Single nucleotide polymorphism in sugar pathway and disease resistance genes in sugarcane.
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.
National Research Centre on Plant Biotechnology, New Delhi, 110012, India.|National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
Swarup K
SK
Parida
National Research Centre on Plant Biotechnology, New Delhi, 110012, India.|Department of Biotechnology, CGO Complex, Lodhi Road, New Delhi, 110003, India.
Sanjay
S
Kalia
National Research Centre on Plant Biotechnology, New Delhi, 110012, India.|National Centre for Biological Sciences, Bengaluru, 560065, Karnataka , India.
Awadhesh
A
Pandit
Utkal University, Vanivihar, Bhubaneswar, Odisha, 751004, India.
Preetam
P
Nayak
U.P. Council of Sugarcane Research, Shahjahanpur, Uttar Pradesh, 242001, India.
Ram Kushal
RK
Singh
National Research Centre on Plant Biotechnology, New Delhi, 110012, India.
Kishor
K
Gaikwad
Department of Biotechnology, Jamia Hamdard University, New Delhi, 110062, India.
Prem Shankar
PS
Srivastava
National Research Centre on Plant Biotechnology, New Delhi, 110012, India.
Nagendra K
NK
Singh
National Research Centre on Plant Biotechnology, New Delhi, 110012, India. tmnrcpb@gmail.com.|Indian Council of Agricultural Research, Krishi Bhavan, New Delhi, 110001, India. tmnrcpb@gmail.com.
Trilochan
T
Mohapatra
D001483:Base Sequence; D050260:Carbohydrate Metabolism / Q000235:genetics*; D060467:Disease Resistance / Q000235:genetics*; D020869:Gene Expression Profiling; D017343:Genes, Plant; D005819:Genetic Markers; D060005:Genotyping Techniques; D006239:Haplotypes / Q000235:genetics; D054643:INDEL Mutation; D010935:Plant Diseases / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D015203:Reproducibility of Results; D031786:Saccharum / Q000235:genetics*; D016415:Sequence Alignment
D005819:Genetic Markers
CAPS; Disease resistance genes; SNPs; Sugar pathway genes; Sugarcane