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8 publications mentioning osa-MIR1861c

Open access articles that are associated with the species Oryza sativa and mention the gene name MIR1861c. Click the [+] symbols to view sentences that include the gene name, or the word cloud on the right for a summary.

1
[+] score: 25
These are i) BLAST hit should not be more than 20 nt lesser than the query and should have an E-value of ≤10 [−4], ii) the mismatches in the mature sequence of desired sized hit with the mature sequence of rice should be ≤2, iii) the sequence should adopt an appropriate hairpin structure when analysed by RNA Fold [76], iv) the minimum free energy of the predicted hairpin structure should be ≤ −15 kcal/mol, v) the maximum bulge size in the hairpin should not be more than 12, vi) the maximum number of mismatches allowed between miRNA and miRNA [*] is 6. The sequences of all miRNA precursors from the 10 Oryza species and their other details are shown in Additional file  1. miR1861 gene family is one of the miRNA gene families that might be organized into distinct compact clusters, and can be transcribed as single units. [score:1]
Precursor sequences of individual members of osa-miR1861 clusters were determined from the miRBase, and then each cluster sequence was used as a query to extract miR1861 clusters from the other Oryza species. [score:1]
Both the tree topologies depict BB- and FF-genomes as the eminent outgroups, whereas O. longistaminata can be seen as the earliest divergent species among the AA-genomes Among the different non-conserved miRNA gene families of rice, miR1861 family is unique in that it is organized into distinct compact clusters that can be transcribed as single units. [score:1]
A possible evolutionary path for nine clusters of osa-miR1861 family (b). [score:1]
In order to analyse the sequence convergence or divergence in nine sequenced miR1861 clusters from the five Oryza species, each cluster from all these species was aligned using Clustal X 1.83 with default parameters. [score:1]
Genomic organization and conservation of miR1861 family in Oryza. [score:1]
Plant materials and PCR reactions for sequencing of miR1861 clusters. [score:1]
The lesser number of miRNA genes and the absence of miR1861 clusters in O. brachyantha might be reasoned out to the finding that illegitimate and unequal homologous recombination in this species have resulted in the elimination of ancient gene families massively which gave rise to its smaller genome size than rice [66]. [score:1]
Here cluster-II represents all the 2-membered miR1861-clusters. [score:1]
These are i) BLAST hit should not be more than 20 nt lesser than the query and should have an E-value of ≤10 [−4], ii) the mismatches in the mature sequence of desired sized hit with the mature sequence of rice should be ≤2, iii) the sequence should adopt an appropriate hairpin structure when analysed by RNA Fold [76], iv) the minimum free energy of the predicted hairpin structure should be ≤ −15 kcal/mol, v) the maximum bulge size in the hairpin should not be more than 12, vi) the maximum number of mismatches allowed between miRNA and miRNA [*] is 6. The sequences of all miRNA precursors from the 10 Oryza species and their other details are shown in Additional file  1. miR1861 gene family is one of the miRNA gene families that might be organized into distinct compact clusters, and can be transcribed as single units. [score:1]
