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Wheat Rust in Asia: Meeting the Challenges with Old and New Technologies

Ravi P. Singh1, Harindra M. William1, Julio Huerta-Espino2 and Garry Rosewarne1

1 International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico DF, Mexico.Email r.singh@cgiar.org

2 Campo Experimental Valle de Mexico-INIFAP, Apdo. Postal 10, 56230, Chapingo, Edo. de Mexico, Mexico.

Abstract

The rust diseases of wheat pose a constant threat to sustainable wheat production and thus food security in Asia. If susceptible wheat cultivars are grown, approximately 60 and 40 million hectares could experience periodic epidemics of leaf rust and stripe rust, respectively. Avoiding major rust epidemics in the region is a complex challenge, given that fewer cultivars are being cultivated over large areas, that several of those cultivars are protected by the same resistance genes, and that there is free movement of new virulent races in most of west and south Asia. Monitoring the evolution and movement of new rust races and diversifying cultivars sown in the region based on genetic information could help reduce losses, provided newly susceptible cultivars are withdrawn quickly. Using race-specific resistance genes in combinations could enhance their longevity. Linked DNA markers show promise for achieving such combinations; however, a national and regional deployment strategy is necessary to achieve long-term success. The most promising long-term control strategy is to breed and deploy cultivars carrying durable resistance based on minor, slow rusting genes with additive effects. CIMMYT studies show that combining 4-5 such genes results in a high level of resistance, comparable to immunity. Traditional genetic and molecular mapping studies have demonstrated high genetic diversity for such minor genes, but significant investment is necessary to identify closely linked markers that could be used effectively in marker-assisted selection. Targeted incorporation of durable resistance genes into mega-cultivars grown in Asia by using a ‘single-backcross selected-bulk breeding scheme’ is being pursued at CIMMYT with encouraging results.

Media summary

Breeding and deploying wheat cultivars with durable rust resistance should provide a long-term solution to leaf and stripe rust diseases of wheat in Asia.

Key words

Puccinia triticina, Puccinia striiformis, Triticum aestivum, resistance,

Introduction

Of the total area (approximately 215 million hectares) sown to hexaploid and tetraploid wheat (Triticum aestivum and T. turgidum var. durum) worldwide, 44% (95 million hectares) is in Asia. Of this, 62 million ha are located in just three countries: China, India, and Pakistan. However, food security and production stability are of paramount importance in most Asian countries, given that a majority of farmers are poor. The rust diseases of wheat have historically been one of the major biotic production constraints both in Asia and the rest of the world. Stem (or black) rust caused by Puccinia graminis has been under control since the semidwarf spring wheats of the green revolution, which are stem rust resistant, occupied most of the area in South and West Asia in the 1960s. Leaf (or brown) rust caused by Puccinia triticina and stripe (or yellow) rust caused by Puccinia striiformis continue to pose a major threat to wheat production over a large area. Leaf rust and stripe rust could affect production on approximately 60 (63%) and 43 (46%) m ha, respectively, in Asia (Table 1), if susceptible cultivars were grown there.

Although the timely application of fungicides can provide adequate control, their use adds to production costs and they are considered unfriendly to the environment. Growing resistant cultivars is thus the most effective and efficient control strategy, as it has no cost to farmers and is environmentally safe. Significant variation for virulence to specific resistance genes in populations of highly specialized rust fungi, combined with the rapid evolution of new virulence through migration, mutation, or recombination and selection of existing virulences, have complicated and will continue to complicate the control strategy.

In this paper we attempt to look critically at past successes and failures in controlling the rust diseases in Asia and will suggest what could be done better in the future to meet the enormous challenge of protecting over 95 m ha of wheat in Asia.

Table 1. Wheat area1 in different countries of Asia where the environment favours the development of leaf rust and stripe rust.

Region/country

Area (m ha)

Estimated rust-prone area (%)

Estimated rust-prone area (m ha)

