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High-throughput SNP discovery and genotyping for constructing a saturated linkage map of chickpea (Cicer arietinum L.).

Gaur R, Azam S, Jeena G, Khan AW, Choudhary S, Jain M, Yadav G, Tyagi AK, Chattopadhyay D, Bhatia S - DNA Res. (2012)

Bottom Line: Of these, 697 SNPs could be successfully used for genotyping, demonstrating a high success rate of 90.75%.The map was used for the synteny analysis of chickpea, which revealed a higher degree of synteny with the phylogenetically close Medicago than with soybean.The first set of validated SNPs and map resources developed in this study will not only facilitate QTL mapping, genome-wide association analysis and comparative mapping in legumes but also help anchor scaffolds arising out of the whole-genome sequencing of chickpea.

View Article: PubMed Central - PubMed

Affiliation: National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box 10531, New Delhi 110067, India.

ABSTRACT
The present study reports the large-scale discovery of genome-wide single-nucleotide polymorphisms (SNPs) in chickpea, identified mainly through the next generation sequencing of two genotypes, i.e. Cicer arietinum ICC4958 and its wild progenitor C. reticulatum PI489777, parents of an inter-specific reference mapping population of chickpea. Development and validation of a high-throughput SNP genotyping assay based on Illumina's GoldenGate Genotyping Technology and its application in building a high-resolution genetic linkage map of chickpea is described for the first time. In this study, 1022 SNPs were identified, of which 768 high-confidence SNPs were selected for designing the custom Oligo Pool All (CpOPA-I) for genotyping. Of these, 697 SNPs could be successfully used for genotyping, demonstrating a high success rate of 90.75%. Genotyping data of the 697 SNPs were compiled along with those of 368 co-dominant markers mapped in an earlier study, and a saturated genetic linkage map of chickpea was constructed. One thousand and sixty-three markers were mapped onto eight linkage groups spanning 1808.7 cM (centiMorgans) with an average inter-marker distance of 1.70 cM, thereby representing one of the most advanced maps of chickpea. The map was used for the synteny analysis of chickpea, which revealed a higher degree of synteny with the phylogenetically close Medicago than with soybean. The first set of validated SNPs and map resources developed in this study will not only facilitate QTL mapping, genome-wide association analysis and comparative mapping in legumes but also help anchor scaffolds arising out of the whole-genome sequencing of chickpea.

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Syntenic relationships of chickpea LGs: CaLG2 with Mt4, Mt5 and Mt6; CaLG3 with Mt5 and Mt7; CaLG1 with Gm9, Gm13 and Gm15; CaLG3 with Gm1, Gm3 and Gm19. Coloured regions represent syntenic blocks observed in chromosomes of Medicago and soybean.
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DSS018F3: Syntenic relationships of chickpea LGs: CaLG2 with Mt4, Mt5 and Mt6; CaLG3 with Mt5 and Mt7; CaLG1 with Gm9, Gm13 and Gm15; CaLG3 with Gm1, Gm3 and Gm19. Coloured regions represent syntenic blocks observed in chromosomes of Medicago and soybean.

Mentions: Chickpea-Medicago synteny. The chickpea-Medicago synteny was observed for 315 (34.35%) of 917 markers for which 404 significant matches were obtained on different chromosomes of Medicago. Synteny blocks were observed between chickpea and most Medicago chromosomes except Mt6 (Supplementary Fig. S1), indicating an evolutionary relationship between the two species. Many of the CaLGs were found to have syntenic blocks with more than one LG of Medicago. CaLG3 showed maximum synteny, since 68 markers showed 86 hits with Medicago chromosomes (Table 3), majority of which (35 and 23) were located on Mt7 and Mt5, respectively (Fig. 3). Similarly, synteny blocks from CaLG2 were observed on Mt4, Mt5 and Mt6 (Fig. 3). Moreover, CaLG1, CaLG4 and CaLG5 showed distinct synteny with Mt2, Mt1 and Mt3 chromosomes, respectively (Supplementary Figs. S1 and S2). Additionally, CaLG6 and CaLG7 were seen to be highly syntenic with Mt8, whereas CaLG8 was found to be syntenic with Mt4 (Supplementary Figs. S1 and S2). The number of markers that found hits in Medicago in comparison with soybean was more; however, very limited collinearity was observed between the chickpea-Medicago syntenic blocks.Figure 3.


