AUTHOR=Guo Naihui , Wang Yakun , Chen Wei , Tang Shengjia , An Ruihu , Wei Xiangjin , Hu Shikai , Tang Shaoqing , Shao Gaoneng , Jiao Guiai , Xie Lihong , Wang Ling , Sheng Zhonghua , Hu Peisong 

TITLE=Fine mapping and target gene identification of qSE4, a QTL for stigma exsertion rate in rice (Oryza sativa L.)

JOURNAL=Frontiers in Plant Science

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2022.959859

DOI=10.3389/fpls.2022.959859

ISSN=1664-462X

ABSTRACT=<p>The stigma exsertion rate (SER) is a complex agronomy phenotype controlled by multiple genes and climate and a key trait affecting the efficiency of hybrid rice seed production. Using a japonica two-line male sterile line (DaS) with a high SER as the donor and a tropical japonica rice (D50) with a low SER as the acceptor to construct a near-isogenic line [NIL (<italic>qSE4</italic><sup>DaS</sup>)]. Populations were segregated into 2,143 individuals of BC<sub>3</sub>F<sub>2</sub> and BC<sub>4</sub>F<sub>2</sub>, and the stigma exsertion quantitative trait locus (QTL) <italic>qSE4</italic> was determined to be located within 410.4 Kb between markers RM17157 and RM17227 on chromosome 4. Bioinformatic analysis revealed 13 candidate genes in this region. Sequencing and haplotype analysis indicated that the promoter region of <italic>LOC_Os04g43910</italic> (<italic>ARF10</italic>) had a one-base substitution between the two parents. Further Reverse Transcription-Polymerase Chain Reaction (RT-PCR) analysis showed that the expression level of <italic>ARF10</italic> in DaS was significantly higher than in D50. After knocking out <italic>ARF10</italic> in the DaS background, it was found that the SER of <italic>arf10</italic> (the total SER of the <italic>arf10-1</italic> and the <italic>arf10-2</italic> were 62.54 and 66.68%, respectively) was significantly lower than that of the wild type (the total SER was 80.97%). Transcriptome and hormone assay analysis showed that <italic>arf10</italic> had significantly higher auxin synthesis genes and contents than the wild type and the expression of auxin signaling-related genes was significantly different, Similar results were observed for abscisic acid and jasmonic acid. These results indicate that <italic>LOC_Os04g43910</italic> is mostly likely the target gene of <italic>qSE4</italic>, and the study of its gene function is of great significance for understanding the molecular mechanisms of SER and improving the efficiency of hybrid seed production.</p>