Open access peer-reviewed chapter - ONLINE FIRST

Past, Current and Future of Wheat Diseases in Kenya

Written By

Ruth Wanyera and Mercy Wamalwa

Submitted: January 17th, 2022Reviewed: January 25th, 2022Published: April 3rd, 2022

DOI: 10.5772/intechopen.102854

WheatEdited by Mahmood-ur-Rahman Ansari

From the Edited Volume

Wheat [Working Title]

Dr. Mahmood-Ur-Rahman Ansari

Chapter metrics overview

27 Chapter Downloads

View Full Metrics


Wheat (Triticum aestivum L.) is an important cereal and is among the crops that contribute significantly to food security in Kenya. However, wheat diseases are among the biotic factors that affect wheat production. Considerable progress has been made to control wheat diseases through host plant resistance breeding and chemical applications. Frequent changes in the pathogens population still present a major challenge to achieving durable resistance. Disease surveillance and monitoring of the pathogens have revealed the changes in virulence across the region, justifying the need to develop and deploy more efficient and sustainable strategies to manage the diseases. Understanding the genetic variability and composition of the diseases is important for variety release with appropriate resistance gene combinations for sustainable disease management. This review highlights the prevalence, distribution of wheat diseases, host plant resistance in the key wheat-growing regions of Kenya, and future prospects in Kenya.


  • wheat
  • diseases
  • challenges
  • control strategies

1. Introduction

Wheat (Triticum aestivumL) is the second most important cereal crop in Kenya after maize and is produced mainly under rainfed conditions on 0.4% of the arable land [1, 2]. The crop has greater potential in the country where it is grown in Agro-ecological zones: UH2-UH3; LH2-LH3) [3]. Annual estimated area under production is 150,000 hectares [4] with a production of 320,000MT in 2019 compared to local consumption of 2,450,000MT [5]. The national demand for wheat and wheat consumption is on the increase, partly due to the high population growth, increased urbanization, and changing diet [6, 7]. The local wheat production has not been able to meet this demand leading to the importation of large quantities to fill the gap between supply and demand [8]. However, this is unlikely to be satisfied partly due to pre-harvest sprouting, lodging, losses caused by re-emerging diseases, insect pests, intermittent droughts [6, 9], inadequate seed systems, and poor crop practices under resource-constrained small scale farming conditions. The crop grows in a considerably wide range of altitudes in the country, maturing between 90−145 days depending on the location and cultivars.

There are various wheat diseases such as fungal, which include stem or black rust, caused by Puccinia graminisf. sp. triticiErikss and Henning (Pgt), yellow/stripe rust, caused by Puccinia striiformisf. sp. tritici(Pst), leaf/brown rust caused by Puccinia triticina(Pt) and Fusarium caused by Gibberella zeaethat infect wheat in Kenya. Other diseases include Septoria leaf and glume blotch caused by S. triticiand S. nodorum, respectively Spot blotch (Bipolaris sorokiniana), Loose smut (Ustilago tritici), Take All (Gaeumannomyces graminisvar. tritici) and a viral disease, Barley Yellow Dwarf, causal agent Barley Yellow Dwarf Virus (BYDV) [10].

1.1 Wheat rust diseases in Kenya

Among the wheat diseases, rusts have become the most destructive diseases of wheat in Kenya resulting in yield losses of up to 100% in susceptible cultivars [10, 11]. Breeders have been breeding for wheat rust resistance, since 1908, but up to date, there is no permanent solution to the rust diseases as the pathogens keep on evolving rendering the resistant cultivars ineffective [12]. Since the beginning of the wheat breeding program in Kenya in the 1900s, until early 1980s, stem rust was the most serious disease of the three wheat rusts and therefore was given a high research priority by the breeding program. Consequently, many resistant wheat cultivars were developed and the disease seemed to have been controlled. It was until between 1985 and 1988 that trace amounts of the disease were observed in the experimental plots in Njoro; in 1996, it was recorded in some commercial cultivars in Mau-Narok and Molo, and in the year 2000 all the cultivars had become susceptible [10, 12].

Stem or black rust of wheat, caused by Pgtis known historically for causing severe losses to wheat production and was the most feared disease in various countries where wheat is grown [13]. The common host is wheat with other small grain cereals, durum wheat (Triticum durum), barley (Hordeum vulgareL), Rye (Secale cereaelL.), oats (Avena fatuaL.), wild barley, goatgrass and forage grasses [14]. Although the disease has been under control through widespread use of resistant cultivars, the re-emergence of a new virulent race, Ug99 [15] first keyed to pathotype TTKS [16] using the North American nomenclature [17] and later as TTKSK after a fifth set of differentials was adapted to further expand the characterization [18]. Prior to the official reporting of the new race, trace amounts of the disease were observed in experimental plots in Njoro between 1985 and 1988, in 1996 the disease was recorded in some commercial cultivars in Mau-Narok and Molo (high altitude areas) in 1996 and in 2000 all the cultivars had become susceptible [10, 12]. This Ug99 race group has evolved and is now composed of 15 races in 14 countries [19, 20, 21] with 12 variants (TTKSK, TTKST, TTTSK, PTKSK, PTKST, TTKTT, TTKTK, TTHSK, PTKTK, TTHST, TTKTT+, TTHTT) present in Kenya reversing the gains made by breeders, posing a new and significant threat to wheat production in the Eastern Africa region [16]. In the year 2016, race TKTTF (Digalu race) was genotyped in Kenya for the first time. A new variant TTKTT+with additional virulence on Sr8155B1 was detected in 2019 and another new variant, TTHTT detected in Kenya in 2020 [22]. This is an indication that Ug99 race group is spreading faster specifically, in the areas where close to one billion people reside and the majority of this population consumes wheat and its products [23].

Wheat yellow or stripe rust, caused by Pst, is one of the key economical diseases of wheat worldwide [24, 25]. In Kenya, it occurred as early as 1908 and is prevalent in the Rift valley region [12, 26, 27]. Since then it has become a major threat every year as no commercial cultivar is resistant [2829]. Serious attacks of the pathogen occur annually and newly introduced resistant cultivars lose their resistance within a short time.

Stripe rust to limits wheat production by affecting the yield and quality of kernels as it develops at an early crop stage when temperatures are favorable for rust development [30]. Stripe rust destroys leaves at jointing to booting growth stages. Consequently, infection of stripe rust on wheat reduces photosynthetic area as early as tillering and jointing stages of development. Stripe rust epidemic has occurred in more than 60 countries in every continent causing yield losses of up to 100% in susceptible cultivars [31]. In East Africa, Kenya, and Ethiopia the epidemics caused yield loss of 67−100% in the year 2010 [25]. In Kenya, wheat is grown throughout the year in different agro-ecological zones, and this increases the concentration of the urediniospores in the air making it difficult to control the disease in susceptible varieties [12, 16]. Yield losses of up to 80% have been estimated but some fields with susceptible cultivars go up to 100% [10, 25].

Stripe rust is a global problem evolving into different races, either from their wild ancestor or their host through introductions [32]. In Kenya and Ethiopia Yr9and Yr27based cultivars broke down due to evolution of virulent stripe rust races to these genes resulting to yield losses of up to 40% in commercial cultivars like Paa that carried Yr9gene [12, 33]. Stripe rust race 134 with virulence for Yr7, 6, 9+ genes were present in Ethiopia, Kenya, Syria, and Yemen [34]. Thirteen races with virulence corresponding to stripe rust resistance genes Yr1, Yr2, Yr3, Yr6, Yr7, Yr8, Yr9, Yr17, Yr25, Yr27,and Avocet Sare present in wheat-growing regions of Kenya [35], these races belong to either strain Pst1or Pst2which might have been present much earlier than 1982 and 1970.

Wheat leaf rust caused by Ptis the most common and widely distributed of the three wheat rusts and occurs in more regions than stem rust and stripe rust [36, 37]. Leaf rust mostly infects wheat in low to medium altitude wheat-growing areas of Kenya [38, 39]. The earliest epidemics of this rust were reported in Kenya as early as 1908 [26]; therefore, it is considered to be among the major three wheat rusts (stem, yellow and leaf) responsible for depressing crop yields drastically depending on the cultivar because of its high frequency and widespread occurrence. Yield losses attributed to leaf rust have been reported to range from 5–16% on average, and up to 40% in epidemic years [40]. Yield losses are usually the result of lower kernel weights and decreased number of kernels as the pathogen may kill wheat seedlings by elevating respiration rate, reducing photosynthetic area on the leaf surfaces, and lessening translocation of carbohydrates [41]. In Kenya, the disease appears sporadically and has not been a problem for the past 20 years, but it has recently emerged in the wheat fields, and experimental plots, including the Kenya Agricultural and Livestock Research Organization (KALRO), Njoro international screening nursery with severity of over 50% [42]. One of the recent studies [43] reported a high reduction in grain yield and kernel weight in some of the Kenyan wheat cultivars.

