Pan-genomics and genome-editing technologies are revolutionizing breeding of global crops 1,2 . A transformative opportunity lies in exchanging genotype-to-phenotype knowledge between major crops (that is, those cultivated globally) and indigenous crops (that is, those locally cultivated within a circumscribed area) 3-5 to enhance our food system. However, species-specific genetic variants and their interactions with desirable natural or engineered mutations pose barriers to achieving predictable phenotypic effects, even between related crops 6,7 . Here, by establishing a pan-genome of the crop-rich genus Solanum 8 and integrating functional genomics and pan-genetics, we show that gene duplication and subsequent paralogue diversification are major obstacles to genotype-to-phenotype predictability. Despite broad conservation of gene macrosynteny among chromosome-scale references for 22 species, including 13 indigenous crops, thousands of gene duplications, particularly within key domestication gene families, exhibited dynamic trajectories in sequence, expression and function. By augmenting our pan-genome with African eggplant cultivars 9 and applying quantitative genetics and genome editing, we dissected an intricate history of paralogue evolution affecting fruit size. The loss of a redundant paralogue of the classical fruit size regulator CLAVATA3 (CLV3) 10,11 was compensated by a lineage-specific tandem duplication. Subsequent pseudogenization of the derived copy, followed by a large cultivar-specific deletion, created a single fused CLV3 allele that modulates fruit organ number alongside an enzymatic gene controlling the same trait. Our findings demonstrate that paralogue diversifications over short timescales are underexplored contingencies in trait evolvability. Exposing and navigating these contingencies is crucial for translating genotype-to-phenotype relationships across species.

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Background Dai, Hani, and Yao people, in the trans-boundary region between China, Laos, and Vietnam, have gathered plentiful traditional knowledge about wild edible plants during their long history of understanding and using natural resources. The ecologically rich environment and the multi-ethnic integration provide a valuable foundation and driving force for high biodiversity and cultural diversity in this region. However, little study has uncovered this unique and attractive culture to the world. Methods We conducted ethnobotanical survey in 20 villages of Jiangcheng County from 2016 to 2020. Altogether 109 local Dai, Hani, and Yao people were interviewed, and their traditional knowledge about wild edible plants was recorded. Voucher specimens were identified by the authors and deposited in the herbarium of Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences (HITBC). The use value was used as a quantitative index to evaluate the consumption frequency and relative importance of the wild edible plants. The Jaccard index was calculated to assess the usage similarity of different areas. The relationship of age and recognized wild edible plants by different ethnic people was performed by R. Results A total of 211 wild edible plants, belonging to 71 families and 151 genera, were recorded. These plants were consumed as wild edible vegetables, seasonal fruits, salads, spices, sour condiments, tonic soups, tea substitutes, liquor brewing, or dyeing materials. The use value (UV), current cultivation, market availability, and the quantitative traditional knowledge inheritance situation of these wild edible plants among different generations, were analyzed. Based on the data from the threatened species list of China's higher plants and the IUCN Red List, the food plant list for Asia Elephant, the Subject Database of China Plant, and the calculated UV score, the top 30 most important wild edible plants were selected for further cultivation in some local villages. Conclusion Traditional knowledge of wild edible plants, owned by Dai, Hani, and Yao people in Jiangcheng County, is rich but at risk of being lost among the young generation. Diversified cultivation of wild edible plants by the local communities could be a solution for the sustainable use of natural resources and to conserve the endangered species in this trans-boundary region.

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Brinjal (Solanum melongena), scarlet (S. aethiopicum) and gboma (S. macrocarpon) eggplants are three Old World domesticates. The genomic DNA of a collection of accessions belonging to the three cultivated species, along with a representation of various wild relatives, was characterized for the presence of single nucleotide polymorphisms (SNPs) using a genotype-by-sequencing approach. A total of 210 million useful reads were produced and were successfully aligned to the reference eggplant genome sequence. Out of the 75,399 polymorphic sites identified among the 76 entries in study, 12,859 were associated with coding sequence. A genetic relationships analysis, supported by the output of the FastSTRUCTURE software, identified four major sub-groups as present in the germplasm panel. The first of these clustered S. aethiopicum with its wild ancestor S. anguivi; the second, S. melongena, its wild progenitor S. insanum, and its relatives S. incanum, S. lichtensteinii and S. linneanum; the third, S. macrocarpon and its wild ancestor S. dasyphyllum; and the fourth, the New World species S. sisymbriifolium, S. torvum and S. elaeagnifolium. By applying a hierarchical FastSTRUCTURE analysis on partitioned data, it was also possible to resolve the ambiguous membership of the accessions of S. campylacanthum, S. violaceum, S. lidii, S. vespertilio and S. tomentsum, as well as to genetically differentiate the three species of New World Origin. A principal coordinates analysis performed both on the entire germplasm panel and also separately on the entries belonging to sub-groups revealed a clear separation among species, although not between each of the domesticates and their respective wild ancestors. There was no clear differentiation between either distinct cultivar groups or different geographical provenance. Adopting various approaches to analyze SNP variation provided support for interpretation of results. The genotyping-by-sequencing approach showed to be highly efficient for both quantifying genetic diversity and establishing genetic relationships among and within cultivated eggplants and their wild relatives. The relevance of these results to the evolution of eggplants, as well as to their genetic improvement, is discussed.