SAT- O. sativa (indica), BRA- O. brachyantha, GLA- O. glaberrima, NIV- O. nivara, RUF- O. rufipogon To study the relationship among the miR1861 clusters of rice, multiple sequence alignment was performed among them. [score:1]
Fig. 6A probable evolutionary history of nine osa-miR1861 clusters in rice. [score:1]
As per the similarity among the osa-miRNA1861 clusters, an apparent evolutionary pathway of the nine clusters was developed. [score:1]
Fig. 5Mining of nine miR1861-clusters from the different species of Oryza genus. [score:1]
The deletion of 22 nt immediately downstream of the mature sequence in the second precursor (as found by Zhu et al. [64] in osa-miR1861 family of rice) of all the two-membered miR1861 clusters was consistently present in all the Oryza species (Additional file  16 B), suggesting that this deletion in the two-membered clusters was under the strong purifying selection. [score:1]
Relationship among the nine clusters of osa-miR1861 family based on their sequence similarity as depicted by percentage numbers (a). [score:1]
The osa-miR1861 family was put into its current configuration by a final 2-duplication event followed a likely deletion in the clusters II and IV, consequently bringing about a 2-membered (Cluster VIII) and a 1-membered (cluster IX) cluster. [score:1]
The miR1861 family organised into nine distinct compact clusters in the studied Oryza species except O. brachyantha. [score:1]
Since the origin of the ancestral osa-miR1861 gene is not well-defined, we assumed on the basis of phylogenetic tree (Fig.   6a) that osa-miR1861a and osa-miR1861h (cluster I and V) pre-existed in the ancestor of cultivated rice. [score:1]
SAT- O. sativa (indica), BRA- O. brachyantha, GLA- O. glaberrima, NIV- O. nivara, RUF- O. rufipogon To study the relationship among the miR1861 clusters of rice, multiple sequence alignment was performed among them. [score:1]
Fig. 4 Genomic organization of the rice osa-miR1861 gene family as the nine distinct clusters on eight different chromosomes. [score:1]
The recent divergence in the Oryza is hence proven from the conservation in the sequence and structure of the miR1861 family members. [score:1]
Despite the significant sequence conservation, the genomic configuration of miR1861 clusters was found not to be conserved due to the random scattering of clusters across the Oryza genomes. [score:1]
All miR1861-clusters could be retrieved from the genomes of the Oryza species except O. brachyantha, which could be due to the high level of divergence of O. brachyantha from the rice (Oryza sativa subsp. [score:1]
In order to extract these clusters from the 10 Oryza species, BLAST search was performed in gramene against each species with the miR1861-clusters from rice as queries. [score:1]
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2
[+] score: 18
Genes targeted by those differentially expressed miRNAs (i. e. miR156, miR164, miR167, miR397, miR1861, and miR1867) were recognized to play roles in multiple developmental and signaling pathways related to plant hormone homeostasis and starch accumulation. [score:6]
