Dataset Information

Leveraging orthology within maize and Arabidopsis QTL to identify genes affecting natural variation in gravitropism.

ABSTRACT: Plants typically orient their organs with respect to the Earth's gravity field by a dynamic process called gravitropism. To discover conserved genetic elements affecting seedling root gravitropism, we measured the process in a set of Zea mays (maize) recombinant inbred lines with machine vision and compared the results with those obtained in a similar study of Arabidopsis thaliana. Each of the several quantitative trait loci that we mapped in both species spanned many hundreds of genes, too many to test individually for causality. We reasoned that orthologous genes may be responsible for natural variation in monocot and dicot root gravitropism. If so, pairs of orthologous genes affecting gravitropism may be present within the maize and Arabidopsis QTL intervals. A reciprocal comparison of sequences within the QTL intervals identified seven pairs of such one-to-one orthologs. Analysis of knockout mutants demonstrated a role in gravitropism for four of the seven: CCT2 functions in phosphatidylcholine biosynthesis, ATG5 functions in membrane remodeling during autophagy, UGP2 produces the substrate for cellulose and callose polymer extension, and FAMA is a transcription factor. Automated phenotyping enabled this discovery of four naturally varying components of a conserved process (gravitropism) by making it feasible to conduct the same large-scale experiment in two species.

SUBMITTER: Yoshihara T

PROVIDER: S-EPMC9546580 | biostudies-literature | 2022 Oct

REPOSITORIES: biostudies-literature

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Leveraging orthology within maize and Arabidopsis QTL to identify genes affecting natural variation in gravitropism.

Yoshihara Takeshi T Miller Nathan D ND Rabanal Fernando A FA Myles Hannah H Kwak Il-Youp IY Broman Karl W KW Sadkhin Boris B Baxter Ivan I Dilkes Brian P BP Hudson Matthew E ME Spalding Edgar P EP

Proceedings of the National Academy of Sciences of the United States of America 20220926 40

Plants typically orient their organs with respect to the Earth's gravity field by a dynamic process called gravitropism. To discover conserved genetic elements affecting seedling root gravitropism, we measured the process in a set of <i>Zea mays</i> (maize) recombinant inbred lines with machine vision and compared the results with those obtained in a similar study of <i>Arabidopsis thaliana</i>. Each of the several quantitative trait loci that we mapped in both species spanned many hundreds of g ...[more]

PMID: 36161933

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Project description:Low-temperature germination ability (LTGA) is an important characteristic for spring sowing maize. However, few maize genes related to LTGA were confirmed, and the regulatory mechanism is less clear. Here, maize-inbred lines Ye478 and Q1 with different LTGA were used to perform transcriptome analysis at multiple low-temperature germination stages, and a co-expression network was constructed by weighted gene co-expression network analysis (WGCNA). Data analysis showed that 7964 up- and 5010 down-regulated differentially expressed genes (DEGs) of Ye478 were identified at low-temperature germination stages, while 6060 up- and 2653 down-regulated DEGs of Q1 were identified. Gene ontology (GO) enrichment analysis revealed that ribosome synthesis and hydrogen peroxide metabolism were enhanced and mRNA metabolism was weakened under low-temperature stress for Ye478, while hydrogen peroxide metabolism was enhanced and mRNA metabolism was weakened for Q1. DEGs pairwise comparisons between the two genotypes found that Ye478 performed more ribosome synthesis at low temperatures compared with Q1. WGCNA analysis based on 24 transcriptomes identified 16 co-expressed modules. Of these, the MEbrown module was highly correlated with Ye478 at low-temperature stages and catalase and superoxide dismutase activity, and the MEred, MEgreen, and MEblack modules were highly correlated with Ye478 across low-temperature stages, which revealed a significant association between LTGA and these modules. GO enrichment analysis showed the MEbrown and MEred modules mainly functioned in ribosome synthesis and cell cycle, respectively. In addition, we conducted quantitative trait loci (QTL) analysis based on a doubled haploid (DH) population constructed by Ye478 and Q1 and identified a major QTL explanting 20.6% of phenotype variance on chromosome 1. In this QTL interval, we found three, four, and three hub genes in the MEbrown, MEred, and MEgreen modules, of which two hub genes (Zm00001d031951, Zm00001d031953) related to glutathione metabolism and one hub gene (Zm00001d031617) related to oxidoreductase activity could be the candidate genes for LTGA. These biological functions and candidate genes will be helpful in understanding the regulatory mechanism of LTGA and the directional improvement of maize varieties for LTGA.

Dataset Information

Leveraging orthology within maize and Arabidopsis QTL to identify genes affecting natural variation in gravitropism.

Publications

Leveraging orthology within maize and Arabidopsis QTL to identify genes affecting natural variation in gravitropism.

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