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OsLG3 contributing to rice grain length and yield was mined by Ho-LAMap

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ABSTRACT

Background: Most agronomic traits in rice are complex and polygenic. The identification of quantitative trait loci (QTL) for grain length is an important objective of rice genetic research and breeding programs.

Results: Herein, we identified 99 QTL for grain length by GWAS based on approximately 10 million single nucleotide polymorphisms from 504 cultivated rice accessions (Oryza sativa L.), 13 of which were validated by four linkage populations and 92 were new loci for grain length. We scanned the Ho (observed heterozygosity per locus) index of coupled-parents of crosses mapping the same QTL, based on linkage and association mapping, and identified two new genes for grain length. We named this approach as Ho-LAMap. A simulation study of six known genes showed that Ho-LAMap could mine genes rapidly across a wide range of experimental variables using deep-sequencing data. We used Ho-LAMap to clone a new gene, OsLG3, as a positive regulator of grain length, which could improve rice yield without influencing grain quality. Sequencing of the promoter region in 283 rice accessions from a wide geographic range identified four haplotypes that seem to be associated with grain length. Further analysis showed that OsLG3 alleles in the indica and japonica evolved independently from distinct ancestors and low nucleotide diversity of OsLG3 in indica indicated artificial selection. Phylogenetic analysis showed that OsLG3 might have much potential value for improvement of grain length in japonica breeding.

Conclusions: The results demonstrated that Ho-LAMap is a potential approach for gene discovery and OsLG3 is a promising gene to be utilized in genomic assisted breeding for rice cultivar improvement.

Electronic supplementary material: The online version of this article (doi:10.1186/s12915-017-0365-7) contains supplementary material, which is available to authorized users.

No MeSH data available.


Related in: MedlinePlus

OsLG3 is a nuclear-localized transcriptional activator. a Subcellular localization of OsLG3. b Transactivation assay of truncated OsLG3. Fusion proteins of the GAL4 DNA-binding domain and different portions of OsLG3 were expressed in yeast strain AH109. A1 indicates the full-length coding sequence of OsLG3; A2 to A5 indicate the mutated forms of OsLG3 (nucleotide positions were labeled in the diagrams), respectively. P and N indicate the positive and negative control, respectively. The culture solution of the transformed yeast was dropped onto the control plate SD/-Trp or selective plate (SD/-Trp/-Ade/-His/X-α-gal). The plates were incubated for 3 days
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Fig3: OsLG3 is a nuclear-localized transcriptional activator. a Subcellular localization of OsLG3. b Transactivation assay of truncated OsLG3. Fusion proteins of the GAL4 DNA-binding domain and different portions of OsLG3 were expressed in yeast strain AH109. A1 indicates the full-length coding sequence of OsLG3; A2 to A5 indicate the mutated forms of OsLG3 (nucleotide positions were labeled in the diagrams), respectively. P and N indicate the positive and negative control, respectively. The culture solution of the transformed yeast was dropped onto the control plate SD/-Trp or selective plate (SD/-Trp/-Ade/-His/X-α-gal). The plates were incubated for 3 days

Mentions: As OsLG3 encodes an AP2 domain class transcription factor, we speculated that OsLG3 is localized in the nucleus. To determine subcellular localization of OsLG3, we expressed an OsLG3-green fluorescent protein (GFP) fusion protein under the control of the 35S promoter in onion epidermal cells. As shown in Fig. 3a, GFP fluorescence in 35S: OsLG3-GFP transgenic epidermal cells was observed exclusively in nuclei. Thus, this result suggests that OsLG3 is a nuclear-localized protein, consistent with its proposed function as a transcription regulator.Fig. 3


OsLG3 contributing to rice grain length and yield was mined by Ho-LAMap
OsLG3 is a nuclear-localized transcriptional activator. a Subcellular localization of OsLG3. b Transactivation assay of truncated OsLG3. Fusion proteins of the GAL4 DNA-binding domain and different portions of OsLG3 were expressed in yeast strain AH109. A1 indicates the full-length coding sequence of OsLG3; A2 to A5 indicate the mutated forms of OsLG3 (nucleotide positions were labeled in the diagrams), respectively. P and N indicate the positive and negative control, respectively. The culture solution of the transformed yeast was dropped onto the control plate SD/-Trp or selective plate (SD/-Trp/-Ade/-His/X-α-gal). The plates were incubated for 3 days
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC5383996&req=5

Fig3: OsLG3 is a nuclear-localized transcriptional activator. a Subcellular localization of OsLG3. b Transactivation assay of truncated OsLG3. Fusion proteins of the GAL4 DNA-binding domain and different portions of OsLG3 were expressed in yeast strain AH109. A1 indicates the full-length coding sequence of OsLG3; A2 to A5 indicate the mutated forms of OsLG3 (nucleotide positions were labeled in the diagrams), respectively. P and N indicate the positive and negative control, respectively. The culture solution of the transformed yeast was dropped onto the control plate SD/-Trp or selective plate (SD/-Trp/-Ade/-His/X-α-gal). The plates were incubated for 3 days
Mentions: As OsLG3 encodes an AP2 domain class transcription factor, we speculated that OsLG3 is localized in the nucleus. To determine subcellular localization of OsLG3, we expressed an OsLG3-green fluorescent protein (GFP) fusion protein under the control of the 35S promoter in onion epidermal cells. As shown in Fig. 3a, GFP fluorescence in 35S: OsLG3-GFP transgenic epidermal cells was observed exclusively in nuclei. Thus, this result suggests that OsLG3 is a nuclear-localized protein, consistent with its proposed function as a transcription regulator.Fig. 3

View Article: PubMed Central - PubMed

ABSTRACT

Background: Most agronomic traits in rice are complex and polygenic. The identification of quantitative trait loci (QTL) for grain length is an important objective of rice genetic research and breeding programs.

Results: Herein, we identified 99 QTL for grain length by GWAS based on approximately 10 million single nucleotide polymorphisms from 504 cultivated rice accessions (Oryza sativa L.), 13 of which were validated by four linkage populations and 92 were new loci for grain length. We scanned the Ho (observed heterozygosity per locus) index of coupled-parents of crosses mapping the same QTL, based on linkage and association mapping, and identified two new genes for grain length. We named this approach as Ho-LAMap. A simulation study of six known genes showed that Ho-LAMap could mine genes rapidly across a wide range of experimental variables using deep-sequencing data. We used Ho-LAMap to clone a new gene, OsLG3, as a positive regulator of grain length, which could improve rice yield without influencing grain quality. Sequencing of the promoter region in 283 rice accessions from a wide geographic range identified four haplotypes that seem to be associated with grain length. Further analysis showed that OsLG3 alleles in the indica and japonica evolved independently from distinct ancestors and low nucleotide diversity of OsLG3 in indica indicated artificial selection. Phylogenetic analysis showed that OsLG3 might have much potential value for improvement of grain length in japonica breeding.

Conclusions: The results demonstrated that Ho-LAMap is a potential approach for gene discovery and OsLG3 is a promising gene to be utilized in genomic assisted breeding for rice cultivar improvement.

Electronic supplementary material: The online version of this article (doi:10.1186/s12915-017-0365-7) contains supplementary material, which is available to authorized users.

No MeSH data available.


Related in: MedlinePlus