Molecular Mapping of a Stripe Rust Resistance Gene YrH9020a Transferred from Psathyrostachys huashanica Keng on Wheat Chromosome 6D

Journal of Integrative Agriculture 2014, 13(12): 2577-2583

December 2014

RESEARCH ARTICLE

Molecular Mapping of a Stripe Rust Resistance Gene YrH9020a Transferred from Psathyrostachys huashanica Keng on Wheat Chromosome 6D LIU Ze-guang, YAO Wei-yuan, SHEN Xue-xue, CHAO Kai-xiang, FAN Yu, LI Min-zhou, WANG Baotong, LI Qiang and JING Jin-xue State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, P.R.China

Abstract Stripe rust (yellow rust), caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most devastating diseases of wheat throughout the world. H9020-1-6-8-3 is a translocation line originally developed from interspecific hybridization between wheat line 7182 and Psathyrostachys huashanica Keng and is resistant to most Pst races in China. To identify the resistance gene(s) in the translocation line, H9020-1-6-8-3 was crossed with susceptible cultivar Mingxian 169, and seedlings of the parents, F1, F2, F3, and BC1 generations were tested with prevalent Chinese Pst race CYR32 under controlled greenhouse conditions. The results indicated that there is a single dominant gene, temporarily designated as YrH9020a, conferring resistance to CYR32. The resistance gene was mapped by the F2 population from Mingxian 169/H9020-1-6-8-3. It was linked to six microsatellite markers, including Xbarc196, Xbarc202, Xbarc96, Xgpw4372, Xbarc21, and Xgdm141, flanked by Xbarc96 and Xbarc202 with at 4.5 and 8.3 cM, respectively. Based on the chromosomal locations of these markers and the test of Chinese Spring (CS) nullitetrasomic and ditelosomic lines, the gene was assigned to chromosome 6D. According to the origin and the chromosomal location, YrH9020a might be a new resistance gene to stripe rust. The flanking markers linked to YrH9020a could be useful for marker-assisted selection in breeding programs. Key words: Puccinia striiformis f. sp. tritici, Psathyrostachys huashanica Keng, resistance gene, genetic analysis, SSR markers

INTRODUCTION Stripe rust (yellow rust), caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most devastating diseases of wheat throughout the world (Line 2002). China is the largest epidemiologic region of stripe rust in the world in terms of wheat area affected by the disease and the disease has become a major threat to wheat production due to the appearance of new virulent races (Wellings

2011). Host resistance is considered to be the most effective, economic and environmentally sound to control the disease (Chen and Line 1995; Wan et al. 2004; Chen 2005). However, race-specific resistance can be easily overcome by the variability of the predominant races and results in the loss of wheat stripe rust resistance (Li and Zeng 2002; Line 2002; Lin and Chen 2008). Normally, it takes about 5 yr for a new race of the pathogen to overcome race-specific resistance of planting cultivars (Wang et al. 1988). For instance, great yield losses were caused by the appearance of CYR32 and CYR33 since

Received 7 November, 2013 Accepted 27 March, 2014 LIU Ze-guang, E-mail: [email protected]; Correspondence WANG Bao-tong, Mobile: 13572410050, E-mail: [email protected]; LI Qiang, Mobile: 15319489826, E-mail: [email protected]

© 2014, CAAS. All rights reserved. Published by Elsevier Ltd. doi: 10.1016/S2095-3119(14)60755-3