Highly effective durable resistance to leaf rust has been difficult to achieve due to the high degree of virulence variation in the Ptpopulation and the rapid selection of races with virulence to effective Lrgenes in wheat genotypes [44]. This high degree of specificity has made durable rust resistance in wheat difficult to achieve because the virulence of leaf rust against wheat resistance genes is highly diverse resulting in the existence of many different pathogenic races [37]. For instance, the novel race BBG/BN and its variant BBG/BP overcame the resistance of widely adapted durum cultivars in northwestern Mexico. In Kenya, leaf rust samples collected from wheat-growing areas were found to have virulence for leaf rust resistance genes Lr1, Lr2b, Lr3, Lr9, Lr11, Lr12, Lr14a, Lr14b, Lr18, Lr20, Lr22a, Lr23, Lr24, Lr26, and Lr27. The race for an isolate collected from Ololulung’a, Narok in the South Rift region was designated as LBBTN [45].

1.2 Other wheat diseases in Kenya

Fusarium diseases, mainly Fusarium head blight of wheat (FHB), also called head scab, are caused mainly by the fungus Gibberella zeae(also known as Fusarium graminearum),periodically causes significant yield losses and reduced grain quality. Gibberella zeaealso produces mycotoxins [46]. All Kenya wheat cultivars are susceptible to Fusarium infection [47]. Studies done in Kenya show that the prevalence of FHB and yield loss due to FHB varies from trace to 100% [47, 48].

Septoria diseases are caused by S. triticiand S. nodorum[49]. Yield losses attributed to heavy incidences of S. triticiand S. nodorumhave been reported to range from 31–53% resulting in shriveled kernels [49]. The occurrence of Septoria diseases in the wheat-growing areas of Kenya is sporadic and severe infection leading to shriveled grain is observed (Wanyera, Personal observation). Some of the foliar fungicides recommended for the control of rust diseases in wheat have been observed to reduce Septoria disease infection when applied at the right time. These foliar fungicides include: (azoxystrobin200 g/L+ tebuconazole300 g/L (Stamina 500 SC); benzovindiflupy30 g/L + azoxystrobin114G/L + propiconazole132 g/L (Elatus Arc 265.14 SE); difenaconazole125 g/L + azoxystrobin200g/L (Token 325 SC); (trifloxystrobin250g/Kg/L + tebuconazole500 g/Kg (Shadow 750 WG).

Spot blotch caused by Bipolaris sorokiniana(Sacc) Shoemaker, perfect stage Cochliobolus sativus(S.Ito & Kurib) also causes black point, root rot, and crown rot in wheat. It is known to occur worldwide in warmer environments and is a serious constraint in wheat production in India, Bangladesh, and Nepal [50]. It is also a serious problem on barley. The disease can attack all parts of the wheat plant (seed, roots, shoots and leaves) causing seed-rot, seedling emergence, reduced yield affecting end-use quality of the harvested grain [51, 52]. Bipolarissp. is known to reduce seed viability in wheat and also causes a significant reduction in seed quality and flour [53]. Yield loss estimates of 15−25% and 30% have been reported [54] and on barley in Canada [55].

The sudden upsurge of Bipolaris sp. in certain areas of the country has been associated with acid soils. It is estimated that 30% of the soil in the wheat-growing areas is acidic. High infection has been recorded on wheat cultivars Ngamia in Uasin Gishu county (North Rift) and Kenya Nyangumi in Rongai areas of Nakuru county (Central Rift) (Wanyera, Personal observation).

The highland areas of wheat production in Kenya: Molo, Mau Narok (Central Rift), Eldoret and Endebess (North Rift) have a pH of 4.3−5.5 [56]. All wheat cultivars grown in these areas have shown susceptibility to the pathogen but no direct screening has been done. Aluminum toxicity in acid soils has been documented as the primary factor in the reduction of the crop yields [56]. Seed borne nature of the disease has been reported in wheat cultivars in Kenya [57, 58], and studies on disease management revealed that the pathogen can be reduced by the use of seed treatment fungicides [59]. Biological control methods have also been reported [60, 61].

Loose smut caused by Ustilago triticiis seed-borne and common in the wheat-growing areas of the world. Infection occurs during flowering through wind-borne spores. In Kenya, the disease occurs rarely and is mostly observed in recycled wheat seeds.

Take All (Gaeumannomyces graminisvar. tritici) is soil and debri-borne, detected mostly in fields that are continuously cultivated with cereals. Both Loose smut and Take All are well managed through use of certified seed, cultural control, and seed treatment fungicides. Some of the recommended seed treatment fungicides are: prothioconazole100 g/L (Redigo FS100), difenoconazole92g/L + metalaxyl-M23 g/L (Dividend Extreme 115 FS), and azoxystrobin141.4 g/L+ propiconazole122.4 g/L (Quilt Excel 263.5 SE) [6].

Apart from fungal diseases, another disease that threatens wheat production in Kenya is the Barley Yellow Dwarf Virus (BYDV), which is an important virus disease of cereals globally and has a wide host range that includes wheat, barley, oats, triticale, and over 150 grass species [51]. The disease was first reported in Kenya in 1984 and causes serious damage in barley, wheat, and oats and estimated losses range from 16.5−54.7% [62, 63]. Cereal aphids are vectors of the barley yellow dwarf and five strains have been known to occur in Kenya: RPV (Rhopalosiphumpadi), RMV (R. maidis), MAV (Sitobionavenae), SGV (Schizaphis graminum), and PAV (R. padi, S. avenae[63]. Outbreaks are frequent, and management practices require use of seed dressing insecticides: Gaucho 350FS (Imidacloprid), Cruiser 350FS (Thiamethoxam), Redigo Deter 350FS (Clothianidin + prothioconazole), Celest Top 312FS (Thiamethoxam + fludioxonil +difenoconozole, and (ii) foliar-applied insecticides (Karate Zeon (Lambda-cyhalothrin), Bulldock star 262.5EC (Betacyfluthrin + Chlorpyrifos), Thunder OD 145 (Imidacloprid + Betacyfluthrin), Keshet 2.5EC (Deltamethrin),Twigathoate 40EC (Dimethoate), Nurelle D 50/505 EC (Cypermethrin + Chlorpyrifos), Alphadime (Alpha-cypermethrin + Dimethoate), Cyclone 505EC (Cypermethrin + Chlorpyrifos), and Pirimor 50WG (Pirimicarb) [6, 64, 65].

Under favorable environmental conditions, infection of the wheat crop with these diseases can reduce quantity and quality of the grain. Disease surveillance is an epidemiological practice by which the spread is monitored to establish patterns of progression and is key in identifying new diseases and races which can be used in risk assessment and resistance breeding. This review highlights the prevalence, distribution of wheat diseases, host plant resistance in the key wheat-growing regions, and future prospects in Kenya.

1.3 Distribution of diseases in wheat-growing regions of Kenya

Surveys were conducted in the farmer fields in the major wheat-growing regions (Central Rift, South Rift, North Rift, and Mount (Mt) Kenya from 2011 to 2019. The objective was to determine the prevalence and distribution of the wheat diseases and host plant resistance in these regions. Farms were randomly picked along the routes, stopping at every 3 to 5 kilometers. Crops were observed for disease symptoms. An International Standardized survey form was used to keep the records on disease incidence and severity, cultivar grown, production area, and growth stage [66], also any other data that was useful. The Global positioning system (GPS) tool was used to collect precise information on latitude, longitude, and elevation of the sampled farms. Stem, yellow, and leaf rust severities were taken using modified Cobb scale, 0−100% where; 0- immune and 100- susceptible [67]. The host plant response to infection was scored as resistant (R), moderately resistant (MR), moderately susceptible (MS), and susceptible(S) [68]. Incidence and severity of other diseases observed during the surveys were also taken using recommended scales. Septoria diseases were assessed using 0−9 scale [49], where 0 = Free from infection and 9 = Very susceptible/severe infection. Similarly, barley yellow dwarf virus was assessed on a scale of 0−9 [69], where 0 = no symptoms and 9 = full symptom expression, and the Fusarium disease score rating system was 0−5 [70]. Tables 1 and 2 show the occurrence (percent infection and severity & plant response) of the diseases in all the wheat-growing regions. Rust diseases are common in the wheat fields and stem rust is widespread in all the regions. This explains the importance of stem rust, Ug99 race group, since its detection in Uganda and spread to the wheat-growing areas of Kenya, throughout eastern Africa, Yemen, Sudan, Iran, Zimbabwe, Tanzania, South Africa, Mozambique, Zimbabwe, and Iraq [15, 16, 22]. The prediction for the rust diseases to spread towards North Africa, Middle East, Asia and beyond, raises serious concerns of major epidemics that could destroy the world’s wheat crop [19].

