AUTHOR=Liu Sicheng , Xiong Zhuang , Zhang Zuolin , Wei Youbo , Xiong Dongliang , Wang Fei , Huang Jianliang 

TITLE=Exploration of chlorophyll fluorescence characteristics gene regulatory in rice (Oryza sativa L.): a genome-wide association study

JOURNAL=Frontiers in Plant Science

VOLUME=14

YEAR=2023

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2023.1234866

DOI=10.3389/fpls.2023.1234866

ISSN=1664-462X

ABSTRACT=<p>Chlorophyll content and fluorescence parameters are crucial indicators to evaluate the light use efficiency in rice; however, the correlations among these parameters and the underlying genetic mechanisms remain poorly understood. Here, to clarify these issues, we conducted a genome-wide association study (GWAS) on 225 rice accessions. In the phenotypic and Mendelian randomization (MR) analysis, a weak negative correlation was observed between the chlorophyll content and actual quantum yield of photosystem II (<inline-formula><mml:math display="inline" id="im1" xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:msub><mml:mtext>Φ</mml:mtext><mml:mrow><mml:mi>I</mml:mi><mml:mi>I</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>). The phenotypic diversity observed in <italic>SPAD</italic>, <inline-formula><mml:math display="inline" id="im2" xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi>N</mml:mi><mml:mi>P</mml:mi><mml:msub><mml:mi>Q</mml:mi><mml:mi>t</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, <inline-formula><mml:math display="inline" id="im3" xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:msub><mml:mtext>Φ</mml:mtext><mml:mrow><mml:mi>N</mml:mi><mml:mi>P</mml:mi><mml:mi>Q</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>, and <inline-formula><mml:math display="inline" id="im4" xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:msub><mml:mi>F</mml:mi><mml:mi>v</mml:mi></mml:msub><mml:mo stretchy="false">/</mml:mo><mml:msub><mml:mi>F</mml:mi><mml:mi>m</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> among accessions was affected by genetic background. Furthermore, the GWAS identified 78 SNPs and 17 candidate genes significantly associated with <italic>SPAD</italic>, <inline-formula><mml:math display="inline" id="im5" xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi>N</mml:mi><mml:mi>P</mml:mi><mml:msub><mml:mi>Q</mml:mi><mml:mi>t</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>, <inline-formula><mml:math display="inline" id="im6" xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:msub><mml:mtext>Φ</mml:mtext><mml:mrow><mml:mi>I</mml:mi><mml:mi>I</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>, <inline-formula><mml:math display="inline" id="im7" xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:msub><mml:mtext>Φ</mml:mtext><mml:mrow><mml:mi>N</mml:mi><mml:mi>P</mml:mi><mml:mi>Q</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>, <inline-formula><mml:math display="inline" id="im8" xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:msub><mml:mi>q</mml:mi><mml:mi>L</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> and <inline-formula><mml:math display="inline" id="im9" xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:msub><mml:mi>q</mml:mi><mml:mi>P</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula>. Combining GWAS on 225 rice accessions with transcriptome analysis of two varieties exhibiting distinct fluorescence characteristics revealed two potential candidate genes (<italic>Os03g0583000</italic> from <inline-formula><mml:math display="inline" id="im10" xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:msub><mml:mtext>Φ</mml:mtext><mml:mrow><mml:mi>I</mml:mi><mml:mi>I</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> &amp; <inline-formula><mml:math display="inline" id="im11" xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:msub><mml:mi>q</mml:mi><mml:mi>P</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> traits and <italic>Os06g0587200</italic> from <inline-formula><mml:math display="inline" id="im12" xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi>N</mml:mi><mml:mi>P</mml:mi><mml:msub><mml:mi>Q</mml:mi><mml:mi>t</mml:mi></mml:msub></mml:mrow></mml:math></inline-formula> trait), which are respectively associated with peroxisomes, and protein kinase catalytic domains might involve in regulating the chlorophyll content and chlorophyll fluorescence. This study provides novel insights into the correlation among chlorophyll content and fluorescence parameters and the genetic mechanisms in rice, and offers valuable information for the breeding of rice with enhanced photosynthetic efficiency.</p>