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<p>The mitochondrial genome of cotton holds significant genetic diversity, yet its polymorphic sites remain underexplored. Our study focused on a highly polymorphic SSR&#xa0;(simple sequence repeat) locus (SSR160), located 160 bp downstream of the mitochondrial <i>atpA</i> gene, across 29 cotton species. This locus has been identified as the most polymorphic SSR site currently known in the cotton mitochondrial genome. Sequencing revealed a compound SSR motif, (TAA)m(TA)n, with distinct repeat patterns across cottons of different genomes: (TAA)7(TA)6 in A-, B-, and AD-genomes; (TAA)5(TA)5–6 in C-genomes; (TAA)3–4(TA)2–3 in D-genomes; and (TAA)4–5(TA)4–6 in G-genomes. We identified 68 single nucleotide polymorphisms (SNPs), including 26 within SSR160, and developed two novel markers: (1) an mtSSR-sequence characterized amplified region (SCAR) marker targeting <i>G. raimondii</i> (D5 genome) using unique deletions at 170–185 bp and SNP "T" specificity, and (2) an mtSSR-InDel marker for <i>G. armourianum</i> (D2-1 genome) based on a pentanucleotide "TTTTA" repeat. Capillary electrophoresis confirmed marker specificity, enabling rapid differentiation of these species. Phylogenetic analysis grouped the 29 species into 17 clusters, aligning with geographic origins and genome types. These markers address critical gaps in cotton germplasm identification, offering robust tools for evolutionary research, breeding programs, and conservation of genetic resources.</p>

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Comparative analysis of mitochondrial atpA 3’-flanking simple sequence repeat (SSR) polymorphisms in diploid and tetraploid cotton (Gossypium spp.)

  • 期刊论文

  • 发表日期：

    2025年12月16日

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  • Yan Song,
  • JiaQi Ding,
  • YaXin Yan,
  • YiQiong Wang,
  • Bing Zhang,
  • Xiao Zhang,
  • Rui Zhang

摘要

The mitochondrial genome of cotton holds significant genetic diversity, yet its polymorphic sites remain underexplored. Our study focused on a highly polymorphic SSR (simple sequence repeat) locus (SSR160), located 160 bp downstream of the mitochondrial atpA gene, across 29 cotton species. This locus has been identified as the most polymorphic SSR site currently known in the cotton mitochondrial genome. Sequencing revealed a compound SSR motif, (TAA)m(TA)n, with distinct repeat patterns across cottons of different genomes: (TAA)7(TA)6 in A-, B-, and AD-genomes; (TAA)5(TA)5–6 in C-genomes; (TAA)3–4(TA)2–3 in D-genomes; and (TAA)4–5(TA)4–6 in G-genomes. We identified 68 single nucleotide polymorphisms (SNPs), including 26 within SSR160, and developed two novel markers: (1) an mtSSR-sequence characterized amplified region (SCAR) marker targeting G. raimondii (D5 genome) using unique deletions at 170–185 bp and SNP "T" specificity, and (2) an mtSSR-InDel marker for G. armourianum (D2-1 genome) based on a pentanucleotide "TTTTA" repeat. Capillary electrophoresis confirmed marker specificity, enabling rapid differentiation of these species. Phylogenetic analysis grouped the 29 species into 17 clusters, aligning with geographic origins and genome types. These markers address critical gaps in cotton germplasm identification, offering robust tools for evolutionary research, breeding programs, and conservation of genetic resources.