Status of the resistance of selected rice (Oryzasativa) varieties to bacterial blight strains in Senegal

doi:10.21203/rs.3.rs-3454462/v1

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Status of the resistance of selected rice (Oryzasativa) varieties to bacterial blight strains in Senegal

https://doi.org/10.21203/rs.3.rs-3454462/v1

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Rice plays an important role in achieving and maintaining food and nutritional security in the world. However, its productivity is affected by various constraints, including biotic and abiotic stresses, and several socio-economic constraints. Regarding biotic factors, bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is a major bacterial disease that causes severe yield losses of more than 70%, thereby threatening food and income security in most rice growing countries, including Senegal. Optimal control of this disease requires the use of host plant resistance, as it is economical and environmentally sustainable. Nevertheless, in the context of Senegal, the available sources of resistance are limited, and the potential for resistance among Senegalese rice varieties has been inadequately investigated. In this study we evaluated local rice germplasms for resistance to bacterial blight in Senegal. A trial was conducted in glasshouse conditions using a split-plot experimental design with 32 rice varieties as the main factor and five strains of Xanthomonas oryzae pv. oryzae (Xoo) as the secondary factor. Seven (07) of the popular rice varieties, including two (02) lowland (TOX 728-1 and BG 90 − 2), four (04) irrigated (ISRIZ 04, ISRIZ 05, ISRIZ 14 and SAHEL 202) and the variety GIGANTE exhibited full resistance against all strains tested. These varieties are suggested to be grown in Xoo-prone areas, and can be used for improving the resistance of other commercial varieties in other regions where Xoo is prevalent. A significant interaction between strains and varieties was detected, suggesting that pathogen race diversity may contribute to the determination of rice resistance to Xoo strains in Senegal. Among all bacterial strains, S82-4-1 of the race S4 exhibited the highest virulence. This strain can be used as reference for screening rice varieties in West-Africa.

Bacterial blight

Oryza sativa L.

resistance

Senegal

Xanthomonas oryzae pv. oryzae

Rice is one of the most widely consumed cereals in the world. It represents the main staple food of the Senegalese population with an average annual consumption of about 100 kg per resident (Mendez Del Villar & Dia, 2019). The rice cultivated area in Senegal is estimated to be more than 403,727 ha with a highly variable production of about 1,349,723 tons (FAOSTAT, 2020).

Among the problems facing rice production, biotic damage, especially bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is prominent. BB is a devastating rice disease worldwide, and particularly in Africa where high yield losses have been reported in several countries of the West African region (Naqvi, 2019ré & Nacro, 1992). In Senegal, BB occurs mainly in Saint-Louis and Kedougou regions with an estimated incidence of 50% (Tall et al., 2020). BB development is favored by climatic factors such as high temperatures, high humility, strong winds and excess of fertilizers, especially nitrogen (Sharma et al., 2017). The symptoms of the disease appear on leaves as pale green to grey green lesions; water-soaked streaks appear near the leaf tips and margins. These lesions coalesce and become yellow-white with wavy edges as the infection progresses. The whole leaf may be affected becoming white or grey and then turns necrotic. Infection at the seedling stage leads to practically total crop loss while infection at the tillering stage may cause more than 70% loss of grain yield in favorable conditions (Dash et al., 2016; Khan et al., 2021). Bacterial blight can also induce a physiological disruption of the plants, which can either result in the death of the plants or the production of unfilled grains at maturity (Noer et al., 2018).

Several methods (cultural, chemical, botanical, biological) are recommended for controlling BB, but the development of resistant varieties is recognized as the most effective and less costly option to producers and has less negative environmental impact (Kim et al., 2015; Suh et al., 2009). Several studies have been conducted in Asia on BB resistance, leading to the identification of about 44 resistance genes and more than 20 QTLs related with Xoo resistance (Kumar et al., 2020). Contrarily, studies conducted on the African Xoo revealed that most of the genes conferring resistance against Asian strains are not effective against African strains (Djedatin et al., 2016). It has also been pointed out that West African strains are different from the Asian and American strains in their genetic profiles, including the distribution of virulence factors like transcription activator-like effectors (TALE), with African Xoo having fewer and less diverse TALe than Asian strains (Poulin et al., 2015). As a result of this, the question of whether African strains possess the ability to effectively differentiate between resistant and susceptible varieties holds considerable implications in the development of resistant varieties.

