Chromosome-scale reference genome of an ancient landrace: unveiling the genetic basis of seed weight in the food legume crop pigeonpea (Cajanus cajan)

Abstract

Pigeonpea (Cajanus cajan) is a nutrient-rich and versatile food legume crop of tropical and subtropical regions. In this study, we describe the de novo assembly of a high-quality genome for the ancient pigeonpea landrace ‘D30’, achieved through a combination of Pacific Biosciences high-fidelity (PacBio HiFi) and high-throughput chromatin conformation capture (Hi-C) sequencing technologies. The assembled ‘D30’ genome has a size of 813.54 Mb, with a contig N50 of 10.74 Mb, a scaffold N50 of 73.07 Mb, and a GC content of 35.67%. Genomic evaluation revealed that the ‘D30’ genome contains 99.2% of Benchmarking Universal Single-Copy Orthologs (BUSCO) and achieves a 29.06 long terminal repeat (LTR) assembly index (LAI). Genome annotation indicated that ‘D30’ encompasses 431.37 Mb of repeat elements (53.02% of the genome) and 37 977 protein-coding genes. Identification of single-nucleotide polymorphisms (SNPs), insertions/deletions (indels), and structural variations between ‘D30’ and the published genome of pigeonpea cultivar ‘Asha’ suggests that genes affected by these variations may play important roles in biotic and abiotic stress responses. Further investigation of genomic regions under selection highlights genes enriched in starch and sucrose metabolism, with 42.11% of these genes highly expressed in seeds. Finally, we conducted genome-wide association studies (GWAS) to facilitate the identification of 28 marker-trait associations for six agronomic traits of pigeonpea. Notably, we discovered a calmodulin-like protein (CcCML) that harbors a dominant haplotype associated with the 100-seed weight of pigeonpea. Our study provides a foundational resource for developing genomics-assisted breeding programs in pigeonpea.

Acknowledgements

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).

Author contributions

P.L. conceived the project and designed the experiments. C.L. performed genome assembly, annotation, transcriptomic, and population analyses. G.L. provided funding and performed supervision. X.D. provided ‘D30’ pigeonpea germplasm. Y.W., J.Z., R.H., and X.L. planted and collected pigeonpea samples. C.L. wrote the manuscript. P.L. revised the manuscript. All authors read and approved the final manuscript.

Data availability

The raw genomic sequencing data, including PacBio HiFi, BGISEQ, Hi-C, and transcriptome sequencing data, are available in the National Genomics Data Center (NGDC) under PRJCA024778. DNA resequencing data of 292 Cajanus accessions (BioProject: PRJNA383013), NGS data (SRR5922906), and TGS data (SRR10053121) of ‘Asha’ were retrieved from the SRA database (https://www.ncbi.nlm.nih.gov/sra/). The genome assembly and gene annotation reported in this paper have been deposited in the Genome Warehouse in National Genomics Data Center, Beijing Institute of Genomics (China National Center for Bioinformation), Chinese Academy of Sciences, under accession number GWHETRU00000000.1, which is publicly accessible at https://bigd.big.ac.cn/gwh.

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary data

Supplementary data are available at Horticulture Research online.

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