基于基因组重测序揭示栽培欧菱遗传多样性及‘南湖菱’的起源驯化历史

doi:10.17520/biods.2024212

生物多样性 ›› 2024, Vol. 32 ›› Issue (9): 24212. DOI: 10.17520/biods.2024212 cstr: 32101.14.biods.2024212

基于基因组重测序揭示栽培欧菱遗传多样性及‘南湖菱’的起源驯化历史

姚祥坦¹, 张心怡²^,³, 陈阳⁴, 袁晔¹, 程旺大⁵^,^*(), 王天瑞²^,⁶^,^*()(), 邱英雄²^,^*()()

1.嘉兴市农业科学研究院经济作物研究所, 浙江嘉兴 314016
2.中国科学院武汉植物园植物多样性研究中心, 武汉 430074
3.浙江大学生命科学学院, 杭州 310058
4.宁波市农业科学研究院, 浙江宁波 315040
5.嘉兴职业技术学院, 浙江嘉兴 314036
6.中国科学院大学, 北京 100049

收稿日期:2024-05-30 接受日期:2024-08-01 出版日期:2024-09-20 发布日期:2024-09-02
通讯作者: * E-mail: chwd228@163.com; wangtianrui231@mails.ucas.ac.cn; qiuyingxiong@wbgcas.cn
基金资助:
嘉兴市科技计划项目(2019AY11001);嘉兴市科技计划项目(2021AZ10013)

Genomic resequencing reveals the genetic diversity of the cultivated water caltrop, and the origin and domestication of ‘Nanhuling’

Xiangtan Yao¹, Xinyi Zhang²^,³, Yang Chen⁴, Ye Yuan¹, Wangda Cheng⁵^,^*(), Tianrui Wang²^,⁶^,^*()(), Yingxiong Qiu²^,^*()()

1. Institute of Economic Crop Research, Jiaxing Academy of Agricultural Sciences, Jiaxing, Zhejiang 314016, China
2. Research Center for Plant Diversity, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
3. College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
4. Ningbo Academy of Agricultural Sciences, Ningbo, Zhejiang, 315040, China
5. Jiaxing Vocational Technical College, Jiaxing, Zhejiang, 314036, China
6. University of Chinese Academy of Sciences, Beijing 100049, China

Received:2024-05-30 Accepted:2024-08-01 Online:2024-09-20 Published:2024-09-02
Contact: * E-mail: chwd228@163.com; wangtianrui231@mails.ucas.ac.cn; qiuyingxiong@wbgcas.cn
Supported by:
Jiaxing Science and Technology Project(2019AY11001);Jiaxing Science and Technology Project(2021AZ10013)

摘要/Abstract

摘要：

阐明栽培作物的起源驯化历史, 深入解析作物驯化改良的过程对于理解人类文明的进程至关重要。欧菱(Trapa natans)隶属于千屈菜科, 为一年生水生浮叶草本, 其果实俗称菱角, 是我国传统的水生蔬菜作物。然而, 相较于主粮作物, 我们对栽培欧菱种质资源的遗传多样性和起源驯化历史仍知之甚少。本研究基于31份不同品种(系)的二倍体栽培欧菱和23份二倍体野生欧菱的全基因组重测序(resequencing)数据, 利用群体基因组学分析方法, 对栽培欧菱的遗传多样性和我国特有的栽培品种‘南湖菱’的起源驯化历史进行研究。群体遗传结构与遗传分化的结果表明, 野生欧菱和栽培欧菱分属不同的基因池, 栽培欧菱起源于长江流域的二倍体野生欧菱。栽培欧菱遗传多样性水平整体低于野生欧菱(0.68 × 10⁻³ vs. 1.35 × 10⁻³), 有效群体大小相比野生欧菱也急剧收缩(~4,000 vs. ~7,700), 表明栽培欧菱经历了驯化瓶颈作用。栽培欧菱中, ‘南湖菱’的遗传多样性水平最低, 连锁不平衡的衰减速度最慢, 可能与其驯化程度高、选择强度大有关。基于FASTSIMCOAL2溯祖模拟的群体动态历史结果表明, ‘南湖菱’、‘乌菱’与其他栽培欧菱均发生了基因交流事件, ‘南湖菱’驯化发生在距今大约669年前, 这与明代文学记载信息相吻合。综上所述, 本研究通过探讨栽培欧菱的遗传多样性和‘南湖菱’的驯化历史, 对深入理解栽培欧菱驯化起源过程及其遗传演化特征具有重要意义。

