Genome-Wide Association Study Unravels <i>LRK1</i> as a Dark Respiration Regulator in Rice (<i>Oryza sativa</i> L.)
Respiration is a major plant physiological process that generates adenosine triphosphate (ATP) to support the various pathways involved in the plant growth and development. After decades of focused research on basic mechanisms of respiration, the processes and major proteins involved in respiration...
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MDPI AG
2020-07-01
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| Series: | International Journal of Molecular Sciences |
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| author | Mingnan Qu Jemaa Essemine Ming Li Shuoqi Chang Tiangen Chang Gen-Yun Chen Xin-Guang Zhu |
| author_facet | Mingnan Qu Jemaa Essemine Ming Li Shuoqi Chang Tiangen Chang Gen-Yun Chen Xin-Guang Zhu |
| author_sort | Mingnan Qu |
| collection | DOAJ |
| description | Respiration is a major plant physiological process that generates adenosine triphosphate (ATP) to support the various pathways involved in the plant growth and development. After decades of focused research on basic mechanisms of respiration, the processes and major proteins involved in respiration are well elucidated. However, much less is known about the natural variation of respiration. Here we conducted a survey on the natural variation of leaf dark respiration (<i>R</i><sub>d</sub>) in a global rice minicore diversity panel and applied a genome-wide association study (GWAS) in rice (<i>Oryza sativa</i> L.) to determine candidate loci associated with <i>R</i><sub>d</sub>. This rice minicore diversity panel consists of 206 accessions, which were grown under both growth room (GR) and field conditions. We found that <i>R</i><sub>d</sub> shows high single-nucleotide polymorphism (SNP) heritability under GR and it is significantly affected by genotype-environment interactions. <i>R</i><sub>d</sub> also exhibits strong positive correlation to the leaf thickness and chlorophyll content. GWAS results of <i>R</i><sub>d</sub> collected under GR and field show an overlapped genomic region in the chromosome 3 (Chr.3), which contains a lead SNP (3m29440628). There are 12 candidate genes within this region; among them, three genes show significantly higher expression levels in accessions with high <i>R</i><sub>d</sub>. Particularly, we observed that the <i>LRK1</i> gene, annotated as leucine rich repeat receptor kinase, was up-regulated four times. We further found that a single significantly associated SNPs at the promoter region of <i>LRK1</i>, was strongly correlated with the mean annual temperature of the regions from where minicore accessions were collected. A rice <i>lrk1</i> mutant shows only ~37% <i>R</i><sub>d</sub> of that of WT and retarded growth following exposure to 35 °C for 30 days, but only 24% reduction in growth was recorded under normal temperature (25 °C). This study demonstrates a substantial natural variation of <i>R</i><sub>d</sub> in rice and that the <i>LRK1</i> gene can regulate leaf dark respiratory fluxes, especially under high temperature. |
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| issn | 1661-6596 1422-0067 |
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| spelling | doaj.art-9866d670bd174a859e7f3bbc2dc8748c2023-11-20T06:35:35ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672020-07-012114493010.3390/ijms21144930Genome-Wide Association Study Unravels <i>LRK1</i> as a Dark Respiration Regulator in Rice (<i>Oryza sativa</i> L.)Mingnan Qu0Jemaa Essemine1Ming Li2Shuoqi Chang3Tiangen Chang4Gen-Yun Chen5Xin-Guang Zhu6State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai 200032, ChinaState Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai 200032, ChinaShanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, ChinaState Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, ChinaState Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai 200032, ChinaLaboratory of Photosynthesis and Environmental Biology, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, ChinaState Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai 200032, ChinaRespiration is a major plant physiological process that generates adenosine triphosphate (ATP) to support the various pathways involved in the plant growth and development. After decades of focused research on basic mechanisms of respiration, the processes and major proteins involved in respiration are well elucidated. However, much less is known about the natural variation of respiration. Here we conducted a survey on the natural variation of leaf dark respiration (<i>R</i><sub>d</sub>) in a global rice minicore diversity panel and applied a genome-wide association study (GWAS) in rice (<i>Oryza sativa</i> L.) to determine candidate loci associated with <i>R</i><sub>d</sub>. This rice minicore diversity panel consists of 206 accessions, which were grown under both growth room (GR) and field conditions. We found that <i>R</i><sub>d</sub> shows high single-nucleotide polymorphism (SNP) heritability under GR and it is significantly affected by genotype-environment interactions. <i>R</i><sub>d</sub> also exhibits strong positive correlation to the leaf thickness and chlorophyll content. GWAS results of <i>R</i><sub>d</sub> collected under GR and field show an overlapped genomic region in the chromosome 3 (Chr.3), which contains a lead SNP (3m29440628). There are 12 candidate genes within this region; among them, three genes show significantly higher expression levels in accessions with high <i>R</i><sub>d</sub>. Particularly, we observed that the <i>LRK1</i> gene, annotated as leucine rich repeat receptor kinase, was up-regulated four times. We further found that a single significantly associated SNPs at the promoter region of <i>LRK1</i>, was strongly correlated with the mean annual temperature of the regions from where minicore accessions were collected. A rice <i>lrk1</i> mutant shows only ~37% <i>R</i><sub>d</sub> of that of WT and retarded growth following exposure to 35 °C for 30 days, but only 24% reduction in growth was recorded under normal temperature (25 °C). This study demonstrates a substantial natural variation of <i>R</i><sub>d</sub> in rice and that the <i>LRK1</i> gene can regulate leaf dark respiratory fluxes, especially under high temperature.https://www.mdpi.com/1422-0067/21/14/4930dark respirationCRISPR/CAS9GWAS<i>LRK1</i>rice populationmolecular genetics |
| spellingShingle | Mingnan Qu Jemaa Essemine Ming Li Shuoqi Chang Tiangen Chang Gen-Yun Chen Xin-Guang Zhu Genome-Wide Association Study Unravels <i>LRK1</i> as a Dark Respiration Regulator in Rice (<i>Oryza sativa</i> L.) International Journal of Molecular Sciences dark respiration CRISPR/CAS9 GWAS <i>LRK1</i> rice population molecular genetics |
| title | Genome-Wide Association Study Unravels <i>LRK1</i> as a Dark Respiration Regulator in Rice (<i>Oryza sativa</i> L.) |
| title_full | Genome-Wide Association Study Unravels <i>LRK1</i> as a Dark Respiration Regulator in Rice (<i>Oryza sativa</i> L.) |
| title_fullStr | Genome-Wide Association Study Unravels <i>LRK1</i> as a Dark Respiration Regulator in Rice (<i>Oryza sativa</i> L.) |
| title_full_unstemmed | Genome-Wide Association Study Unravels <i>LRK1</i> as a Dark Respiration Regulator in Rice (<i>Oryza sativa</i> L.) |
| title_short | Genome-Wide Association Study Unravels <i>LRK1</i> as a Dark Respiration Regulator in Rice (<i>Oryza sativa</i> L.) |
| title_sort | genome wide association study unravels i lrk1 i as a dark respiration regulator in rice i oryza sativa i l |
| topic | dark respiration CRISPR/CAS9 GWAS <i>LRK1</i> rice population molecular genetics |
| url | https://www.mdpi.com/1422-0067/21/14/4930 |
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