SeedExtractor

SeedExtractor extracts quantitative seed shape and color metrics from scanned seed images to support phenotypic analyses for breeding and genome-wide association studies.

Key Features:

• Quantitative measurements: Extracts seed size and shape metrics including area, perimeter, length, width, circularity, and centroid from images.
• Color analysis: Assesses seed color from scanned images as part of phenotype extraction.
• Processing speed: Processes individual seed images in approximately 2 seconds each.
• Image input and species applicability: Operates on scanned seed images and has been applied to seeds from multiple crops, including rice.
• Validation: Validated on mature rice seeds from 231 accessions in the Rice Diversity Panel 1, and extracted phenotypes were used in genome-wide association analysis that recovered loci GS3 (seed length) and qSW5/GW5 (seed width).

Scientific Applications:

• Genome-wide association studies (GWAS): Provides quantitative phenotypes for GWAS to map loci associated with seed traits.
• Breeding and trait quantification: Quantifies yield-related seed size traits to support agricultural breeding programs.
• Genetic and developmental research: Supports basic research into the genetic determinants of seed size and seed development.

Methodology:

Performs image processing to extract seed size, shape, centroid, and color metrics; extracted phenotypes were used in genome-wide association analysis that identified GS3 and qSW5/GW5.