YearRegionNo. of sampled farmsSr% Infection (%)Sr% severity and plant responseYrinfection (%)Yr% severity and plant responseLr Infection (%)Lr% severity (%)
2011Central Rift6270.90-100S17.7TR -60S17.7TR-40S
South Rift12568.8TR-100S6.4TR- 20S17.7TR-20S
North Rift7348.3TR-90S10.9TR- 20S10.9TR-20S
Mt. Kenya region6768.0TR- 60S10.40 - 40S13.4TR-20S
2012Central Rift6765.7TR-80S4.55-50S11.95-30S
South Rift715.6TR-20S
North Rift10126.7TR-70S5.95-70S3.910-50S
Mt. Kenya region3958.9TR-50S5.1%5-60S2.630S
2013Central Rift9771.0TR-70S8.3TR-50S6.7TR-50S
South Rift10468.3TR-100S3.810S–30S5.8TR-50S
North Rift7833.3TR-70S10.3TR-50S6.5TR-50S
Mt. Kenya region5425.9TR-60S7.410S–30S00
2014Central Rift9282.5TR-80S6.2TR -50S6.210S–50S
South Rift7972.2TR-80S8.9TR- 60S
North Rift9555.8TR-80S6.3TR- 40S5.30 - 40S
Mt. Kenya region7157.7TR- 60S15.55S - 60S1.40-40S
2015Central Rift6654.54TR-80S5.85S–40S1.50-30S
South Rift10135.6TR-60S
North Rift10675.5TR-50S8.5TR-40S1.9TR-30S
Mt. Kenya region6371.4TR-60S
2016Central Rift6088.3TR-80S16.7TR-60S3.330S–50S
South Rift8176.5TR-70S4.9TR-10S1.20-50S
North Rift9872.4TR-80S13.3TR-40S10.2TR-50S
Mt. Kenya region6180.3TR-90S1.6TR
2017Central Rift5487.03TR-70S8.90 -30S
South Rift7969.2TR-100S3.79TR- 10S
North Rift7864.1TR-60S8.97TR- 30S24.4TR-40S
Mt. Kenya region3844.1TR- 30S10.5TR - 40S
2018Central Rift6474.05-50S10.05-60S10.0TR-30S
South Rift8542.25-70S3.310S–30S1.1TR-40S
North Rift8925.845-80S19.15S–60S24.355S–70S
Mt. Kenya region6247.95-40S2.8110S–30S
2019Central Rift5682.2TR-50S2.20-40S
South Rift8783.13TR-80S1.2TR
North Rift10122.77TR-40S7.92TR-40S4.95TR-20S
Mt. Kenya region4663.04TR-50S10.8615S–60S6.55S–30S

Table 1.

Occurrence of wheat rust diseases in the commercial fields in year 2011−2019.

Sr = Stem rust; Yr = Yellow rust; Lr = Leaf rust; TR- trace; S = susceptible; − = no disease observed.

YearRegionNo of sampled farmsDisease incidence (%)
2011Central Rift6216.19.60
South Rift12541.60.8
North Rift7327.412.30
Mt. Kenya671.500
2012Central Rift6742.88.916.4
South Rift7146.52.80
North Rift10141.80.90.9
Mt. Kenya3917.92.70
2013Central Rift978.26.22.1
South Rift10414.40.90.9
North Rift7828.200
Mt. Kenya5445.31.90

Table 2.

Occurrence of Septoriadiseases, Fusariumsp. and Barley yellow dwarf virus (BYDV) in commercial wheat field year 2011, 2012, and 2013.

Yellow rust, which was first described in 1777, and attacked wheat in Kenya as early as 1908 [26], was observed in low incidences but high severities across all the regions (Table 1). The disease is also a major threat as no cultivar is resistant [28, 29]. Newly introduced resistant varieties lose their resistance within a short time and farmers are forced to spray to save on yields. Serious attacks of the pathogen occur annually and the disease severity increases with altitude [33]. Serious epidemics also occur in the lower latitudes areas. All the wheat-growing areas are prone to disease in low medium and high altitudes areas.

In Kenya, leaf rust has been sporadic and has not been a problem for the past 20 years, but it has recently emerged in the wheat fields (Table 1), and experimental plots, including the international screening nursery with a severity of over 50%. Our cultivars are now at risk given the fact that virulences and new races have been identified in Njoro and also South Rift, Ololulung’a areas (data not shown).

The growing of wheat in diverse agro-ecological zones throughout the year [71, 72] in Kenya creates a significant pool of airborne urediniospores, which coupled with favorable climatic conditions and the presence of host plants, favors rapid build up of inoculum and the occurrence of epidemics. This implies that there is a shift in races present each year, which affects different cultivars of wheat. There is continuous attack, due to the presence of wheat crops throughout the year. The breakdown in resistance could also be attributed to mutations [24]. It is, therefore, a problem to reduce the disease infection in susceptible cultivars and also not possible to grow a profitable crop of wheat without the application of fungicides [10, 16]. Septoria diseases, Fusarium spp., Barley yellow dwarf virus are also becoming more prevalent in the commercial fields (Table 2), year 2011 to 2013. Disease incidence varied from year to year depending on the chemical/spray applied. Data for the occurrence of these diseases from 2014 to 2019 was not shown because it was similar as shown in Table 2.

1.4 Wheat breeding in Kenya

Conventional breeding, which includes testing genotypes in different environments to determine the adaptability of the varieties has been used largely in Kenyan wheat breeding programs to identify resistant varieties [72]. Crop improvement by traditional methods, involves collection, hybridization, and inbreeding that has been practiced since the beginning of 20th Century. However, it has now been realized that these methods are insufficient to make further breakthroughs or cope with the increasing demand for improvement in crop varieties [73]. Some of the limitations of conventional breeding include the exhaustion of the gene pool, low response to biotic and abiotic stress of the introduced materials, and low combining ability, especially with complex characters. In Kenya, diverse agro-ecological zones and favorable environs highly contribute to the emergence of new races. The cultivars grown are at high risk of being infected with diseases, therefore, it is necessary to identify and incorporate genes that confer durable resistance to contain major epidemics [74, 75]. There are various strategies employed to control these diseases in wheat. These include incorporation of genetic resistance into susceptible wheat genotypes, crop management plus use of fungicides. Despite the fact that it takes a long-time, breeding for durable resistance remains to be a cost-effective strategy of minimizing loss due to wheat diseases [76]. Therefore, host resistance is the primary tool to protect wheat crops from wheat fungal rust diseases and other biotic stresses [77]. Breeding for vertical (qualitative) resistance based on major genes and horizontal (quantitative) influenced by several minor genes for wheat disease resistance has been going on in Kenya since wheat introduction in the 19th century. However, due to pathogen evolution, most of the genotypes with qualitative and quantitative resistance become susceptible to the new races, especially wheat rusts pathogens. For instance, wheat cultivars Robin and Eagle 10 released in Kenya as resistant varieties in 2009 and 2010 were overcome by Ug99 variant SrTmp [78, 79]. Durable resistance by selecting resistant wheat varieties has been going on in Kenya for the past decades, most of the varieties released with resistant genes are now ineffective against the evolving wheat rusts pathogens (Table 3).

NoVarietyRegion and variety area planted (%)
Central RiftSouth RiftNorth RiftMt.Kenya
2KS Mwamba50.414.912.350.415.520.245.228.726.933.825.625.9

Table 3.

Commonly grown cultivars in the key wheat-growing regions in the year 2011−2013.

-cultivar not planted.

Kenyan wheat cultivars Robin, NjoroBW2, KS Mwamba, Kwale, Kenya Korongo, Robin, Eagle 10, Kenya Black Hawk 12 (Tables 3 and 4), and Kenya Seed Company cultivars were grown by most farmers in the wheat-growing regions of Kenya.

Commercial NamePedigreeYield potential tons/HaDays to MaturityYear of releaseResistant status
RobinBABAX/LR42//BABAX*2/3/TUKURU8.1110–1202009Overcome by TTKTT race in 2014
Eagle10EMB16/CBRD//CBRD6.5100–1102010Good resistance to stem rust (Ug99 strain).
Kenya WrenTHELIN#2/TUKURU8.5120–1302012APR to both yellow and stem rust diseases.
Kenya TaiND643/2*WBLLI6.5100–1102012Resistant to both stem rust and yellow rust.
Kenya SunbirdND643/2*WBLLI6.5100–1102012Resistance to stem rust,
Kenya KorongoBABAX/LR42//BABAX*2/4/SNI/TRAP#1/3KAUZ*2/TRAP//KAUZ8.5120–1302012Overcome by TTKTT race in 2014
Kenya KingbirdTAM-200/TUI/6/PAVON-76//CAR-422/ANAHUAC-75/5/BOBWHITE/CROW//BUCKBUCK/PAVON-76/3/YECORA-70/4/TRAP-16.090–1102012Developed for Adult plant resistance to both stem rust and yellow rust.
Black Hawk12URES/JUN//KAUZ/3/BABAX/4/TILHI8.0120–1302012Overcome by TTKTT race in 2014
Kenya HornbillPASTOR//HXL7573/2*BAU/3/SOKOLL/WBLL17.5110–1202016High APR to yellow rust and moderate resistance to stem rust.
Kenya DeerPBW343*2/KUKUNA*2//YANAC7.8100–1102016High adult plant resistance to stem rust and yellow.
Kenya WeaverbirdPRINIA/3/ALTAR84/AE. SQ //2*OPATA/4/CHEN/AEGILOPS SQUARROSA(TAUS)//BCN/3/BAV928.0110–1202016High APR to stem rust.
Kenya PeacockQUAIU/3/PGO/SERI/BAV92120–1302016High APR to both stem and yellow rusts.
Kenya FalconKSW/5/2*ATLAR 84/AE. SQUARROSA (221)//3*BORL95/3/URES/JUN/KAUZ/4/WBLL18.0100–1152016Excellent seedling and APR to stem rust. Highly resistant to yellow rust
Kenya SongbirdKSW/5/2*ALTAR 84/AE. SQUARROSA (221)//3*BORL95/3/URES/JUN/KAUZ/4/WBLL18.2110–1202016_
Kenya PelicanKSW/5/2*ALTAR84 /AE. AQUARROSA (221)//3*BORL95/3/URES/JUN/KAUZ/4/WBLL18.5120–1302016High APR to stem rust.
Kenya JacanaKSW/SAUAL//SAUAL/3/REEDLING #16.5–8.0110–130 Days2019Moderately resistant to original Ug99 races. In warmer weather, susceptible to race “TTKTT”
Kenya KasukoKSW/SAUAL//SAUAL/3/REEDLING #17.0–8.0110–120 Days2019Moderately resistant to original Ug99 races. In warmer weather, susceptible to race “TTKTT”

Table 4.

