Genome-Wide Association Analysis Identifies Resistance Loci for Bacterial Leaf Streak Resistance in Rice (Oryza sativa L.)

Sattayachiti, Wannapa; Wanchana, Samart; Arikit, Siwaret; Nubankoh, Phakchana; Patarapuwadol, Sujin; Vanavichit, Apichart; Darwell, Clive T.; Toojinda, Theerayut

doi:10.3390/plants9121673

Cited by 20 publications

(19 citation statements)

References 42 publications

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“…We also tried crossing DH and KV with IR, but after multiple attempts, we were unsuccessful. To avoid the bias of xa5 and other QTLs associated with BLS resistance in rice (Sattayachiti et al, 2020), which are present in DH (Iyer and McCouch, 2004) but not in PT1, we used F 3 individuals segregating for the mega-papillae trait that were derived from F 2 individuals where the xa5 and other QTLs were absent (Supplementary Figure 2). From a pool of 88 F 3 individuals, we selected 26 plants with "normal" SCP and 26 plants with mega-papillae to test for pathogen resistance (Figures 5A,B).…”

Section: Mega-papillae Hybrid Plants Have Reduced Bacterial Leaf Streak Symptomsmentioning

confidence: 99%

Rice Stomatal Mega-Papillae Restrict Water Loss and Pathogen Entry

et al. 2021

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Rice (Oryza sativa) is a water-intensive crop, and like other plants uses stomata to balance CO2 uptake with water-loss. To identify agronomic traits related to rice stomatal complexes, an anatomical screen of 64 Thai and 100 global rice cultivars was undertaken. Epidermal outgrowths called papillae were identified on the stomatal subsidiary cells of all cultivars. These were also detected on eight other species of the Oryza genus but not on the stomata of any other plant species we surveyed. Our rice screen identified two cultivars that had “mega-papillae” that were so large or abundant that their stomatal pores were partially occluded; Kalubala Vee had extra-large papillae, and Dharia had approximately twice the normal number of papillae. These were most accentuated on the flag leaves, but mega-papillae were also detectable on earlier forming leaves. Energy dispersive X-Ray spectrometry revealed that silicon is the major component of stomatal papillae. We studied the potential function(s) of mega-papillae by assessing gas exchange and pathogen infection rates. Under saturating light conditions, mega-papillae bearing cultivars had reduced stomatal conductance and their stomata were slower to close and re-open, but photosynthetic assimilation was not significantly affected. Assessment of an F3 hybrid population treated with Xanthomonas oryzae pv. oryzicola indicated that subsidiary cell mega-papillae may aid in preventing bacterial leaf streak infection. Our results highlight stomatal mega-papillae as a novel rice trait that influences gas exchange, stomatal dynamics, and defense against stomatal pathogens which we propose could benefit the performance of future rice crops.

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Section: Mega-papillae Hybrid Plants Have Reduced Bacterial Leaf Streak Symptomsmentioning

confidence: 99%

Rice Stomatal Mega-Papillae Restrict Water Loss and Pathogen Entry

et al. 2021

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“…For QTL-seq analysis, Xanthomanas oryzae pv.oryzicola (Xoc) isolate SP7-5, one of the representatives of Thai Xoc isolates [30], was used for the inoculation of the F 2 population (IR62266 × HCS). For marker validation, another Xoc isolate, 2NY2-2, was used for the inoculation of the six F 2 populations.…”

Section: Inoculum Preparation and Phenotypingmentioning

confidence: 99%

“…The tray was then removed from the box and kept in the greenhouse with a misting system to control the humidity (75% relative humidity). Fourteen days after inoculation, BLS disease assessment was performed using the International Rice Research Institution (IRRI) Standard Evaluation System (SES) as previously described [30], with the following scale: 0, no lesions observed; 1, small brown specks of pin-point size or larger brown specks with no sporulation center; 3, lesion type the same as in scale 2 but with a significant number of lesions on the upper leaves; 5, typical lesions infecting 4-10% of the leaf area; 7, typical lesions infecting 26-50% of the leaf area; and 9, more than 75% of the leaf area is affected (Figure S1).…”

Section: Inoculum Preparation and Phenotypingmentioning

confidence: 99%

“…IR62266 is an indica rice variety developed by the International Rice Research Institute (IRRI) and used as a source of BLB resistance [34,35]. This rice variety also has high resistance to several Thai Xoc isolates and has been recommended as a potential source of BLS resistance [30]. The BLS disease was evaluated 14 days after inoculation using the leaf lesion scoring index (with scores from 1 to 9 indicating highly resistant and highly susceptible, respectively).…”

Section: Phenotype Of F 2 Population and The Construction Of Resistant And Susceptible Bulksmentioning

confidence: 99%

“…Although BLS has been confirmed as an important disease in Asia, especially in the tropical and subtropical regions, not many studies on BLS resistance gene/QTL identification have been reported from Thailand. In a recent study, 12 QTLs associated with Thai Xoc strains were identified using the GWAS approach [30]. Two QTLs on chromosomes 2 and 5 have been proposed as promising QTLs for broad-spectrum resistance to BLS cuased by Thai Xoc strains.…”

Section: Introductionmentioning

confidence: 99%

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Identification and Validation of a QTL for Bacterial Leaf Streak Resistance in Rice (Oryza sativa L.) against Thai Xoc Strains

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Pitaloka

et al. 2021

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Rice is one of the most important food crops in the world and is of vital importance to many countries. Various diseases caused by fungi, bacteria and viruses constantly threaten rice plants and cause yield losses. Bacterial leaf streak disease (BLS) caused by Xanthomonas oryzae pv. oryzicola (Xoc) is one of the most devastating rice diseases. However, most modern rice varieties are susceptible to BLS. In this study, we applied the QTL-seq approach using an F2 population derived from the cross between IR62266 and Homcholasit (HSC) to rapidly identify the quantitative trait loci (QTL) that confers resistance to BLS caused by a Thai Xoc isolate, SP7-5. The results showed that a single genomic region at the beginning of chromosome 5 was highly associated with resistance to BLS. The gene xa5 was considered a potential candidate gene in this region since most associated single nucleotide polymorphisms (SNPs) were within this gene. A Kompetitive Allele-Specific PCR (KASP) marker was developed based on two consecutive functional SNPs in xa5 and validated in six F2 populations inoculated with another Thai Xoc isolate, 2NY2-2. The phenotypic variance explained by this marker (PVE) ranged from 59.04% to 70.84% in the six populations. These findings indicate that xa5 is a viable candidate gene for BLS resistance and may help in breeding programs for BLS resistance.

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