Fine mapping of a stripe rust resistance gene YrZM175 in bread wheat

doi:10.21203/rs.3.rs-1537017/v1

Download PDF

Research Article

Fine mapping of a stripe rust resistance gene YrZM175 in bread wheat

https://doi.org/10.21203/rs.3.rs-1537017/v1

This work is licensed under a CC BY 4.0 License

You are reading this latest preprint version

Stripe rust, caused by Puccinia striiformis f. sp. tritici (PST), is a worldwide wheat disease that causes large losses in production. Fine mapping and cloning of resistance genes are important for accurate marker-assisted breeding. Here, we report the fine mapping and candidate gene analysis of stripe rust resistance gene YrZM175 in a Chinese wheat cultivar Zhongmai 175. Fifteen F₁, 7,325 F₂ plants and 117 F2:3 lines derived from cross Avocet S/Zhongmai 175 were inoculated with PST race CYR32 at the seedling stage in a greenhouse, and F2:3 lines were also evaluated for stripe rust reaction in the field using mixed PST races. BSR-seq analyses revealed 13 SNPs in the region 762.50–768.52 Mb on chromosome arm 2AL. By genome mining we identified SNPs and InDels between the parents and contrasting bulks, and mapped YrZM175 to a 0.72-cM, 636.4-kb interval spanned by YrZM175-InD1 and YrZM175-InD2 (763,452,916–764,089,317 bp) including two putative disease resistance genes based on IWGSC RefSeq v1.0. Collinearity analysis indicated similar target genomic intervals in Chinese Spring, Aegilops tauschii (2D: 647.7–650.5 Mb), Triticum urartu (2A: 750.7–752.3 Mb), Triticum dicoccoides (2A: 771.0–774.5 Mb), Triticum turgidum (2B: 784.7–788.2 Mb), and T. aestivum cv. Aikang 58 (2A: 776.3–778.9 Mb) and Jagger (2A: 789.3–791.7 Mb). Through collinearity analysis, sequence alignments of resistant and susceptible parents and gene expression level analysis, we predicted TRITD2Bv1G264480 from Triticum turgidum to be a candidate gene for map-based cloning of YrZM175. A gene-specific marker for TRITD2Bv1G264480 co-segregated with the resistance gene. Molecular marker analysis and stripe rust response data revealed that YrZM175 was different from genes Yr1, Yr17, Yr32 and YrJ22 located on chromosome 2A. Fine mapping of YrZM175 lays a solid foundation for functional gene analysis and marker-assisted selection for improved stripe rust resistance in wheat.

Candidate gene

Disease resistance

Molecular marker

Puccinia striiformis

T. aestivum

A stripe rust resistance gene YrZM175 in Chinese wheat cultivar Zhongmai 175 was mapped to a genomic interval of 636.4 kb on chromosome arm 2AL, and a candidate gene was predicted.

Wheat (Triticum aestivum L.) is a staple food crop worldwide, providing substantial amounts of nutrients for humans (Shewry 2009; Shewry and Hey 2015). The estimated global wheat production in 2021 was 770 million tonnes (FAO, http://www.fao.org/worldfoodsituation/en/). Wheat stripe rust (or yellow rust), caused by Puccinia striiformis f. sp. tritici (PST), is a widely distributed disease that causes millions of tonnes of yield losses every year (Chen and Kang 2017). Stripe rust occurred in 1.78 million ha of wheat in China during 2011–2016 and has since increased to about 5 million ha annually (Huang et al. 2020). Resistant cultivars are the most environment-friendly approach to control stripe rust (Xia et al. 2007). Although many resistance genes have been identified, relatively few of them, such as Yr5, Yr15 and Yr18, continue to confer resistance in China. Therefore, it is necessary to mine new stripe rust resistance genes and to deploy them in wheat cultivars, preferably in multiple gene combinations.

More than 80 stripe rust resistance genes (Yr1–Yr83) have been formally catalogued (McIntosh et al. 2017; Feng et al. 2018; Nsabiyera et al. 2018; Gessese et al. 2019; Pakeerathan et al. 2019; Li et al. 2020). Among formally catalogued and other named genes nine have been cloned (Yr5/YrSP, Yr7, Yr10, Yr15, Yr18, Yr36, Yr46, YrAS2388 and YrU1). Yr18, Yr36 and Yr46 confer adult-plant resistance and encode a putative ATP-binding cassette (ABC) transporter (Krattinger et al. 2009), a protein with a kinase domain and a lipid binding domain (Fu et al. 2009), and a hexose transporter (Moore et al. 2015), respectively. Yr5/YrSP (alleles), Yr7, Yr10, Yr15, YrAS2388 and YrU1 are all-stage resistance genes. Yr15 encodes a protein with kinase-pseudokinase domains, and the others encode various nucleotide-binding site and leucine-rich repeat (NBS-LRR) proteins. Yr5/YrSP and Yr7 belong to a gene cluster originated from Triticum spelta (Marchal et al. 2018); YrAS2388 was come from Aegilops tauschii (Liu et al. 2014, Zhang et al. 2019); Yr15 was derived from Triticum dicoccoides (Klymiuk et al. 2018) and YrU1 was from Triticum urartu (Wang et al. 2020).

Wheat cultivar Zhongmai 175 is widely grown in the North Winter Wheat Zone of China; it has high yield and good resistance to stripe rust. It also shows moderate to high resistance in Sichuan and Gansu provinces, the hotspots for stripe rust epidemics and year-round survival in China. One of the parents of Zhongmai 175 was the French line VPM1 which had high resistance to powdery mildew, stem rust, leaf rust and stripe rust, and was widely used as a disease resistant germplasm by breeders. Zhongmai 175 carries Yr17 from VPM1 and a putatively new stripe rust resistance gene YrZM175 that was located in chromosome 2A (Lu et al. 2016). The aims of this study were to fine-map YrZM175, predict a candidate gene for further analysis, and to develop gene-specific markers for research and breeding.

Plant materials

A total of 7,325 F2 plants derived from the cross of Avocet S/Zhongmai 175 were used for fine mapping of YrZM175. One hundred and seventeen random F2:3 lines were evaluated for stripe rust reaction in the greenhouse and field to confirm the results from the F2 population.

Evaluation of stripe rust reaction

Fifteen F1, 7,325 F2 plants and 117 F2:3 lines of Avocet S/Zhongmai 175 and the parents were inoculated at the seedling stage in controlled greenhouse conditions with PST race CYR32, kindly provided by Dr. Gangming Zhan (Northwest A & F University, Yangling, Shaanxi). CYR32 is avirulent to Zhongmai 175 and virulent to Avocet S. Ten to 15 seeds were planted in a 9 × 9 × 9 cm plastic pot, along with three seeds of susceptible cultivar Mingxian 169 as control. Seedlings were inoculated with CYR32 at 1.5-leaf stage (7–8 days old) by brushing fresh urediniospores from fully infected Mingxian 169 leaves. Inoculated plants were kept in plastic boxes with 100% humidity at 10 °C in darkness for 24 h, then transferred to 15 ± 2 °C conditions with 16 h of light (20,000 lux) daily. Infection types (ITs) were scored 14–18 days after inoculation based on a 0–4 scale (0–2 as resistant, 3–4 as susceptible) (Bariana and McIntosh 1993).

