Decoding pigeonpea: Ancient landrace yields insights for modern agriculture

A recent study has uncovered the genetic foundations of seed weight in pigeonpea (Cajanus cajan), a tropical legume prized for its nutritional value and resilience. The research introduces a high-quality chromosome-scale reference genome for the ancient pigeonpea landrace 'D30', marking a transformative step in genomics-assisted breeding. This breakthrough provides a powerful genetic resource, allowing scientists to pinpoint key genes responsible for stress tolerance and seed development, with the potential to revolutionize strategies for improving this essential crop.

Pigeonpea, a cornerstone food legume in tropical and subtropical regions, has long faced challenges in genomic research due to the absence of a high-quality reference genome. This gap has hindered efforts to fully understand its genetic diversity and unlock its potential for crop enhancement. As climate change and population growth place increasing pressure on global food systems, there is an urgent need to explore the pigeonpea genome in depth to create varieties better equipped to endure environmental stresses and increase nutritional output.

In an achievement, researchers from the Tropical Crops Genetic Resources Institute have assembled the first-ever high-quality genome of the ancient pigeonpea landrace 'D30'. Published (DOI: 10.1093/hr/uhae201) in Horticulture Research on July 30, 2024, the study utilizes cutting-edge sequencing technologies, including Pacific Biosciences high-fidelity (PacBio HiFi) and high-throughput chromatin conformation capture (Hi-C), to uncover the genetic variations crucial for crop improvement.

The study presents a comprehensive chromosome-scale reference genome for 'D30', spanning 813.54 Mb with remarkable accuracy. The genome assembly boasts a contig N50 of 10.74 Mb, scaffold N50 of 73.07 Mb, and a GC content of 35.67%. This treasure trove of genomic data includes 431.37 Mb of repeat elements and 37,977 protein-coding genes. Notably, the research identifies single-nucleotide polymorphisms (SNPs), insertions/deletions (indels), and structural variations between 'D30' and the widely studied 'Asha' cultivar. These variations are linked to stress responses, with a standout discovery being a calmodulin-like protein (CcCML) that is associated with 100-seed weight—a dominant haplotype with the potential to significantly influence seed size, a crucial trait for crop yield. These findings not only deepen our understanding of pigeonpea genetics but also pave the way for more targeted breeding efforts aimed at enhancing both yield and resilience.

Dr. Pandao Liu, a principal investigator on the project, highlights the far-reaching impact of the research: “Our work not only fills a critical gap in pigeonpea genomics but also provides us with the tools to reshape breeding practices. By pinpointing genetic markers linked to vital agronomic traits, we are now positioned to develop pigeonpea varieties that are not only more productive but also more resilient—key to ensuring food security in regions where pigeonpea is a primary source of protein.”

The implications of this research extend far beyond the lab. With the genetic blueprint of pigeonpea now unlocked, scientists can accelerate the development of new, high-yielding varieties that are more nutritious and better equipped to withstand environmental challenges like drought and disease. This genomic resource will play a crucial role in enhancing agricultural sustainability in tropical and subtropical regions, where smallholder farmers rely on pigeonpea for both nutrition and economic stability. The ability to improve this crop could drive significant advances in food production and economic resilience, helping to combat food insecurity and malnutrition in vulnerable regions around the world.

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References

DOI

10.1093/hr/uhae201

Original Source URL

https://doi.org/10.1093/hr/uhae201

Funding information

The research was financially supported by the Natural Science Foundation of Hainan Province (No. 323CXTD387), the earmarked fund for China Agriculture Research System—Green Manure (No. CARS-22), the earmarked fund for CARS (No. CARS-34), the Young Elite Scientists Sponsorship Program by CAST (No. 2019QNRC001), the Agricultural Research Outstanding Talents and Innovation Team of MARA (No. 13210268), and the Central Public-interest Scientific Institution Basal Research Fund for CATAS (No. 1630032022023).

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, 2022. 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.