短穗竹居群遗传结构及气候适应性分析

doi:10.11983/CBB24094

植物学报 ›› 2025, Vol. 60 ›› Issue (3): 407-424.DOI: 10.11983/CBB24094 cstr: 32102.14.CBB24094

短穗竹居群遗传结构及气候适应性分析

张如礼¹, 李德铢², 张玉霄¹^,^*()

¹西南林业大学云南生物多样性研究院, 昆明 650224
²中国科学院昆明植物研究国西南野生生物种质资源库, 昆明 650201

收稿日期:2024-06-19 接受日期:2024-11-15 出版日期:2025-05-10 发布日期:2024-11-26
通讯作者: *张玉霄, 博士, 副研究员, 硕士生导师。主要从事植物系统与演化研究, 以竹亚科为主要研究对象, 开展分类学、分子系统发育学、系统发育基因组学和DNA条形码研究。主持国家自然科学基金项目3项, 科技部科技基础资源调查专项1项, 中国科学院大科学工程装置开放研究项目子课题1项, 云南省科技厅农业基础研究联合专项2项, 获得2019年“云南省万人计划青年拔尖人才”专项资助, 参与国家自然科学基金项目10余项。参编论著(译著) 7部, 发表学术论文40余篇, 其中以第一作者发表被SCI数据库收录期刊论文10余篇。E-mail: yxzhang811203@163.com
基金资助:
国家自然科学基金(31100148);云南省高层次人才培养计划青年拔尖人才专项(YNWR-QNBJ-2019-148)

Population Genetic Structure and Climate Adaptation Analysis of Brachystachyum densiflorum

Zhang Ruli¹, Li Dezhu², Zhang Yuxiao¹^,^*()

¹Yunnan Academy of Biodiversity, Southwest Forestry University, Kunming 650224, China
²Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China

Received:2024-06-19 Accepted:2024-11-15 Online:2025-05-10 Published:2024-11-26
Contact: *E-mail: yxzhang811203@163.com

1. 附录.pdf(1689KB)

摘要/Abstract

摘要： 短穗竹(Brachystachyum densiflorum)是中国特有种。近年来, 由于气候变化和人类活动加剧, 短穗竹栖息地遭到破坏, 破碎化加剧, 居群数量呈减少趋势。该研究对短穗竹6个居群36个个体开展简化基因组测序(RAD-seq), 获得了16 583个单核苷酸多态性(SNPs)位点, 据此评估短穗竹居群遗传结构, 并整合景观遗传学和物种分布模型, 探讨短穗竹对气候变化的适应机制。结果表明, 短穗竹具有中等水平的遗传多样性(PIC=0.722 5, Ho=0.087, He=0.284 3, π=0.317 5), 将不同居群划分为2组, 各居群间存在中度分化(F_ST=0.102)和较高的基因流(Nm=2.442)。基因型-环境关联分析表明, 短穗竹对气候的局部适应推动2个组的分化, 温差、低温和降水共同驱动遗传变异, 筛选出544个与温差、低温(Bio2、Bio6、Bio11和Bio7)和降水量(Bio19)显著相关的适应性位点。物种分布模型显示, 从末次盛冰期到当前, 短穗竹明显向北迁移, 且其分布面积增加了89.5%。预计在2021-2040年和2041-2060年2个时段适生区波动较小, 2061-2080年适生区范围缩小, 安徽境内高适生区部分衰退和破碎化。研究结果为短穗竹的保护利用提供了理论依据。

