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<p>Blade thickness is a quantitative trait in <i>Pyropia haitanensis</i> regulated by multiple genes, significantly influencing its taste and value-added potential. However, research on identifying candidate genes related to this trait remains limited. In this study, a double haploid (DH) population derived from the cross of&#xa0;<i>P. haitanensis</i>&#xa0;was utilized. Two DNA pools were constructed from strains with extremely thick and thin blades, respectively. Through bulk segregant analysis sequencing (BSA-seq), seven candidate regions associated with blade thickness were identified on chromosome 1, encompassing a total of 220 genes. To further explore these findings, one extremely thick and one extremely thin strain were selected for transcriptome sequencing (RNA-seq) of their 35-day-old blades. The analysis revealed that differentially expressed genes (DEGs) were mainly associated with carbon metabolism and the cell cycle. Notably, 38 DEGs were located within the thickness-related candidate regions. Subsequently, using ΔSNP-index = 1 as a strict screening criterion, 17 candidate genes were preliminarily identified. Nine SNP sites within the exons of these candidate genes were selected for validation across multiple extremely thick and thin strains. Remarkably, the success rate of selecting blade thickness traits for all SNP sites was 100%. Among the candidate genes, two genes (<i>Ph1g02152</i> and <i>Ph1g02161</i>) encoded SUF4 domain protein and Cupin domain protein, respectively, and were involved in cell wall synthesis. In addition, RT-qPCR results showed significant differences in the expression levels of three candidate genes (<i>Ph1g02176, Ph1g02177</i>, and <i>Ph1g02296</i>) between three extremely thick strains and three extremely thin strains. It is speculated that these genes are highly likely to be associated with the thickness trait of&#xa0;<i>P. haitanensis</i>. The results of this research are crucial for promoting accurate molecular breeding strategies in&#xa0;<i>P. haitanensis</i>, thereby accelerating the cultivation of high-quality varieties.</p>

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Integrated analysis of BSA-seq and RNA-seq identified the candidate genes for blades thickness in Pyropia haitanensis

  • 期刊论文

  • 发表日期：

    2025年8月7日

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  • Ye-Fan Qiu,
  • Hong-Chang Ding,
  • Xing-Hong Yan

摘要

Blade thickness is a quantitative trait in Pyropia haitanensis regulated by multiple genes, significantly influencing its taste and value-added potential. However, research on identifying candidate genes related to this trait remains limited. In this study, a double haploid (DH) population derived from the cross of P. haitanensis was utilized. Two DNA pools were constructed from strains with extremely thick and thin blades, respectively. Through bulk segregant analysis sequencing (BSA-seq), seven candidate regions associated with blade thickness were identified on chromosome 1, encompassing a total of 220 genes. To further explore these findings, one extremely thick and one extremely thin strain were selected for transcriptome sequencing (RNA-seq) of their 35-day-old blades. The analysis revealed that differentially expressed genes (DEGs) were mainly associated with carbon metabolism and the cell cycle. Notably, 38 DEGs were located within the thickness-related candidate regions. Subsequently, using ΔSNP-index = 1 as a strict screening criterion, 17 candidate genes were preliminarily identified. Nine SNP sites within the exons of these candidate genes were selected for validation across multiple extremely thick and thin strains. Remarkably, the success rate of selecting blade thickness traits for all SNP sites was 100%. Among the candidate genes, two genes (Ph1g02152 and Ph1g02161) encoded SUF4 domain protein and Cupin domain protein, respectively, and were involved in cell wall synthesis. In addition, RT-qPCR results showed significant differences in the expression levels of three candidate genes (Ph1g02176, Ph1g02177, and Ph1g02296) between three extremely thick strains and three extremely thin strains. It is speculated that these genes are highly likely to be associated with the thickness trait of P. haitanensis. The results of this research are crucial for promoting accurate molecular breeding strategies in P. haitanensis, thereby accelerating the cultivation of high-quality varieties.