Genome-wide assessment of population structure and genetic diversity for Anabasis aphylla based on specific length amplification fragment sequencing

ABSTRACT

Anabasis aphylla is a salt and alkali resistant shrub grows in arid and semi-arid areas, which is also a constructive species of desert soil. To reveal the population structure and genetic diversity in populations of A. aphylla, a total of 106 samples were used as experimental materials for sequencing by specific-locus amplified fragment sequencing. In total, we obtained 300105 SNP which had high consistency. Phylogenetic tree of A. aphylla result showed there was a certain difference between these samples, which can be divided into two groups. The Shanon–Wiener index of A. aphylla was 0.4440 and the Nei diversity index was 0.2854. AMOVA analysis showed there was genetic differentiation among the seven groups to a certain level. The genetic diversity analysis showed the genetic variation of A. aphylla mainly from groups. This study provides a reference for further comprehensive study of the genetic structure and evolutionary adaptation of A. aphylla.

KEYWORDS:

• Anabasis aphylla
• SLAF-seq
• population structure
• genetic diversity

Acknowledgements

Guangming Chu and Yaling Chang designed the study. Mei Wang, Yaling Chang, Guangming Chu and Mengwen Peng performed the experiments and collected the data. Mei Wang and Yaling Chang designed and performed the data analysis. Yaling Chang led the writing of the manuscript. Guangming Chu and Mei Wang reviewed and edited the manuscript. All authors participated in data interpretation and revised the manuscript.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

The raw data of sequencing data have been published in NCBI (https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA549341).

Additional information

Funding

This work was supported by the Program of the National Natural Science Foundation of China [grant number 31460187], General Financial Grant of the China Postdoctoral Science Foundation [grant number 2017M613253] and Scientific Research Foundation of Shihezi University for Advanced Talents [grant numbers RCZX201518, RCZX201521].

Notes on contributors

Yaling Chang

Yaling Chang is a master’s degree student, studied at the Agricultural College of Shihezi University, Xinjiang, China. Her main research direction is forest ecology.

Mengwen Peng

Mengwen Peng is a master’s degree student, studied at the Agricultural College of Shihezi University, Xinjiang, China. Her main research direction is forest ecology.

Guangming Chu

Guangming Chu is an associate professor of ecology, focuses on forest ecology and conservation and utilization of woody plant resources. His main works include the research on the construction of artificial oasis protection ecological security system (Xinjiang, China, 2012) and the physiological and ecological responses and adaptation strategies of vegetation in arid and semi-arid regions (Xinjiang, China, 2010).

Mei Wang

Mei Wang is an associate professor of ecology, focuses on forest ecology and conservation biology. Her main works include the research on the construction of artificial oasis protection ecological security system (Xinjiang, China, 2012) and the ecological and conservation techniques of endangered plant populations in Qinling (Xinjiang, China, 2015).