AUTHOR=Han Zhenyun , Li Fei , Qiao Weihua , Nong Baoxuan , Cheng Yunlian , Zhang Lifang , Huang Jingfen , Wang Yanyan , Lou Danjing , Ge Jinyue , Xing Meng , Fan Weiya , Nie Yamin , Guo Wenlong , Wang Shizhuang , Liu Ziran , Li Danting , Zheng Xiaoming , Yang Qingwen 

TITLE=Identification of candidate genes and clarification of the maintenance of the green pericarp of weedy rice grains

JOURNAL=Frontiers in Plant Science

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2022.930062

DOI=10.3389/fpls.2022.930062

ISSN=1664-462X

ABSTRACT=<p>The weedy rice (<italic>Oryza sativa</italic> f. <italic>spontanea</italic>) pericarp has diverse colors (e.g., purple, red, light-red, and white). However, research on pericarp colors has focused on red and purple, but not green. Unlike many other common weedy rice resources, LM8 has a green pericarp at maturity. In this study, the coloration of the LM8 pericarp was evaluated at the cellular and genetic levels. First, an examination of their ultrastructure indicated that LM8 chloroplasts were normal regarding plastid development and they contained many plastoglobules from the early immature stage to maturity. Analyses of transcriptome profiles and differentially expressed genes revealed that most chlorophyll (Chl) degradation-related genes in LM8 were expressed at lower levels than Chl <italic>a</italic>/<italic>b</italic> cycle-related genes in mature pericarps, suggesting that the green LM8 pericarp was associated with inhibited Chl degradation in intact chloroplasts. Second, the F<sub>2</sub> generation derived from a cross between LM8 (green pericarp) and SLG (white pericarp) had a pericarp color segregation ratio of 9:3:4 (green:brown:white). The bulked segregant analysis of the F<sub>2</sub> populations resulted in the identification of 12 known genes in the chromosome 3 and 4 hotspot regions as candidate genes related to Chl metabolism in the rice pericarp. The RNA-seq and sqRT-PCR assays indicated that the expression of the Chl <italic>a</italic>/<italic>b</italic> cycle-related structural gene <italic>DVR</italic> (encoding divinyl reductase) was sharply up-regulated. Moreover, genes encoding magnesium-chelatase subunit D and the light-harvesting Chl <italic>a</italic>/<italic>b</italic>-binding protein were transcriptionally active in the fully ripened dry pericarp. Regarding the ethylene signal transduction pathway, the <italic>CTR</italic> (encoding an ethylene-responsive protein kinase) and <italic>ERF</italic> (encoding an ethylene-responsive factor) genes expression profiles were determined. The findings of this study highlight the regulatory roles of Chl biosynthesis- and degradation-related genes influencing Chl accumulation during the maturation of the LM8 pericarp.</p>