# Identification and analysis of genomic regions influencing leaf morpho-physiological traits related to stress responses in greater yam (Dioscorea alata L.)

## TL;DR

This study identifies genetic regions in greater yam linked to leaf traits that help the plant respond to stress, which can aid in breeding more resilient crops.

## Contribution

The study provides new insights into the genetic basis of stress-related leaf traits in greater yam using GWAS and allele analysis.

## Key findings

- 24 significant associations were identified across 11 chromosomes for leaf traits related to stress responses.
- Candidate genes like Dioal.18G049300 and Dioal.12G033600 were linked to stomatal density and net photosynthesis, respectively.
- High heritability was observed for traits like transpiration rate and stomatal density, indicating potential for breeding improvement.

## Abstract

Yams (Dioscorea spp.) are significant food security crops especially in West Africa. With the increasing tuber demand and climate change challenges, it is pertinent to strengthen breeding programs for developing high-yielding cultivars with climate resilience. The current study aimed at deciphering the genetic basis of leaf traits related to stress responses in a diverse panel of Dioscorea alata genotypes.

Phenotypic characterization of 12 traits, including leaf dry matter content, mean leaf area, net photosynthesis, transpiration rate, transpiration use efficiency, stomatal density, stomatal index, preformed node count, leaf thickness, competitor, stress-tolerator, ruderal ecological strategies emphasized significant variations among the genotypes and across two planting locations. Weak correlations were observed among most of traits, suggesting that breeding simultaneously for some of these stress response-related traits would be possible. Heritability was highest for transpiration rate, leaf area and stomatal density, while it was lowest for stress-tolerator, ruderal ecological strategies. Genome-wide association study (GWAS) using high-quality single nucleotide polymorphism (SNPs) identified 24 significant associations on 11 chromosomes, where the association signals were consistent across two locations for traits with high heritability, viz., stomatal density (Chr18) and transpiration rate (Chr3). Further characterization of the significant signals and their related alleles identified advantageous alleles contributing positively to the studied traits. Moreover, 44 putative candidate genes were identified. Dioal.18G049300 (3 keto acyl-coenzyme A synthase) was identified as a strong candidate gene for stomatal density, while Dioal.12G033600 (Phosphatidyl inositol monophosphate 5 kinase 4) was identified for net photosynthesis.

Taken together, GWAS and allele segregation analysis for key SNPs provided significant insights into the marker-trait associations, which can be further utilized in breeding programs to improve climate resilience in greater yam.

The online version contains supplementary material available at 10.1186/s12870-025-07595-3.