Rice landraces are vital genetic resources for agronomic and quality traits but the undeniable collection of Kerala landraces remains poorly delineated. To effectively conserve, manage, and use these resources, understanding the genomic structure of germplasm is essential. Genotyping by sequencing (GBS) enables identification of an immense number of single nucleotide polymorphism (SNP) and insertion deletion (InDel) from 96 rice germplasm. In the present study, a total of 16.9 × 10⁷ reads were generated, and among that 16.3 × 10⁷ reads were mapped to the indica reference genome. Exploring GBS data unfolded a wide genomic variations including 82,59,639 SNPs and 1,07,140 Indels. Both neighbor-joining tree and principal coordinate analysis with InDel markers revealed the selected germplasm in this study as highly diverse in structure. We assembled unmapped reads which were further employed for gene ontology analysis. These unmapped sequences that are generally expelled from subsequent studies of GBS data analysis may exist as an unexplored resort for several novel significant biological findings. The discovery of SNPs from the haplotyping results of GS3 and GIF1 genes provided insight into marker- assisted selection based on grain size and yield and can be utilized for rice yield improvement. To our knowledge, this is the first report on structural variation analysis using the GBS platform in rice landraces collected from Kerala. Genomic information from this study endows with valuable resources for perceptive rice landrace structure and can also facilitate sequencing-based molecular breeding.

水稻地方品种是农艺和品质性状的重要遗传资源，但不可否认的喀拉拉邦地方品种的收藏仍然很难界定。为了有效地保存，管理和使用这些资源，了解种质的基因组结构至关重要。通过测序（GBS）进行基因分型可以鉴定96种水稻种质中的大量单核苷酸多态性（SNP）和插入缺失（InDel）。在本研究中，总共产生了16.9×10 ^7个读数，其中16.3×10 ⁷将读段定位到the参考基因组。探索GBS数据揭示了广泛的基因组变异，包括82,59,639个SNP和1,07,140个Indel。邻居连接树和使用InDel标记的主坐标分析都揭示了本研究中所选种质的结构高度多样化。我们组装了未映射的读段，将其进一步用于基因本体分析。这些未映射的序列通常是从GBS数据分析的后续研究中删除的，可能作为一些新颖的重要生物学发现的未开发手段而存在。从GS3和GIF1的单体型分析结果中发现SNP这些基因提供了基于颗粒大小和产量的标记辅助选择的见识，可用于提高水稻产量。就我们所知，这是关于使用GBS平台从喀拉拉邦收集的稻种中进行结构变异分析的第一份报告。这项研究的基因组信息为了解水稻的地方品种结构提供了宝贵的资源，也可以促进基于测序的分子育种。