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Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection.

Duitama J, Silva A, Sanabria Y, Cruz DF, Quintero C, Ballen C, Lorieux M, Scheffler B, Farmer A, Torres E, Oard J, Tohme J - PLoS ONE (2015)

Bottom Line: We identified repetitive elements and recurrent copy number variation covering about 200 Mbp of the rice genome.Genotyping of over 18 million polymorphic locations within O. sativa allowed us to reconstruct the individual haplotype patterns shaping the genomic background of elite varieties used by farmers throughout the Americas.We expect that both the analysis methods and the genomic information described here would be of great use for the rice research community and for other groups carrying on similar sequencing efforts in other crops.

View Article: PubMed Central - PubMed

Affiliation: Agrobiodiversity research area, International Center for Tropical Agriculture, Cali, Colombia.

ABSTRACT
Current advances in sequencing technologies and bioinformatics revealed the genomic background of rice, a staple food for the poor people, and provided the basis to develop large genomic variation databases for thousands of cultivars. Proper analysis of this massive resource is expected to give novel insights into the structure, function, and evolution of the rice genome, and to aid the development of rice varieties through marker assisted selection or genomic selection. In this work we present sequencing and bioinformatics analyses of 104 rice varieties belonging to the major subspecies of Oryza sativa. We identified repetitive elements and recurrent copy number variation covering about 200 Mbp of the rice genome. Genotyping of over 18 million polymorphic locations within O. sativa allowed us to reconstruct the individual haplotype patterns shaping the genomic background of elite varieties used by farmers throughout the Americas. Based on a reconstruction of the alleles for the gene GBSSI, we could identify novel genetic markers for selection of varieties with high amylose content. We expect that both the analysis methods and the genomic information described here would be of great use for the rice research community and for other groups carrying on similar sequencing efforts in other crops.

No MeSH data available.


Observed haplotype patterns within the gene GBSSI for O. sativa accessions.Alleles of the temperate japonica variety Haginomae Mochi (dashed rectangle), which has the defective alleles for Waxy-1 to Waxy-7, are colored blue. Arrows indicate locations within the gene for the discriminative SNPs Waxy-1 to Waxy-7. Colors in the left panel differentiate the following groups: aromatic (ARO), temperate japonica (TEJ), tropical japonica (TRJ), indica (IND), aus (AUS) and admixed (ADM). The table below shows the six haplotype configurations in an independent group of 48 indica elite varieties with variable amylose contents. The last two columns are the number of samples showing the haplotype and the average amylose content for each haplotype. Characters a, b, c and d in the last column differentiate haplotypes with significant differences in amylose content.
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pone.0124617.g004: Observed haplotype patterns within the gene GBSSI for O. sativa accessions.Alleles of the temperate japonica variety Haginomae Mochi (dashed rectangle), which has the defective alleles for Waxy-1 to Waxy-7, are colored blue. Arrows indicate locations within the gene for the discriminative SNPs Waxy-1 to Waxy-7. Colors in the left panel differentiate the following groups: aromatic (ARO), temperate japonica (TEJ), tropical japonica (TRJ), indica (IND), aus (AUS) and admixed (ADM). The table below shows the six haplotype configurations in an independent group of 48 indica elite varieties with variable amylose contents. The last two columns are the number of samples showing the haplotype and the average amylose content for each haplotype. Characters a, b, c and d in the last column differentiate haplotypes with significant differences in amylose content.

Mentions: For breeding purposes, one of the main goals of performing sequencing of elite cultivars is the identification of markers that could be used for marker assisted selection. Bearing this in mind, we investigated the variation observed within the gene GBSSI, located at 1.76Mbp of chromosome 6, which is known to be related to amylose content [43]. We identified a total of 112 SNPs close to this gene, 82 of them only variable in the admixed variety HaishaCaman (Fig 4). From the remaining 30 SNPs, the minor allele of 17 was carried by at least four varieties. Three of these SNPs (termed Waxy-1, Waxy-2, and Waxy-3) were previously reported as markers for amylose content [44, 45]. Waxy-1 is located in the first splicing site of one of the transcripts identified for GBSSI which probably blocks transcription of this isoform. In this case the defective allele is the minor allele in our population and it is mostly present in temperate japonica accessions. Waxy-2 and Waxy-3 produce single amino acid changes in exons 6 and 10 respectively. For both markers, the advantageous allele is more frequent in indica than in japonica, although the advantageous allele of Waxy-2 is also frequent in temperate japonica. Besides these markers, we selected four additional SNPs with the minor allele present mostly in indica cultivars and we termed them Waxy-4, Waxy-5, Waxy-6 and Waxy-7. Waxy-4 and Waxy-5 are located about 800 bp before the transcription start site. Waxy-6 is located within the first intron, and Waxy-7 is a synonymous SNP in exon 9.


Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection.

Duitama J, Silva A, Sanabria Y, Cruz DF, Quintero C, Ballen C, Lorieux M, Scheffler B, Farmer A, Torres E, Oard J, Tohme J - PLoS ONE (2015)

Observed haplotype patterns within the gene GBSSI for O. sativa accessions.Alleles of the temperate japonica variety Haginomae Mochi (dashed rectangle), which has the defective alleles for Waxy-1 to Waxy-7, are colored blue. Arrows indicate locations within the gene for the discriminative SNPs Waxy-1 to Waxy-7. Colors in the left panel differentiate the following groups: aromatic (ARO), temperate japonica (TEJ), tropical japonica (TRJ), indica (IND), aus (AUS) and admixed (ADM). The table below shows the six haplotype configurations in an independent group of 48 indica elite varieties with variable amylose contents. The last two columns are the number of samples showing the haplotype and the average amylose content for each haplotype. Characters a, b, c and d in the last column differentiate haplotypes with significant differences in amylose content.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4414565&req=5

pone.0124617.g004: Observed haplotype patterns within the gene GBSSI for O. sativa accessions.Alleles of the temperate japonica variety Haginomae Mochi (dashed rectangle), which has the defective alleles for Waxy-1 to Waxy-7, are colored blue. Arrows indicate locations within the gene for the discriminative SNPs Waxy-1 to Waxy-7. Colors in the left panel differentiate the following groups: aromatic (ARO), temperate japonica (TEJ), tropical japonica (TRJ), indica (IND), aus (AUS) and admixed (ADM). The table below shows the six haplotype configurations in an independent group of 48 indica elite varieties with variable amylose contents. The last two columns are the number of samples showing the haplotype and the average amylose content for each haplotype. Characters a, b, c and d in the last column differentiate haplotypes with significant differences in amylose content.
Mentions: For breeding purposes, one of the main goals of performing sequencing of elite cultivars is the identification of markers that could be used for marker assisted selection. Bearing this in mind, we investigated the variation observed within the gene GBSSI, located at 1.76Mbp of chromosome 6, which is known to be related to amylose content [43]. We identified a total of 112 SNPs close to this gene, 82 of them only variable in the admixed variety HaishaCaman (Fig 4). From the remaining 30 SNPs, the minor allele of 17 was carried by at least four varieties. Three of these SNPs (termed Waxy-1, Waxy-2, and Waxy-3) were previously reported as markers for amylose content [44, 45]. Waxy-1 is located in the first splicing site of one of the transcripts identified for GBSSI which probably blocks transcription of this isoform. In this case the defective allele is the minor allele in our population and it is mostly present in temperate japonica accessions. Waxy-2 and Waxy-3 produce single amino acid changes in exons 6 and 10 respectively. For both markers, the advantageous allele is more frequent in indica than in japonica, although the advantageous allele of Waxy-2 is also frequent in temperate japonica. Besides these markers, we selected four additional SNPs with the minor allele present mostly in indica cultivars and we termed them Waxy-4, Waxy-5, Waxy-6 and Waxy-7. Waxy-4 and Waxy-5 are located about 800 bp before the transcription start site. Waxy-6 is located within the first intron, and Waxy-7 is a synonymous SNP in exon 9.

Bottom Line: We identified repetitive elements and recurrent copy number variation covering about 200 Mbp of the rice genome.Genotyping of over 18 million polymorphic locations within O. sativa allowed us to reconstruct the individual haplotype patterns shaping the genomic background of elite varieties used by farmers throughout the Americas.We expect that both the analysis methods and the genomic information described here would be of great use for the rice research community and for other groups carrying on similar sequencing efforts in other crops.

View Article: PubMed Central - PubMed

Affiliation: Agrobiodiversity research area, International Center for Tropical Agriculture, Cali, Colombia.

ABSTRACT
Current advances in sequencing technologies and bioinformatics revealed the genomic background of rice, a staple food for the poor people, and provided the basis to develop large genomic variation databases for thousands of cultivars. Proper analysis of this massive resource is expected to give novel insights into the structure, function, and evolution of the rice genome, and to aid the development of rice varieties through marker assisted selection or genomic selection. In this work we present sequencing and bioinformatics analyses of 104 rice varieties belonging to the major subspecies of Oryza sativa. We identified repetitive elements and recurrent copy number variation covering about 200 Mbp of the rice genome. Genotyping of over 18 million polymorphic locations within O. sativa allowed us to reconstruct the individual haplotype patterns shaping the genomic background of elite varieties used by farmers throughout the Americas. Based on a reconstruction of the alleles for the gene GBSSI, we could identify novel genetic markers for selection of varieties with high amylose content. We expect that both the analysis methods and the genomic information described here would be of great use for the rice research community and for other groups carrying on similar sequencing efforts in other crops.

No MeSH data available.