Leaf rust

Stripe rust

Leaf rust

Stripe rust

East Asia

China

24.00

50

40

12.0

9.6

Mongolia

0.26

80

0

0.2

0.0

North Korea

0.08

80

0

0.1

0.0

South Asia

Bangladesh

0.70

100

0

0.7

0.0

India

26.95

80

35

21.6

9.4

Myanmar

0.10

100

0

0.1

0.0

Nepal

0.64

80

30

0.5

0.2

Pakistan

8.35

80

70

6.7

5.8

West Asia

Afghanistan

2.08

20

80

0.4

1.7

Iran

5.47

20

80

1.1

4.4

Iraq

1.52

60

30

0.9

0.5

Saudi Arabia

0.45

80

0

0.4

0.0

Syria

1.68

20

80

0.3

1.3

Turkey

9.30

30

80

2.8

7.4

Yemen

0.10

10

100

0.0

0.1

Central Asia

Kazakhstan

11.00

90

10

9.9

1.1

Kyrgyzstan

0.46

100

0

0.5

0.0

Tajikistan

0.33

100

100

0.3

0.3

Turkmenistan

0.51

100

100

0.5

0.5

Uzbekistan

1.30

80

80

1.0

1.0

Total

95.27

63

46

60.0

43.4

1 Modified from Aquino et al. (2002).

Defining the problem

The nature of rust fungi

Rust fungi are obligate parasites and must survive on living plants. Survival during the off-season occurs on either self-sown (or voluntary) wheat plants or other grass species that can also be infected. High-input, irrigated agriculture and the existence of cool highlands in different parts of Asia promote the carryover of inoculum between seasons. Moreover, conditions favorable to disease development (i.e., temperature and high humidity leading to dew formation) occur most years throughout the growing season. The presence of races capable of overcoming different resistance genes, or their combinations, has been demonstrated for all three rust fungi; numerous races are now known to occur worldwide. New races may arise through sexual recombination (not known for P. striiformis), mutation, or somatic hybridization followed by selection if a new race has a selective advantage. Being an airborne pathogen, new races may also be introduced into a new area through migration. A P. striiformis race with virulence for resistance gene Yr9 recently migrated from the Eastern African highlands to South Asia, through West Asia (Figure 1). This suggests that the entire wheat area in Asia (except China) may comprise a single epidemiologic zone. Therefore, if a new race arises anywhere in this area, given time it could spread throughout the epidemiologic region. It should be noted that the Yr9 virulence in China evolved independently in 1985 (Figure 1), as many winter wheat cultivars grown in China at that time carried this gene.

Figure 1. Movement of Yr9-virulent race of Puccinia striiformis from the East African highlands to the Indian Subcontinent and an independent evolution of Yr9-virulent race in China.

Lack of appropriate races and optimum disease pressure at breeding sites

The probability of identifying resistant parents and resistant progenies is increased through the use of a reliable screening methodology and an environment favorable to disease development. Protocols for screening for resistance to rust diseases are well established (Roelfs et al. 1992). For example, using artificial inoculation with desired races, inclusion of resistant and susceptible check cultivars to assess disease pressure and degree of resistance, and choosing appropriate field sites with reliable environmental conditions, are crucial to making continuous breeding progress. Unfortunately, we have observed that several breeding programs in Asia currently depend on natural epidemics and, as a result, in most years selection is done under insufficient rust pressure or with inappropriate races. Although stem rust is a major disease in Asia historically, it should be noted that practically no one in Asia currently selects wheat for stem rust resistance, as this disease is not considered important at present. This is a precarious situation, as highly virulent P. graminis races from Eastern Africa could migrate to Asia as has happened with stripe rust.

Deployment of cultivars with hypersensitive, race-specific resistance genes

With the discoveries of the genetic basis of resistance by Biffen (1905), physiological specialization in rust pathogens by Stakman and Levine (1922), and gene-for-gene interaction by Flor (1956), the utilization of the hypersensitive (race-specific) type of resistance has dominated wheat improvement during the last 50 years. Identifying numerous new sources of resistance genes either in wheat or in related species and genera, and their transfer to wheat through wide hybridization supported the strategy. Utilization of such genes is very attractive, both from the crop cleanliness point of view and because they are simple to incorporate into improved germplasm. Although it must be acknowledged that rusts were controlled effectively through the use of race-specific genes, their use led to “boom-and-bust” production cycles where varieties succumb in a short time to a new virulent race of the pathogen, leading to significant losses. Combining effective race-specific genes is an attractive strategy for increasing the longevity of this resistance but, to be successful, their deployment has to be planned at both the regional and global levels, as the pathogen is known to accumulate virulences for the combined resistance genes in a stepwise manner, if these genes are also deployed singly. Furthermore, when race-specific resistance is used in breeding, a parallel investment is required to monitor the evolution of pathogen and pests, and to continually search for new, effective resistance genes.

In recent years the use of DNA marker-assisted incorporation of multiple race-specific resistance genes has been suggested and is being attempted by a few breeding programs. DNA markers are currently known for only a few resistance genes (Table 2). Unfortunately, the options for selecting such genes is further narrowed down as several genes are now ineffective or the markers are not close enough. Perfect markers are available only for resistance genes located on chromosome segments that were transferred to wheat from alien species or genera. How many such chromosome segments could be put together in a single genotype without having an adverse effect on grain yield and quality remains undetermined.

Table 2. Race-specific genes for resistance to leaf rust and stripe rust for which linked DNA markers are reported in the literature and also given in McIntosh et al. (2003).

