International Workshop on Facilitating

International Research Collaboration on Transboundary Plant Pests

Draft report of discussion group on

Fusarium wilt of Banana (Fusarium oxysporum f.sp. cubense Tropical race 4)

1. Organization of basic data on the pest

Distribution of the pest: Fusarium oxysporum f.sp. cubense Tropical race 4 (TR4)

In Taiwan, symptoms of Fusarium wilt on Cavendish cultivars were first observed in 1967. In 1972, the results of

pathogenicity tests suggested that the isolates belonged to race 1, but isolates tested in 1977 were designated as

race 4. In 1989, a previously undescribed VCG, designated VCG 01213, was identified in samples from Taiwan.

The vulnerability of Cavendish cultivars to what would become known as TR4 was underscored in the early 1990s,

when Fusarium wilt decimated newly established plantations of Cavendish bananas in Indonesia and Malaysia. The

TR4 isolates introduced to Taiwan probably came from one of those places.

By the end of the 20th century, TR4 had been found in Taiwan, Malaysia, Indonesia (Java, Sumatra, Sulawesi,

Halmahera, Kalimantan on the island of Borneo, and Papua Province on the island of New Guinea), mainland China

(Guangdong, Hainan, Guangxi, Fujian and Yunnan), and Australia (Northern Territory). In 2008, it was reported to

be in the Philippines' island of Mindanao since at least 2005. Since then, the number of first reports has increased

exponentially, although they have not all been formally published.

Though not formally published, TR4 is in Oman. It seems to have been present since at least 2012.

In 2013, TR4 was reported to be in Jordan, the first official report of TR4 outside the Southeast Asia-Pacific region.

A 2014 survey revealed another infected area north of the original outbreak. At the end of 2013, TR4 was also

reported to be in Africa, where it was confirmed to be in an export banana plantation located in northern

Mozambique. The Matanuska farm in Nampula province filed for insolvency in 2018, after which it was bought by

Jacaranda Agricultura Lda and renamed Jacaranda Monapo. In 2014, TR4 was reported to be present in two other

Jacaranda farms (Lúrio, in Nampula, and Ocua, in Cabo Delgado province).

In 2015, TR4 was reported to be in Queensland, Australia, as well as in Lebanon and Pakistan. An analysis of

isolates from Pakistan and the Phillipines showed that they were closely related. The incursion in Lebanon has also

been shown to be associated with the one in Jordan. In 2017, TR4 was reported in Laos and Vietnam.

In 2018, TR4 was confirmed to be in Myanmar. The analysis of isolates from Laos, Vietnam and Myanmar provided

evidence that the particular TR4 strain in these countries was likely introduced from China.

In 2018, Israel's National Plant Protection Organization (NPPO) officially announced that TR4 had been found in

two farms in Israel (the Carmel coastal plain and the eastern shores of Lake Galilee) in 2016. After taking measures

to contain the incursions, the NPPO declared that the fungal strain had been eradicated from Israel. The

declaration drew comments that TR4 had been contained rather than eradicated. In 2019, the pest status was

amended to "actionable, under eradication" following the discovery of TR4 at a number of sites close to the

eastern/southern Lake Galilee area.

In 2018, TR4 was officially reported to be in India, based on isolates collected in the state of Uttar Pradesh in 2017.

However, wilting symptoms on Cavendish cultivars had previously been observed, in 2015, by a banana grower

from Barari village in the state of Bihar. Isolates were collected and the presence of TR4 in the Katikar and Purnea

districts was confirmed in 2019. TR4 is said to have spread from Bihar to the states of Uttar Pradesh, Madhya

Pradesh and Gujarat.

In August 2019, the Instituto Colombiano Agropecuario (ICA) confirmed the presence of TR4 in an area of 175 ha in

Colombia's La Guajira department. Symptomatic plants had been spotted in June and the area quarantined on 11

June. It is the first report of TR4 in Latin America.A suspected case of TR4 in a plantation operated by a Chinese

company was reported in June 2019 in the Chiang Rai province of Thailand.TR4 is also present at the Eden

Project's indoor rainforest biome in Cornwall, England.

