1. Introduction
Bread wheat (
Triticum aestivum) is one of the most important food crops for mankind and the security of wheat production benefits economic development and social stability. However, wheat production in China is continually challenged by diseases, including rusts, powdery mildew, and Fusarium head blight. Stripe rust, caused by
Puccinia striiformis f. sp.
tritici (
Pst), is one of the most devastating fungal diseases in many areas around the world. Beddow et al. [
1] estimated that up to 88% of the world’s wheat cultivars had become susceptible since 1960 and that annual losses amounted to 5.47 million tonnes. Resistance is recognized as the most effective, economic, and environmentally safe strategy for control of stripe rust, although fungicides can also effectively control the disease, provided they are used in a timely and safe manner [
2,
3].
Resistance to stripe rust is generally categorized as seeding (or all-stage) resistance and adult-plant resistance (APR, including high temperature APR) according to the growth stage at which it is expressed [
2,
4]. Up until now, seventy-nine genes for stripe rust resistance (
Yr1 to
Yr79) have been permanently named, but dozens of temporarily designated and hundreds of quantitative trait loci (QTL) have been reported and mapped to the wheat genome [
5,
6]. Among the formally designated stripe rust resistance genes, 55 confer seeding resistance and 24 genes are described as APR genes [
6,
7,
8,
9,
10]. Some of these genes have been very widely deployed in agriculture by major epidemics following the emergence and increase of new virulent pathogen races. Examples of such occurrences of “boom and bust” situations in China include the use of
Yr1 from the 1950s,
Yr9 from the 1970s (overcome by Chinese yellow rust race CYR29), so-called Fan 6 resistance from the 1990s (race CYR31), and
Yr24/
Yr26 from the 2000s (CYR34). At the time of its downfall in the late 1990s,
Yr9, present in a 1RS·1BL translocation, was deployed in more than 80% of the released cultivars in China [
11]. The lessons learnt from these events were that widespread deployment of a single highly effective resistance gene ultimately leads to failure, with detrimental effects proportional to area of wheat cultivars bearing that gene. With the aim to avoid the overuse of individual resistance genes, avoid deployment of combinations of effective resistance genes, and to use resistance, sources with reputed durability were generally applied. It is therefore necessary to find new sources of stripe rust resistance to identify the underlying genes for resistance and to convince breeders that they are worthy of use in current breeding programs.
The stripe rust in Sichuan province is the most serious foliar disease affecting wheat production. Wheat cultivars Chuanmai 42 (CH42) and Chuanmai 55 (CH55) developed by the Crop Research Institute, Sichuan Academy of Agricultural Sciences, were released in 2004 and 2009, respectively. CH42 was a synthetic wheat derivative with
YrCH42 (
=Yr24/Yr26) [
12] and maintained novel stripe rust resistance before 2010 in Sichuan [
13]. As a new high-yielding and excellent quality variety, CH55 was selected from the cross SW3243/SW8688. It displayed a high level of resistance to stripe rust over a decade. However, the molecular genetic basis of CH55 for stripe rust resistance at adult plant stage has not been investigated.
Specific locus amplified fragment sequencing (SLAF-seq) is a recently developed, high-throughput strategy for large-scale single nucleotide polymorphism (SNP) discovery and genotyping, based on next generation sequencing (NGS) technology [
14]. It is also cost-effective. SLAF-seq technology has been used in various species and different types of populations. For example, a high-density genetic map of cucumber (
Cucumis sativus L.) spanning 845.87-cM with an average genetic distance of 0.45 cM was constructed for an F
2 population [
15]. Zhang et al. [
16] similarly applied an SLAF-seq strategy in constructing a genetic map of 907.8 cM for a segregating
Agropyron F
1 population. Hu et al. [
17] identified and cloned a candidate gene associated with thousand-grain weight (TGW) in wheat using DNA bulks of recombinant inbred lines (RILs). Yin et al. [
18] fine-mapped the stripe rust resistance gene
YrR39 to a 17.39 Mb segment on wheat chromosome 4B using SLAF-seq combined with bulked segregant analysis (BSA) of F
2 and BC
1 progenies. However, SLAF-seq has not been used to construct a high-density genetic map for an entire wheat RIL population and then identify QTLs for disease resistance.
In this study, an RIL population from a cross between CH42 and CH55 were developed for QTL mapping of stripe rust resistance and the SLAF-seq for individual RILs was used to construct a high-density genetic map for identifying the QTLs from CH55 and CH42 backgrounds.
3. Discussion
In order to determine the relationship between the three QTLs identified in the present study and other
Yr genes and QTLs reported previously, we compared their physical locations by basic local alignment search tool (BLAST) analysis of the International Wheat Genome Sequencing Consortium (IWGSC) RefSeq v1.0 genome, which was shown in
Figure 4 and
Table 9.