Gene

Ch. location

Marker type

Marker designation

Origin

Leaf rust

Lr1

5DL

RFLP/SSR

Xpsr567, Xgwm272

T. aestivum

Lr9

6BL

STS

J13/1, J13/2

Ae. umbellulata

Lr10

1AS

STS

F1.2245, Lr10-6/r2

T. aestivum

Lr13

2BS

RFLP/RAPD

 

T. aestivum

Lr19

7DL

STS

STSLr19130

Th. elongatum

Lr20

7AL

STS

STS638-L, STS638-R

T. aestivum

Lr21

1DL,1DS

STS

KSUD14

Ae. tauschii

Lr23

2BS

RFLP/RAPD

Xtam72-2BS

T. aestivum

Lr24

3DL

SCAR

SC-H5

Th. elongatum

Lr25

4BS

RFLP/RAPD

 

Secale cereale

Lr26

1BL-1RS

SCAR

IB267, iag95

Secale cereale

Lr27

3BS

RFLP/RAPD

 

T. aestivum

Lr28

4AL

STS

Lr28-01, Lr28-02

Ae. speltoides

Lr29

7DS

RFLP/RAPD

 

Th. Elongatum

Lr31

4BL

RFLP/RAPD

 

T. aestivum

Lr35

2B

STS

BCD260F1, 35R2

Ae. speltoides

Lr37

2AS, 2NS

PCR, CAPS, SNP

VENTRIUP-LN2, URIC-LN2,

Ae. ventricosa

Lr39/Lr41

2DS

SSR

Xgdm35

Ae. tauschii

Lr47

7AS

CAPS

PS10R, PS10L

Ae. speltoides

Lr50

2BL

SSR

Xgwm382, Xgdm87

T. timopheevii

Stripe rust

Yr5

2BL

RGAP

Xwpg17 and Xwpg18

T. spelta album

Yr9

1BL-1RS

STS

IB267, iag95

Secale cereale

Yr10

1BS

RGAP

 

T. aestivum

Yr15

1BS

SSR

Xgwm11

T. dicoccoides

Yr17

2AS

PCR, CAPS, SNP

VENTRIUP-LN2, URIC-LN2,

Ae. ventricosa

Yr28

4DS

RFLP

 

Ae. tauschii

Yr32

2AL

SSR

 

T. aestivum

The diversity of resistance in Asia can be maintained by growing cultivars that carry different resistance genes. However, there is a general tendency for farmers to grow only one or a few favored cultivars, which, as a result, come to occupy large areas. An example of this is cultivation of varieties ‘PBW343’ and ‘Inqualab 91’ on 7 and 6 million hectares in India and Pakistan, respectively. These cultivars are also grown in other countries under different names. Unfortunately, both cultivars are protected from stripe rust by the same resistance gene Yr27, for which virulence was detected recently in Asia. Growing fewer cultivars that carry race-specific resistance genes thus leads to greater genetic uniformity and, consequently, greater disease vulnerability.

Strategies to safeguard the wheat crop in Asia

The wheat crop can be protected from rust, or at least the occurrence of epidemics in Asia could be reduced, by emphasizing the following three strategies: 1) regional cooperation in monitoring the evolution and migration of new races of rust fungi, 2) enhanced information on the genetic basis of resistance in important wheat cultivars, and 3) shift towards breeding and deploying wheat cultivars with durable resistance.

1. Regional cooperation in monitoring the evolution and migration of new races of rust fungi

Monitoring the evolution and migration of new, virulent races of P. triticina and P. striiformis should be a high priority in Asia, especially because 1) the spores of these fungi can move freely over long distances (Fig. 1), 2) several current widely grown cultivars carry race-specific resistance genes, 3) the same cultivars are being grown in more than one country, and 4) the same genes confer resistance to several cultivars grown in different countries. Political tensions in the region often do not permit scientists in some countries to collaborate and communicate with each other directly and hence the presence of a politically neutral institution such as CIMMYT is important to coordinate such effort. It may also be necessary to test cultivars at hot-spot locations outside the region, as virulence for certain resistance genes may already be present in the pathogen population. Virulence for stripe rust resistance gene Yr9 was known in China, Eastern Africa, and Central America in the mid 1980s, long before epidemics occurred on cultivars carrying Yr9 in West and South Asia. Similarly, virulence for gene Yr27, present in two leading cultivars in India and Pakistan, was present in Mexico since the mid 1990s. Such testing is useful in determining the cultivars’ level of background susceptibility and identifying additional resistant cultivars at a low cost in a short time. This could alert national programs to a forthcoming problem. CIMMYT currently coordinates a rust monitoring network in Asia, Africa and South America. Based on information gathered through the network, CIMMYT predicted that cultivars PBW343 and Inqualab 91 would become susceptible to Yr27-virulent races of stripe rust in Asia.

