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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.


SNP haplotype-based neighbour-joining phylogenetic tree of 128 diverse rice genotypes, including wild rice, land races, improved cultivars and Sub1 backcross derivatives of mega rice varieties.Four major distinct groups are: wild rice with ‘sathi’ (blue), wild rice with Aus rice cultivars (green), wild rice with Indica rice cultivars (red) and Japonica rice cultivars (cyan).
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f2: SNP haplotype-based neighbour-joining phylogenetic tree of 128 diverse rice genotypes, including wild rice, land races, improved cultivars and Sub1 backcross derivatives of mega rice varieties.Four major distinct groups are: wild rice with ‘sathi’ (blue), wild rice with Aus rice cultivars (green), wild rice with Indica rice cultivars (red) and Japonica rice cultivars (cyan).

Mentions: Haplotype-based phylogenetic analysis unravels the origin of mutations and provides clues to the evolution of genetic diversity in populations. The SC gene based 50 K rice SNP chip was used to study the genetic diversity and phylogenetic relationship among 128 diverse rice germplasm, including wild rice accessions, traditional rice varieties, and genetically improved rice cultivars. Of the total 192 samples used for chip validation, 64 samples were excluded from this analysis because one sample had a low call rate, four samples were in replicates, and 59 samples were breeding lines and bulk samples (Supplementary Table 3). Haplotype based analysis separated the 128 genotypes into four major groups (Fig. 2, Supplementary Table 3). Group I comprised entirely of wild rice accessions including both O. rufipogon and O. nivara. This group represented the eastern states of India including Uttar Pradesh, Bihar, West Bengal, and Odisha. Only exception in this group was a unique extra-early maturing rice landrace Sathi_NKSLR-9 [matures in 60 (sath) days; therefore, named Sathi], which was clustered with Group I along with wild rice accessions collected from the Indo-Gangetic Plain. Group II comprised wild rice accessions along with rice landraces, including well-known Aus varieties, namely Nagina 22 and FR 13A, which seem to have evolved from O. nivara. Wild rice collected from widespread geographical regions of India were represented in this group, including those collected from Himachal Pradesh, Uttar Pradesh, Bihar, Bengal, Gujarat, and Maharashtra. Group III comprised mainly of well-known indica rice varieties, namely ADT 39, CR 1009, IR 64, MTU 1010, Pokkali, Pusa 44, Ranjit, Swarna, and their Sub1 derivatives, along with five wild rice accessions (O. nivara), of which four accessions were from Uttar Pradesh and one accession was from Himachal Pradesh. Group IV included two accessions of japonica rice cultivars Nipponbare and Taipei 309 and no clustering of wild rice accessions.


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)

SNP haplotype-based neighbour-joining phylogenetic tree of 128 diverse rice genotypes, including wild rice, land races, improved cultivars and Sub1 backcross derivatives of mega rice varieties.Four major distinct groups are: wild rice with ‘sathi’ (blue), wild rice with Aus rice cultivars (green), wild rice with Indica rice cultivars (red) and Japonica rice cultivars (cyan).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f2: SNP haplotype-based neighbour-joining phylogenetic tree of 128 diverse rice genotypes, including wild rice, land races, improved cultivars and Sub1 backcross derivatives of mega rice varieties.Four major distinct groups are: wild rice with ‘sathi’ (blue), wild rice with Aus rice cultivars (green), wild rice with Indica rice cultivars (red) and Japonica rice cultivars (cyan).
Mentions: Haplotype-based phylogenetic analysis unravels the origin of mutations and provides clues to the evolution of genetic diversity in populations. The SC gene based 50 K rice SNP chip was used to study the genetic diversity and phylogenetic relationship among 128 diverse rice germplasm, including wild rice accessions, traditional rice varieties, and genetically improved rice cultivars. Of the total 192 samples used for chip validation, 64 samples were excluded from this analysis because one sample had a low call rate, four samples were in replicates, and 59 samples were breeding lines and bulk samples (Supplementary Table 3). Haplotype based analysis separated the 128 genotypes into four major groups (Fig. 2, Supplementary Table 3). Group I comprised entirely of wild rice accessions including both O. rufipogon and O. nivara. This group represented the eastern states of India including Uttar Pradesh, Bihar, West Bengal, and Odisha. Only exception in this group was a unique extra-early maturing rice landrace Sathi_NKSLR-9 [matures in 60 (sath) days; therefore, named Sathi], which was clustered with Group I along with wild rice accessions collected from the Indo-Gangetic Plain. Group II comprised wild rice accessions along with rice landraces, including well-known Aus varieties, namely Nagina 22 and FR 13A, which seem to have evolved from O. nivara. Wild rice collected from widespread geographical regions of India were represented in this group, including those collected from Himachal Pradesh, Uttar Pradesh, Bihar, Bengal, Gujarat, and Maharashtra. Group III comprised mainly of well-known indica rice varieties, namely ADT 39, CR 1009, IR 64, MTU 1010, Pokkali, Pusa 44, Ranjit, Swarna, and their Sub1 derivatives, along with five wild rice accessions (O. nivara), of which four accessions were from Uttar Pradesh and one accession was from Himachal Pradesh. Group IV included two accessions of japonica rice cultivars Nipponbare and Taipei 309 and no clustering of wild rice accessions.

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.