Dataset Information

Overcoming collinearity in path analysis of soybean [Glycine max (L.) Merr.] grain oil content.

ABSTRACT: Path analysis allows understanding the direct and indirect effects among traits. Multicollinearity in correlation matrices may cause a bias in path analysis estimates. This study aimed to: a) understand the correlation among soybean traits and estimate their direct and indirect effects on gain oil content; b) verify the efficiency of ridge path analysis and trait culling to overcome colinearity. Three different matrices with different levels of collinearity were obtained by trait culling. Ridge path analysis was performed on matrices with strong collinearity; otherwise, a traditional path analysis was performed. The same analyses were run on a simulated dataset. Trait culling was applied to matrix R originating the matrices R1 and R2. Path analysis for matrices R1 and R2 presented a high determination coefficient (0.856 and 0.832, respectively) and low effect of the residual variable (0.379 and 0.410 respectively). Ridge path analysis presented low determination coefficient (0.657) and no direct effects greater than the effects of the residual variable (0.585). Trait culling was more effective to overcome collinearity. Mass of grains, number of nodes, and number of pods are promising for indirect selection for oil content.

SUBMITTER: Viotto Del Conte M

PROVIDER: S-EPMC7244132 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Overcoming collinearity in path analysis of soybean [Glycine max (L.) Merr.] grain oil content.

Viotto Del Conte Murilo M Carneiro Pedro Crescêncio Souza PCS Vilela de Resende Marcos Deon MD Lopes da Silva Felipe F Peternelli Luiz Alexandre LA

PloS one 20200522 5

Path analysis allows understanding the direct and indirect effects among traits. Multicollinearity in correlation matrices may cause a bias in path analysis estimates. This study aimed to: a) understand the correlation among soybean traits and estimate their direct and indirect effects on gain oil content; b) verify the efficiency of ridge path analysis and trait culling to overcome colinearity. Three different matrices with different levels of collinearity were obtained by trait culling. Ridge ...[more]

PMID: 32442213

Similar Datasets

Project description:Soybean (Glycine max) seed yields rely on the efficiency of photosynthesis, which is poorly understood in soybean. Chlorophyll, the major light harvesting pigment, is crucial for chloroplast biogenesis and photosynthesis. Magnesium chelatase catalyzes the insertion of Mg2+ into protoporphyrin IX in the first committed and key regulatory step of chlorophyll biosynthesis. It consists of three types of subunits, ChlI, ChlD, and ChlH. To gain a better knowledge of chlorophyll biosynthesis in soybean, we analyzed soybean Mg-chelatase subunits and their encoding genes. Soybean genome harbors 4 GmChlI genes, 2 GmChlD genes, and 3 GmChlH genes, likely evolved from two rounds of gene duplication events. The qRT-PCR analysis revealed that GmChlI, GmChlD, and GmChlH genes predominantly expressed in photosynthetic tissues, but the expression levels among paralogs are different. In silicon promoter analyses revealed these genes harbor different cis-regulatory elements in their promoter regions, suggesting they could differentially respond to various environmental and developmental signals. Subcellular localization analyses illustrated that GmChlI, GmChlD, and GmChlH isoforms are all localized in chloroplast, consistent with their functions. Yeast two hybrid and bimolecular fluorescence complementation (BiFC) assays showed each isoform has a potential to be assembled into the Mg-chelatase holocomplex. We expressed each GmChlI, GmChlD, and GmChlH isoform in Arabidopsis corresponding mutants, and results showed that 4 GmChlI and 2 GmChlD isoforms and GmChlH1 could rescue the severe phenotype of Arabidopsis mutants, indicating that they maintain normal biochemical functions in vivo. However, GmChlH2 and GmChlH3 could not completely rescue the chlorotic phenotype of Arabidopsis gun5-2 mutant, suggesting that the functions of these two proteins could be different from GmChlH1. Considering the differences shown on primary sequences, biochemical functions, and gene expression profiles, we conclude that the paralogs of each soybean Mg-chelatase subunit have diverged more or less during evolution. Soybean could have developed a complex regulatory mechanism to control chlorophyll content to adapt to different developmental and environmental situations.

Dataset Information

Overcoming collinearity in path analysis of soybean [Glycine max (L.) Merr.] grain oil content.

Publications

Overcoming collinearity in path analysis of soybean [Glycine max (L.) Merr.] grain oil content.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets