Developing KASP markers on a major stripe rust resistance QTL in TAM 111 using 90K array and genotyping-by-sequencing SNPs

Authors: YANG, YAN - Texas A&M Agrilife; BASNET, BHOJA - International Maize & Wheat Improvement Center (CIMMYT); IBRAHIM, AMIR - Texas A&M University; RUDD, JACKIE - Texas A&M Agrilife; Chen, Xianming; Bowden, Robert; XUE, QINGWU - Texas A&M Agrilife; WANG, SHICHEN - Texas A&M Agrilife; JOHNSON, CHARLES - Texas A&M Agrilife; METZ, RICHARD - Texas A&M Agrilife; MASON, RICHARD - University Of Arkansas; HAYS, DIRK - Texas A&M University; LIU, SHUYU - Texas A&M Agrilife

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/8/2018
Publication Date: 12/20/2018
Citation: Yang, Y., Basnet, B.R., Ibrahim, A.M., Rudd, J.C., Chen, X., Bowden, R.L., Xue, Q., Wang, S., Johnson, C., Metz, R., Mason, R.E., Hays, D.B., Liu, S. 2018. Developing KASP markers on a major stripe rust resistance QTL in TAM 111 using 90K array and genotyping-by-sequencing SNPs. Crop Science. 59(1):165-175. https://doi.org/10.2135/cropsci2018.05.0349.
DOI: https://doi.org/10.2135/cropsci2018.05.0349

Interpretive Summary: Stripe rust is an important disease of wheat in the United States and many other areas of the world. In order to identify the genetic basis of resistance in the winter wheat cultivar ‘TAM 111’, a mapping population of 124 recombinant inbred lines (RILs) developed from the cross “TAM 112/TAM 111” was evaluated against the stripe rust pathogen populations over eight field environments in the United States and against race PST-100 in the greenhouse. A high-density genetic map was constructed using the wheat 90K iSelect array and genotyping-by-sequencing (GBS) markers. A set of 6343 markers covering all 21 chromosomes were used for quantitative trait locus (QTL) analyses. The largest and most consistent stripe rust resistance QTL QYr.tamu-2B was identified on chromosome 2B and explained 12.0% to 76.1% of the phenotypic variance in infection type (IT) and 9.4% to 57.1% of the variance in disease severity (DS) across the environments in field and greenhouse. Six tightly linked single-nucleotide polymorphism (SNP) markers were converted to Kompetitive allele specific PCR (KASP) markers for high throughput screening of this 2B QTL. The 2B QTL was involved with significant epistatic interactions for both DS and IT as well as epistasis by environment interactions with QTL QYr.tamu-2A1 for DS only. These QTL can be combined with effective major genes to enhance the stripe rust resistance, and corresponding diagnostic markers can be applied through marker-assisted breeding.

Technical Abstract: Stripe rust, caused by Puccinia striiformis Westend. f. sp. tritici Erikss. (Pst), is an important disease of wheat (Triticum aestivum L.) in the United States and many other areas of the world. In order to identify the genetic basis of resistance in the winter wheat cultivar ‘TAM 111’, a mapping population of 124 F6 recombinant inbred lines (RILs) developed from the cross “TAM 112/TAM 111” was evaluated against Pst populations over eight field environments in the United States and against race PST-100 in the greenhouse. A high-density genetic map was constructed using the wheat 90K iSelect array and genotyping-by-sequencing (GBS) markers. A set of 6343 markers covering all 21 chromosomes, including 16 SSR and STS, 3335 GBS, and 2992 SNP markers from 90K array were used for QTL analyses. The largest and most consistent stripe rust resistance QTL QYr.tamu-2B was identified on chromosome 2B and explained 12.0% to 76.1% of the phenotypic variance in Infection type (IT) and 9.4% to 57.1% of the variance in disease severity (DS) across the environments in field and greenhouse. Six tightly linked SNP markers were converted to Kompetitive allele specific PCR (KASP) markers for high throughput screening of this 2B QTL. This QTL QYr.tamu-2B was involved with significant epistatic interactions both DS and IT as well as epistasis by environment interactions with QYr.tamu-2A1 for DS only. These QTL can be combined with effective major genes to enhance the stripe rust resistance, and corresponding diagnostic markers can be applied through marker-assisted breeding.