Current wheat varieties released in Kenya, their yield potential and resistant attributes.

In 2011, KS Mwamba occupied the largest area in Central and South Rift (50.4%), North Rift (45.2%), and in Mount Kenya region 33.8% (Table 3). In 2012, the area planted with NjoroBW2 increased: 34.3%, 39.4%, 60.4%, while it decreased for KS Mwamba, 14.9%, 15.5%, and 28.7% in Central, South, and North Rift, respectively (Table 3). Cultivar Kwale was highly grown in Central Rift (20.9%), Mt. Kenya (23.1%), and South Rift (20.2%) in 2013. For the cultivars released in 2010 with adult plant resistance (APR) to the wheat stem rust race Ug99, Robin occupied 20.6% in Central Rift, 22.2% in Mt. Kenya, 7.7% in North Rift (2013). Cultivar Eagle 10 occupied 1.6% in Mt. Kenya region and 0.9% in South Rift. Mixed and other unknown cultivars were common across the regions and this could be due to the high cost of certified seed.

In 2014, cultivar Robin was highest in Central Rift (43.3%), South Rift (41.8%), and Mt. Kenya region (43.7%) while cultivar NjoroBW2 was highest in North Rift (64.2%), Central Rift (15.5%), Mt. Kenya (12.7%), and South Rift (8.9%). KS Mwamba was highest in North Rift (16.4%), Central Rift (15.5%), South Rift (11.4%), and Mount Kenya (9.9%). The area under cultivar Kwale was highest in Central Rift (10.3%), followed by South Rift and Mt. Kenya region (7.6% and 7.0%), respectively. The area under cultivar Eagle 10 was only noted in South Rift 18.9% and overall occupied only 4.4% across the region. Mixed and other unknown cultivars were common in Mt. Kenya region: Kenya Ibis occupied 1.2%, Duma (0.6%), mixed cultivars (1.8%).

In 2015, the area planted with NjoroBW2 increased in North Rift from 63.2% in 2014 to 70.6% in 2015 cultivar Robin increased in Mt. Kenya region (66.7%) as opposed to 2014 (43.7%), but decreased in Central Rift from to 21.2%. The area under production in North Rift increased from to 16.5% and decreased in South Rift from 35.6%. Cultivar Eagle 10 was only observed in South Rift (20.8%) of the sampled fields. Cultivars Kenya Wren and Kenya Hawk12 were observed only in the South Rift (1.9%).

The area planted on NjoroBW2 decreased in North Rift to 64.3% Mt. Kenya 49.2% in 2016. Cultivar Eagle 10 was only grown in South Rift (9.9%) and in North Rift (2.0%) of the sampled fields. Cultivars Kenya Wren was grown in South Rift (2.5%) and North Rift (1.0%) while Kenya Hawk12 was grown in the South Rift (6.2%). Kenya Korongo was grown in South Rift (8.3%) and North Rift (1.0%).

In 2017, cultivar NjoroBW2 was popular in North Rift (69.2%), Central Rift (40.7%), and South Rift (32.9%). Robin was popular in Mt. Kenya region (32.4%), followed by South Rift (20.3%), Central Rift (10.7%), and North Rift (7.7%). Kenya Korongo was only popular in the Central Rift (27.8%). Kwale was popular in Central Rift (7.4%), South Rift (6.3%), and Mt. Kenya (5.3%) area under production of the sampled fields. Cultivar NjoroBW2 occupied the largest area in North Rift (69.2%) and Central Rift (40.7%). Cultivar Eagle 10 was recorded in South Rift (13.9%), Central Rift (1.9%), and in North Rift (1.3%) of the sampled fields. While variety Duma was popular in Mt. Kenya region (42.1%) area under production of the sampled fields. Kenya Wren was grown in Central Rift 1.9.3%), South Rift (1.3%), and North Rift (1.0%) while Kenya Black Hawk12 was grown in South Rift (6.2%) and North Rift (1.3%). Kingbird was only grown in South Rift (2.5%) and North Rift (1.3%) area under production of the sampled fields.

In 2018, cultivar NjoroBW2 was popular in all the regions: North Rift (70.8%), Central Rift (44.0%), South Rift (34.4%), and Mt. Kenya region (14.08%). Robin was grown in North Rift (16.0%), Mt. Kenya (14.6%), Central Rift (12.0%), and South Rift (11.8). Kenya Korongo was only popular in the Mt. Kenya region (36.6%) while Kwale was grown in Central Rift (8.0%) and South Rift (4.7%). Variety Eagle 10 was only popular in South Rift (14.0%) area under production of the sampled fields. The area under production of variety Eagle 10 remained the same in the South Rift as the previous year. Kenya Wren was only grown in South Rift (3.5%), Kenya Black Hawk12 was grown in North Rift (2.5%). while Kingbird was grown in South Rift (1.2%) and North Rift (1.3%).

In 2019 cultivar NjoroBW2 was popular in Mt. Kenya (43.5%). North Rift (42.5%), Central Rift (39.28%), South Rift (31.0%). Kenya Korongo was grown in Mt. Kenya (23.9%), Central Rift (16.0%), South Rift (11.5%), and North Rift (7.92%). Cultivar Robin was popular in the Mt. Kenya (23.9%), South Rift (13.8%), and Central Rift (5.4%). Kwale was grown in North Rift (9.9.0%), South Rift (8.0%), Mt. Kenya (6.5%), Central Rift (5.4%) area under production of the sampled fields. Cultivar Eagle 10 was only popular in South Rift (14.9%) and Central Rift (7.1%) area under production of the sampled fields. The Kenya Seed Company cultivars were more popular in the North Rift (24.8%) area under production of the sampled fields.

Over fifty percent of the previously released varieties (Table 4) are now susceptible to the Ug99 race. Robin, Kenya Black Hawk12, Kenya Korongo, Kenya Jacana, and Kenya Kasuko are susceptible to Ug99 races (TTKTK and TTKTT) that were detected on Robin with virulence to SrTmp and virulence to Sr24, respectively. The resistance in Kwale and other genotypes like Kenya Plume (not included) is due to adult plant resistance (APR) genes and others associated with variable levels of disease symptoms, which show recessive inheritance and is expressed primarily during the APR which has been deployed in a breeding program in Kenya [80]. Stem rust resistance gene Sr2is an APR gene present in some of the Kenyan genotypes such as Kwale, Kenya Swara, Kenya Nyangumi, and Kenya Popo together with other APR genes condition resistance to stem rust [11, 81].

There is a long history of wheat breeding in Kenya as early as 1908, however, the use of molecular breeding tools is very limited thereby hampering the rate of genetic gains achieved. As such, the national breeding program has depended on introductions of wheat lines from international wheat breeding programs including CIMMYT and ICARDA. Understanding the composition and diversity of fungal wheat disease resistance in Kenya wheat germplasm is important for defining breeding strategies and prioritizing trait targets for wheat improvement [82].

Biotechnological approaches in wheat breeding such as double haploid (DH) and mutational breeding have been used to speed up breeding by complementing conventional breeding [72]. DH which shortens the breeding period by a single cycle has been used in Kenya to produce varieties such as K. Ibis. Mutation breeding brings about genetic variation and accelerates the outcome of variety release has been applied at KARLO, Njoro to release varieties NjoroBW2 and K. Heroe by irradiation using gamma rays [72, 83]. Conventional method of gene pyramiding is time-consuming, hence, the incorporation of molecular breeding is efficient in breeding for biotic and abiotic stresses in wheat for quick release of resistant varieties. The use of molecular markers enhances phenotypic selection because it makes it more efficient, effective, reliable, and cost-effective compared to conventional plant breeding, hence improving the latter [84]. There has been some concern about the incorporation of DNA marker technology in many plant-breeding institutions and most institutions can now develop their own markers [85, 86]. Molecular markers such as SSR, AFLP, and KASP markers have been developed to evaluate genotypes for biotic stresses such as diseases in Kenyan varieties [7, 82, 87].

1.5 Control of wheat diseases in Kenya

Other than host plant resistance, cultural and chemical methods have been used to control wheat diseases in Kenya. Cultural control techniques such as growing resistant genotypes, late planting, reduced irrigation, avoidance of excessive nitrogen use, and elimination of volunteer and grass plants can reduce stripe rust severities as they limit exposure time to inoculum [25]. Altering planting date and separating the vulnerable crop from the pathogen in either time or space controls certain airborne disseminated pathogens of wheat [88]. Although the cultural techniques are used, they are either not profitable, conflict with conservation farming, or reduce yield potential [89]. Genetic resistance combined with chemical treatments, although expensive to the poor resource farmers may often be very effective in controlling wheat diseases [90]. Some of the fungicides used by farmers in Kenya are listed in Table 5. The application of seed treatment chemicals such as triadimenol(sterol biosynthesis inhibitors) and carboxin(respiratory inhibitors) and the use of moderately resistant cultivars is effective in controlling wheat diseases as it provides the most efficient use of fungicides at the lowest rates [91, 92]. Reduced chemical applications could also minimize the potential development of resistance to the chemicals [90]. Although wheat diseases have been controlled by timely use of effective chemicals, the cost of chemicals and their application creates a huge burden for growers. In Kenya, large-scale farmers are the only ones who can afford to spray chemicals, but it costs about $ 8 million annually [10]. Fungicides can be used to control fungal diseases, but they cause environmental hazards and lead to fungicide tolerant strains [25]. Re-emergence of new virulent races has reversed the gains made by breeders, posing a new and significant threat to wheat breeding in Kenya [16]. Resistance in the commercial wheat cultivars in Kenya, including those released in the last decade, has been overcome by the new races making it impossible to grow a profitable crop of wheat without the use of fungicides [10, 90].