关键词: 短穗竹, 简化基因组测序, 遗传多样性, 遗传结构, 物种分布模型

Abstract: INTRODUCTION: Genetic diversity is considered as a crucial aspect in assessment and conservation of rare and endangered species. Brachystachyum densiflorum is a species endemic to eastern China. In recent years, with rapid economic development, accelerated urbanization, and escalating pollutant emissions, the habitat of B. densiflorum has been continuously degraded, habitat fragmentation has intensified, and its populations have shown a tendency to decline. RATIONALE: Genetic diversity endows species with abundant genetic resources and plays a pivotal role in shaping their capacity to adapt to new environments. To elucidate the genetic diversity of B. densiflorum and evaluate the influence of climate change on its genetic variation, reduced-representation genome sequencing technology was employed to obtain single nucleotide polymorphisms (SNPs), and subsequently population genetics and landscape genetics together with species distribution modelling were analyzed. RESULTS: B. densiflorum had a moderate level of genetic diversity. Six populations were divided into two groups, and there was moderate differentiation (F_ST=0.102) and high gene flow (Nm=2.442) between them. Genotype-environment association analysis indicated that the two groups were diverged attributable to local adaptation to the climate. Temperature differences and low-temperature regimes interacting together with precipitation gave rise to genetic variation of this species. In total, 544 adaptive loci were identified, which displayed significant correlations with temperature difference, low-temperature factors (Bio2, Bio6, Bio11, and Bio7), and precipitation factors (Bio19). B. densiflorum migrated evidently northward from the Last Glacial Maximum to the current, with its distribution area increased by 89.5%. However, during the period from 2061 to 2080, the extent of the suitable area for this species will be contracted, and there will be partial degradation and fragmentation occurring in highly suitable areas within Anhui Province. CONCLUSION: B. densiflorum showed a moderate level of genetic diversity and a moderate degree of genetic differentiation. Local adaptation drove the formation of the current genetic pattern of B. densiflorum, and temperature differences, low-temperature, and precipitation led to genetic variation. B. densiflorum has evidently migrated northward from the Last Glacial Maximum to the current with increase of distribution area. However, niche modelling indicated that during the period from 2061 to 2080, the suitable habitat area of B. densiflorum would be contracted, with partial degradation and fragmentation occurring in highly suitable areas within Anhui Province. These results provide the basis for conservation and utilization of B. densiflorum.

Population genetic structure analysis of Brachystachyum densiflorum

Key words: Brachystachyum densiflorum, reduced-representation genome sequencing, genetic diversity, genetic structure, species distribution model

张如礼, 李德铢, 张玉霄. 短穗竹居群遗传结构及气候适应性分析. 植物学报, 2025, 60(3): 407-424.

Zhang Ruli, Li Dezhu, Zhang Yuxiao. Population Genetic Structure and Climate Adaptation Analysis of Brachystachyum densiflorum. Chinese Bulletin of Botany, 2025, 60(3): 407-424.

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链接本文: https://www.chinbullbotany.com/CN/10.11983/CBB24094

https://www.chinbullbotany.com/CN/Y2025/V60/I3/407

图/表 8

表1 短穗竹居群采集信息

Table 1 Sampling information of Brachystachyum densiflorum populations

Population	Locality	Sample individuals	Longitude	Latitude
AHYX	Yuexi, Anhui	7	116°14′49″ E	30°55′27″ N
AHHS	Huoshan, Anhui	4	116°26′38″ E	31°24′01″ N
AHGD	Guangde, Anhui	9	119°14′10″ E	30°48′56″ N
JSLY	Liyang, Jiangsu	3	119°28′30″ E	31°14′39″ N
JSYX	Yixing, Jiangsu	10	119°47′54″ E	31°16′49″ N
ZJCX	Changxing, Zhejiang	3	119°52′31″ E	31°07′24″ N

表2 6个居群遗传多样性指标

Table 2 Genetic diversity indices of six populations

Population	PIC	Ho	He	π	Fis	Ne (95% CI)
AHYX	0.8102	0.0880	0.3051	0.3295	0.6466	5.4 (5.2, 5.7)
AHHS	0.6412	0.0863	0.2712	0.3099	0.4899	9.4 (8.4, 10.4)
AHGD	0.8802	0.0885	0.3148	0.3339	0.7123	3.8 (3.6, 4.0)
JSLY	0.5502	0.0841	0.2492	0.2990	0.4098	Inf (inf, inf)
JSYX	0.9069	0.0884	0.3183	0.3358	0.7385	4.0 (3.9, 4.2)
ZJCX	0.5462	0.0865	0.2474	0.2969	0.4017	4.8 (4.5, 5.1)
Mean	0.7225	0.0870	0.2843	0.3175	0.5665	5.6 (5.1, 5.9)

图1 短穗竹居群遗传结构分析 (A) 系统进化树和K=2, 3, 4时每个个体的遗传成分, 分支上方的数字表示靴带值; (B) 主成分分析(PCA); (C) 主成分判别分析(DAPC)。AHYX、AHHS、AHGD、JSLY、JSYX和ZJCX同表1。

Figure 1 Population genetic structure analysis of Brachystachyum densiflorum (A) Phylogenetic tree and individual genetic components at K=2, 3, 4, the numbers above the branch are the bootstrap values; (B) Principal component analysis (PCA); (C) Discriminant analysis of principal components (DAPC). AHYX, AHHS, AHGD, JSLY, JSYX, and ZJCX are the same as shown in Table 1.

