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<p>Cytoplasmic male sterility (CMS) is widely utilized in hybrid rice seed production, yet the plastid genomes of CMS lines remain poorly characterized. To address this gap, the first de novo plastome assemblies of CMS A/B lines for rice were generated, along with a comparative characterization of the complete chloroplast genomes of the male-sterile A-line and maintainer B-line of Mestizo 1 (NSIC 1997 Rc72H). Both genomes exhibited the typical quadripartite circular structure, comprising a large single-copy (LSC) region, a small single-copy (SSC) region, and two inverted repeats (IRs). Sequence comparison revealed that the A-line plastome had the highest sequence similarity to <i>Oryza rufipogon</i> plastomes, whereas the B-line plastome was most similar to <i>O. sativa</i> plastomes. Phylogenetic reconstruction based on 26 <i>Oryza</i> chloroplast genomes confirmed that the B-line formed a close relationship with <i>O. sativa</i>, while the A-line grouped with <i>O. rufipogon</i>, its wild progenitor. Comparative plastome analysis further identified single-nucleotide polymorphisms and insertion-deletion polymorphisms across 12 genic regions, including the widely used barcoding locus <i>rps16</i>. These results indicate&#xa0;that the CMS A-line of Mestizo 1 carries a plastome closely related to <i>O. rufipogon</i>, while its maintainer B-line carries a plastome characteristic of&#xa0;the&#xa0;domesticated <i>O. sativa</i>. These findings highlight the contribution of wild maternal lineages in shaping CMS cytoplasms and provide the first plastome assemblies for a rice CMS A/B pair. We also underscore the need to document maternal backgrounds of parental lines in released cultivars.</p>

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First plastome assembly of rice cytoplasmic male sterility (CMS) A/B lines reveals wild maternal origin

  • 期刊论文

  • 发表日期：

    2026年6月29日

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  • Renerio P. Gentallan Jr.,
  • Edelweiss E. Sajise,
  • Juan Rodrigo A. Vera Cruz,
  • Bjorn Q. Manuel,
  • Kristine Joyce O. Quiñones-Arribado,
  • Jeremaiah L. Estrada,
  • Emmanuel Bonifacio S. Timog,
  • Patricia Izabelle M. Lopez,
  • Wendy A. Gaspar,
  • Sancho G. Bon,
  • Mark Ian C. Calayugan,
  • Teresita H. Borromeo

摘要

Cytoplasmic male sterility (CMS) is widely utilized in hybrid rice seed production, yet the plastid genomes of CMS lines remain poorly characterized. To address this gap, the first de novo plastome assemblies of CMS A/B lines for rice were generated, along with a comparative characterization of the complete chloroplast genomes of the male-sterile A-line and maintainer B-line of Mestizo 1 (NSIC 1997 Rc72H). Both genomes exhibited the typical quadripartite circular structure, comprising a large single-copy (LSC) region, a small single-copy (SSC) region, and two inverted repeats (IRs). Sequence comparison revealed that the A-line plastome had the highest sequence similarity to Oryza rufipogon plastomes, whereas the B-line plastome was most similar to O. sativa plastomes. Phylogenetic reconstruction based on 26 Oryza chloroplast genomes confirmed that the B-line formed a close relationship with O. sativa, while the A-line grouped with O. rufipogon, its wild progenitor. Comparative plastome analysis further identified single-nucleotide polymorphisms and insertion-deletion polymorphisms across 12 genic regions, including the widely used barcoding locus rps16. These results indicate that the CMS A-line of Mestizo 1 carries a plastome closely related to O. rufipogon, while its maintainer B-line carries a plastome characteristic of the domesticated O. sativa. These findings highlight the contribution of wild maternal lineages in shaping CMS cytoplasms and provide the first plastome assemblies for a rice CMS A/B pair. We also underscore the need to document maternal backgrounds of parental lines in released cultivars.