High-throughput SNP discovery and genotyping for constructing a saturated linkage map of chickpea (Cicer arietinum L.).

Gaur R, Azam S, Jeena G, Khan AW, Choudhary S, Jain M, Yadav G, Tyagi AK, Chattopadhyay D, Bhatia S - DNA Res. (2012)

Syntenic relationships of chickpea LGs: CaLG2 with Mt4, Mt5 and Mt6; CaLG3 with Mt5 and Mt7; CaLG1 with Gm9, Gm13 and Gm15; CaLG3 with Gm1, Gm3 and Gm19. Coloured regions represent syntenic blocks observed in chromosomes of Medicago and soybean.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3473369&req=5

DSS018F3: Syntenic relationships of chickpea LGs: CaLG2 with Mt4, Mt5 and Mt6; CaLG3 with Mt5 and Mt7; CaLG1 with Gm9, Gm13 and Gm15; CaLG3 with Gm1, Gm3 and Gm19. Coloured regions represent syntenic blocks observed in chromosomes of Medicago and soybean.
Mentions: Chickpea-Medicago synteny. The chickpea-Medicago synteny was observed for 315 (34.35%) of 917 markers for which 404 significant matches were obtained on different chromosomes of Medicago. Synteny blocks were observed between chickpea and most Medicago chromosomes except Mt6 (Supplementary Fig. S1), indicating an evolutionary relationship between the two species. Many of the CaLGs were found to have syntenic blocks with more than one LG of Medicago. CaLG3 showed maximum synteny, since 68 markers showed 86 hits with Medicago chromosomes (Table 3), majority of which (35 and 23) were located on Mt7 and Mt5, respectively (Fig. 3). Similarly, synteny blocks from CaLG2 were observed on Mt4, Mt5 and Mt6 (Fig. 3). Moreover, CaLG1, CaLG4 and CaLG5 showed distinct synteny with Mt2, Mt1 and Mt3 chromosomes, respectively (Supplementary Figs. S1 and S2). Additionally, CaLG6 and CaLG7 were seen to be highly syntenic with Mt8, whereas CaLG8 was found to be syntenic with Mt4 (Supplementary Figs. S1 and S2). The number of markers that found hits in Medicago in comparison with soybean was more; however, very limited collinearity was observed between the chickpea-Medicago syntenic blocks.Figure 3.

Bottom Line: Of these, 697 SNPs could be successfully used for genotyping, demonstrating a high success rate of 90.75%.The map was used for the synteny analysis of chickpea, which revealed a higher degree of synteny with the phylogenetically close Medicago than with soybean.The first set of validated SNPs and map resources developed in this study will not only facilitate QTL mapping, genome-wide association analysis and comparative mapping in legumes but also help anchor scaffolds arising out of the whole-genome sequencing of chickpea.

View Article: PubMed Central - PubMed

Affiliation: National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box 10531, New Delhi 110067, India.

ABSTRACT
The present study reports the large-scale discovery of genome-wide single-nucleotide polymorphisms (SNPs) in chickpea, identified mainly through the next generation sequencing of two genotypes, i.e. Cicer arietinum ICC4958 and its wild progenitor C. reticulatum PI489777, parents of an inter-specific reference mapping population of chickpea. Development and validation of a high-throughput SNP genotyping assay based on Illumina's GoldenGate Genotyping Technology and its application in building a high-resolution genetic linkage map of chickpea is described for the first time. In this study, 1022 SNPs were identified, of which 768 high-confidence SNPs were selected for designing the custom Oligo Pool All (CpOPA-I) for genotyping. Of these, 697 SNPs could be successfully used for genotyping, demonstrating a high success rate of 90.75%. Genotyping data of the 697 SNPs were compiled along with those of 368 co-dominant markers mapped in an earlier study, and a saturated genetic linkage map of chickpea was constructed. One thousand and sixty-three markers were mapped onto eight linkage groups spanning 1808.7 cM (centiMorgans) with an average inter-marker distance of 1.70 cM, thereby representing one of the most advanced maps of chickpea. The map was used for the synteny analysis of chickpea, which revealed a higher degree of synteny with the phylogenetically close Medicago than with soybean. The first set of validated SNPs and map resources developed in this study will not only facilitate QTL mapping, genome-wide association analysis and comparative mapping in legumes but also help anchor scaffolds arising out of the whole-genome sequencing of chickpea.

Show MeSH
Related in: MedlinePlus