NoChemical nameCommon nameRate L/ha
1trifloxystrobin100gL+ tebuconazole200 g/LlNativo 300SC1.0
2prothioconazole125gL + tebuconazole125gLlProsaro 250EC1.0
3epoxiconazole250 g/LTwiga Epox GF1.0
4tebuconazole200 g/LFezan 250 EW GF1.0
5picoxystrobin200 g/L + cyproconazole80 g/LAcanto Plus1.0
6epoxiconazole62.5 g/L + pyraclostrobin62.5 g/LAbacus SE1.0
7epoxiconazole18 g/L + thiophanate methyl310 g/LRexduo SE1.0
8metconazole27.5 g/L+ epoxiconazole37.5 g/L + 200 g/L picoxystrobin + 80 g/L cyproconazoleOsiris EC1.0
9propiconazole62.5 g/L+ chlorothalonil375 g/L + cyproconazole50 g/LCherokee 487.5 SE1.0
10propiconazole250 g/L + cyproconazole60 g/LMenara 410EC0.5
11tebuconazole430 g/LTebulis 430 SC0.5
12tebuconazole200 g/L + azoxystrobin200 g/LAzimut SC1.0
13bixafen75 g/L + prothioconazole100 g/L + tebuconazole100g/LSkyway Xpro 275 EC1.2
14propiconazole150 g/L + difeconazole150 g/LAtlas 300EC1.0
15propiconazole172.4 g/L + azoxystrobin141.1 g/LQuilt Excel 265 SE1.25
16epoxiconazole187 g/L + thiophanate methyl310 g/LSwing Xtra 497 SC1.0
17monopotassium phosphate43% + dipotassiumphosphate19%Fosphite Liquid4.0
18azoxystrobin80 g/L+ chlorothalonil400 g/LAmizoc 480 EC1.8
19bixafen50 g/L+ tebuconazole166 g/LZantara 216 EC1.0
20fluxapyroxad41.6 g/L + epoxiconazole41.6 g/L + pyraclostrobin66.60 g/LCeriax 149.8 EC1.0
21azoxystrobin200 g/L+ tebuconazole300 g/LStamina 500SC0.9
22difenaconazole125 g/L + azoxystrobin200g/LToken 325 SC0.75
23benzovindiflupy30 g/L + azoxystrobin114G/L + propiconazole132 g/LElatus Arc 265.14 SE1.0
24tebuconazole/tridimenolSilvacur 375 EC1.0
25tebuconazoleFolicur 250 EC1.0
26(trifloxystrobin250g/Kg/L + tebuconazole500 g/Kg))Shadow 750 WG SC400 g

Table 5.

Recommended fungicides for control/reduction of foliar wheat diseases in Kenya.

* Can control Fusarium Head Blight (FHB) when spayed at flowering**Can control Fusarium Head Blight (FHB) and Septoria diseases GF- Generic fungicide.

During surveys, we noted that farmers who sprayed following the right recommendations of fungicides in Table 5 had good yields compared to those who did not spray or sprayed without following the proper recommendations hence losing the crop to the disease. Majority of the farmers sprayed the fungicides to reduce/suppress disease infections, particularly the rusts, but some sprayed farms were noted to have high disease infections. These are farms that either had been sprayed late or the timing/ chemical concentrations were not right.

1.6 Future of breeding for wheat diseases resistance in Kenya

Despite the occurrence of wheat diseases in Kenya, information on the genetic basis of the diseases and wheat cultivars is limited. Molecular genetic markers have been advanced from phenotypic and protein-based markers to DNA sequence polymorphism, this accelerates the process of plant breeding when coupled with conventional breeding [93]. Since many traits valued by plant breeders are complex and polygenic, it is essential to involve the deliberate combination of various genomic regions from many different individuals in the development of an adapted elite variety [94]. Sequencing polymorphism markers are important in identifying genetic diversity in cultivated and wild genotypes, the source of novel genomic regions, alleles, and traits [95].

In crops, marker-assisted selection (MAS) has been made efficient by designation of markers associated with economic importance, for instance, disease resistance (wheat rust), response to abiotic stress and seed quality [96, 97]. The use of molecular markers enhances phenotypic selection because it makes it more efficient, effective, reliable, and cost-effective compared to conventional plant breeding hence improving the latter [84]. There has been some concern about the incorporation of DNA marker technology in many plant-breeding institutions but most institutions can now develop their own markers [85, 86].

In genetic studies of wheat, genetic markers such as amplified fragment length polymorphism (AFLP), restriction fragment length polymorphism (RFLP), random amplified polymorphic DNA (RAPD), simple sequence repeat (SSR), and single nucleotide polymorphism (SNP) have been used but they are limited in their own ways [98]. These limitations are being overcome by improving already available techniques to form next-generation sequencing (NGS) [98]. With next-generation sequencing (NGS) technologies, SNP markers have been discovered in wheat, which is a good choice due to their abundance in the genome as they are distributed across all the wheat chromosomes [99]. These technologies offer easier means to map polymorphic genetic loci and identify genes for important traits [98]. Microsatellite markers have been used to determine the genetic diversity of wheat stem rust races in Kenya ([100]; Wanyera, unpublished data).

1.6.1 Single nucleotide polymorphism (SNP) markers

Single nucleotide variations in genome sequences of individuals of a population are known as SNPs. They result when DNA sequence differs by a single base and are the most abundant molecular markers in the genome [101]. SNPs and flanking sequences are found by library construction and sequencing or through the screening of readily available sequence databases [102]. Genotyping methods, including DNA chips, allele-specific PCR, and primer extension approaches based on SNPs, are particularly attractive for their high data throughput and for suitability for automation [103]. They are used for a wide range of purposes, including rapid identification of crop cultivars and construction of ultra-high-density genetic maps [103, 104]. SNPs markers have been used in wheat in identifying resistance genes for stripe rust Yr5, leaf rust Lr16, stem rust Sr6, the waxy starch gene Wx-D, and Karnal bunt resistance among others [105, 106, 107].

1.6.2 Kompetitive allele specific PCR (KASP) markers

Application of modern marker-assisted breeding approaches can help accelerate variety development efforts, single nucleotide polymorphisms (SNPs) markers have emerged as powerful tools for many genetic applications mainly due to their low assay cost, high abundance, co-dominant inheritance, high-throughput, and ease of use [101]. Numerous genotyping platforms have therefore been developed for SNP genotyping [108, 109] including KASP (Kompetitive Allele Specific PCR) which is a gel-free and fluorescent-based genotyping platform. KASP is fast emerging as a global benchmark in SNP genotyping [110, 111] developed and validated 70 KASP assays for functional genes controlling economically important traits such as plant height, disease resistance, yield, and quality in bread wheat. KASP markers have been used to determine alleles for important agronomic traits in wheat in East Africa, Kenya, and Ethiopia [82].

1.6.3 Use of sequence-characterized-amplified region (SCAR)

The application of molecular markers in different epidemiological studies is crucial in developing strain-specific markers such as Sequence-characterized-amplified-region (SCAR) markers [112]. The SCAR markers are codominant, while others are dominant single locus which allows for quick and easy PCR amplification-based detection and hence used in the studies of pathogens [113]. The SCAR markers are efficient in testing large samples and useful in tracing the origin and spread of microbial pathogens with the ability for long-distance disposal and invasion like yellow rust [114]. SCAR markers SCAR1265 and SCAR1400 were developed in wheat to identify powdery mildew (B. graminis) gene Pm21,which was located on 6AL/6Vs same locus for gene Yr26[115]. Species-specific sequence-characterized-amplified-region (SCAR) markers have been used to characterize stripe rust races in Kenya [35].


2. Conclusion

There are high disease incidences and severity of wheat diseases particularly wheat rusts in the farmers’ fields, which is attributed to the use of highly susceptible wheat cultivars and also climate change contributing to emerging of new diseases. For example, the evolution and spread of Ug99 race group and additional races like Digalu race (TKTTF) are spreading very fast causing epidemics subjecting the wheat germplasm to vulnerability.

Other wheat diseases such as Septoriaand Fusariumalthough sporadic are also a major concern in the wheat-growing regions in the country. The increase in the spread of these diseases is largely due to the widespread of cultivars that are highly susceptible. The favorable climatic conditions and additional costs of fungicides qualify the diseases as damaging with a strong impact on wheat production. Varieties with adequate resistance are now being released and continued monitoring of disease virulences throughout the country is necessary to detect shifts in the pathogen population as early as possible and therefore to effect an appropriate breeding strategy. Effective genetic control of the diseases using the state of the art molecular techniques will require a coordinated effort, including race monitoring, collection, and characterization of sources of resistance and resistance breeding.

