Liu Chun, Ding Xipeng, Wu Yuanhang, Zhang Jianyu, Huang Rui, Li Xinyong, Liu Guodao, Liu Pandao
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.
Hortic Res. 2024 Jul 30;11(9):uhae201. doi: 10.1093/hr/uhae201. eCollection 2024 Sep.
Pigeonpea () is a nutrient-rich and versatile food legume crop of tropical and subtropical regions. In this study, we describe the 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 () 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.
木豆（Cajanus cajan）是热带和亚热带地区一种营养丰富且用途广泛的食用豆类作物。在本研究中，我们描述了通过结合太平洋生物科学公司的高保真（PacBio HiFi）和高通量染色质构象捕获（Hi-C）测序技术，对古老的木豆地方品种“D30”进行高质量基因组组装的过程。组装后的“D30”基因组大小为813.54 Mb，重叠群N50为10.74 Mb，支架N50为73.07 Mb，GC含量为35.67%。基因组评估显示，“D30”基因组包含99.2%的基准通用单拷贝直系同源基因（BUSCO），并实现了29.06的长末端重复序列（LTR）组装指数（LAI）。基因组注释表明，“D30”包含431.37 Mb的重复元件（占基因组的53.02%）和37977个蛋白质编码基因。对“D30”与已发表的木豆品种“Asha”基因组之间的单核苷酸多态性（SNP）、插入/缺失（indel）和结构变异的鉴定表明，受这些变异影响的基因可能在生物和非生物胁迫反应中发挥重要作用。对选择区域的进一步研究突出了富含淀粉和蔗糖代谢的基因，其中42.11%的这些基因在种子中高度表达。最后，我们进行了全基因组关联研究（GWAS），以促进对木豆六个农艺性状的28个标记-性状关联的鉴定。值得注意的是，我们发现了一种类钙调蛋白（CML），它具有与木豆百粒重相关的显性单倍型。我们的研究为木豆基因组辅助育种计划的开发提供了基础资源。