2. Enhanced information on the genetic basis of resistance in important wheat cultivars

Promoting cultivars that have distinct resistance genes can enhance genetic diversity in farmers’ fields. Generation of such information often has low priority, as conducting detailed genetic analysis is time consuming and often considered academic. Several Asian countries lack proper greenhouse facilities, trained personnel, or the financial resources needed to conduct such research. A simple technique is to test cultivars as seedlings in the greenhouse with an array of diverse races of known avirulence/virulence combinations and to use the host-pathogen interaction data to postulate the presence of known resistance genes (Singh and Rajaram 1991). Further testing in the field of adult plants with known races at selected sites in Asia, outside the region, and at laboratories in specialist institutions could help determine the effectiveness of such seedling resistance genes and the presence of additional adult-plant resistance. Often this kind of testing, combined with pedigree information, may be enough to enhance knowledge of genetic diversity, but genetic analysis may be necessary to confirm the gene postulations. If DNA markers become available for the most important, useful resistance genes, they could be used for characterizing the presence of such genes in cultivars in a relatively short time and at little cost. Currently the major limitation is the lack of tightly linked DNA markers for several resistance genes and the presence of non-catalogued race-specific genes in wheat, at least for stripe rust resistance. If this strategy is to be applied successfully, significant investment will be needed to generate such markers.

3. Shift towards breeding and deploying cultivars with durable resistance

The phenomenon of the erosion of race-specific resistance genes, or their combinations, has led scientists to look for alternative approaches to resistance management. The multilineal approach promoted by Jensen (1952) and Borlaug (1953) emerged out of frustrations associated with the frequent failure of race-specific genes. Van der Plank (1963) was the first epidemiologist to clearly define the theoretical basis of concepts of resistance. In the late 1960s and 1970s, there was a revival of the concept of general (race-nonspecific) resistance and its application in crop improvement (Caldwell 1968). This approach was advocated for breeding stem rust resistance in wheat by Borlaug (1972), leaf rust resistance by Caldwell (1968) and yellow rust resistance by Johnson (1988). The wide-scale application of such a concept in breeding for leaf rust resistance, commonly known as slow rusting, has dominated in CIMMYT’s bread wheat improvement for almost 30 years with major impacts (Marasas et al. 2002). Today, we understand better the genetic basis of durable resistance to rust diseases, and this knowledge is being applied in breeding at least at CIMMYT. The genetic basis of durable resistance to three rusts is described below. We believe that deployment of such resistance will provide a long-term genetic solution to rust control in Asia and other countries.

Sr2 and other minor genes for durable resistance to stem rust

Resistance gene Sr2, in addition to other unknown minor genes derived from cultivars Hope and H-44, provided the foundation for durable resistance to stem rust in germplasm from the University of Minnesota in the USA and from Sydney University in Australia, and in the spring wheat germplasm developed by Dr. N.E. Borlaug as part of a program sponsored by the Mexican Government and the Rockefeller Foundation. Cultivar Yaqui 50, released in Mexico during the 1950s, and other Sr2-carrying wheats released since then have stabilized the stem rust situation in Mexico and other countries where modern semidwarf wheats were adopted. Changes in stem rust races have not been observed in Mexico in recent years and natural infections are non-existent. Released in 1960 in the Indian Subcontinent and subsequently grown on millions of hectares, the cultivar Sonalika has also remained resistant. When present alone, the Sr2 gene confers slow rusting that is not adequate under heavy disease pressure, but does provide adequate resistance in combination with other minor genes. Unfortunately, not much is known about the other genes in the Sr2 complex and their interactions. Knott (1988) has shown that adequate levels of multigenic resistance to stem rust can be achieved by accumulating approximately five minor genes. In his studies the genes were different from Sr2.

Lr34, Lr46 and other minor genes for durable resistance to leaf rust

The South American cultivar Frontana is considered one of the best sources of durable resistance to leaf rust, (Roelfs 1988). The Mexican-Rockefeller Program first used the variety in the 1950s. Later derivatives such as Penjamo 62, Torim 73, and Kalyan/Bluebird showed slow rusting characteristics possibly derived from Frontana. Genetic analysis of Frontana and several CIMMYT wheats possessing excellent slow rusting resistance to leaf rust worldwide has indicated that such adult plant resistance is based on the additive interaction of Lr34 and two or three additional slow rusting genes (Singh and Rajaram 1992). Leaf rust severity observed in Mexico on most slow rusting cultivars was related to the number of minor genes they carry (Figure 2). When susceptible cultivars display 100% leaf rust severity, cultivars with only Lr34 display approximately 40% severity; cultivars with Lr34 and one or two additional minor genes display 10-15% severity; and cultivars with Lr34 and two or three additional genes display 1-5% severity (Table 3). Leaf rust may increase to unacceptable levels on cultivars carrying only Lr34, or Lr34 and one or two additional genes. However, cultivars with Lr34 and two or three additional genes show a stable response in all environments tested so far, with final leaf rust ratings lower than 10%. The presence of Lr34 can be indicated by the presence of leaf tip necrosis in adult plants, which is closely linked with it (Singh 1992a).