In Kenya, different research groups consisting of plant breeders, plant pathologists, agronomists, international partners, and farmers are working towards achieving host plant resistance and ways to combat wheat diseases in order to achieve high yields and contribute to food security.



The authors wish to acknowledge the technical staff of the Plant Pathology section KALRO, Njoro, for assistance in collating pertinent information for this article.


  1. 1.Republic of Kenya. National Food and Nutrition Security Policy. Cathedral Road, Nairobi, Kenya: Agricultural Sector Coordination Unit (ASCU), Kilimo House; 2011
  2. 2.Kenya Agricultural Research Institute. Strategic Plan. Annual Reports, KARI, Nairobi- Kenya; 2009. pp. 2009-2014
  3. 3.Jaetzold R, Schmidt H, Hornetz B, Shisanya C. Farm management Handbook. 2nd ed. Vol. II. Part B Central Kenya. Subpart B1a: Southern Rift Valley. Ministry of Agriculture, Kenya, in Cooperation with the German Agency for Technical Corporation; 2010
  4. 4.Economic Review of Agriculture. Ministry of Agriculture. Nairobi, Kenya; 2013. p. 109
  5. 5.FAOSTAT. 2019. Available at:
  6. 6.Kamwaga J, Macharia G, Boyd L, Chiurugwi T, Midgley I, Canales C, et al. Kenya Wheat Production Handbook. Nairobi, Kenya: Kenya Agricultural and Livestock Research Organization; 2016. ISBN 978-9966-30-025-6
  7. 7.Macharia G, Waweru B. Wheat in Kenya: Past and twenty-first century breeding. In: Wanyera R, Owuoche J, editors. Wheat Improvement, Management and Utilization. Rijeka: InTech; 2017. ISBN: 978-953-51-3151-9, Online: ISBN: 978-953-51-3152-6
  8. 8.FAOSTAT. 2020. Statistical Database of the Food and Agriculture of the United Nations. Available from:
  9. 9.Kenya Agricultural Research Institute. 2009. Strategic Plan Implementation Frame Work. Annual Reports, KARI, Nairobi, Kenya; 2009-2014
  10. 10.Wanyera R, Macharia JK, Kilonzo SM, Kamundia JW. Foliar fungicides to control wheat stem rust, race TTKS (Ug99) in Kenya. Plant Disease. 2009;93:929-932
  11. 11.Wamalwa MN, Owuoche J, Ogendo J, Wanyera R. Multi-pathotype testing of selected Kenyan wheat germplasm and Watkin landraces for resistance to wheat stripe rust (Puccinia striiformisf. sptritici) races. Agronomy. 2019;9(11):770
  12. 12.Fetch TG, Park RF, Pretorius ZA, Depauw RM. Stem rust: Its history in Kenya and research to combat a global wheat threat. Canadian Journal of Plant Pathology, (just-accepted). 2021;43:S275-S297. DOI: 10.1080/07060661.2021.1902860
  13. 13.Singh VK. Pathophenotyping and genome guided characterization of rust fungi infecting wheat and other cereals-A training manual. In: The Cereal Rusts in History. Vol. 10. 2020
  14. 14.Li A, Liu D, Yang W, Kishii M, Mao L. Synthetic hexaploid wheat: Yesterday, today, and tomorrow. Engineering. 2018;4(4):552-558
  15. 15.Pretorius ZA, Singh RP, Wagoire WW, Payne TS. Detection of virulence to wheat stem rust resistance geneSr31inPuccinia graminisf. sp.triticiin Uganda. Plant Disease. 2000;84:203
  16. 16.Wanyera R, Kinyua MG, Jin Y, Singh R, Roelfs AP. The spread of stem rust caused byPuccinia graminisf. sp.tritici, with virulence onSr31in wheat in eastern Africa. Plant Disease. 2006;90:113
  17. 17.Roelfs AP, Singh RP, Saari EE. Rust Diseases of Wheat: Concepts and Methods of Disease Management. Mexico, D.F: CIMMYT; 1992
  18. 18.Jin Y, Szabo LJ, Pretorius ZA, Singh RP, Ward R, Fetch T. Detection of virulence to resistance gene Sr24 within race TTKS ofPuccinia graminisf. sp.tritici. Plant Disease. 2008;92:923-926
  19. 19.Singh RP, Hodson DP, Jin Y, Lagudah ES, Ayliffe MA, Bhavani S, et al. Emergence and spread of new races of wheat stem rust fungus: Continued threat to food security and prospects of genetic control. Phytopathology. 2015;105:872-884
  20. 20.Newcomb M, Olivera PD, Rouse MN, Szabo LJ, Johnson J, Gale S, et al. (2016). Characterization of Kenyan isolates ofPuccinia graminisf. sp.triticifrom 2008 to 2014 reveals virulence toSrTmpin the Ug99 race group. Phytopathology. 2016;100:986-996
  21. 21.Nazari K, Al-Maaroof E, Kurtulus E, Kavaz H, Hodson D, Ozseven I. First report of Ug99 race TTKTT of wheat stem rust (Puccinia graminisf. sp.tritici) in Iraq. Plant Disease. 2021;105(9):2719
  22. 2020 Pathotype Tracker – Where Is Ug99? Retrieved from:
  23. 23.Olson EL. Broadening the wheat gene pool for stem rust resistance through genomic-assisted introgressions fromAegilops tauschii[PhD thesis]. Kansas State University: Manhattan, Kansas; 2012
  24. 24.Hovmøller MS. Sources of seedling and adult plant resistance toPuccinia striiformisf. sp.triticiin European wheat. Plant Breeding. 2007;126:225-233
  25. 25.Chen XM. Pathogens which threaten food security:Puccinia striiformis, the wheat stripe rust pathogen. Food Security. 2020;12(2):239-251
  26. 26.Thorpe HC. Wheat Breeding in Kenya. Canada: First International wheat Genetics Symposium, University of Manitoba; 1959
  27. 27.Wanyera R. The status of rust diseases of wheat in Kenya. In: Breeding for disease resistance with emphasis on durability. In: Daniel DL, editor. Proceedings of a Regional Workshop for Eastern, Central and Southern Africa. Njoro, Kenya. 1994. pp. 222-225
  28. 28.Bonthuis H. Survival of stripe rust (Puccinia striiformis) on wheat in the Kenyan highlands and the consequences for virulence. Mededelingen van de Faculteit landbouwwetenschappen. Rijksuniversiteit Gent. 1985;50(4):1109-1117
  29. 29.Kenya Agricultural Research Institute. Annual Reports, KARI, Nairobi, Kenya; 1990-2012
  30. 30.Braun HJ, Singh RP, Huerta-Espino J, Herrera-Foessel SA, Lan CX, Basnet BR. Global status of yellow rust on wheat and strategies for its short- and long-term control. In: Proceedings of the 2nd International Wheat Stripe Rust Symposium, Regional Cereal Rust Research, Center Izmir, Turkey, 28th April – 1st May 2014. 2014. p. 25
  31. 31.Aggarwal R, Kulshreshtha D, Sharma S, Singh VK, Manjunatha C, Bhardwaj SC, et al. Molecular characterization of Indian pathotypes ofPuccinia striiformisf. sp.triticiand multigene phylogenetic analysis to establish inter-and intraspecific relationships. Genetics and Molecular Biology. 2018;41:834-842
  32. 32.Hartmann FE, Rodríguez de la Vega RC, Carpentier F, Gladieux P, Cornille A, Hood ME, et al. Understanding adaptation, coevolution, host specialization, and mating system in castrating anther-smut fungi by combining population and comparative genomics. Annual Review of Phytopathology. 2019;57:431-457
  33. 33.Danial DL, Stubbs RW, Parlevliet JE. Evolution of virulence patterns in yellow rust races and its implications for breeding for resistance in wheat in Kenya. Euphytica. 1994;80:165-170
  34. 34.Ding Y, Cuddy WS, Wellings CR, Zhang P, Thach T, Hovmøller MS, et al. Incursions of divergent genotypes, evolution of virulence and host jumps shape a continental clonal population of the stripe rust pathogenPuccinia striiformis. Molecular Ecology. 2021;00:1-19
  35. 35.Wamalwa M, Wanyera R, Rodriguez-Algaba J, Boyd L, Owuoche J, Ogendo J, et al. Distribution ofPuccinia striiformisf. sp. tritici races and virulence in wheat growing regions of Kenya from 1970 TO 2014. Plant Disease. 2021;PDIS-11
  36. 36.Kolmer JA, Long DL, Hughes ME. Physiological specialization ofPuccinia triticinaon wheat in the United States in 2003. Plant Disease. 2005;89:1201-1206
  37. 37.Kolmer J. Leaf rust of wheat: Pathogen biology, variation and host resistance. Forests. 2013;4(1):70-84
  38. 38.Roelfs AP, Singh RP, Saari EE. Rust Diseases of Wheat: Concepts and Methods of Disease Management. Mexico, D.F: CIMMYT; 1992
  39. 39.Marasas CN, Smale M, Singh RP. The economic impact of productivity maintenance research: Breeding for leaf rust resistance in modern wheat. Agricultural Economics. 2003;29:253-263
