Information report for GL3.1;qGL3-1
Gene Details
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Functional Descriptions
- Here, we report the cloning and functional characterization of a major grain length QTL, qGL3, which encodes a putative protein phosphatase with Kelch-like repeat domain (OsPPKL1).
- Transgenic studies showed that OsPPKL1 and OsPPKL3 function as negative regulators of grain length, whereas OsPPKL2 as a positive regulator.
- Rare allele of OsPPKL1 associated with grain length causes extra-large grain and a significant yield increase in rice.
- Field trials showed that the application of the qGL3 allele could significantly increase grain yield in both inbred and hybrid rice varieties, due to its favorable effect on grain length, filling, and weight.
- We found a rare allele qgl3 that leads to a long grain phenotype by an aspartate-to-glutamate transition in a conserved AVLDT motif of the second Kelch domain in OsPPKL1.
- In particular, qGL3-1, a newly-identified grain length QTL with the highest LOD value and largest phenotypic variation, was fine-mapped to the 17 kb region of chromosome 3.
- The novel quantitative trait locus GL3.1 controls rice grain size and yield by regulating Cyclin-T1;3.
- Comparative analysis of primary panicle transcriptomes in the four NILs revealed that the genes affected by GS3 and qGL3 partially overlapped, and both loci might be involved in brassinosteroid signaling.
- The additive effects of GS3 and qGL3 on rice grain length regulation revealed by genetic and transcriptome comparisons.
- By comparing the grain lengths of 93-11, NIL-GS3, NIL-qGL3 and NIL-GS3/qGL3, we investigated the effects of GS3, qGL3 and GS3 × qGL3 interaction on grain length based on two-way ANOVA.
- We found that GS3 and qGL3 had additive effects on rice grain length regulation.
Functional Keywords
- grain-length , grain-yield , grain , yield , grain-size , panicle , brassinosteroid
Literature and News
- The novel quantitative trait locus GL3.1 controls rice grain size and yield by regulating Cyclin-T1;3 . DOI: 10.1038/cr.2012.151 ; PMID: 23147796
- A Kelch motif-containing serine/threonine protein phosphatase determines the large grain QTL trait in rice . DOI: 10.1111/jipb.12008 ; PMID: 23137285
