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Single-copy gene based 50 K SNP chip for genetic studies and molecular breeding in rice.

Singh N, Jayaswal PK, Panda K, Mandal P, Kumar V, Singh B, Mishra S, Singh Y, Singh R, Rai V, Gupta A, Raj Sharma T, Singh NK - Sci Rep (2015)

Bottom Line: The chip incorporates 50,051 SNPs from 18,980 different genes spanning 12 rice chromosomes, including 3,710 single-copy (SC) genes conserved between wheat and rice, 14,959 SC genes unique to rice, 194 agronomically important cloned rice genes and 117 multi-copy rice genes.The usefulness of the chip in genetic diversity and phylogenetic studies of cultivated and wild rice germplasm was demonstrated.Furthermore, its efficacy was validated for analysing background recovery in improved mega rice varieties with submergence tolerance developed through marker-assisted backcross breeding.

View Article: PubMed Central - PubMed

Affiliation: 1] National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi 110012, India [2] Rayat and Bahra Institute of Engineering and Bio-Technology, Mohali, Punjab Technical University, Jalandhar 140104, India.

ABSTRACT
Single nucleotide polymorphism (SNP) is the most abundant DNA sequence variation present in plant genomes. Here, we report the design and validation of a unique genic-SNP genotyping chip for genetic and evolutionary studies as well as molecular breeding applications in rice. The chip incorporates 50,051 SNPs from 18,980 different genes spanning 12 rice chromosomes, including 3,710 single-copy (SC) genes conserved between wheat and rice, 14,959 SC genes unique to rice, 194 agronomically important cloned rice genes and 117 multi-copy rice genes. Assays with this chip showed high success rate and reproducibility because of the SC gene based array with no sequence redundancy and cross-hybridisation problems. The usefulness of the chip in genetic diversity and phylogenetic studies of cultivated and wild rice germplasm was demonstrated. Furthermore, its efficacy was validated for analysing background recovery in improved mega rice varieties with submergence tolerance developed through marker-assisted backcross breeding.

No MeSH data available.


Distribution of different kinds of rice genes and number of SNPs in the Affymetrix 50 K rice SNP chip (OsSNPnks): (a) Number of genes in different categories; (b) Number of SNPs in different categories of genes; (c) Number of SNPs in different regions of the genes.
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f1: Distribution of different kinds of rice genes and number of SNPs in the Affymetrix 50 K rice SNP chip (OsSNPnks): (a) Number of genes in different categories; (b) Number of SNPs in different categories of genes; (c) Number of SNPs in different regions of the genes.

Mentions: The custom-designed Affymetrix rice SNP genotyping chip ‘OsSNPnks’ includes 50,051 high-quality non-redundant SNPs, mostly representing SC genes from the entire 12 rice chromosomes. Four categories of rice genes used for the chip design were, conserved SC genes between wheat and rice (CSCWR), unique SC rice genes (SCR), agronomically important cloned rice genes (AGCR), and multi-copy rice genes (MCR), of which the highest proportion of genes (79%) was from the SCR category, followed by 19% from the CSCWR category (Fig. 1a). In total, 48,217 (96%) SNPs on the chip were from SC genes, and the remaining 4% SNPs, including 1,216 (3%) from AGCR and 618 (1%) from MCR genes, were included for molecular breeding applications and MCR used as control (Fig. 1b). This rice chip had 38% SNPs from exons, including 8,798 (18%) synonymous and 10,148 (20%) non-synonymous types with the potential to affect gene function, 41% SNPs from introns, and 21% SNPs from 5′ and 3′ UTR regions (Fig. 1c). The chip has a high-density genome-wide coverage with an average distance of 0.745 kbp between adjacent SNPs (Supplementary Figure 1). The AGCR genes had a high number of 6.26 SNPs per gene (1.21 SNP/kbp) perhaps due to more extensive re-sequencing studies performed on these genes. Of the two categories of SC genes, the CSCWR genes showed an over three-fold higher number of 6 SNPs per gene (1.25 SNP/kbp) than the SCR genes that showed only 1.73 SNPs per gene (0.85 SNP/kbp). The MCR genes showed a medium number of 5 SNPs per gene (1.07 SNP/kbp). However, in the chip, 26,001 (~52%) of all SNPs were from the SCR category because of the much larger number of SCR genes (Table 1). The higher average number of SNPs in the CSCWR genes than in the SCR genes is attributed to both the larger average size (4,782 bp for CSCWR vs 2,036 bp for SCR) and the ancient origin of the CSCWR genes, allowing the accumulation of more SNPs2125. The complete array information of the 50 K rice SNP chip is provided in Supplementary Table 1.


