1. Introduction
Suaeda spp., which has more than 100 species, is a genus of flowering plants that belongs to the family Amaranthaceae [
1]. These plants are halophytic herbs or shrubs commonly found in Asia, Europe, North America, and seashores worldwide [
2].
Suaeda plants are highly adapted to extreme salt and water conditions [
3]. They have a unique structure that allows them to store water and tolerate high levels of salinity in the soil [
4]. In addition to their medicinal properties, some species of
Suaeda are used for reclamation of degraded saline lands, as well as in the production of biofuels due to their high oil content [
5].
Suaeda represents a significant ecological and economic resource for many countries around the world [
3].
Suaeda aralocaspica is a plant species with succulent leaves that belongs to the family Amaranthaceae. This annual halophyte plant is native to Central Asia and can be found in the salty deserts of the region. In China, this plant is found in the cold desert regions of the Junggar Basin in Xinjiang [
6,
7]. It carries out complete C
4 photosynthesis within individual cells but lacks the characteristic leaf anatomy of other C
4 plants. These features make it potentially valuable in biotechnology of higher photosynthetic efficiencies in agriculturally important C
3 carbon fixation species such as rice [
8]. Seed heteromorphism, which refers to the presence of two distinct types of seeds within a single plant, is a unique characteristic of this species. The two types of seeds are black and brown, and they differ in their size, color, and germination behavior [
9,
10,
11,
12]. Conservation measures are imperative for the survival of
S. aralocaspica, as its population is rapidly diminishing, requiring urgent protection against further decline and potential extinction.
Genetic diversity, also known as gene diversity, is the total range of genetic variation present in different individuals among various populations as well as within the same population [
13]. It is considered a fundamental and essential component of biodiversity. Genetic diversity level is critical in determining the long-term survivability and evolutionary capacity of a specific species [
14]. A decrease in genetic diversity can lead to a reduction in species’ fitness, ultimately increasing their risk of extinction. For this reason, genetic diversity is often utilized as a predictive tool in studies concerning endangered species and species trend analysis [
15,
16].
There are several methods for studying genetic diversity, such as morphological tests, cytological markers, biochemical markers, and molecular markers [
17,
18]. However, molecular markers, in particular, have become one of the most prevalent methods due to their high reliability, independence from environmental factors, and high number [
19]. Among molecular markers, microsatellite markers are increasingly popular for conducting genetic studies. Microsatellite markers, also known as simple sequence repeats (SSR) or short tandem repeat (STR) data, a segment of DNA consisting of 1-6bp repeat units in tandem, offer several advantages, including high information content, co-dominance, and multiple alleles. Therefore, they are widely used in various genetic studies as an effective molecular marker [
20,
21].
There have been limited research efforts focused on exploring the genetic diversity of
Suaeda species [
22,
23]. This could be attributed to the fact that molecular markers specific to the
Suaeda genus have not been extensively developed. Genetic diversity of
S. corniculata from Bunge in Eastern Siberia was analyzed by using five inter-simple sequence repeats (ISSRs) markers [
24]. In a study conducted by Prinz (2013), the genetic diversity and differentiation of 31 populations of
S. maritima from coastal and inland areas of Central Europe were compared using 10 polymorphic microsatellite markers. The findings revealed that there were significant differences in the genetic diversity between populations of
S. maritima from coastal and inland areas. This suggests that the addition of anthropogenic salt sites may have a facilitative effect on gene flow in inland populations of saline plants [
25]. Prinz (2009) also developed a set of 12 polymorphic microsatellite markers specifically designed for analyzing the genetic diversity of
S. maritima. These polymorphic markers were also found to be cross-amplifiable across related species, such as
S. glauca and
S. salsa. Of the 12 markers, 11 were shown to be reproducible and effective for conducting genetic analyses of
Suaeda populations [
8]. The limited research on genetic diversity in
Suaeda species suggests moderate to high levels of genetic diversity within populations and variable levels of diversity among populations. The genome of
S. aralocaspica, comprising 452 Mb, has been sequenced to provide a data base for the analysis and development of SSR markers for
S. aralocaspica and even the genus
Suaeda [
26].
The habitat of S. aralocaspica is facing significant fragmentation and degradation caused by human activities and climate change in China. This fragmentation is posing a potential threat to the species as it may reduce gene flow among isolated populations. The primary aim of this research is to conduct a comprehensive genome-wide study to characterize and develop SSR markers in S. aralocaspica. This study also aims to analyze the genetic diversity of SSRs in S. aralocaspica populations to understand the species’ population structures. The developed SSR markers can be used to identify genetic variations and patterns in different populations of S. aralocaspica, which may be useful in conservation planning and germplasm management in the future.
