QTL Mapping and Validation of Adult Plant Resistance to Stripe Rust in Chinese Wheat Landrace Humai 15

Abstract

Stripe rust caused by Puccinia striiformis f. sp. tritici (Pst) is a devastating foliar disease that affects common wheat and barley throughout the world. The reasonable deployment of adult plant resistance (APR) wheat varieties is one of the best methods for controlling this disease. Wheat landraces are valuable resources for identifying the genes/QTLs responsible for disease resistance. Humai 15 is a Chinese spring wheat landrace and it has exhibited adequate levels of APR to the prevalent Pst races in field environments for many years. In this study, a population of 177 recombinant inbred lines (RILs) was derived from Humai 15 × Mingxian 169. After screening based on a 90K chip array using 45 RILs and Kompetitive Allelic Specific PCR marker genotyping for the population of RILs, a major effect QTL in Humai 15 was located on the centromere of chromosome 2B, where it accounted for up to 47.2% of the phenotypic variation. Two other minor QTL genes from Humai 15 were located on chromosome arms 3BS and 4BL. The Yr18 gene was identified on chromosome arm 7DS in Mingxian 169.

Keywords: Puccinia striiformis f. sp. tritici; Triticum aestivum; adult plant resistance (APR); fluorescence in situ hybridization (FISH); quantitative trait loci (QTL).

Figure 1

Frequency distribution of the relative area under the disease progress curve (rAUDPC) for the F_2:3 population in Yangling and Tianshui during 2012–2013 (A). Maximum disease severity (MDS) for the 177 RILs from Mingxian 169 × Humai 15 evaluated in Yangling, Jiangyou, and Tianshui during 2015–2016 and 2016–2017 (B). Mean values for the parents, Mingxian 169, and Humai 15 are indicated by arrows.

Figure 2

QTLs related to stripe rust resistance on chromosomes 2B (A–C), 4B/6A (D–F), 3B (G,H), and 7D (I). The QTLs were detected based on the relative area under the disease progress curve (rAUDPC) in the F_2:3 population (A,D), and by MDS in sub-populations (B,E,G,I) and the population of 177 RILs (C,F,H). The QTLs were identified by inclusive composite interval mapping (ICIM) with LOD peak values of more than 2.5.

Figure 3

Haplotypes of 149 common wheat cultivars in the QYrhm.nwafu-2BC interval. Two-dimensional (row and column) hierarchical clustering analysis was performed to group lines into haplotypes, as indicated by the colorized dendrogram along the top X-axis and the similarly marker order is shown along the left Y-axis. The matrix comprises 660K genotypic data where SNPs with the same alleles as Humai 15 allele are shaded in green, whereas SNPs with different alleles to Mingxian 169 are shaded in orange. The name and physical position of each 660K probe were anchored to the physical position based on IWGSC_refseqv1.0. The mean stripe rust disease severity score for each line is shown in the bar chart along the top X-axis. *n, Numbers of lines collapsed into a single haplotype (Table S2).

Figure 4

Fluorescence in situ hybridization (FISH) analysis of wheat lines Humai 15 (A) and Mingxian 169 (B). Karyotypes of all the wild type chromosomes and translocations of 5B (C), 7B (C), 4B (D), and 6A (D). FISH was conducted using Oligo-pTa535 (red) and Oligo-pSc119.2 (green) as probes.