De novo SSR markers development and genetic diversity assessment in Ailanthus excelsa in India

Ailanthus excelsa 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 A. excelsa. 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_e = 0.71; A_r = 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 A. excelsa, essential for conservation and long-term genetic improvement programs.

The online version contains supplementary material available at 10.1007/s12298-025-01566-6.