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. 2024 May 9:15:1373028.
doi: 10.3389/fgene.2024.1373028. eCollection 2024.

Development and application of microsatellite markers in Hippophae rhamnoides subsp. sinensis Rousi (Hippophae rhamnoides L.) based on transcriptome sequencing

Qingqing Liu  1   2 , Guisheng Ye  1 , Yuhua Ma  1
Affiliations

Development and application of microsatellite markers in Hippophae rhamnoides subsp. sinensis Rousi (Hippophae rhamnoides L.) based on transcriptome sequencing

Qingqing Liu et al. Front Genet. .

Abstract

Hippophae rhamnoides subsp. sinensis Rousi is a cold- and drought-tolerant pioneer species with significant economic and ecological value. Evaluating its genetic diversity and population structure is of great importance for guiding the development and utilization of resources. In this study, a total of 41,804 SSRs were generated by transcriptome sequencing of Hippophae rhamnoides subsp. sinensis Rousi. Among the different SSR motif types, mononucleotide repeats (26,972) were the most abundant, followed by trinucleotides, tetranucleotides, and pentanucleotides. 200 pairs of SSR primers were selected to detect polymorphisms, of which 15 pairs primers were selected as validated polymorphic SSRs used for genetic diversity and population structure analysis. A total of 63 alleles were identified with 15 pairs primers, with Nei's genetic diversity index ranged from 0.27 to 0.83 (average: 0.54), and the expected heterozygosity ranged from 0.16 to 0.73 (average: 0.46). The polymorphism information content ranged from 0.23 to 0.81 (average: 0.48). Genetic structure analyses showed that the 10 populations could be broadly categorized into two groups. AMOVA denoted that genetic variations primarily originated from within the populations, with minimal differences observed between the groups, accounting for only 7% of the total genetic variation. This implies that mutation in H. rhamnoides subsp. sinensis Rousi mainly occurred within the populations. The results showed that the 10 populations of H. rhamnoides subsp. sinensis Rousi are rich in genetic diversity, with low levels of population differentiation and a high degree of gene exchange, which should be taken into consideration for the future work of germplasm resource preservation and seedling breeding.

Keywords: Hippophae rhamnoides subsp. sinensis Rousi; SSR; genetic diversity evaluation; population genetic structure; primer development.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Sample collection map of Hippophae rhamnoides subsp. sinensis.
FIGURE 2
FIGURE 2
Nr Annotation of the Hippophae rhamnoides subsp. sinensis. (A) E-value distribution. (B) similarity distribution. (C) species classification.
FIGURE 3
FIGURE 3
The number distribution of SSR motif unit in Hippophae rhamnoides subsp. sinensis. transcriptome.
FIGURE 4
FIGURE 4
Frequency distribution of genome-SSRs based on motif numbers.
FIGURE 5
FIGURE 5
The principal coordinate analysis (PCoA). The cluster numbers represent the following: 1: Huzhu, 2: Tongde, 3: Maqin, 4: Datong, 5: Menyuan, 6: Qilian, 7: Banma, 8: Huangyuan, 9: Minhe, 10: Guinan.
FIGURE 6
FIGURE 6
Dendrogram of the Hippophae rhamnoides subsp. sinensis Rousi populations constructed using UPGMA methods UPGMA methods based on matrices of pairwise Nei′s genetic distances. Note:The clusters represented by the numbers are: 1: Huzhu, 2: Tongde, 3: Maqin, 4: Datong, 5: Menyuan, 6: Qilian, 7: Banma, 8: Huangyuan, 9: Minhe, 10: Guinan.
FIGURE 7
FIGURE 7
Variation law of ΔK value with K value.
FIGURE 8
FIGURE 8
Structure of optimal K value. Note: The residence groups represented by each cluster number are: 1: Huzhu, 2: Tongde, 3: Maqin, 4: Datong, 5: Menyuan, 6: Qilian, 7: Banma, 8: Huangyuan, 9: Minhe, 10: Guinan.
See this image and copyright information in PMC

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