Kun Chai

A k-mer-based genome-wide association study approach empowering gene mining in polyploids

Shuai Chen, Xinlong Liu, Shenyang Qu, Yuhan Song et autres

Genome-wide association studies in complex polyploids are hindered by genotyping ambiguity and allele dosage complexity. Here we present KMERIA, a k-mer-based framework specifically designed to address these challenges, enabling efficient genotyping and robust association mapping in complex polyploid genomes. Rigorous benchmarking with …

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Genetic architecture of sugarcane traits in a polyploid genomics framework

Yi-Xiang Wang, Xiaofeng Li, Yibin Wang, Jishan Lin et autres

Sugarcane (Saccharum spp.) is a vital sugar and bioenergy crop with an exceptionally complex polyploid genome (10–12 sets of chromosomes). This complexity resulted from nobilization—a historical breeding process involving interspecific hybridization and repeated backcrossing1. However, the extreme ploidy has long impeded efforts …

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A k-mer-based GWAS approach empowering gene mining in polyploids

Xingtan Zhang, Shuai Chen, Xinlong Liu, Shenyang Qu et autres

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Pan-genomic analysis highlights genes associated with agronomic traits and enhances genomics-assisted breeding in alfalfa

Fei He, Shuai Chen, Yangyang Zhang, Kun Chai et autres

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Multiomics Analysis Reveals the Genetic Basis of Volatile Terpenoid Formation in Oolong Tea

Kun Chai, Shuai Chen, Pengjie Wang, Weilong Kong et autres

Oolong tea has gained great popularity in China due to its pleasant floral and fruity aromas. Although numerous studies have investigated the aroma differences across various tea cultivars, the genetic mechanism is unclear. This study performed multiomics analysis of three varieties suitable …

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A telomere-to-telomere reference genome of ficus ( Ficus hispida ) provides new insights into sex determination

Zhenyang Liao, Tianwen Zhang, Wen‐Long Lei, Yibin Wang et autres

Abstract A high-quality reference genome is indispensable for resolving biologically essential traits. Ficus hispida is a dioecious plant. A complete Ficus reference genome will be crucial for understanding their sex evolution and important biological characteristics, such as aerial roots, mutualistic symbiosis with …

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Gene mining and genomics-assisted breeding empowered by the pangenome of tea plant Camellia sinensis

Shuai Chen, Pengjie Wang, Weilong Kong, Kun Chai et autres

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5mC DNA methylation modification-mediated regulation in tissue functional differentiation and important flavor substance synthesis of tea plant (Camellia sinensis L.)

Weilong Kong, Qiufang Zhu, Qing Zhang, Yiwang Zhu et autres

Abstract In plants, 5mC DNA methylation is an important and conserved epistatic mark involving genomic stability, gene transcriptional regulation, developmental regulation, abiotic stress response, metabolite synthesis, etc. However, the roles of 5mC DNA methylation modification (5mC methylation) in tea plant growth and …

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Pan-transcriptome assembly combined with multiple association analysis provides new insights into the regulatory network of specialized metabolites in the tea plant Camellia sinensis

Weilong Kong, Mengwei Jiang, Yibin Wang, Shuai Chen et autres

Abstract Specialized metabolites not only play important roles in biotic and abiotic stress adaptation of tea plants (Camellia sinensis (L.) O. Kuntze) but also contribute to the unique flavor of tea, the most important nonalcoholic beverage. However, the molecular networks and major …

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