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2001, which are virulent to wheat variety Fan 6 and its derivatives, carrying Yr3b and Yr4b and widely used in wheat breeding programs in China (Wan et al. 2004). Therefore, there is a great need to identify new genes for effective resistance and develop molecular markers for pyramiding genes into wheat cultivars in order to attain durable resistance. To date, 54 stripe rust resistance genes have been officially designated, among which 17 genes, including Yr5, Yr7, Yr8, Yr9, Yr15, Yr17, Yr24, Yr26, Yr28, Yr35, Yr36, Yr37, Yr38, Yr40, Yr42, Yr50 (Liu et al. 2013), and Yr53 (Xu et al. 2013), originate from alien species (Chen 2005; McIntosh et al. 2007; Cheng and Chen 2010). It could be concluded that there are plenty of novel resistance genes available for stripe rust resistance in wild relatives of common wheat. These genes from wheat wild relatives greatly enriched the stripe rust resistance gene pool and genetic diversity. Some of these genes like Yr9, Yr24 and Yr26 have been widely used to control stripe rust in China (Chen 2005). Psathyrostachys huashanica Keng (2n=2x=14, NsNs) is a wild relative of common wheat which has been found only to grow in Huashan Mountain in Shaanxi Province, China. P. huashanica possesses many excellent traits, including early maturation, dwarfing, salinity and drought tolerance and most importantly disease resistance (Chen et al. 1991). Many types of wheatP. huashanica hybrid genetic stocks have been successfully created through interspecific hybridization and chromosomal engineering, including nullisomic heptaploid lines, alien chromosomal substitution lines, addi-

tion lines and translocation lines (Chen et al. 1991, 1996; Hou et al. 1997). A series of genes resistant to stripe rust, including Yrhua in H9020-17-5 (Cao et al. 2008), YrH122 in H122 (Tian et al. 2011), YrHs and YrH9020 (temporarily named) in H9020-1-6-8-3 (Liu et al. 2008; Li et al. 2012), YrH9014 and YrHA in H9014-14-4-6-1 and H9014-121-5-5-9 (Ma et al. 2013a, b), have been identified and molecular-mapped from P. huashanica. Wheat line H9020-1-6-8-3 was developed from the hybridization between donor parent P. huashanica accession 0503383 and receptor parent 7182 (Li et al. 2012). The objectives of this study were to identify the gene(s) conferring all-stage resistance to predominant stripe rust race CYR32 in H9020-1-6-8-3, map the resistance gene(s) in the material with SSR markers and develop molecular markers for wheat breeding.

RESULTS Inheritance of the resistance to stripe rust in H9020-1-6-8-3 The seedling infection type (IT) data tested with nine Pst races on H9020-1-6-8-3, Mingxian 169, P. huashanica and 7182 were summarized in Table 1, which showed that H9020-1-6-8-3 had resistance to 8 of 9 races. The infection data for the parents, F1, F2, F3, and BC1 generations to CYR32 were summarized in Table 2. All F1 plants from cross Mingxian 169/H9020-1-6-8-3 showed

Table 1 Infection type (IT) of wheat line H9020-1-6-8-3 and associate lines/species produced by Puccinia striiformis f. sp. tritici (Pst) races in seedling stage under controlled greenhouse condition Material H9020-1-6-8-3 Mingxian 169 P.huashanica 7182

CYR25 0 4 0 3

CYR27 3 4 0 3

CYR29 0 4 0 3

CYR30 0 4 0 4

Pst races CYR31 0 4 0 4

CYR32 0 4 0 4

CYR33 0 4 0 4

SUN11-4 0 4 0 4

SUN11-11 0 4 0 4

Table 2 Inheritance analysis of H9020-1-6-8-3 for stripe rust resistance to CY32 Race CYR32

1)

Cross H9020-1-6-8-3 Mingxian169 F1 F2 BC1 F3

Observed number of plants or lines1) Res. Seg. Sus. 16 0 0 0 0 18 16 0 0 64 26 11 9 22 41 23

Total 16 18 16 90 20 86

Expected ratio (Res.:Seg.:Sus.) 　

χ2

P

　

　

3:1 1:1 1:2:1

0.73 0.20 0.21

0.39 0.65 0.90

Res., resistant; Seg., segregate; Sus., susceptible.

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Molecular Mapping of a Stripe Rust Resistance Gene YrH9020a Transferred from Psathyrostachys huashanica Keng

to be resistant (IT 0), similar to the resistant parent H9020-1-6-8-3. Among all 90 F2 plants, there were 64 resistant and 26 susceptible individuals, fitting a 3:1 resistant/susceptible ratio (χ2=0.73, P=0.39). In the F3 generations, 22 lines were homozygous resistant (HR), 41 segregating (Seg) and 23 homozygous susceptible (HS), which fitted a 1:2:1 ratio (χ2=0.21, P=0.90). Of 20 BC1 plants, 11 plants were resistant and 9 susceptible, fitting a 1 resistance: 1 susceptible ratio (χ2=0.20, P=0.65). All the results above demonstrated that there was a single dominant resistance gene for stripe rust race CYR32 in H9020-1-6-8-3, temporarily designated as YrH9020a.

Molecular mapping of the resistance gene to stripe rust in H9020-1-6-8-3 In this study, the F2 population from the cross Mingxian 169/H9020-1-6-8-3 was used to map the stripe rust resistance gene. In total, five hundred simple sequence repeat (SSR) markers covering all 21 wheat chromosomes were chosen for initial screening for polymorphisms between H9020-1-6-8-3 and Mingxian 169. Six SSR markers, including Xbarc196, Xbarc202, Xbarc96, Xgpw4372, Xbarc21, and Xgdm141, displayed clear and stabilized polymorphisms between the two parents as well as the resistant and susceptible bulks. Then all 90 F2 plants were genotyped with the six polymorphic markers. The six markers segregated in 1:2:1 ratios (A:H:B), indicating that these markers were single loci markers (Table 3). Linkage analysis based on the phenotypic and genotypic data of the whole F2 population illustrated that the resistance gene YrH9020a was linked to the six SSR loci, with genetic distances of 4.5 to 33.1 centimorgans

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(cM) (Fig. 1). The two closest linked flanking SSR markers, Xbarc96 and Xbarc202, were 4.5 and 8.3 cM from the gene YrH9020a, respectively (Fig. 2). According to the reported chromosomal location of the six polymorphic markers, YrH9020a was temporarily localized on chromosome 6D. Besides, Xbarc96 and Xbarc202, the two flanking markers of the resistance gene, were published to be located on the long arm of chromosome 6D (http://wheat.pw.usda.gov/GG2/ index.shtml). Thus, the gene was deduced to be on 6DL. The microsatellite primer Xbarc96 was used for testing 21 Chinese Spring (CS) nullitetrasomic lines. The target fragment, same as the resistant parent, was present in CS and all lines except N6DT6A, confirming that the resistance gene in H9020-1-6-8-3 was located on chromosome 6D indeed (Fig. 3).

Likely origin of the stripe rust resistance gene Wheat line H9020-1-6-8-3 was derived from hybridization between receptor parent wheat line 7182 and donor parent P. huashanica accession 0503383. According to the seedling test IT with the nine predominant Pst races on H9020-1-6-8-3, Mingxian 169, P. huashanica and 7182 showed in Table 1, H9020-1-6-8-3 were resistant (IT 0) to eight of the tested races (CYR25, CYR29, CYR30, CYR31, CYR32, CYR33, Su11-4, and Su11-11) and susceptible (IT 3) to CYR27. Whilst Mingxian 169 and 7182 were susceptible (IT 3-4) to all nine tested races. P. huashanica accession 0503383, as for the donor parent, was highly resistant to all tested races (Table 1). Thus, the resistance gene in H9020-1-6-8-3 against the eight races was probably derived from P. huashanica. To determine the origin of the resistance gene in H9020-1-6-8-3, two closely linked flanking markers

Table 3 Simple sequence repeat (SSR) markers linked to resistance gene to CYR32 and their genotype, presence (+) and absence (-) in H90201-6-8-3 (Pr), Mingxian 169 (Ps) and Chinese Spring (CS), number of F2 population of the cross with or without the bands, and χ2 and probability values for goodness of fit to 3:1 ratios for dominant markers and 1:2:1 ratios for co-dominant markers Marker Xbarc196 Xbarc202 Xbarc96 Xgpw4372 Xbarc21 Xgdm141 1)

Pr A A A A A A

Present (+)/Absent (-) Ps B B B B B B

CS +(170 bp) +(660 bp) +(430 bp) +(270 bp) +(650 bp) +(290 bp)

　

A 23 25 20 22 22 27

No. of F2 plant1) H 41 40 44 44 40 39

B 26 25 26 24 28 24

χ2(1:2:1)

P

0.91 1.11 0.84 0.13 1.91 1.80

0.63 0.57 0.66 0.94 0.38 0.41

A, banding pattern of the resistant parent; H, heterotic banding pattern; B, banding pattern of the susceptible parent.

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Xbarc196

P1 P2 CS 1 2

3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 M

12.5 Xbarc202 8.3 4.5

YrH9020a Xbarc96

15.9 Xgpw4372 10.7 2.0

Xbarc21 Xgdm141

Fig. 1 Genetic linkage map of stripe rust resistance gene YrH9020a constructed with six simple sequence repeat (SSR) markers on chromosome 6D. Locus names are indicated on the right side of the map. Kosambi map distances (cM) are shown on the left side.

A

Fig. 3 PCR profile of Xbarc96 in H9020-1-6-8-3, Mingxian 169, and Chinese Spring (CS) nullitetrasomic lines. 1, CS N1AT1B; 2, CS N1BT1A; 3, CS N1DT1A; 4, CS N2AT2B; 5, CS N2BT2A; 6, CS N2DT2A; 7, CS N3AT3B; 8, CS N3BT3D; 9, CS N3DT3A; 10, CS N4AT4B; 11, CS N4BT4D; 12, CS N4DT4A; 13, CS N5AT5B; 14, CS N5BT5D; 15, CS N5DT5A; 16, CS N6AT6B; 17, CS N6BT6D; 18, CS N6DT6A; 19, CS N7AT7B; 20, CS N7BT7A; 21, CS N7DT7A.

A

P1

P2

1

2

3

4

5

6

M P1 P2 Br Bs R R R R R R R R S S S S S S S S

B

B

M

M

P1

P2

1

2

3

4

5

6

M P1 P2 Br Bs R R R R R R R R S S S S S S S S

Fig. 2 Electrophoresis of polymerase chain reaction products amplified with SSR markers Xbarc96 (A) and Xbarc202 (B) in F2 plants from the cross Mingxian 169 with H9020-1-6-8-3. M, DNA ladder; P1, H9020-1-6-8-3; P2, Mingxian 169; the same as below. Br, resistant pool; Bs, susceptible pool; R, resistant plant; S, susceptible plant.

(Peng et al. 2000), Xbarc96 and Xbarc202, were used to test 7182, P. huashanica line and four other wheatP. huashanica translocation lines. When Xbarc202 was used to test these materials, all the four translocation lines (H9014-121-5-5-9, H122, H9020-17-5, H9014-14-4-6-1) and the P. huashanica line had the same specific band of H9020-1-6-8-3, whilst all the lines except H122 had the same specific band of H9020-1-6-8-3 when Xbarc96 was used (Fig. 4). The target bands were absent in 7182 when the two markers were used. Thus, the resistance gene YrH9020a in H9020-1-6-8-3 was presumably originated from P. huashanica. Additionally, there might

Fig. 4 PCR amplification profiles using SSR markers Xbarc96 (A) and Xbarc202 (B). 1, P. huashanica Keng accession 0503383; 2, 7182; 3, H9014-121-5-5-9; 4, H122; 5, H9020-17-5; 6, H9014-14-4-6-1.

be the same resistance gene in these tested translocation lines with H9020-1-6-8-3 except H122.

DISCUSSION There are many exotic genes for wheat resistance improvement from wild relatives of wheat in China. P. huashanica is one of the most important wild relatives, due to its excellent traits like early maturation, dwarfing, salinity and drought tolerance and most importantly disease resistance (Chen et al. 1991). A number of researches have shown that there were valuable disease resistance genes in wheat-P. huashanica hybrid lines. Yrhua, which is a single dominant resistance gene to CYR30, was identified from H9020-17-5 and located on the chromo© 2014, CAAS. All rights reserved. Published by Elsevier Ltd.

