High-density QTL mapping and candidate gene identification uncover the genetic architecture of leaf anatomy, growth kinetics and tuber yield in greater yam (Dioscorea alata L)

Greater yam ( Dioscorea alata L.) is a staple orphan crop critical for food security and climate resilience in tropical regions. While genetic improvement has historically focused on tuber quality traits like starch and dry matter, the genomic regions and genetic architecture governing yield stability, vegetative vigor, and resource-use efficiency remain poorly understood. Understanding the genetic basis of growth-related and leaf micro-anatomical traits is essential for identifying leverage points for simultaneously improving biomass accumulation, tuber filling capacity, and environmental adaptation. In this study, we combined high-throughput phenotyping of leaf anatomy and growth kinetics with parent-resolved high-density QTL mapping tailored to the complex genomic architecture of D. alata . We identified 49 QTLs and prioritized 51 candidate genes associated with leaf anatomical traits, vegetative growth dynamics, and tuber yield components. Together, these QTLs and candidate genes highlighted coordinated genetic modules potentially contributing to (i) leaf anatomical variation associated with gas exchange capacity, (ii) vegetative vigor and source capacity, (iii) hormonal regulation of tuber initiation, and (iv) sink strength, resource remobilization, and tuber filling. By connecting leaf micro-anatomical traits and canopy growth dynamics with genomic regions, this study provides a foundation for dissecting complex efficiency-related traits in greater yam. The identified QTLs and candidate genes represent valuable resources for future functional validation and the development of molecular breeding strategies in this underexplored crop species.