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http://223.31.159.10:8080/jspui/handle/123456789/670
Title: | Single nucleotide polymorphism in sugar pathway and disease resistance genes in sugarcane |
Authors: | Parida, Swarup K. Kalia, Sanjay Pandit, Awadhesh Nayak, Preetam Singh, Ram Kushal Gaikwad, Kishor Srivastava, Prem Shankar Singh, Nagendra K. Mohapatra, Trilochan |
Keywords: | CAPS Disease resistance genes SNPs Sugar pathway genes Sugarcane |
Issue Date: | 2016 |
Publisher: | Springer |
Citation: | Plant Cell Reports, 35(8): 1629 – 1653 |
Abstract: | 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. |
Description: | Accepted date: 21 March 2016 |
URI: | http://172.16.0.77:8080/jspui/handle/123456789/670 |
ISSN: | 1432-203X |
Appears in Collections: | Institutional Publications |
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File | Description | Size | Format | |
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Parida SK_2016_6.pdf Restricted Access | 6.29 MB | Adobe PDF | View/Open Request a copy |
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