A high-density intraspecific SNP linkage map of pigeonpea (Cajanas cajan L. Millsp.)

Pigeonpea (Cajanus cajan (L.) Millsp.) is a major food legume cultivated in semi-arid tropical regions including the Indian subcontinent, Africa, and Southeast Asia. It is an important source of protein, minerals, and vitamins for nearly 20% of the world population. Due to high carbon sequestration and drought tolerance, pigeonpea is an important crop for the development of climate resilient agriculture and nutritional security. However, pigeonpea productivity has remained low for decades because of limited genetic and genomic resources, and sparse utilization of landraces and wild pigeonpea germplasm. Here, we present a dense intraspecific linkage map of pigeonpea comprising 932 markers that span a total adjusted map length of 1,411.83 cM. The consensus map is based on three different linkage maps that incorporate a large number of single nucleotide polymorphism (SNP) markers derived from next generation sequencing data, using Illumina GoldenGate bead arrays, and genotyping with restriction site associated DNA (RAD) sequencing. The genotyping-by-sequencing enhanced the marker density but was met with limited success due to lack of common markers across the genotypes of mapping population. The integrated map has 547 bead-array SNP, 319 RAD-SNP, and 65 simple sequence repeat (SSR) marker loci. We also show here correspondence between our linkage map and published genome pseudomolecules of pigeonpea. The availability of a high-density linkage map will help improve the anchoring of the pigeonpea genome to its chromosomes and the mapping of genes and quantitative trait loci associated with useful agronomic traits.木豆（Cajanus cajan (L.) Millsp.）是一类主要食用豆科作物，广泛种植于印度次大陆、非洲及东南亚等半干旱热带区域。全球近20%的人口将其作为蛋白质、矿物质与维生素的重要供给来源。由于具备较高的碳固存能力与耐旱特性，木豆是发展气候韧性农业、保障营养安全的核心作物之一。然而，受限于有限的遗传与基因组资源，以及地方品种和野生木豆种质资源的开发利用不足，木豆的单产数十年来始终处于低位。本研究构建了一张高密度木豆种内连锁图谱，包含932个标记位点，总校正图谱长度达1411.83 cM。该整合连锁图谱基于三套独立的连锁图谱构建，整合了大量源自下一代测序数据的单核苷酸多态性（Single Nucleotide Polymorphism, SNP）标记，分型技术涵盖Illumina GoldenGate芯片阵列与限制性酶切位点相关DNA（Restriction Site Associated DNA, RAD）测序。测序分型技术虽有效提升了标记密度，但由于作图群体各基因型间缺乏通用标记，其应用效果未能达到预期。本整合图谱共包含547个芯片阵列SNP标记、319个RAD-SNP标记以及65个简单序列重复（Simple Sequence Repeat, SSR）标记位点。本研究同时验证了该连锁图谱与已发表的木豆基因组假分子之间的对应关系。高密度连锁图谱的问世，将有助于完善木豆基因组与染色体的锚定工作，并推动与优良农艺性状相关的基因及数量性状位点的定位研究。