Qyr.saas-1B, contributed by CH55, was significantly associated with resistance to stripe rust in all environments. It was physically located between 664.08 Mbp and 673.64 Mbp in the distal region of chromosome 1BL (
Table 9,
Table S1,
Figure 4a). This region is rich in stripe rust resistance genes and QTLs, such as
Yr21 [
20],
Yr24/
Yr26 [
21], and
Yr29 [
22,
23]. The physical interval of
Qyr.saas-1B overlapped with
Yr29,
QYr.cim-1BL1 [
24],
QYr.cim-1BL2 [
25],
QYr.spa-1B [
26],
QYr.ucw-1BL [
23,
27], and
QYr.sicau-1B.3 [
28]. We concluded that
Qyr.saas-1B was most likely
Yr29. However, more work is needed to conclude that
Qyr.saas-1B is
Yr29. The
Yr29 is an APR gene first reported in cultivar Pavon 76 [
29], but has since been identified in many different genetic backgrounds, including Pastor [
30], Francolin#1 [
24], and Klein Chajá [
27]. In the present study, CH55 showed high resistance to stripe rust in all four environments with low disease severities of 15–40, with
Qyr.saas-1B explaining 6.24%–34.22% of the phenotypic variation. This indicates that
Qyr.saas-1B is relatively effective in Sichuan. Moreover, extremely low disease severity scores occurred when
Qyr.saas-1B was combined with the other two QTLs with rather positive additive effects also being detected (
Table 8). Therefore, the
Qyr.saas-1B is considered to be a valuable component of resistance for use in Sichuan breeding programs combined with other genes.
Qyr.saas-7B, derived from CH42, also had consistent QTLs across the environments; it was physically located between 678.64 Mbp and 706.81 Mbp in the distal region of chromosome 7BL (
Table 9,
Table S1,
Figure 4c). Several permanently- and temporarily-named stripe rust resistance genes have been mapped to chromosome 7BL (
Table 9), including
Yr2 [
31],
Yr39 [
32],
Yr52 [
33],
Yr59 [
34],
Yr67 (
YrC591) [
35],
Yr79 [
6],
YrZH84 [
36], and
YrMY37 [
7]. None of the physical intervals for these genes overlapped with
Qyr.saas-7B (
Table 9,
Figure 4c). A number of QTLs were also mapped to chromosome 7BL (
Table 9), including
QTL-7B.1 [
37],
QTL-7B.2 [
38],
QTL-7B.3 [
39],
QYr.nsw-7B [
40],
QYr.caas-7BL.1, and
QYr.caas-
7BL.2 [
33]. The physical interval of
QYr.nsw-7B from Tiritea [
40] overlapped with
Qyr.saas-7B (
Table 9,
Figure 4c), suggesting they could be the same locus. Similar to the genetic variation across environments, both
QYr.nsw-7B [
40] and the present
Qyr.saas-7B could be important as a component of multiple-gene resistance to stripe rust. Previous study has located a stripe rust resistance gene
YrCH42 on the 1B chromosome of CH42 [
12], but the QTL of
Qyr.saas-7B from CH42 was not detected as it was in this study. It is possible that the stripe rust resistance of
YrCH42 was overcome with the occurrence of
Pst race CYR34, which was inoculated in this study [
13]. There is another possibility that the present study used the high-throughput SLAF markers to screen an entire wheat RIL population between CH45 and CH42, which is higher resolution than the previous study for CH42 by SSR-PCR assay [
12].
A minor QTL from CH55 was identified on chromosome 2AL. The
Qyr.saas-2A was physically located between 677.90 Mbp and 701.74 Mbp in chromosome 2AL (
Table 9,
Table S1,
Figure 4b).
Yr1 [
41],
Yr32 [
42], and
YrJ22 [
43] were mapped to 2AL, but these were genes of large effect.
Qyr.saas-2A was likely to be a new stripe rust resistance locus based on its different physical location (
Table 9,
Figure 4b). This QTL was detected only in XD2017 and JT2017, which explained 3.77% and 5.29% of the phenotypic variation, respectively (
Table 7). The effect of
Qyr.saas-2A was much smaller than that of
Qyr.saas-1B and
Qyr.saas-7B. However, a significant additive effect in
Qyr.saas-2A was observed. Singh et al. [
44] indicated that an adequate level of slow rusting resistance could be achieved by the additive/complementary effects of three to five genes. This has been supported by many reports, including those of Yang et al. [
45], Lan et al. [
24], and Rosewarne et al. [
46]. Similarly, the disease severities of RILs approached immunity when
Qyr.saas-2A was combined with two other QTLs,
Qyr.saas-1B and
Qyr.saas-7B, in XD2016. There is repeated evidence that an effective and stable level of adult plant stripe rust resistance can be achieved by using combinations of genes that individually confer relatively small effects. Therefore, although the effect of
Qyr.saas-2A was small, it provided enhancement effects and therefore could be useful in Sichuan wheat breeding for multiple gene resistance to stripe rust.
Based on the studies of chromosome composition of CH55 revealed by FISH analysis (
Figure 1), we found that CH55 contained both 1RS·1BL and 5B-7B reciprocal translocation chromosomes. The 1RS·1BL translocation is still widely used in wheat breeding because of the superior genes for grain yield and stress tolerances in 1RS [
47]. In the present study, the 1BL arm of 1RS·1BL in CH55 carried the stripe rust resistance QTL
Qyr.saas-1B. According to a previous study, the alien chromatin suppresses the recombination between normal and translocated chromosomes [
48]. Therefore, the selection of 1RS·1BL accumulates excellent agronomic characteristics and resistance with high frequency in breeding practice. Moreover, the 5B–7B reciprocal translocation is possibly of French origin according to the genealogy of CH55. It was found that the stripe rust resistance QTL
QYr.ufs-5B was located on 5BS in the 5B–7B reciprocal translocation [
49], which requires further validation by
Pst races in different environments for CH55.