Heatmap shows the expressional levels [log2(normalized miRNA expression)] of different miRNA family members including miR156, miR159, miR164, miR167, miR397, miR1861, and miR1867 families in superior (S, on left part of the map) and inferior (I, on right part of the map) spikelets at different rice grain filling stages. [score:5]
Additionally, miR1861 has been demonstrated to target genes that encode beta-amylase and starch -binding domain containing proteins and thus may also play curial roles during rice seed development [16],[33]. [score:4]
Interestingly, miR1861 expressed much lower in inferior spikelets than in superior ones during all the grain filling stages (Figure  5, Additional file 2 and Additional file 3). [score:3]
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3
[+] score: 14
Other miRNAs from this paper: osa-MIR156a, osa-MIR156b, osa-MIR156c, osa-MIR156d, osa-MIR156e, osa-MIR156f, osa-MIR156g, osa-MIR156h, osa-MIR156i, osa-MIR156j, osa-MIR160a, osa-MIR160b, osa-MIR160c, osa-MIR160d, osa-MIR164a, osa-MIR164b, osa-MIR166a, osa-MIR166b, osa-MIR166c, osa-MIR166d, osa-MIR166e, osa-MIR166f, osa-MIR167a, osa-MIR167b, osa-MIR167c, osa-MIR169a, osa-MIR397a, osa-MIR397b, osa-MIR398a, osa-MIR398b, osa-MIR156k, osa-MIR156l, osa-MIR159a, osa-MIR159b, osa-MIR159c, osa-MIR159d, osa-MIR159e, osa-MIR159f, osa-MIR319a, osa-MIR319b, osa-MIR160e, osa-MIR160f, osa-MIR164c, osa-MIR164d, osa-MIR164e, osa-MIR166k, osa-MIR166l, osa-MIR167d, osa-MIR167e, osa-MIR167f, osa-MIR167g, osa-MIR167h, osa-MIR167i, osa-MIR169b, osa-MIR169c, osa-MIR169d, osa-MIR169e, osa-MIR169f, osa-MIR169g, osa-MIR169h, osa-MIR169i, osa-MIR169j, osa-MIR169k, osa-MIR169l, osa-MIR169m, osa-MIR169n, osa-MIR169o, osa-MIR169p, osa-MIR169q, osa-MIR166g, osa-MIR166h, osa-MIR166i, osa-MIR393b, osa-MIR408, osa-MIR167j, osa-MIR166m, osa-MIR166j, osa-MIR164f, osa-MIR390, osa-MIR528, osa-MIR529a, osa-MIR812a, osa-MIR812b, osa-MIR812c, osa-MIR812d, osa-MIR812e, osa-MIR815c, osa-MIR818d, osa-MIR529b, osa-MIR1425, osa-MIR1428a, osa-MIR169r, osa-MIR1436, osa-MIR1428b, osa-MIR1428c, osa-MIR1428d, osa-MIR1428e, osa-MIR1858a, osa-MIR1861a, osa-MIR1861b, osa-MIR1861d, osa-MIR1861e, osa-MIR1861f, osa-MIR1861g, osa-MIR1861h, osa-MIR1861i, osa-MIR1861j, osa-MIR1861k, osa-MIR1861l, osa-MIR1861m, osa-MIR1861n, osa-MIR812f, osa-MIR1862d, osa-MIR812g, osa-MIR812h, osa-MIR812i, osa-MIR812j, osa-MIR1428f, osa-MIR1428g, osa-MIR812k, osa-MIR812l, osa-MIR812m, osa-MIR812n, osa-MIR812o, osa-MIR812p, osa-MIR812q, osa-MIR812r, osa-MIR812s, osa-MIR812t, osa-MIR812u, osa-MIR812v, osa-MIR1861o
Os01g63810, encoding a starch -binding domain containing protein (SBD), is targeted by a miR1861 family that was strongly accumulated during rice grain filling (Fig. 7E ), while transcript-encoding β-amylase (Os10g32810), targeted by miR1861, has been validated by degradome data [65]. [score:5]
Os01g63810 is the predicted target of miR1861, encoding a starch -binding domain-containing protein. [score:3]
However, the main cleavage site detected was 29 nt upstream of the predicted miR1861 target site, which was probably caused by an unknown small RNA cleavage mechanism (Fig. 5 ). [score:3]
MiR156 and miR166 play a role in overall spikelets development, while miR167, miR164, miR812, miR1861, miR1428 and miR45 play a specific role in the differentiation during rice grain filling (Fig. 8 ). [score:2]
