Overcoming chromosomal roadblocks in banana breeding

Banana production worldwide is threatened by narrow genetic diversity, pests, diseases, and climate pressures. Addressing these challenges requires new cultivars with higher yield, improved fruit quality, and greater resilience. A large-scale genetic study of over 2,700 triploid banana hybrids has now identified dozens of quantitative trait loci (QTLs) linked to yield components, plant and fruit architecture, and harvest timing. By accounting for complex chromosomal rearrangements that often hinder genetic analysis, researchers uncovered key regions of the genome associated with favorable traits. These findings provide a roadmap for accelerating breeding strategies, offering breeders powerful genetic resources to guide the development of stronger, more sustainable banana varieties.

Bananas (Musa spp.) are both a staple food and a major cash crop for millions of people in tropical and subtropical regions. Yet global production relies heavily on a few hybrid cultivars, particularly the 'Cavendish', which accounts for more than half of exports. Such dependence on a narrow genetic base leaves the crop highly vulnerable to disease outbreaks, pests, and environmental fluctuations. Traditional banana breeding has been slow and difficult due to sterility, low fertility, and long growth cycles. Due to these problems, there is an urgent need for in-depth research on the genetic architecture of agronomic traits to accelerate the breeding of improved varieties.

A research team from CIRAD and partners has published (DOI: 10.1093/hr/uhae307) a comprehensive genome-wide association study (GWAS) of triploid bananas in Horticulture Research on February 1, 2025. The study examined 2,723 hybrids and used advanced statistical models to account for large chromosomal rearrangements, a common but overlooked feature of banana genomes. The researchers identified 62 consensus quantitative trait loci (QTLs) linked to traits such as yield, fruit size, bunch angle, and days to maturity. These insights mark a significant step toward modern, genomics-driven banana breeding.

The team evaluated 24 agro-morphological traits in three crop cycles, covering aspects from pseudostem height and leaf size to bunch weight and fruit grade. Over 200,000 SNP markers were genotyped across a subset of 1,129 hybrids. Standard GWAS methods often lose statistical power when genomes contain structural heterozygosities like reciprocal translocations. To overcome this, the researchers introduced a chromosome-specific kinship model (Kc model) that excluded SNPs from rearranged chromosomes, enabling the detection of signals previously hidden.

As a result, the study identified 62 consensus QTLs across 23 traits, distributed over 10 chromosomes. Notably, key QTLs were linked to shorter fruiting cycles (chromosome 4), larger fruit diameter (chromosome 3), and improved bunch weight (chromosome 3 and 5). Some QTLs showed pleiotropic effects, influencing multiple traits simultaneously—for example, alleles from the banksii ancestral group were associated with both increased bunch weight and reduced time to maturity. This level of genetic detail provides breeders with a map of favorable alleles and highlights the crucial role of wild ancestral germplasm in modern banana improvement.

“Banana breeding has always been constrained by low fertility and complex genomes, but this study shows we can unlock valuable genetic variation despite these barriers,” said Guillaume Martin, CIRAD researcher and co-author. “By pinpointing where favorable alleles originate and how chromosomal rearrangements influence trait inheritance, we can design more efficient breeding schemes. This knowledge empowers breeders to make smarter cross choices and apply genomic prediction tools, ultimately speeding up the creation of resilient banana cultivars for farmers and consumers worldwide”.

The discovery of QTLs underlying yield and quality traits opens the door to applying molecular markers and genomic prediction in banana breeding. Breeders can now screen parental lines for favorable alleles, prioritize promising crosses, and perform early selection in progeny, saving years of costly field trials. Importantly, identifying allele ancestries also directs attention to wild germplasm, such as banksii, as reservoirs of beneficial traits. Beyond bananas, the new GWAS approach—accounting for chromosomal rearrangements—offers a methodological advance for crops with structurally complex genomes, from sugarcane to wheat. These innovations hold promise for building more diverse, sustainable, and climate-resilient food systems.

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References

DOI

10.1093/hr/uhae307

Original Source URL

https://doi.org/10.1093/hr/uhae307

Funding information

This research was supported by the Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD) and Genoscope (from French Alternative Energies and Atomic Energy Commission (CEA)), the European Agricultural Fund for Rural Development (FEADER) and Région Guadeloupe through 'Plan Banane Durable 1' and 'Plan Banane Durable 2′ programmes, the France Génomique (ANR-10-INBS-09-08) project DYNAMO, the CGIAR Research Programme on Roots, Tubers and Bananas and the Agropolis Fondation (ID 1504-006) 'GenomeHarvest' project through the French Investissements d’Avenir programme (Labex Agro: ANR- 10-LABX-0001-01).

About Horticulture Research

Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.