Os01g0848400

Please input one-sentence summary here.

Molecular cloning of major quantitative trait loci (QTLs) responsible for the reduction of rice grain shattering, a hallmark of cereal domestication, provided opportunities for in-depth investigation of domestication processes. Here, we studied nucleotide variation at the shattering loci, sh4 and qSH1, for cultivated rice, Oryza sativa ssp. indica and Oryza sativa ssp. japonica, and the wild progenitors, Oryza nivara andOryza rufipogon. The nonshattering sh4 allele was fixed in all rice cultivars, with levels of sequence polymorphism significantly reduced in both indica and japonica cultivars relative to the wild progenitors. The sh4 phylogeny together with the neutrality tests and coalescent simulations suggested that sh4 had a single origin and was fixed by artificial selection during the domestication of rice. Selection on qSH1 was not detected in indica and remained unclear in japonica. Selection on sh4 could be strong enough to have driven its fixation in a population of cultivated rice within a period of c. 100 yr. The slow fixation of the nonshattering phenotype observed at the archeological sites might be a result of relatively weak selection on mutations other than sh4 in early rice cultivation. The fixation of sh4 could have been achieved later through strong selection for the optimal phenotype.

Loss of seed shattering was a key event in the domestication of major cereals. We revealed that the qSH1 gene, a major quantitative trait locus of seed shattering in rice, encodes a BEL1-type homeobox gene and demonstrated that a single-nucleotide polymorphism (SNP) in the 5' regulatory region of the qSH1 gene caused loss of seed shattering owing to the absence of abscission layer formation. Haplotype analysis and association analysis in various rice collections revealed that the SNP was highly associated with shattering among japonica subspecies of rice, implying that it was a target of artificial selection during rice domestication.

Lin-Bin Zhang; Qihui Zhu; Zhi-Qiang Wu; Jeffrey Ross-Ibarra; Brandon S. Gaut; Song Ge; Tao Sang

Selection on grain shattering genes and rates of rice domestication An SNP Caused Loss of Seed Shattering During Rice Domestication