Similar trends were observed in miR156, miR164, miR166, and miR1861 (Fig. 7B–E ), but were not apparent for miR812 (Fig. 7F ). [score:1]
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[+] score: 8
Other miRNAs from this paper: osa-MIR156a, osa-MIR156b, osa-MIR156c, osa-MIR156d, osa-MIR156e, osa-MIR156f, osa-MIR156g, osa-MIR156h, osa-MIR156i, osa-MIR156j, osa-MIR160a, osa-MIR160b, osa-MIR160c, osa-MIR160d, osa-MIR162a, osa-MIR164a, osa-MIR164b, osa-MIR166a, osa-MIR166b, osa-MIR166c, osa-MIR166d, osa-MIR166e, osa-MIR166f, osa-MIR167a, osa-MIR167b, osa-MIR167c, osa-MIR169a, osa-MIR171a, osa-MIR393a, osa-MIR394, osa-MIR395b, osa-MIR395d, osa-MIR395e, osa-MIR395g, osa-MIR395h, osa-MIR395i, osa-MIR395j, osa-MIR395k, osa-MIR395l, osa-MIR395s, osa-MIR395t, osa-MIR395c, osa-MIR395a, osa-MIR395f, osa-MIR395u, osa-MIR396a, osa-MIR396b, osa-MIR396c, osa-MIR397a, osa-MIR397b, osa-MIR398a, osa-MIR398b, osa-MIR399a, osa-MIR399b, osa-MIR399c, osa-MIR399d, osa-MIR399e, osa-MIR399f, osa-MIR399g, osa-MIR399h, osa-MIR399i, osa-MIR399j, osa-MIR399k, osa-MIR156k, osa-MIR156l, osa-MIR159a, osa-MIR159b, osa-MIR159c, osa-MIR159d, osa-MIR159e, osa-MIR159f, osa-MIR319a, osa-MIR319b, osa-MIR160e, osa-MIR160f, osa-MIR162b, osa-MIR164c, osa-MIR164d, osa-MIR164e, osa-MIR166k, osa-MIR166l, osa-MIR167d, osa-MIR167e, osa-MIR167f, osa-MIR167g, osa-MIR167h, osa-MIR167i, osa-MIR168a, osa-MIR168b, osa-MIR169b, osa-MIR169c, osa-MIR169d, osa-MIR169e, osa-MIR169f, osa-MIR169g, osa-MIR169h, osa-MIR169i, osa-MIR169j, osa-MIR169k, osa-MIR169l, osa-MIR169m, osa-MIR169n, osa-MIR169o, osa-MIR169p, osa-MIR169q, osa-MIR171b, osa-MIR171c, osa-MIR171d, osa-MIR171e, osa-MIR171f, osa-MIR171g, osa-MIR172a, osa-MIR172b, osa-MIR172c, osa-MIR166g, osa-MIR166h, osa-MIR166i, osa-MIR171h, osa-MIR393b, osa-MIR408, osa-MIR172d, osa-MIR171i, osa-MIR167j, osa-MIR166m, osa-MIR166j, osa-MIR164f, osa-MIR426, osa-MIR390, osa-MIR396e, osa-MIR528, osa-MIR530, osa-MIR395m, osa-MIR395n, osa-MIR395o, osa-MIR395p, osa-MIR395q, osa-MIR395v, osa-MIR395w, osa-MIR395r, osa-MIR810a, osa-MIR812a, osa-MIR812b, osa-MIR812c, osa-MIR812d, osa-MIR812e, osa-MIR820a, osa-MIR1423, osa-MIR1425, osa-MIR1432, osa-MIR169r, osa-MIR810b, osa-MIR1436, osa-MIR1441, osa-MIR1861a, osa-MIR1861b, osa-MIR1861d, osa-MIR1861e, osa-MIR1861f, osa-MIR1861g, osa-MIR1861h, osa-MIR1861i, osa-MIR1861j, osa-MIR1861k, osa-MIR1861l, osa-MIR1861m, osa-MIR1861n, osa-MIR1862a, osa-MIR1862b, osa-MIR1862c, osa-MIR812f, osa-MIR1873, osa-MIR1862d, osa-MIR1862e, osa-MIR812g, osa-MIR812h, osa-MIR812i, osa-MIR812j, osa-MIR827, osa-MIR396f, osa-MIR2873a, osa-MIR2878, osa-MIR396g, osa-MIR396h, osa-MIR396d, osa-MIR395x, osa-MIR395y, osa-MIR812k, osa-MIR812l, osa-MIR812m, osa-MIR1862f, osa-MIR1862g, osa-MIR812n, osa-MIR812o, osa-MIR2873b, osa-MIR5071, osa-MIR5074, osa-MIR5075, osa-MIR5077, osa-MIR5080, osa-MIR5081, osa-MIR5144, osa-MIR812p, osa-MIR812q, osa-MIR812r, osa-MIR5795, osa-MIR812s, osa-MIR5802, osa-MIR812t, osa-MIR812u, osa-MIR5805, osa-MIR812v, osa-MIR5807, osa-MIR2873c, osa-MIR6253, osa-MIR1861o
The predicted targets of osa-MIR1861 include structural maintenance of chromosomes protein (SMC5), receptor-like protein kinase, glutathione peroxidase 4, mitotic control protein DIS3 and pentatricopeptide repeat –containing protein, which may indicate that osa-MIR1861 are regulating different important molecular functions in the rice plant. [score:4]
