Integration of genetic and imaging data to detect QTL for root traits in Interspecific soybean populations

Authors: ISLAM, SHAFIQUL - Kyungpook National University; Song, Qijian; LEE, JEONG-DONG - Kyungpook National University; JO, HYUN - Kyungpook National University; KIM, YOONHA - Kyungpook National University

Submitted to: International Journal of Molecular Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/27/2025
Publication Date: 1/28/2025
Citation: Islam, S.M., Song, Q., Lee, J., Jo, H., Kim, Y. 2025. Integration of genetic and imaging data to detect QTL for root traits in Interspecific soybean populations. International Journal of Molecular Sciences. 26(3):1152. https://doi.org/10.3390/ijms26031152.
DOI: https://doi.org/10.3390/ijms26031152

Interpretive Summary: Wild soybean is known for its ability to adapt to environmental stresses, providing valuable traits to enrich the narrow genetic diversity of cultivated soybean. By focusing on root traits that are critical for water and nutrient absorption, researchers aim to improve soybean adaptability and productivity, especially under challenging environmental conditions. However, evaluating root traits in field environments is difficult and expensive, resulting in fewer reports aiming to identify genes controlling root traits. To address this issue, the researchers created a mapping population by crossing cultivated soybean varieties with wild soybean germplasm. They used imaging software to analyze root traits and identified 39 regions on 10 chromosomes that affect key root characteristics, including total root length and surface area. Notably, five of these regions were found to have significant effects on root traits and were enriched with favorable genetic variation in both wild and cultivated soybean. The team identified specific genes within these regions that affect root growth and development. By incorporating these root-enhancing genes into breeding programs, breeders may optimize soybean water and nutrient absorption and improve soybean adaptability and yield in different environments.

Technical Abstract: Wild soybean, which has many desirable traits, such as adaptability to climate change-related stresses, is a valuable resource for expanding the narrow genetic diversity of cultivated soybean. Plants require roots to adapt to different environments and optimize water and nutrient uptake to support growth and facilitate storage of metabolites, however, it is challenging and costly to evaluate root traits under field conditions. Previous studies of quantitative trait loci (QTLs) have been mainly based on cultivated soybean populations. In this study, an interspecific mapping population from a cross between wild soybean ‘PI483463’ and cultivar ‘Hutcheson’ was used to investigate QTLs associated with root traits using image data. Our results showed that 39 putative QTLs were distributed across 10 chromosomes (chr.). Seventeen of these were clustered in regions on chr. 8, 14, 15, 16, and 17, accounting for 19.92% of the phenotypic variation. We identified five significant QTL clusters influencing root-related traits, such as total root length, surface area, lateral total length, and number of tips, across five chr., with favorable alleles from both wild or cultivated soybeans. Furthermore, we identified eight candidate genes controlling these traits based on functional annotation. These genes were highly expressed in root tissues and directly or indirectly affecting soybean root growth and development. Our results provide valuable insights for breeders aiming to optimize soybean root traits and leveraging genetic diversity from wild soybean species to develop varieties with improved root morphological traits, ultimately enhancing overall plant growth, productivity, and resilience.