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ARS Home » Plains Area » Lubbock, Texas » Cropping Systems Research Laboratory » Plant Stress and Germplasm Development Research » Research » Publications at this Location » Publication #347693

Title: Marker assisted selection in sorghum using KASP assay for detection of single nucleotide polymorphism/insertion deletion

item Burow, Gloria
item Chopra, Ratan
item Hughes, Halee
item Burke, John
item Xin, Zhanguo

Submitted to: Methods in Molecular Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/17/2018
Publication Date: 12/1/2018
Citation: Burow, G.B., Chopra, R., Hughes, H.J., Burke, J.J., Xin, Z. 2018. Marker assisted selection in sorghum using KASP assay for detection of single nucleotide polymorphism/insertion deletion. Methods in Molecular Biology. 1931:75-84.

Interpretive Summary: Development of modern sorghum varieties is a time consuming process; however, new technologies including marker assisted selection (MAS) maybe able to expedite the process. The translation of causal single nucleotide polymorphisms (SNPs) into perfect DNA markers for rapid assay and accurate prediction of a phenotype is an important goal and application of marker assisted selection during introgression and for majority of desirable traits needed in continued crop improvement. This report focusses on the description of methods pertaining to development and assay of SNP/Insertion deletion (InDel) markers found in the causal gene using the SNPs for lack of wax covering the underside of the leaves and stem (bloomless trait) of sorghum as a case study to demonstrate rapid genotyping and efficient selection for the trait in a marker assisted backcrossing project . The application of Kompetitive Allele Specific Polymerase Chain Reaction(KASP) assay is described here as the genotyping technology, because of its ease of use, consistency and cost effectiveness. In sorghum, marker assisted backcrossing using KASP can expedite the development of near isogenic lines to 3 years compared to 5- 6 years using conventional method of backcrossing and improved overall efficiency both in cost and accuracy of introgression.

Technical Abstract: Marker assisted selection (MAS), an advance tool in plant breeding that allows accurate and efficient introgression of important agronomic trait(s) from a germplasm source to desired elite lines, is applied to sorghum recently. Here, we report the methods for deployment of MAS for trait introgression using endpoint genotyping technology for single nucleotide polymorphism (SNP) /insertion deletion (InDel) coupled with application of KASP (Kompetitive Allele Specific Polymerase Chain Reaction[PCR]) chemistry towards selection of parents for advancement of generation without going through the laborious and time consuming phenotypic selection and additional generations for selection of desired individuals. This MAS-SNP marker assisted backcrossing scheme can be applied to accurately select heterozygotes for use as allele donor parent in each backcross generation, thus expediting the backcrossing scheme and resulting in time savings of three years compared to conventional methods of introgression practiced in sorghum breeding and improvement.