Fifteen F1 plants and 117 F2:3 lines along with both parents with 30–40 seedlings each were also evaluated for stripe rust reaction at Pidu Experimental Station, Sichuan Academy of Agricultural Sciences in Chengdu, in the 2017–2018 and 2018–2019 cropping seasons. F2:3 lines were sown in two replications. Avocet S was used as a susceptible control and spreader, inoculated with mixed PST races (CYR32, CYR33, and CYR34). Infection types (ITs) and disease severity (DS) were recorded twice at 4- to 5-day intervals when the DS of Avocet S reached 90–100%. DS was scored as the percentage of infected leaf area. ITs were scored similarly to those at seedling stage mentioned above.

DNA and RNA extraction

Leaf samples of plants were used to extract genomic DNA using the CTAB method (Saghai-Maroof et al. 1984). For F2:3 lines, equal amounts of leaf tissue from 8–10 plants of each line were mixed for DNA extraction. Because of large genome differences between Zhongmai 175 and Avocet S and the absence of some genes in the target region in Avocet S, we later chose Mingxian 169 as a susceptible control for RNA isolation. Fresh leaf tissues of Zhongmai 175 and Mingxian 169 inoculated with CYR32 were collected before inoculation (0 h) and at 2, 4, 6, 8, 10, 12, 24 h post inoculation (hpi), and at 10 a.m daily in 2 to 14 days post inoculation (dpi) with three biological replications for RNA extraction using the Plant RNA Kit (Omega Biotek, Inc. Norcross, Georgia USA).

BSR-seq assay

Based on phenotypic evaluations at 14 dpi, 50 resistant (IT = 0;) and 50 susceptible plants (IT = 4) were separately mixed to form resistant (R) and susceptible (S) pools for RNA extraction and sequencing. The pooled leaf samples and parents were sent to Novogene (Tianjin, China) for RNA-Seq. After quality testing, single RNA libraries were constructed for each sample and sequenced in an Illumina HiSeq4000 platform, generating 150 bp paired-end reads. BWA (Burrows-Wheeler Aligner) (Li et al. 2009) was used to align the clean reads of each sample against the reference genome of Chinese Spring, Aegilops tauschii ssp. strangulata accession AL8/78 (Luo et al. 2017), Triticum urartu accession G1812 (Ling et al. 2018), Triticum turgidum ssp. dicoccoides accession Zavitan (Avni et al. 2017), Triticum turgidum ssp. durum cv. Svevo (Maccaferri et al. 2019), and Triticum aestivum cv. Aikang 58 and Jagger (Walkowiak et al. 2020) (https://www.ncbi.nlm.nih.gov/assembly/?term=triticeae), respectively, after a series of quality control (QC) procedures. SNPs/InDels calling between the two pools was performed using the Unified Genotyper function in GATK (McKenna et al. 2010). The homozygous SNPs/InDels were extracted to calculate the SNP/InDel index. The sliding window method was used to present the SNP/InDel index of polymorphic sites in whole genome. The differences in SNP/InDel indices between the two pools were calculated as the delta SNP/InDel index to determine the target region of the resistance gene. SNPs/InDels with delta SNP/InDel index of 1 or -1 are considered highly reliable.

Marker development through BSR-seq and genome mining

Highly reliable SNPs from BSR-seq analyses were converted into cleaved amplified polymorphic sequence (CAPS) markers following Thiel et al. (2004) based on their 700–1,000 bp flanking sequences identified in the Chinese Spring reference genome RefSeq v1.0 (IWGSC 2018) and the six other genome sequences mentioned above. Chromosome-specific primers for each SNP were designed with DNAMAN 8.0 software. Due to the limited number of SNPs from BSR-seq, more variations between the parents were identified from gene sequences in the target region in reference to the RefSeq v1.0 (IWGSC 2018). According to gene annotations from RefSeq v1.0 (IWGSC 2018) and the six other genome sequences, gene-specific primers were designed from putative disease resistance genes in the target scaffolds to isolate gene sequences in the parents. PCR sequencing results for the parents were aligned to identify the polymorphic SNPs/InDels using Geneious Prime 2019.0.3 software. InDels between the parents were converted to sequence-tagged site (STS) markers, whereas CAPS markers were developed from SNPs.

Genetic map construction

Chi-squared (χ²) tests were conducted to determine the goodness-of-fit of the observed and expected ratios of segregation in the F₂ and F_2:3 populations using SAS 9.2 (SAS Institute, Cary, NC, USA). All susceptible F₂plants were tested by molecular markers in the target region for linkage analysis with the resistance gene. Genetic distances between polymorphic SNP, STS and SSR markers linked to the stripe rust resistance gene were calculated using the Kosambi mapping function (Kosambi 1943) computed by Mapmaker 3.0 with an LOD threshold of 3.0 (Lincoln et al. 1993). The linkage map was graphically drawn with MapDraw V2.1 (Liu and Meng 2003).

Collinearity analysis of homologous sequences

Collinear alignment of genes and homoeologous intervals was performed using TGT website (http://wheat.cau.edu.cn/TGT/) by blasting markers flanking YrZM175 to obtain physical positions of homologous sequences in related species in Triticum multi-omics center databases on WheatOmics 1.0 (http://wheatomics.sdau.edu.cn/) and to confirm corresponding homoeologous intervals. Gene annotations within homoeologous intervals were searched and downloaded in EnsemblPlants (http://plants.ensembl.org/index.html) and related disease resistance genes were checked.

Genome walking to get sequences of candidate genes

Genome walking is an effective technique to obtain unknown sequences adjacent to known sequences. To find the physical position of the start point with different sequences in the target region between Zhongmai 175 and Chinese Spring to perform genome walking, we designed chromosome-specific primers at 763.83 Mb upstream of TraesCS2A02G562800 in Chinese Spring RefSeq v1.0 to perform PCR with Zhongmai 175 and Chinese Spring as templates. If sequences of PCR products were common between Zhongmai 175 and Chinese Spring we continued to design primers to amplify downstream sequences from 763.83 Mb until sequences of PCR products showed polymorphisms between Zhongmai 175 and Chinese Spring. Then the position of the polymorphic sequence was set as the start point for genome walking using the Genome Walking Kit (TaKaRa, Dalian). Walking primer designing and PCR amplifications were performed following the manufacturer’s protocol. Purified PCR products were ligated with pEASY-T5 Blunt-Zero cloning vectors at 25°C for 2 h and transformed into Trans1-T1 competent cells by the heat shock (TransGen Biotech Co., Ltd., Beijing). After coating the plate and incubating at 37°C for 24 h, 6–10 positive clones from each PCR product were randomly selected and sequenced by Shanghai Sangon Biotech Co., Ltd (http://www.sangon.com/).

Quantitative real-time PCR

First-strand cDNA was synthesized using the PrimeScript RT Reagent Kit with gDNA Eraser (TaKaRa, Kyoto, Japan). The cDNA products of Zhongmai 175 and Mingxian 169 were used for quantitative real-time PCR (qPCR) assays in a BioRad CFX system with the iTaq Universal SYBR Green Supermix (BioRad). Gene-specific primers for candidate genes and the ACTIN gene as internal control were designed using DNAMAN 8.0 software. Each sample had three biological replicates. Relative gene expression was calculated using the 2^–^∆∆Ct equation (Schmittgen and Livak 2008).

Stripe rust resistance of Zhongmai 175 at seedling stage

Zhongmai 175 confers resistance to a broad spectrum of PST races (Lu et al. 2016) and displays high resistance at all growth stages (Fig. S1). Among 7,325 F₂ plants derived from Avocet S/Zhongmai 175, 5,532 and 1,793 plants were resistant and susceptible, respectively, conforming with a 3:1 ratio (χ² = 1.06, P = 0.30). The F_2:3 lines segregated 33 homozygous resistant, 56 segregating and 28 homozygous susceptible, conforming with a 1:2:1 ratio (χ² = 0.35, P = 0.84) (Table 1). Thus, the stripe rust resistance in Zhongmai 175 was conferred by a single dominant gene.

Table 1

Seedling reactions of Zhongmai 175, Avocet S, F₁, F₂ plants and F_2:3 lines from the cross of Avocet S/ Zhongmai 175 to PST race CYR32
Material	Total no.	Infection type						Expected ratio	χ²	P
Material	Total no.	0	0;	1	2	3	4	Expected ratio	χ²	P
Zhongmai 175	15	11	4
Avocet S	12					3	9
F₁	15	10	5
F₂	7,325	1,277	3,817	283	155	774	1,019	3:1	1.06	0.30
		RR^a		Rr^b		rr^c
F_2:3	117	33		56		28		1:2:1	0.64	0.73
^a homozygous resistant
^b segregating
^c homozygous susceptible

Fine mapping of YrZM175

BSR-seq analysis revealed 13 highly reliable SNPs in the genomic region 762.50–768.52 Mb on chromosome arm 2AL based on the Chinese Spring RefSeq v1.0 (IWGSC, 2018) (Figs. 1A and S2). We initially screened 35 simple sequence repeat (SSR) markers on chromosome 2A and identified nine markers polymorphic between the parents; among them, Xwmc658, Xgwm382 and Xgwm311 on 2AL were linked to YrZM175 with genetic distances of 6.51 cM, 5.12 cM and 5.12 cM, respectively (Figs. 1B and S3). The physical positions of Xwmc658 and Xgwm382 (Xgwm311) are at 771.16 Mb and 772.96 Mb, respectively, in agreement with the results of BSR-seq. The 13 polymorphic SNPs were mainly concentrated in two physical positions, i.e., four SNPs at 762.50–762.64 Mb and six around 768.52 Mb on 2AL (Table S1). We developed CAPS markers YrZM175-CAPS1 and YrZM175-CAPS2 (Table S2), based on a SNP at 762.50 Mb and another at 768.52 Mb, with genetic distances of 0.81 cM and 2.57 cM from YrZM175, respectively.

Many polymorphic SNPs/InDels between parents were identified by sequencing genes in the target region and were converted to CAPS or STS markers (Table S2). YrZM175 was then mapped in a genetic interval of 1.41 cM between YrZM175-CAPS1 and YrZM175-InD1, spanning a 1.58 Mb (762.50–764.08 Mb) genomic region containing 35 high-confidence genes, including six putative disease resistance genes (Table S3) based on IWGSC RefSeq v1.0. After designing gene-specific PCR primers (Table S4) and sequencing six putative resistance genes in Zhongmai 175, Avocet S and Mingxian 169, TraesCS2A02G560600 showed a SNP between Zhongmai 175 and Mingxian 169 in the CDS domain, but the gene was absent in Avocet S. During genome walking and mining, we identified two polymorphic sites and converted them to markers YrZM175-CAPS5 and YrZM175-InD2 (Fig. S3) with genetic distances of 0.27 cM and 0.12 cM from the resistance gene, respectively. Finally, we mapped YrZM175 in a genetic interval of 0.72 cM between YrZM175-InD1 and YrZM175-InD2, spanning a 636.4 kb (763,452,916–764,089,317 bp) on chromosome arm 2AL (Figs. 1B and 2A). There were nine high-confidence genes in this genomic region based on IWGSC RefSeq v1.0, including putative disease resistance genes TraesCS2A02G562800 and TraesCS2A02G563200.

Analysis of genes in the 636.4 kb interval of Chinese Spring

The NBS-LRR gene TraesCS2A02G563200 showed no difference between Zhongmai 175, Avocet S and Mingxian 169, indicating that it was not a gene candidate. No PCR product was obtained following amplification of kinase gene TraesCS2A02G562800 in all three genotypes, exhibiting that this gene also was not a candidate. The genome sequence was quite different or absent in the three cultivars compared with Chinese Spring (Fig. 2B). After two cycles of genome walking from 763.83 Mb upstream of TraesCS2A02G562800 we obtained a 3,860-bp genome sequence from Zhongmai 175. Blasting of this sequence against the Triticum genome databases in WheatOmics 1.0 we found that this sequence was identical with a receptor-like kinase gene TRITD2Bv1G265970 on chromosome arm 2BL in Triticum turgidum ssp. durum cv. Svevo (Maccaferri et al. 2019). Isolation of the entire 7,739-bp open-reading frame (ORF) of TRITD2Bv1G265970 in Zhongmai 175, Mingxian 169 and Avocet S with gene-specific primers (Table S5) according to the reference genome of Svevo found no sequence difference between Zhongmai 175 and Avocet S in the ORF domain, whereas the sequence of the ORF in Mingxian 169 was different from that in Zhongmai 175. Sequencing following amplification of a 3,000-bp promoter sequence upstream of the ATG start codon by genomic-specific primers (Table S6) referring to Svevo revealed three SNPs, single 1-bp and 11-bp insertions, and single 9-bp, 11-bp and 23-bp deletions in Avocet S compared with Zhongmai 175 (Fig. S4). Annotation of the promoter sequence of Zhongmai 175 on database PLACE (https://www.dna.affrc.go.jp/PLACE/?action=newplace) indicated that the SNPs/InDels could change several important cis-acting regulators such as ABA responsive element (ABRE), carbohydrate metabolite signal responsive element 1 (CMSRE-1) and salicylic acid regulatory element GT-1 motif. However, tests of all susceptible F₂ plants with a gene-specific marker developed from a polymorphic site between Zhongmai 175 and Avocet S in the promoter, and the marker located 0.21 cM from the resistance gene failed to show an association. We concluded that TRITD2Bv1G265970 was not the gene candidate for YrZM175.

Collinearity analysis of the target genomic interval

Based on Triticum genome databases (Aegilops tauschii, Triticum urartu, Triticum dicoccoides, Triticum turgidum and 10+ Genomes) at TGT website, we performed collinearity analysis of the closest marker YrZM175-InD2 and the targeted genomic region according to the genome sequence of Chinese Spring RefSeq v1.0 (IWGSC, 2018). The 636.4-kb mapping interval showed a good collinearity with 10+ Genome varieties, whereas most of the wild relatives had inversions, duplications and deletions of genes compared with Chinese Spring (Fig. S5). The genomic interval flanked by YrZM175-CAPS5 and YrZM175-InD1 in Chinese Spring RefSeq v1.0 was similar to corresponding intervals in Ae. tauschii ssp. strangulata accession AL8/78 (2D: 647.7–650.5 Mb), T. urartu accession G1812 (2A: 750.7–752.3 Mb), T. turgidum ssp. dicoccoides accession Zavitan (2A: 771.0–774.5 Mb), T. turgidum ssp. durum cv. Svevo (2A: 773.2–775.1 Mb), T. turgidum ssp. durum cv. Svevo (2B: 784.7–788.2 Mb), and T. aestivum cv. Aikang 58 (2A: 776.3–778.9 Mb) and Jagger (2A: 789.3–791.7 Mb), including eight, five, twelve, eight, eleven, three and four putative disease resistance genes in the target intervals, respectively (Fig. S6).

Analysis of genes in the collinear interval of other wheat varieties and related species

Based on BSR-seq analysis using genome sequence information from five species (Ae. tauschii, T. urartu, T. dicoccoides, T. turgidum, and T. aestivum cv. Aikang 58 and Jagger), there was an obvious single peak on homoeologous group 2 chromosomes in all species (Fig. S7). Based on two polymorphic SNPs between R and S pools from BSR-seq analysis in the collinear interval on chromosome 2AL referring Triticum dicoccoides and Triticum turgidum genome sequences, respectively, molecular markers were developed and tested on susceptible F₂ plants from cross Avocet S/Zhongmai 175, and the linkage distances of two SNPs with YrZM175 were 0.12 cM. The results confirmed sequence similarity between Chinese Spring, T. dicoccoides and T. turgidum. Based on collinearity and homology analysis of genes in the collinear interval at website TGT, there were ten putative disease resistance genes in the region upstream of marker YrZM175-InD2 on chromosomes 2A or 2D based on four Triticum reference genomes (T. turgidum, T. dicoccoides, T. urartu, and Ae. tauschii), whereas these genes were absent in Chinese Spring (Fig. 3). Amplifying and sequencing all ten genes (TRITD2Av1G295090, TRITD2Av1G295160, TRITD2Av1G295250, TRIDC2AG082340, TRIDC2AG082360, TRIDC2AG082430, TuG1812G0200006348, TuG1812G0200006350, AET2Gv21292200, AET2Gv21292500) in Zhongmai 175 and Avocet S indicated that these genes were also not present in Zhongmai 175 and Avocet S. Therefore, we inferred that Zhongmai 175 does not contain these gene sequences on chromosome arm 2AL.

A putative disease-resistance-like gene isolated in the target interval of chromosome arm 2AL in Zhongmai 175 by genome walking was almost the same (with two SNPs in the intron) as a kinase gene TRITD2Bv1G265970 on chromosome arm 2BL in T. turgidum. This indicated that chromosome arm 2AL in Zhongmai 175 might carry genes originating from chromosome arm 2BL in T. turgidum. Analysis of 11 putative disease resistance genes (Table S7) in the collinear interval of 2BL in T. turgidum in Zhongmai 175 and Mingxian 169 detected differential expression of TRITD2Bv1G264470 and TRITD2Bv1G264480. The expression levels of TRITD2Bv1G264470 were significantly higher at 5–14 dpi than at 0 dpi in both cultivars, with higher expression in Mingxian 169 (Fig. 4A). The expression of TRITD2Bv1G264480 was first observed in Zhongmai 175 at 2 hpi, then significantly increased at 1–14 dpi, with constantly higher expression level than in Mingxian 169 (Fig. 4B). TRITD2Bv1G264470 and TRITD2Bv1G264480 are NBS-LRR genes. Amplifying parental lines with gene-specific primers (Table S8) indicated no sequence difference at CDS domain of TRITD2Bv1G264470 between Zhongmai 175 and Mingxian 169 or Avocet S. The ORF sequence of TRITD2Bv1G264480 was 23,559 bp with a 5,661-bp CDS domain in T. turgidum. The homoeologous CDS sequences of TRITD2Bv1G264480 were amplified in the target interval on chromosome arm 2AL in Zhongmai 175, Mingxian 169 and Avocet S (Fig. S8). Based on one SNP at CDS domain between Zhongmai 175 and Avocet S, we developed a molecular marker CAPS6 (Table S2) and tested all susceptible F₂ plants. CAPS6 co-segregated with the resistance gene. Therefore, we considered that TRITD2Bv1G264480 was a gene candidate for YrZM175.

Identification of candidate genes for YrZM175

After anchoring the genomic interval of YrZM175 according to the Chinese Spring genome sequence we found that the target region contained a cluster of putative resistance genes. We cloned six putative disease resistance genes in this interval; four had no sequence difference between Zhongmai 175 and Avocet S or Mingxian 169; NLR gene TraesCS2A02G560600 had a SNP in exon 2 between Zhongmai 175 and Mingxian 169, and no PCR product for kinase gene TraesCS2A02G562800 was obtained from Zhongmai 175 and Avocet S or Mingxian 169. We performed transgenic assays of TraesCS2A02G560600 using two transgenic vectors; one was the CDS domain driven by Ubi promoter and another was the 6,251-bp ORF (including coding and intron region) with a 2,770-bp presumed native promoter and 1,500-bp terminator (3’-UTR). All the positive T₁ plants were susceptible to race CYR32 in seedling stage tests, indicating that TraesCS2A02G560600 was not a gene candidate for YrZM175. We amplified five and two genes upstream and downstream, respectively, of TraesCS2A02G562800 according to the Chinese Spring genome and again failed to obtain PCR products, indicating great sequence differences of this genomic region between Zhongmai 175 and the Chinese Spring reference genome. With the release of reference genomes such as T. turgidum ssp. durum cv. Svevo (Maccaferri et al. 2019), T. aestivum cv. Zang1817 (Guo et al. 2020), 10 + Genome (Walkowiak et al. 2020), and T. aestivum cv. Fielder (Sato et al. 2021) we were able to extend our investigation. Since TraesCS2A02G562800 was the only undetermined putative resistance gene in the 636.4-kb target interval on chromosome arm 2AL of Zhongmai 175 according to the Chinese Spring genome, we performed genome walking to obtain the unknown sequence corresponding to TraesCS2A02G562800 in Zhongmai 175. After sequencing and blasting, we found that products corresponding to TraesCS2A02G562800 on 2AL in Zhongmai 175 were almost the same as a genome sequence (TRITD2Bv1G265970) on chromosome arm 2BL of durum wheat Svevo. Tests of relative TRITD2Bv1G265970 expression in infected leaf samples of Zhongmai 175 and Mingxian 169 at 0–7 dpi showed that relative expression of TRITD2Bv1G265970 in Zhongmai 175 was 3.8-fold higher than in Mingxian 169 at 1 dpi. However, the linkage distance between TRITD2Bv1G265970 and the resistance gene was 0.21 cM, indicating that TRITD2Bv1G265970 was not the gene candidate for YrZM175.

We amplified and sequenced ten putative disease resistance genes in the collinear chromosome arm 2AL interval in five Triticum genomes in Zhongmai 175 and obtained no candidate gene sequences. Finally, we assessed TRITD2Bv1G264480 on chromosome arm 2BL in T. turgidum as a candidate gene based on a co-segregating marker, sequence alignment of resistant and susceptible parents and gene expression patterns. Our research indicated that Zhongmai 175 has complicated genetic origins that caused difficulties in mapping the target genes according to single reference genome. In addition to the Chinese Spring genome sequence, it is also very necessary to refer other available genome sequences of wheat and related species for fine mapping and cloning of disease resistance genes in bread wheat.

