Genome-wide association studies reveal genetic diversity and regulatory loci underlying dwarfing traits in banana

doi:10.1111/jipb.70002

• Research Article •

Genome-wide association studies reveal genetic diversity and regulatory loci underlying dwarfing traits in banana

Yuqi Li^1,2,3†, Junting Feng^2†, Liu Yan^1,2, Shouxing Wei⁴, Huigang Hu⁵, Juhua Liu², Yixian Xie⁶, Bingyu Cai², Kai Li², Yankun Zhao², Yufeng Chen², Qifeng Cheng², Miaomiao Cao², Yi Wang¹, Yongzan Wei², Wei Li^1,3*, Wei Wang^2*, Jianghui Xie^2* and Zhenhai Han^1,3*

1. Sanya Institute of China Agricultural University, Sanya 572000, China
2. National Key Laboratory of Biological Breeding of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
3. Institute for Horticultural Plants, China Agricultural University, Beijing 100193, China
4. Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences (CARTA), Danzhou 571737, China
5. Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, National Field Genebank for Tropical Fruit, South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Science, Zhanjiang 524091, China
6. Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Hainan Institute for Tropical Agricultural Resources, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101,China

^†These authors contributed equally to this work.
^*Correspondences: Wei Li (liwei0522898@163.com); Wei Wang (wangwei@itbb.org.cn); Jianghui Xie (xiejianghui@itbb.org.cn); Zhenhai Han (rschan@cau.edu.cn, Dr. Han is fully responsible for the distribution of all materials associated with this article)

Received:2025-01-20 Accepted:2025-06-29 Online:2025-07-29
Supported by:
The work was supported by the Research Program of Sanya Yazhou Bay Science and Technology City (SYND‐2021‐05, SYND‐2022‐13), the Natural Science Foundation of Hainan (321MS066), the Central Public‐interest Scientific Institution Basal Research Fund (1630052022006, CATASCXTD202309), the National Natural Science Foundation of China (32360706, U22A20487), the Project of National Key Laboratory for Tropical Crop Breeding (NKLTCBCXTD27, NKLTCB202311), the Social Public‐Interest Scientific Institution Reform Special Fund (1630052024003), and the China Agriculture Research System (CARS‐31).

Abstract

Abstract: Bananas (Musa ssp.) are globally important staple crops increasingly constrained by biotic stressors, climatic instability, and the high labor demands of cultivation. The genetic improvement of dwarf phenotypes offers a strategic pathway to enhance mechanization and reduce production costs. In this study, we have carried out whole-genome resequencing of 300 Musa accessions to analyze genome-wide allelic diversity and identify loci associated with shoot architecture. Our analysis uncovered extensive genetic variation within the A subgenome, pivotal for environmental adaptability, and detected introgression from Musa itinerans (subgroup A) into cultivated varieties (subgroup F), suggesting a broadened genetic base amenable to breeding. A genome-wide association study (GWAS) pinpointed MabHLH30 as a crucial gene associated plant stature. Functional validation confirmed MabHLH30 as a critical regulator of plant stature and leaf morphology. Leveraging this finding, we developed molecular markers for MabHLH30, enabling marker-assisted selection (MAS) to accelerate the breeding of compact, high-yielding cultivars. Collectively, these results provide a genomic framework for the targeted improvement of banana architecture and represent a valuable resource for cultivar development under diverse agroecological conditions.

Key words: GWAS, hormone, molecular marker, Musa, plant height

Yuqi Li, Junting Feng, Liu Yan, Shouxing Wei, Huigang Hu, Juhua Liu, Yixian Xie, Bingyu Cai, Kai Li, Yankun Zhao, Yufeng Chen, Qifeng Cheng, Miaomiao Cao, Yi Wang, Yongzan Wei, Wei Li, Wei Wang, Jianghui Xie, Zhenhai Han. Genome-wide association studies reveal genetic diversity and regulatory loci underlying dwarfing traits in banana[J]. J Integr Plant Biol., DOI: 10.1111/jipb.70002.

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Genome-wide association studies reveal genetic diversity and regulatory loci underlying dwarfing traits in banana

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