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

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

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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.

Chun Liu、Xipeng Ding、Yuanhang Wu、Jianyu Zhang、Rui Huang、Xinyong Li、Guodao Liu、Pandao Liu

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Tropical Crops Genetic Resources Institute,National Key Laboratory for Tropical Crop Breeding,Chinese Academy of Tropical Agricultural Sciences,Haikou/Sanya 571101/572024,China

Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China,Ministry of Agriculture and Rural Affairs,Haikou 571101,China

Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province,Haikou 571101,China

School of Tropical Agriculture and Forestry,Sanya Institute Bree

School of Nuclear Technology and Chemistry & Biology,Hubei University of Science and Technology,Xianning 437100,China

School of Tropical Agriculture and Forestry,Sanya Institute Breeding and Multiplication,Hainan University,Haikou/Sanya 570228/572025,China

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2024

10.1093/hr/uhae201

园艺研究(英文)

园艺研究(英文)

CSTPCD
ISSN：
年,卷(期)：2024.11(9)