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

doi:10.17520/biods.2024212

Abstract

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

Xiangtan Yao, Xinyi Zhang, Yang Chen, Ye Yuan, Wangda Cheng, Tianrui Wang, Yingxiong Qiu. Genomic resequencing reveals the genetic diversity of the cultivated water caltrop, and the origin and domestication of ‘Nanhuling’[J]. Biodiv Sci, 2024, 32(9): 24212.

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URL: https://www.biodiversity-science.net/EN/10.17520/biods.2024212

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Figures/Tables 6

References 62

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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