Additional file 8 shows that all 12 mature miRNAs of osa-MIR1861 family [miRBase:MIPF0000567] were found to be differentially expressed in our analysis. [score:3]
They are mature miRNAs from osa-MIR1423, osa-MIR1425, osa-MIR1861, osa-MIR1862, osa-MIR1873, osa-MIR2873, osa-MIR2878, osa-MIR5144, osa-MIR528, osa-MIR530, osa-MIR5795, osa-MIR5802, osa-MIR5805, osa-MIR5807, osa-MIR6253, osa-MIR810 and osa-MIR812 families. [score:1]
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[+] score: 8
Other miRNAs from this paper: osa-MIR156a, osa-MIR156b, osa-MIR156c, osa-MIR156d, osa-MIR156e, osa-MIR156f, osa-MIR156g, osa-MIR156h, osa-MIR156i, osa-MIR156j, osa-MIR160a, osa-MIR160b, osa-MIR160c, osa-MIR160d, osa-MIR164a, osa-MIR164b, osa-MIR166a, osa-MIR166b, osa-MIR166c, osa-MIR166d, osa-MIR166e, osa-MIR166f, osa-MIR167a, osa-MIR167b, osa-MIR167c, osa-MIR396a, osa-MIR396b, osa-MIR396c, osa-MIR156k, osa-MIR156l, osa-MIR159f, osa-MIR160e, osa-MIR160f, osa-MIR164c, osa-MIR164d, osa-MIR164e, osa-MIR166k, osa-MIR166l, osa-MIR167d, osa-MIR167e, osa-MIR167f, osa-MIR167g, osa-MIR167h, osa-MIR167i, osa-MIR168a, osa-MIR168b, osa-MIR166g, osa-MIR166h, osa-MIR166i, osa-MIR408, osa-MIR167j, osa-MIR166m, osa-MIR166j, osa-MIR164f, osa-MIR396e, osa-MIR444a, osa-MIR531a, osa-MIR810a, osa-MIR812a, osa-MIR812b, osa-MIR812c, osa-MIR812d, osa-MIR812e, osa-MIR820a, osa-MIR820b, osa-MIR820c, osa-MIR444b, osa-MIR444c, osa-MIR444d, osa-MIR444e, osa-MIR444f, osa-MIR810b, osa-MIR531b, osa-MIR1846d, osa-MIR1846a, osa-MIR1846b, osa-MIR1861a, osa-MIR1861b, osa-MIR1861d, osa-MIR1861e, osa-MIR1861f, osa-MIR1861g, osa-MIR1861h, osa-MIR1861i, osa-MIR1861j, osa-MIR1861k, osa-MIR1861l, osa-MIR1861m, osa-MIR1861n, osa-MIR1862a, osa-MIR1862b, osa-MIR1862c, osa-MIR812f, osa-MIR1874, osa-MIR1862d, osa-MIR1862e, osa-MIR812g, osa-MIR812h, osa-MIR812i, osa-MIR812j, osa-MIR1846c, osa-MIR1846e, osa-MIR396f, osa-MIR2103, osa-MIR2105, osa-MIR396g, osa-MIR396h, osa-MIR396d, osa-MIR812k, osa-MIR812l, osa-MIR812m, osa-MIR1862f, osa-MIR1862g, osa-MIR812n, osa-MIR812o, osa-MIR812p, osa-MIR812q, osa-MIR812r, osa-MIR812s, osa-MIR812t, osa-MIR812u, osa-MIR812v, osa-MIR1861o, osa-MIR531c
There were a few exceptions; four rice-specific miRNAs, osa-miR1861, osa-miR1862, osa-miR812, and osa-miR820, displayed relatively high expression during grain filling, suggesting that they may be important regulators of rice grain development. [score:5]
osa-miR1861, whose target mRNAs encode a starch -binding domain-containing protein (Os01g63810), are involved in starch degradation [51]. [score:3]
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[+] score: 5
More interestingly, a glyoxalase gene (BGIOSGA027518) was predicted and validated as the target of miR1861, a rice specific miRNA. [score:3]
These observations suggested that miR1861 and its mediated glyoxalase pathway could play a role in innate immunity. [score:1]
It was reported that miR1861 is responded to arsenate and arsenite stress 36, and glyoxalase is also reported to be associated with biotic and abiotic stimulation in A. thaliana 37 38. [score:1]
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[+] score: 5