Candidate gene TRITD2Bv1G264480

The putative resistance gene TRITD2Bv1G264480 encodes an NBS-LRR protein that belongs to two overlapping homologous superfamilies: P-loop containing nucleoside triphosphate hydrolase, and apoptotic protease-activating factors (helical domain) (http://www.ebi.ac.uk/interpro/entry/InterPro/IPR002182/). The predicted protein of TRITD2Bv1G264480 is closest to TRIDC2BG090350 on chromosome 2B from T. dicoccoides (Fig. S9). The paralogous genes on chromosome 2A in genomes of seven bread wheat varieties clustered together phylogenetically (Fig. S9), with 89% and 66% sequence similarities in the CDS domain to TRITD2Bv1G264480 on chromosome 2B and the paralogous gene TRITD2Av1G294930 on chromosome 2A in T. turgidum, respectively, indicating much closer phylogenetic relationship with TRITD2Bv1G264480 from chromosome 2B in T. turgidum, whereas the orthologous genes on chromosome 2B in T. aestivum cv. CDC Landmark, cv. CDC Stanley, cv. Fielder and cv. Julius showed 67.4% similarity with TRITD2Bv1G264480. In addition, paralogous genes on chromosomes 2A in T. Urartu and 2D in Ae. tauschii and orthologous genes on chromosome 2B in T. spelta also had quite distant phylogenetic relationships with TRITD2Bv1G264480 (Fig. S9). Therefore, we inferred TRITD2Bv1G264480 was transferred from chromosome 2B to 2A during evolution from an old crossover event of bread wheat. The CDS domain of candidate gene in Zhongmai 175 showed 97.8% and 96.8% similarities with TRITD2Bv1G264480 (T. turgidum) and TRIDC2BG090350 (T. dicoccoides), respectively, whereas the sequence similarities with homologues genes on chromosome 2A in other bread wheat varieties (Zang1817, Jagger, Fielder, Mace, CDC Landmark and Norin 61) were relatively low (all below 88.3%), indicating multiple allelic variations or haplotypes of the candidate gene present in bread wheat during evolution.

The relationship between YrZM175 and other Yr genes on chromosome 2A

Zhongmai 175 has been widely grown in the North Winter Wheat Zone of China since 2008. It was derived from the cross between Jing 411 and BPM27 (Fig. S10). BPM27 is a disease-resistant line developed by Prof. Zuomin Yang at China Agricultural University in the 1980s; one of its parents was VPM1, a French line derived from crosses of Ae. ventricosa, T. turgidum L. var. carthlicum (T. persicum) and common wheat cv. Marne (Fig. S10). The 2NS translocation fragment with Yr17 in Zhongmai 175 came from Ae. ventricosa.

Lu et al. (2016) mapped YrZM175 on chromosome arm 2AS using 344 F₂ plants and 147 F_2:3 lines derived from cross Lunxuan 987/Zhongmai 175 tested with CYR29. The present study used many more F2 plants from a cross of Avocet S and Zhongmai 175 but employed race CYR32. The discrepancy of gene locations can be attributed to different mapping populations, molecular markers and PST races used in the two studies. Unfortunately, the PST race CYR29 used previously (Lu et al. 2016) was no longer available to test the present population, thus we are not very sure whether the resistance genes are the same or not. The race CYR32 is virulent to VPM1 (Yr17) (Table S9). Screening of the 1,793 susceptible F₂ plants in the Avocet S/Zhongmai 175 population with the marker URIC/LN2 (Helguera et al. 2003) as proxy for Yr17 indicated linkage of 55.2 cM. YrZM175 is located at the distal end (763,452,916–764,089,317 bp) of chromosome arm 2AL, whereas Yr17 is located at the distal (25.0–38.0 cM linkage interval) of chromosome arm 2AS (Cruz et al. 2016) (Fig. S11). Lu et al. (2016) performed multi-pathotype test on VPM1 (Yr17) and Zhongmai 175 (Yr17 and YrZM175), the two lines showed different reactions to 7 PST races at the seedling stage (Table S9). A test with the marker URIC/LN2 in 92 susceptible F₂ plants indicated that the linkage distance between Yr17 and YrZM175 was 39.0 cM (Lu et al. 2016), being similar to the present study.

To date, three Yr genes have been mapped on chromosome arm 2AL, i.e., Yr1, Yr32 and YrJ22 (Lupton and Macer 1962; Eriksen et al. 2004; Chen et al. 2016). Yr1 is linked to Xgwm382 (Fig. 5B), with a genetic distance of 5.6 cM (Zheng et al. 2017; Bansal et al. 2009). Xgwm382 (at 772.96 Mb) was tested on all 1,793 susceptible F₂ plants from Avocet S/Zhongmai 175; it was linked to YrZM175 (763,452,916–764,089,317 bp) with a genetic distance of 5.1 cM (Fig. 5C). The EST-SSR marker BU099658 (763.69 Mb) may accurately show the presence of Yr1 (Hasancebi et al. 2014), which locates at almost the same physical position as YrZM175. Because Zhongmai 175 and Chinese 166 have different pedigrees and different responses to PST races (Lu et al. 2016; Chen et al. 2016) (Table S9), we believe YrZM175 and Yr1 are different. Based on the linkage maps and physical positions of linked markers, the physical position of YrZM175 is close to Yr1, possibly indicating allelism. To clarify their relationship, tests of allelism and gene cloning should be carried out. Xgwm382 is also closely linked to YrJ22 with a genetic distance of 2.5 cM (Fig. 5D) (Chen et al. 2016). The physical position of YrJ22 is at 768.0–769.0 Mb on 2AL (Personal communication with Dr. Can Chen), a 5 Mb physical distance from YrZM175. As Jimai 22 and Zhongmai 175 have different pedigrees and different arrays of reactions to PST races (Table S9) we assume that YrZM175 and YrJ22 are different genes or alleles.

Eriksen et al. (2004) found that the marker Xcdo678 linked with Yr32 in a genetic distance of 35 cM, while Xcdo678 is co-segregating with Pm4 (Ma et al. 1994). Pm4 and Yr1 are closely linked to each other with a genetic distance of 2.0 cM (McIntosh and Arts 1996). As a result, the genetic distance between Yr32 and Yr1 is about 33 cM (Fig. 5A) (Yang et al. 2019), indicating that Yr32 is far away from YrZM175 and Yr1. Based on linkage maps and molecular marker analyses we conclude that YrZM175 is different from Yr1, Yr17, Yr32 and YrJ22.

Complexity Of The Distal Genome Region Of Chromosome 2al

Structural genomic variation such as presence-absence variations (PAVs) and copy number variations (CNVs) have been recognized to have the potential to generate phenotypic variation in maize (Springer et al. 2009) and barley (Muñoz-Amatriaín et al. 2013). Megabase-scale PAVs of Tripsacum origin were confirmed to be under selection during maize domestication and adaptation (Huang et al. 2021). Rimbert et al. (2018) also found high frequencies of PAVs in the distal regions of wheat chromosomes. Akhunov et al. (2003) found that duplicated loci were most frequently located in the distal regions of chromosomes, and their distribution was positively correlated with recombination rate. The higher recombination rate indicates that these regions are fast-evolving in adapting to biotic and abiotic stresses. Besides, there are higher polymorphisms in the distal regions of chromosomes with the decreased levels of synteny between homoeologous chromosomes as distance from centromeres increase (Akhunov et al. 2003). Our experimental results on chromosome arm 2AL in Zhongmai 175 were in agreement with these related reports mentioned above; this is reflected by the result that the candidate gene TRITD2Bv1G264480 for YrZM175 likely originated from chromosome arm 2BL of Triticum turgidum. The distal region of chromosome has great structural genomic variations, therefore is easier to evolve new alleles that trigger phenotypic variation.

In conclusion, YrZM175 is a stripe rust resistance gene that confers moderate to high resistance to stripe rust in the field. We fine mapped YrZM175 and identified a candidate gene based on a high-resolution linkage map, collinearity analysis and gene expression analysis. Transgenic assays are ongoing to validate the functions of gene candidate for YrZM175. The identification and fine mapping of YrZM175 provide options for deployment in combination with other effective resistance genes.

Authors’ contribution statement:

J. C. Wu performed the experiments and data analysis and wrote the paper.

D. A. Xu and L. P. Fu contributed to data analysis.

L. Wu participated in field trials.

J. H. Li participated in the transgenic assay.

W. H. Hao, Y. Dong, Y. Y. Wu contributed to scoring stripe rust in greenhouse.

F. J. Wang helped the population construction.

Z. H. He, H. Q. Si, C. X. Ma, and X. C. Xia designed the experiment and assisted in writing the paper.

All authors read and approved the final manuscript.

Acknowledgments

We thank Prof. R. A. McIntosh, Plant Breeding Institute, University of Sydney, for critical review of this manuscript. This work was funded by the National Natural Science Foundation of China (31971929, 31961143007), the National Key Research and Development Program of China (2016YFD0101802, 2016YFE0108600), and CAAS Science and Technology Innovation Program.

Conflict of interest:

We declare no conflicts of interest in regard to this manuscript.

Ethical Standards:

These experiments complied with the ethical standards in China.