Asia and Australia: Australia (Northern Territories & Queensland), China (Guandong, Hainan, Guagxi, Fujian,Yunnan),India (Bihar, Uttar Pradesh, Madhya Pradesh, Gujarat), Indonesia (Java, Sumatra, Sulawesi, Halmahera, Kalimantan, New Guinea), Taiwan, Laos, Malaysia, Myanmar, The Philippines (Island of Mindanao), Vietnam, Pakistan

Middle-East: Israël, Jordan, Lebanon, Oman Africa: Mozambique Latin America: Colombia

Panama disease caused by F. oxysporum was found In 2016, in Miyakojima, Okinawa prefecture, Japan (Nitani et

al. 2018).

Epidemiological data Panama disease of banana, also called Fusarium wilt, is caused by 3 races of Fusarium oxysporum f.sp.

cubense (Foc): race 1, race 2, race 4. The Tropical Race 4 (TR4) is most dangerous to the global banana

production since it affects the widely grown Cavendish group.

o Host Range:

Banana of the groups Cavendish (AAA), Gros Michel (AAA), Pisang Awak (ABB), Silk and Pome (AAB),

Bluggoe (ABB) and cooking ABB; the status of Plantains (AAB) is uncertain. In addition to Cavendish

cultivars, TR4 affects cultivars susceptible to races 1 and 2 as well as hitherto unaffected cultivars such

as, 'Barangan' (Lakatan subgroup, AAA genome group) and 'Pisang Mas'. The often cited figure that TR4

affects cultivars that account for more than 80% of the world's banana production assumed that

Plantains were also susceptible. At the time, however, the only Plantain-like material that had been

evaluated against TR4 were hybrids produced by breeders. The reaction of the Plantains domesticated in

Africa, along with another group of locally domesticated bananas, the East African highland bananas

(EAHB), was not known. The first field screening of these two subgroups was conducted in 2011-2012 in

the Philippines using accessions from the ITC genebank. Most of the accessions tested were slightly to

moderately susceptible. Except for the 'Obubit Ntanga' Plantain accession that was still symptom-free

after 10 months (a relatively short time given the perennial nature of most banana production), the

disease incidence was below 5%, with the exception of 'Ibwi', for which the disease incidence was 29%.

However, the ploidy of the ITC accession called Ibwi (2x/3x) suggests that the material tested might not

be the EAHB cultivar 'Ibwi'.

The FHIA improvement programme has produced hybrids that are resistant to races 1 and 4, while the

Taiwan Banana Research Institute (TBRI) has released Giant Cavendish tissue-culture variants (GCTCV)

that are partially resistant to TR4. In field trials conducted in China, FHIA-01, FHIA-02, FHIA-18, FHIA-25,

Pisang Jari Buaya, Rose (AA), and to a lesser extent GCTCV-119 and FHIA-03, have shown resistance to

TR4. In a field trial conducted in the Philippines, only 1% of the GCTCV-219 plants exhibited symptoms of

Fusarium wilt in the second crop cycle, whereas none of plants of the Cardava cultivar (Saba subgroup)

did.TR4 was also found on some weeds in Australia: Poaceae (Chloris inflata), Euphorbiaceae (Euphorbia

heterophylla), Asteraceae (Cyanthillium cinereum, Tridax procumbens) (Dita et al 2018).Infectivity of TR4

to other crop species is not documented.

o Dispersal means.

The fungus is commonly spread through infected planting material, infested soil and water.Dispersion

is mediated mainly by contaminated plant material, along with soil particles sticking on truck and tractor

wheels, workers tools and shoes. Dissemination can also occur through water (watercourses and rivers),

but to our knowledge no data are available on dispersal distances mediated by these means.

Planting material:

Symptomless but infected suckers or rhizomes can transmit the disease when planted in a new area.

Infected planting material is often responsible for the local, national and international spread of the

disease. Certified tissue-culture plantlets should be free of the fungus and would not contribute to the

spread of the disease.

Soil:

Staff and visitors to a banana plantation have the potential of moving the fungus in or out through

infested soil attached to vehicles, tools and shoes. Untreated soil used as a potting medium can transmit

the fungus and animals can also move around fungal spores present in soil.

Water:

Spores can be carried in surface run-off water. They can also contaminate irrigation reservoirs. It is said

that in China pumping water from sources contaminated with TR4 spores contributed to the spread of

the Fusarium wilt in plantations of Cavendish bananas.

2. Integration and implementation of pest management technologies

Diagnostic technologies

o Current effective technologies: Most techniques are molecular techniques targeting DNA regions. One reference diagnostic method is the determination of Vegetative Compatibility Groups (VCG); since the TR4 lineage corresponds uniquely to the VCG 01213/16. This method is however labor-intensive and time-consuming.

