Pigeonpea (Cajanus cajan) is a vital legume for millions of farmers across Asia, Africa, and Latin America. Its natural resilience to heat, drought, and poor soils makes it especially valuable in regions facing environmental challenges. Yet despite its importance, pigeonpea remains under-researched compared to other major crops, in part due to the lack of a robust reference genome. Previous assemblies, such as that of the modern cultivar 'Asha', lacked the resolution needed to deeply explore the species' genetic diversity. Due to these limitations, there is an urgent need to develop a more complete genomic blueprint to unlock its full breeding potential.
A research team from the Chinese Academy of Tropical Agricultural Sciences has made a major contribution to pigeonpea genetics by publishing a chromosome-level genome assembly of the landrace 'D30'. Their study (DOI: 10.1093/hr/uhae201), appearing July 30, 2024, in Horticulture Research, reveals high-impact genomic regions associated with seed traits. Combining PacBio HiFi, Hi-C, and NGS technologies, the researchers not only mapped the genome with exceptional accuracy but also uncovered a candidate gene—CcCML—whose dominant haplotype correlates with increased 100-seed weight, a key productivity trait in pigeonpea.
By sequencing and assembling the 813.5 Mb genome of 'D30', the researchers achieved a contig N50 of 10.74 Mb and anchored 92.8% of the genome to 11 chromosomes—surpassing previous assemblies in continuity and completeness. Detailed annotation identified nearly 38,000 protein-coding genes. Through resequencing 294 Cajanus accessions, the team detected genetic variations under selection, particularly in starch and sucrose metabolism pathways—many of which showed high expression in seeds. In parallel, genome-wide association studies (GWAS) pinpointed 28 genetic markers linked to six agronomic traits. One region on chromosome 11 stood out: a 163-kb linkage block harboring CcCML, a calmodulin-like protein gene. This gene showed strong expression in seeds and pods, and its dominant haplotype—distinguished by two non-synonymous SNPs—was associated with significantly heavier seeds. The findings suggest CcCML plays a previously underappreciated role in seed development, offering a promising target for crop improvement.
“Our high-quality genome of 'D30' fills a critical gap in pigeonpea genomics,” said Dr. Pandao Liu, senior author of the study. “By tracing seed weight to a specific gene haplotype, we're not only expanding our understanding of pigeonpea biology, but also offering a tangible tool for breeders. This work bridges traditional landrace diversity and modern genomics, which is exactly what's needed to revitalize this orphan crop for the future.”
The newly sequenced genome provides a powerful foundation for precision breeding programs aimed at enhancing pigeonpea yield and adaptability. The identification of functional haplotypes in CcCML opens new avenues for marker-assisted selection focused on seed size. Beyond seed weight, the study's comprehensive data on gene expression and variation can inform breeding for stress resistance and nutritional quality. Looking ahead, functional validation of CcCML and similar genes will help breeders develop improved pigeonpea varieties—better suited to the needs of farmers and consumers in a changing climate.
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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, 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.