Genomic regions affecting seed shattering and seed dormancy in rice

Cai, Hongwei; Morishima, Hajime

doi:10.1007/s001220051360

Cited by 162 publications

(147 citation statements)

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“…Many dormancy QTLs have been identified from model plants and major cereal crops. For example, dormancy QTLs are distributed over all five chromosomes (chr) in Arabidopsis (Arabidopsis thaliana) ( Van der Schaar et al, 1997;Alonso-Blanco et al, 2003;Clerkx et al, 2004) and 11 of the 12 chr in cultivated (Oryza sativa) (Wan et al, 1997;Lin et al, 1998;Dong et al, 2002;Miura et al, 2002), wild (O. rufipogon) (Cai and Morishima, 2000;Thomson et al, 2003), and weedy (O. sativa) (Gu et al, 2004) rice. Dormancy QTLs in barley (Oberthur et al, 1995;Li et al, 2003;Prada et al, 2004), sorghum (Lijavetzky et al, 2000), and wheat (Anderson et al, 1993;Kato et al, 2001;Mares and Mrva, 2001;Groos et al, 2002;Osa et al, 2003;Kulwal et al, 2004) have been identified to seek gene resources to impart resistance to preharvest sprouting (PHS) and to manipulate germination programs in the malting process.…”

Section: Introductionmentioning

confidence: 99%

Isolation of three dormancy QTLs as Mendelian factors in rice

2005

Heredity

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Seed dormancy is a key adaptive trait under polygenic control in many plants. We introduced the chromosomal regions containing the dormancy QTLs qSD1, qSD7-1, and qSD12 from an accession of weedy rice into a nondormant genetic background to examine component genetic effects and their interactions with time of afterripening (DAR). A BC 4 F 2 plant, which was heterozygous for the three loci, was selected to develop the BC 4 F 3 population. Single point analysis detected only qSD7-1 and qSD12 (R 2 ¼ 38-72%) at 10, 30, and 50 DAR in the population. However, multiple linear regression analysis detected genetic effects of the three QTLs and their trigenic epistasis, an environmental effect of DAR (E), and interactions of E with qSD12 and with the qSD1 Â qSD7-1 and qSD7-1 Â qSD12 epistases. The linear model demonstrates that QTL main effects varied with DAR, and that some epistasis or epistasis-by-DAR interactions partially counteract the main effects. The three QTLs were isolated as single Mendelian factors from the BC 4 F 3 population and estimated for component genic effects based on the BC 4 F 4 populations. Isolation improved estimation of the qSD1 effect and confirmed the major effect of qSD12. The qSD1 and qSD12 loci displayed a gene-additive effect. The qSD7-1, which was further narrowed to a chromosomal region encompassing the red pericarp color gene Rc, displayed gene additive and dominant effects. Heredity (2006) 96, 93-99.

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Section: Introductionmentioning

confidence: 99%

Isolation of three dormancy QTLs as Mendelian factors in rice

2005

Heredity

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“…The sh2 and Sh4 loci are reported to be related to the formation of the abscission layer (Fukuta et al 1994;Oba et al 1995;Fukuta and Yagi 1998). In addition, QTL for shattering have been reported on chromosomes 1, 3, 4, 7, 8, and 11 (Xiong et al 1999;Cai and Morishima 2000;Bres-Patry et al 2001;Thomson et al 2003).…”

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confidence: 99%

Characterization and Mapping of a Shattering Mutant in Rice That Corresponds to a Block of Domestication Genes

