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<p><i>Buchanania cochinchinensis</i> (Lour.) M.R. Almeida syn. <i>Buchanania lanzan</i>, commonly known as Chironji, is an economically important nontimber forest tree valued for its kernels and medicinal properties but is threatened by overexploitation and habitat fragmentation. The genomic resources for this species are limited. In this study, low-coverage Illumina paired-end sequencing produced 6.29&#xa0;Gb of high-quality data, from which 36,584 simple sequence repeats (SSRs) were identified. A total of 50 primers were randomly selected from the sequenced data. Among these, 13 highly polymorphic SSR markers, including two cross-amplified primers, were validated. These markers were then used to assess genetic diversity and population structure across 120 accessions from five populations in Central India. The validated SSR primers presented high polymorphic information content (PIC), ranging from 0.754 to 0.882, indicating their strong discriminatory power. The observed heterozygosity (Ho) ranged from 0.257 to 0.462, the expected heterozygosity (He) ranged from 0.334 to 0.461, and the average Shannon’s information index value was 0.587. Bayesian STRUCTURE analysis revealed four distinct genetic clusters with minimal admixture, as supported by&#xa0;the&#xa0;unweighted pair group method with arithmetic mean (UPGMA) clustering and&#xa0;the analysis of molecular variance (AMOVA), which confirmed significant genetic differentiation among populations. These findings underscore the impact of geographic isolation and limited gene flow on population structure. This study reports the first de novo development of SSR markers for <i>B. cochinchinensis</i>, providing valuable genomic resources for future breeding, conservation, and management programs. The developed markers will facilitate marker-assisted selection, diversity monitoring, and the formulation of strategies for preserving the genetic integrity of this ecologically and economically vital species.</p>

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Development of microsatellite markers for population genetic analysis of the socioeconomically important tree Buchanania cochinchinensis (Lour.) M. R. Almeida

  • 期刊论文

  • 发表日期：

    2026年5月6日

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  • Ankur Dahayat,
  • Naseer Mohammad

摘要

Buchanania cochinchinensis (Lour.) M.R. Almeida syn. Buchanania lanzan, commonly known as Chironji, is an economically important nontimber forest tree valued for its kernels and medicinal properties but is threatened by overexploitation and habitat fragmentation. The genomic resources for this species are limited. In this study, low-coverage Illumina paired-end sequencing produced 6.29 Gb of high-quality data, from which 36,584 simple sequence repeats (SSRs) were identified. A total of 50 primers were randomly selected from the sequenced data. Among these, 13 highly polymorphic SSR markers, including two cross-amplified primers, were validated. These markers were then used to assess genetic diversity and population structure across 120 accessions from five populations in Central India. The validated SSR primers presented high polymorphic information content (PIC), ranging from 0.754 to 0.882, indicating their strong discriminatory power. The observed heterozygosity (Ho) ranged from 0.257 to 0.462, the expected heterozygosity (He) ranged from 0.334 to 0.461, and the average Shannon’s information index value was 0.587. Bayesian STRUCTURE analysis revealed four distinct genetic clusters with minimal admixture, as supported by the unweighted pair group method with arithmetic mean (UPGMA) clustering and the analysis of molecular variance (AMOVA), which confirmed significant genetic differentiation among populations. These findings underscore the impact of geographic isolation and limited gene flow on population structure. This study reports the first de novo development of SSR markers for B. cochinchinensis, providing valuable genomic resources for future breeding, conservation, and management programs. The developed markers will facilitate marker-assisted selection, diversity monitoring, and the formulation of strategies for preserving the genetic integrity of this ecologically and economically vital species.