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Article

Identification and Mapping of QTLs for Adult Plant Resistance in Wheat Line XK502

by
Xianli Feng
,
Ming Huang
,
Xiaoqin Lou
,
Xue Yang
,
Boxun Yu
,
Kebing Huang
and
Suizhuang Yang
*
Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
*
Author to whom correspondence should be addressed.
Plants 2024, 13(17), 2365; https://doi.org/10.3390/plants13172365
Submission received: 23 July 2024 / Revised: 20 August 2024 / Accepted: 22 August 2024 / Published: 25 August 2024
(This article belongs to the Section Plant Genetics, Genomics and Biotechnology)
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Abstract

:
Stripe rust is a serious wheat disease occurring worldwide. At present, the most effective way to control it is to grow resistant cultivars. In this study, a population of 221 recombinant inbred lines (RILs) derived via single-seed descent from a hybrid of a susceptible wheat line, SY95-71, and a resistant line, XK502, was tested in three crop seasons from 2022 to 2024 in five environments. A genetic linkage map was constructed using 12,577 single-nucleotide polymorphisms (SNPs). Based on the phenotypic data of infection severity and the linkage map, five quantitative trait loci (QTL) for adult plant resistance (APR) were detected using the inclusive composite interval mapping (ICIM) method. These five loci are QYrxk502.swust-1BL, QYrxk502.swust-2BL, QYrxk502.swust-3AS, QYrxk502.swust-3BS, and QYrxk502.swust-7BS, explaining 5.67–19.64%, 9.63–36.74%, 9.58–11.30%, 9.76–23.98%, and 8.02–12.41% of the phenotypic variation, respectively. All these QTL originated from the resistant parent XK502. By comparison with the locations of known stripe rust resistance genes, three of the detected QTL, QYrxk502.swust-3AS, QYrxk502.swust-3BS, and QYrxk502.swust-7BS, may harbor new, unidentified genes. From among the tested RILs, 16 lines were selected with good field stripe rust resistance and acceptable agronomic traits for inclusion in breeding programs.

1. Introduction

Wheat stripe rust, caused by Puccinia striiformis Westend. f. sp. tritici Erikss. (Pst) [1], is one of the most serious diseases in the world. Losses due to stripe rust typically range from 10% to 70% in commercial production environments [2]. Between 1975 and 2012, the average losses of susceptible cultivars of winter and spring wheat near Pullman, Washington, USA, were 36% and 30%, respectively [3]. In 2008, wheat stripe rust in Punjab, India, caused losses of about INR 236 million [4]. In 2010, wheat stripe rust that swept through Central and West Asia caused yield losses of 20% to 70% in different countries [5]. In the winter and spring wheat regions of Northwest China, Southwest China, North China, and the Yellow and Huaihai Seas, the annual incidence of stripe rust is estimated to be about 4–5.3 million hectares [6].
The identification and deployment of new genes for stripe rust resistance is an ongoing struggle [7,8,9,10]. To date, 86 stripe rust resistance genes (Yr1–Yr86) have been formally named, mainly from common wheat [11]. In addition, more than 300 quantitative trait loci (QTL) have been reported [11,12,13,14,15]. According to the expression period of stripe rust resistance genes, they can be divided into all-stage resistance (ASR) genes and adult plant resistance (APR) genes. A single ASR gene is easily overcome by new Pst races [5,16,17,18]. Adult plant resistance genes usually provide race-nonspecific resistance and are more durable, which can better solve the current difficulties faced by wheat stripe rust resistance breeding [19,20]. Combining APR genes with effective ASR genes in the future is the best way to breed wheat cultivars with high levels of durable resistance [21].
At present, single-nucleotide polymorphism (SNP) markers are often used for quantitative trait locus (QTL) detection, which has higher accuracy and density than other molecular markers [22,23,24,25,26,27,28]. It has been widely used in wheat QTL positioning and whole-genome association analysis, providing valuable markers and information for genetic analysis and breeding [29]. The wheat 55K SNP array was developed by the Chinese Academy of Agricultural Sciences based on the 660K SNP array combined with thousands of local materials [30]. It is more suitable for the research of domestic wheat germplasm materials and is also of great significance for cultivar identification and gene positioning [31].
In this study, 221 RILs and a 55K SNP array consisting of the mapping population SY95-71/XK502 were used to profile the wheat line XK502, which showed a high level of resistance in many years of field trials, to explore the stripe rust resistance line of XK502, detect QTLs, obtain molecular markers closely linked to them, and identify QTLs by comparing their chromosomal locations with previously reported stripe rust resistance QTLs.

