files.
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About this article
Cite this article
Wang H, Liu J, Xu X, Li Y, Yuan J, et al. 2024. MGCPdb, a collective resource for mulberry genome size, chromosome number, and ploidy. Forestry Research 4: e027 doi: 10.48130/forres-0024-0024
MGCPdb, a collective resource for mulberry genome size, chromosome number, and ploidy
- Received: 06 February 2024
- Revised: 13 July 2024
- Accepted: 22 July 2024
- Published online: 13 August 2024
Abstract: Mulberry is a critical economic tree with a high diversity of germplasm resources. However, the lack of primary data on genome size, chromosome number, and ploidy for this species limits the exploitation of mulberry resources. In this study, the genome size of 323 mulberry germplasm resources were examined using flow cytometry and chromosome numbers analyzed. The genome sizes ranged from 0.36 to 3.08 Gb, and seven different ploidies of mulberry germplasm resources were identified, with chromosome numbers ranging from 14 to 308. Correlation analysis indicated that genome size (1C) and chromosome number positively correlated. Here, the genome size, chromosome number, and ploidy database MGCPdb (
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Key words:
- Flow cytometry /
- Chromosome count /
- Mulberry germplasm resources