A comprehensive suite of tools for allele discovery and phenotype improvement in crops
No Thumbnail Available
Authors
Meeting name
Sponsors
Date
Journal Title
Format
Thesis
Subject
Abstract
[EMBARGOED UNTIL 05/01/2026] The rapid advancements in sequencing technologies have significantly expanded genomic research and generating vast amounts of genomics and phenomics data. With constantly growing data, whole-genome re-sequencing data has become an invaluable resource that enables precise identification of alleles and functional elements within genomes. In order to perform analyses and obtain meaning insights, a comprehensive suite of computational tools and pipelines have been designed and developed to enhance genomic analysis and facilitate agricultural innovation. These tools and pipelines include the SnakyVC variant calling pipeline, Allele Catalog pipeline, Allele Catalog Tool, Genomic Variation Explorer, Phenotype Distribution pipeline, Phenotype Distribution Tool, Multiple Allele Discovery Tool, and Paralog Allele Catalog Tool. By integrating data mining methodologies and leveraging these tools, researchers can pinpoint causative alleles, link genomic variations to phenotypic traits, and explore regulatory differences, including variations within promoter regions and copy number variations. The Allele Catalog Tool supports allele discovery and improvement efforts, while the Genomic Variation Explorer provides insights into the genetic and regulatory components influencing specific phenotypic traits. Additionally, the Phenotype Distribution Tool aids in analyzing phenotype distribution differences at the allele level and identifying candidate alleles and genes suitable for phenotype improvement. Moreover, the Multiple Allele Discovery Tool enables researchers to identify alleles within genes that act cooperatively to influence phenotypic traits. The Paralog Allele Catalog Tool facilitates comparative analyses of paralogous genes by leveraging allele landscapes and phenotype distributions to support candidate paralogous gene selections for crop improvement. These tools collectively empower researchers and breeders to make informed decisions in selective breeding, translational research, and phenotype improvement strategies. Ultimately, these advancements accelerate the development of improved crop varieties and contribute to sustainable agriculture, food security, and economic success.
Table of Contents
DOI
PubMed ID
Degree
PhD