2. Results

2.1. Phenotypic Analysis

According to the seedling identification in the greenhouse, the parents SY95-71, XK502, and the susceptible control Mingxian 169 (MX169) showed high susceptibility with infection type (IT) = 8,9 to Pst minor races CRY32, CRY33, and CRY34 (Figure 1A–C), and the surface of the leaves was covered with numerous spore mounds.
The identification of wheat stripe rust resistance took place in five environments: in Jiangyou (JY; 31°31′ N, 104°51′ E) in 2022 (22), in both Mianyang (MY; 31°27′ N, 104°68′ E) and Jiangyou in 2023 (23), and in the experimental fields of Guangyuan (GY; 31°88′ N, 106°01′ E) and Jiangyou in 2024 (24), in Sichuan Province. In all environments, SY95-71 showed high susceptibility, with IT = 8,9 and a disease severity (DS) of ≥85% (Figure 1D); the MX169 was also highly susceptible (IT = 8,9; DS ≥ 80%). The resistant parent XK502 (Figure 1D) exhibited high resistance characteristics (IT = 1–3, DS = 0–5%), suggesting that XK502 is a resistant line at the adult plant stage. The IT of the RIL population was in the range of 0–9 (Figure 2), and DS was in the range of 0–100%; additionally, IT and DS were continuously distributed and approximately normally distributed, indicating the presence of quantitative trait loci in the SY95-71/XK502 recombinant inbred line population (Figure 3).
A correlation analysis showed that 221 RILs had significant correlations between IT and DS in the five environments (r = 0.49–0.75, p < 0.001 for IT; r = 0.53–0.73, p < 0.001 for DS) (Table 1). In the analysis of variance (ANOVA), IT and DS showed extremely significant differences among different genotypes, different environments, and the interaction between different genotypes × different environments (p < 0.001). The broad-sense heritability (h2b) of IT was 0.90 and that of DS was 0.89, indicating that this trait variation was less affected by the environment and was mainly controlled by genes. Resistance genes play an important role in reducing the severity of the disease (Table 2).

2.2. QTL Analysis of Stripe Rust Resistance

A genetic map was constructed using 12,577 SNP markers with known chromosomal locations. On average, there were 599 markers distributed on each chromosome, and the average genetic distance between two markers was 0.97 cM. The genetic map was combined with IT and DS data to preliminarily detect the stripe rust resistance QTL using the inclusive composite interval mapping (ICIM) method. A total of five adult plant resistance QTLs were detected, which were located at chromosomes 1BL, 2BL, 3AS, 3BS, and 7BS, tentatively named QYrxk502.swust-1BL, QYrxk502.swust-2BL, QYrxk502.swust-3AS, QYrxk502.swust-3BS, and QYrxk502.swust-7BS, respectively. All QTLs were derived from the resistant parent XK502 (Supplemental Table S1, Figure 4). Among them, QYrxk502.swust-1BL, QYrxk502.swust-2BL, QYrxk502.swust-3BS, and QYrxk502.swust-7BS have appeared in four or more environments and were considered stable QTLs.
QYrxk502.swust-1BL, located between markers AX-109335890 and AX-109389405, with a genetic distance of 80.46–81.54 cM, explained 5.96–19.64% and 5.67–19.60% of the phenotypic variation of IT and DS, respectively. QYrxk502.swust-2BL, located between markers AX-108884194 and AX-110024591, with a genetic distance of 361.45–362.20 cM, explained 10.04–36.74% and 9.63–34.50% of the phenotypic variation of IT and DS, respectively. QYrxk502.swust-3AS, located between markers AX-111631905 and AX-109308178, with a genetic distance of 307.78–317.30 cM, explained 10.26–10.88% and 9.58–11.30% of the phenotypic variation of IT and DS, respectively. QYrxk502.swust-3BS, located between markers AX-108747357 and AX-109438796, with a genetic distance of 47.20–57.27 cM, explained 9.76–20.79% and 11.27–23.98% of the phenotypic variation of IT and DS, respectively. QYrxk502.swust-7BS, located between markers AX-109968088 and AX-110982135, with a genetic distance of 405.25–406.79 cM, explained 8.02–11.90% and 8.81–12.41% of the phenotypic variation of IT and DS, respectively. Different effects of the same QTL in different environments may be caused by specific environments and different disease pressures. Inclusive composite interval mapping of digenic EPI static (ICIM-EPI) analysis was used to perform pairwise analysis of the QTL regions of chromosomes 1BL, 2BL, 3AS, 3BS, and 7BS. The results showed that there was no epistasis between these five QTLs.
Among the five QTLs, QYrxk502.swust-1BL and QYrxk502.swust-3BS overlapped with Yr29 and Yr30 in Chinese spring wheat and had the same resistance type, so these two QTLs may be Yr29 and Yr30. However, Yr29 is closely linked to the leaf tip necrosis (LTN) gene (leaf tip necrosis occurs when this gene is present), but XK502 was not observed to exhibit leaf tip necrosis in this study, so QYrxk502.swust-1BL was not Yr29. Yr30 was linked to the morphological marker pseudo-black husk (PBC), and wheat carrying this gene will gradually turn black in the husk and internodes in the late grain-filling period. Although the resistant parent XK502 in this study showed the characteristic of blackening of glumes in the late grain-filling period (Figure 5A), we detected the flanking marker WMS533 of Yr30 but failed to find it in XK502 (Figure 5B), so QYrxk502.swust-3BS was not Yr30 either.

