Why do bird's eye chili fruits grow upward? Are bell peppers naturally non-pungent? Recently, a new study constructed high-quality genomic maps of wild and cultivated chili peppers, unraveling the mysteries of chili pepper trait evolution. The research was completed by a scientific team from the Institute of Vegetables and Flowers of the Chinese Academy of Agricultural Sciences (hereinafter referred to as "IVF") and was published as a cover article in Nature Plants.

Chili peppers are one of China's most widely planted vegetable crops, with an annual planting area exceeding 20 million mu. The genus Capsicum includes over 30 species, including five cultivated species such as the widely grown annual chili and numerous wild species, which exhibit rich genetic diversity but have an unclear evolutionary trajectory.

According to the China Food Exhibition, using advanced sequencing technologies, researchers have completed high-quality assemblies of five cultivated and six wild species. Two of the genomes achieved "telomere-to-telomere" complete maps, thereby unlocking the genetic code of chili pepper evolution.

How many chromosomes did the chili pepper ancestor have? The academic community has not reached a consensus. Thanks to multiple high-quality genomic maps, researchers reconstructed the ancestral model of the Capsicum genus and confirmed its original karyotype as 12 pairs of chromosomes. Transposons, known as "active genomic elements," were found to have distinct burst events in different chili genomes. These transposons triggered extensive structural variations in the genome, directly contributing to the phenotypic diversity of chili peppers. For example, the fruits of Chinese chili peppers mainly grow downward. However, a deletion in the promoter region of the gene regulating fruit orientation altered gene expression, causing some chili fruits to grow upward instead.

By constructing a complete haplotype map of chili peppers, researchers also discovered that the annual chili continuously optimizes its traits through "genetic borrowing." For example, by hybridizing with its sister species, the shrub chili, genetic diversity was enriched; some bell peppers introduced disease-resistant genes from Chinese chili peppers to combat the chili pepper mild mottle virus; and by selectively breeding specific haplotypes of the pungency-related Pun1 gene, the transition from spicy to sweet was achieved. "These findings are like a 'roadmap' for chili breeding, providing new ideas for improving the efficiency of superior variety selection," said Wang Lihao, a researcher at IVF and co-corresponding author of the paper.

"This study powerfully demonstrates China's original innovative capabilities in the field of chili peppers," said Zou Xuexiao, an expert in chili breeding and an academician of the Chinese Academy of Engineering. He believes that the results are of great guiding significance for promoting the transformation of chili breeding from "experience-driven" to "data-driven."

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Source: People's Daily

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