关键词: 起源驯化, 菱角, 孤儿作物, 水生植物, 基因组重测序

Abstract

Aims: Understanding the origins and domestication processes of cultivated crops, is crucial for understanding human civilization. Trapa, commonly known as water caltrop, belongs to the family Lythraceae and is an annual floating-leaf aquatic herb. As a traditional aquatic vegetable crop, the fruit of Trapa has long been a significant food source in early Chinese agricultural societies. However, in recent years, rapid urbanization in China has resulted in habitat destruction, posing a serious threat to its genetic diversity. Moreover, ‘Nanhuling’, a major cultivar of Trapa, holds high economic and cultural value, yet its origin and domestication history are not fully understood.
Methods: In this study, we employed population genomics to investigate the genetic diversity of cultivated water caltrop and the domestication history of ‘Nanhuling’. The dataset for this study was generated by whole-genome resequencing of 31 diploid cultivated T. natans and 23 diploid wild T. natans samples.
Results: Population genetic structure and differentiation indicated that wild and cultivated T. natans belonged to distinct gene pools. Cultivated T. natans originated from the diploid wild T. natans in the Yangtze River Basin. The overall genetic diversity level of cultivated T. natans is lower than that of wild T. natans (0.68 × 10⁻³ vs. 1.35 × 10⁻³), and the effective population size is significantly reduced compared to wild T. natans (~4,000 vs. ~7,700), suggesting that cultivated T. natans experienced a genetic bottleneck during domestication. Among cultivated T. natans, ‘Nanhuling’ exhibited the lowest level of genetic diversity and the slowest decay rate of linkage disequilibrium, which may be related to its high degree of domestication and strong selection pressure. Based on the population dynamic history inferred from the FASTSIMCOAL2 ancestral simulation model, we found that there had been gene flow events among ‘Nanhuling’, ‘Wuling’, and other cultivated T. natans. The domestication of ‘Nanhuling’ occurred approximately 669 years ago, consistent with literary records from the Ming Dynasty.
Conclusions: This study is significant as it deepens our understanding of the domestication and genetic evolution of cultivated T. natans. Insights gained from this work may help improve agriculturally valuable characteristics of T. natans, such as crop yields and nutrient content.

Key words: origin and domestication, water caltrop, orphan crops, aquatic plants, genome resequencing

姚祥坦, 张心怡, 陈阳, 袁晔, 程旺大, 王天瑞, 邱英雄 (2024) 基于基因组重测序揭示栽培欧菱遗传多样性及‘南湖菱’的起源驯化历史. 生物多样性, 32, 24212. DOI: 10.17520/biods.2024212.

Xiangtan Yao, Xinyi Zhang, Yang Chen, Ye Yuan, Wangda Cheng, Tianrui Wang, Yingxiong Qiu (2024) Genomic resequencing reveals the genetic diversity of the cultivated water caltrop, and the origin and domestication of ‘Nanhuling’. Biodiversity Science, 32, 24212. DOI: 10.17520/biods.2024212.

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链接本文: https://www.biodiversity-science.net/CN/10.17520/biods.2024212

https://www.biodiversity-science.net/CN/Y2024/V32/I9/24212

图/表 6

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模型 Models	参数Parameters	Delta似然值 Delta likelihood	AIC	AIC权重 AIC’s weight
Model 1	23	55,516.96	2,597,573.64	1
Model 2	21	56,021.93	2,640,483.74	0
Model 3	19	59,304.03	2,615,594.33	0
Model 4	17	71,677.36	2,672,571.65	0
Model 5	15	69,289.32	2,661,570.30	0
Model 6	21	55,952.22	2,610,162.71	0
Model 7	17	67,543.76	2,653,535.73	0
Model 8	19	65,390.88	2,698,162.24	0

模型 Models	参数Parameters	Delta似然值 Delta likelihood	AIC	AIC权重 AIC’s weight
Model 1	23	55,516.96	2,597,573.64	1
Model 2	21	56,021.93	2,640,483.74	0
Model 3	19	59,304.03	2,615,594.33	0
Model 4	17	71,677.36	2,672,571.65	0
Model 5	15	69,289.32	2,661,570.30	0
Model 6	21	55,952.22	2,610,162.71	0
Model 7	17	67,543.76	2,653,535.73	0
Model 8	19	65,390.88	2,698,162.24	0