There have been reports of promising sources of resistance in African germplasm, including the New Rice for Africa (NERICA) varieties, which are derived from a cross between Oryza sativa and O. glaberrima (CG14). This resistance is race specific (i.e NERICA lines, and other accessions derived from O. glaberrima are highly susceptible to Xoo Race A1, despite being resistant to Race A3) (Djedatin et al., 2011). In Senegal, few studies have been conducted with regards to this, and the identification of new sources of resistance to bacterial blight. Prior research successfully identified cultivars that are partially or highly resistant to Xoo in irrigated rice ecosystems (Tall et al., 2022). However, the disease has recently emerged as a significant threat in rainfed ecologies (Islam et al., 2016; Kumar et al., 2020), and currently there is lack of varieties that combine high resistance and good agronomic performance in rainfed conditions. This scarcity of resistant to BB and agronomically desirable rice genotypes in rainfed ecologies calls for evaluation of local accessions as a stopgap measure. This study was therefore conducted to compare the response of irrigated and rainfed varieties to BB strains, especially those from Senegal, classify variety-strain interaction patterns and to uncover additional sources of resistance that can be deployed in Xoo hotspots or in breeding for resistance against African Xoo strains.

Study site

The experiments were conducted in 2021/2022, in greenhouse conditions, at the ‘’Centre d'Etude Régional pour l'Amélioration de l'Adaptation à la Sécheresse’’ (CERAAS) in Thiès, Senegal. Thiès is located at 14° 50'03'' North latitude and 17° 06'21'' West longitude.

Plant material

The plant materials used in this study were sourced from AfricaRice and the ‘’Institut Sénégalais de Recherches Agricoles’’ (ISRA). The dataset consists of a total of twenty-nine (29) varieties that are representative of the rice varieties grown in Senegal. Additionally, two (2) Xoo susceptible control varieties, namely IR 24 and NIPPONBARE, and a Malian Xoo resistant control variety, GIGANTE (Tekete et al., 2020), were included in this study (Table 1).

Table 1

List of the varieties used
S/N	Ecology	Name of varieties	Parents
1	Lowland	TOX 728-1	MAHSURI / IET 1444
2	Lowland	BG 90 − 2	(PETA 3 * TN 1) / REMADJA
3	Lowland	ITA 123 (FKR 28)	Mutant OF OS 6
4	Lowland	DJ 11–509	H4xSe 288 D
5	Upland	ITA 150	63–83 * Dourado
6	Upland	WAB 56 − 50	IDSA 6 * IAC 164
7	Upland	NERICA 1	WAB 56–104/CG 14
8	Upland	NERICA 5	WAB 56–104/CG 14
9	Upland	NERICA 6	WAB 56–104/CG 14
10	Irrigated	IR 1529-68O-3	Segadis 2/TNI * IR 24
11	Irrigated	IR 8 (-288 3)	Peta * Dec-Geo-Wo-Gen
12	Irrigated	JAYA	Taichung Native 1 * 141
13	Irrigated	NERICA-S-21	Tog 5681/2*IR 64/IR 31785
14	Irrigated	ISRIZ 01	ISRIZ-J1-127
15	Irrigated	ISRIZ 02	ISRIZ-J4-145
16	Irrigated	ISRIZ 03	ISRIZ-J3-128
17	Irrigated	ISRIZ 04	Namcheon (Myrlang 103) / Namyeong (Myrlang82)
18	Irrigated	ISRIZ 05	Suweom450 / SR21356-1-13
19	Irrigated	ISRIZ 06	IR 1317-316-5-1/IR 24
20	Irrigated	ISRIZ 07	IR 24*2/IR 747-B2-6-3
21	Irrigated	ISRIZ 08	BAS 320/IR 661
22	Irrigated	ISRIZ 09 H	Hybrid from Sahel
23	Irrigated	ISRIZ 10	IR 4630-22-2/IR 31785-58-1-2-3-3
24	Irrigated	ISRIZ 11	IR 20/IR 24//IR 65195-3B-13-2-3 (PSB RC 86)
25	Irrigated	ISRIZ 12	08 FAN 10
26	Irrigated	ISRIZ 14	FAROX 521-288-H1
27	Irrigated	ISRIZ 15	CT8837-1-17-9-21// Oryza-1/Oryzica Lianos-4
28	Irrigated	SAHEL 202	TOX 494–3696 / TOX711 / BG6812
29	Irrigated	SAHEL 201	IR 2071 − 586/BG 400-1
30		NIPPONBARE	Susceptible control variety
31		IR 24	Susceptible control variety
32		GIGANTE	Resistant control variety