图2 K值对应的交叉检验错误率

Figure 2 The cross-validation error rate of K value

表3 6个居群间遗传分化值(FST, 左下三角)和基因流(Nm, 右上三角)

Table 3 Genetic differentiation (FST, lower left triangle) and gene flow (Nm, upper right triangle) among six populations

Population	AHGD	AHYX	AHHS	JSLY	JSYX	ZJCX
AHGD	0.000	3.596	2.497	2.065	4.958	2.108
AHYX	0.065	0.000	2.382	1.869	3.848	1.887
AHHS	0.091	0.095	0.000	1.523	2.591	1.562
JSLY	0.108	0.118	0.141	0.000	2.154	1.406
JSYX	0.048	0.061	0.088	0.104	0.000	2.177
ZJCX	0.106	0.117	0.138	0.151	0.103	0.000

图3 冗余分析(RDA)和梯度森林(GF)分析 (A), (C), (E) 气候和地理与遗传结构之间的关联分析; (B) 梯度森林分析; (D), (F) Bio2和Bio6响应曲线。Bio2: 平均气温日较差; Bio6: 最冷月份最低温度; Bio7: 气温年较差; Bio8: 最湿季度平均温度; Bio11: 最冷季度平均温度; Bio15: 降水量季节性变化; Bio17: 最湿季度降水量; Bio19: 最冷季度降水量。AHYX、AHHS、AHGD、JSLY、JSYX和ZJCX同表1。

Figure 3 Redundancy analysis (RDA) and gradient forest (GF) analysis (A), (C), (E) Association analysis between climate, geography and genetic structure; (B) Gradient forest analysis; (D), (F) Bio2 and Bio6 response curves. Bio2: Average daily temperature range; Bio6: The lowest temperature in the coldest month; Bio7: Annual temperature range; Bio8: The average temperature of the wettest quarter; Bio11: The average temperature of the coldest quarter; Bio15: Seasonal variation of precipitation; Bio17: The wettest season precipitation; Bio19: The coldest season precipitation. AHYX, AHHS, AHGD, JSLY, JSYX, and ZJCX are the same as shown in Table 1.

图4 利用3种方法筛选的异常单核苷酸多态性(SNP)位点 (A) BayeScan软件筛选; (B) 冗余分析(RDA)筛选; (C) 潜在因素混合模型(LFMM)筛选。FST: 遗传分化指数。Bio2、Bio6、Bio7、Bio11和Bio19同图3。

Figure 4 Screening of outlier single nucleotide polymorphism (SNP) sites by three methods (A) Screening by BayeScan software; (B) Screening by redundancy analysis (RDA); (C) Screening by latent factor mixed modeling (LFMM). FST: Fixation index of subdivision. Bio2, Bio6, Bio7, Bio11, and Bio19 are the same as shown in Figure 3.

图5 不同时期短穗竹适宜性生境分布 (A) 当前(1970-2000年)气候条件下; (B) 全新世中期气候条件下; (C) 末次盛冰期气候条件下; (D), (G) 2021-2040年间气候; (E), (H) 2041-2060年间气候; (F), (I) 2061-2080年间气候

Figure 5 Distribution of suitable habitats for Brachystachyum densiflorum in different periods (A) Current (1970‒2000) climate scenarios; (B) Mid Holocene climate scenarios; (C) Last Glacial Maximum climate scenarios; (D), (G) 2021-2040 climate scenarios; (E), (H) 2041-2060 climate scenarios; (F), (I) 2061-2080 climate scenarios

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短穗竹居群遗传结构及气候适应性分析

Population Genetic Structure and Climate Adaptation Analysis of Brachystachyum densiflorum

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