The reference diagnostic method of ANSES (France) uses real-time PCR to detect and diagnose FocTR4 from infected tissues, using Aguayo 2017 primers. There are several TR4-specific PCR primers and reactions, e.g. Dita et al 2010 (target gene:IGS), Yang et al 2013 , Aguayo et 2017 (target gene: putative pathogenicity gene). There are also Loop-Mediated Isothermal (LAMP) methods. Li et al primers target a SCAR marker sequence; Ordonez primers target regions TR4-specific identified in DARTseq data. The test is based on a scientific paper published in Plos One (Aguayo et al. 2017). It targets a putative virulence gene. The test is a hydrolysis probe-based assay (real-time PCR) that can be used directly on banana tissues. It has been conceived to detect tropical strains of Fusarium oxysporum f. sp cubense race 4 (VCGs 01213/16 and 0121).

A recent publication by Magdama et al. (2019) suggests that molecular methods targeting the putative virulence gene of the French official test are currently the most robust and reliable in the detection of FOCTR4.

o Challenges related to the above technologies One main challenge is TR4-specificity. The Magdama study points out the limitations of several molecular detection methods, with some methods identifying non-pathogenic strains as TR4 (false-positive). Sensitivity is also an issue, in particular to detect any latent infections in banana plants. Moreover, these methods require a laboratory equipment of good level, and also implies to extract DNA from suspected material. Need of rapid FOC TR4 detection kits like LAMP and/or RPA PCR for detection in the field to speed up the alertprocess.This must be coupled with trainings in these detection methods for people working in the field (banana growers, agents of the Agricultural institutions, etc.). This will allow taking efficient measures to avoid further spread of the disease during the confirmation analysis by the NRL. Most developing countries do not have the access to molecular technologies and lack to the trained/qualified personal capacities in collecting and analyzing samples. Markers might not function perfectly in all conditions and at all times.Thus it is recommended to carry out cross checking approach for accurate diagnosis.

o Future directions for research collaboration related to the above technologies

- Development of high -resolution diagnostic tools, highly sensitive and specific.The study of genomic diversity of TR4 strains spreading out of Asia will help to identify conserved regions and further gain in specificity.

- Evaluation of the diagnostic tools in field conditions and on several host. Need of developing robust and reliable detection methods to detect early stages of infection (asymptomatic banana for example.

- Validation and optimization of reliable and robust field detection kits as LAMP or RPA PCR, including optimization of rapid DNA extraction methods.

- For epidemiological studies, molecular tools should be also able to detect and quantify the pathogen in soil and water.

- More building capacities activities are needed at regional and national level for diagnosis; more simple diagnosis protocols also will be much appreciated. Refinements of the protocols would be valuable also through collective efforts.

Monitoring technologies

o Current effective technologies Technologies are currently under development, using the diagnostic methods detailed above. But they are not validated in field conditions.For example, research is currently in Stellenbosch University (South Africa) to develop a molecular quantitative method able to distinguish viable fungal spores from dead spores in the environment (water, soil).Monitoring banana fields by drones or remote sensing methods to localize yellowing banana trees.

o Challenges related to the above technologies The challenge is linked to lack of validated in-field monitoring methods.Need of disposing reliable and robust detection and diagnostic tool for infected banana trees

o Future directions for research collaboration related to the above technologies Phenotyping and detection of diseased plants by unmanned aerial vehicle (UAV) and artificial intelligence (DeChant et al. 2017. Validation of statistic model for sampling with the current information on the introduction and spread of the pest. Facilitation of surveys in countries where capacities and expertise are lacking, international collaboration and information sharing. There is a need to develop a monitoring system for TR4 counting on collecting geo referenced data at the field level with a tracking system for the collected samples and the results of analyzing these samples.

Border measures to avert introduction

o Current effective technologies At country level, phytosanitary measures and regulations have to be assessed/ develped / updated and implemented effectively. It must be ensured that imported invitro banana plant material must be subject to specific rules/ protocol to ensure guarantees of the absence of quarantine pathogens such as FOC TR4 (indexation of the mother-plant with molecular diagnostic tests to certify the absence of Foc TR4).Because FOC TR4 is a telluric pathogen, it must be necessary to grow mother plants under strict conditions (proof greenhouses or fields free from the pest) with substrate or soils, water for irrigation, certified free of telluric pathogens (especially FOC TR4).

