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Score: 8.00 |
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| Title: Different patterns of genealogical relationships found in the two major QTLs causing reduction of seed shattering during rice domestication .
| | Author: Onishi K Takagi K Kontani M Tanaka T Sano Y | | Journal: Genome Citation: V : 50 P : 757-66 Year: 2007 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub17893735 Accession (PMID): 17893735 | | Abstract: The three quantitative trait loci ( qSH1 , qSH3 , and qSH4 ) causing reduction of seed shattering were investigated to examine their relative importance during rice domestication .
The qSH1 and qSH4 loci showed a distinct effect on the reduction of shattering , compared with the qSH3 locus .
Fine mapping and sequence analysis strongly suggested that the qSH1 and qSH4 loci are the same as the recently reported genes .
A non-shattering allele at qSH1 drastically changed the shattering phenotype to a non-shattering phenotype even in the presence of shattering alleles at the qSH3 and qSH4 loci , showing that qSH1 is genetically epistatic to the other loci .
The level of the reduction in sequence diversity was compared between the qSH1 and qSH4 regions .
The sequence diversity was severely reduced in the qSH1 region of Oryza sativa subsp . japonica compared with that of O sativa subsp . indica , despite that the level of diversity was similarly reduced at the qSH4 region in the 2 subspecies .
Phylogenetic reconstruction based on the combined sequences of the flanking sites showed different patterns in the 2 subspecies .
The 2 subspecies formed a single clade with respect to qSH4 , whereas they were separated into different lineages with respect to qSH1 , suggesting that these loci had different histories during rice domestication .
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[ Sen. 4, subscore: 2.00 ]: A non-shattering allele at qSH1 drastically changed the shattering phenotype to a non-shattering phenotype even in the presence of shattering alleles at the qSH3 and qSH4 loci , showing that qSH1 is genetically epistatic to the other loci .
[ Sen. 1, subscore: 1.00 ]: The three quantitative trait loci ( qSH1 , qSH3 , and qSH4 ) causing reduction of seed shattering were investigated to examine their relative importance during rice domestication .
[ Sen. 2, subscore: 1.00 ]: The qSH1 and qSH4 loci showed a distinct effect on the reduction of shattering , compared with the qSH3 locus .
[ Sen. 3, subscore: 1.00 ]: Fine mapping and sequence analysis strongly suggested that the qSH1 and qSH4 loci are the same as the recently reported genes .
[ Sen. 5, subscore: 1.00 ]: The level of the reduction in sequence diversity was compared between the qSH1 and qSH4 regions .
[ Sen. 6, subscore: 1.00 ]: The sequence diversity was severely reduced in the qSH1 region of Oryza sativa subsp . japonica compared with that of O sativa subsp . indica , despite that the level of diversity was similarly reduced at the qSH4 region in the 2 subspecies .
[ Sen. 8, subscore: 1.00 ]: The 2 subspecies formed a single clade with respect to qSH4 , whereas they were separated into different lineages with respect to qSH1 , suggesting that these loci had different histories during rice domestication .
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Score: 4.00 |
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| Title: Allelic interaction at seed-shattering loci in the genetic backgrounds of wild and cultivated rice species .
| | Author: Ishikawa R Thanh PT Nimura N Htun TM Yamasaki M Ishii T | | Journal: Genes Genet Syst Citation: V : 85 P : 265-71 Year: 2010 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub21178306 Accession (PMID): 21178306 | | Abstract: It is known that the common cultivated rice ( Oryza sativa ) was domesticated from Asian wild rice , O rufipogon .
Among the morphological differences between them , loss of seed shattering is one of the striking characters specific for the cultivated forms .
In order to understand the genetic control on shattering habit , QTL analysis was carried out using BC ( 2 ) F ( 1 ) backcross population between O sativa cv .
Nipponbare ( a recurrent parent ) and O rufipogon acc .
W630 ( a donor parent ) .
As a result , two strong QTLs were detected on chromosomes 1 and 4 , and they were found to be identical to the two major seed-shattering loci , qSH1 and sh4 , respectively .
The allelic interaction at these loci was further examined using two sets of backcross populations having reciprocal genetic backgrounds , cultivated and wild .
In the genetic background of cultivated rice , the wild qSH1 allele has stronger effect on seed shattering than that of sh4 .
In addition , the wild alleles at both qSH1 and sh4 loci showed semi-dominant effects .
On the other hand , in the genetic background of wild rice , non-shattering effects of Nipponbare alleles at both loci were examined to inspect rice domestication from a viewpoint of seed shattering .