Bacterial strains

The strains used in this study consisted of five strains of Xoo that were representative of the races documented in Senegal (Table 2). These strains were isolated from rice leaf samples collected from two regions of Senegal under lowland and irrigated environment from 2013 to 2015 and preserved at the ‘’Institut de Recherche pour le Développement’’ (IRD) in Montpellier (Tall et al., 2020). The bacteria strains were cultured on PSA medium (per liter: 10 g Peptone, 10 g Sucrose, 15 g Agar, 1 g glutamic Acid, pH 7.0) at 28°C. The strains were revived by culturing on PSA medium 24 h before inoculation.

Inoculation of bacterial strains to rice plants

A suspension of 10⁸ CFU mL^− 1 bacterial cells from a one-day old culture was prepared for each strain and inoculated to 45 days old rice plants using the leaf clipping method. The inoculation process involved cutting the leaf at 4–5 cm centimeters from the tip using sterilized scissors and dipping the cut edge of the leaf into the bacterial suspension (Kauffman, 1975). The last two youngest leaves of two plants in each pot were inoculated, totaling four leaves per pot. Each strain was inoculated on each variety seeded in three pots. Sterile distilled water was used as a negative control. The inoculated plants were placed in the greenhouse at 27 ± 1°C, 80% relative humidity with 12 hours of alternating light and darkness.

Table 2

List of *Xanthomonas oryzae* pv. *oryzae* strains
S/N	Name of strains	Origin (Locality)	Region	Country	Race
1	S69-1-1	Ndioum	Saint-louis	Senegal	A1
2	S62-2-5	Ndiaye	Saint-louis	Senegal	S2
3	S82-4-1	Bandafassi	Kédougou	Senegal	S4
4	S62-2-22	Ndiaye	Saint-louis	Senegal	S5
5	S62-2-26	Ndiaye	Saint-louis	Senegal	S6

Experimental design and management of experiment

The experiment was conducted in a split-plot design replicated 3 times with varieties as the main factor and strains as the secondary factor. Pots of 10L were filled to a depth of 20 cm with natural potting soil. The pots were then placed in the greenhouse with controlled temperature and moisture and each pot was planted with four seeds of a given variety at a depth of 3 cm. The pots were then watered and their moisture levels was kept-up until the seedlings emerged. After the 14th day, the plant number per pot was thined to two. The pots were irrigated every morning to maintain the water level in the pots at 5 cm. Fertilization using 3g of DAP (Di-Ammonic Phosphate: 18-46-0) was added on each pot at 15th, 25th and 35th day after sowing (Tekete et al., 2020). Whenever necessary, weeds were manually removed.

Data collection

The length of the lesions were measured on the 15th day after inoculation with a graduated ruler. Lesion length on inoculated leaves of different varieties evaluated was classified according to the method of Kauffman et al. (1973). The varieties with the lesion size of less than 5 cm were considered resistant whereas those with a lesion length longer than 5 cm were categorized as susceptible (Quibod et al., 2016). The most virulent strain was determined to be the one that elicited the most extensive leaf lesions.

Statistical analysis

Data analysis was performed with R statistical software version 4.1.2. Lesion lengths for each combination variety/strain and the measured parameters were subjected to analysis of variance (ANOVA) with the package ''Agricolae''. To test the ANOVA model hypothesis, Shapiro-Wilk normality tests (Shapiro & Wilk, 1965) and homogeneity Bartlet of variance test (Bartlett, 1937) were performed on the residuals of the model. Tukey test was used for multiple comparisons between varieties. The confidence interval considered was 95%. The data on lesion length was used to perform the Hierarchical Ascending Classification (HAC) by grouping the varieties according to their response to the set of strains. The linear model used for the analysis of variance is as follows:

X_ijk = µ + α_i + β_j + γ_k + α_i β_j + e_ik + e_ijk

X_ijk = Response observed on the variety j in contact with the strain i in block k; µ = general average effect; α_i = effect of the strain i; β_j = effect of the variety j; γ_k = effect of block k; α_i β_j = effect of the first order interaction between Strain and variety factors; e_ik = residual effect between sub-blocks; e_ijk = residual effect between plots.

The different figures were created using R software and the bioinformatics tool ''Shiny'' (https://bioinfo-shiny.ird.fr/AnalyseSymptoms/) developed by IRD.

Response of the varieties to inoculation with bacterial blight strains from Senegal

Two lowland rainfed rice varieties, TOX 728-1 and BG 90 − 2, as well as four irrigated rice varieties, ISRIZ 04, ISRIZ 05, ISRIZ 14 and SAHEL 202, exhibited mild blight symptoms, which affected less than 1 cm of leaf surface (Table 3). A total of 11 varieties, of which two lowland varieties (ITA 123 (FKR 28), DJ 11–509), one upland variety (NERICA 6) and eight irrigated varieties (IR 8 (-288 3), JAYA, NERICA-S-21, ISRIZ 08, ISRIZ 09H, ISRIZ 10, ISRIZ 15, SAHEL 201) exhibited lesion lengths exceeding 5 cm for all the five bacterial strains. Interestingly, a particular variety may exhibit resistance to one bacterial strain while simultaneously displaying sensitivity to another strain (Table 3). This is for example the case of the two upland varieties NERICA 1, NERICA 5, as well as the irrigated variety ISRIZ 11 that showed lesion length exceeding 5 cm when inoculated with strains S69-1-1 and S82-4-1. In contrast, when the same varieties were inoculated with bacterial strains S62-2-5, S62-2-22, and S62-2-26, the blight symptoms remained below 5 cm. The varieties SAHEL 201, ISRIZ 10, JAYA, NERICA 6, and DJ11-509 exhibited significantly larger lesions compared to the susceptible control varieties used.

Table 3

Lesion length of 32 varieties inoculated with five bacterial strains
Varieties	Strains
Varieties	S62-2-22	S62-2-26	S62-2-5	S69-1-1	S82-4-1
BG 90 − 2	0.07 ± 0.06	0.20 ± 0.03	0.14 ± 0.04	0.17 ± 0.01	0.14 ± 0.03
DJ 11–509	19.42 ± 0.98	22.28 ± 0.08	25.13 ± 2.97	28.43 ± 1.44	35.41 ± 0.46
GIGANTE	0.00 ± 0.00	0.01 ± 0.01	0.00 ± 0.00	0.08 ± 0.05	0.00 ± 0.00
IR 1529-68O-3	2.10 ± 0.29	2.53 ± 0.13	2.03 ± 0.92	4.55 ± 0.92	8.12 ± 0.49
IR 24	10.17 ± 1.00	10.87 ± 0.25	10.27 ± 0.15	19.77 ± 2.50	15.97 ± 0.23
IR 8 (-288 3)	13.33 ± 0.46	12.83 ± 0.3	9.90 ± 0.63	22.64 ± 0.78	19.84 ± 1.10
ISRIZ 01	12.13 ± 0.78	3.73 ± 0.08	7.71 ± 0.76	4.25 ± 0.50	5.58 ± 0.07
ISRIZ 02	5.06 ± 0.54	3.10 ± 0.38	6.65 ± 0.54	26.53 ± 2.75	25.53 ± 1.13
ISRIZ 03	6.36 ± 0.36	6.73 ± 0.11	3.95 ± 0.98	10.18 ± 2.22	12.61 ± 0.22
ISRIZ 04	0.13 ± 0.01	0.11 ± 0.04	0.12 ± 0.06	0.12 ± 0.04	0.10 ± 0.03
ISRIZ 05	0.08 ± 0.08	0.13 ± 0.03	0.11 ± 0.04	0.16 ± 0.01	0.08 ± 0.00
ISRIZ 06	7.63 ± 0.32	10.24 ± 0.14	3.33 ± 0.74	4.09 ± 1.39	7.29 ± 0.22
ISRIZ 07	10.98 ± 0.29	8.58 ± 0.15	3.81 ± 0.41	12.60 ± 0.85	10.63 ± 0.23
ISRIZ 08	8.46 ± 1.22	10.68 ± 1.21	9.17 ± 1.45	13.01 ± 2.74	15.87 ± 0.65
ISRIZ 09 H	9.94 ± 1.79	14.72 ± 0.19	5.28 ± 0.62	20.07 ± 3.20	8.48 ± 0.19
ISRIZ 10	10.47 ± 0.36	7.65 ± 0.20	7.19 ± 0.81	20.28 ± 1.61	21.78 ± 0.30
ISRIZ 11	2.59 ± 0.55	3.22 ± 0.21	0.19 ± 0.08	9.38 ± 1.40	7.63 ± 0.57
ISRIZ 12	2.30 ± 0.29	2.66 ± 0.22	0.50 ± 0.35	2.48 ± 0.75	5.06 ± 0.36
ISRIZ 14	0.26 ± 0.01	0.08 ± 0.04	0.13 ± 0.04	0.15 ± 0.03	0.05 ± 0.03
ISRIZ 15	7.08 ± 0.79	10.66 ± 0.10	5.07 ± 0.42	18.80 ± 2.86	15.84 ± 0.97
ITA 123 (FKR 28)	11.04 ± 1.37	6.16 ± 0.05	12.72 ± 2.04	20.81 ± 2.79	17.18 ± 0.13
ITA 150	2.83 ± 0.44	4.09 ± 0.06	21.00 ± 3.54	5.88 ± 0.33	31.58 ± 1.21
JAYA	15.28 ± 0.95	20.94 ± 0.82	14.41 ± 1.99	25.71 ± 1.00	27.73 ± 0.31
NERICA-S-21	8.53 ± 0.78	11.03 ± 0.21	11.58 ± 1.30	12.45 ± 0.73	17.79 ± 0.18
NERICA 1	4.19 ± 0.48	2.59 ± 0.19	4.11 ± 0.77	10.68 ± 1.37	13.60 ± 0.29
NERICA 5	2.67 ± 0.40	3.14 ± 0.19	4.28 ± 0.48	14.66 ± 0.79	12.15 ± 0.62
NERICA 6	11.50 ± 1.05	12.93 ± 0.13	14.33 ± 2.82	25.78 ± 1.52	19.28 ± 0.27
NIPPONBARE	15.50 ± 0.35	12.37 ± 2.64	10.17 ± 0.81	17.17 ± 1.17	17.63 ± 0.31
SAHEL 201	11.88 ± 0.50	17.90 ± 0.16	15.75 ± 1.00	26.07 ± 3.36	26.80 ± 0.26
SAHEL 202	0.03 ± 0.03	0.10 ± 0.03	0.00 ± 0.00	0.14 ± 0.03	0.07 ± 0.03
TOX 728-1	0.08 ± 0.07	0.07 ± 0.03	0.05 ± 0.03	0.13 ± 0.04	0.11 ± 0.03
WAB 56 − 50	3.99 ± 1.13	2.33 ± 0.11	3.33 ± 0.78	7.67 ± 0.23	3.29 ± 0.37

