Genetic diversity and genetic structure of Haloxylon ammodendron in the Turpan and Hami area, Xinjiang, China

doi:10.17521/cjpe.2024.0214

Abstract

Abstract:

Aims In this study, we analyzed the genetic diversity and structure of Haloxylon ammodendron populations in the Turpan-Hami area, Xinjiang. The objective is to reveal the genetic diversity and genetic structure of the Haloxylon ammodendron population in the region, so as to provide a scientific basis for the conservation of Haloxylon resources in these areas.

Methods We sampled 154 individuals from 13 natural populations of H. ammodendron. Based on single nucleotide polymorphism (SNP) and chloroplast sequences genome data obtained by population resequencing, nucleotide diversity, haplotype diversity and genetic differentiation coefficient were calculated. The genetic structure was assessed by conducting ADMIXTURE, principal components analysis (PCA), phylogenetic tree and chloroplast haplotype network analyses.

Important findings The SNPs variations indicated that population Qitai exhibited higher nucleotide diversity compared to Barikun, Xishan and Qincheng Township in Hami City. Haloxylon ammodendron populations in the Turpan-Hami area can be divided into four groups. Populations in the Barkol County of Hami City has similar genetic composition with populations in the southeast of Junggar Basin and Gansu Province, and unique genetic compositions were retained in the Gaochang District and Xishan Township. The chloroplast genome analyses results showed that 39 haplotypes were detected, and Qitai region had the most diverse haplotypes and the highest genetic diversity. The haplotypes from Qitai were found in both Turpan-Hami and Gansu populations. This may suggest that H. ammodendron populations in the Turpan-Hami region originated from Qitai and dispersed eastward.

Key words: Haloxylon ammodendron, genome resequencing, population genetic structure, chloroplast genome haplotype, nucleotide diversity

ZHANG Wang, TAN Si-Yi, TU Wen-Qin, LOU An-Ru. Genetic diversity and genetic structure of Haloxylon ammodendron in the Turpan and Hami area, Xinjiang, China[J]. Chin J Plant Ecol, 2025, 49(11): 1858-1868.

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URL: https://www.plant-ecology.com/EN/10.17521/cjpe.2024.0214

https://www.plant-ecology.com/EN/Y2025/V49/I11/1858

Figures/Tables 8

Table 1 Sampling information and genetic diversity of the 13 Haloxylon ammodendron populations

序号 ID	地点 Locality	编号 Code	经度 Longitude (E)	纬度 Latitude (N)	样本量 Sample size	单倍型 Haplotypes	核苷酸多样性 Nucleotide diversity (π)
新疆昌吉回族自治州 Changji Hui Autonomous Prefecture, Xinjiang
1	奇台 Qitai	QT	89.63°	44.19°	12	H3(3), H4(1), H5(2), H6(1), H14(1), H15(1), H34(1), H35(1), 36(1)	0.004	-0.604	0.929
2	木垒 Mori	ML	90.78°	44.03°	12	H11(10), H29(1), H30(1)	0.003	-0.050	0.318
新疆吐鲁番和哈密地区 Turpan and Hami area, Xinjiang
3	星星峡 Xingxingxia	XXX	95.17°	41.72°	12	H20(10)	0.003	0.440	0.000
4	镜儿泉 Jing’erquan	JEQ	95.34°	42.35°	12	H7(1), H8(9), H28(1)	0.004	0.194	0.345
5	沁城 Qincheng	QCN	94.61°	42.60°	12	H6(3), H12(2), H13(2), H14(1), H31(1), H32(1), H33(1)	0.003	-0.748	0.909
6	西山乡 Xishan Township	XSN	93.35°	43.06°	12	H5(1), H18(8), H19(1), H20(1)	0.003	0.419	0.491
7	亚勒曼 Yaleman	YLM	95.70°	43.05°	12	H8(7), H40(5)	0.003	-0.010	0.530
8	三塘湖 Santanghu	STH	93.21°	44.11°	12	H6(7), H15(1), H16(1), H37(1), H38(1), 39(1)	0.003	-0.771	0.682
9	老爷庙 Laoyemiao	LYM	93.93°	44.66°	12	H9(7), H10(5)	0.003	-0.164	0.530
10	汉水泉 Hanshuiquan	HSQ	92.05°	44.52°	12	H6(4), H24(4), H25(1), H26(1), H27(1)	0.002	-0.843	0.782
11	吐鲁番 Turpan	TLF	88.86°	43.28°	12	H17(11), H18(1)	0.004	0.493	0.167
甘肃 Gansu
12	敦煌 Dunhuang	DH	94.70°	40.11°	12	H3(3), H4(4), H5(4)	0.004	-0.292	0.727
13	阿克塞 Aksay	AKS	94.36°	39.72°	12	H1(8), H2(2), H22(1), H23(1)	0.003	-0.630	0.561

Fig. 1 Estimation of cross-validation errors (CV error) for K values ranging from 1 to 6 of the13 Haloxylon ammodendron populations.

Fig. 2 Results of population genetic structure and geographical distribution of Haloxylon ammodendron obtained based on single nucleotide polymerphism (SNP) markers. A, ADMIXTURE results for 151 samples from 13 populations at K = 4. B, Geographical distribution of the genetic structure of 13 H. ammodendron populations with ADMIXTURE at K = 4. The abbreviations indicate population codes, as shown in Table 1.

Fig. 3 Neighbor-Joining tree (A) and principal components analysis (PCA) (B) of 13 Haloxylon ammodendron populations obtained based on single nucleotide polymorphism markers. G-I-G-IV represents the four groups divided according to the ADMIXTURE result. The abbreviations indicate population codes, as shown in Table 1.

Table 2 Pairwise genetic differentiation (Fst) of the four groups in this study

类群 Inferred group	G-I	G-II	G-III	G-IV
G-I	-	0.048	0.110	0.038
G-II		-	0.136	0.059
G-III			-	0.118
G-IV				-

Fig. 4 Geographical distribution of 39 haplotypes of 13 Haloxylon ammodendron populations. The abbreviations indicate population codes, as shown in Table 1. In the fan chart, the color represents different haplotypes, and the size of the fan represents the proportion of haplotypes in the population. Clade I-IV represent four clades divided according to chloroplast genomes.

Fig. 5 A maximum likelihood phylogenetic tree of the 149 Haloxylon ammodendron based on chloroplast genomes. The end of each branch represents 149 individuals in 13 H. ammodendron populations, QT is red, TLF is light blue, HSQ, STH, QCN is purple, LYM is orange, XSN is brown, ML is green, JEQ, YLM, XXX is dark blue, AKS, DH is yellow. The information of populations is shown in Table 1. The outmost colored strips (Clade I-IV) indicate four clades divided according to chloroplast genomes.

Fig. 6 Haplotype (Hap) network for the 39 haplotypes of Haloxylon ammodendron based on chloroplast genomes. The circles represent haplotypes, the size of the circle represents the number of individuals with the haplotype, and different colors represent different populations. The abbreviations indicate population codes, as shown in Table 1. The black circle represents the unsampled or extinct haplotypes, and the white circle represents the haplotype of Haloxylon persicum. The fan size indicates the proportion of individuals from different populations with a certain haplotype. Clade I-IV represent four clades divided according to chloroplast genomes.

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