参数 Parameters	点估计 Point estimation	95%置信区间 95% confidence intervals
参数 Parameters	点估计 Point estimation	置信下限 Lower bound	置信上限 Upper bound
野生欧菱有效群体大小 Effective population size of wild T. natans	7,685	3,873	10,423
‘乌菱’有效群体大小 Effective population size of ‘Wuling’	1,465	770	2,128
‘南湖菱’有效群体大小 Effective population size of ‘Nanhuling’	1,087	586	2,526
其他栽培欧菱有效群体大小 Effective population size of other cultivated T. natans	4,823	3,088	6,492
栽培欧菱祖先有效群体大小 Effective population size of the ancestor of cultivated T. natans	4,068	3,293	7,602
‘南湖菱’和其他栽培欧菱的祖先有效群体大小 Effective population size of the ancestor of ‘Nanhuling’ and other cultivated T. natans	5,245	4,995	8,423
欧菱祖先有效群体大小 Effective population size of the ancestor of T. natans	31,528	18,113	42,355
‘南湖菱’驯化时间 Domestication time of ‘Nanhuling’	669	285	983
‘乌菱’驯化时间 Domestication time of ‘Wuling’	839	661	1,428
栽培欧菱驯化时间 Domestication time of cultivated T. natans	6,741	4,658	8,237
‘南湖菱’向‘乌菱’迁移率 Migration rate from ‘Nanhuling’ to ‘Wuling’	6.68E-6	3.27E-6	4.12E-5
‘乌菱’向‘南湖菱’迁移率 Migration rate from ‘Wuling’ to ‘Nanhuling’	1.16E-5	6.67E-6	4.82E-5
其他栽培欧菱向‘南湖菱’迁移率 Migration rate from other cultivated T. natans to ‘Nanhuling’	2.29E-5	3.31E-6	4.44E-5
‘南湖菱’向其他栽培欧菱迁移率 Migration rate from ‘Nanhuling’ to other cultivated T. natans	3.40E-5	4.67E-6	9.73E-5
‘南湖菱’和其他栽培欧菱祖先向‘乌菱’迁移率 Migration rate from the ancestor of ‘Nanhuling’ and other cultivated T. natans to ‘Wuling’	1.52E-3	7.24E-4	4.29E-3
‘乌菱’向‘南湖菱’和其他栽培欧菱祖先迁移率 Migration rate from ‘Wuling’ to the ancestor of ‘Nanhuling’ and other cultivated T. natans	1.27E-3	6.28E-4	4.64E-3
野生欧菱向栽培欧菱迁移率 Migration rate from wild T. natans to cultivated T. natans	9.25E-3	2.92E-3	1.76E-2
栽培欧菱向野生欧菱迁移率 Migration rate from cultivated T. natans to wild T. natans	1.75E-4	7.66E-5	1.13E-3
其他栽培欧菱向‘乌菱’迁移率 Migration rate from other cultivated T. natans to ‘Wuling’	1.95E-6	2.58E-7	8.69E-5
‘乌菱’向其他栽培欧菱迁移率 Migration rate from ‘Wuling’ to other cultivated T. natans	3.70E-6	3.31E-6	1.35E-5

参数 Parameters	点估计 Point estimation	95%置信区间 95% confidence intervals
参数 Parameters	点估计 Point estimation	置信下限 Lower bound	置信上限 Upper bound
野生欧菱有效群体大小 Effective population size of wild T. natans	7,685	3,873	10,423
‘乌菱’有效群体大小 Effective population size of ‘Wuling’	1,465	770	2,128
‘南湖菱’有效群体大小 Effective population size of ‘Nanhuling’	1,087	586	2,526
其他栽培欧菱有效群体大小 Effective population size of other cultivated T. natans	4,823	3,088	6,492
栽培欧菱祖先有效群体大小 Effective population size of the ancestor of cultivated T. natans	4,068	3,293	7,602
‘南湖菱’和其他栽培欧菱的祖先有效群体大小 Effective population size of the ancestor of ‘Nanhuling’ and other cultivated T. natans	5,245	4,995	8,423
欧菱祖先有效群体大小 Effective population size of the ancestor of T. natans	31,528	18,113	42,355
‘南湖菱’驯化时间 Domestication time of ‘Nanhuling’	669	285	983
‘乌菱’驯化时间 Domestication time of ‘Wuling’	839	661	1,428
栽培欧菱驯化时间 Domestication time of cultivated T. natans	6,741	4,658	8,237
‘南湖菱’向‘乌菱’迁移率 Migration rate from ‘Nanhuling’ to ‘Wuling’	6.68E-6	3.27E-6	4.12E-5
‘乌菱’向‘南湖菱’迁移率 Migration rate from ‘Wuling’ to ‘Nanhuling’	1.16E-5	6.67E-6	4.82E-5
其他栽培欧菱向‘南湖菱’迁移率 Migration rate from other cultivated T. natans to ‘Nanhuling’	2.29E-5	3.31E-6	4.44E-5
‘南湖菱’向其他栽培欧菱迁移率 Migration rate from ‘Nanhuling’ to other cultivated T. natans	3.40E-5	4.67E-6	9.73E-5
‘南湖菱’和其他栽培欧菱祖先向‘乌菱’迁移率 Migration rate from the ancestor of ‘Nanhuling’ and other cultivated T. natans to ‘Wuling’	1.52E-3	7.24E-4	4.29E-3
‘乌菱’向‘南湖菱’和其他栽培欧菱祖先迁移率 Migration rate from ‘Wuling’ to the ancestor of ‘Nanhuling’ and other cultivated T. natans	1.27E-3	6.28E-4	4.64E-3
野生欧菱向栽培欧菱迁移率 Migration rate from wild T. natans to cultivated T. natans	9.25E-3	2.92E-3	1.76E-2
栽培欧菱向野生欧菱迁移率 Migration rate from cultivated T. natans to wild T. natans	1.75E-4	7.66E-5	1.13E-3
其他栽培欧菱向‘乌菱’迁移率 Migration rate from other cultivated T. natans to ‘Wuling’	1.95E-6	2.58E-7	8.69E-5
‘乌菱’向其他栽培欧菱迁移率 Migration rate from ‘Wuling’ to other cultivated T. natans	3.70E-6	3.31E-6	1.35E-5

基于基因组重测序揭示栽培欧菱遗传多样性及‘南湖菱’的起源驯化历史

Genomic resequencing reveals the genetic diversity of the cultivated water caltrop, and the origin and domestication of ‘Nanhuling’

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