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Single nucleotide polymorphism in sugar pathway and disease resistance genes in sugarcane

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Title Single nucleotide polymorphism in sugar pathway and disease resistance genes in sugarcane
 
Creator Parida, Swarup K.
Kalia, Sanjay
Pandit, Awadhesh
Nayak, Preetam
Singh, Ram Kushal
Gaikwad, Kishor
Srivastava, Prem Shankar
Singh, Nagendra K.
Mohapatra, Trilochan
 
Subject CAPS
Disease resistance genes
SNPs
Sugar pathway genes
Sugarcane
 
Description Accepted date: 21 March 2016
Single nucleotide polymorphism in sugar pathway and disease resistance genes showing genetic association with sugar content and red rot resistance would be useful in marker-assisted genetic improvement of sugarcane. Validation and genotyping of potential sequence variants in candidate genes are necessary to understand their functional significance and trait association potential. We discovered, characterized, validated and genotyped SNPs and InDels in sugar pathway and disease resistance genes of Saccharum complex and sugarcane varieties using amplicon sequencing and CAPS assays. The SNPs were abundant in the non-coding 3'UTRs than 5'UTRs and coding sequences depicting a strong bias toward C to T transition substitutions than transversions. Sequencing of cloned amplicons validated 61.6 and 45.2 % SNPs detected in silico in 21 sugar pathway and 16 disease resistance genes, respectively. Sixteen SNPs in four sugar pathway genes and 10 SNPs in nine disease resistance genes were validated through cost-effective CAPS assay. Functional and adaptive significance of SNP and protein haplotypes identified in sugar pathway and disease resistance genes was assessed by correlating their allelic variation with missense amino acid substitutions in the functional domains, alteration in protein structure models and possible modulation of catalytic enzyme activity in contrasting high and low sugar and moderately red rot resistant and highly susceptible sugarcane genotypes. A strong genetic association of five SNPs in the sugar pathway and disease resistance genes, and an InDel marker in the promoter sequence of sucrose synthase-2 gene, with sugar content and red rot resistance, was evident. The functionally relevant SNPs and InDels, detected and validated in sugar pathway and disease resistance genes, and genic CAPS markers designed, would be of immense use in marker-assisted genetic improvement of sugarcane for sugar content and disease resistance.
This work was carried out at the National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi in the project on “Development and use of molecular markers for mapping genes for red rot resistance and sugar traits in sugarcane” funded by the Department of Biotechnology (DBT), Government of India.
 
Date 2016-08-04T09:46:09Z
2016-08-04T09:46:09Z
2016
 
Type Article
 
Identifier Plant Cell Reports, 35(8): 1629 – 1653
1432-203X
http://172.16.0.77:8080/jspui/handle/123456789/670
http://link.springer.com/article/10.1007/s00299-016-1978-y?view=classic
10.1007/s00299-016-1978-y
 
Language en_US
 
Publisher Springer