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<p>The majority of the dehydration industries require onion with high total soluble solid (TSS) content (&gt; 15°Bx) to produce high-quality processed products. An effort has been made to identify genes associated with total soluble solids content using genotyping-by-sequencing (GBS) and transcriptome sequencing. A total of 7734 filtered SNPs were mined, and GWAS models (GLM, MLM, MLMM, FarmCPU, and BLINK) were applied. An SNP at locus SCAJJJL010074204.1_52690 was found to be strongly associated with TSS content, which was able to explain up to 65% of the total phenotypic variation. Integration of the GWAS-identified SNP SCAJJJL010074204.1_52690 with the set of differentially expressed genes of high TSS (HTSS)_vs_ low TSS(LTSS) revealed that transcripts E1.U.164657 and E1.U.58798 contained this SNP and encoded ATP synthase subunit alpha. Within the ± 50&#xa0;kb flanking region of E1.U.164657 and E1.U.58798 transcripts, more than twofold upregulated DNA/RNA polymerase, TRAFAC class myosin-kinesin ATPase superfamily, pentatricopeptide repeat-containing protein, heat shock protein 70, plastidal glycolate/glycerate translocator, and the electron transfer flavoprotein subunit beta were reported. RNA sequencing of HTSS_vs_LTSS onion lines revealed that, in addition to the SCAJJJL010074204.1_52690 SNP-containing transcript and within the ± 50&#xa0;kb flanking region of it, higher expression of other ATP synthase (26), carbohydrate metabolism (65) genes in HTSS lines likely contributes to elevating TSS level in HTSS lines. Further metabolome analysis of HTSS_vs_LTSS lines revealed that HTSS lines had upregulated carbohydrate metabolism. Hence, the SCAJJJL010074204.1_52690 SNP loci, E1.U.164657 and E1.U.58798 transcripts responsible for ATP synthase subunit alpha, and HTSS-containing lines (S74, S75, and S76) identified in the current study, are of prime importance for industrial application and genotypic improvement of wild and cultivated Alliums. Targeted genome editing to convert the C allele to the T allele at SCAJJJL010074204.1_52690 SNP loci could further enhance TSS levels and elevate crop quality.</p>

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Genome-Wide Association and Transcriptome Analysis Unraveling Putative Genes Responsible for High TSS of Allium cepa

  • 期刊论文

  • 发表日期：

    2026年1月28日

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  • Deepanshu Jayaswal,
  • Deepesh Kumar,
  • Vijay Mahajan,
  • Nandita Banerjee,
  • Sonia Sood,
  • Isha Sharma,
  • Sanjay Kumar,
  • Kuldip Jayaswall

摘要

The majority of the dehydration industries require onion with high total soluble solid (TSS) content (> 15°Bx) to produce high-quality processed products. An effort has been made to identify genes associated with total soluble solids content using genotyping-by-sequencing (GBS) and transcriptome sequencing. A total of 7734 filtered SNPs were mined, and GWAS models (GLM, MLM, MLMM, FarmCPU, and BLINK) were applied. An SNP at locus SCAJJJL010074204.1_52690 was found to be strongly associated with TSS content, which was able to explain up to 65% of the total phenotypic variation. Integration of the GWAS-identified SNP SCAJJJL010074204.1_52690 with the set of differentially expressed genes of high TSS (HTSS)_vs_ low TSS(LTSS) revealed that transcripts E1.U.164657 and E1.U.58798 contained this SNP and encoded ATP synthase subunit alpha. Within the ± 50 kb flanking region of E1.U.164657 and E1.U.58798 transcripts, more than twofold upregulated DNA/RNA polymerase, TRAFAC class myosin-kinesin ATPase superfamily, pentatricopeptide repeat-containing protein, heat shock protein 70, plastidal glycolate/glycerate translocator, and the electron transfer flavoprotein subunit beta were reported. RNA sequencing of HTSS_vs_LTSS onion lines revealed that, in addition to the SCAJJJL010074204.1_52690 SNP-containing transcript and within the ± 50 kb flanking region of it, higher expression of other ATP synthase (26), carbohydrate metabolism (65) genes in HTSS lines likely contributes to elevating TSS level in HTSS lines. Further metabolome analysis of HTSS_vs_LTSS lines revealed that HTSS lines had upregulated carbohydrate metabolism. Hence, the SCAJJJL010074204.1_52690 SNP loci, E1.U.164657 and E1.U.58798 transcripts responsible for ATP synthase subunit alpha, and HTSS-containing lines (S74, S75, and S76) identified in the current study, are of prime importance for industrial application and genotypic improvement of wild and cultivated Alliums. Targeted genome editing to convert the C allele to the T allele at SCAJJJL010074204.1_52690 SNP loci could further enhance TSS levels and elevate crop quality.