Detection of SNPs from Gossypium barbadense L. Cotton through whole-genome resequencing and their utilization

Working group session: 
Structural Genomics
Presentation type: 
15 minute Oral
Authors: 
Ishwarappa, S Katageri
N V, Mohan Kumar
S, Anjan Gowda
Author Affliation: 
Associate Director of Research and Professor, Regional Agricultural Research Station, UAS Campus, Vijayapura-586 101, India.
Research Associate, Research, Regional Agricultural Research Station, UAS Campus, Vijayapura-586 101, India.
Ph.D Scholar, Department of Genetics and Plant Breeding, University of Agricultural Sciences, Dharwad-580008, India.
Abstract: 
Upland cotton (Gossypium hirsutum) dominates the production of most-utilized natural textile fibre crop and contributes 95 per cent of the world’s cotton production but, it's fibre qualities are less superior than G. barbadense and this is the only best genetic resource among cultivated species for improving fibre quality traits of upland cotton. Higher the counts of the yarn, finer is the garment. G. hirsutum cotton produces 30-50's counts yarn whereas, G. barbadense is known for superior quality fibre, produces 60-120's counts yarn. Identification of more number of molecular markers in G. barbadense is very much necessary to construct a high-density linkage map/fine gene map/QTL map, which will ease the precise introgression of fibre QTLs in to upland cotton. The present study explored the feasibility of identifying single nucleotide polymorphism (SNP) markers between Suvin (known as Jewel in the Indian cotton crown for fiber quality) and BCS23-18-7 (known for high-yielding and early maturity) genotypes of G. barbadense cotton through whole genome re-sequencing. After filtering out poor quality reads, a total of 1,176,543,126 and 1,301,334,450 reads were obtained from Suvin and BCS23-18-7 respectively. By aligning the sequences with reference genomes, they recorded highest alignment with G. barbadense reference genome (97.44 & 95.27 % respectively) followed by G. hirsutum (95.03 & 93.03 % respectively), G. arboreum (78.29 & 77.05 % respectively), G. raimondii (95.16 & 54.47 % respectively). The highest number of 12,276,464 SNPs (10,110,752 homozygous) and Indels (1,248,940) were observed between Suvin and BCS23-18-7 when G. hirstum used as a reference genome. Whereas, 2,604,107 SNPs (1,020,162 homozygous) and Indels (592,364) were observed with reference genome G. barbadense. The total size of 1.98 Gb and 1.99 Gb scaffold assembly with the coverage of 77 and 77.6 percent of G. barbadense genome was constructed from Suvin and BCS23-18-7 respectively. Based on gene annotation for these polymorphic SNPs through reference genome, 20K SNPs responsible for fiber, abiotic and biotic stress related traits were considered for inclusion in SNP chip preparation. These SNP chip will be used for genotyping. Keywords: QTL, SNP, Assembly, Reference and Aligning