Figure 2. Relationship between the progress of stripe/leaf rust and the number of minor genes present in a wheat cultivar.

Rubiales and Niks (1995) studied the infection process and indicated that slow rusting resistance due to gene Lr34 was based on a reduced rate of haustorium formation in the early stages of infection, in association with relatively little, or no, cell necrosis. Electron microscopic studies by Alvarez-Zamorano (1995) showed an accumulation of unknown electro-dense substances in the cells of Lr34 lines near the site where haustorial mother cells try to dissolve the cell wall of mesophyll cells for the formation of haustoria. It appears that the accumulation (cell wall apposition) causes a thickening of cell walls, and reduces the establishment of the haustorial tube. If haustoria are formed, slow mycelial growth may be due to restricted movement of the fungus from one cell to another by a similar phenomenon. Alvarez-Zamorano (1995) also observed structural change in the Lr34 line leading to invagination, or contraction of the cell wall, which may delay the completion of the infection process. These observations indicate a different mechanism for Lr34-based slow rusting compard with hypersensitivity, which is associated with the action of race-specific resistance .

Slow rusting resistance to leaf rust is common in spring wheat germplasm. Our studies have shown that at least 10-12 slow rusting genes are involved in the adult plant resistance of CIMMYT wheats. We have also identified lines, such as Amadina (Table 3), where Lr34 is absent, but whose level of resistance is high. We therefore believe that durable resistance is feasible even in the absence of Lr34. This is the case of variety Pavon 76 (Table 3), where we have identified a new gene Lr46 for slow rusting on chromosome 1BL (Singh et al. 1998, William et al. 2003a). Gene Lr46 also functions in a similar manner to Lr34 (Martinez et al. 2001).

Table 3. Seedling susceptible bread wheats that carry adult plant resistance to leaf rust in field trials at Mexico and other countries.

Genotype(s)

Usual leaf rust response1

Additive genes2 for resistance

Jupateco 73S

100S(N)

Susceptible (check)

Jupateco 73R

50MSS

Lr34

Nacozari 76

30MSS

Lr34+ 1 gene

Sonoita 81, Bacanora 88, Rayon 89

20MSS

Lr34 + 1 or 2 genes

Frontana, Parula, Trap, Tonichi 81

10MSS

Lr34 + 2 or 3 genes

Chapio, Tukuru, Kukuna, Vivitsi

1MSS

Lr34 + 3 or 4 genes

Pavon 76, Attila

40MSS

Lr46 + 1 gene

Amadina

5MSS

4 genes

1 Leaf rust response evaluated in Mexico has two components: % severity based on the modified Cobb scale (Peterson et al. 1948) and reaction based on Roelfs et al. (1992). The reactions are: MSS = moderately susceptible to susceptible, i.e., medium- to large-sized uredinia without chlorosis or necrosis; S = susceptible, i.e. large uredinia without chlorosis or necrosis; N = necrotic leaves following high leaf rust severity.

2 Minimum numbers estimated from genetic analysis.

Yr18, Yr29 and other minor genes for durable resistance to stripe rust

Singh (1992b) and McIntosh (1992) indicated that the moderate level of durable adult plant resistance to stripe rust of the CIMMYT-derived US wheat cultivar Anza and winter wheats such as Bezostaja is controlled in part by the Yr18 gene. This gene is completely linked to the Lr34 gene. The level of resistance it confers is usually not adequate when present alone. However, combinations of Yr18 and 3-4 additional slow rusting genes result in adequate resistance levels in most environments (Singh and Rajaram 1994). Cultivars carrying such Yr18 complexes are listed in Table 4. Genes Lr34 and Yr18 occur frequently in germplasm developed at CIMMYT and in various countries. The recently identified slow rusting gene Yr29 is completely linked to gene Lr46, which confers moderate resistance to leaf rust (William et al. 2003a).


Table 4. Seedling susceptible bread wheats that carry adult plant resistance to stripe rust in field trials at Mexico and other countries.

Genotype(s)

Usual stripe rust response1

Additive genes for resistance2

Jupateco 73S

100MS

Moderately susceptible (check)

Jupateco 73R

50M

Yr18 + Yr30

Parula, Trap, Cook

15M

Yr18+ 2 genes

Tonichi 81, Sonoita 81, Yaco

10M

Yr18 + 2 or 3 genes

Chapio, Tukuru, Kukuna, Vivitsi

1M

Yr18 + 3 or 4 genes

Pavon 76, Attila

20M

Yr29 + 2 genes

Amadina

30M

3 genes

1 Yellow rust response data from Mexico has two components, % severity based on modified Cobb scale (Peterson et al. 1948) and reaction based on Roelfs et al. (1992). The reactions are M = moderately resistant to moderately susceptible, sporulating stripes with necrosis and chlorosis; and S = sporulating stripes without chlorosis or necrosis.

