Cytoplasmic male sterility (CMS) systems have revolutionised hybrid seed production by eliminating the need for manual pollen removal.
However, success depends on the ability to restore fertility in hybrid offspring using nuclear-encoded restorer genes (Rf). While CMS-Rf systems have been well studied in crops like rice and maize, similar progress in pepper has been hampered by the absence of genetic information and genotyping tools. This has constrained breeding efficiency and slowed the development of superior pepper hybrids.
A research team from Hunan Agricultural University in China says it has made a significant breakthrough towards improving hybrid pepper breeding by identifying a novel restorer gene, CaRf, and launching a powerful genotyping platform known as PepperSNP50K. The new study combines cutting-edge genetic mapping, transcriptome analysis, and molecular validation to tackle longstanding bottlenecks in CMS-based breeding.
The scientists began by examining fertility traits in the CMS line 9704A and the restorer line Zhangshugang. While the sterile 9704A failed to produce viable pollen, Zhangshugang restored fertility in hybrid offspring. Using bulked-segregant analysis and fine mapping, the team pinpointed CaRf, a dominant restorer gene, on chromosome 6. To support breeding at scale, the researchers developed PepperSNP50K, a 51,172-marker SNP chip derived from resequencing 176 diverse pepper lines. The chip offers uniform genome coverage, high polymorphism, and accurate genotype calls, making it ideal for studying genetics and breeding.
The team’s work not only provides the first functional validation of a pepper Rf gene but also delivers a versatile SNP chip capable of accelerating precision breeding across diverse pepper varieties.
“This is a milestone for pepper genetics,” said Dr Feng Liu, co-corresponding author and professor at Hunan Agricultural University. “For the first time, we have functionally verified a restorer gene in pepper and paired it with a high-throughput genotyping tool. CaRf allows us to control fertility restoration with precision, and the PepperSNP50K chip ensures that we can do so rapidly, efficiently, and at scale. It’s the kind of integrated solution breeders have been waiting for—one that transforms complex breeding challenges into streamlined, data-driven strategies.”
These strategies enable breeders to develop male-sterile and restorer lines more quickly, improving the efficiency of three-line hybrid production. It also facilitates genome-wide selection for disease resistance, fruit quality, and other key traits. Looking forward, the team plan to build a pepper “speed breeding” facility inspired by rice platforms, aiming to compress breeding cycles to under two years.