Nudix hydrolase 14 influences plant development and grain chalkiness in rice

Abstract

Nudix hydrolases (NUDX) can hydrolyze a wide range of organic pyrophosphates and are widely distributed in various organisms. Previous studies have shown that NUDXs are extensively involved in biotic and abiotic stress responses in different plant species; however, the role of NUDXs in plant growth and development remains largely unknown. In the present study, we identified and characterized OsNUDX14 localized in the mitochondria in rice. Results showed that OsNUDX14 is constitutively expressed in various tissues and most strongly expressed in mature leaves. We used CRISPR/Cas9 introducing mutations that editing OsNUDX14 and its encoding product. OsNUDX14-Cas9 (nudx14) lines presented early flowering and a larger flag leaf angle during the reproductive stage. In addition, OsNUDX14 affected grain chalkiness in rice. Furthermore, transcript profile analysis indicated that OsNUDX14 is associated with lignin biosynthesis in rice. Six major haplotypes were identified by six OsNUDX14 missense mutations, including Hap_1 to Hap_6. Accessions having the Hap_5 allele were geographically located mainly in South and Southeast Asia with a low frequency in the Xian/indica subspecies. This study revealed that OsNUDX14 is associated with plant development and grain chalkiness, providing a potential opportunity to optimize plant architecture and quality for crop breeding.

Establishing an optimized ATAC-seq protocol for the maize

“…To have a better sense of the ATAC-seq data from 2500 or 5000 maize nuclei, we showed four genes (lipoxygenases 10, S-adenosyl methionine decarboxylase 2, plasma-membrane H+ATPase2, and nudix hydroxylase 4), including their expression levels and ATAC-seq abundance in our 2500 N and 5000 N libraries using a genome browser ( Supplementary Figure 1 ). These genes, or their family members, have been linked to plant defense and early development ( Suzuki and Hirasawa, 1980 ; Christensen et al., 2013 ; Liu et al., 2022 ), suggesting that their open state may enhance gene transcription, leading to improved development and adaptation. We generated peaks distribution across genomic features using ChIPSeeker and ATACgraph.…”

Identification of QTLs Conferring Rice Leaf Inclination Angle and Analysis of Candidate Genes

“…LOC_Os08g01330 encodes NAC transcription factor; NAC transcription factors play a key role in the regulation of secondary wall biosynthesis, thereby affecting the mechanical strength of plants [55]. LOC_Os08g28860 and LOC_Os09g38040 encode Nudix hydrolase; it can specifically hydrolyze ADP ribose in the cytoplasm, leading to downregulation of genes related to lignin biosynthesis [56], thereby reducing the mechanical strength of the plant. LOC_Os09g32080 encodes a chitinase-like protein, which is necessary for cellulose biosynthesis and will affect plant mechanical strength [44].…”