Genotyping-by-sequencing (GBS) allows rapid identification of markers for use in development of linkage maps, which expedite efficient breeding programs. In the present study, we have utilized GBS approach to identify and genotype single-nucleotide polymorphism (SNP) markers in an inter-specific RIL population of Cicer arietinum L. X C. reticulatum. A total of 141,639 raw SNPs were identified using the TASSEL-GBS pipeline. After stringent filtering, 8208 candidate SNPs were identified of which ~ 37% were localized in the intragenic regions followed by genic regions (~ 30%) and intergenic regions (~ 27%). We then utilized 6920 stringent selected SNPs from present study and 6714 SNPs and microsatellite markers available from previous studies for construction of linkage map. The resulting high-density linkage map comprising of eight linkage groups contained 13,590 markers which spanned 1299.14 cM of map length with an average marker density of 0.095 cM. Further, the derived linkage map was used to improve the available assembly of desi chickpea genome by anchoring 443 previously unplaced scaffolds onto eight linkage groups. The present efforts have refined anchoring of the desi chickpea genome assembly to 55.57% of the ~ 520 Mb of assembled desi genome. To the best of our knowledge, the linkage map generated in the present study represents one of the most dense linkage map developed for the crop till date. It will serve as a valuable resource for fine mapping and positional cloning of important quantitative trait loci (QTLs) associated with agronomical traits and also for anchoring and ordering of future genome sequence assemblies.

通过测序进行基因分型（GBS）可以快速鉴定用于连锁图谱开发的标记，从而加快了有效的育种程序。在本研究中，我们已利用GBS方法中的一个具体的帧间RIL群体，以确定和基因型单核苷酸多态性（SNP）标记物鹰嘴豆L. X C.网藻。使用TASSEL-GBS管道共鉴定了141,639个原始SNP。经过严格过滤后，鉴定出8208个候选SNP，其中〜37％位于基因内区域，其次是基因区域（〜30％）和基因间区域（〜27％）。然后，我们利用了本研究中的6920个严格选择的SNPs和6714个SNPs和微卫星标记，这些标记可从以前的研究中获得，用于构建连锁图。所得的由八个连锁组组成的高密度连锁图谱包含13,590个标记，这些标记跨越1299.14 cM的图谱长度，平均标记密度为0.095 cM。此外，派生的链接图用于改进desi的可用组装鹰嘴豆基因组通过将443个先前未放置的支架锚定在八个连接基团上来实现。目前的努力已将德西鹰嘴豆基因组装配的锚定细化到组装的德西基因组的约520 Mb的55.57％。据我们所知，本研究中生成的连锁图代表了迄今为止为农作物开发的最密集的连锁图之一。它将为重要的与农艺性状相关的数量性状基因座（QTL）的精细定位和位置克隆，以及未来基因组序列装配的锚定和排序提供宝贵的资源。