Molecular Mapping of a Stripe Rust Resistance Gene YrH9020a Transferred from Psathyrostachys huashanica Keng

some 6AL (Cao et al. 2008). YrH122, located on 1DL in H122, was considered to confer resistance to SUN11-4 (Tian et al. 2011). In wheat-P. huashanica translocation line H9020-1-6-8-3, YrHs and YrH9020 have been localized on chromosome 2D, which were resistant to CYR29 and CYR33, respectively (Liu et al. 2008; Li et al. 2012). YrH9014 and YrHA were identified to be resistant to SUN11-4 and CYR31 in H9014-14-4-6-1 and H9014-121-5-5-9, respectively (Ma et al. 2013a, b). These studies suggested that P. huashanica and its hybrid lines with wheat could be very useful in wheat resistance improvement. In this study, we identified a resistance gene to CYR32 on chromosome 6D from translocation line H9020-1-6-8-3, temporarily designated YrH9020a. In the initial SSR markers screening, several primers located on 2D, including those linked to YrHs and YrH9020, did showed polymorphic between the parents. However, when they were tested between resistant and susceptible bulks, no polymorphic was detected. According to the chromosome location and molecular detection, YrH9020a might be different from the YrHs and YrH9020 (both temporarily named) reported on 2D from H9020-1-6-8-3. To date, there were only two officially named stripe rust resistance genes, Yr20 and Yr23, located on chromosome 6D (Chen et al. 1995). According to research, Yr20 and Yr23 were originated from Triticum aestivum while YrH9020a in our study was transferred from P. huashanica. Therefore, YrH9020a should be different from Yr20 and Yr23, and might be a novel resistance gene to stripe rust. However, to confirm difference among these genes, further researches are required to be carried out. According to the genetic analysis, H9020-1-6-8-3 displayed resistance to most stripe rust races including the predominant races CYR32 and CYR33. Due to the resistance resources restricted, the resistance gene YrH9020a derived from wild relative P. huashanica could be useful for resistance improvement of wheat cultivars in wheat breeding programs. Based on the bulk segregant analysis and SSR markers analysis in the present study, YrH9020a was linked with six SSR markers. Of the six markers, Xbarc96 and Xbarc202 were the two closest flanking markers with genetic distance of 4.5 and 8.3 cM. Application of these SSR

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markers could highly accelerate pyramiding of the gene with other effective resistance genes to develop wheat cultivars with potentially durable stripe rust resistance.

CONCLUSION Traditional genetic analysis suggested that a single dominant gene was present in H9020-1-6-8-3 for resistance to stripe rust race CYR32. The dominant gene, temporarily named YrH9020a, was flanked by SSR markers Xbarc202 and Xbarc96 with genetic distances of 4.5 and 8.3 cM, respectively. Presumably this gene was derived from P. huashanica.

MATERIALS AND METHODS Plant materials and pathogens Wheat line H9020-1-6-8-3, a wheat-P. huashanica translocation line, which was developed from the hybridization between donor parent P. huashanica accession 0503383 and receptor parent 7182 (Li et al. 2012), was provided by the State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, China. The segregation populations were developed by crossing susceptible material Mingxian 169 with the resistant donor H9020-1-6-8-3. The F1, F2, F3, and BC1 progenies were made to conduct genetic analysis in the greenhouse. The F2 population was further used to map the stripe rust resistance gene(s) using microsatellite markers. Chinese Spring (CS) and its complete set of 21 nullitetrasomic lines were used to test the chromosomal location of the SSR markers linked to the resistance gene in H9020-1-6-8-3. Four other common wheat-P. huashanica translocation lines, H9020-17-5, H122, H9014-121-5-5-9 and H9014-14-4-6-1 (Cao et al. 2008; Tian et al. 2011; Ma et al. 2013a, b) were used to analyze the origin and the relationship of these genes. Nine Pst races (CYR25, CYR27, CYR29, CYR30, CYR31, CYR32, CYR33, SUN11-4, and SUN11-11), which were prevalent in China, were used to conduct seedling test in the greenhouse in order to identify the reaction patterns of Mingxian 169, H9020-1-6-8-3 and their progenies as well as their donor parent P. huashanica and receptor parent 7182.

