Multiple Areas Investigation Reveals the Genes Related to Vascular Bundles in Rice

Overview

Journal Rice (N Y)

Date 2019 Mar 23

PMID 30900100

Citations 8

Authors

Cheng Fei

Xin Geng

Zhengjin Xu

Quan Xu

Affiliations

Soon will be listed here.

Abstract

Background: The vascular bundle in the panicle neck is a crucial trait in rice (Oryza sativa) production that differs between the indica and japonica subspecies. However, the effect of indica/japonica genetic background on the vascular bundles remains unknown.

Results: A series of recombinant inbred lines (RILs) derived from a cross between japonica and indica were planted in three areas. High-throughput sequencing was conducted to determine the indica pedigree percentage and for quantitative trait locus (QTL) analysis. The indica pedigree affected the number of large vascular bundles (LVBs), but not the number of small vascular bundles (SVBs). QTL analysis identified a locus (qLVB9) that was pleiotropic for both LVBs and SVBs in all three areas, and qLVB9 appeared synonymous with DENSE AND ERECT PANICLE 1 (DEP1). Using CRISPR/Cas9 gene editing and gene overexpression technology, we confirmed that the truncated dep1 allele increased the number of LVBs, and resulted in LVBs more closely associated to the indica pedigree. RNA sequencing showed that the truncated dep1 allele downregulated the AP2-like gene family. The double mutant for the DEP1 and AP2-like genes (OsAP2-39) showed decreased endogenous abscisic acid (ABA) level and insensitivity to exogenous ABA treatment, confirming that both DEP1 and OsAP2-39 are involved in the ABA response mechanism.

Conclusions: The present study showed the qLVB9/DEP1 affects LVBs, and involved in ABA signaling via regulating the AP2-like gene family. These results offer new insights into the function of qLVB9/DEP1 in rice.

Citing Articles

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References

Terao T, Nagata K, Morino K, Hirose T . A gene controlling the number of primary rachis branches also controls the vascular bundle formation and hence is responsible to increase the harvest index and grain yield in rice. Theor Appl Genet. 2010; 120(5):875-93. DOI: 10.1007/s00122-009-1218-8. View

Fujita D, Trijatmiko K, Tagle A, Sapasap M, Koide Y, Sasaki K . NAL1 allele from a rice landrace greatly increases yield in modern indica cultivars. Proc Natl Acad Sci U S A. 2013; 110(51):20431-6. PMC: 3870739. DOI: 10.1073/pnas.1310790110. View

Hsu P, Scott D, Weinstein J, Ran F, Konermann S, Agarwala V . DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotechnol. 2013; 31(9):827-32. PMC: 3969858. DOI: 10.1038/nbt.2647. View

Cui K, Peng S, Xing Y, Yu S, Xu C, Zhang Q . Molecular dissection of the genetic relationships of source, sink and transport tissue with yield traits in rice. Theor Appl Genet. 2003; 106(4):649-58. DOI: 10.1007/s00122-002-1113-z. View

Qi J, Qian Q, Bu Q, Li S, Chen Q, Sun J . Mutation of the rice Narrow leaf1 gene, which encodes a novel protein, affects vein patterning and polar auxin transport. Plant Physiol. 2008; 147(4):1947-59. PMC: 2492643. DOI: 10.1104/pp.108.118778. View

Sun J, Liu D, Wang J, Ma D, Tang L, Gao H . The contribution of intersubspecific hybridization to the breeding of super-high-yielding japonica rice in northeast China. Theor Appl Genet. 2012; 125(6):1149-57. DOI: 10.1007/s00122-012-1901-z. View

Nishimura A, Aichi I, Matsuoka M . A protocol for Agrobacterium-mediated transformation in rice. Nat Protoc. 2007; 1(6):2796-802. DOI: 10.1038/nprot.2006.469. View

Garris A, Tai T, Coburn J, Kresovich S, McCouch S . Genetic structure and diversity in Oryza sativa L. Genetics. 2005; 169(3):1631-8. PMC: 1449546. DOI: 10.1534/genetics.104.035642. View

Yuan Q, Saito H, Okumoto Y, Inoue H, Nishida H, Tsukiyama T . Identification of a novel gene ef7 conferring an extremely long basic vegetative growth phase in rice. Theor Appl Genet. 2009; 119(4):675-84. DOI: 10.1007/s00122-009-1078-2. View

10.

Li X, Wu L, Wang J, Sun J, Xia X, Geng X . Genome sequencing of rice subspecies and genetic analysis of recombinant lines reveals regional yield- and quality-associated loci. BMC Biol. 2018; 16(1):102. PMC: 6145349. DOI: 10.1186/s12915-018-0572-x. View

11.

Lucas W, Groover A, Lichtenberger R, Furuta K, Yadav S, Helariutta Y . The plant vascular system: evolution, development and functions. J Integr Plant Biol. 2013; 55(4):294-388. DOI: 10.1111/jipb.12041. View

12.

Murray M, Thompson W . Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res. 1980; 8(19):4321-5. PMC: 324241. DOI: 10.1093/nar/8.19.4321. View

13.

Xu Q, Zhao M, Wu K, Fu X, Liu Q . Emerging insights into heterotrimeric G protein signaling in plants. J Genet Genomics. 2016; 43(8):495-502. DOI: 10.1016/j.jgg.2016.06.004. View

14.

Zhang D, Zhou Y, Yin J, Yan X, Lin S, Xu W . Rice G-protein subunits qPE9-1 and RGB1 play distinct roles in abscisic acid responses and drought adaptation. J Exp Bot. 2015; 66(20):6371-84. DOI: 10.1093/jxb/erv350. View

15.

Huang X, Qian Q, Liu Z, Sun H, He S, Luo D . Natural variation at the DEP1 locus enhances grain yield in rice. Nat Genet. 2009; 41(4):494-7. DOI: 10.1038/ng.352. View

16.

Wan L, Zhang J, Zhang H, Zhang Z, Quan R, Zhou S . Transcriptional activation of OsDERF1 in OsERF3 and OsAP2-39 negatively modulates ethylene synthesis and drought tolerance in rice. PLoS One. 2011; 6(9):e25216. PMC: 3180291. DOI: 10.1371/journal.pone.0025216. View

17.

Huang X, Wei X, Sang T, Zhao Q, Feng Q, Zhao Y . Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet. 2010; 42(11):961-7. DOI: 10.1038/ng.695. View

18.

Li C, Qiao Z, Qi W, Wang Q, Yuan Y, Yang X . Genome-wide characterization of cis-acting DNA targets reveals the transcriptional regulatory framework of opaque2 in maize. Plant Cell. 2015; 27(3):532-45. PMC: 4558662. DOI: 10.1105/tpc.114.134858. View

19.

Yaish M, El-Kereamy A, Zhu T, Beatty P, Good A, Bi Y . The APETALA-2-like transcription factor OsAP2-39 controls key interactions between abscisic acid and gibberellin in rice. PLoS Genet. 2010; 6(9):e1001098. PMC: 2936520. DOI: 10.1371/journal.pgen.1001098. View

20.

Bai X, Wu B, Xing Y . Yield-related QTLs and their applications in rice genetic improvement. J Integr Plant Biol. 2012; 54(5):300-11. DOI: 10.1111/j.1744-7909.2012.01117.x. View