Abstract
Chinese pepper, referring to Zanthoxylum bungeanum Maxim. and Zanthoxylum armatum DC. species, is an important spice crop that has long attracted people’s interest due to its extensive application in Asian cuisine to improve taste. Numerous cultivars have been developed during the long history of domestication and cultivation. However, little to no information is available on the genetic diversity and evolutionary relationships of Chinese pepper cultivars and their historical diversification has not been clarified. Herein, we sequenced two nrDNA non-coding region markers, the external transcribed spacer (ETS) and the internal transcribed spacer 2 (ITS2), to assess genetic diversity and phylogenetic relationships among 39 cultivated and wild populations of Chinese pepper from eight provinces and to address the question of ancient demographic trends which were probably influenced by changing climate during evolutionary history. In total, 31 haplotypes were identified based on 101 polymorphism sites. Our results revealed relatively high level of genetic variation despite long-term cultivation of this crop. AMOVA revealed that genetic variation existed predominantly within provinces rather than among provinces. The genetic structure result based on haplotype network analysis largely reflected historical records, which suggested a Gansu origin for Chinese pepper and an ancient west-to-east spread of Chinese pepper circulating in China. We also provided evidence that changing Pleistocene climates had shaped the demographic trends of Chinese pepper. Taken together, our findings not only suggest that Chinese pepper is a dynamic genetic system that responds to evolutionary forces, but it also provides a fundamental genetic profile for the conservation and responsible exploitation of the extant germplasm of Chinese pepper and for improving the genetic basis for breeding the cultivars.
Highlights
Zanthoxylum, a genus of both economical and ecological importance in the Rutaceae family, consists of 250 species spreading in tropical and subtropical areas, including Asia, Africa, Oceania, and North America [1]
In order to explore the demographic history of both Chinese pepper species, we examined the frequency distributions of pairwise mismatch between sequences using Arlequin 3.5 [30] and
To analyze changes in relative population sizes over time, we reconstructed demographic histories independently in both species by using the Bayesian skyline plot [35] as implemented in BEAST 1.8 [31], with the divergence time between Z. armatum and Z. bungeanum informed by previous phylogenetic analysis [36] as the calibration point. We modeled these calibrations as an normal distribution with a sigma of 1.4 and an offset that equaled the median age of the calibration
Summary
Zanthoxylum, a genus of both economical and ecological importance in the Rutaceae family, consists of 250 species spreading in tropical and subtropical areas, including Asia, Africa, Oceania, and North America [1]. Z. bungeanum is the most popular Chinese pepper species due to its fruitful (a fruit spike with many fruitlets) and bright red fruits (Figure 1A) This species is believed to be native to China [2,6], and the first description of this plant can be traced back to Shijing (Classic of Poetry) written 2,600 years ago. According to historical records of Shijing, Fanzi Jiran (Master Fan’s Questions to Jiran, an ancient agricultural treatise), Shan Hai Jing (Classic of Mountains and Seas), Chu state poet Qu Yuan, the main distribution of wild Z. bungeanum during the period of pre-Qin Dynasty covered the north Sichuan, south Gansu, southwest Shaanxi, south Shanxi, southeast Henan, and the mountain regions of Hunan and Hubei
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