Dataset Information

Genome-Wide Association Study Identifies a Plant-Height-Associated Gene OsPG3 in a Population of Commercial Rice Varieties.

ABSTRACT: Plant height is one of the most crucial components of plant structure. However, due to its complexity, the genetic architecture of rice plant height has not been fully elucidated. In this study, we performed a genome-wide association study (GWAS) to determine rice plant height using 178 commercial rice varieties and identified 37 loci associated with rice plant height (LAPH). Among these loci, in LAPH2, we identified a polygalacturonase gene, OsPG3, which was genetically and functionally associated with rice plant height. The rice plant exhibits a super dwarf phenotype when the knockout of the OsPG3 gene occurs via CRISPR-Cas9 gene-editing technology. RNA-Seq analysis indicated that OsPG3 modulates the expression of genes involved in phytohormone metabolism and cell-wall-biosynthesis pathways. Our findings suggest that OsPG3 plays a vital role in controlling rice plant height by regulating cell wall biosynthesis. Given that rice architecture is one of the most critical phenotypes in rice breeding, OsPG3 has potential in rice's molecular design breeding toward an ideal plant height.

SUBMITTER: Peng S

PROVIDER: S-EPMC10380248 | biostudies-literature | 2023 Jul

REPOSITORIES: biostudies-literature

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Genome-Wide Association Study Identifies a Plant-Height-Associated Gene <i>OsPG3</i> in a Population of Commercial Rice Varieties.

Peng Shasha S Liu Yanchen Y Xu Yuchen Y Zhao Jianhua J Gao Peng P Liu Qi Q Yan Shuangyong S Xiao Yinghui Y Zuo Shi-Min SM Kang Houxiang H

International journal of molecular sciences 20230714 14

Plant height is one of the most crucial components of plant structure. However, due to its complexity, the genetic architecture of rice plant height has not been fully elucidated. In this study, we performed a genome-wide association study (GWAS) to determine rice plant height using 178 commercial rice varieties and identified 37 loci associated with rice plant height (LAPH). Among these loci, in LAPH2, we identified a polygalacturonase gene, <i>OsPG3</i>, which was genetically and functionally ...[more]

PMID: 37511211

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Project description:Drought is one of the vitally critical environmental stresses affecting both growth and yield potential in rice. Drought resistance is a complicated quantitative trait that is regulated by numerous small effect loci and hundreds of genes controlling various morphological and physiological responses to drought. For this study, 270 rice landraces and cultivars were analyzed for their drought resistance. This was done via determination of changes in plant height and grain yield under contrasting water regimes, followed by detailed identification of the underlying genetic architecture via genome-wide association study (GWAS). We controlled population structure by setting top two eigenvectors and combining kinship matrix for GWAS in this study. Eighteen, five, and six associated loci were identified for plant height, grain yield per plant, and drought resistant coefficient, respectively. Nine known functional genes were identified, including five for plant height (OsGA2ox3, OsGH3-2, sd-1, OsGNA1, and OsSAP11/OsDOG), two for grain yield per plant (OsCYP51G3 and OsRRMh) and two for drought resistant coefficient (OsPYL2 and OsGA2ox9), implying very reliable results. A previous study reported OsGNA1 to regulate root development, but this study reports additional controlling of both plant height and root length. Moreover, OsRLK5 is a new drought resistant candidate gene discovered in this study. OsRLK5 mutants showed faster water loss rates in detached leaves. This gene plays an important role in the positive regulation of yield-related traits under drought conditions. We furthermore discovered several new loci contributing to the three investigated traits (plant height, grain yield, and drought resistance). These associated loci and candidate genes significantly improve our knowledge of the genetic control of these traits in rice. In addition, many drought resistant cultivars screened in this study can be used as parental genotypes to improve drought resistance of rice by molecular breeding.

Project description:BackgroundMendelian randomization (MR) has been used to identify drug targets in many conditions. Height is a classic complex trait affected by genetic and early-life environmental factors. No systematic screening has been conducted to identify drugs that interact with height. We investigated the causal relationship between genes and height, and systematically screened for interactive drugs that may promote or delay growth.MethodsWe performed MR using summary statistics from the Genetic Investigation of ANthropometric Traits consortium (N=253,288), the UK Biobank (N=461,950), and the BioBank Japan Project (N=159,095). Gene expression-single-nucleotide polymorphism associations represented by cis-expression quantitative trait loci data were obtained from the Genotype-Tissue Expression study and were used as genetic instruments. We performed annotation and enrichment analyses of the genes. Interactive drugs were identified through drug-gene interactions.ResultsOf the 27,094 genes screened, 209 had causal associations with height, including genes associated with height and short stature phenotypes (AMZ1, GNA12, NPPC, UQCC1, and ZBTB38), genes associated with height in a few studies (ANKIB1, CEP250, DCAF16, HIST1H4E, and HLA-C), and genes without previous evidence (BTN2A2 and RBMS1P1). Enrichment analysis showed that transcriptional regulation by RUNX1 was the most enriched pathway. Interactive drugs were identified, including amoxicillin, atenolol, infliximab, colchicine, propionyl-L-carnitine, BMN-111, and tamoxifen, which were known to have a positive effect on height. We also identified drugs that had a negative effect on height, including antineoplastic drugs, corticosteroids, and antiepileptic drugs. Moreover, many interactive drugs have not been previously reported to be associated with height.ConclusionsOur results suggest that many genes have causal effects on height. By interrogating drug-gene interactions, interactive drugs have been identified as having both positive and negative effects on growth, which would help make clinical decisions.

Dataset Information

Genome-Wide Association Study Identifies a Plant-Height-Associated Gene OsPG3 in a Population of Commercial Rice Varieties.

Publications

Genome-Wide Association Study Identifies a Plant-Height-Associated Gene <i>OsPG3</i> in a Population of Commercial Rice Varieties.

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