Structured Information

Gene Name	Os01g0848400
Description	Acid phosphatase/vanadium-dependent haloperoxidase family protein
Version	NM_001051339.1 GI:115441048 GeneID:4324855
Length	4496 bp
Definition	Oryza sativa Japonica Group Os01g0848400, complete gene.
Source	Oryza sativa Japonica Group ORGANISM Oryza sativa Japonica Group Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP clade; Ehrhartoideae; Oryzeae; Oryza.
Chromosome	Chromosome 1
Location	Chromosome 1:38201303..38205798
Sequence Coding Region	38201457..38202047,38202155..38202215,38203339..38203718,38204543..38205349
Expression	GEO Profiles:Os01g0848400
Genome Context	<gbrowseImage1> name=NC_008394:38201303..38205798 source=RiceChromosome01 preset=GeneLocation </gbrowseImage1>
Gene Structure	<gbrowseImage2> name=NC_008394:38201303..38205798 source=RiceChromosome01 preset=GeneLocation </gbrowseImage2>
Coding Sequence	<cdnaseq>atgtcgtccgccgctgggggcggcgggtacggcggcggccagggtggaggcgcggagcaccaccaccaccaccacgggcacgccggtcacctcctgctccaccaccatccgcagcacgtggccggcgcggccgttgcggcagcggccgcggcggcgggcgggcagatgtaccacgtgccccagcacagccggcgcgagaagctccggttcccgccggacgccggggactcgccaccgcctcatggtcatggtcatggtcatgccccgcagcagcagcagcagcacgggtcgtggcctccgcccccggcgttctactcgtacgcgtcctcgtcgtcgtcgtactccccgcacagccctactctagcgcaggcgcagctggtggcgcacgggctggcgccgccgctcccgcagatcccgacgcagaacttctcgctgtcgctctcctccgcgtcgtcgaatcctccaccaccgcaggcgcagccgaggaggcagctcggcggcctcgcgcaggccacggggccgttcggtcccttcaccggctacgccgccgtgctcggccggtcccgtttcctcggcccggcagagaagctgttcgaggagatctgcgacgtcggcggcgctgcttcgcacgtcgaccgcaccatctccgacgagggcctgctcgacgcggatccgatggacggcgtcgatcatgacgtcgttgatcacgacctcggcggcgctgaccgcgcagcggccgacgctggccccatctcgggggccgagcagcagtggaagaagacgaagctcatctccatgatggaagaggtttgcaagaggtaccggcagtactaccagcaggttcaggctgtgatggcctcgttcgagaccgtcgccgggttcagcaacgccgcgccgttcgcggcattggcgctgagggcgatggcgaagcacttcaagtgcttgaagagcatgattctgaaccagctgcgcaacacgagcaacaaggtcgctgtgaaggacgggctaaacaaggagatcgccgtgttcgggctcgccgggggtagcagcggcggcgccggcctccagcgagcgaacagcgcgagcgcgttcggccagccgcacaatatttggcgcccacagagggggctccccgagcgcgctgtgtccgttttacgcgcgtggctgttcgaacacttcctgcacccgtatcctaccgatggtgataagcaaatgctagcaaaacaaacaggcttgacacgcaaccaggtatcgaactggtttatcaacgcaagggttaggttgtggaagccaatggtggaagaaattcacaacctagagatgaggcaaatgcacaagcactcggtggttgacaagggccagcatagcgtgcatcatcaggcccagcattcttcgcagtgcagcgggaatccctccgttccttcggactcccatcctggacagagcagcagcataactcggaaccacaacaccgctgcctcccagggcttcccggatgagctctcccagatgtcccagtccatccagggacaggtgagcttcgcatacaacgggctgacctcgcagcacaacattgcatcaccacatcatcagcaccagcaggtcggcggtgttggtatcggaggcggcaatggcggtgtctccctcacccttggtcttcaccagaacaacagggtctgcatcgccgagcctctcccggctgctctcccggccaacctagctcaccgtttcggactggaggaagtcagtgacgcctatgtgatgagctcatttggaggtcaggaccggcatttcgggaaggagattggtggtcacttgctgcatgattttgtcgggtga</cdnaseq>
Protein Sequence	<aaseq>MSSAAGGGGYGGGQGGGAEHHHHHHGHAGHLLLHHHPQHVAGAA VAAAAAAAGGQMYHVPQHSRREKLRFPPDAGDSPPPHGHGHGHAPQQQQQHGSWPPPP AFYSYASSSSSYSPHSPTLAQAQLVAHGLAPPLPQIPTQNFSLSLSSASSNPPPPQAQ PRRQLGGLAQATGPFGPFTGYAAVLGRSRFLGPAEKLFEEICDVGGAASHVDRTISDE GLLDADPMDGVDHDVVDHDLGGADRAAADAGPISGAEQQWKKTKLISMMEEVCKRYRQ YYQQVQAVMASFETVAGFSNAAPFAALALRAMAKHFKCLKSMILNQLRNTSNKVAVKD GLNKEIAVFGLAGGSSGGAGLQRANSASAFGQPHNIWRPQRGLPERAVSVLRAWLFEH FLHPYPTDGDKQMLAKQTGLTRNQVSNWFINARVRLWKPMVEEIHNLEMRQMHKHSVV DKGQHSVHHQAQHSSQCSGNPSVPSDSHPGQSSSITRNHNTAASQGFPDELSQMSQSI QGQVSFAYNGLTSQHNIASPHHQHQQVGGVGIGGGNGGVSLTLGLHQNNRVCIAEPLP AALPANLAHRFGLEEVSDAYVMSSFGGQDRHFGKEIGGHLLHDFVG</aaseq>
Gene Sequence	<dnaseqindica>3752..4342#3584..3644#2081..2460#450..1256#cggcctttctgctttcgctttcacagtttcacggcttaccatttccttcccatctctccctcccgccacccccctctttctccccctccgtgtctcgcctttgcagaaagaaaggcgccacgaacccagcaacaacacccagcacaaaggcgaaacggggaaaaagaggaggaaaacaacaagaggacgcgaggggtcggggtgggagagggaggctacactacagcagcagcagaagcagagcgggagagtgatgagggagtgagaccaggccagccaagccaggcccgggcgctcggaaagtgcggagccgtttcccctctatctccactctctccagggccaggtgctcactgcgctgcgcctcttcgcacgcaccacccgtactacgtgcccacccgcgcgcgcgccgaggagaagagacccacgaccgtacgtgcgtgcgcgccatgtcgtccgccgctgggggcggcgggtacggcggcggccagggtggaggcgcggagcaccaccaccaccaccacgggcacgccggtcacctcctgctccaccaccatccgcagcacgtggccggcgcggccgttgcggcagcggccgcggcggcgggcgggcagatgtaccacgtgccccagcacagccggcgcgagaagctccggttcccgccggacgccggggactcgccaccgcctcatggtcatggtcatggtcatgccccgcagcagcagcagcagcacgggtcgtggcctccgcccccggcgttctactcgtacgcgtcctcgtcgtcgtcgtactccccgcacagccctactctagcgcaggcgcagctggtggcgcacgggctggcgccgccgctcccgcagatcccgacgcagaacttctcgctgtcgctctcctccgcgtcgtcgaatcctccaccaccgcaggcgcagccgaggaggcagctcggcggcctcgcgcaggccacggggccgttcggtcccttcaccggctacgccgccgtgctcggccggtcccgtttcctcggcccggcagagaagctgttcgaggagatctgcgacgtcggcggcgctgcttcgcacgtcgaccgcaccatctccgacgagggcctgctcgacgcggatccgatggacggcgtcgatcatgacgtcgttgatcacgacctcggcggcgctgaccgcgcagcggccgacgctggccccatctcgggggccgagcagcagtggaagaagacgaagctcatctccatgatggaagaggtgagtgagctccgctagccgcctcaattcctccttccaggtttcttgtggcgaccatctttttcaccttgtttcggcgttacaattatcgctactcctgggtggagaagaatcttgcacatagtggtcatgtcaccgatgcagttgcggattgcttttatttactgtggttgcatgtgcttttgatttgatgatgatttcctttgctgctgatacatcttttgatttgttctctctcttctttttcctcgagtggtttgagcttgtacagttctgcactgttcatgatgaatagtagtgttcctccgcgtcttatcaccaaagattgtattttgatcggctgtttagcactactgtgagtgcttgaaaagatagtcctccacatgaaattagaactaaccgtcctttcaaagtcttgagacatgacccatgggcgatgccagatgccattaattctctcttgttggtgtcctctggtgagaatagtggcgctgctaaaagcttcgagctttgaaatgcgctctcctctacgatgtcggagcatggcaattaggagtatactacatgagcatctacgtaggagtacaatgtagaaagcttctatttttggaaccctctgtaaggcaattttgtttgcctgtgttcttcaataacatctctctcccataattgggagctacgcttgctttgttcgtgtcatatccacatgaaaacaaaagcacactgcttccttttcctaacatggatatctttttatctaatcattctttgttggtagattatctctcatcgaattctaacccaacagcaatatctttttttaggtttgcaagaggtaccggcagtactaccagcaggttcaggctgtgatggcctcgttcgagaccgtcgccgggttcagcaacgccgcgccgttcgcggcattggcgctgagggcgatggcgaagcacttcaagtgcttgaagagcatgattctgaaccagctgcgcaacacgagcaacaaggtcgctgtgaaggacgggctaaacaaggagatcgccgtgttcgggctcgccgggggtagcagcggcggcgccggcctccagcgagcgaacagcgcgagcgcgttcggccagccgcacaatatttggcgcccacagagggggctccccgagcgcgctgtgtccgttttacgcgcgtggctgttcgaacacttcctgcacccgtaagccctttgatcttcttattgctttatggttaactctgggttcattagctgcacgcattccaagacaatgatgatgatgctacagttgcttgctttagatgaggataacagtagtccctaagcatttgtggtgagtgtggttgttcctttttgatatgatcagtagtacgtgacactggaaccgtggggttgatccgttgatggtttggtgatagcaagcgaccctgcctgtctgatagaaggctatggcctcatgcaggcatggcttccaatccatcattaacataacttttaaacctgtacctaactgtgtgttgagctgtactactagagatcatactttcgacttggtgatctaaatagtggcattcctgctgcttgtttgatgcattcttaatcacgtattaacttcctggatttgttgtttctggctgtaatgtatgaatgtggtggcccggcttctcataagtagagtggcttttagaacacgttaatgctggaattaacttgccagatgggcattacttcgaactaaatcttaaaagtacataccttaggctataataagcatcatcataatgtagtttgtttggcatattctttttagtttttgtagtatgatcattttgcattatatatatgatctaaaggctgtagctaagccctactggtggttacatcaagttgattgacatgtgctcgagatattcagtttgagataattagtacagtagtttagtgctagccattttcatccagtaaggggtttgtctgtctgtttattactttaaaaaaaggatcagtcatcatctttaaaaaaagtcactgaaatccattatttgtcagatgttggtcctagtgttattagttcccgtattgatcaaatcctttgtaaggttcgacttggaagatgtgtttgcctacatctttgcttggatattcgccatgtaaaatatttgttgtgatcctgtaaaccatcgttaagcatgcacatcacaagtgtcttttgtaatagcggaaatttcttgattatttgattttgcgctatatctggtactttgttcttttagaaaacactataattttgcatcagtgacattttcagattccaatcgtgcaggtatcctaccgatggtgataagcaaatgctagcaaaacaaacaggcttgacacgcaaccaggtaaatagaaatgcttctaggtgtgttcaagaatagattgcacagtatatcaggctagattgttttgttttcaggacattttgattgaatttgtgatgctggtgcaggtatcgaactggtttatcaacgcaagggttaggttgtggaagccaatggtggaagaaattcacaacctagagatgaggcaaatgcacaagcactcggtggttgacaagggccagcatagcgtgcatcatcaggcccagcattcttcgcagtgcagcgggaatccctccgttccttcggactcccatcctggacagagcagcagcataactcggaaccacaacaccgctgcctcccagggcttcccggatgagctctcccagatgtcccagtccatccagggacaggtgagcttcgcatacaacgggctgacctcgcagcacaacattgcatcaccacatcatcagcaccagcaggtcggcggtgttggtatcggaggcggcaatggcggtgtctccctcacccttggtcttcaccagaacaacagggtctgcatcgccgagcctctcccggctgctctcccggccaacctagctcaccgtttcggactggaggaagtcagtgacgcctatgtgatgagctcatttggaggtcaggaccggcatttcgggaaggagattggtggtcacttgctgcatgattttgtcgggtgattgtggctgctgcctcaggttgctggtgatgcacttgtaatgtactgctagtatgatgttaggatggtatataagtcaatcacttggcgacatggcttgatgatcagtctgaatcaatttgttcggagggtgaaaaaacattgatcttcccttc</dnaseqindica>
External Link(s)	NCBI Gene:Os01g0848400, RefSeq:Os01g0848400