A novel miR167a-OsARF6-OsAUX3 module regulates grain length and weight in rice

Abstract

Grain size is one of the most important factors that control rice yield, as it is associated with grain weight (GW). To date, dozens of rice genes that regulate grain size have been isolated; however, the regulatory mechanism underlying GW control is not fully understood. Here, the quantitative trait locus qGL5 for grain length (GL) and GW was identified in recombinant inbred lines of 9311 and Nipponbare (NPB) and fine mapped to a candidate gene, OsAUX3. Sequence variations between 9311 and NPB in the OsAUX3 promoter and loss of function of OsAUX3 led to higher GL and GW. RNA sequencing, gene expression quantification, dual-luciferase reporter assays, chromatin immunoprecipitation-quantitative PCR, and yeast one-hybrid assays demonstrated that OsARF6 is an upstream transcription factor regulating the expression of OsAUX3. OsARF6 binds directly to the auxin response elements of the OsAUX3 promoter, covering a single-nucleotide polymorphism site between 9311 and NPB/Dongjin/Hwayoung, and thereby controls GL by altering longitudinal expansion and auxin distribution/content in glume cells. Furthermore, we showed that miR167a positively regulate GL and GW by directing OsARF6 mRNA silencing. Taken together, our study reveals that a novel miR167a-OsARF6-OsAUX3 module regulates GL and GW in rice, providing a potential target for the improvement of rice yield.

MicroRNAs Are Involved in Regulating Plant Development and Stress Response through Fine-Tuning of TIR1/AFB-Dependent Auxin Signaling

“…OsmiR167-guided OsARF12 expression regulates root elongation and iron accumulation in rice [ 41 ], while OsmiR167a represses its targets, OsARF12/17/25, to control rice tiller angle by modulating the asymmetric auxin distribution in shoots [ 42 ]. Recently, the OsmiR167a-OsARF6-OsAUX3 module has been reported to regulate grain length and weight in rice, indicating the OsmiR167a-mediated auxin distribution may be important for rice yield improvement [ 43 ]. Overall, miR160 and miR167 may modulate auxin signaling not only through the simple cleavage of ARFs, but also through influencing auxin homeostasis and response during specific developmental processes ( Figure 2 A).…”

Multi-Environmental Genetic Analysis of Grain Size Traits Based on Chromosome Segment Substitution Line in Rice (Oryza sativa L.)

“…To date, QTL mapping for rice grain size traits using different populations, which derived from various biparental crosses, has been reported in many previous studies [7][8][9][10][11][12][13][14][15][16][17]. Some of QTLs identified in these populations have been cloned, such as GS3 [18], GW2 [19], GW5/qSW5/GSE5 [20][21][22][23], GS5 [24], qGL3/GL3.1/ OsPPKL1 [25][26][27], GW8/OsSPL16 [28], TGW6 [29], GW6a [30], GW7/GL7/SLG7 [31][32][33], GS2/GL2/ GLW2/PT2 [34][35][36][37][38], GLW7 [39], GS9 [40], qLGY3/OsLG3b [41,42], TGW3/qTGW3/GL3.3/OsSK41 [43][44][45], TGW2 [46], OsAUX3 [47]. Although a large number of QTLs for grain size traits have been mapped or cloned, and these results have facilitated a better understanding of the genetic basis of the grain size, it still needs to identify new QTL or genes to understand the complex mechanisms of grain size traits.…”

“…The substitution lines are the complete integration of the substituted segments with the stability of a certain character, which could reduce the interference of background noise and improve the accuracy of QTL mapping [48]. A large number of CSSLs sets have been developed to identify the QTLs for rice agronomic traits, including the grain size traits [47,[49][50][51][52][53].…”

Control of Thousand-Grain Weight by OsMADS56 in Rice

“…Six genes, namely GW2 [ 5 ], TGW2 [ 6 ], GS5 [ 7 ], GSE5 [ 8 ], GW6 [ 9 ] and GW8 [ 10 ], mainly regulated TGW and GW. The other 13 genes, namely qTGW1.2b [ 11 ], GS2 / GL2 [ 12 , 13 ], OsLG3 [ 14 ], OsLG3b / qLGY3 [ 15 , 16 ], GS3 [ 17 ], SG3 [ 18 ], GL3.1 / qGL3 [ 19 , 20 ], qTGW3 [ 21 ], qGL5 [ 22 ], TGW6 [ 23 ], GW6a [ 24 ], GL6 [ 25 ] and GLW7 [ 26 ], mainly regulated TGW and GL. These genes are distributed on all the rice chromosomes except chromosomes 4, 10, 11 and 12.…”