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Background <p>Genomic resources for underutilized crops like sorghum [<i>Sorghum bicolor</i> (L.) Moench] often lag behind major staples, hindering efforts to link genetic diversity to agronomic traits. Improvements in genomic sequencing and bioinformatics have advanced crop genomics, yet species-specific challenges persist in the lack of tailored genomic resources, limiting precision breeding and applied genomics applications.</p> Results <p>This study presents the addition of a SorghumHub to the KBCommons web portal, an applied genomics platform for Sorghum. The core focus of this framework is the Sorghum Allele Catalog Tool, with a web-based interface enabling researchers to query, visualize, and download allelic variants from curated sorghum datasets of 988 resequenced accessions. The newly improved Allele Catalog Tool now features the ability to connect variant positions with phenotype information collected for Plant Introduction (PI) accessions in the Germplasm Resource Information Network (GRIN). On the SorghumHub, users can also find the Protein Sequence Logos, a new tool complementary to the Allele Catalog Tool, which allows users to graphically explore missense amino acid sequence changes for conservation and frequency. These custom genomic tools available on the SorghumHub enable users to query genomic variants, allele frequency, and trait-associated genotype–phenotype relationships leveraging data produced through our group’s computational pipelines for variant calling and processing into curated Allele Catalog datasets.</p> Conclusions <p>This research work demonstrates practical application of Sorghum Allele Catalog Tool and Protein Sequence Logos by highlighting different candidate alleles for the predicted flowering time (FT-like) gene <i>SbFT12</i> (<i>Sobic.006G047700</i>) in <i>Sorghum bicolor</i>; additionally, we discovered a relatively rare missense allele of the betaine aldehyde dehydrogenase (BADH2) gene that may provide a new avenue for fragrant/scented sorghum. The tools in SorghumHub allow researchers to optimize the accession selection process with efficient trait targeting and bridge the gaps between genomics and breeding. This approach can assist breeders and researchers in the development of resilient and high yielding crop varieties with broader positive outcomes for the agricultural industry and global food security.</p>

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SorghumHub: featuring the next phase for the KBCommons web portal with new molecular biology features

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年7月16日

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  • Nathan Grant,
  • Yen On Chan,
  • Anser Mahmood,
  • Jana Biová,
  • Mária Škrabišová,
  • Trupti Joshi,
  • Kristin Bilyeu

摘要

Background

Genomic resources for underutilized crops like sorghum [Sorghum bicolor (L.) Moench] often lag behind major staples, hindering efforts to link genetic diversity to agronomic traits. Improvements in genomic sequencing and bioinformatics have advanced crop genomics, yet species-specific challenges persist in the lack of tailored genomic resources, limiting precision breeding and applied genomics applications.

Results

This study presents the addition of a SorghumHub to the KBCommons web portal, an applied genomics platform for Sorghum. The core focus of this framework is the Sorghum Allele Catalog Tool, with a web-based interface enabling researchers to query, visualize, and download allelic variants from curated sorghum datasets of 988 resequenced accessions. The newly improved Allele Catalog Tool now features the ability to connect variant positions with phenotype information collected for Plant Introduction (PI) accessions in the Germplasm Resource Information Network (GRIN). On the SorghumHub, users can also find the Protein Sequence Logos, a new tool complementary to the Allele Catalog Tool, which allows users to graphically explore missense amino acid sequence changes for conservation and frequency. These custom genomic tools available on the SorghumHub enable users to query genomic variants, allele frequency, and trait-associated genotype–phenotype relationships leveraging data produced through our group’s computational pipelines for variant calling and processing into curated Allele Catalog datasets.

Conclusions

This research work demonstrates practical application of Sorghum Allele Catalog Tool and Protein Sequence Logos by highlighting different candidate alleles for the predicted flowering time (FT-like) gene SbFT12 (Sobic.006G047700) in Sorghum bicolor; additionally, we discovered a relatively rare missense allele of the betaine aldehyde dehydrogenase (BADH2) gene that may provide a new avenue for fragrant/scented sorghum. The tools in SorghumHub allow researchers to optimize the accession selection process with efficient trait targeting and bridge the gaps between genomics and breeding. This approach can assist breeders and researchers in the development of resilient and high yielding crop varieties with broader positive outcomes for the agricultural industry and global food security.