Kant Rama, Meena Rajendra K, Garg Rimpee, Yadav Abhishek, Bhandari Maneesh S
Division of Genetics and Tree Improvement, ICFRE-Forest Research Institute, Dehradun, Uttarakhand 248 195 India.
Physiol Mol Biol Plants. 2025 Mar;31(3):357-373. doi: 10.1007/s12298-025-01566-6. Epub 2025 Mar 5.
is a fast-growing, multipurpose agroforestry tree species of Indian Arid Regions (IAR). It is widely cultivated as tree outside forests (TOFs) on farm lands, roadside, canal banks, etc., where the genetic stocks were randomly planted. To ensure the availability of quality planting materials (QPM) for industrial profitability, the germplasm must undergo a systematic genetic improvement program. Genetic variability in the base population is crucial for effective selection, but the lack of genomic resources and marker impedes this process. This study aimed to generate genome sequence information and de novo development of simple sequence repeats (SSRs) in . About 96 million raw reads were generated using Illumina platform, assembled into ~ 183,000 contigs with 33% GC content and an N50 value of 641 bp. A total of 7,667 microsatellite repeats were identified, with di-nucleotides being the most abundant. AT rich repeats were more prevalent than GC rich motifs. A total of 3,696 primer pairs were designed, and 150 of these were selected for validation. In PCR, 145 SSRs were positively amplified and 15 showed polymorphic banding pattern. These polymorphic SSRs were used to characterize 213 individuals from northern and central India. SSR analysis revealed high gene diversity (H = 0.71; A = 9.12) with negligible genetic differentiation in populations. The study presents a comprehensive set of de novo SSR markers and provides baseline knowledge of genetic structure of , essential for conservation and long-term genetic improvement programs.
The online version contains supplementary material available at 10.1007/s12298-025-01566-6.
是印度干旱地区（IAR）一种快速生长的多用途农林业树种。它作为非林地树木（TOFs）广泛种植于农田、路边、运河堤岸等地，其遗传种质是随机种植的。为确保有优质种植材料（QPM）以实现产业盈利，种质必须经历系统的遗传改良计划。基础种群中的遗传变异性对于有效选择至关重要，但基因组资源和标记的缺乏阻碍了这一进程。本研究旨在生成基因组序列信息并从头开发该树种的简单序列重复（SSRs）。使用Illumina平台产生了约9600万个原始读数，组装成约183,000个重叠群，GC含量为33%，N50值为641 bp。共鉴定出7667个微卫星重复序列，其中二核苷酸最为丰富。富含AT的重复序列比富含GC的基序更为普遍。共设计了3696对引物，其中150对被选用于验证。在PCR中，145个SSR得到阳性扩增，15个呈现多态性条带模式。这些多态性SSR被用于对来自印度北部和中部的213个个体进行表征。SSR分析显示基因多样性高（H = 0.71；A = 9.12），种群间遗传分化可忽略不计。该研究提供了一套全面的从头开发的SSR标记，并提供了该树种遗传结构的基础知识，这对于保护和长期遗传改良计划至关重要。
在线版本包含可在10.1007/s12298-025-01566-6获取的补充材料。