- Rare allele of OsPPKL1 associated with grain length causes extra-large grain and a significant yield increase in rice . DOI: 10.1073/pnas.1219776110 ; PMID: 23236132
- The additive effects of GS3 and qGL3 on rice grain length regulation revealed by genetic and transcriptome comparisons . DOI: 10.1186/s12870-015-0515-4 ; PMID: 26105598
- Bin-based genome-wide association studies reveal superior alleles for improvement of appearance quality using a 4-way MAGIC population in rice . DOI: 10.1016/j.jare.2020.08.001 ; PMID: 33364055
- Bin-based genome-wide association studies reveal superior alleles for improvement of appearance quality using a 4-way MAGIC population in rice . DOI: 10.1016/j.jare.2020.08.001 ; PMID: 33364055
- A cryptic inhibitor of cytokinin phosphorelay controls rice grain size . DOI: 10.1016/j.molp.2021.09.010 ; PMID: 34562665
- qGL3/OsPPKL1 induces phosphorylation of 14-3-3 protein OsGF14b to inhibit OsBZR1 function in brassinosteroid signaling . DOI: 10.1093/plphys/kiab484 ; PMID: 34662408
Gene Resources
- UniProt: Q10G19
- EMBL: DP000009
- AlphaFoldDB: Q10G19
- EnsemblPlants: Os03t0646900-01
- Gramene: Os03t0646900-01
- KEGG: osa:107277011
- InterPro: IPR004843, IPR006186, IPR012391
- PANTHER: PTHR46422, PTHR46422:SF4
- SUPFAM: SSF117281, SSF56300
- PROSITE: PS00125
- Gene3D: 2.120.10.80, 3.60.21.10
- OrthoDB: Q10G19
- SWISS-MODEL: Q10G19
- Conserved Domain Database: cd07419
Sequences
cDNA Sequence
- >LOC_Os03g44500.1
ATGGACGTGGACTCCCGCATGACGACGGAGTCGGACTCCGACTCCGACGCCGCCGCCACCGCCGCCGCCTCCGCCTCGGTTGCTGCGCAAGGAGGCTTAGCGAGCGAGACCTCGTCGTCGTCGTCGGCCTCGGCCCCGTCCACGCCAGGGACGCCCACGGTAGCTCCGGCTCCTGCGGCCGCGGGAGCCACGGGGCCCAGGCCGGCGCCGGGGTACACGGCGGTCAGCGCTGTGATCGAGAAGAAGGAGGACGGGCCGGGCTGCCGCTGCGGGCACACGCTCACGGCGGTGCCGGCCGTCGGGGAGGAAGGCACGCCGGGGTACATCGGCCCACGCCTCATCCTCTTCGGGGGCGCCACGGCGCTCGAGGGCAACTCCGCCACGCCACCCTCCTCGGCCGGCAGTGCTGGGATCCGTCTTGCCGGTGCCACAGCAGATGTCCACTGTTATGATGTGTTATCAAATAAGTGGAGCAGGCTTACTCCACAAGGTGAGCCTCCTTCACCAAGAGCCGCACATGTAGCAACTGCAGTTGGAACCATGGTTGTCATCCAGGGTGGCATTGGCCCTGCTGGTTTATCTGCCGAGGATCTTCATGTTCTAGACCTTACACAACAACGACCGCGATGGCACAGAGTGGTGGTTCAAGGACCTGGTCCAGGTCCACGATATGGGCATGTCATGGCCTTGGTTGGACAGAGGTTTTTGTTGACAATTGGTGGAAATGATGGGAAACGGCCGCTGGCAGATGTATGGGCTCTAGATACTGCAGCTAAGCCATACGAATGGAGGAAACTTGAACCAGAAGGTGAAGGACCGCCACCATGCATGTATGCCACTGCCAGTGCACGCTCTGATGGTCTTCTTTTACTTTGTGGTGGGAGGGATGCCAACAGTGTGCCGCTGGCAAGTGCATATGGTCTTGCAAAACACAGAGATGGGCGATGGGAGTGGGCAATCGCCCCTGGTGTTTCTCCATCACCCAGATATCAACATGCAGCTGTTTTTGTGAATGCACGTCTCCATGTATCAGGAGGAGCTCTTGGAGGTGGTCGGATGGTAGAAGACTCCTCAAGTGTTGCAGTGCTAGACACAGCTGCTGGAGTCTGGTGCGACACAAAGTCAGTTGTCACAACTCCCAGGATAGGAAGATATAGTGCAGATGCAGCAGGGGGTGATGCTGCTGTTGAACTTACACGGCGGTGCAGGCATGCAGCTGCTGCTGTTGGTGATCAAATATTCATTTATGGAGGTCTACGAGGAGGGGTACTGCTAGATGATCTTCTTGTAGCTGAAGATCTTGCTGCTGCTGAAACGACAACCGCTGCTAATCATGCAGCGGCAAGTGCAGCAGCCACTAATGTACAAAGCGGAAGAACACCCGGAAGATATGCTTATAATGATGAGCGAGCGAGACAAACAGCTCCAGAATCAGCTCAGGATGGATCTGTAGTTCTTGGAACTCCAGTTGCCCCTCCTGTCAACGGTGACATGTACACTGATATCAGCCCTGAGAATGCTGTGCTTCAGGGACAGAGGAGATTAAGCAAAGGTGTCGATTACTTAGTTGAAGCATCAGCAGCAGAGGCAGAGGCTATTAGTGCAACTTTAGCTGCAGTGAAGGCTAGGCAGGTTAACGGTGAGATGGAGCAATTGCCTGACAAGGAGCAATCTCCAGATTCCGCATCGACCAGCAAGCATTCAAGCCTCATCAAACCAGACAGTATTCTCTCTAACAACATGACGCCTCCACCTGGGGTTCGGTTGCATCATAGAGCTGTTGTAGTGGCTGCAGAAACTGGAGGTGCCTTAGGTGGCATGGTCAGGCAGCTGTCAATTGACCAATTTGAAAATGAGGGAAGAAGAGTCAGCTATGGCACCCCTGAGAATGCAACTGCTGCAAGAAAGTTGCTAGATCGACAGATGTCCATTAATAGTGTTCCTAAAAAGGTGATTGCATCTCTATTGAAACCTCGTGGTTGGAAGCCCCCTGTGCGAAGACAGTTCTTCTTGGACTGCAATGAGATTGCAGATCTATGTGATAGTGCTGAGAGAATATTTTCAAGTGAACCAAGTGTTCTGCAACTTAAAGCTCCTGTTAAGATATTTGGTGATTTACATGGTCAATTTGGTGACCTCATGCGATTGTTTGATGAGTATGGTGCTCCTTCAACAGCAGGAGACATTGCTTACATTGATTATCTCTTCTTGGGTGATTATGTGGATCGTGGCCAGCATAGCTTAGAAACAATGACTCTTCTTCTTGCATTGAAGGTTGAGTATCCTCAGAATGTACATTTGATTCGTGGAAATCATGAAGCTGCAGATATTAATGCTTTGTTTGGCTTCCGAATAGAGTGCATAGAGCGAATGGGTGAGAGAGATGGTATTTGGACATGGCACCGAATGAATAGATTATTTAACTGGCTTCCTTTGGCTGCACTTATCGAAAAGAAAATTATATGTATGCATGGTGGAATTGGTCGGTCAATCAACCATGTTGAGCAAATTGAGAATCTTCAGAGACCAATTACCATGGAAGCAGGCTCTGTTGTCCTTATGGATCTTCTATGGTCTGATCCAACCGAGAATGACAGTGTTGAAGGATTGAGACCAAATGCTCGAGGCCCTGGCCTTGTTACGTTTGGGCCTGATCGTGTTATGGAGTTTTGCAACAATAATGATCTTCAACTAATTGTGCGAGCGCATGAGTGTGTGATGGATGGCTTTGAGCGCTTTGCTCAAGGTCACCTGATCACTCTTTTCTCTGCAACAAACTATTGTGGTACTGCAAATAATGCCGGTGCTATCTTAGTTTTGGGCAGAGATCTTGTGGTCGTTCCAAAACTGATTCATCCTTTGCCCCCGGCAATCACATCACCTGAGACCTCTCCGGAGCATCATATTGAGGACACATGGATGCAGGAGCTGAATGCAAACAGACCACCGACTCCAACAAGGGGCCGCCCCCAAGTAGCAGCTAACGATCGAGGTTCTCTTGCCTGGATATAGTAGAGTGGCCAGATATTGATTAATCTGATCTATATATGAAGTCTCGATCGGCGCGATCTTGCTATTTTTATTTTTTTCTGCACAGAGTAAAGTGATTTGTGTTTGCGAGACAGTGGCCCACAGCCATGCCAAAAGGTAAACATTTAAAGTGAGCAAGGTAGTAGATAAGATGGATGAACAGATGATCATCCTGAACAGCGCCGTCCAGTCCAAGCTGTTTCCCGAACACGACAGTAAAACAATTCAATTCACAGAGATTATCTGGAGATCGACGAGGCTTCACTTCACCTGTATATACTCGGCTGCTGGTGGATAGGCAGTTGTATGTGGTTTTTGCATCCAATTGGAATGGCAAAAAGGAATAGTGTTATTGTACTAGCTATTCTTTCCTCTCTTTTTTTTTTTCCTTTCTTTTTGGGATCTTGAGTTCTGATTTTGCAAGGTGCTTCTGAACTGCTGGAGAGAGACCGATGGCTGGTGTTCGTGGTCCAGTCGTGTATAATAGCCTTCCCTCCTGCTACTTTCGTCGCAGCATACCCCTTGTAATTTCAGTCTGATGATGCTGATGTACAATTTTGTGTTCCAAGTTTTGGGTGGCGAATGGAGTTTGATTTGGTTTACTAGAAGGAGAGAGATGTGGTGTTACTCATGGTGGTTGTACAAAAATTCAATTATATCTTGTTTGGCTCCGAATTGAATTCGATTCATTCAATTGGATTTTGGGCTATATG
CDS Sequence
- >LOC_Os03g44500.1
ATGGACGTGGACTCCCGCATGACGACGGAGTCGGACTCCGACTCCGACGCCGCCGCCACCGCCGCCGCCTCCGCCTCGGTTGCTGCGCAAGGAGGCTTAGCGAGCGAGACCTCGTCGTCGTCGTCGGCCTCGGCCCCGTCCACGCCAGGGACGCCCACGGTAGCTCCGGCTCCTGCGGCCGCGGGAGCCACGGGGCCCAGGCCGGCGCCGGGGTACACGGCGGTCAGCGCTGTGATCGAGAAGAAGGAGGACGGGCCGGGCTGCCGCTGCGGGCACACGCTCACGGCGGTGCCGGCCGTCGGGGAGGAAGGCACGCCGGGGTACATCGGCCCACGCCTCATCCTCTTCGGGGGCGCCACGGCGCTCGAGGGCAACTCCGCCACGCCACCCTCCTCGGCCGGCAGTGCTGGGATCCGTCTTGCCGGTGCCACAGCAGATGTCCACTGTTATGATGTGTTATCAAATAAGTGGAGCAGGCTTACTCCACAAGGTGAGCCTCCTTCACCAAGAGCCGCACATGTAGCAACTGCAGTTGGAACCATGGTTGTCATCCAGGGTGGCATTGGCCCTGCTGGTTTATCTGCCGAGGATCTTCATGTTCTAGACCTTACACAACAACGACCGCGATGGCACAGAGTGGTGGTTCAAGGACCTGGTCCAGGTCCACGATATGGGCATGTCATGGCCTTGGTTGGACAGAGGTTTTTGTTGACAATTGGTGGAAATGATGGGAAACGGCCGCTGGCAGATGTATGGGCTCTAGATACTGCAGCTAAGCCATACGAATGGAGGAAACTTGAACCAGAAGGTGAAGGACCGCCACCATGCATGTATGCCACTGCCAGTGCACGCTCTGATGGTCTTCTTTTACTTTGTGGTGGGAGGGATGCCAACAGTGTGCCGCTGGCAAGTGCATATGGTCTTGCAAAACACAGAGATGGGCGATGGGAGTGGGCAATCGCCCCTGGTGTTTCTCCATCACCCAGATATCAACATGCAGCTGTTTTTGTGAATGCACGTCTCCATGTATCAGGAGGAGCTCTTGGAGGTGGTCGGATGGTAGAAGACTCCTCAAGTGTTGCAGTGCTAGACACAGCTGCTGGAGTCTGGTGCGACACAAAGTCAGTTGTCACAACTCCCAGGATAGGAAGATATAGTGCAGATGCAGCAGGGGGTGATGCTGCTGTTGAACTTACACGGCGGTGCAGGCATGCAGCTGCTGCTGTTGGTGATCAAATATTCATTTATGGAGGTCTACGAGGAGGGGTACTGCTAGATGATCTTCTTGTAGCTGAAGATCTTGCTGCTGCTGAAACGACAACCGCTGCTAATCATGCAGCGGCAAGTGCAGCAGCCACTAATGTACAAAGCGGAAGAACACCCGGAAGATATGCTTATAATGATGAGCGAGCGAGACAAACAGCTCCAGAATCAGCTCAGGATGGATCTGTAGTTCTTGGAACTCCAGTTGCCCCTCCTGTCAACGGTGACATGTACACTGATATCAGCCCTGAGAATGCTGTGCTTCAGGGACAGAGGAGATTAAGCAAAGGTGTCGATTACTTAGTTGAAGCATCAGCAGCAGAGGCAGAGGCTATTAGTGCAACTTTAGCTGCAGTGAAGGCTAGGCAGGTTAACGGTGAGATGGAGCAATTGCCTGACAAGGAGCAATCTCCAGATTCCGCATCGACCAGCAAGCATTCAAGCCTCATCAAACCAGACAGTATTCTCTCTAACAACATGACGCCTCCACCTGGGGTTCGGTTGCATCATAGAGCTGTTGTAGTGGCTGCAGAAACTGGAGGTGCCTTAGGTGGCATGGTCAGGCAGCTGTCAATTGACCAATTTGAAAATGAGGGAAGAAGAGTCAGCTATGGCACCCCTGAGAATGCAACTGCTGCAAGAAAGTTGCTAGATCGACAGATGTCCATTAATAGTGTTCCTAAAAAGGTGATTGCATCTCTATTGAAACCTCGTGGTTGGAAGCCCCCTGTGCGAAGACAGTTCTTCTTGGACTGCAATGAGATTGCAGATCTATGTGATAGTGCTGAGAGAATATTTTCAAGTGAACCAAGTGTTCTGCAACTTAAAGCTCCTGTTAAGATATTTGGTGATTTACATGGTCAATTTGGTGACCTCATGCGATTGTTTGATGAGTATGGTGCTCCTTCAACAGCAGGAGACATTGCTTACATTGATTATCTCTTCTTGGGTGATTATGTGGATCGTGGCCAGCATAGCTTAGAAACAATGACTCTTCTTCTTGCATTGAAGGTTGAGTATCCTCAGAATGTACATTTGATTCGTGGAAATCATGAAGCTGCAGATATTAATGCTTTGTTTGGCTTCCGAATAGAGTGCATAGAGCGAATGGGTGAGAGAGATGGTATTTGGACATGGCACCGAATGAATAGATTATTTAACTGGCTTCCTTTGGCTGCACTTATCGAAAAGAAAATTATATGTATGCATGGTGGAATTGGTCGGTCAATCAACCATGTTGAGCAAATTGAGAATCTTCAGAGACCAATTACCATGGAAGCAGGCTCTGTTGTCCTTATGGATCTTCTATGGTCTGATCCAACCGAGAATGACAGTGTTGAAGGATTGAGACCAAATGCTCGAGGCCCTGGCCTTGTTACGTTTGGGCCTGATCGTGTTATGGAGTTTTGCAACAATAATGATCTTCAACTAATTGTGCGAGCGCATGAGTGTGTGATGGATGGCTTTGAGCGCTTTGCTCAAGGTCACCTGATCACTCTTTTCTCTGCAACAAACTATTGTGGTACTGCAAATAATGCCGGTGCTATCTTAGTTTTGGGCAGAGATCTTGTGGTCGTTCCAAAACTGATTCATCCTTTGCCCCCGGCAATCACATCACCTGAGACCTCTCCGGAGCATCATATTGAGGACACATGGATGCAGGAGCTGAATGCAAACAGACCACCGACTCCAACAAGGGGCCGCCCCCAAGTAGCAGCTAACGATCGAGGTTCTCTTGCCTGGATATAG
Protein Sequence
- >LOC_Os03g44500.1
MDVDSRMTTESDSDSDAAATAAASASVAAQGGLASETSSSSSASAPSTPGTPTVAPAPAAAGATGPRPAPGYTAVSAVIEKKEDGPGCRCGHTLTAVPAVGEEGTPGYIGPRLILFGGATALEGNSATPPSSAGSAGIRLAGATADVHCYDVLSNKWSRLTPQGEPPSPRAAHVATAVGTMVVIQGGIGPAGLSAEDLHVLDLTQQRPRWHRVVVQGPGPGPRYGHVMALVGQRFLLTIGGNDGKRPLADVWALDTAAKPYEWRKLEPEGEGPPPCMYATASARSDGLLLLCGGRDANSVPLASAYGLAKHRDGRWEWAIAPGVSPSPRYQHAAVFVNARLHVSGGALGGGRMVEDSSSVAVLDTAAGVWCDTKSVVTTPRIGRYSADAAGGDAAVELTRRCRHAAAAVGDQIFIYGGLRGGVLLDDLLVAEDLAAAETTTAANHAAASAAATNVQSGRTPGRYAYNDERARQTAPESAQDGSVVLGTPVAPPVNGDMYTDISPENAVLQGQRRLSKGVDYLVEASAAEAEAISATLAAVKARQVNGEMEQLPDKEQSPDSASTSKHSSLIKPDSILSNNMTPPPGVRLHHRAVVVAAETGGALGGMVRQLSIDQFENEGRRVSYGTPENATAARKLLDRQMSINSVPKKVIASLLKPRGWKPPVRRQFFLDCNEIADLCDSAERIFSSEPSVLQLKAPVKIFGDLHGQFGDLMRLFDEYGAPSTAGDIAYIDYLFLGDYVDRGQHSLETMTLLLALKVEYPQNVHLIRGNHEAADINALFGFRIECIERMGERDGIWTWHRMNRLFNWLPLAALIEKKIICMHGGIGRSINHVEQIENLQRPITMEAGSVVLMDLLWSDPTENDSVEGLRPNARGPGLVTFGPDRVMEFCNNNDLQLIVRAHECVMDGFERFAQGHLITLFSATNYCGTANNAGAILVLGRDLVVVPKLIHPLPPAITSPETSPEHHIEDTWMQELNANRPPTPTRGRPQVAANDRGSLAWI*