Quarantine. -Tools to detect banana plants, and plants associated with passengers pathways (plane, train, boats), example: sniffer dogs educated to detect plant material (Costa Rica), Inspection of containers by customs officers . -Disinfection of the containers if they have to go to plantation (disinfection measures with dodecyl, dimethyl ammonium chloride at 12% or benzylkonium chloride at 25%)Avoid entrance and exit of trucks into plantations infested with TR4. - At the airport: there should be warning signboards, posters or screen messages warning not to carry plant materials, carpet with quaternary ammonium (Costa-Rica)

o Challenges related to the above technologies - Monitoring is lack of adequate surveillance due to shortage of capacity and reluctance to

disclose the survey information in some cases. - Custom teams should have tools (molecular or others) to check easily large and numerous

pathways in terminals (ports and airports). - Countries should adopt a national monitoring system counting on registering banana farms

and mapping the banana cultivation with a certified protocol for collecting and analyzing samples. On banana material.

- Authorized only the introduction of fruits and tissue culture material (with import permit). - Quarantine: keep the banana plant tissue culture 3 monthsand ensure they are free from foc

TR4 with molecular tests before give them to the producers. - Extend the quarantine for plants and substrateswhich come from infected area and practice

monitoring on this material.

o Future directions for research collaboration related to the above technologies - Facilitation of surveys in countries where capacities and expertise are lacking, - International collaboration and information sharing. - There is a need to develop a monitoring system for TR4 counting on collecting geo referenced

data at the field level with a tracking system for the collected samples and the results of analyzing these samples.

- A lot of work should be done on detection and quantitative assessment in the environment (water, soil, weeds, growing compost and substrate,...etc.) to anticipate TR4 introduction and prevent the onset of an epidemics.

- Develop a traceability system to facilitate the track of the imported materials (planting materials, planting substrates, second hand machinery….etc.) and help in contain any new infestations

Measures for prevention and control

o Current effective technologies Since the fungus lives and infects the plants through the root control with chemicals is almost impossible. Fungicide applications in large areas is not practical and they get decomposed when in contact with soil. Control and management of irrigation water is critical to avoid spread. The best approach to avoid damage is to contain the plots where it is detected first and apply quarantine. For the long term, development and use of resistant varieties is the ideal strategy but these would have to be acceptable to the consumers. For the court term, using clean planting materials/reinforcing drastic biosecurity measures at the field level/control the visitor mobility and the movement of tools, soils, water from or into the banana farms are considered crucial. Resistant varieties: There are some somaclonal variants GCTCV, developed in Taiwan, which helped mitigating losses in Taiwan and the Philippines (GCTCV-218 (Formosana) and GCTCV-219), and were recently planted in Mozambique (Dita et al 2018).Some CIRAD hybrids have been rated as resistant to highly resistant to TR4 in greenhouse tests, these can be further evaluated for adaptability to different environments and acceptability by the consumers. GM-resistant bananas were developed by the University of Queensland (Australia) and gave promising results in TR4-infested fields of Northern Territories, Australia. RGA2-3 and Ced9-21 were found immune after 3 years of field screening, thesealso need to be further evaualted for adaptability to different environements and acceptability by the consumers. All these somaclonal variants would have to be further evaluated and checked for adaptability and acceptability by the consumers. In host resistance, the main challenge is to combine resistance level with agronomically acceptable traits. Since most of the varieties promoted nowadays are actually partially resistant, there is a risk they could latently multiply the inoculum, and favor dispersal of the fungus from TR4-infected to disease-free areas. Therefore, epidemiological studies have to be done to follow the level of the inoculum in resistant varieties plantation. Moreover, banana resistance level as measured in greenhouse screening tests is not always correlated with field resistance. Thus resistant candidate need anyway to be evaluated in the field. The other challenge is related to the acceptability of GM-resistant bananas in the TR4-affected countries. Soil management practices:crop plantation and interpolating of banana Cavendish with Manihot esculenta, in Indonesia, led to reduction of disease incidence to less than 5%, maintianed over three cropping cycles (Buddenhagen 2009).