Seedling tests Seedling tests were carried out under controlled greenhouse conditions. About 20 seeds for each of the two parents, BC1

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and the F1, 200 seeds of the F2 population and 20 seeds for each of the F3 lines were planted for genetic analysis. Around 15 to 20 seeds were planted in each of the 10-cm-diameter pots. Mingxian 169, the highly susceptible cultivar, was used as a control. Inoculation was carried out when the first leaves of the plants were fully expanded. After inoculated, seedling plants were kept in a dew chamber at 10°C and 100% relative humidity for 24 h and then moved into an environmentally controlled greenhouse with a daily cycle of 16 h of light at 18°C and 8 h of darkness at 10°C. Plants reactions were scored on a 0-4 scale, 18-21 d after inoculation when the susceptible control, Mingxian 169, was heavily infected (Li et al. 2006; Wang et al. 2009).

Chromosome assignment and linkage analysis Chromosomal location of the resistance gene was identified by the location of the linked microsatellite markers published by the GrainGenes website. Chinese Spring nullisomic tetrasomic lines were used to further confirm the putative location. In order to evaluate the deviations of observed data from theoretically expected segregation ratios, the chi-squared (χ2) tests for goodness of fit were used in this study. MapMaker 3.0 (Lincoln et al. 1992) was used to analyse linkages between the polymorphic markers and the resistance gene. Mapdraw V2.1 was used to draw a linkage map (Liu and Meng 2003).

Acknowledgements DNA extraction and bulk segregant analysis The two parents and 90 F2 plants from hybridization Mingxian 169/H9020-1-6-8-3 were used for SSR analysis. All the plants were collected separately and genomic DNA was extracted from leaf tissue samples by the CTAB method (Yan et al. 2003; Li et al. 2011). Resistant (Br) and susceptible (Bs) bulks were obtained by mixing equal amount of DNA from ten resistant and ten susceptible F2 plants, respectively (Michelmore et al. 1991; Li et al. 2011).

SSR analysis SSR markers were used to identify markers linked to the resistance gene. SSR primer sequences were obtained from the GrainGenes website (http://wheat.pw.usda.gov) (Röder et al. 1998) and synthesized by Sangon Biotech (Shanghai) Co., Ltd. One marker from each of the microsatellite (SSR) marker series was chosen approximately 10 cM along the chromosomes according to the reported consensus map for the initial polymorphic marker survey (Somers et al. 2004). A 15-μL reaction mixture consisted of 1.5 μL PCR 10× buffer, 2.1 μL DNA template (50 ng μL-1), 0.3 μL dNTPs (2.5 mmol L-1 each), 1.2 μL MgCl2 (mmol L-1), 1.5 μL each of forward and reverse primers, 0.15 μL Taq DNA polymerase (5 U μL-1) and 6.75 μL ddH2O. PCR amplification was performed in a MJ Research PTC-200 thermal cycler as follows: initial denaturation at 94°C for 5 min, followed by 35 cycles of 45 s denaturation at 94°C, 45 s annealing at 50-68°C depending on primers and 45 s extensions at 72°C, and a final extension at 72°C for 10 min. After amplification, 6 μL of formamide loading buffer (98% formamide, 10 mmol L-1 EDTA (pH 8.0), 0.5 % (w/v) xylene cyanol and 0.5% (w/v) bromophenol blue) was added to the PCR product. About 5-7 μL mixture of the PCR product and loading buffer for each sample was loaded for electrophoresis on 6% polyacrylamide gels, and then visualized by silver staining (Bassam et al. 1991).

The research was supported by the Programme of Introducing Talents of Discipline to Universities, Ministry of Education, China (111 Project, B07049), the National Basic Research Program of China (973 Program, 2013CB127700), the Science and Technology Co-ordinating Innovative Engineering Project of Shaanxi Province, China (2012KTCL02-10), the National Natural Science Foundation of China (30771397), and the China Postdoctoral Science Foundation (2012M512034).

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Molecular Mapping of a Stripe Rust Resistance Gene YrH9020a Transferred from Psathyrostachys huashanica Keng

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