biostudies-literatureUnknown16Khade YPAlliums, including vital crops such as onion, garlic, chives, bunching onion, and leek, are globally prized for their culinary applications and medicinal attributes. However, their genetic improvement remains constrained by large genome size, high heterozygosity, and limited characterization of genetic resources. To bridge this gap, we developed chloroplast simple sequence repeat (cp-SSR) markers, which are particularly suitable for population genetics studies because of their maternal inheritance, low recombination rates, and high variability. Leveraging the chloroplast genome of <i>Allium fistulosum</i>, we identified 22 cp-SSR loci, with tetranucleotides being the most prevalent, followed by di-, tri-, and pentanucleotides. Screening 96 underutilized <i>Allium</i> accessions using polymFrontiers in plant science1645145https://www.ebi.ac.uk/biostudies/studies/S-EPMC12477137biostudies-literatureHarnessing chloroplast SSRs to decipher genetic diversity in underutilized &lt;i&gt;Allium&lt;/i&gt; species.PMC12477137Gupta AJJadhav MBhandari HRHembade VLKhade YPSinhasane SRPatil AKhar AMainkar PRadhakrishna AChandanshive AKale RBMahajan VRai KMMore SJPrakash KfalseHarnessing chloroplast SSRs to decipher genetic diversity in underutilized &lt;i&gt;Allium&lt;/i&gt; species.Alliums, including vital crops such as onion, garlic, chives, bunching onion, and leek, are globally prized for their culinary applications and medicinal attributes. However, their genetic improvement remains constrained by large genome size, high heterozygosity, and limited characterization of genetic resources. To bridge this gap, we developed chloroplast simple sequence repeat (cp-SSR) markers, which are particularly suitable for population genetics studies because of their maternal inheritance, low recombination rates, and high variability. Leveraging the chloroplast genome of <i>Allium fistulosum</i>, we identified 22 cp-SSR loci, with tetranucleotides being the most prevalent, followed by di-, tri-, and pentanucleotides. Screening 96 underutilized <i>Allium</i> accessions using polym2025-01-01T00:00:00Z20252026-06-30T03:29:54.533Z2026-06-30T03:22:54.19ZS-EPMC124771374103130010.3389/fpls.2025.1645145