Genomic prediction using a cost-effective mid-density SNP platform in spring wheat

Area of Science:

• Plant breeding
• Genomics
• Agricultural science

Background:

• Genotyping cost limits genomic selection adoption in wheat breeding.
• Evaluating different single nucleotide polymorphism (SNP) platforms is crucial for cost-effective genomic prediction.

Purpose of the Study:

• Compare low-density 4K SNP and high-density 90K SNP genotyping platforms for genomic prediction in wheat.
• Assess the impact of incorporating competitive allele specific PCR (KASP) markers on prediction accuracy.
• Identify cost-effective strategies for genomic selection in wheat breeding programs.

Main Methods:

• Evaluated five models: 4K SNP-only, 4K SNP + KASP, 90K SNP-only, 90K SNP + KASP, and KASP-only.
• Used a training population of 224 spring wheat lines and a new population of 141 spring wheat lines.
• Assessed prediction for grain yield (YLD), thousand kernel weight (TKW), heading date (HD), and plant height (PHT).

Main Results:

• The 90K SNP array showed slightly higher predictive ability for YLD, while the 4K SNP panel performed better for TKW in the training population.
• Incorporating KASP markers significantly improved prediction for YLD, HD, and PHT in both 4K and 90K SNP models.
• KASP-only models outperformed SNP-only models for HD and PHT in cross-population predictions.

Conclusions:

• A mid-density marker platform, specifically the 4K SNP + KASP model, offers a cost-effective strategy for genomic prediction in wheat.
• KASP-only genotyping provides a practical, ultra-low-cost option for screening specific traits like heading date and plant height.
• These findings support the wider adoption of genomic selection by providing viable, economical genotyping solutions for wheat breeding.