2.3. Additive Effect Analysis for QTL

In order to determine the effects of different QTL on stripe rust, 221 RILs were divided into five groups (Table 3), and the effect sizes of these five QTL were determined based on the average infection type and disease severity as QYrxk502.swust-3BS > QYrxk502.swust-2BL > QYrxk502.swust-7BS > QYrxk502.swust-3AS > QYrxk502.swust-1BL. Obviously, the average IT and DS of RILs carrying any QTL were lower than those without QTL. The 221 recombinant inbred lines were divided into six groups according to the number of QTLs they contained (Figure 6). The average IT and DS of RILs without QTL were 8.21 and 82.57%, respectively, which were similar to those of the susceptible parent SY95-71. The average IT and DS of RILs containing one QTL were 7.12 and 70.60%, respectively, which were 13.42% and 14.50% lower than those without QTLs; the average IT and DS of RILs containing two QTL were 5.04 and 40.97%, respectively, which were 38.61% and 50.38% lower than those without QTL; the average IT and DS of RILs containing three QTL were 4.39 and 30.60%, respectively, which were 46.53% and 62.94% lower than those without QTL. The average IT and DS of RILs containing four QTL were 3.46 and 17.55%, respectively, which were 57.86% and 78.75% lower than those without QTL. The average IT and DS of RILs containing five QTL were 2.9 and 7.8%, respectively, which were reduced by 64.68% and 90.55% compared with RILs without QTL, and were comparable to the resistant parent XK502. This indicates that the clustering of multiple QTL for adult plant resistance can enhance wheat resistance to stripe rust.

2.4. Selection of Breeding Lines

The average plant height (PH) of the parents SY95-71 and XK502 was 83.58 cm and 97.75 cm, respectively, and the average PH of the RILs was 66.92–110.83 cm. The average productive tiller number (PTN) of SY95-71 and XK502 was 7 and 9, respectively, and the average PTN of the RILs was 5–12. The average spike length (SL) of SY95-71 and XK502 was 8.33 cm and 10.38 cm, respectively, and the average SL of RILs was 6.68–12.83 cm. The average thousand-kernel weight (TKW) of SY95-71 and XK502 was 33.68 g and 44.12 g, respectively, and the average TKW of the RILs was 28.78–61.14 g. The average grain length (GL) of SY95-71 and XK502 was 5.5 and 6.62 mm, respectively, and the average GL of the RILs was 5.29–7.08 mm. The average grain width (GW) of SY95-71 and XK502 was 2.92 and 3.14 mm, respectively, and the average GW of the RILs was 2.53–3.65 mm. The average grain length–width ratio (LWR) of SY95-71 and XK502 was 1.90 and 2.12, respectively, and the average LWR of the RILs was 1.71–2.34. Correlation analysis showed that IT and DS were extremely significantly negatively correlated with the first six agronomic traits (p < 0.001), which showed that the key to improving wheat agronomic traits is to ensure the resistance of the crop (Table 4).
The criteria for screening RILs are as follows: PH = 80–90 cm, PTN = 6–11 spikes, spike length > 8.5 cm, TKW > 40 g, grain length > 5.5 mm, grain width > 3 mm, length–width ratio = 1.5–2.5. A total of 16 eligible families were selected from the 221 RILs (Supplemental Table S2). These lines contained at least two QTL and, at most, four QTL.

