Genetic Analysis of Adult Plant Resistance to Stripe Rust in Common Wheat Cultivar "Pascal"

Abstract

Wheat stripe rust is an important foliar disease that affects the wheat yield globally. Breeding for resistant wheat varieties is one of the most economically and environmentally effective ways to control this disease. The common wheat (Triticum aestivum L.) cultivar "Pascal" exhibited susceptibility to stripe rust at the seedling stage but it showed high resistance to stripe rust at the adult plant stage over 20 years in Gansu, a hotspot of the disease in northwestern China. To understand the genetic mechanism of stripe rust resistance in this cultivar, a 55K SNP array was used to analyze the two parents and the 220 recombinant inbred lines (RILs) derived from the cross of "Huixianhong" × "Pascal." We detected three new stripe rust adult plant resistance (APR) quantitative trait locus (QTL) contributed by Pascal, viz. QYr.gaas-1AL, QYr.gaas-3DL, and QYr.gaas-5AS, using the inclusive composite interval mapping method. They were flanked by SNP markers AX-111218361-AX-110577861, AX-111460455-AX-108798599, and AX-111523523-AX-110028503, respectively, and explained the phenotypic variation ranging from 11.0 to 23.1%. Bulked segregant exome capture sequencing (BSE-Seq) was used for fine mapping of QYr.gaas-1AL and selection of candidate genes, TraesCS1A02G313700, TraesCS1A02G313800, and TraesCS1A02G314900 for QYr.gaas-1AL. KASP markers BSE-1A-12 and HXPA-3D for QYr.gaas-1AL and QYr.gaas-3DL were developed for breeders to develop durable stripe rust-resistant wheat varieties.

Keywords: adult plant resistance; genetic mapping; quantitative traits; stripe rust; wheat.

FIGURE 1

The two parents Huixianhong (left) and Pascal (right) showed susceptible against stripe rust race CYR32 (A) and CYR33 (B) at the seedling stage. The response of susceptible parent Huixianhong (C) and the resistant parent Pascal (D) in the adult plant stage under Gansu province field test.

FIGURE 2

Frequency distributions of 220 Huixianhong/Pascal F₅ recombinant inbred lines (RILs) for final disease severity of stripe rust in field traits at Gansu Province during 2017–2018 (GS2018), 2018–2019 (GS2019), and at Sichuan Province during 2018–2019 (SC2019).

FIGURE 3

Likelihood plots of quantitative trait loci (QTL) for adult plant resistance to stripe rust on chromosomes 1AL (A) after adding three KASP markers BSE-1A-2, BSE-1A-6, and BSE-1A-12, 3DL (B) after adding KASP marker HXPA-3D and 5AS (C) identified by IciMapping 4.1 in the Huixianhong/Pascal RIL population. The significant LOD threshold was based on 1,000 permutations. Positions (in cM) of the molecular markers along chromosomes are shown on the vertical axes using cumulated genetic distances. KASP markers BSE-1A-2, BSE-1A-6, and BSE-1A-12 near QYr.gaas-1AL were designed based on the SNP of BSE-Seq in the interval of original marker AX-111218361—AX-110577861. New marker BSE-1A-12 and SNP marker AX-110577861 were closely linked with QYr.gaas-1AL identified in the present study. we converted SNP marker AX-109580758 as a KASP marker named HXPA-3D to detect 220 RIL families. KASP marker HXPA-3D was closely linked with QYr.gaas-3DL identified in the present study. GS2018, final stripe rust severity during Gansu 2017–2018; GS2019, final stripe rust severity, during Gansu 2018–2019; SC2019, final stripe rust severity during Sichuan 2018–2019; YRM, the mean final disease severity of each season; BLUP, best linear unbiased prediction.

FIGURE 4

Results of the BSE-Seq analysis method. Fitted ED on chromosome 1A (A) and ED after zooming in the area near the maximum (B). SNP count between R bulk same as Pascal and S bulk same as Huixianhong on chromosome 1A (C), and SNP count after zooming in the area near the maximum (D).