Akhunov ED, Akhunova AR, Linkiewicz AM, Dubcovsky J, Hummel D, Lazo G, Chao SM, Anderson OD, David J, Qi LL, Echalier B, Gill BS, Miftahudin, Gustafson JP, Rota ML, Sorrells ME, Zhang DS, Nguyen HT, Kalavacharla V, Hossain K, Kianian SF, Peng JH, Lapitan NLV, Wennerlind EJ, Nduati V, Anderson JA, Sidhu D, Gill KS, McGuire PE, Qualset CO, Dvorak J (2003) Synteny perturbations between wheat homoeologous chromosomes caused by locus duplications and deletions correlate with recombination rates. Proc Natl Acad Sci U S A 100:10836–10841
Akhunov ED, Goodyear AW, Geng S, Qi LL, Echalier B, Gill BS, Miftahudin, Gustafson JP, Lazo G, Chao SM, Anderson OD, Linkiewicz AM, Dubcovsky J, Rota ML, Sorrells ME, Zhang DS, Nguyen HT, Kalavacharla V, Hossain K, Kianian SF, Peng JH, Lapitan NLV, Gonzalez-Hernandez JL, Anderson JA, Choi DW, Close TJ, Dilbirligi M, Gill KS, Walker-Simmons MK, Steber C, McGuire PE, Qualset CO, Dvorak J (2003) The organization and rate of evolution of wheat genomes are correlated with recombination rates along chromosome arms. Genome Res 13:753–763
Avni R, Nave M, Barad O, Baruch K, Twardziok SO, Gundlach H, Hale I, Mascher M, Spannagl M, Wiebe K, Jordan KW, Golan G, Deek J, Ben-Zvi B, Ben-Zvi G, Himmelbach A, MacLachlan RP, Sharpe AG, Fritz A, Ben-David R, Budak H, Fahima T, Korol A, Faris JD, Hernandez A, Mikel MA, Levy AA, Steffenson B, Maccaferri M, Tuberosa R, Cattivelli L, Faccioli P, Ceriotti A, Kashkush K, Pourkheirandish M, Komatsuda T, Eilam T, Sela H, Sharon A, Ohad N, Chamovitz DA, Mayer KFX, Stein N, Ronen G, Peleg Z, Pozniak CJ, Akhunov ED, Distelfeld A (2017) Wild emmer genome architecture and diversity elucidate wheat evolution and domestication. Science 357:93–97
Bansal UK, Hayden MJ, Keller B, Wellings CR, Park RF, Bariana HS (2009) Relationship between wheat rust resistance genes Yr1 and Sr48 and a microsatellite marker. Plant Pathol 58:1039–1043
Bariana HS, McIntosh RA (1993) Cytogenetic studies in wheat XV Location of rust resistance in VPM1 and their genetic linkage with other disease resistance genes in chromosome 2A. Genome 36:476–482
Chen C, He ZH, Lu JL, Li J, Ren Y, Ma CX, Xia XC (2016) Molecular mapping of stripe rust resistance gene YrJ22 in Chinese wheat cultivar Jimai 22. Mol Breed 36:118
Chen XM, Kang ZS (2017) Chap. 7 - Stripe rust research and control: conclusions and perspectives. In: Chen XM, Kang ZS (eds) Stripe Rust. Springer, Dordrecht Publishing, pp 601–630
Cruz CD, Peterson GL, Bockus WW, Kankanala P, Dubcovsky J, Jordan KW, Akhunov E, Chumley F, Baldelomar FD, Valent B (2016) The 2NS Translocation from Aegilops ventricosa Confers Resistance to the Triticum Pathotype of Magnaporthe oryzae. Crop Sci 56:990–1000
Eriksen L, Afshari F, Christainsen MJ, McIntosh RA, Jahoor A, Wellings CR (2004) Yr32 for resistance to stripe (yellow) rust present in the wheat cultivar Carstens V. Theor Appl Genet 108:567–575
Feng JY, Wang MN, Deven RS, Chao SM, Zheng YL, Chen XM (2018) Characterization of Novel Gene Yr79 and four additional quantitative trait loci for all-stage and high-temperature adult-plant resistance to stripe rust in spring wheat PI 182103. Phytopathology 108:737–747
Fu DL, Uauy C, Distelfeld A, Blechl A, Epstein L, Chen XM, Sela H, Fahima T, Dubcovsky J (2009) A Kinase-START gene confers temperature-dependent resistance to wheat stripe rust. Science 323:1357–1360
Gessese M, Bariana H, Wong D, Hayden M, Bansal U (2019) Molecular mapping of stripe rust resistance gene Yr81 in a common wheat landrace Aus27430. Plant Dis 103:1166–1171
Guo WL, Xin MM, Wang ZH, Yao YY, Hu ZR, Song WJ, Yu KH, Chen YM, Wang XB, Guan PF, Appels R, Peng HR, Ni ZF, Sun QX (2020) Origin and adaptation to high altitude of Tibetan semi-wild wheat. Nat Commun 11:5085
Hasancebi S, Mert Z, Ertugrul F, Akan K, Aydin Y, Senturk Akfirat F, Altinkut Uncuoglu A (2014) An EST-SSR marker, bu099658, and its potential use in breeding for yellow rust resistance in wheat. Czech J Genet Plant Breeding 50:11–18
Helguera M, Khan IA, Kolmer J, Lijavetzky D, Li ZQ, Dubcovsky J (2003) PCR assays for cluster of rust resistance genes and their use to develop isogenic hard red spring wheat lines. Crop Sci 43:1839–1847
Huang C, Jiang YY, Li CG (2020) Analysis on the occurrence, damage and evolution of main wheat diseases and insect pests in my country from 1987 to 2018. Plant Prot 46:186–193 (in Chinese with English abstract)
Huang YM, Huang W, Meng Z, Braz GT, Li YF, Wang K, Wang H, Lai JS, Jiang JM, Dong ZB, Jin WW (2021) Megabase-scale presence-absence variation with Tripsacum origin was under selection during maize domestication and adaptation. Genome Biol 22:237
International Wheat Genome Sequencing Consortium (IWGSC) (2018) Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science 361:eaar7191
Klymiuk V, Yaniv E, Huang L, Raats D, Fatiukha A, Chen SS, Feng LH, Frenkel Z, Krugman T, Lidzbarsky G, Chang W, Jääskeläinen M, Schudoma C, Paulin L, Laine P, Bariana H, Sela H, Saleem K, Sørensen CK, Hovmøller MS, Distelfeld A, Chalhoub B, Dubcovsky J, Korol AB, Schulman AH, Fahima T (2018) Cloning of the wheat Yr15 resistance gene sheds light on the plant tandem kinase-pseudokinase family. Nat Commun 9:3735
Kosambi DD (1943) The estimation of map distances from recombination values. Ann Eugen 12:172–175
Krattinger SG, Lagudah ES, Spielmeyer W, Singh RP, Huerta-Espino J, McFadden H, Bossolini E, Selter LL, Keller B (2009) A putative ABC transporter confers durable resistance to multiple fungal pathogens in wheat. Science 323:1360–1363
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup (2009) The sequence alignment format and SAMtools. Bioinformatics 25:2078–2079
Li JB, Dundas L, Dong CM, Li GR, Trethowan R, Yang ZJ, Hoxha S, Zhang P (2020) Identification and characterization of a new stripe rust resistance gene Yr83 on rye chromosome 6R in wheat. Theor Appl Genet 133:1095–1107
Lincoln SE, Daly MJ, Lander ES (1993) Constructing genetic linkage maps with Mapmaker/eXP3.0. Whitehead Institute Techn rep, 3rd edn. Whitehead Institute, Cambridge
Ling HQ, Ma B, Shi X, Liu H, Dong L, Sun H, Cao Y, Gao Q, Zheng S, Li Y, Yu Y, Du H, Qi M, Li Y, Lu H, Yu H, Cui Y, Wang N, Chen C, Wu H, Zhao Y, Zhang J, Li Y, Zhou W, Zhang B, Hu W, van Eijk MJT, Tang J, Witsenboer HMA, Zhao S, Li Z, Zhang A, Wang D, Liang C (2018) Genome sequence of the progenitor of wheat A subgenome Triticum urartu. Nature 557:424–428
Liu RH, Meng JL (2003) MapDraw: a microsoft excel macro for drawing genetic linkage maps based on given genetic linkage data. Hereditas 25:317–321
Liu W, Frick M, Huel R, Nykiforuk CL, Wang XM, Gaudet DA, Eudes F, Conner RL, Kuzyk A, Chen Q, Kang ZS, Laroche A (2014) The stripe rust resistance gene Yr10 encodes an evolutionary-conserved and unique CC-NBS-LRR sequence in wheat. Mol Plant 7:1740–1755
Lu JL, Chen C, Liu P, He ZH, Xia XC (2016) Identification of a new stripe rust resistance gene in Chinese winter wheat Zhongmai 175. J Integr Agr 15:2461–2468
Luo MC, Gu YQ, Puiu D, Wang H, Twardziok SO, Deal KR, Huo N, Zhu T, Wang L, Wang Y, McGuire PE, Liu S, Long H, Ramasamy RK, Rodriguez JC, Van SL, Yuan L, Wang Z, Xia Z, Xiao L, Anderson OD, Ouyang S, Liang Y, Zimin AV, Pertea G, Qi P, Bennetzen JL, Dai X, Dawson MW, Müller HG, Kugler K, RivarolaDuarte L, Spannagl M, Mayer KFX, Lu FH, Bevan MW, Leroy P, Li P, You FM, Sun Q, Liu Z, Lyons E, Wicker T, Salzberg SL, Devos KM, Dvořák J (2017) Genome sequence of the progenitor of the wheat D genome Aegilops tauschii. Nature 551:498–502