  40. 40.Bolton MD, Kolmer JA, Garvin DF. Wheat leaf rust caused by Puccinia triticina. Molecular Plant Pathology. 2008;9:563-575
  41. 41.Arslan U, Karbulut OA, Yagdi K. Reaction of wheat lines to leaf rust (Puccinia triticina) in Turkey. Bangladesh Journal of Botany. 2007;36(2):163-166
  42. 42.Kenya Agricultural Research Institute. Annual Reports. Kenya: Nairobi; 2011
  43. 43.Nyamu GA, Owuoche JO, Ojwang PR, Wanyera R. Evaluation of Kenyan wheat (Triticum aestivumL.) genotypes for leaf rust (Puccinia triticinaEriks) at adult plant stage. International Journal Agronomic Agriculture Research. 2017;11(6):66-78
  44. 44.Jin Y, Kolmer JA, Long DL. Wheat leaf rust and stem rust in the United States. Australian Journal of Agricultural Research. 2007;58:631-638
  45. 45.Wamalwa M, Wanyera R. Characterization of wheat (Triticum aestivum L.) leaf rust (Puccinia triticina) races in Kenya. In: Proceedings of EAAPP Mini-Conference and Stakeholders Open Day 12-15 November 2013. Naivasha, Kenya: RDCoE/Morendat Training Centre; 2014
  46. 46.Windels CE. Economic and social impacts of fusarium head blight: Changing farms and rural communities in the northern Great Plains. Phytopathology. 2000;90:17-21
  47. 47.Muthomi JW, Oerke EC, Dehne HW, Mutitu EW. Susceptibility of Kenyan wheat varieties to head blight, fungal invasion and Deoxynivalenol accumulation inoculated with fusarium graminearum. Journal of Phytopathology. 2002;150(1):30-36
  48. 48.Wagacha JM, Steiner U, Dehne HW, Zuehlke S, Spiteller M, Muthomi JW, et al. Diversity in mycotoxins and fungal species infecting wheat in Nakuru district, Kenya. Journal of Phytopathology. 2010;157:527-535
  49. 49.Eyal Z, Scharen AL, Prescott JM, Van Ginkel M. The Septoria Diseases of Wheat Concepts and Methods of Diseases Management. Mexico, D.F: CIMMYT; 1987. ISBN: 968-6127-06-02
  50. 50.Gupta PK, Chand R, Vasistha NK, Pandey SP, Kumar U, Mishra VK, et al. Spot blotch disease of wheat: The current status of research on genetics and breeding. Plant Pathology. 2018;67:508-531
  51. 51.Wiese MV. Compendium of Wheat Diseases. St. Paul, MN: APS Press; 1987
  52. 52.Mathur SB, Cunfer BM. Seed Borne Diseases and Seed Health Testing of Wheat. Copenhagen: Danish Government Institute of Seed Pathology for Developing Countries; 1993. p. 168
  53. 53.Mehta YR. Constraints on the integrated management of spot blotch of wheat. In: Duveiller E, Dubin HJ, Reeves J, McNab A, editors. Helminthosporium Blight of Wheat: Spot Blotch and Tan Spot. Mexico, DF: CIMMYT; 1998. pp. 18-27
  54. 54.Dubin HJ, van Ginkel M. The status of wheat diseases and disease research in the warmer areas. Wheat for the nontraditional warm areas: a proceedings of the International Conference July 29-August 3 1990 Foz do Iguaçu, Brazil. CIMMYT; 1991. pp. 125-45
  55. 55.Ghazvini H, Tekauz A. Virulence diversity in the population ofBipolaris sorokiniana. Plant Disease. 2007;91(7):814-821
  56. 56.Nyachiro JM. Development of Aluminum-tolerant bread wheat varieties in Kenya. In: Saunders DA, editor. Wheat for the Non-traditional Warm Areas. Mexico, D.F: CIMMYT; 1990. pp. 486-490
  57. 57.Wanyera R, Kinyua MG, Kongsdal O, Hynkemejer A. Detection of seed- bornefungal pathogens infecting some crops in Kenya. In: Korir JK, Gohole LS, Muasya RM, editors. Proceedings of the Stakeholders workshop on Seed Industry in Kenya. Agrotech; 2004. p. 82-88. ISSN: 1727-8155
  58. 58.Wanyera R. Seed-health status in wheat varieties Kenya. Proceedings of the First EgertonUniversity/NPBRC-NJORO Symposium in Agricultural Research. For Development (eds. J.N. Nanua, et al.); 2001. p. 249-256
  59. 59.Wanyera R. Seed-borne pathogens of wheat in Kenya. Regional Wheat Workshop for Eastern, Central and Southern Africa, 10; University of Stellenbosch, South Africa; 14-18 Sep 1998. In: TRegional Wheat Workshop for Eastern, Central and Southern Africa, 10; University of Stellenbosch, South Africa; 14-18 Sep 1998 Addis Ababa (Ethiopia)CIMMYT C1999 (No. Look under series title. CIMMYT.). Centro Internacional de Mejoramiento de Maiz y Trigo (CIMMYT), Addis Ababa (Ethiopia). 1999
  60. 60.Villa-Rodríguez E, Parra-Cota F, Castro-Longoria E, López-Cervantes J, de los Santos-Villalobos S.Bacillus subtilisTE3: A promising biological control agent againstBipolaris sorokiniana, the causal agent of spot blotch in wheat (Triticum turgidumL. subsp. durum). Biological Control. 2019;132:135-143
  61. 61.Singh UB, Malviya D, Singh S, Kumar M, Sahu PK, Singh HV, et al. Trichoderma harzianum- and methyl Jasmonate-induced resistance toBipolaris sorokinianathrough enhanced Phenylpropanoid activities in bread wheat (Triticum aestivumL.). Frontiers in Microbiology. 2019;10:3389
  62. 62.Wangai AW. Effects of barley yellow dwarf virus on cereals in Kenya. In: Burnett PA, editor. World Perspectives on Barley Yellow Dwarf Virus. Mexico, D.F: CIMMYT; 1990. pp. 391-393
  63. 63.Munene M, Nyakwara ZA, Njuguna MN, Maina IN. The occurrence of cereal aphids in Rainfed wheat in Kenya: The problem and possible integrated Pest management strategies. In: Wanyera R, Owuoche J, editors. Wheat Improvement, Management and Utilization. Rijeka: IntechOpen; 2017. DOI: 10.5772/67115. Available from:
  64. 64.Wanjama JK. Review of wheat aphid as a pest of cereals in the Rift Valley province Kenya. Entomologist Newsletter. 1979;9:2-3
  65. 65.Migui SM, Macharia M, Muthangyia PM, Wanjama JK. Evaluation of insecticides for the control of cereal aphids transmitting barley yellow dwarf virus in barley. Pp-203-210. In: Tanner DG, Mwangi W, editors. Seventh Regional Wheat Workshop for Eastern, Central and Southern Africa. Nakuru, Kenya: CIMMYT; 1992
  66. 66.Zadoks JC, Chang TT, Konzak CF. A decimal code for the growth stages of cereals. Weed Research. 1974;14:415-421
  67. 67.Peterson RF, Campell AB, Hannah AE. A diagrammatic scale for estimating rust intensity of leaves and stems of cereals. Canadian Journal of Research. 1984;26:496-500
  68. 68.Roelfs AP, Singh RP, Saari EE. Rust Diseases of Wheat: Concepts and Methods of Disease Management. Mexico, D.F: CIMMYT; 1992
  69. 69.Muthangya PM, Macharia M, Wanjama JK. Effects of Imidacloprid seed dressing and foliar aphicide on cereal aphids and BYDV on barley in Kenya. In: Tanner DG, Payne TS, Abdalla OS, editors. The Nineth Regional Wheat Workshop: For Eastern, Central and Southern Africa. 1993
  70. 70.James C. A Manual of Assessment Keys for Plant Diseases. No. BOOK. American Phytopathological Society; 1971
  71. 71.Green GJ, Martens JW, Ribeiro O. Epidemiology and specialization of wheat and oat stem rusts in Kenya in 1968. Phytopathology. 1970;60:309-314
  72. 72.Njau PN, Kimurto PK, Kinyua MG, Okwaro HK, Ogolla JB. Wheat productivity improvement in the drought prone areas of Kenya. African Crop Science Journal. 2006;14(1):49-57
  73. 73.Kinyua M, Malinga JN, Wanyama J, Karanja L, Njau P, Leo T, Alomba E (2001) Improvement of wheat for resistance to Russian wheat aphid.
  74. 74.Dawit WK, Flath WE, Weber E, Schumann MS, Röderand S, Chen X. Postulation and mapping of seedling stripe rust resistance genes in Ethiopian bread wheat cultivars. Plant Pathology. 2012;94:403-409
  75. 75.Kang ZS, Zhao J, Han DJ, Zhang HC, Wang XJ, Wang CF, et al. Status of wheat rust research and control in China. In: BGRI 2010 Technical Workshop, 30-31 May 2010, St Petersburg, Russia. PP; 2010. p. 38
  76. 76.Yuen GY, Schoneweis SD. Strategies for managing fusarium head blight and deoxynivalenol accumulation in wheat. International Journal of Food Microbiology. 2007;119(1-2):126-130
  77. 77.Loughman A, Fitzgerald JR, Brennan MP, Higgins J, Downer R, Cox D, et al. Roles for fibrinogen, immunoglobulin and complement in platelet activation promoted byStaphylococcus aureusclumping factor A. Molecular Microbiology. 2005;57(3):804-818