2 Minimum numbers estimated from genetic analysis.


Because stripe rust can develop systemically, it is different from the other two rusts, where every new pustule develops from a new infection. The epidemiology of stripe rust is also different from that of the other two rusts. Johnson (1988) presented examples of adult plant resistance genes that are race-specific in nature. It is difficult to distinguish such resistances from the resistances conferred by race-nonspecific adult plant resistance genes . Low disease severity to stripe rust is most often associated with at least some reduction in infection type. However, we have observed that in the case of potentially durable slow rusting resistance, the first uredinia to appear are moderately susceptible to susceptible. Subsequent growth of the fungal mycelium causes some chlorosis and necrosis; therefore, the final infection type is usually rated as moderately resistant-moderately susceptible. Durability of such resistance can be expected if the cultivar’s low disease severity is due to the additive interaction of several (4 to 5) partially effective genes.

Advances in identifying molecular markers for slow rusting, minor genes

Significant advances have been made in characterizing genes that confer resistance to biotic stresses in several crops, thanks to the use of molecular markers. Although molecular markers have been successfully applied to characterize race-specific resistance genes, finding markers closely associated with durable resistance genes is comparatively more challenging. Because several minor genes are needed in a cultivar to achieve adequate protection under high disease pressure, the mapping populations generated often segregate for a number of these genes as quantitative trait loci (QTLs). Usually populations of doubled haploid (DH) or nearly homozygous recombinant inbred lines (RILs) are used for mapping in wheat. Initial efforts aimed at identifying QTLs for durable rust resistance were documented by Nelson et al. (1997) involving linkage mapping using the ITMI reference population, and by William et al. (1997) using bulked segegant analysis (Michelmore et al. 1991) in a CIMMYT spring wheat cross. PCR-based markers such as microsatellites (SSRs) and amplified fragment length polymorphisms (AFLPs) has made it possible to have more success in characterizing adult resistance genes for a number of diseases including leaf rust and yellow rust. The advantages of using DH or RIL populations is that an identical set of segregating material can be screened under multiple environments, providing more reliable data with which to estimate environmental interactions. At CIMMYT, we have used full linkage mapping as well as bulked segregant analysis with multiple populations to determine the number and genomic locations of genes conferring durable resistance and to identify molecular markers with strong linkages with resistance alleles. Other research groups have also used mapping involving spring and winter wheats to identify minor genes for resistance to the rust diseases.

Populations used in marker application efforts hitherto and the resulting QTLs for adult plant-effective slow rusting resistance genes for leaf rust and yellow rust, as well as their relative effects and genome locations, are given in Table 5. Known slow rusting resistance genes for leaf rust and yellow rust include Lr34/Yr18, Lr46/Yr29, and Yr30. Nelson et al. (1997) using RFLPs first associated molecular markers with Lr34/Yr18 on the ITMI reference mapping population. The ITMI population exhibited considerable polymorphism as it is derived from the cross of the spring wheat cultivar ‘Opata 85’ and a synthetic hexaploid wheat. However, these markers did not show polymorphism in several other mapping populations involving spring wheat cultivars at CIMMYT. The availability of a large number of SSR markers with adequate coverage of the wheat genome and other marker systems such as AFLPs has helped to associate markers with genes such as Lr34/Yr18 (Suenaga et al. 2003). These have subsequently been validated in other populations (William et al. 2003b; Schnubusch et al. 2003). Using molecular markers, we have shown the presence of loci that reduce leaf rust and yellow rust severities simultaneously (William et al. 2003b). The presence of at least some common loci facilitates the accumulation of sufficient minor genes to achieve resistance to both rust diseases. The relative effects of minor genes vary widely, ranging from about 5 to 50% of phenotypic variations (Table 5). The effectiveness of utilizing markers to manipulate these genes depends on finding closely linked or flanking markers for each gene. Because there seems to be a multitude of these resistance genes in the wheat genome, current efforts could concentrate on further characterization of genes with larger effects on more than one disease, so that they can be manipulated and deployed effectively in breeding as soon as possible. Understanding their function and developing cloning strategies for such genes would also enhance their utilization through transformation aimed at overexpression from a single copy or introgression of multiple copies at different genomic location.

