Multi-locus genome-wide association study reveal genomic regions underlying root system architecture traits in Ethiopian sorghum germplasm

Authors: DURESSO, MASARAT - Ethiopia Haramaya University; CHERE, DIRIBA - Kansas State University; LULE, DAGNACHEW - Ethiopia Agricultural Transformation Agency; Serba, Desalegn; TIRFESSA, ALEMU - Ethiopian Institute Of Agricultural Research; GELMESA, DANDENA - Ethiopia Haramaya University; TESSO, TESFAYE - Kansas State University; BANTTE, KASSAHUN - Jimma University; MENAMO, TEMESGEN - Jimma University

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/24/2024
Publication Date: 2/15/2024
Citation: Duresso, M.E., Chere, D.H., Lule, D., Serba, D.D., Tirfessa, A., Gelmesa, D., Tesso, T., Bantte, K., Menamo, T.M. 2024. Multi-locus genome-wide association study reveal genomic regions underlying root system architecture traits in Ethiopian sorghum germplasm. The Plant Genome. 17(2). Article e20436. https://doi.org/10.1002/tpg2.20436.
DOI: https://doi.org/10.1002/tpg2.20436

Interpretive Summary: It is vital to identify the genetic factors underlying root system architecture (RSA) and their genomic regions for fast tracking the improvement of crops for stress tolerance using genomic-assisted breeding. This study was aimed to identify quantitative trait nucleotides (QTNs) linked to RSA in 274 Ethiopian sorghum accessions. A multi-locus genome-wide association study using 265,944 single nucleotide polymorphism (SNP) markers identified 17 quantitative trait nucleotides (QTNs) significantly associated with root angle, number of roots, root length, or root dry weight. Five QTNs were found intragenic, with genes responsible for plant growth hormone-induced RSA, that may regulate root development in seedling stage. Further analysis on these genes could dissect the genetic structure of RSA in sorghum.

Technical Abstract: The identification of genomic regions underlying the root system architecture (RSA)is vital for improving crop abiotic stress tolerance. To improve sorghum (Sorghum bicolor L. Moench) for environmental stress tolerance, information on genetic variability and genomic regions linked to RSA traits is paramount. The aim of thisstudy was, therefore, to investigate common quantitative trait nucleotides (QTNs) via multiple methodologies and identify genomic regions linked to RSA traits in a panel of 274 Ethiopian sorghum accessions. Multi-locus genome-wide association study was conducted using 265,944 high-quality single nucleotide polymorphism markers. Considering the QTN detected by at least three different methods, a total of 17 reliable QTNs were found to be significantly associated with root angle, number, length, and dry weight. Four QTNs were detected on chromosome SBI-05, followed by SBI-01and SBI-02 with three QTNs each. Among the 17 QTNs, 11 are colocated with previously identified root traits quantitative trait loci and the remaining six are genome regions with novel genes. A total of 118 genes are colocated with these up- and down-streams of the QTNs. Moreover, five QTNs were found intragenic. These QTNs are S5_8994835 (number of nodal roots), S10_55702393 (number of nodal roots),S1_56872999 (nodal root angle), S9_1212069 (nodal root angle), and S5_5667192(root dry weight) intragenic regions of Sobic.005G073101, Sobic.010G198000,Sobic.001G273000,Sobic.009G013600, andSobic.005G054700, respectively. Particularly, Sobic.005G073101, Sobic.010G198000, and Sobic.009G013600 were found responsible for the plant growth hormone-induced RSA. These genes may regulate root development in the seedling stage. Further analysis on these genes might be important to explore the genetic structure of RSA of sorghum.