Xoo virulence and strains classification

All the five bacterial strains used in this study induced typical bacterial blight lesions one week after inoculation on the susceptible control varieties. The length of the lesions ranged from 10.17 cm with the strain S62-2-5 to 17.63 cm with the strain S82-4-1 for NIPPONBARE and from 10.17 cm with the strain S62-2-22 to 19.77 cm with the strain S69-1-1 for IR 24. The strain, S82-4-1, belonging to race S4 exhibited the highest level of virulent on NIPPONBARE while the strain S69-1-1 belong to race A1 displayed the highest level of virulence on IR 24. The analysis of variance showed a highly significant interaction between variety and strain (p < 0.001) (Table 4). As a result, we performed an analysis of variance for each strain, which revealed a highly significant varietal effect (p < 0.001) (Table 5). Lesions length on the different rice varieties ranged from 0 to 35.41 cm, 15 days after inoculation (Fig. 1). Bacterial strain S82-4-1 belonging to race S4, exhibited the highest lesion size on most varieties followed by the strain S69-1-1 of race A1. Based on varietal response to Xoo inoculation above, an ascending hierarchical classification was performed on Xoo strains. The results showed three groups (Fig. 2). Group I consisted of the two most virulent strains S69-1-1 and S82-4-1. The strain S62-2-5 belongs to Group II, and strains S62-2-22 and S62-2-26 belong to Group III. The strains of all the three groups were virulent on all class 6 varieties, but not to the class 1 varieties. Group I bacterial strains were virulent on NERICA 1, NERICA 5 and ISRIZ 11. Strain S82-4-1, classified under group I exhibited virulence to the varieties IR 1529-680-3 and ISRIZ 12. Group I as well as group III strains, were virulent to the varieties ISRIZ 03 and ISRIZ 07. Group I and II bacterial strains were virulent on ITA 150.