Breeding for durable resistance

Breeding for durable resistance based on minor additive genes has been challenging and often slow, for several reasons: 1) a sufficient number of minor genes may not be present in a single source genotype, 2) a source genotype may be poorly adapted, 3) there may be confounding effects from the segregation of both major and minor genes in the population, 4) crossing and selection schemes and population sizes are more suitable for selecting major genes, 5) reliable molecular markers for several minor genes are unavailable, and 6) the cost associated with identifying and utilizing multiple markers, is high. One approach suggested in the literature is to use recurrent selection schemes to accumulate several minor genes in a single genetic background. Such selection schemes have often been of scientific interest rather than actually applied in wheat. Selection for resistance alone will not generate important popular cultivars, unless it is simultaneously combined with other traits such as high yield and quality. However, such germplasm carrying combinations of minor genes should be very useful in transferring these genes to adapted local cultivars.

Table 5. Quantitative trait loci (QTLs) reported in the literature to reduce wheat leaf rust and stripe rust severities .

Cross

QTL (No.)

Chromosome location

Range of effect

Lr1

Yr2

(% R2)

Parula x Siete Cerros3

3

-

1BS, 7B, 7DS

10 – 27 (Lr)

Frontana x INIA664

4

4

LR: 1BL*, 3DL, 5B, 7DS*

5 – 46 (Lr)

YR: 1BL*, 2BL, 3BS, 7DS*

4 – 25 (Yr)

Avocet x Pavon 765

3

5

LR: 1BL*, 4B*, 6A*

7 – 50 (Lr)

YR: 1BL*, 4B*, 6A*, 6B, 3BS

9 – 35 (Yr)

Avocet x Parula5

3

3

LR: 1BL*, 7B, 7DS*

10 – 58 (Lr)

YR: 1BL*, 3BS, 7B, 7DS*

12 – 64 (Yr)

Avocet x Tonichi 815

3

6

LR: 7DS*, 7D*, 7B? *

10 – 56 (Lr)

YR: 3BS, 6B, 7B*, 7D*, 7DS*, AFLP12

10 – 24 (Yr)

Fuko-kumughi x Oligoculm6

2

7

LR: 1BL, 7DS*

15 – 41 (Lr)

YR: 3BS, 4BL, 4DL, 5BL, 6B, 7BS, 7DS*

2 – 13 (Yr)

Opata 85 x Synthetic wheat7

7

5

LR: 2AL, 2B, 2DS, 3BS, 7BL, 7DS*

9 – 33 (Lr)

YR: 3BS, 3DS, 4DS, 5DS, 7DS*

13 – 20 (Yr)

Camp Remy x Michigan Amber8

-

2

YR: 2A, 2B

11 – 46 (Yr)

CD87 x Katepawa9

-

3

YR: 1BL, 2DS, 7D

9 –15 (Yr)

Forno x Oberkulmer10

7

-

1BS, 2B, 3A, 4B, 4DL, 5DL, 7B

7 – 35 (Lr)

Arina x Forno11

8

-

1BS, 2AL, 2DS, 2DL, 4BS, 7BS, 7BL, 7DS

9 – 43 (Lr)

1Leaf rust, 2Stripe (yellow) rust, 3William et al. (1997), 4Khairallah et al. (unpublished), 5William et al. (2003a &b), 6Suenaga et al. (2003), 7Nelson et al. (1997) and Singh et al. (2000b), 8Boukhatem et al. (2002), 9Bariana et al. (2001), 10Messmer et al. (2000), 11Schnurbusch et al. (2003), 12 Not chromosomally located.
* Positive effects in reducing severities of both leaf and stripe rusts.

A successful example of breeding for resistance based on minor genes is the resistance to leaf and stripe rusts in wheat, which took about 30 years of continuous effort at CIMMYT. In the early 1970s, S. Rajaram, influenced by the concepts of slow rusting resistance to leaf rust in wheat advocated by R. Caldwell and partial resistance to late blight of potato demonstrated by J. Niederhauser, made a strategic decision to initiate selection for slow rusting resistance to leaf rust in CIMMYT spring wheat germplasm. In the early phase of breeding he maintained plants and lines in segregating populations that showed 20-30% rust severity with compatible (susceptible) infection types. This strategy led to the release of several successful wheat cultivars, such as Pavon 76 and Nacozari 76, in Mexico and other countries. These slow rusting lines were used heavily in the crossing program and resulted in the wide distribution of minor genes within CIMMYT spring wheat germplasm.

The genetic basis of such resistance started to become clear in the early 1990s. High-yielding lines that combined four or five additive, minor genes for both leaf rust and stripe rust and show near-immune levels of resistance were developed in the 1990s. To achieve this, three or four lines carrying different minor genes were crossed (3-way and 4-way crosses), and plants in large segregating populations were selected under artificially created rust epidemics. Races of pathogens that have virulence for race-specific resistance genes present in the parents were used to create the epidemics (Singh et al. 2000a). The resulting highly resistant lines are now being used in a planned manner to transfer these minor resistance genes to cultivars that are currently grown over large areas but have become susceptible to rust races in Mexico. Based on genetic information on the number of additive, minor genes that must be transferred to achieve the desired level of resistance, the crossing and selection scheme described below was developed and applied. This strategy has allowed simultaneous transfer not only of resistance genes but also other quantitative traits that increase the yield potential or improve the grain quality of an adapted cultivar.