3. Discussion

Genes for adult plant resistance are important in wheat stripe rust resistance research. They have a longer-lasting resistance than the ASR gene. In the recombinant inbred line population composed of SY95-71/XK502, we detected five adult plant resistance QTL, temporarily named QYrxk502.swust-1BL, QYrxk502.swust-2BL, QYrxk502.swust-3AS, QYrxk502.swust-3BS, and QYrxk502.swust-7BS. To determine the relationship between the QTL mapped in this study and the reported “Yr” genes/QTLs, we compared the relative physical distances of these loci based on Chinese spring wheat (IWGSC Ref Seq v.1.0).
QYrxk502.swust-1BL is located between markers AX-109335890 and AX-109389405 in the physical interval 670,382,321–670,593,327 bp. The genes that have been officially named on wheat chromosome 1BL are Yr21, Yr26, and Yr29, of which, Yr21 [33] and Yr26 [34] are ASR genes. Yr29 is an APR gene that is closely linked to the SSR marker Xwmc44 and has a physical location of 678,736,681 bp [35]. It is also closely associated with the leaf tip necrosis LTN gene, but no leaf tip necrosis was observed in XK502 in the field in this study, so QYrxk502.swust-1BL is not Yr29. The Yr29 is widely distributed in CIMMYT wheat germplasm. QYr.hebau-1BL [36], QYr.ucw-1BL [37], QYr.crc-1BL [38], QYr.cim-1BL [39], QYrCW357-1BL [40], QYr.sicau-1BL [26], and QYr.hazu-1BL [41] are all likely to be Yr29. In addition, several tentatively named QTL have been previously reported on chromosome 1BL, with YrNS-1 flanking markers Xgwm124 and Xwmc719, and a physical interval of 638,898,514–664,520,756 bp [42]. QYrsv.swust-1BL.1 is flanked by markers IWB5732 and IWB4839, with a physical range of 670,783,574–671,505,487 bp [43]. The flanking markers for QYr.sdau-1BL are KASP_63005 and KASP_19405, with a physical interval of 655.7–677.3 Mb [9]. QYr.gaas.1B.1 was flanked by AX-108745931 and AX-110017315, with a physical interval of 667,012,868–667,229,049 bp [44]. QYr.sicau-1B.1 is linked to SSR marker Xwmc156, with a physical location of 462,460,534 bp [45]. QYrxk502.swust-1BL lies within the physical interval of QYr.sdau-1BL, and further research is needed to confirm the relationship.
QYrxk502.swust-2BL is located between markers AX-108884194 and AX-110024591, with a physical range of 683,285,668–690,205,985 bp. The genes that have been officially named on wheat chromosome 2BL are Yr5 [46], Yr7 [47], Yr43 [48], Yr44 [49], and Yr53 [50], all of which belong to the ASR genes, whereas QYrxk502.swust-2BL belongs to the APR genes. In addition, several QTL were located on chromosome 2BL: QYr.hbaas-2BL flanking marker is IWA586, and its physical location is 453.3 Mb [51]. The QYr.niab-2B.1 flanking marker is Kukri_c9118_1774, and its physical location is 683.05 Mb [52]. The QYrPI660122.swust-2BL flanking markers are AX-109349804 and AX-109849173, with a physical interval of 777,831,275–779,847,527 bp [53]. The QYr.niab-2B flanking marker is WPT-9190, and its physical location is 750.12 Mb [54]. QYrhm.nwafu-2BC is located between markers IWB26631 and IWB40714 in the physical interval 212.58–215.2 Mb [26]. The QYR1 flanking marker is Xgwm501, and its physical location is 672.08 Mb [55]. The QYr.caas-2BL flanking markers are Xwmc441 and Xwmc361, with a physical interval of 598,064,477–779,339,263 bp [56]. QYrxk502.swust-2BL is different from QYraq.cau-2BL (HTAP gene), but its relationship with QYr.niab-2B.1 and QYr.caas-2BL needs further study and confirmation.