Table 4

Analysis of variance of variety, strain and their interaction
Source of variation	DF	P
Strain (S)	4	3.077e-12 ***
Variety (V)	31	‹ 2.2e-16 ***
S : V	124	‹ 2.2e-16 ***
*** Significant at the .001 probability level

Table 5

Analysis of variance for each strain
Strain	S62-2-22	S62-2-26	S62-2-5	S69-1-1	S82-4-1
Variety	‹ 2.2e-16 ***	‹ 2.2e-16 ***	‹ 2.2e-16 ***	‹ 2.2e-16 ***	‹ 2.2e-16 ***
*** Significant at the .001 probability level

Classification of rice varieties based on their reaction to bacterial strains

Based on the reaction of the different varieties to Xoo inoculation above, the 29 local varieties and the resistant control GIGANTE were categorized into 6 classes. Class 1 consists of varieties that are resistant to all strains. It includes TOX 728-1, SAHEL 202, ISRIZ 14, ISRIZ 05, ISRIZ 04, BG 90 − 2 and the resistant control GIGANTE (Fig. 3). In contrast, Class 6 is composed of varieties that are susceptible to all strains. It includes ISRIZ 10, ISRIZ 09H, DJ 11–509, IR 8 (-288 3), ISRIZ 08, ISRIZ 15, ITA 123, JAYA, NERICA 6, NERICA-S-21 and SAHEL 201. Varying degrees of resistance also exist within and between class 1 and 6. For instance, varieties ISRIZ 12, IR 1529 − 680 3 and WAB 56 − 50 belonging to class 2 exhibited a resistance level of 83.33% against all the strains. On the other hand, varieties ISRIZ 11, NERICA 1 and NERICA 5 from class 3 had a resistance level of 66.67%. A resistance level of 50% was observed in the varieties ISRIZ 01, ISRIZ 06 and ITA 150 within class 4, while the varieties ISRIZ 02, ISRIZ 03 and ISRIZ 07 belonging to class 5 had just 33.33% resistance to BB strains.

Bacterial blight is one of the most damaging bacterial diseases that affects rice production in several rice-producing countries globally. Senegal, a prominent rice-producing country in West Africa, has recently documented a significant prevalence of this disease over most of its rice cultivation regions (Tall et al., 2020). The unanticipated expansion of BB to rainfed ecologies is occurring in the absence of varieties that possess resistance in Senegalese rainfed environments.

The objective of this study was to evaluate the resistance levels of 32 rice varieties sourced from AfricaRice and ISRA in order to identify potential sources of resistance that may be either maintained as cultivars by farmers or used by breeders to improve BB resistance and alleviate the growing disease burden. Among these varieties, 29 are already cultivated in Senegal. Evaluation was conducted under controlled conditions using five strains of Xoo, which were selected to represent the races identified in Senegal.

