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<Emphasis Type="BoldItalic">Key message</Emphasis> <p><b> Development of </b><Emphasis Type="BoldItalic">de novo</Emphasis> <b>SSR markers in jamun with high PIC and high cross-species transferability provide a valuable resource for genetic diversity analysis, conservation, and molecular breeding in</b> <Emphasis Type="BoldItalic">S. cumini.</Emphasis></p> Abstract <p><i>Syzygium cumini</i> (Jamun) is an underutilized tropical fruit tree valued for its nutritional and therapeutic properties, particularly high content of antioxidants, flavonoids, and phenolic compounds. Despite its economic and medicinal potential, genomic resources for jamun remain limited. In this study, partial genome sequencing of the cultivar ‘Dupdal’ was done using the Illumina HiSeq 2500 platform, yielding a 432&#xa0;Mb assembly and identifying 72,464 simple sequence repeats (SSRs), with predominant di-nucleotide motifs. Thirty polymorphic SSR primers were utilized to genotype 254 jamun accessions. The markers exhibited high informativeness, with polymorphic information content (PIC) values ranging from 0.80 to 0.94 (mean: 0.88). Observed and expected heterozygosity ranged from 0.33 to 0.84 and 0.62–0.94, respectively. Population structure analyses using neighbor-joining dendrogram, STRUCTURE, and principal component analysis (PCA) revealed two distinct genetic clusters, generally corresponding to geographic origin. Analysis of molecular variance (AMOVA) indicated that 21.54% of the total genetic variation resided among populations, while 78.44% was within populations, with a significant fixation index (FST = 0.2159; <i>p</i> = 0.001) suggesting high genetic differentiation. The newly developed genome-wide SSR markers demonstrated high cross-species transferability and also provide a valuable resource for genetic diversity analysis, conservation, and molecular breeding in <i>S. cumini</i> and related Syzygium species.</p>

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De Novo SSR marker development and genetic diversity analysis in Indian Jamun (Syzygium cumini L.) germplasm

  • 期刊论文

  • 发表日期：

    2025年12月3日

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  • Abhilasha Krishnamurthy,
  • Malarvizhi Mathiazhagan,
  • Sukhen Chandra Das,
  • Prasenjit Debnath,
  • Debasree Podder,
  • Ajitha Rekha,
  • Kodthalu S. Shivashankara,
  • Kundapura V. Ravishankar

摘要

Key message

Development of de novo SSR markers in jamun with high PIC and high cross-species transferability provide a valuable resource for genetic diversity analysis, conservation, and molecular breeding in S. cumini.

Abstract

Syzygium cumini (Jamun) is an underutilized tropical fruit tree valued for its nutritional and therapeutic properties, particularly high content of antioxidants, flavonoids, and phenolic compounds. Despite its economic and medicinal potential, genomic resources for jamun remain limited. In this study, partial genome sequencing of the cultivar ‘Dupdal’ was done using the Illumina HiSeq 2500 platform, yielding a 432 Mb assembly and identifying 72,464 simple sequence repeats (SSRs), with predominant di-nucleotide motifs. Thirty polymorphic SSR primers were utilized to genotype 254 jamun accessions. The markers exhibited high informativeness, with polymorphic information content (PIC) values ranging from 0.80 to 0.94 (mean: 0.88). Observed and expected heterozygosity ranged from 0.33 to 0.84 and 0.62–0.94, respectively. Population structure analyses using neighbor-joining dendrogram, STRUCTURE, and principal component analysis (PCA) revealed two distinct genetic clusters, generally corresponding to geographic origin. Analysis of molecular variance (AMOVA) indicated that 21.54% of the total genetic variation resided among populations, while 78.44% was within populations, with a significant fixation index (FST = 0.2159; p = 0.001) suggesting high genetic differentiation. The newly developed genome-wide SSR markers demonstrated high cross-species transferability and also provide a valuable resource for genetic diversity analysis, conservation, and molecular breeding in S. cumini and related Syzygium species.