Genome-wide Association Studies for Soybean Epicotyl Length in Two Environments Using 3VmrMLM

Overview

Journal Front Plant Sci

Date 2022 Dec 1

PMID 36452100

Authors

Huilong Hong

Mei Li

Yijie Chen

Haorang Wang

Jun Wang

Bingfu Guo

Huawei Gao

Honglei Ren

Ming Yuan

Yingpeng Han

Lijuan Qiu

Affiliations

Soon will be listed here.

Abstract

Germination of soybean seed is the imminent vital process after sowing. The status of plumular axis and radicle determine whether soybean seed can emerge normally. Epicotyl, an organ between cotyledons and first functional leaves, is essential for soybean seed germination, seedling growth and early morphogenesis. Epicotyl length (EL) is a quantitative trait controlled by multiple genes/QTLs. Here, the present study analyzes the phenotypic diversity and genetic basis of EL using 951 soybean improved cultivars and landraces from Asia, America, Europe and Africa. 3VmrMLM was used to analyze the associations between EL in 2016 and 2020 and 1,639,846 SNPs for the identification of QTNs and QTN-by-environment interactions (QEIs)".A total of 180 QTNs and QEIs associated with EL were detected. Among them, 74 QTNs (ELS_Q) and 16 QEIs (ELS_QE) were identified to be associated with ELS (epicotyl length of single plant emergence), and 60 QTNs (ELT_Q) and 30 QEIs (ELT_QE) were identified to be associated with ELT (epicotyl length of three seedlings). Based on transcript abundance analysis, GO (Gene Ontology) enrichment and haplotype analysis, ten candidate genes were predicted within nine genic SNPs located in introns, upstream or downstream, which were supposed to be directly or indirectly involved in the process of seed germination and seedling development., Of 10 candidate genes, two of them (Glyma.04G122400 and Glyma.18G183600) could possibly affect epicotyl length elongation. These results indicate the genetic basis of EL and provides a valuable basis for specific functional studies of epicotyl traits.

Citing Articles

QTL Mapping and Data Mining to Identify Genes Associated with Soybean Epicotyl Length Using Cultivated Soybean and Wild Soybean.

Chen L, Ma S, Li F, Li L, Yu W, Yu L Int J Mol Sci. 2024; 25(6).

PMID: 38542270 PMC: 10970105. DOI: 10.3390/ijms25063296.

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