Nature Genetics | Zhejiang University And Fujian Agriculture And Forestry University Analyze The Genome Of Cultivated Banana, Revealing Its Origin And Unearthing Key Genes For Disease Resistance And Fruit Ripening

Nature Genetics | Zhejiang University and Fujian Agriculture and Forestry University analyze the genome of cultivated banana, revealing its origin and unearthing key genes for disease resistance and fruit ripening

Banana (Musa ssp) is the most traded fresh fruit in the world, and is also an important food crop in tropical and subtropical developing countries. on December 11, 2023, Zhang Liangsheng's group from the College of Agriculture, Zhejiang University, together with a number of units from Fujian Agriculture and Forestry University, published an article in Nature Genetics, entitled "Origin and evolution of the triploid cultivated banana genome". The research paper entitled Origin and evolution of the triploid cultivated banana genome was published online in the prestigious international journal Nature Genetics, which analyzed the genome of the cultivated banana, revealed its origin, and unearthed the key genes for disease resistance and fruit ripening.

More than 90% of the cultivated bananas on the market belong to the triploid Cavendish and Gros Michel subgroups. This study assembled high-quality chromosome-level genomes of these two widely grown triploid cultivated bananas, as well as a high-quality genome of the wild diploid banana zebrina (Zebrina v2.0) (Figure 1). The ancestral origin of the triploid cultivated banana A genome was clarified, which was mainly derived from three wild diploids, Musa acuminata ssp. banksii, malaccensis and zebrina (Fig. 1). The banana wilt Foc race 1 and TR4 resistance loci were identified and mined, and the Brazilian banana resistance to wilt No. 1 was probably obtained from wild zebrina (Fig. 2). Banana was not resistant to wilt 4 probably due to transposon insertion resulting in non-expression of the resistance gene (RGA). New key genes (MaNAP4 and MaNAP5) regulating fruit ripening were identified (Fig. 3).

High-quality chromosome-level genomes of Cavendish and Gros Michel were completed using PacBio single-molecule sequencing and Hi-C technology in combination with the trio-binning algorithm.The final assembled genome sizes of Cavendish and Gros Michel were 1.48 and 1.33 Gb, and BUSCO assessed completenesses, respectively as high as 97.0% and 96.9%. The chromosomes were mounted using two different strategies, Hi-C and reference-guided, and then subgenome typing was performed using the trio-binning algorithm, which resulted in the classification of three subgenomes each: Ban, Dh, and Ze. Three subgenomes each from Cavendish and Gros Michel were selected, and four published AA wild diploids were identified. Banana: Banskii, DH-Pahang, Zebrina and Calcutta 4, and SS wild diploid banana M. schizocarpa were selected from a total of seven species. Using both phylogenetic and comparative genomics, it was clarified that the three subgenomes of the triploid cultivated bananas, Ban, Dh, and Ze, were mainly derived from Musa acuminata ssp. banksii. acuminata ssp. banksii, malaccensis and zebrina (Figure 1).

Fig. 1 Analysis of two cultivated banana species and their origins.

Banana has been threatened by banana wilt caused by Fusarium oxysporum f.sp. cubense (Foc). Using assembled high-quality Cavendish (Foc race 1-resistant) and Gros Michel (Foc race 1-susceptible) genomes, a complete deletion of one RLP gene cluster located on chromosome 10 in the Ze subgenome of the susceptible banana, Gros Michel, was found (Fig. 2b-d). In addition, a comparative analysis of the Foc TR4 resistance gene RGA2 revealed the insertion of small repetitive fragments in the RGA2 promoter region in most wild and cultivated bananas (Fig. 2). These results suggest that the retention and deletion of key resistance genes (clusters) or alteration of regulatory sites in the genome may be closely related to whether bananas are resistant to Fusarium wilt.

Fig. 2 Comparative analysis of resistance genes/QTL for resistance to minor species 1 and 4 in Brazilian and barley bananas and their wild ancestor species.

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