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. 2024 Oct 17;13(20):2910.
doi: 10.3390/plants13202910.

Identification of New Cultivar and Different Provenances of Dendrocalamus brandisii (Poaceae: Bambusoideae) Using Simple Sequence Repeats Developed from the Whole Genome

Ruiman Geng  1 , Junlei Xu  1 , Jutang Jiang  1 , Zhanchao Cheng  1 , Maosheng Sun  2 , Nianhe Xia  3 , Jian Gao  1
Affiliations

Identification of New Cultivar and Different Provenances of Dendrocalamus brandisii (Poaceae: Bambusoideae) Using Simple Sequence Repeats Developed from the Whole Genome

Ruiman Geng et al. Plants (Basel). .

Abstract

Dendrocalamus brandisii is a high-quality bamboo species that can be used for both bamboo shoots and wood. The nutritional components and flavors of D. brandisii vary from different geographical provenances. However, the unique biological characteristics of bamboo make morphological classification methods unsuitable for distinguishing them. Although the new cultivar 'Manxie No.1' has significant differences in the branch characteristics and the color of shoot sheaths compared to the D. brandisii, it still lacks precise genetic information at the molecular level. This study identified 231,789 microsatellite markers based on the whole genome of D. brandisii and analyzed their type composition and distribution on chromosomes in detail. Then, using TP-M13-SSR fluorescence-labeling technology, 34 pairs of polymorphic primers were screened to identify the new cultivar 'Manxie No.1' and 11 different geographical provenances of D. brandisii. We also constructed DNA fingerprinting profiles for them. At the same time, we mapped six polymorphic SSRs to the gene of D. brandisii, among which SSR673 was mapped to DhB10G011540, which is related to plant immunity. The specific markers selected in this study can rapidly identify the provenances and the new cultivar of D. brandisii and help explore candidate genes related to some important traits.

Keywords: D. brandisii; DNA fingerprinting; bamboo species identification; genetic diversity analysis; microsatellite development; molecular characterization of plants; plant genetic markers; provenances and cultivar identification; ‘Manxie No.1’.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
The proportion of different types of microsatellites. (A) The number and proportion of different types of microsatellites. The black numbers and corresponding shapes represent the number and proportion of single and composite SSRs in all SSRs. The gray numbers and corresponding shapes represent the number and proportion of different types of perfect SSRs in all perfect SSRs. (B) Trends in the number of perfect SSRs with different repetitive motifs.
Figure 2
Figure 2
Changes in the content of 2–6 nt motifs with different repetitions. The horizontal axis represents the number of repetitions of 2–6 nt motifs; the vertical axis represents the proportion of a certain type of motif with a certain number of repetitions.
Figure 3
Figure 3
Localization of SSR on the Dendrocalamus brandisii chromosome. (A) The proportion of SSRs successfully located on chromosomes. (B) The proportion of SSR on 70 chromosomes. The right side of the two orange arrows represents the number of SSRs on DbrChrA01–A35 in a clockwise direction, while the left side of the two orange arrows represents the number of SSRs on DbrChrB01–B35 in a clockwise direction. (C) Localization of SSRs on the 5’UTR, 3’UTR, exon, intron, intergenic, and multi-mapped D. brandisii. (D) The distribution of SSR on 70 chromosomes of D. brandisii.
Figure 4
Figure 4
Diagram of cis-acting elements in the promoters of DhB21G011140, DhB31G002880, DhB31G019250, DhA19G015160, DhA19G013950, and DhB10G011540.
Figure 5
Figure 5
Cluster analysis of 12 materials based on SSR markers. * represents Cangyuan County, Lincang City, Yunnan Province, China, and ** represents Linxiang District, Lincang City, Yunnan Province, China.
Figure 6
Figure 6
DNA fingerprinting of 12 materials constructed based on 34 pairs of SSR primers. On the right side of the image is the information of 12 materials, with the SSR name above. The number below the image represents the size of all fragments that the corresponding SSR can amplify. Blue and gray, respectively, represent the presence or absence of fragments. * represents Cangyuan County, Lincang City, Yunnan Province, China, and ** represents Linxiang District, Lincang City, Yunnan Province, China.
Figure 7
Figure 7
Sampling site labeling diagram for 11 samples of D. brandisii and 1 sample of ‘Manxie No.1’. The figure above shows the location of the sampling sites on a world map. In the figure below, green, red, blue, and purple represent the sampling sites in Yunnan Province, China; Guangdong Province, China; Yenbai Province, Vietnam; and Chiang Mai Province, Thailand.
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