Crop rotation of Banana Cavendish with Allium tuberosum in China, induced a 97% reduction in disease incidence, due to antifungal volatiles released by A. tuberosum (Huang et al 2012, Zhang et al 2013). Same result with rotation with Ananas squamosa in China (Wang et al 2015). Diversity is also key to prevention: diversification of crops on plantations through intercropping and other agroecological practices to support sustainability in the long term. There are some agronomic approaches are claimed to improve soil health but these have to be verified under diverse conditions. Biological control was investigated for many years but with no success in the field. The use of non-pathogenic Fusarium strains as biocontrol agents, was found completely inefficient to control TR4 in the field (A. VILJOEN, pers.comm.2019), like for Subtropical race 4 (SR4) (Belgrove et al 2011). Organic amendments (cattle or pig manure compost, bio-organic fertilizer) have given variable disease reduction rates, notably in China (Shen et al 2013). But the efficiency of such amendments is greatly variable across years, and across farms and countries. The portability of cultural control methods from its region of development to a larger area is often a challenge, since the efficiency of such methods is highly dependent of the environmental conditions.

o Challenges related to the above technologies Prevention is the main strategy to combat Fusarium oxysporum f. sp cubense tropical race 4 (Foc TR4), also known as Tropical race 4 (TR4), due to the following challenges and issues:

o Presently, there is no way of getting rid of the fungus, once it’s in the soil; o Fungicides and soil fumigants are not efficient in controlling or eradicating the disease

from infested soil; o The spores of the fungus persist in the soil for decades; o Since the greatest risk of introducing pests is caused by human mobility, it is necessary

to apply greater controls to passengers coming from countries that report the presence of TR4, according to existing hazard profiles;

o The most effective approach to combat TR4 is prevention of its spread into non-infected areas and immediate containment when it is detected;

o If a plantation becomes infested, the only way to contain the pathogen is to destroy all of the plants according to specific phytosanitary standards, and take the farm out of production for many years—while trying to prevent the spores from escaping in run-off.

o TR4 support is needed for disease management and recovery in affected countries, and for this, both international collaboration and local actions are essential.

o Future directions for research collaboration related to the above technologies

- International collaboration should be promoted for collective breeding programmes and multi-location testing of genetic materials as well as agronomic measures.

- There have been several initiatives for identifying biocontrol agents (e.g. in course in Stellenbosch University, IITA-Tanzania and -Uganda), notably bacterial endophytes to mitigate TR4 infection and harmfulness.

- The characterization of the microbiome of TR4-suppressive soils may lead to the identification of candidate biocontrol agents.

- Test of suppressive cover crops should be done in TR4-infected fields with very strict quarantine practices, e.g. Colombia, Mozambique, Laos. CIRAD agroecological research

teams have now a high expertise on the positive effect of cover crops on banana field growth.

- There is currently no mapping of FOC-resistance genes or QTLs in banana, which makes breeding for FOC-resistance a challenging task.

- Molecular test to quantify the inoculum in area where there are resistantvarieties Evaluation of the effect of spatial arrangement of different varieties onthe soil inoculum.

- Gene editing tool is expected to introduce resistance against TR4 to banana. (https://www.nature.com/articles/d41586-019-02770-7)

3. Others

Proposed actions for international research collaboration - Internationals reference lab network for the diagnostic of Foc TR4 (international references for

diagnosis tests). - To coordinate and improve public plant health epidemiological network on banana diseases and

especially on FOC TR4. - Publication of an international bulletin could a good opportunity to create links. Regional Plant

Health Organizations all over the world may be in charge of this objective because of their missions and knowledge on plant health networks and data bases.0

- International collaboration should be promoted i) collective breeding programmes and multi-location testing of genetic materials, ii) efficiency of agronomic practices in improving soil health and suppressing the fungal population.

- An International network of screening platforms is needed to evaluate efficiency, stability, durability of banana resistance to TR4.

Other issues - There is a general tendency in search for a single simple solution such as developing / finding a

resistant variety. The problem is a systematic problem and a holistic approach should be taken focusing on prevention, finding a resistant variety and also thinking of long term management strategy. However, banana is also local staple food for some area. We should also consider disease management method for minor banana cultivars susceptible to Foc.

- The commercial banana production in Japan is only 150 tons/year, and the yield is going down year-to-year. On the other hand, Japan imports bananas exceed 1.5 million tons/year mainly from Philippine. Therefore, we think we have to contribute to solve Foc occurred worldwide in international research collaboration.

- National TR4 prevention strategies, programmes and action plans must be developed and implements and in this context i)Capacities of regional and national plant protection organizations must be strengthened; ii)Pest risk analysis must be conducted; seed certification and production systems must be strengthened iv)Institutional coordination mechanisms must be established and v)Appropriate policies must be developed and implemented, vi) Awareness has to be increased at all levels using the most effective communication means and tools

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