Identification of quantitative trait loci controlling root morphological traits in an interspecific soybean population using 2D imagery data

Authors: ISLAM, SHAFIGUL - Kyungpook National University; GHIMIRE, AMIT - Kyungpook National University; LAY, LINY - Kyungpook National University; KHAN, WALEED - Kyungpook National University; LEE, JEONG-DONG - Kyungpook National University; Song, Qijian; JO, HYAN - Kyungpook National University; KIM, YOONHA - Kyungpook National University

Submitted to: International Journal of Molecular Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/23/2024
Publication Date: 4/25/2024
Citation: Islam, S.M., Ghimire, A., Lay, L., Khan, W., Lee, J., Song, Q., Jo, H., Kim, Y. 2024. Identification of quantitative trait loci controlling root morphological traits in an interspecific soybean population using 2D imagery data. International Journal of Molecular Sciences. 25(9). Article e4687. https://doi.org/10.3390/ijms25094687.
DOI: https://doi.org/10.3390/ijms25094687

Interpretive Summary: Roots are the most important feature of plants for absorbing or transporting water and nutrients and interacting with microorganisms. Compared with cultivated soybeans, wild soybeans have very obvious differences in root morphology. Some accessions even have a better ability to absorb water and nutrients from deep soil, making them resistant to drought and flooding. However, genetic studies of these traits, especially in wild soybean, have been limited due to difficulties in measuring root diameter, surface area, and volume. In this study, we used 2D root images and image processing software to more accurately and efficiently phenotype these traits in a wild and cultivated soybean hybrid population. We identified the major genomic regions controlling these traits as well as the desired alleles on both chromosomes in wild and cultivated soybean. We also identified six candidate genes within these regions that influence the root traits. This report provides useful information on the use of wild soybean alleles to improve cultivated soybean root morphological traits and potentially enhance soybean root development.

Technical Abstract: Roots are the hidden and most important part of plants. They serve as stabilizers and channels for uptaking water and nutrients and play a crucial role in the growth and development of plants. Here, two-dimensional image data were used to identify quantitative trait loci (QTL) controlling root traits in an inter-specific mapping population derived from a cross between wild soybean ‘PI366121’ and cultivar ‘Williams 82’. A total of 2830 single-nucleotide polymorphisms were used for constructing genetic linkage maps and analyzing QTLs. Forty-two QTLs were identified on twelve chromosomes, twelve of which were identified as major QTLs, with a phenotypic variation range of 36.12% to 39.11% and a logarithm of odds value range of 12.01 to 17.35. Two significant QTL regions for the average diameter, root volume were detected on chromosomes 3 and 13, both wild and cultivated soybeans contributed positive alleles. Six candidate genes Glyma.03G027500 (transketolase/glycoaldehyde transferase), Gly-ma.03G014500 (dehydrogenases), Glyma.13G341500 (leucine-rich repeat receptor-like protein ki-nase), Glyma.13G341400 (AGC kinase family protein), Glyma.13G331900 (60S ribosomal protein), and Glyma.13G333100 (aquaporin transporter) showed higher expression in root tissues based on publicly available transcriptome data. These results will help breeders improve soybean genetic components and enhance soybean root morphological traits using desirable alleles from wild soybean.