Differences were observed in the response of varieties following inoculation with the five Xoo strains. The varieties TOX 728-1, BG 90 − 2, ISRIZ 04, ISRIZ 05, ISRIZ 14, SAHEL 202, and the resistant control, GIGANTE, showed complete resistance to all Xoo strains. In contrast, ISRIZ 10, ISRIZ 09H, DJ 11–509, IR 8 (-288 3), ISRIZ 08, ISRIZ 15, ITA 123, JAYA, NERICA 6, NERICA-S-21, and SAHEL 201, exhibited susceptibility to all strains of Xoo tested in this study. These varieties apparently lack resistance genes, or if they are there, they may not effectively combat Senegalese strains or may be peculiar to other races. Given that these cultivars are now under cultivation by farmers, it will be imperative to introduce resistance genes into them in order to improve productivity in Xoo prone areas. Disease pressure could also be controlled by the deployment of disease-resistant varieties identified in this study, such as BG 90 − 2 and TOX 728-1. BG 90 − 2 is a lowland and irrigated variety, and TOX 728-1 is grown on hydromorphic soil with characteristics intermediate between upland and lowland. TOX 728-1 was developed through a controlled breeding process using parental varieties, Mashuri and IET 1444, and exhibits appreciable adaptability to upland ecologies. The initial assessment of the testing lines that served as parents for IET 1444 breeding demonstrated resistance to BB in India (Ahuja, 1984). It is possible that these lines could be the primary origin of resistance in TOX 728-1. The rice variety BG 90 − 2 contains Xa21 gene, which has been proven to confer resistance against Xoo (Gnanamanickam et al., 1999; Vo et al., 2018). The presence of this specific gene in BG 90 − 2 is a potential basis for the resistance it exhibits against Xoo in Senegal. The ISRIZ series was developed via a selective breeding project that encompassed the hybridization of two distinct varieties of rice, specifically Namyeong and Namcheon. Namcheon has gained popularity for its resistance against Xoo in Korea (Fred et al., 2016). It is conceivable that ISRIZ 04, 05 and 14 may have inherited the resistance genes from Namcheon, hence explaining its resistance to Xoo strains tested in this study. SAHEL 202 (ITA 306) was developed through a hybridization process including TOX 494–3696 and TOX 711/BG 6812. Previous studies conducted by Tall et al. (2022) demonstrated the resistance of SAHEL 202 to Xoo in Senegal. The results of our study provide additional evidence supporting the resistance of SAHEL 202. Nevertheless, the underlying genetic mechanisms for resistance against Xoo in SAHEL 202 are still not fully understood. GIGANTE is resistant against Malian Xoo strains (Tekete et al., 2020). Evidence suggests that resistance in GIGANTE is controlled by the Xa1 gene (Tekete, 2020). Our study provides evidence of the probable involvement of this gene in resistance against Senegalese Xoo strains. Considering the close geographical location between Senegal and Mali, it is conceivable that Xa1 could be deployed to manage Xoo in both countries.

Our data as a whole points to the possibility that additional resistant varieties identified in this study habor one or several genes that provide resistance to Xoo strains, as demonstrated by the cases of BG 90 − 2 and GIGANTE. The cultivation of these varieties in areas marked by a substantial prevalence of Xoo infections could potentially mitigate yield losses associated with this disease in Senegal. Likewise, these varieties can be used to improve the resistance of other elite genetic resources in other countries in the region.

When exploring potential sources of resistance, it is also crucial to understand the impact of variety-strain interaction. It is possible for a particular variety to exhibit susceptibility to a specific bacterial strain while simultaneously demonstrating resistance to another strain. Such varieties may be considered for cultivation in regions where the prevailing strains are those against which they exhibit resistance. We analyzed the response of some varieties, such as ISRIZ 12, which exhibited resistance to strains S69-1-1, S62-2-5, S62-2-22, and S62-2-26, while displaying susceptibility to S82-4-1. ISRIZ 12 has the potential to effectively control Xoo in the Saint-Louis region of Senegal. However, its effectiveness in other regions remains uncertain due to its susceptibility to S82-4-1. Other varieties that exhibit divergent responses include NERICA 1, NERICA 5, and ISRIZ 11. These varieties demonstrated resistance to Xoo strains S62-2-5, S62-2-22, and S62-2-26 collected from the Ndiaye region. In contrast, these varieties displayed susceptibility to S69-1-1 strain from the Ndioum region. We also observed that WAB 56 − 50 exhibited resistance against all strains, except for S69-1-1, which was collected from Ndioum region. Furthermore, the lowland variety DJ11-509 exhibited high susceptibility when exposed to strains obtained from both irrigated and lowland environments. Moreover, DJ11-509 demonstrated even a higher level of susceptibility than the susceptible controls, NIPPONBARE and IR24, despite its adaptability to lowland ecologies. Upland cultivars WAB 56 − 50, NERICA 5, and NERICA 6 also provided additional support for these varying responses by exhibiting high susceptibility mostly to the Xoo strain S69-1-1 isolated from Ndioum irrigated fields. Previous studies (Balanagouda et al., 2017; Safrizal et al., 2020) indicated that WAB 56 − 50 exhibited resistance to 80% of Xoo strains. Subsequently, Liu et al. (2021) confirmed this finding by demonstrating that WAB 56 − 50 displayed resistance to several Xoo strains. This observation aligns with our findings; nonetheless, the susceptibility of WAB 56 − 50 to S69-1-1 suggests that some Xoo strains overcome its resistance. In a similar vein, we observed that both ITA 150 and NERICA 1 exhibited high susceptibility to S82-4-1, which was collected from the lowland region in Bandafassi. Furthermore, the lowland cultivar ITA 123 (FKR 28) had a higher susceptibility to strains collected from the irrigated area in Saint-Louis, in contrast to strains obtained from Ndiaye region. These findings provide further evidence that there is a considerable interaction between strains and varieties in determining rice resistance to Xoo and are in line with previous studies (Acharya et al., 2018; Aye et al., 2007; Dossa et al., 2017; Fordjour et al., 2020; Hasan et al., 2020; Naqvi et al., 2015; Noor et al., 2006; Tekete et al., 2020).

