Scientists from the Peking University Institute of Advanced Agricultural Sciences has accomplished the construction of Telomere-to-telomere Citrullus super-pangenome. The advancement allows innovation and breeding in watermelon enter a new era.

The pangenome represents the collective genomic information of all individuals within a species. Constructing a pangenome effectively addresses the issues of missing information and analytical biases that arise from relying on a single reference genome. The super-pangenome, on the other hand, encompasses the genomic information of all species within a genus, particularly incorporating abundant genomic variations found in wild species. It represents a further expansion of the pangenome and holds significant prospects for applications such as distant hybridization and gene exploration.

Watermelon is recognized as one of the world's important horticultural crops. It is rich in antioxidants like lycopene and citrulline, which enhance blood circulation. With its sweet taste, watermelon enjoys the reputation of being the "King of Fruits" in the summer and is highly favored by consumers worldwide. The global annual production of watermelon approaches nearly 100 million tons, with China being the largest producer and consumer, accounting for over 60% of the global total. The watermelon industry plays a vital role in rural revitalization and the prosperity of farmers. The rapid development of the watermelon industry in China relies on excellent varieties and the relentless efforts of generations of breeders. China has become the most active country in the innovation of watermelon germplasm and variety selection. However, watermelon production faces significant challenges due to the intensifying climate change and increasing pest and disease threats.

To maintain high-quality and environmentally friendly development in China's watermelon industry, it is crucial to address the key issue of incorporating desirable disease-resistant and stress-tolerant genes that are lacking in existing superior varieties. Cultivated watermelons have undergone a narrowing of genetic diversity due to the pursuit of quality and yield during domestication and variety improvement. This has resulted in the substantial loss of genes associated with disease resistance and stress tolerance. However, the wild ancestors of watermelon exhibit extensive genetic and phenotypic diversity, including rich genetic resources for abiotic and biotic resistance. They serve as a valuable treasure trove for genetic improvement and germplasm innovation in watermelon.

On July 8, 2024, scientists from Peking University Institute of Advanced Agricultural Sciences published a groundbreaking research achievement titled "Telomere-to-telomere Citrullus super-pangenome provides direction for watermelon breeding" in the prestigious international journal Nature Genetics. This publication marks a significant breakthrough in the field of watermelon research.

 

 

The study generated telomere-to-telomere (T2T) high-quality genome assemblies for 28 representative materials from all seven species within the watermelon genus, resulting in the construction of the first genus-level T2T super-pangenome. This encompassed a total of 768.5 megabases (Mb) and 32,513 gene families, which is 1.5 times larger than a single watermelon genome, incorporating 11,225 genes that were not found in cultivated watermelons. Utilizing the T2T high-quality genome assemblies, this study conducted the first comprehensive comparison of centromere sequences in the watermelon genus, revealing abundant variations and unique evolutionary relationships that influenced hybridization compatibility among different species. As a result, the super-pangenome significantly expanded the genetic pool for watermelon genetic improvement. (Figure 1)

 

 

Figure 1 Diversity and pangenome map of 28 representative materials from the seven species within the watermelon genus

 

Using genomic sequences, this study expanded the classification system of the watermelon genus, confirming the theory that watermelon originated from Africa and uncovering the possibility of additional ancestors in cultivated watermelons apart from the previously reported cordophanus subspecies. Moreover, three significant chromosomal rearrangement events and two large segment inversions were identified within the watermelon genus. These chromosomal rearrangements significantly affected disease resistance, quality-related genes, and the three-dimensional genome structure of watermelon, which have been retained in cultivated varieties. These discoveries also provided a genomic basis for minimizing linkage drag during backcross breeding. (Figure 2)

 

 

Figure 2 Evolution of the watermelon genus and the origins of cultivated watermelon

 

The super-pangenome identified over 461,987 structural variations (SVs) within the watermelon genus, with a graphic pan-genome for watermelon constructed. Through SV-based genome-wide association studies (SV-GWAS), this study identified key genes lost and gained during domestication. It further unearthed structural variations in functional genes related to important traits such as cucurbitacin content, sugar content, and flesh color. During watermelon domestication, a significant expansion of gene clusters associated with increased sweetness and red flesh color occurred, while a large number of gene clusters related to disease resistance were lost. This study provides breeders with the most comprehensive genomic resources for watermelon, facilitating a deeper understanding of the complexity and diversity of the watermelon genome and the efficient exploration and utilization of favorable genes from wild watermelon species. (Figure 3)

 

Figure 3 Structural variation map of genes associated with important traits in the watermelon genus

 

Lastly, utilizing the genomic sequences of wild watermelons and information on disease-resistant genes, this study successfully bred a self-pollinating line, 'PKR6,' which exhibits resistance to multiple diseases. Candidate genes associated with Fusarium wilt disease resistance in watermelon were also identified. This research provides a paradigm for utilizing wild germplasm to create outstanding breeding materials, enabling the deliberate reintroduction of disease-resistant genes that were lost during domestication into cultivated varieties. This has profound implications for accelerating the breeding of disease-resistant varieties and promoting the efficient development of the watermelon industry (Figure 4).

Figure 4 Genomic composition of the distinctive interspecific hybrid 'PKR6' with improved disease resistance

 

The Telomere-to-telomere Citrulluss super-pangenome represents the highest quality and most comprehensive genomic sequence and variation map for watermelon. It reveals the genomic evolutionary history of Citrulluss, explores the rich genetic diversity within wild watermelon species, and provides a new paradigm for the creation of superior breeding materials using wild germplasm. Additionally, it points the way towards constructing super-pangenomes for other crops and harnessing the potential of wild germplasm.

Dr. Xingping Zhang and Dr. Yun Deng from the Crop Genetics and Germplasm Innovation Platform at PKU-IAAS, along with Dr. Hang He from the Agricultural Omics Big Data Platform, are the corresponding authors of this research paper. PhD candidate Yilin Zhang, Associate Researcher Mingxia Zhao from PKU-IAAS, Research Assistant Jingsheng Tan, and Dr. Minghan Huang are the co-first authors of this paper. Academician Xing Wang Deng, Research Professors Bosheng Li and Guochen Qin from PKU-IAAS provided crucial support for this study. Researchers Xiao Chu, Yan Li, Xue Han, Taohong Fang, Yao Tian, Dongdong Lu, Yijun Chen, Lifang Xue, and Xiaoni Li from PKU-IAAS, and Research Professor Yudong Sun from Huaiyin Agricultural Science Institute, Jiangsu, as well as Dr. Robert Jarret from the United States Department of Agriculture's Germplasm Resources Center, made significant contributions to this research. Funding for this study was provided by the Shandong Provincial Technology Innovation Fund, the Agricultural Breeding Special Project of Ningxia Hui Autonomous Region, Key Research and Development Project of Shandong Province, Major Science and Technology Project of Ningbo City, and the Innovation Team of Seed Industry in Weifang City.

Expert Commentary:

Dr. Sanwen Huang, an Academician of the Chinese Academy of Sciences, spoke highly of this achievement: "This research represents an incredible, detailed, and exquisite study in the field of watermelon."

Dr. Amnon Levi, a senior researcher at the Vegetable Laboratory of the United States Department of Agriculture and a recipient of the Lifetime Achievement Award at the International Symposium on Cucurbits, also provided a commendation: "It is an amazing and most detailed and beautiful work ever in watermelon."