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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.


Background recovery analysis in Sub1 derivatives of four mega rice varieties:(a) Percentage similarity between recipient variety and its backcross derived submergence tolerant version (b) Snapshot of chromosome wise (1-12) similarity between Swarna and Swarna-Sub1, alleles of donor parent are indicated in red color, while Sub1B gene is highlighted in yellow color on chromosome 9.
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f3: Background recovery analysis in Sub1 derivatives of four mega rice varieties:(a) Percentage similarity between recipient variety and its backcross derived submergence tolerant version (b) Snapshot of chromosome wise (1-12) similarity between Swarna and Swarna-Sub1, alleles of donor parent are indicated in red color, while Sub1B gene is highlighted in yellow color on chromosome 9.

Mentions: The 50 K rice SNP chip was used to analyse the percentage similarity of four submergence tolerant mega rice varieties, namely Swarna-Sub1, CR1009-Sub1, IR64-Sub1, and Samba Mahsuri-Sub1, with their respective recipient parents. These rice varieties were developed by introgression of Sub1A gene located on the rice chromosome 9 through marker-assisted backcross breeding27. Backcross-derived lines with maximum recipient genome recovery (background selection) in these lines were identified using low-density SSR markers and phenotypic selection. The overall background genomes of Swarna-Sub1, CR1009-Sub1, IR64-Sub1, and Samba Mahsuri-Sub1 estimated using the 50 K rice SNP chip were 97.7%, 91.9%, 91.7%, and 78.7%, respectively. As expected, because of linkage drag, background recovery of chromosome 9, bearing the target Sub1A gene, was slightly lower at 94.0%, 91.5%, 86.03%, and 78.5%, respectively (Supplementary Table 4). High density background analysis by using the 50 K rice SNP chip clearly showed that a significant proportion of the residual donor background genome was present in all the four varieties spread across all the 12 rice chromosomes, with the highest background recovery in Swarna-Sub1 (Fig. 3a, b).


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)

Background recovery analysis in Sub1 derivatives of four mega rice varieties:(a) Percentage similarity between recipient variety and its backcross derived submergence tolerant version (b) Snapshot of chromosome wise (1-12) similarity between Swarna and Swarna-Sub1, alleles of donor parent are indicated in red color, while Sub1B gene is highlighted in yellow color on chromosome 9.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f3: Background recovery analysis in Sub1 derivatives of four mega rice varieties:(a) Percentage similarity between recipient variety and its backcross derived submergence tolerant version (b) Snapshot of chromosome wise (1-12) similarity between Swarna and Swarna-Sub1, alleles of donor parent are indicated in red color, while Sub1B gene is highlighted in yellow color on chromosome 9.
Mentions: The 50 K rice SNP chip was used to analyse the percentage similarity of four submergence tolerant mega rice varieties, namely Swarna-Sub1, CR1009-Sub1, IR64-Sub1, and Samba Mahsuri-Sub1, with their respective recipient parents. These rice varieties were developed by introgression of Sub1A gene located on the rice chromosome 9 through marker-assisted backcross breeding27. Backcross-derived lines with maximum recipient genome recovery (background selection) in these lines were identified using low-density SSR markers and phenotypic selection. The overall background genomes of Swarna-Sub1, CR1009-Sub1, IR64-Sub1, and Samba Mahsuri-Sub1 estimated using the 50 K rice SNP chip were 97.7%, 91.9%, 91.7%, and 78.7%, respectively. As expected, because of linkage drag, background recovery of chromosome 9, bearing the target Sub1A gene, was slightly lower at 94.0%, 91.5%, 86.03%, and 78.5%, respectively (Supplementary Table 4). High density background analysis by using the 50 K rice SNP chip clearly showed that a significant proportion of the residual donor background genome was present in all the four varieties spread across all the 12 rice chromosomes, with the highest background recovery in Swarna-Sub1 (Fig. 3a, b).

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.