QYrxk502.swust-3AS is located between markers AX-109308178 and AX-111631905, with a physical range of 37,303,271–46,005,047 bp. The only officially named gene on wheat chromosome 3AS is Yr76 [57], which is an ASR gene. There are also a number of QTL that have been located to chromosome 3AS. The QYrsv.swust-3AS flanking markers are IWB7237 and IWB8523, with a physical interval of 21.26–22.48 Mb [43]. The QYr.niab-3A.1 flanking marker is Kukri_c28650_111, and its physical location is 7.92 Mb [52]. The QYr.hbau-3AS flanking markers are AX-111491666 and AX-110551014, with a physical interval of 45.78–54.87 Mb [36]. The QYrto.swust-3AS flanking markers are AX-95240191 and AX-94828890, with a physical range of 7,920,927–10,144,518 bp [58]. The QYr.spa-3A.1 flanking marker is BS00021981_51, and its physical location is 61,349,059 bp [59]. The QYr.dms-3A flanking markers are Tdurum_contig74920_757 and RAC875_c45016_79, with a physical interval of 51,177,286–53,837,108 bp [60]. The QYr.ifa-3AS flanking markers are wPt-9634 and wPt-0714, with a physical interval of 11,379,461–25,903,821 bp [61]. The QYr.caas-3AS flanking marker is Kukri_c96747_274, and its physical location is 19,181,736 bp [62]. QYrxk502.swust-3AS is different from these QTL and may be a new QTL.
QYrxk502.swust-3BS is located between markers AX-109438796 and AX-108747357, with a physical distance range of 933,501–7,529,669 bp. The genes that have been officially named on wheat chromosome 3BS are Yr4a [11], Yr4b [63], Yr30, Yr57 [64], and Yr58, among which, Yr4a, Yr4b, and Yr57 are ASR genes, and Yr30 and Yr58 are APR genes. The Yr58 flanking marker is Xbarc75, with a physical location of 3,395,500 bp [65]. The flanking markers of Yr30 are Xgwm389 and Xgwm533, with a physical location of 806,388–35,326,710 bp; it is linked to the morphological marker pseudo-black chaff (PBC), and if wheat contains this gene, the husk and internodes will gradually darken in the late grain-filling period [66]. The resistant parent XK502 in this study showed the trait of blackening of glumes in the late grain-filling period, and QYrxk502.swust-3BS was within the physical interval of Yr30. Therefore, we tested the chain marker WMS533 for Yr30 in XK502 but did not detect the marker, and QYrxk502.swust-3BS was not Yr30. Yr30 has been mapped in many wheat germplasms. QYrlov.nwafu-3BS located in wheat P10057 is Yr30, and the flanking markers are IWB57990 and IWB6491, which are linked to the flanking markers Xgwm389 and Xgwm533 of Yr30, respectively. The parent P10057 showed dark glumes in the late grain-filling period, and the color of the glumes’ offspring was basically consistent with the haplotype of the KASP marker [67]. The flanking markers of QYr.hbaas-3BS [51], QYr.nafu-3BS [68], QYr.ccsu-3B.1 [69], QYrto.swust-3BS [58], QYr.cim-3BS [39], QYrhm.nwafu-3BS [70], and QYr.ifa-3BS [61] are within the physical interval corresponding to Yr30 and may be Yr30. QYrxk502.swust-3BS is likely a new QTL.
QYrxk502.swust-7BS is located between markers AX-110982135 and AX-109968088, with a physical interval of 15,508,999–18,217,648 bp. The officially named stripe rust resistance genes on wheat chromosome 7BS are Yr6 [71] and Yr63 [11], which are ASR genes. QYrxk502.swust-7BS is different from these officially named genes. Few QTLs have been reported on the short arm of chromosome 7BS, and the QYrcw.nwafu-7BS flanking markers AX-94670534 and AX-94488627, with physical intervals ranging from 23,490,588 to 49,139,449 bp [38], are different from QYrxk502.swust-7BS and are likely to be a new QTL.