It was serendipitous that the backcross plants individually having Nipponbare homozygous alleles at either shattering locus ( qSH1 or sh4 ) shed all the seeds .
This fact strongly indicates that the non-shattering behavior was not obtained by a single mutation in the genetic background of wild rice .
Probably , some other minor genes are still associated with the formation or activation of abscission layer , which enhance the seed shattering .
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[ Sen. 6, subscore: 1.00 ]: As a result , two strong QTLs were detected on chromosomes 1 and 4 , and they were found to be identical to the two major seed-shattering loci , qSH1 and sh4 , respectively .
[ Sen. 8, subscore: 1.00 ]: In the genetic background of cultivated rice , the wild qSH1 allele has stronger effect on seed shattering than that of sh4 .
[ Sen. 9, subscore: 1.00 ]: In addition , the wild alleles at both qSH1 and sh4 loci showed semi-dominant effects .
[ Sen. 11, subscore: 1.00 ]: It was serendipitous that the backcross plants individually having Nipponbare homozygous alleles at either shattering locus ( qSH1 or sh4 ) shed all the seeds .
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Score: 3.00 |
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| Title: Identification of QTLs with main , epistatic and QTL x environment interaction effects for salt tolerance in rice seedlings under different salinity conditions .
| | Author: Wang Z Cheng J Chen Z Huang J Bao Y Wang J Zhang H | | Journal: Theor Appl Genet Citation: V : 125 P : 807-15 Year: 2012 Type: In-Data-Review | | Literature: oryza Field: abstract Doc ID: pub22678666 Accession (PMID): 22678666 | | Abstract: Salt tolerance of rice ( Oryza sativa L ) at the seedling stage is one of the major determinants of its stable establishment in saline soil .
One population of recombinant inbred lines ( RILs , F ( 2 : 9 ) ) derived from a cross between the salt-tolerant variety Jiucaiqing and the salt-sensitive variety IR26 was used to determine the genetic mechanism of four salt tolerance indices , seedling height ( SH ) , dry shoot weight ( DSW ) , dry root weight ( DRW ) and Na/K ratios ( Na/K ) in roots after 10 days in three salt concentrations ( 0 . 0 , 0 . 5 and 0 . 7 % NaCl ) .
The main effect QTLs ( M-QTLs ) and epistatic QTLs ( E-QTLs ) were detected by QTL IciMapping program using single environment phenotypic values .
Eleven M-QTLs and 11 E-QTLs were identified for the salt tolerance indices .
There were six M-QTLs and two E-QTLs identified for SH , three M-QTLs and five E-QTLs identified for DSW , two M-QTLs and one E-QTL identified for DRW , and three E-QTLs identified for Na/K The phenotypic variation explained by each M-QTL and E-QTL ranged from 7 . 8 to 23 . 9 % and 13 . 3 to 73 . 7 % , respectively .
The QTL-by-environment interactions were detected by QTLNetwork program in the joint analyses of multi-environment phenotypic values .
Six M-QTLs and five E-QTLs were identified .
The phenotypic variation explained by each QTL and QTL x environment interaction ranged from 0 . 95 to 6 . 90 % and 0 . 02 to 0 . 50 % , respectively .
By comparing chromosomal positions of these M-QTLs with those previously identified , five M-QTLs qSH1 . 3 , qSH12 . 1 , qSH12 . 2 , qDSW12 . 1 and qDRW11 might represent novel salt tolerance genes .
Five selected RILs with high salt tolerance had six to eight positive alleles of the M-QTLs , indicating that pyramiding by marker-assisted selection ( MAS ) of M-QTLs can be applied in rice salt tolerance breeding programs .
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[ Sen. 9, subscore: 3.00 ]: By comparing chromosomal positions of these M-QTLs with those previously identified , five M-QTLs qSH1 . 3 , qSH12 . 1 , qSH12 . 2 , qDSW12 . 1 and qDRW11 might represent novel salt tolerance genes .
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Score: 2.00 |
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| Title: An SNP caused loss of seed shattering during rice domestication .
| | Author: Konishi S Izawa T Lin SY Ebana K Fukuta Y Sasaki T Yano M | | Journal: Science Citation: V : 312 ( 5778 ) P : 1392-6 Year: 2006 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub16614172 Accession (PMID): 16614172 | | Abstract: 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 . | Matching Sentences:
[ Sen. 2, subscore: 2.00 ]: 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 .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 2.00 |
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| Title: Selection on grain shattering genes and rates of rice domestication .
| | Author: Zhang LB Zhu Q Wu ZQ Ross-Ibarra J Gaut BS Ge S Sang T | | Journal: New Phytol Citation: V : 184 P : 708-20 Year: 2009 Type: In-Process | | Literature: oryza Field: abstract Doc ID: pub19674325 Accession (PMID): 19674325 | | Abstract: 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 .
