Genetic Architecture of Seed Dormancy in U.S. Weedy Rice in Different Genetic Backgrounds

Subudhi, Prasanta K.; Parco, Arnold; Singh, Pawan K.; DeLeon, Teresa; Karan, Ratna; Biradar, Hanamareddy; Cohn, Marc Alan; Brar, D. S.; Sasaki, Takuji

doi:10.2135/cropsci2012.04.0228

Cited by 30 publications

(51 citation statements)

References 59 publications

(99 reference statements)

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“…More QTL were detected for wild and crop-mimic traits in this than in the reported research on weedy rice (Bres-Patry et al 2001; Gu et al 2005a; Jing et al 2008; Subudhi et al 2012; Thurber et al 2013). In addition to the difference in the parental combination of mapping population from the previous research, a larger population size, the greenhouse condition, and more trait measurements used in this research must have also contributed to the QTL detection.…”

Section: Discussionmentioning

confidence: 43%

Quantitative Trait Locus and Haplotype Analyses of Wild and Crop-Mimic Traits in U.S. Weedy Rice

Mispan

Zhang

Feng

et al. 2013

G3 Genes|Genomes|Genetics

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Conspecific weeds retained characteristics from wild ancestors and also developed crop mimicries for adaptation and competitiveness. This research was conducted to identify quantitative trait loci (QTL) associated with the wild and crop-mimic traits and to determine haplotype variants for QTL-rich regions in U.S. weedy rice. An F2 population from the cross between a cultivated (EM93-1) and a U.S. weedy (US1) rice line was evaluated for six wild and eight crop-mimic traits in a greenhouse to identify the QTL. A core collection of 27 U.S. weedy red rice lines and 14 AA-genome wild rice lines were determined for the haplotype variants. A total of 49 QTL were identified, with 45 collocated as clusters on 14 genomic segments. The number of haplotypes across the 14 segments was lower in the weedy (6.1 ± 2.4) than in the wild (7.5 ± 1.8) rice sample. Both samples shared ~50% haplotypes (wild-like). The EM93-1−like haplotypes accounted for a greater proportion (30 ± 26%) of the haplotypes in the weedy than in the wild (7 ± 10%) rice. Based on haplotype patterns for the 14 QTL cluster regions, 26 of the 28 red rice lines were clustered into two groups corresponding to the black-hull awned and straw-hull awnless morphological types, respectively. The QTL analysis demonstrated that conspecific weed-crop differentiation involved many genomic segments with multiple loci regulating natural variation for adaptation and competitiveness. The haplotype analysis revealed that U.S. weedy rice retained large blocks of linkage disequilibrium for the multiple loci from the wild relatives and also incorporated haplotypes from cultivars.

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Section: Discussionmentioning

confidence: 43%

Quantitative Trait Locus and Haplotype Analyses of Wild and Crop-Mimic Traits in U.S. Weedy Rice

Mispan

Zhang

Feng

et al. 2013

G3 Genes|Genomes|Genetics

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“…This Rc -specific pattern suggests that selection may be playing a role in elevating Rc allele frequencies in Malaysian weedy rice. Given the known functional importance of Rc in maintaining rice seed dormancy (Gu et al 2011; Subudhi et al 2012), this disproportionate occurrence of wild-type Rc alleles could potentially reflect selection to maintain seed dormancy alleles introgressed from wild O. rufipogon into Malaysian weed populations.…”

Section: Resultsmentioning

confidence: 99%

“…However, the adaptive value of functional Rc alleles may be more likely to come from the gene’s effects in maintaining seed dormancy. The ability of agricultural weed seeds to remain dormant in the soil over multiple planting seasons plays a key role in their persistence and proliferation (Delouche and Labrada 2007; Vigueira et al 2013b), and the Rc locus has been identified as one of the two major effect QTL for seed dormancy in United States weedy rice (Subudhi et al 2012). While the functional effects of Rc sequence variation on seed dormancy have not been explicitly examined, it is reasonable to expect that wild-type sequences that can successfully regulate proanthocyanidin synthesis would also be functional in establishing seed dormancy.…”

