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

文献类型： 外文期刊

作者： Liu, Chun 1 ; Ding, Xipeng 1 ; Wu, Yuanhang 5 ; Zhang, Jianyu 4 ; Huang, Rui 1 ; Li, Xinyong 1 ; Liu, Guodao 1 ; Liu, Pandao 1 ;

作者机构： 1.Chinese Acad Trop Agr Sci, Trop Crops Genet Resources Inst, Natl Key Lab Trop Crop Breeding, Haikou Sanya 572024, Peoples R China

2.Minist Agr & Rural Affairs, Key Lab Crop Gene Resources & Germplasm Enhancemen, Haikou 571101, Peoples R China

3.Key Lab Trop Crops Germplasm Resources Genet Impro, Haikou 571101, Peoples R China

4.Hainan Univ, Sanya Inst Breeding & Multiplicat, Sch Trop Agr & Forestry, Haikou Sanya 572025, Peoples R China

5.Hubei Univ Sci & Technol, Sch Nucl Technol & Chem & Biol, Xianning 437100, Peoples R China

期刊名称：HORTICULTURE RESEARCH （ 影响因子：8.5； 五年影响因子：9.1 ）

ISSN： 2662-6810

年卷期： 2024 年 11 卷 9 期

页码：

收录情况： SCI

摘要： 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.

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