Development and application of new genomics platforms for wheat breeding and pre-breeding

Awais Rasheed1,2

1* Quaid-i-Azam University, Pakistan

2* CIMMYT, China office

arasheed@qau.edu.pk

Abstract

Functional markers (FMs) are the most valuable markers for crop breeding. Low-cost and high-throughput genotyping for FMs could provide an excellent opportunity to effectively practice marker-assisted selection in breeding. Based on FMs, we developed and validated kompetitive allele specific PCR (KASP) assays for genes that underpin economically important traits in bread wheat including adaptability, grain yield, quality, and biotic and abiotic stress resistances. Finally, a KASP platform with a robust marker toolkit for high-throughput and cost-effective screening of 90 functional gene/loci in wheat was developed. It has three advantages: (1) high-throughput, 1536 cultivars can be genotyped with 142 available markers in 2-3 days; (2) low-cost, 9 cents USD per data point including DNA extraction; (3) good quality, highly consistent with normal PCR markers. It has potential application in wheat breeding to accelerate the characterization of crossing parents and advanced lines for marker-assisted selection of known genes. We also developed new 55K and 15K wheat TraitBreed Affymetrix SNP arrays, and a targeted genotyping-by-sequencing (GBS) platform “Triticum Geneseizer”. Such genotyping platforms have significant potential to apply for academic wheat research and applied breeding.

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​Keywords: Functional markers; Molecular Breeding; KASP markers; SNP chip; NGS