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[ Sen. 2, subscore: 1.00 ]: 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 .
[ Sen. 5, subscore: 1.00 ]: Selection on qSH1 was not detected in indica and remained unclear in japonica .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 2.00 |
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| Title: Genetic control of seed shattering in rice by the APETALA2 transcription factor shattering abortion1 .
| | Author: Zhou Y Lu D Li C Luo J Zhu BF Zhu J Shangguan Y Wang Z Sang T Zhou B Han B | | Journal: Plant Cell Citation: V : 24 P : 1034-48 Year: 2012 Type: In-Process | | Literature: oryza Field: abstract Doc ID: pub22408071 Accession (PMID): 22408071 | | Abstract: Seed shattering is an important agricultural trait in crop domestication .
SH4 ( for grain shattering quantitative trait locus on chromosome 4 ) and qSH1 ( for quantitative trait locus of seed shattering on chromosome 1 ) genes have been identified as required for reduced seed shattering during rice ( Oryza sativa ) domestication .
However , the regulatory pathways of seed shattering in rice remain unknown .
Here , we identified a seed shattering abortion1 ( shat1 ) mutant in a wild rice introgression line .
The SHAT1 gene , which encodes an APETALA2 transcription factor , is required for seed shattering through specifying abscission zone ( AZ ) development in rice .
Genetic analyses revealed that the expression of SHAT1 in AZ was positively regulated by the trihelix transcription factor SH4 .
We also identified a frameshift mutant of SH4 that completely eliminated AZs and showed nonshattering .
Our results suggest a genetic model in which the persistent and concentrated expression of active SHAT1 and SH4 in the AZ during early spikelet developmental stages is required for conferring AZ identification . qSH1 functioned downstream of SHAT1 and SH4 , through maintaining SHAT1 and SH4 expression in AZ , thus promoting AZ differentiation .
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[ Sen. 2, subscore: 1.00 ]: SH4 ( for grain shattering quantitative trait locus on chromosome 4 ) and qSH1 ( for quantitative trait locus of seed shattering on chromosome 1 ) genes have been identified as required for reduced seed shattering during rice ( Oryza sativa ) domestication .
[ Sen. 8, subscore: 1.00 ]: Our results suggest a genetic model in which the persistent and concentrated expression of active SHAT1 and SH4 in the AZ during early spikelet developmental stages is required for conferring AZ identification . qSH1 functioned downstream of SHAT1 and SH4 , through maintaining SHAT1 and SH4 expression in AZ , thus promoting AZ differentiation .
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Score: 1.00 |
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| Title: The contribution of intersubspecific hybridization to the breeding of super-high-yielding japonica rice in northeast China .
| | Author: Sun J Liu D Wang JY Ma DR Tang L Gao H Xu ZJ Chen WF | | Journal: Theor Appl Genet Citation: V : P : Year: 2012 Type: Publisher | | Literature: oryza Field: abstract Doc ID: pub22660631 Accession (PMID): 22660631 | | Abstract: Hybridization between indica and japonica rice combined with utilization of ideal plant type has led to the development of high-yielding japonica rice in northern China .
However , the contribution at the genomic level of intersubspecific hybridization to the increased yield of northern Chinese japonica rice is uncertain .
In this study , we analyzed the genomic pedigree of descendants of hybridization between indica and japonica rice grown in northeastern China between 1963 and 2008 .
Simple sequence repeat markers indicated that since 1990 the genetic diversity among northern japonica cultivars was enriched .
Genome-wide analysis with subspecies-specific indel and intron length polymorphism markers showed indica-allele frequencies were significantly increased in cultivars bred after 1990 , and were significantly positively correlated with spikelet number per panicle and significantly negatively correlated with panicle number per plant .
Among eight genes controlling agronomic traits , GN1a and GS3 were partially fixed in the genome of northern japonica cultivars .
In contrast , Waxy and qSH1 were eliminated , whereas DEP1 and qSW5 were retained .
Indica germplasm is an important contributor to the increased yield of northern japonica rice .
Breeding for high yield and grain quality in combination is a complicated process and difficult to achieve when relying on only one or several functional genes , thus the selection expertise of the breeder remains critical | Matching Sentences:
[ Sen. 7, subscore: 1.00 ]: In contrast , Waxy and qSH1 were eliminated , whereas DEP1 and qSW5 were retained .
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