Single-copy gene based 50 K SNP chip for genetic studies and molecular breeding in rice.

Singh N, Jayaswal PK, Panda K, Mandal P, Kumar V, Singh B, Mishra S, Singh Y, Singh R, Rai V, Gupta A, Raj Sharma T, Singh NK - Sci Rep (2015)

Distribution of different kinds of rice genes and number of SNPs in the Affymetrix 50 K rice SNP chip (OsSNPnks): (a) Number of genes in different categories; (b) Number of SNPs in different categories of genes; (c) Number of SNPs in different regions of the genes.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4481378&req=5

f1: Distribution of different kinds of rice genes and number of SNPs in the Affymetrix 50 K rice SNP chip (OsSNPnks): (a) Number of genes in different categories; (b) Number of SNPs in different categories of genes; (c) Number of SNPs in different regions of the genes.
Mentions: The custom-designed Affymetrix rice SNP genotyping chip ‘OsSNPnks’ includes 50,051 high-quality non-redundant SNPs, mostly representing SC genes from the entire 12 rice chromosomes. Four categories of rice genes used for the chip design were, conserved SC genes between wheat and rice (CSCWR), unique SC rice genes (SCR), agronomically important cloned rice genes (AGCR), and multi-copy rice genes (MCR), of which the highest proportion of genes (79%) was from the SCR category, followed by 19% from the CSCWR category (Fig. 1a). In total, 48,217 (96%) SNPs on the chip were from SC genes, and the remaining 4% SNPs, including 1,216 (3%) from AGCR and 618 (1%) from MCR genes, were included for molecular breeding applications and MCR used as control (Fig. 1b). This rice chip had 38% SNPs from exons, including 8,798 (18%) synonymous and 10,148 (20%) non-synonymous types with the potential to affect gene function, 41% SNPs from introns, and 21% SNPs from 5′ and 3′ UTR regions (Fig. 1c). The chip has a high-density genome-wide coverage with an average distance of 0.745 kbp between adjacent SNPs (Supplementary Figure 1). The AGCR genes had a high number of 6.26 SNPs per gene (1.21 SNP/kbp) perhaps due to more extensive re-sequencing studies performed on these genes. Of the two categories of SC genes, the CSCWR genes showed an over three-fold higher number of 6 SNPs per gene (1.25 SNP/kbp) than the SCR genes that showed only 1.73 SNPs per gene (0.85 SNP/kbp). The MCR genes showed a medium number of 5 SNPs per gene (1.07 SNP/kbp). However, in the chip, 26,001 (~52%) of all SNPs were from the SCR category because of the much larger number of SCR genes (Table 1). The higher average number of SNPs in the CSCWR genes than in the SCR genes is attributed to both the larger average size (4,782 bp for CSCWR vs 2,036 bp for SCR) and the ancient origin of the CSCWR genes, allowing the accumulation of more SNPs2125. The complete array information of the 50 K rice SNP chip is provided in Supplementary Table 1.

Bottom Line: The chip incorporates 50,051 SNPs from 18,980 different genes spanning 12 rice chromosomes, including 3,710 single-copy (SC) genes conserved between wheat and rice, 14,959 SC genes unique to rice, 194 agronomically important cloned rice genes and 117 multi-copy rice genes.The usefulness of the chip in genetic diversity and phylogenetic studies of cultivated and wild rice germplasm was demonstrated.Furthermore, its efficacy was validated for analysing background recovery in improved mega rice varieties with submergence tolerance developed through marker-assisted backcross breeding.

View Article: PubMed Central - PubMed

Affiliation: 1] National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi 110012, India [2] Rayat and Bahra Institute of Engineering and Bio-Technology, Mohali, Punjab Technical University, Jalandhar 140104, India.

ABSTRACT
Single nucleotide polymorphism (SNP) is the most abundant DNA sequence variation present in plant genomes. Here, we report the design and validation of a unique genic-SNP genotyping chip for genetic and evolutionary studies as well as molecular breeding applications in rice. The chip incorporates 50,051 SNPs from 18,980 different genes spanning 12 rice chromosomes, including 3,710 single-copy (SC) genes conserved between wheat and rice, 14,959 SC genes unique to rice, 194 agronomically important cloned rice genes and 117 multi-copy rice genes. Assays with this chip showed high success rate and reproducibility because of the SC gene based array with no sequence redundancy and cross-hybridisation problems. The usefulness of the chip in genetic diversity and phylogenetic studies of cultivated and wild rice germplasm was demonstrated. Furthermore, its efficacy was validated for analysing background recovery in improved mega rice varieties with submergence tolerance developed through marker-assisted backcross breeding.

No MeSH data available.