4. Materials and Methods

4.1. Plant Materials

Wheat line XK502 was developed by the Wheat Research Institute of Southwest University of Science and Technology using a cross-breeding method in 2005. The line had demonstrated excellent stripe rust resistance at the adult plant stage for the last two decades in field. SY95-71 is a wheat material highly susceptible to stripe rust and is suitable for resistant breeding research [45]. SY95-71 and XK502 were hybridization, and a mapping population of 221 RILs of the F7 generation was obtained via single-seed descent, which was used to locate QTLs for resistance to stripe rust. MX169 and Avocet S (AvS) are both wheat cultivars that are highly susceptible to stripe rust and are often used as susceptible controls.

4.2. Phenotypic Identification

4.2.1. Greenhouse Tests

Through a greenhouse seedling experiment, the response of SY95-71 and XK502 to stripe rust at the seedling stage was evaluated. Plants SY95-71, XK502, and MX169 were placed in small separate flowerpots with a diameter of 8 cm. Three Chinese Pst races, CYR32, CYR33, and CYR34, propagated in single-spore isolation were used for single-race infection. During the one-tip–one-leaf stage of wheat, the leaves were dewaxed, and then Pst races and talcum powder were mixed in a ratio of 1:20 and dipped in a cotton swab to apply to the front of the leaves. After the inoculation was completed, the wheat seedlings were placed in a dark environment at 8–12 °C and sprayed with water to moisturize. They were taken out after 24 h and moved to a greenhouse at 13–17 °C to continue infection. During this period, the environment was maintained with light for 16 h, no light for 8 h, and a relatively humid atmosphere. The infection type (IT) was recorded 15–20 days after inoculation using a 0–9 scale [72].

4.2.2. Field Tests

For the identification of field phenotypic responses to stripe rust of 221 recombinant inbred lines from parents SY95-71, XK502, and F6, F7, and F8 generations, the study was conducted in 22JY, in both 23MY and 23JY, and in the experimental fields of 24GY and 24JY, in Sichuan Province. Each field trial site adopted a completely randomized block design with two replicate groups. In the experimental field, the row length was set to 1 m, and approximately 30 seeds were sown in each row, with a row spacing of 30 cm. MX169 was planted every 20 rows as a susceptible control and spore spreader to increase stripe rust pressure and uniformity in the nursery spend. The highly susceptible stripe rust cultivar AvS was planted between the experimental plots to increase the Pst inoculum amount. The survey method of IT was the same as that of seedling identification. The DS survey was identified and recorded according to the Cobb’s scale standard [73]. A total of three surveys were conducted, and the final results were averaged. This systematic experimental design aims to comprehensively assess the resistance of both parental and recombinant inbred line populations across various environments.

4.2.3. Determination of Agronomic Traits

The agronomic traits of the parent lines SY95-71 and XK502, as well as 221 RILs, were evaluated across four environments: 23MY, 23JY, 24GY, and 24JY. We investigated PH, PTN, SL, TKW, GL, GW, and LWR [74]. By combining these seven agronomic traits, RILs with strong resistance and excellent agronomic traits were screened.

4.3. DNA Extraction and Genotyping

Genomic DNA was extracted from the leaves of uninfected seedlings of 221 recombinant inbred lines in the parental and F7 generations using a modified CTAB method [75] and the DNA concentration was diluted to 100 ng/μL in a volume of 80 μL according to the requirements of China Golden Marker (Beijing, China) Biotech. The company was commissioned to use the Affymetrix wheat 55K SNP array [76] to perform sequencing on the parental and recombinant inbred lines to obtain genotype data.

4.4. Genetic Linkage Map Construction and QTL Analysis

Creating a wheat genetic map is one of the key steps in conducting genome analysis and studying phenotypic variation in wheat. Previously, analysis of variance was performed on the phenotypic data of stripe rust in multiple environments to determine genetic, environmental, and genetic × environmental interaction effects, and calculate the Pearson correlation coefficient between phenotypic data in different environments [77,78]. To compare paired RIL phenotypic responses in different environments, the genetic linkage group of the recombinant inbred line was constructed through the software IciMapping4.2, and the BIN tool was first used to remove redundant markers with a deletion rate greater than 20%. Recombination rates were converted to genetic distances (cM) using the Kosambi [79] function. Genetic maps and inclusion composite interval mapping were used to detect IT and DS data of stripe rust in different environments for preliminary QTL positioning. Subsequently, in order to determine the additive effect of QTL, the effect of QTL combination was verified by plotting a box plot of the average IT and average DS of recombinant inbred lines with the same number of beneficial alleles.

