Genome-Wide Association Study of Topsoil Root System Architecture in Field-Grown Soybean [Glycine max (L.) Merr.]

Abstract

Water and nutrient acquisition is a critical function of plant root systems. Root system architecture (RSA) traits are often complex and controlled by many genes. This is the first genome-wide association study reporting genetic loci for RSA traits for field-grown soybean (Glycine max). A collection of 289 soybean genotypes was grown in three environments, root crowns were excavated, and 12 RSA traits assessed. The first two components of a principal component analysis of these 12 traits were used as additional aggregate traits for a total of 14 traits. Marker–trait association for RSA traits were identified using 31,807 single-nucleotide polymorphisms (SNPs) by a genome-wide association analysis. In total, 283 (non-unique) SNPs were significantly associated with one or more of the 14 root traits. Of these, 246 were unique SNPs and 215 SNPs were associated with a single root trait, while 26, four, and one SNPs were associated with two, three, and four root traits, respectively. The 246 SNPs marked 67 loci associated with at least one of the 14 root traits. Seventeen loci on 13 chromosomes were identified by SNPs associated with more than one root trait. Several genes with annotation related to processes that could affect root architecture were identified near these 67 loci. Additional follow-up studies will be needed to confirm the markers and candidate genes identified for RSA traits and to examine the importance of the different root characteristics for soybean productivity under a range of soil and environmental conditions.

Effects of irrigation on root growth and development of soybean: A 3-year sandy field experiment

“…To date, studies have been conducted on the root systems of wheat (Chen et al, 2020), rice (Phung et al, 2016;Kadam et al, 2017;Guimarães et al, 2020), maize (Li et al, 2015), and soybean (Falk et al, 2020;Kim et al, 2021). However, most of these studies were carried out in controlled environments, with the exception of a study of Dhanapal et al (2021), which investigated only the topsoil part of the root system. Phenotyping of roots under controlled conditions, including laboratories or greenhouses, can be done with a large number of genotypes at a reasonable cost.…”

Genome-Wide Association Study Reveals Influence of Cell-specific Gene Networks on Soybean Root System Architecture

“…In comparison to earlier GWAS studies, our analysis aligns with past sample sets, typically involving several hundred samples ranging from 137 to 397 varieties (Salim et al 2021;Dhanapal et al 2020;Seck, Torkamaneh, and Belzile 2020;Prince et al 2019;S.-H. Kim et al 2023;Chandnani et al 2023;Falk et al 2020). These studies measured between seven and thirteen traits and identified two to 70 candidate genes, spanning a wide range of annotations (Salim et al 2021;Dhanapal et al 2020;Seck, Torkamaneh, and Belzile 2020;Prince et al 2019;S.-H. Kim et al 2023;Chandnani et al 2023;Falk et al 2020). Our analysis identified overlaps with two specific loci adding to the credibility of the discovered associations.…”