3. Discussion
Suaeda is a valuable representative plant species among saline plants, with significant research potential. However, the development of molecular markers for Suaeda has been limited, hindering the progress of molecular ecology and population genetics studies on this genus. To address this gap, we utilized the sequencing data of S. aralocaspica to identify SSRs on its genome and subsequently developed 38 SSR markers with good polymorphism. These markers can be used to analyze the genetic diversity of S. aralocaspica and contribute to the study of genetic diversity and structure of the Suaeda plants.
After performing the analysis, we discovered that the frequency of SSRs in
S. aralocaspica’s entire genome was 393.37 SSRs/Mb. This amount was significantly higher when compared to
Anemone coronaria (65.52 SSRs/Mb),
Solanum melongena (120 SSRs/Mb), and
Triticum aestivum (36.68 SSRs/Mb) [
27,
28,
29]. Therefore, it can be inferred that SSRs were abundant in the whole genome of
S. aralocaspica. Dinucleotide and trinucleotide repeats were the most common SSRs in the genome of
S. aralocaspica, similar to Tartary buckwheat [
30]. However, there is a difference in abundance between the two, as dinucleotide repeats were the most common in Tartary buckwheat (63.95%), whereas trinucleotide repeats were more common in
S. aralocaspica (75.74%).
In this study, we examined the genetic diversity of
S. aralocaspica using 38 pairs of SSR primers developed for various populations. We found that the expected heterozygosity (He) and Shannon’s information index (I) values for the three populations ranged from 0.288 to 0.805 and 0.642 to 1.085, respectively. A comparison of our results with those obtained for other species, such as
S. maritima (He = 0.37, I = 0.97) [
25],
S. corniculata subsp.
mongolica (I = 0.1688),
S. “jacutica” (I = 0.0878), and
S. corniculata s. str [
23].
Nuphar submersa (He = 0.42),
Pedicularis kansuensis (He = 0.441, I = 0.781),
Ruta oreojasme (He = 0.687),
Vincetoxicum atratum (He = 0.67),
Ammi seubertianum (He = 0.66, I = 1.28),
Ammi trifoliatum (He = 0.67, I = 1.35), and
Tapiscia sinensis (He = 0.6904, I = 1.4368), revealed some variation in values [
31,
32,
33,
34,
35,
36]. It is essential to note that different plants and SSR loci, as well as the number of markers used, can all affect genetic diversity analysis results.
The genetic diversity analysis of S. aralocaspica populations from three distinct regions revealed differences in their genetic diversity. Specifically, the genetic diversity of S. aralocaspica populations in Fukang was significantly greater than that of populations in Shihezi and Shawan. This may be due to the different habitats of the three populations. For instance, the S. aralocaspica population in Fukang is located near a protected reservoir, making it less susceptible to human activities and boasting relatively stable conditions. It also has a larger habitat area and population size compared to those in Shihezi and Shawan. Conversely, the S. aralocaspica populations in Shihezi and Shawan are more frequently impacted by human activities and experience greater environmental volatility. This may explain the significant differences in genetic diversity observed between the three populations.
In this study, we compared the genetic identity and actual geographic distance of three distinct S. aralocaspica populations. Our findings revealed that the S. aralocaspica populations of Shihezi and Shawan had the closest geographic distance and the highest genetic identity. Conversely, the Fukang and Shawan populations showed the greatest geographic distance and the lowest genetic similarity. These results indicate an inverse relationship between genetic identity and geographic distance among the three S. aralocaspica populations. This suggests that geographic distance may play a vital role in influencing gene flow among different S. aralocaspica populations.
Gene flow has a reducing effect on genetic differentiation between populations, particularly where gene flow is greater than 1 number of migrants (Nm). However, when Nm is less than 1, local differentiation between populations tends to occur. Despite this, the collected samples of
S. aralocaspica indicate greater genetic differentiation, with mean Fst values above 0.25. This suggests that
S. aralocaspica may have undergone local adaptation due to high selection pressure, which can occur even in the presence of high levels of gene flow, according to Endler et al. [
37]. In combination with other data, it is possible that high selection pressure has contributed to the local adaptation of
S. aralocaspica [
38]. Factors that influence plant genetic diversity include species-related factors such as mating systems, bottleneck effects, evolution, and life history, as well as anthropogenic factors.
Heterozygous species typically exhibit greater genetic diversity than self-incompatible species [
39,
40]. Although there is no definitive evidence on the mating system of
S. aralocaspica, its monoecious annual nature and inbreeding coefficients exceeding 0.5 in all three populations suggest a likelihood of more pronounced inbreeding. Further analysis is necessary to determine the exact mating system. Mating among close relatives in small populations often happens out of necessity and results in high inbreeding coefficients and a decline in genetic diversity [
41].
S. aralocaspica populations exhibit high genetic diversity and this may be attributed to natural or anthropogenic factors that have caused severe habitat fragmentation and a significant reduction in population size, with the small populations inheriting a fraction of the genetic variation from the original large populations. Further investigation is needed to establish the exact causes of this phenomenon.