Section: Discussionmentioning

confidence: 99%

Little White Lies: Pericarp Color Provides Insights into the Origins and Evolution of Southeast Asian Weedy Rice

Cui

Song

et al. 2016

G3 Genes|Genomes|Genetics

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Weedy rice is a conspecific form of cultivated rice (Oryza sativa L.) that infests rice fields and results in severe crop losses. Weed strains in different world regions appear to have originated multiple times from different domesticated and/or wild rice progenitors. In the case of Malaysian weedy rice, a multiple-origin model has been proposed based on neutral markers and analyses of domestication genes for hull color and seed shattering. Here, we examined variation in pericarp (bran) color and its molecular basis to address how this trait evolved in Malaysian weeds and its possible role in weed adaptation. Functional alleles of the Rc gene confer proanthocyanidin pigmentation of the pericarp, a trait found in most wild and weedy Oryzas and associated with seed dormancy; nonfunctional rc alleles were strongly favored during rice domestication, and most cultivated varieties have nonpigmented pericarps. Phenotypic characterizations of 52 Malaysian weeds revealed that most strains are characterized by the pigmented pericarp; however, some weeds have white pericarps, suggesting close relationships to cultivated rice. Phylogenetic analyses indicate that the Rc haplotypes present in Malaysian weeds likely have at least three distinct origins: wild O. rufipogon, white-pericarp cultivated rice, and red-pericarp cultivated rice. These diverse origins contribute to high Rc nucleotide diversity in the Malaysian weeds. Comparison of Rc allelic distributions with other rice domestication genes suggests that functional Rc alleles may confer particular fitness benefits in weedy rice populations, for example, by conferring seed dormancy. This may promote functional Rc introgression from local wild Oryza populations.

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“…The QTLs for SD and SH were reported earlier for both RIL populations [21, 22]. Here, we report the results for the agronomic traits that were subjected to QTL analysis using composite interval mapping.…”

Section: Resultsmentioning

confidence: 75%

A Chromosome Segment Substitution Library of Weedy Rice for Genetic Dissection of Complex Agronomic and Domestication Traits

et al. 2015

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Chromosome segment substitution lines (CSSLs) are a powerful alternative for locating quantitative trait loci (QTL), analyzing gene interactions, and providing starting materials for map-based cloning projects. We report the development and characterization of a CSSL library of a U.S. weedy rice accession ‘PSRR-1’ with genome-wide coverage in an adapted rice cultivar ‘Bengal’ background. The majority of the CSSLs carried a single defined weedy rice segment with an average introgression segment of 2.8 % of the donor genome. QTL mapping results for several agronomic and domestication traits from the CSSL population were compared with those obtained from two recombinant inbred line (RIL) populations involving the same weedy rice accession. There was congruence of major effect QTLs between both types of populations, but new and additional QTLs were detected in the CSSL population. Although, three major effect QTLs for plant height were detected on chromosomes 1, 4, and 8 in the CSSL population, the latter two escaped detection in both RIL populations. Since this was observed for many traits, epistasis may play a major role for the phenotypic variation observed in weedy rice. High levels of shattering and seed dormancy in weedy rice might result from an accumulation of many small effect QTLs. Several CSSLs with desirable agronomic traits (e.g. longer panicles, longer grains, and higher seed weight) identified in this study could be useful for rice breeding. Since weedy rice is a reservoir of genes for many weedy and agronomic attributes, the CSSL library will serve as a valuable resource to discover latent genetic diversity for improving crop productivity and understanding the plant domestication process through cloning and characterization of the underlying genes.

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Genetic Architecture of Seed Dormancy in U.S. Weedy Rice in Different Genetic Backgrounds

Cited by 30 publications

References 59 publications

Quantitative Trait Locus and Haplotype Analyses of Wild and Crop-Mimic Traits in U.S. Weedy Rice

Quantitative Trait Locus and Haplotype Analyses of Wild and Crop-Mimic Traits in U.S. Weedy Rice

Little White Lies: Pericarp Color Provides Insights into the Origins and Evolution of Southeast Asian Weedy Rice

A Chromosome Segment Substitution Library of Weedy Rice for Genetic Dissection of Complex Agronomic and Domestication Traits

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