5. Conclusions

This study successfully integrated high throughput 55K SNP sequencing with stripe rust phenotypes from both parental lines and 221 mapping populations, leading to the identification of five adult plant resistance QTL. Each of these QTL offers varying levels of resistance to stripe rust, highlighting their potential utility in crop improvement. While the associations between QYrxk502.swust-1BL and QYrxk502.swust-2BL and other QTL require further validation, QYrxk502.swust-3AS, QYrxk502.swust-3BS, and QYrxk502.swust-7BS appear to represent novel contributions to our understanding of stripe rust resistance. Notably, the QTL located on chromosomes 1BL, 2BL, 3BS, and 7BS exhibited stability across conditions, suggesting their reliability for breeding purposes. This study underscores the correlation between the clustering of resistance QTL and enhanced resistance levels, indicating that selecting lines with multiple QTL could yield more resilient cultivars. Furthermore, the identification of 16 promising lines from the 221 RILs through a dual approach of resistance and agronomic trait evaluation indicates a pathway toward the development of commercially viable wheat cultivars. Future efforts can focus on converting the SNP markers linked to these stable major-effect QTL into KASP or SSR markers to facilitate the breeding of wheat cultivars that possess lasting resistance to stripe rust.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/plants13172365/s1, Table S1: Quantitative trait locus of adult plant resistance to stripe rust detected in progenies of SY95-71/XK502 by using inclusive composite interval mapping in five environments; Table S2: Excellent families screened for stripe rust and agronomic traits and the QTL carried by the families.

Author Contributions

Conception and design, X.F. and S.Y.; writing—original draft writing, X.F.; data curation and analysis, X.F.; data collection, X.F., M.H., X.L., B.Y. and X.Y.; cohort construction, S.Y. and K.H.; manuscript revision, S.Y. All authors have read and agreed to the published version of the manuscript.

Funding

This study was financially supported by the Breakthrough in Wheat Breeding Material and Method Innovation and New Variety Breeding (Breeding Research Project, 2021YFYZ0002) and the Major Program of National Agricultural Science and Technology of China (NK20220607).

Data Availability Statement

Data are contained within the article.

Acknowledgments

We thank the anonymous reviewers for their valuable review and comments on the manuscript.

Conflicts of Interest

The authors declare no conflicts of interest.