The susceptible control varieties also exhibited varied responses upon inoculation, thereby indicating the disparity in virulence among Xoo strains. Strain S82-4-1 exhibited the highest lesion length on the majority of the rice varieties screened, suggesting its high level of virulence. This observation could perhaps be associated with the higher abundance of putative TAL effectors in this particular strain, as previously reported by Ji et al. (2014), who found a positive correlation between the number of putative TALE genes and the virulence of bacterial strains. Although the current study was not designed to assess the quantity and diversity of TALE genes in these strains, strain S82-4-1 demonstrates promise as a viable candidate for evaluating rice varieties or lines within breeding programs. Strain S82-4-1 and to some extent S69-1-1 also exhibited the highest lesion length on upland varieties. Studies indicate the emergence of Xoo strains that are adapted to upland environments, consequently acquiring the capacity to infect upland varieties (Islam et al., 2016; Kumar et al., 2020). The emergence of these strains could have a significant negative effect on rice yields in the near future. Therefore, it is imperative to place more emphasis on upland rice research related to Xoo surveillance and characterization. Moreover, the execution of breeding projects targeted at improving upland rice resistance to Xoo holds the potential to serve as a contingency plan in the event of future epidemics.

The present work has provided evidence on the presence of local sources of resistance against Senegalese strains of Xoo, the causal agent of bacterial blight in rice. A total of seven (07) rice varieties exhibited resistance to Xoo, including two (02) lowland rice varieties, four (04) irrigated rice varieties, and the control variety GIGANTE. All of the upland varieties tested in this study exhibit susceptibility to at least one strain of Xoo, Therefore, gaining a comprehensive understanding of the influence of ecological and evolutionary factors associated with Xoo spread in the uplands is crucial in effectively managing disease outbreaks and ensuring the productivity of rice in uplands. The identification of the genetic loci responsible for conferring resistance to Xoo in the resistant varieties identified in this study is a crucial further stage. Once these genes are identified, they could be introduced into elite varieties to improve rice resistance to Xoo. The bacterial strain S82-4-1 exhibited the highest level of virulence. This particular strain can be used in the evaluation of rice germplasm for resistance against Xoo in rice breeding programs.

Declaration of competing interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Ethical approval

Not application.

Acknowledgements

We are grateful to the Deutscher Akademischer AustauschDienst (DAAD) (Grant number: 91782296), for funding this research on improving rice production in Senegal. The Centre d'Etude Régional pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS) for hosting the work. We also thank AfricaRice, IRD and ISRA for providing biological material.

Author contributions

Conceptualization, Project administration and Funding acquisition: Bernadin A. Dossou, Daniel Foncéka, Baboucarr Manneh, Papa M. Diédhiou. Formal analysis: Bernadin A. Dossou, Diarietou Sambakhe. Investigation: Bernadin A. Dossou, Hamidou Tall, Ndjido A. Kane, Omar N. Faye, Boris Szurek, Geoffrey Onaga. Methodology: Bernadin A. Dossou, Hamidou Tall, Boris Szurek, Geoffrey Onaga, Baboucarr Manneh, Papa M. Diédhiou. Validation: Bernadin A. Dossou, Baboucarr Manneh, Papa M. Diédhiou. Writing-original draft: Bernadin A. Dossou, Papa M. Diédhiou. Writing-review & editing: Bernadin A. Dossou, Hamidou Tall, Ndjido A. Kane, Geoffrey Onaga, Daniel Foncéka, Papa M. Diédhiou.

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Status of the resistance of selected rice (Oryzasativa) varieties to bacterial blight strains in Senegal

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Abstract

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Introduction

Materials and methods

Study site

Plant material

Bacterial strains

Inoculation of bacterial strains to rice plants

Experimental design and management of experiment

Data collection

Statistical analysis

Results

Response of the varieties to inoculation with bacterial blight strains from Senegal

Classification of rice varieties based on their reaction to bacterial strains

Discussion

Conclusion

Declarations

References

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