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<p><i>Pyropia yezoensis</i>, an economically significant cultivated seaweed, exhibits blade length as a crucial yield-determining trait. However, limited studies have focused on identifying length-associated candidate genes. This study utilized heterozygous conchocelis derived from the cross between wild-type (<i>W</i>) and red mutant (<i>R</i>) strains of <i>P. yezoensis</i> and constructed a genetic population comprising 200 double haploid (DH) strains using their offspring with four-color-sectored blades. Based on the lengths of the 35-day-old blades of different DH strains, two bulked pools were constructed by selecting 20 extreme-long and 20 extreme-short DH strains. BSA-seq analysis identified 9 candidate regions associated with blade length, encompassing 415 genes. Three strains were respectively selected from the extremely long and extremely short bulked pools, and transcriptome sequencing was performed on their blades at 35 days old, revealing 572 differentially expressed genes (DEGs) at the intersection of three comparison groups of extremely long and extremely short strains. Results of the trend clustering analysis showed that a total of 93 genes displayed the same trend in either the extremely long group or the extremely short group, but there were obvious differences in trends between different groups. These genes are mainly related to pathways such as RNA polymerase activity, ATP-dependent chromatin remodeling, and carbon metabolism. Integrative analysis of BSA-seq and RNA-seq, three candidate genes were screened out, encoding DNA-directed RNA polymerase III subunit (RPC2), ATP-dependent DNA helicase (Pif1), and a protein of unknown function, respectively. qRT-PCR validation confirmed significant expression differences of these three genes between three extremely long and three extremely short strains, demonstrating high correlations with blade length. This study not only deepens our understanding of the regulatory mechanisms of blade length in <i>P. yezoensis</i>, but also provides valuable references for future precision molecular breeding.</p>

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Screening and analysis of candidate genes related to the blade length in Pyropia yezoensis using BSA-seq and RNA-seq techniques

  • 期刊论文

  • 发表日期：

    2025年9月9日

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  • Lai-Hong Dang,
  • Hong-Chang Ding,
  • Xing-Hong Yan

摘要

Pyropia yezoensis, an economically significant cultivated seaweed, exhibits blade length as a crucial yield-determining trait. However, limited studies have focused on identifying length-associated candidate genes. This study utilized heterozygous conchocelis derived from the cross between wild-type (W) and red mutant (R) strains of P. yezoensis and constructed a genetic population comprising 200 double haploid (DH) strains using their offspring with four-color-sectored blades. Based on the lengths of the 35-day-old blades of different DH strains, two bulked pools were constructed by selecting 20 extreme-long and 20 extreme-short DH strains. BSA-seq analysis identified 9 candidate regions associated with blade length, encompassing 415 genes. Three strains were respectively selected from the extremely long and extremely short bulked pools, and transcriptome sequencing was performed on their blades at 35 days old, revealing 572 differentially expressed genes (DEGs) at the intersection of three comparison groups of extremely long and extremely short strains. Results of the trend clustering analysis showed that a total of 93 genes displayed the same trend in either the extremely long group or the extremely short group, but there were obvious differences in trends between different groups. These genes are mainly related to pathways such as RNA polymerase activity, ATP-dependent chromatin remodeling, and carbon metabolism. Integrative analysis of BSA-seq and RNA-seq, three candidate genes were screened out, encoding DNA-directed RNA polymerase III subunit (RPC2), ATP-dependent DNA helicase (Pif1), and a protein of unknown function, respectively. qRT-PCR validation confirmed significant expression differences of these three genes between three extremely long and three extremely short strains, demonstrating high correlations with blade length. This study not only deepens our understanding of the regulatory mechanisms of blade length in P. yezoensis, but also provides valuable references for future precision molecular breeding.