Tracking crop varieties using genotyping-by-sequencing markers: a case study using cassava (Manihot esculenta Crantz)

Area of Science:

• Agricultural Science
• Genetics
• Plant Breeding

Background:

• Accurate crop cultivar identification is vital for evaluating crop improvement research.
• Traditional methods like farmer interviews and morphological traits have limitations in accuracy.
• Genotyping-by-sequencing (GBS) offers a molecular alternative for tracking crop varieties.

Purpose of the Study:

• To assess Genotyping-by-sequencing (GBS) as a method for identifying cassava varieties in farmers' fields.
• To compare molecularly identified varieties with farmer-reported names and traditional identification methods.
• To estimate the genetic ancestry of cassava cultivars using genome-wide SNP data.

Main Methods:

• Collected 917 cassava accessions from 495 farming households in Ghana.
• Genotyped accessions using 56,489 SNP loci and a reference library of 64 released varieties and landraces.
• Employed distance-based hierarchical clustering and model-based ADMIXTURE analysis for cultivar identification and ancestry estimation.

Main Results:

• Genotyping-by-sequencing (GBS) successfully identified 11 major cassava variety groups using complementary clustering methods.
• 30% of farmer-field accessions matched released varieties in the reference library.
• Significant discrepancies were observed between genetically identified cultivars and farmer-reported names, highlighting limitations in traditional identification.

Conclusions:

• Genome-wide SNP markers from GBS, combined with cluster analysis, provide a powerful tool for fine-scale population structure and variety identification.
• Ancestry estimation using GBS data can quantify the genetic contribution of germplasm to improved cultivars.
• This molecular approach enhances the accuracy of tracking crop varieties and understanding their genetic diversity.