Incorporation of rust resistance based on additive, minor slow rusting genes into adapted wheat cultivars

To transfer minor genes based resistance into a susceptible adapted cultivar or any selected genotype, we use a single backcross-selected bulk scheme, where the cultivar/genotype is crossed with a group of 8-10 resistance donors (some listed in Tables 3 and 4); 20 spikes of the F1 plants from each cross are then backcrossed to obtain 400-500 BC1 seeds. Selection is practiced from the BC1 generation onwards for resistance and other agronomic features under high rust pressure. Because additive genes are partially dominant, BC1 plants carrying most of the genes show intermediate resistance and can be selected visually. About 1600 plants per cross are space-grown in the F2, whereas population sizes of about 1000 plants are maintained in the F3-F5 populations. Plants with desirable agronomic features and low to moderate terminal disease severity in early generations (BC1, F2 and F3), and plants with low terminal severities in later generations (F4 and F5) are retained. We use a selected-bulk scheme where one spike from each selected plant is harvested and bulked until the F4 generation. Plants are harvested individually in the F5. Bulking of selected plants poses no restriction on the number of plants that can be selected in each generation, as harvesting and threshing are quick and inexpensive, and the next generation is derived from a sample of the bulked seed. Because high resistance levels require the presence of 4 to 5 additive genes, the level of homozygosity from the F4 generation onwards is usually sufficient to identify plants that combine adequate resistance with good agronomic features. Moreover, selecting plants with low terminal disease severities under high disease pressure means that more additive genes may be present in those plants. Selection for seed characteristics is carried out on seeds obtained from individually harvested F5 plants. Small plots of the F6 lines are then evaluated for agronomic features and homozygosity of resistance, before conducting yield trials.

Resistant derivatives of several cultivars, including PBW343 and Inqualab 91, were recently developed using the above methodology. In each case we identified derived lines that not only carry high levels of resistance to leaf rust or yellow rust or both, but also show about 5-15% higher yield potential than the original cultivars. We believe this approach to wheat improvement allows us to maintain the characteristics of the original cultivar while improving yield potential and rust resistance. We are taking the improved versions of the original cultivars back to the areas where they were/are grown to achieve long-term control of rusts. It should be noted that having minor gene based resistance in several backgrounds should ease future selection for these resistance genes.

Availability for tightly linked DNA markers in the future can be useful in maintaining and diversifying the combinations of additive slow rusting resistance genes in the wheat germplasm and cultivars. The actual use of multiple markers in breeding strategy at CIMMYT is likely be limited to the characterization and selection of parents to be used in specific crosses as the field screening is very reliable and cost-effective. However, if such genes need to be incorporated in adapted cultivar that contains an effective race-specific resistance gene, then markers are the only option and will be used despite the cost.

Prospects of genetic engineering in rust control

Another area of biotechnology that has potential in wheat cultivar development is the use of genetic engineering approaches. The successful deployment of maize and cotton containing Bt genes is well known. Several experiments utilizing other gene constructs such as the coat protein (Cp) gene of rice stripe virus introduced into rice (Hayakawa et al. 1992) and thaumatin-like protein gene introduced into wheat (Chen et al. 1999) have achieved increased levels of protection from plant pathogens. Although genetically modified wheat has not yet been grown commercially, the area under other genetically modified crops continues to increase. Cloning of resistance genes, especially those that confer durable or broad-spectrum disease resistance, could open new possibilities in wheat improvement. Resistance genes, when cloned and used for transformation, may show over-expression of resistance (Horvath et al. 2002). This strategy could be used to improve the effectiveness of individual slow rusting resistance genes that have minor effects. Also, the insertion of multiple copies of such minor genes could lead to better resistance. However, it is worthwhile mentioning that transformation techniques will need further refining, since at present only a few wheat genotypes can be easily transformed. These genotypes are not the currently grown cultivars, and hence at present any transformed gene will need to be transferred to desired cultivars through traditional or DNA marker-assisted backcrossing and rigorous field-testing.

Conclusion

Rust diseases of wheat can be successfully controlled in Asia through a combination of strategies. Regional cooperation is essential for monitoring the evolution of new races and following their migration path. Enhanced information on the genetic basis of resistance will be necessary to maintain genetic diversity in farmers’ fields. Traditional and molecular genetics research to further enhance the understanding of slow rusting resistance based on minor, additive genes should receive high priority in the future. The targeted transfer of durable resistance into widely grown genotypes and the subsequent deployment of their derivatives is an attractive strategy for achieving long-term rust control.

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