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Background Shui communities of southwest China have an extensive history of using wild plants as starters (Xiaoqu) to prepare fermented beverages that serve important roles in interpersonal relationships and cultural events. While the practice of using wild plants as starters for the preparation of fermented beverages was once prevalent throughout China, this tradition has seen a decline nationally since the 1930s. The traditional technique of preparing fermented beverages from wild plant starters remains well preserved in the Shui communities in southwest China and provides insight on local human-environment interactions and conservation of plant biodiversity for cultural purposes. The present study sought to examine the ethnobotany of wild plants used as starters for the preparation of fermented beverages including an inventory of plants used as a starter in liquor fermentation and associated knowledge and practices. Methods Field surveys were carried out that consisted of semi-structured surveys and plant species inventories. One hundred forty-nine informants in twenty Shui villages were interviewed between July 2012 and October 2014 to document knowledge associated with wild plants used as a liquor fermentation starter. The inventories involved plant voucher specimens and taxonomic identification of plant collections. Results A total of 103 species in 57 botanical families of wild plants were inventoried and documented that are traditionally used as starters for preparing fermented beverages by Shui communities. The majority of the species (93.2%) have multiple uses in addition to being used as a starter with medicinal purposes being the most prevalent. Shui women are the major harvesters and users of wild plants used as starters for preparing fermented beverages and transfer knowledge orally from mother to daughter. Conclusions Findings from this study can serve as a basis for future investigation on fermented beverages and foods and associated knowledge and cultural practices. However, with rapid development, utilization of wild plants and the cultural systems that support them are at risk of erosion. Cultural preservation practices are necessary in Shui communities for the continued use and transmission of this ethnobiological knowledge as well as associated biodiversity.

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Background This paper is based on an ethnobotanical investigation that focused on the traditional medicinal plants used by local Maonan people to treat human diseases in Maonan concentration regions. The Maonan people have relied on traditional medicine since ancient times, especially medicinal plants. The aim of this study is to document medicinal plants used by the Maonans and to report the status of medicinal plants and associated traditional knowledge. Methods Ethnobotanical data were collected from June 2012 to September 2014 in Huanjiang Maonan Autonomous County, northern Guangxi, southwest China. In total, 118 knowledgeable informants were interviewed. Following statistically sampling method, eighteen villages from 5 townships were selected to conduct field investigations. Information was collected through the approache of participatory observation, semi-structured interviews, ranking exercises, key informant interviews, focus group discussions, and participatory rural appraisals. Results A total of 368 medicinal plant species were investigated and documented together with their medicinal uses by the Maonans, most of which were obtained from the wild ecosystems. The plants were used to treat 95 human diseases. Grinding was a widely used method to prepare traditional herbal medicines. There were significant relationships between gender and age, and between gender and informants' knowledge of medicinal plant use. Deforestation for agricultural purposes was identified as the most destructive factor of medicinal plants, followed by drought and over-harvest. Conclusions The species diversity of medicinal plants used by the Maonans in the study area was very rich. Medicinal plants played a significant role in healing various human disorders in the Maonan communities. However, the conflicts between traditional inheriting system and recent socio-economic changes (and other factors) resulted in the reduction or loss of both medicinal plants and associated indigenous knowledge. Thus, conservation efforts and policies, and innovation of inheriting system are necessary for protecting the medicinal plants and associated indigenous knowledge. Awareness is also needed to be raised among local Maonans focusing on sustainable utilization and management of both medicinal plants and traditional knowledge.

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