  78. 78.Njau PN, Wanyera R, Singh D, Singh R, Gethi M. Release of stem rust resistant wheat varieties for commercial production in Kenya. Journal of Agricultural Science and Technology. 2011;A1:587-598
  79. 79.Alemu G. Wheat breeding for disease resistance: Review. Journal of Microbiology and Biotechnology. 2019;4(2):000142
  80. 80.Spielmeyer W, Sharp PJ, Lagudah ES. Identification and validation of markers linked to broad-spectrum stem rust resistance geneSr2in wheat (Triticum aestivumL.). Crop Science. 2003;43:333-336
  81. 81.Njau PN, Jin Y, Huerta-Espino J, Keller B, Singh RP. Identification and evaluation of sources of resistance to stem rust race Ug99 in wheat. Plant Disease. 2010;94(4):413-419
  82. 82.Wamalwa M, Tadesse Z, Muthui L, Yao N, Zegeye H, Randhawa M, et al. Allelic diversity study of functional genes in East Africa bread wheat highlights opportunities for genetic improvement. Molecular Breeding. 2020;40(11):1-4
  83. 83.M’mboyi F, Njau P, Olembo N, Kinyua M, Malinga MJ. Application of Biotechnology to Wheat Improvement in Sub-Saharan Africa: The Case of Kenya. Nairobi, Kenya: African Biotechnology Stakeholders Forum (ABSF); 2010
  84. 84.Yang Q, Fang T, Li X, Ma C, Yang S, Kang Z, et al. Improving stripe rust resistance and agronomic performance in three elite wheat cultivars using a combination of phenotypic selection and marker detection ofYr48. Crop Protection. 2021;148:105752
  85. 85.Eagles HA, Barian HS, Ogbonnaya FC, Rebetzke GJ, Hollamby GJ, Henry RJ, et al. Implementation of markers in Australian wheat breeding. Austrialian Journal of Agricultural Research. 2001;52:1349-1356
  86. 86.Kaur P, Sachan S, Sharma A. Weed competitive ability in wheat: A peek through in its functional significance, present status and future prospects. Physiology and Molecular Biology of Plants. 2021;1:15
  87. 87.Malinga J, Kinyua M, Wanjama J, Kamau A, Karanja L, Awala J, et al. Evidence of a new Russian wheat aphid biotype in Kenya adduced from molecular markers. In: 12th Regional Wheat Workshop for Eastern, Central and Southern Africa, Nakuru, Kenya, 22-26 November, 2004. 2005
  88. 88.Ellis JG, Lagudah ES, Spielmeyer W, Dodds PN. The past, present and future of breeding rust resistant wheat. Frontiers of Plant Science. 2014;5:641
  89. 89.Chen XM. Epidemiology and control of stripe rust (Puccinia striiformisf sptritici). Canadian Journal of Plant Pathology. 2005;27:314-337
  90. 90.Chen XM, Kang ZS, editors. Stripe Rust (719 pages). Dordrecht: Springer; 2017
  91. 91.Boshoff WHP, Pretorius ZA, Van BD. Fungicide efficacy and the impact of stripe rust on spring and winter wheat in South Africa. South African Journal of Plant and Soil. 2003;20:11-17
  92. 92.Zobir SAM, Ali A, Adzmi F, Sulaiman MR, Ahmad K. A review on Nano pesticides for plant protection synthesized using the supramolecular chemistry of layered hydroxide hosts. Biology. 2021;10(11):1077
  93. 93.Iqbal M, Shahzad R, Bilal K, Qaisar R, Nisar A, Kanwal S, et al. (2021). DNA fingerprinting of crops and its applications in the field of plant breeding. Journal of Agricultural Research. 2021;59(1):13-28
  94. 94.Peleman JD, van der Voort JR. Breeding by design. Trends in Plant Science. 2003;8:330-334
  95. 95.Li HH, Ribaut JM, Li ZL, Wang JK. Inclusive composite interval mapping (ICIM) for digenic epistasis of quantitative traits in biparental populations. Applied Genetics. 2008;2008(116):243-260
  96. 96.Forster BP, Ellis RP, Thomas WTB, Newton AC, Tuberosa R, This D, et al. The development and application of molecular markers for abiotic stress tolerance in barley. Journal of Experimental Botany. 2000;51(342):19-27
  97. 97.Rana M, Kaldate R, Nabi SU, Wani SH, Khan H. Marker-assisted breeding for resistance against wheat rusts. In: Physiological, Molecular, and Genetic Perspectives of Wheat Improvement. Cham: Springer; 2021. pp. 229-262
  98. 98.Kumar S, Kumar M, Mir RR, Kumar R, Kumar S. Advances in molecular markers and their use in genetic improvement of wheat. In: Physiological, Molecular, and Genetic Perspectives of Wheat Improvement. Cham: Springer; 2021. pp. 139-174
  99. 99.Hussain B, Alaux M, Sehgal D, Appels R, Batley J, Bentley AR, et al. In: Edwards D, editor. Wheat Genomics and Breeding: Bridging the Gap. AgriRxiv. 2021
  100. 100.Okello OE (2019). Analysis of the population structure 2015Pucciniagraminisf. sptritici(Pgt) in Kenya using simple sequence repeats markers. MSC. Thesis, University of Eldoret, Kenya
  101. 101.Bangarwa SK, Balwan KLS, Choudhary M, Choudhary MK. An introduction to DNA-markers and their role in crop improvement. The Pharma Journal. 2021;10(7):638-643
  102. 102.Spooner D, van Treuren R, de Vicente MC. Molecular Markers for Gene Bank Management. IPGRI Technical Bulletin No. 10. Rome, Italy: International Plant Genetic Resources Institute; 2005
  103. 103.Pandurangan S, Workman C, Nilsen K, Kumar S. Introduction to marker-assisted selection in wheat breeding. In: Accelerated Breeding of Cereal Crops. New York, NY: Humana; 2022. pp. 77-117
  104. 104.Mondini L, Noorani A, Pagnotta MA. Assessing plant genetic diversity by molecular tools. Diversity. 2009;1:19-35
  105. 105.Kassa MT, You FM, Hiebert CW, Pozniak CJ, Fobert PR, Sharpe AG, et al. Highly predictive SNP markers for efficient selection of the wheat leaf rust resistance gene Lr16. BMC Plant Biology. 2017;17(1):1-9
  106. 106.Mourad AM, Sallam A, Belamkar V, Wegulo S, Bowden R, Jin Y, et al. Genome-wide association study for identification and validation of novel SNP markers for Sr6 stem rust resistance gene in bread wheat. Frontiers in Plant Science. 2018;9:380
  107. 107.Naruoka Y, Ando K, Bulli P, Muleta KT, Rynearson S, Pumphrey MO. Identification and validation of SNP markers linked to the stripe rust resistance geneYr5in wheat. Crop Science. 2016;56(6):3055-3065
  108. 108.Sobrino B, Brio’n M, and Carracedo A. SNPs in forensic genetics: A review on SNP typing methodologies. Forensic Science International. 2005;154:181-194
  109. 109.Wang L, Liao B, Gong L, Xiao S, Huang Z. Haploid genome analysis reveals a tandem cluster of four HSP20 genes involved in the high-temperature adaptation ofCoriolopsis trogii. Microbiology Spectrum. 2021;9(1):287-221
  110. 110.Kumpatla SP, Buyyarapu R, Abdurakhmonov IY, Mammadov JA. Genomics-assisted plant breeding in the 21st century: Technological advances and progress. In: Abdurakhmonov I, editor. Plant Breeding. Rijeka: InTech publishers; 2012. Available from: genomics-assisted-plant-breeding-in-the-21stcenturytechnological-advances-and-progress
  111. 111.Rasheed A, Wen W, Gao FM, Zhai S, Jin H, Liu JD. Development and validation of KASP assays for functional genes underpinning key economic traits in wheat. Theoretical and Applied Genetics. 2016;129:1843-1860
  112. 112.Hodson DP, Hansen JG, Lassen P, Alemayehu Y, Arista J, Sonder K. Tracking the wheat rust pathogen. In: Proceedings from BGRI Technical Meeting, Beijing, China. 2012. p. 20
  113. 113.Naeimi S, Koscsube S. Strain-specific SCAR markers for the detection ofTrichoderma harzianumAS12- 2, a biological control agent againstRhizoctonia solani, the causal agent of rice sheath blight. Acta Biology Hungary. 2011;62:73-84
  114. 114.Walter S, Ali S, Kemen E, Nazari K, Bahri BA, Enjalbert J, et al. Molecular markers for tracking the origin and worldwide distribution of invasive strains ofPuccinia striiformis. Ecology and Evolution. 2016;6:2790-2804
  115. 115.Liu Z, Sun Q, Ni Z, Yang T. Development of SCAR markers linked to thePm21gene conferring resistance to powdery mildew in common wheat. Plant Breeding. 1999;118:215-219

Written By

Ruth Wanyera and Mercy Wamalwa

Submitted: January 17th, 2022Reviewed: January 25th, 2022Published: April 3rd, 2022