Lupton FGH, Macer RCF (1962) Inheritance of resistance to yellow rust (Puccinia glumarum Erikss. & Henn.) in seven varieties of wheat. Trans Br Mycol Soc 45:21–45
Ma ZQ, Sorrells ME, Tanksley SD (1994) RFLP markers linked to powdery mildew resistance genes Pm1, Pm2, Pm3, and Pm4 in wheat. Genome 37:871–875
Maccaferri M, Harris N, Twardziok SO, Pasam RK, Gundlach H, Spannagl M, Ormanbekova D, Lux T, Prade VM, Milner SG, Himmelbach A, Mascher M, Bagnaresi P, Faccioli P, Cozzi P, Lauria M, Lazzari B, Stella A, Manconi A, Gnocchi M, Moscatelli M, Avni R, Deek J, Biyiklioglu S, Frascaroli E, Corneti S, Salvi S, Sonnante G, Desiderio F, Marè C, Crosatti C, Mica E, Özkan H, Kilian B, Vita PD, Marone D, Joukhadar R, Mazzucotelli E, Nigro D, Gadaleta A, Chao S, Faris JD, Melo AT, Pumphrey M, Pecchioni N, Milanesi L, Wiebe K, Ens J, MacLachlan RP, Clarke JM, Sharpe AG, Koh CS, Liang KY, Taylor GJ, Knox R, Budak H, Mastrangelo AM, Xu SS, Stein N, Hale I, Distelfeld A, Hayden MJ, Tuberosa R, Walkowiak S, Mayer KF, Ceriotti A, Pozniak CJ, Cattivelli L (2019) Durum wheat genome highlights past domestication signatures and future improvement targets. Nat Genet 51:885–895
Marchal C, Zhang JP, Zhang P, Fenwick P, Steuernagel B, Adamski NM, Boyd L, Mclntosh R, Wulff BB, Berry S, Lagudah E, Uauy C (2018) BED-domain-containing immune receptors confer diverse resistance spectra to yellow rust. Nat Plants 4:662–668
McIntosh RA, Arts CJ (1996) Genetic linkage of the Yr1 and Pm4 genes for stripe rust and powdery mildew resistance in wheat. Euphytica 89:401–403
McIntosh RA, Dubcovsky J, Rogers WJ, Morris C, Xia XC (2017) Catalogue of gene symbols for wheat: 2017 Supplement. http:www.shigen.nig.ac.jp/wheat/komugi/genes/macgene/supplement2017.pdf
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA (2010) The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297–1303
Moore JW, Herrera-Foessel S, Lan CX, Schnippenkoetter W, Ayliffe M, Huerta-Espino J, Lillemo M, Viccars L, Milne R, Periyannan S, Kong XY, Spielmeyer W, Talbot M, Bariana H, Patrick JW, Dodds P, Singh R, Lagudah E (2015) A recently evolved hexose transporter variant confers resistance to multiple pathogens in wheat. Nat Genet 47:1494–1498
Muñoz-Amatriaín M, Eichten SR, Wicker T, Richmond TA, Mascher M, Steuernagel B, Scholz U, Ariyadasa R, Spannagl M, Nussbaumer T, Mayer KFX, Taudien S, Platzer M, Jeddeloh JA, Springer NM, Muehlbauer GJ, Stein N (2013) Distribution, functional impact, and origin mechanisms of copy number variation in the barley genome. Genome Biol 14:R58
Nsabiyera V, Bariana HS, Qureshi N, Wong D, Hayden MJ, Bansal UK (2018) Characterisation and mapping of adult plant stripe rust resistance in wheat accession Aus27284. Theor Appl Genet 131:1459–1467
Pakeerathan K, Bariana H, Qureshi N, Wong D, Hayden M, Bansal U (2019) Identification of a new source of stripe rust resistance Yr82 in wheat. Theor Appl Genet 132:3169–3176
Rimbert H, Darrier B, Julien N, Kitt J, Choulet F, Leveugle M, Duarte J, Rivière N, Eversole K, International Wheat Genome Sequencing Consortium, Gouis JL, on behalf The BreedWheat Consortium, Davassi A, Balfouruer F, Paslier MCL, Berard A, Brunel D, Feuillet C, Poncet C, Sourdille P, Paux E (2018) High throughput SNP discovery and genotyping in hexaploid wheat. PLoS ONE 13:e0186329
Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allard RW (1984) Ribosomal DNA spacer-length polymorphisms in barley: mendelian inheritance, chromosomal location, and population dynamics. Proc Natl Acad Sci U S A 24:8014–8018
Sato K, Abe F, Mascher M, Haberer G, Gundlach H, Spannagl M, Shirasawa K, Isobe S (2021) Chromosome-scale genome assembly of the transformation-amenable common wheat cultivar ‘Fielder’. DNA Res 28:dsab008
Schmittgen TD, Livak KJ (2008) Analyzing real-time PCR data by the comparative CT method. Nat Protoc 3:1101–1108
Shewry PR, Shewry PR, Hey SJ (2009) (2015) The contribution of wheat to human diet and health. Food Energy Secur 4 (3):178–202
Springer NM, Ying K, Fu Y, Ji TM, Yeh CT, Jia Y, Wu W, Richmond T, Kitzman J, Rosenbaum H, Iniguez AL, Barbazuk WB, Jeddeloh JA, Nettleton D, Schnable PS (2013) Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content. PLoS Genet 5:e1000734
Thiel T, Kota R, Grosse I, Stein N, Graner A (2004) SNP2CAPS: a SNP and indel analysis tool for CAPS marker development. Nucleic Acids Res 32:e5
Walkowiak S, Gao L, Monat C, Haberer G, Kassa MT, Brinton J, Ramirez-Gonzalez RH, Kolodziej MC, Delorean E, Thambugala D, Klymiuk V, Byrns B, Gundlach H, Bandi V, Siri JN, Nilsen K, Aquino C, Himmelbach A, Copetti D, Ban T, Venturini L, Bevan M, Clavijo B, Koo D-H, Ens J, Wiebe K, N’Diaye A, Fritz AK, Gutwin C, Fiebig A, Fosker C, Fu BX, Accinelli GG, Gardner KA, Fradgley N, Gutierrez-Gonzalez J, Halstead-Nussloch G, Hatakeyama M, Koh CS, Deek J, Costamagna AC, Fobert P, Heavens D, Kanamori H, Kawaura K, Kobayashi F, Krasileva K, Kuo T, McKenzie N, Murata K, Nabeka Y, Paape T, Padmarasu S, Percival-Alwyn L, Kagale S, Scholz U, Sese J, Juliana P, Singh R, Shimizu-Inatsugi R, Swarbreck D, Cockram J, Budak H, Tameshige T, Tanaka T, Tsuji H, Wright J, Wu J, Steuernagel B, Small I, Cloutier S, Keeble-Gagnère G, Muehlbauer G, Tibbets J, Nasuda S, Melonek J, Hucl PJ, Sharpe AG, Clark M, Legg E, Bharti A, Langridge P, Hall A, Uauy C, Mascher M, Krattinger SG, Handa H, Shimizu KK, Distelfeld A, Chalmers K, Keller B, Mayer KFX, Poland J, Stein N, McCartney CA, Spannagl M, Wicker T, Pozniak CJ (2020) Multiple wheat genomes reveal global variation in modern breeding. Nature 588:277–283
Wan AM, Chen XM, He ZH (2007) Wheat stripe rust in China. Aust J Agric Res 58:605–619
Wang H, Zou SH, Li YW, Lin FY, Tang DZ (2020) An ankyrin-repeat and WRKY-domain-containing immune receptor confers stripe rust resistance in wheat. Nat Commun 11:1353
Xia XC, Li ZF, Li GQ, He ZH, Singh RP (2007) Stripe rust resistance in Chinese bread wheat cultivars and lines. Wheat Production in Stressed Environments, pp 77–82
Yang MY, Li GR, Wan HS, Li LP, Li J, Yang WY, Pu ZJ, Yang ZJ, Yang EN (2019) Identification of QTLs for stripe rust resistance in a recombinant inbred line population. Int J Mol Sci 20:3410
Zhang CZ, Huang L, Zhang HF, Hao QQ, Lyu B, Wang MNL, Epstein L, Liu M, Kou CL, Qi J, Chen FJ, Li MK, Gao G, Ni F, Zhang LQ, Hao M, Wang JR, Chen XM, Luo MC, Zheng YL, Wu JJ, Liu DC, Fu DL (2019) An ancestral NB-LRR with duplicated 3’UTRs confers stripe rust resistance in wheat and barley. Nat Commun 10:4023
Zheng SG, Li YF, Lu L, Liu ZH, Zhang CH, Ao DH, Li LR, Zhang CY, Liu R, Luo CP, Wu Y, Zhang L (2017) Evaluating the contribution of Yr genes to stripe rust resistance breeding through marker-assisted detection in wheat. Euphytica 213:50

AdditionalfilesFinal.docx

Download PDF

Editorial decision: Major revisions
23 May, 2022
Reviews received at journal
22 Apr, 2022
Reviewers invited by journal
17 Apr, 2022
Editor assigned by journal
13 Apr, 2022
First submitted to journal
08 Apr, 2022

You are reading this latest preprint version

Fine mapping of a stripe rust resistance gene YrZM175 in bread wheat

Status:

Version 1

Abstract

Figures

Key Message

Introduction

Materials And Methods

Results

Stripe rust resistance of Zhongmai 175 at seedling stage

Discussion

Complexity Of The Distal Genome Region Of Chromosome 2al

Declarations

References

Supplementary Files

Status:

Version 1