et al. 2006

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Easy shattering reduces yield due to grain loss during harvest in cereals. Shattering is also a hindrance in breeding programs that use wild accessions because the shattering habit is often linked to desirable traits. We characterized a shattering mutant line of rice, Hsh, which was derived from a nonshattering japonica variety, Hwacheong, by N-methyl-N-nitrosourea (MNU) treatment. The breaking tensile strength (BTS) of the grain pedicel was measured using a digital force gauge to evaluate the degree of shattering of rice varieties at 5, 10, 15, 20, 25, 30, 35, and 40 days after heading (DAH). The BTS of Hwacheong did not decrease with increasing DAH, maintaining a level of 180-240 gf, while that of Hsh decreased greatly during 10-20 DAH and finally stabilized at 50 gf. Optical microscopy revealed that Hsh had a welldeveloped abscission layer similar to the wild rice Oryza nivara (accession IRGC105706), while Hwacheong did not produce an abscission layer, indicating that the shattering of Hsh was caused by differentiation of the abscission layer. On the basis of the BTS value and morphology of the abscission layer of F 1 plants and segregation data in F 2 populations, it was concluded that the easy shattering of Hsh was controlled by the single recessive gene sh-h. The gene sh-h was determined to be located on rice chromosome 7 by bulked segregant analysis. Using 14 SSR markers on rice chromosome 7, the gene sh-h was mapped between the flanking markers RM8262 and RM7161 at distances of 1.6 and 2.0 cM, respectively. An SSR marker Rc17 cosegregated with the gene sh-h. The locus sh-h for shattering was tightly linked to the Rc locus conferring red pericarp, as well as a QTL qSD s -7-1 for seed dormancy, implying that this region might represent a domestication block in the evolutionary pathway of rice.

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“…For example, the rice sh4 locus accounts for a large proportion of shattering variation in populations derived from crosses between domesticated Oryza sativa and its wild progenitors, the annual species O. nivara (41) and perennial species O. rufipogon (42). However, in some genetic backgrounds, wild rice plants can be homozygous for the sh4 domestication allele and yet still show a shattering phenotype (43) (44).…”

Section: Epistasis Affects Domestication and Crop Improvement Traitsmentioning

confidence: 99%

“…In some cases, mapping studies do not explicitly examine epistatic interactions (e.g., ref. 42), or they only compare them between significant QTL (e.g., ref. 45).…”

Section: Epistasis Affects Domestication and Crop Improvement Traitsmentioning

confidence: 99%

Beyond the single gene: How epistasis and gene-by-environment effects influence crop domestication

Doust

Lukens

Olsen

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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Domestication is a multifaceted evolutionary process, involving changes in individual genes, genetic interactions, and emergent phenotypes. There has been extensive discussion of the phenotypic characteristics of plant domestication, and recent research has started to identify the specific genes and mutational mechanisms that control domestication traits. However, there is an apparent disconnect between the simple genetic architecture described for many crop domestication traits, which should facilitate rapid phenotypic change under selection, and the slow rate of change reported from the archeobotanical record. A possible explanation involves the middle ground between individual genetic changes and their expression during development, where gene-by-gene (epistatic) and gene-by-environment interactions can modify the expression of phenotypes and opportunities for selection. These aspects of genetic architecture have the potential to significantly slow the speed of phenotypic evolution during crop domestication and improvement. Here we examine whether epistatic and gene-byenvironment interactions have shaped how domestication traits have evolved. We review available evidence from the literature, and we analyze two domestication-related traits, shattering and flowering time, in a mapping population derived from a cross between domesticated foxtail millet and its wild progenitor. We find that compared with wild progenitor alleles, those favored during domestication often have large phenotypic effects and are relatively insensitive to genetic background and environmental effects. Consistent selection should thus be able to rapidly change traits during domestication. We conclude that if phenotypic evolution was slow during crop domestication, this is more likely due to cultural or historical factors than epistatic or environmental constraints.QTL | genotype-by-environment interactions | G × E | Setaria | domestication syndrome

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Genomic regions affecting seed shattering and seed dormancy in rice

Cited by 162 publications

References 5 publications

Isolation of three dormancy QTLs as Mendelian factors in rice

Isolation of three dormancy QTLs as Mendelian factors in rice

Characterization and Mapping of a Shattering Mutant in Rice That Corresponds to a Block of Domestication Genes

Beyond the single gene: How epistasis and gene-by-environment effects influence crop domestication

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