References

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Figure 1. Response of the parents SY95-71 and XK502 to stripe rust at seedling and adult stages: seedlings were inoculated with CYR32 (A), CYR33 (B), and CYR34 (C) Puccinia striiformis f. sp. tritici; disease status of flag leaves at adult plant stage (D).
Figure 1. Response of the parents SY95-71 and XK502 to stripe rust at seedling and adult stages: seedlings were inoculated with CYR32 (A), CYR33 (B), and CYR34 (C) Puccinia striiformis f. sp. tritici; disease status of flag leaves at adult plant stage (D).
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Figure 2. Flag leaf infection type (IT) of parental and some RIL adult plants in Jiangyou, Sichuan Province, 2024. The infection type (IT) of RILs was 0–9 from left to right.
Figure 2. Flag leaf infection type (IT) of parental and some RIL adult plants in Jiangyou, Sichuan Province, 2024. The infection type (IT) of RILs was 0–9 from left to right.
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Figure 3. Frequency distribution diagram of average infection type (A) and disease severity (B) of 221 RILs composed of SY95-71/XK502 in five environments.
Figure 3. Frequency distribution diagram of average infection type (A) and disease severity (B) of 221 RILs composed of SY95-71/XK502 in five environments.
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Figure 4. Quantitative trait loci (A–E) associated with stripe rust resistance on chromosomes 1BL, 2BL, 3AS, 3BS, and 7BS were mapped using infection type (IT) and disease severity (DS) data. The y-axis denotes genetic distance (cM), while the x-axis shows LOD values. The red rectangle on the genetic map indicates the location of each QTL.
Figure 4. Quantitative trait loci (A–E) associated with stripe rust resistance on chromosomes 1BL, 2BL, 3AS, 3BS, and 7BS were mapped using infection type (IT) and disease severity (DS) data. The y-axis denotes genetic distance (cM), while the x-axis shows LOD values. The red rectangle on the genetic map indicates the location of each QTL.
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Figure 5. Parental XK502 and SY95-71 grain phenotypes (A); amplification of primer Xwms533 in XK12 and XK502 (B). 1 DNA maker; 2 XK12 (carrying the Yr30 gene) [32]; 3 XK502.
Figure 5. Parental XK502 and SY95-71 grain phenotypes (A); amplification of primer Xwms533 in XK12 and XK502 (B). 1 DNA maker; 2 XK12 (carrying the Yr30 gene) [32]; 3 XK502.
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Figure 6. Effect of different infection type (A) and disease severity (B).
Figure 6. Effect of different infection type (A) and disease severity (B).
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Table 1. Correlation analysis between infection type (IT) and disease severity (DS) in recombinant inbred populations in five environments.
Table 1. Correlation analysis between infection type (IT) and disease severity (DS) in recombinant inbred populations in five environments.
Environment22JY23MY23JY24GY24JY
22JY-
23MY0.57 (0.53) 1-
23JY0.62 (0.73)0.49 (0.61)-
24GY0.58 (0.54)0.68 (0.64)0.63 (0.64)-
24JY0.64 (0.65)0.58 (0.62)0.75 (0.73)0.74 (0.70)-
1 R-values for infection type (IT) and disease severity (DS), all R-values were highly significant, p < 0.001.
Table 2. Analysis of variance for infection type (IT) and disease severity (DS) in a population of recombinant inbred lines.
Table 2. Analysis of variance for infection type (IT) and disease severity (DS) in a population of recombinant inbred lines.
Source of VariationInfection TypeDisease Severity
dfSum of SquaresMean
Square		F ValuedfSum of SquaresMean
Square		F Value
Genotype2206903.9031.3830.92 ***2201,109,579.255043.5434.53 ***
Environment41388.81347.20342.09 ***424,130.666032.6641.3 ***
Genotype × Environment8802919.353.323.27 ***880528,512.63600.584.11 ***
Error10791096.161.02 107957,605.75146.07
h2b 10.90 0.89
*** The difference is highly significant at the p < 0.001 level; 1 h2b broad-sense heritability.
Table 3. Effects of different QTL on stripe rust infection type (IT) and disease severity (DS).
Table 3. Effects of different QTL on stripe rust infection type (IT) and disease severity (DS).
QTLNo. of RILsITDS%
QYrxk502.swust-1BL625.02 39.50
QYrxk502.swust-2BL464.66 34.61
QYrxk502.swust-3AS424.91 37.27
QYrxk502.swust-3BS504.46 30.80
QYrxk502.swust-7BS524.87 36.81
Table 4. Correlation analysis between parent and RIL populations stripe rust phenotypes and agronomic traits.
Table 4. Correlation analysis between parent and RIL populations stripe rust phenotypes and agronomic traits.
Trait NameITDSPHPTNSLTKWGLGWLWR
IT-
DS0.99 ***-
PH−0.25 ***−0.27 ***-
PTN−0.34 ***−0.35 ***0.26 ***-
SL−0.24 ***−0.23 ***0.47 ***0.073 ns-
TKW−0.41 ***−0.42 ***0.45 ***0.19 **0.29 ***-
GL−0.35 ***−0.35 ***0.40 ***0.20 **0.49 ***0.75 ***-
GW−0.32 ***−0.33 ***0.36 ***0.15 *0.16 *0.88 ***0.52 ***-
LWR−0.11 ns−0.10 ns0.12 ns0.07 ns0.37 ***0.05 ns0.60 ***−0.34 ***-
*** Indicates p < 0.001, the correlation is extremely significant; ** indicates p < 0.01, the correlation is extremely significant; * indicates p < 0.05, significant correlation; ns indicates p > 0.05, no correlation.
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Feng, X.; Huang, M.; Lou, X.; Yang, X.; Yu, B.; Huang, K.; Yang, S. Identification and Mapping of QTLs for Adult Plant Resistance in Wheat Line XK502. Plants 2024, 13, 2365. https://doi.org/10.3390/plants13172365

AMA Style

Feng X, Huang M, Lou X, Yang X, Yu B, Huang K, Yang S. Identification and Mapping of QTLs for Adult Plant Resistance in Wheat Line XK502. Plants. 2024; 13(17):2365. https://doi.org/10.3390/plants13172365

Chicago/Turabian Style

Feng, Xianli, Ming Huang, Xiaoqin Lou, Xue Yang, Boxun Yu, Kebing Huang, and Suizhuang Yang. 2024. "Identification and Mapping of QTLs for Adult Plant Resistance in Wheat Line XK502" Plants 13, no. 17: 2365. https://doi.org/10.3390/plants13172365

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