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Related Experiment Video

Updated: Jul 9, 2026

Analysis of Effect of Compound Salt Stress on Seed Germination and Salt Tolerance Analysis of Pepper (Capsicum annuum L.)

Analysis of Effect of Compound Salt Stress on Seed Germination and Salt Tolerance Analysis of Pepper (Capsicum annuum L.)

Published on: November 30, 2022

GWAS-informed genomic selection for cold tolerance in pepper (Capsicum annuum L.).

Kyeongseok Lee¹, Geon Woo Kim¹, Hee-Jin Jeong²

¹Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea.

BMC Plant Biology

|July 7, 2026

Summary

Developing a new cold tolerance index (CTI) and using genome-wide association study (GWAS)-informed genomic selection (GS) improved prediction accuracy for cold tolerance in pepper (Capsicum annuum L.). This approach enhances breeding for climate resilience.

Keywords:

Cold tolerance Cold-tolerance index (CTI)Genome-wide association study (GWAS)Genomic selection (GS)Pepper

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Area of Science:

Plant breeding and genetics
Climate change adaptation
Genomic selection strategies

Background:

Pepper (Capsicum annuum L.) cold tolerance is crucial for climate change adaptation, but breeding is limited by phenotyping challenges and complex genetics.
Genomic selection (GS) can accelerate genetic gain, but its predictive ability is often reduced by uninformative markers in whole-genome sets.

Purpose of the Study:

To develop a robust phenotypic index for adult-stage cold tolerance in pepper.
To implement a genome-wide association study (GWAS)-informed genomic selection (GS) strategy to improve prediction accuracy.

Main Methods:

Phenotyped 192 pepper accessions for cold tolerance using a visual survival score (Surv) and a composite cold-tolerance index (CTI).
Performed genome-wide association study (GWAS) to identify candidate genomic regions associated with cold tolerance.
Applied nested cross-validation (CV) and leave-one-out CV (LOOCV) using GWAS-selected marker sets for genomic prediction.

Main Results:

Both CTI and Surv exhibited moderate heritability (h² ≈ 0.55 and 0.53, respectively), indicating significant additive genetic variance.
GWAS identified 13 candidate genomic regions, including genes like TRM9, CAP1, and PP2A-2, linked to abiotic stress responses.
GWAS-selected marker sets achieved higher prediction accuracies (e.g., 0.349 for CTI in LOOCV) compared to full or random marker sets.

Conclusions:

The CTI effectively assesses cold tolerance, revealing hidden genetic variation by converting ordinal survival data into a continuous spectrum.
The integrated GWAS-informed GS framework successfully identified candidate genes and improved prediction efficiency for complex traits.
This approach provides a practical strategy for understanding adult-stage cold tolerance genetics and enhancing genomic prediction in pepper breeding.