How Genotyping by Target Sequencing is Transforming Agricultural Breeding?

Southern corn rust (SCR), caused by Puccinia polysora, is a growing threat to global corn production, exacerbated by climate change. In China’s Huang-Huai-Hai region, this disease can slash yields by over 20%, costing farmers billions annually. At Molbreeding, we partnered with Hefei Fengle Seed Industry to tackle this challenge using our cutting-edge genotyping by target sequencing (GBTS) technology. In this article, I’ll share how this innovative approach accelerated the development of rust-resistant maize varieties, slashing breeding timelines by up to 2.5 years, and explore what this means for the future of agricultural breeding.

Southern corn rust is no small problem. In China’s Huang-Huai-Hai region, it affects leaves, sheaths, husks, and tassels, disrupting photosynthesis and grain filling. At its peak, SCR impacts 4 million hectares of the region’s 12 million hectares of corn, leading to yield losses of over 6 billion kilograms and economic damages exceeding 12 billion yuan ($1.7 billion USD).

Traditional breeding methods to introduce rust resistance are slow, often taking years to transfer desired traits into elite varieties. In a world of rapidly evolving climate challenges and market demands, this timeline is simply too long. The question became: How can we develop resistant varieties faster without compromising quality?

To address this, Molbreeding teamed up with Hefei Fengle Seed Industry. Our goal was to integrate the broad-spectrum resistance gene RppK into elite maize inbred lines, creating hybrid seeds resistant to southern rust. The key? Our proprietary genotyping by target sequencing (GBTS) technology.

GBTS allows precise identification and tracking of genetic markers, enabling us to select for rust resistance with unprecedented accuracy. Combined with our fully automated, high-throughput laboratory system, we maintained rigorous quality control throughout the breeding process. The result? In just 18 months, we developed rust-resistant elite inbred lines—1.5 to 2.5 years faster than traditional methods.

This speed gave Hefei Fengle a competitive edge, allowing them to bring resistant varieties to market sooner, maintain market share, and support farmers facing SCR’s devastating impacts. This partnership shows how strategic collaboration and biotechnology can transform agricultural challenges into opportunities.

The results speak for themselves. Our GBTS solution has empowered 20 seed companies to enhance 50 maize varieties, covering 3.3 million hectares annually. These varieties are helping farmers in the Huang-Huai-Hai region protect their yields and livelihoods against southern rust, reducing economic losses and strengthening food security.

Beyond the numbers, this work highlights the power of innovation in agriculture. By replacing slow, labor-intensive breeding with precise, technology-driven solutions, we’re enabling the industry to respond faster to emerging threats like climate-driven diseases.

The success of this project is just the beginning. Genotyping by target sequencing is revolutionizing not only maize breeding but also the broader field of crop improvement. Its precision and speed make it ideal for addressing other challenges, from drought tolerance to pest resistance.

At Molbreeding, we’re committed to pushing the boundaries of agricultural science. Our range of crop genotyping panels—from low to high density—offers flexible solutions for breeding programs of all scales. Whether you’re a seed company, researcher, or agribusiness leader, these tools can help you stay ahead in a rapidly changing industry.