High-density genetic maps play an essential role in facilitating discovery of functional genes and comparative analysis of genome structure[42]. However, most current genetic maps contain only about hundreds of markers, due to discovery technologies and genotyping costs [43, 44]. Advances in genome sequencing technologies have paved the way for significant improvements in the rapid detection of genetic variation as well as the throughput and wealth of the information obtained. To date, a number of reduced representation sequencing methods have been developed, such as genotyping by sequencing (GBS), type IIB restriction site associated DNA (2b-RAD)[45], and SLAF-sEq. We chose the latter for this study because of its advantages, such as lower sequencing costs, higher genotyping accuracy, and efficient detection system.
Genetic diversity is the amount of variation observed between DNA sequences from distinct individuals of a given species[46]. This pivotal concept of population genetics has implications for species health, domestication, management and conservation. As Known to all, population diversity and structure is of fundamental importance for crop breeding programs. Normal passport (geography and/or pedigree) and phenotype data, traditionally used for the assessment of genetic architecture of the population, has been recently paralleled by the use of molecular markers. This is because the molecular markers allowed researchers to distinguish closely related samples and give more precise variation information among genotypes. SLAF-seq methods are currently used in a wide range of applications. These applications mainly include constructing high-density linkage maps[20, 47], identifying candidate genes and mutant [48, 49], drafting the genome[50] and constructing the core set for rare species[51]. However, the application of population genetics in endangered plant Ammopiptanthus has not been reported. In this study, a high quality of 111,735,304 80-bp long paired-end reads, 467,735 SLAFs and 1,261,501 SNPs were generated using high-throughput SLAF-sEq. Then we analyzed the genetic diversity(both morphology and molecular)and population structure of 111 kinds of Ammopiptanthus that grow in different locations of China in order to begin to lay a foundation for future yield-improvement endangered plant breeding programs.
Species that are considered threatened or endangered often exhibit low genetic diversity, especially when populations are small or disconnected[52]. Higher levels of genetic diversity allow species to adapt to environmental changes and reduces their susceptibility to catastrophic extinction events[53]. In this study, the 111 Ammopiptanthus lines were used as materials, by comparing the genetic diversity of Ammopiptanthus mongolicus and Ammopiptanthus nanus, most groups can be divided into the independent group, may be experienced the founder effect or the result of the bottleneck effect, GS-MQ group as compared to other Ammopiptanthus nanus on the related closer to the Ammopiptanthus mongolicus group, showing the geographical position close group is affected by the same climate, tending to be more consistent in evolutionary history.
The species evolution is largely related to the genetic diversity. Generally, species with high genetic diversity are better able to adapt to changing ecological environment, while species with low genetic diversity are less adaptable to the environment and are passive in the permanent evolution. In this study, the genetic diversity and genetic structure of different geographic populations in Ammopiptanthus mongolicus and Ammopiptanthus nanus was explored by SLAF for the first time. Previous studies have shown that the heterozygosity is an important measure of overall genetic diversity. Our results showed that the genetic diversity of Ammopiptanthus mongolicus (he = 0.32522, ho = 0.31129) was higher than that of Ammopiptanthus nanus (he = 0.26143, ho = 0.25834). The population differentiation degree of Ammopiptanthus mongolicus was low (FST=0.1248), indicating that the population differentiattion was moderate and the variation mainly existed in the population. While the differentiation degree of Ammopiptanthus nanus population in Xinjiang was high (FST = 0.6989), indicating that Ammopiptanthus nanus population was highly differentiated and the variation mainly existed between populations. The variation of Ammopiptanthus mongolicus and Ammopiptanthus nanus exists between species, which is closely related to the geographical distance between the two species.
Gene flow are integral to interpretation of microevolutionary patterns and geographic structure. Through gene flow, we strive to gain insights into evelutionary independence and potential for population diversification, differentiation and ultimately speciation. Gene flow can halt or reduce genetic divergence that accumulates due to population isolation. In this study, the gene flow value (Nm) among Ammopiptanthus mongolicus population was 3.506, it indicates that genetic differentiation between Ammopiptanthus mongolicus populations was small, while the gene flow value (Nm) among Ammopiptanthus nanus population was 0.431, its genetic differentiation is higher than Ammopiptanthus mongolicus. Overall, the average of gene flow (Nm) was 0.360, indicating that the gene flow level of the whole population was low and the genetic differentiation was high. The main reason may be related to geographical distribution and interspecific isolation. Our analysis results are consistent with the previous studies.
Recently, Ding[54] found that the mountain and monsoon are mainly reasons of terrestrial biodiversity, and by the early to middle Miocene, accelerated diversification and colonization of adjacent regions were likely driven jointly by mountain building and intensification of the monsoon. Similarly, based on our research, we speculate on a possible migration model for Ammopiptanthus species in China. The possible migration route may be from Xinjiang to Gansu, then to Ningxia and Inner Mongolia. It is why we can find some Ammopiptanthus nanus species in Mingqin county of Gansu province. In addition, introduction and cultivation are also the reasons of terrestrial biodiversity, this accuracy of this model needs to be verified in future experiments.
In summary, a SLAF-seq approach for Ammopiptanthus was developed to reveal the genetic diversity, genetic structure and relationship between Ammopiptanthus mongolicus and Ammopiptanthus nanus. Meanwhile, SNP including hundreds of genes between Ammopiptanthus mongolicus and Ammopiptanthus nanus were identifed further. Consequently, our study not only provides a cost-effective approach for Ammopiptanthus genome-wide screening, but also contribute to understanding the diversity and origin of Ammopiptanthus in future research.