Other miRNAs from this paper: osa-MIR156a, osa-MIR156b, osa-MIR156c, osa-MIR156d, osa-MIR156e, osa-MIR156f, osa-MIR156g, osa-MIR156h, osa-MIR156i, osa-MIR156j, osa-MIR164a, osa-MIR164b, osa-MIR166a, osa-MIR166b, osa-MIR166c, osa-MIR166d, osa-MIR166e, osa-MIR166f, osa-MIR167a, osa-MIR167b, osa-MIR167c, osa-MIR169a, osa-MIR171a, osa-MIR393a, osa-MIR394, osa-MIR395f, osa-MIR396a, osa-MIR396b, osa-MIR396c, osa-MIR397a, osa-MIR397b, osa-MIR398b, osa-MIR156k, osa-MIR156l, osa-MIR159a, osa-MIR159b, osa-MIR159c, osa-MIR159d, osa-MIR159e, osa-MIR159f, osa-MIR319a, osa-MIR319b, osa-MIR160f, osa-MIR164c, osa-MIR164d, osa-MIR164e, osa-MIR166k, osa-MIR166l, osa-MIR167d, osa-MIR167e, osa-MIR167f, osa-MIR167g, osa-MIR167h, osa-MIR167i, osa-MIR168a, osa-MIR168b, osa-MIR169b, osa-MIR169c, osa-MIR169d, osa-MIR169e, osa-MIR169f, osa-MIR169g, osa-MIR169h, osa-MIR169i, osa-MIR169j, osa-MIR169k, osa-MIR169l, osa-MIR169m, osa-MIR169n, osa-MIR169o, osa-MIR169p, osa-MIR169q, osa-MIR171b, osa-MIR171c, osa-MIR171d, osa-MIR171e, osa-MIR171f, osa-MIR171g, osa-MIR166g, osa-MIR166h, osa-MIR166i, osa-MIR171h, osa-MIR393b, osa-MIR408, osa-MIR172d, osa-MIR171i, osa-MIR167j, osa-MIR166m, osa-MIR166j, osa-MIR164f, osa-MIR390, osa-MIR396e, osa-MIR444a, osa-MIR528, osa-MIR529a, osa-MIR810a, osa-MIR812a, osa-MIR812b, osa-MIR812c, osa-MIR812d, osa-MIR812e, osa-MIR818a, osa-MIR818b, osa-MIR818c, osa-MIR818d, osa-MIR818e, osa-MIR820a, osa-MIR820b, osa-MIR820c, osa-MIR529b, osa-MIR1425, osa-MIR1430, osa-MIR1432, osa-MIR169r, osa-MIR444b, osa-MIR444c, osa-MIR444d, osa-MIR444e, osa-MIR444f, osa-MIR810b, osa-MIR1440a, osa-MIR531b, osa-MIR1847, osa-MIR1848, osa-MIR1861a, osa-MIR1861b, osa-MIR1861d, osa-MIR1861e, osa-MIR1861f, osa-MIR1861g, osa-MIR1861h, osa-MIR1861i, osa-MIR1861j, osa-MIR1861k, osa-MIR1861l, osa-MIR1861m, osa-MIR1861n, osa-MIR1865, osa-MIR812f, osa-MIR1874, osa-MIR812g, osa-MIR812h, osa-MIR812i, osa-MIR812j, osa-MIR1320, osa-MIR827, osa-MIR2090, osa-MIR396f, osa-MIR2118c, osa-MIR2863a, osa-MIR2863b, osa-MIR396g, osa-MIR396h, osa-MIR396d, osa-MIR812k, osa-MIR812l, osa-MIR812m, osa-MIR3979, osa-MIR3980a, osa-MIR3980b, osa-MIR812n, osa-MIR812o, osa-MIR3981, osa-MIR5082, osa-MIR2863c, osa-MIR5337a, osa-MIR812p, osa-MIR812q, osa-MIR812r, osa-MIR812s, osa-MIR812t, osa-MIR812u, osa-MIR812v, osa-MIR1440b, osa-MIR818f, osa-MIR1861o
Moreover, the expression patterns of miR319, miR166, miR810, and miR1861 were in agreement with our study [21]. [score:3]
2, miR390-3p, miR531b, miR1430, miR1847.2, miR1865-5p, miR1874-3p, and miR5082, whereas 24 miRNAs were identified that were significantly accumulated in the whole roots, including miR156, miR164, miR166, osa-miR169, miR171, miR393, miR408, miR528, miR529, osa-miR812, miR1320, osa-miR1432, miR1861, miR3979, etc. [score:1]
Nine miRNAs, including miR408, miR810, miR319, miR2863, miR444, miR166, miR167, miR818, and miR1861 were also detected in our study. [score:1]
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Our network analysis further showed that osa-miR1861 regulated many genes or TFs in the superior spikelets and had cross-talk with the verified yield -associated osa-miR159a. [score:2]
Most of the SmiRNAs have been reported to be involved in rice grain-filling, including osa-miR444b, osa-miR1861, osa-miR172c, osa-miR1862 and so on [28] (Fig.   3A). [score:1]
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