Mapping and validation of a novel major QTL for resistance to stripe rust in four wheat populations derived from landrace Qishanmai

Abstract

Wheat yield has been constrained by stripe rust disease globally. A wheat landrace (Qishanmai, QSM) consistently showed lower stripe rust severities in multiple year studies than susceptible check varieties including Suwon11 (SW) at the adult plant stage. To detect QTL for reducing the severity in QSM, 1218 recombinant inbred lines (RILs) were developed from SW × QSM. QTL detection was conducted firstly using 112 RILs selected for similarity in pheno-morphological characters. The 112 RILs were assessed for stripe rust severity at the 2nd leaf, 6th leaf and flag leaf stages under field and greenhouse conditions, and genotyping was done primarily with a single nucleotide polymorphism (SNP) array. On the basis of these phenotypic and genotypic data, a major QTL (QYr.cau-1DL) was detected on chromosome 1D at the 6th leaf and flag leaf stages. Further mapping was conducted by genotyping 1218 RILs using new simple sequence repeat (SSR) markers, which were developed by referring to the sequences of the wheat line Chinese Spring (IWGSC RefSeq v1.0). QYr.cau-1DL was mapped within a 0.5 cM (5.2 Mb) interval delimited by the SSR markers 1D-320.58 and 1D-325.79. These markers were applied to select for QYr.cau-1DL by screening F₂ or BC₄F₂ plants of the wheat crosses RL6058 × QSM, Lantian10 × QSM and Yannong21 × QSM. F_2:3 or BC₄F_2:3 families derived from the selected plants were assessed for stripe rust resistance in the fields of two locations and in a greenhouse. Wheat plants carrying the resistant marker haplotype in homozygous state for QYr.cau-1DL showed lower stripe rust severities (by 44% to 48%) than plants lacking this QTL. The trial of RL6058 (a carrier of Yr18) × QSM also indicated that QYr.cau-1DL had larger effect than Yr18 on reducing severity; they acted synergistically, yielding an elevated level of stripe rust resistance.

Keywords: QTL interaction; QTL mapping; disease resistance; marker-assisted selection; stripe rust; wheat landrace.

Figure 1

Frequency distribution of recombinant inbred lines (RILs) of Suwon11 (SW) × Qishanmai (QSM) for stripe rust severity. Disease was recorded on flag leaves in the fields of southern Gansu province (A) and Shandong province (B), and on 6th leaves (C) and 2nd leaves (D) in greenhouses. Mean severities are presented in parentheses.

Figure 2

Genetic map of QYr.cau-1DL region in chromosome arm 1DL and logarithm of the odds (LOD) curves. (A) Location of QYr.cau-1DL mapped using 112 recombinant inbred lines (RILs). (B) Location of QYr.cau-1DL refined based on the map of 1218 RILs. Marker names and intervals (in cM of Kosambi) between adjacent markers are shown along the chromosome orientated with the telomere of 1DL to the right. Arrow suggests approximate position of the centromere. Horizontal lines indicate the threshold LOD of 3.5. Each of the small triangles along the x axis represents a marker used for QTL mapping. For reading ease, only certain marker names are displayed, while all marker names with their positions are presented in Supplementary Table 5 .

Figure 3

DNA fragments produced from the marker loci 1D-320.58 (A) and 1D-325.79 (B) for QYr.cau-1DL, and cssfr5 (C) for Yr18 by PCR amplification with DNA templates from the five tested wheat lines. DNA fragments were separated using polyacrylamide gels for (A, B), while using agrose gel for (C). Primer sequences are presented in Supplementary Table 3 .

Figure 4

Boxplots showing effects of QYr.cau-1DL (represented by the flanking markers 1D-320.58 and 1D-325.79) on reducing stripe rust severity (A) and infection type (B) in Gansu field for LT × QSM and Shandong field for YN × QSM. R-plants carried the marker haplotype of stripe rust resistance in homozygous state at QYr.cau.-1DL and S-plants carried the haplotype of susceptibility in homozygous state. **** Indicates significant difference at α = 0.0001 based on an ANOVA and Tukey test. Small diamond and solid line within a box indicate the mean and median disease value, respectively. The top and bottom edges of a box illustrate the 75th and 25th percentiles, respectively. The whiskers outside a box extend to the extreme data points, and small circles denote outliers.

Figure 5

Boxplots showing the effects of QTL combinations on stripe rust severity in RL6058 × Qishanmai F_2:3 population in a greenhouse. The x-axis defines four F_2:3 family groups with different QTL combinations, i.e., presence of QYr.cau-1DL plus Yr18, QYr.cau-1DL alone, Yr18 alone, and None (neither QYr.cau-1DL nor Yr18), respectively. Refer to the legend of Figure 4 for descriptions of **** and box.

Figure 6

Physical positions of QYr.cau-1DL and the previously reported QTL for resistance to stripe rust on chromosome 1D (10-Mb tick size map) inferred by aligning marker sequences of these QTL to the 1D sequences in the IWGSC RefSeq v1.0 (IWGSC, 2018). Arrows indicate the approximate positions of previously reported QTL. Refer to Supplementary Table 10 for further information and a list of full references.