A novel intragenic marker targeting the ectodomain of bacterial leaf blight resistance gene Xa21 in rice

2019 ◽  
Author(s):  
Dhanesha Lakmali Nanayakkara ◽  
Iresha Kumari Edirisingha ◽  
Lakshika Nivanthi Dissanayake ◽  
Deepika Weerasinghe ◽  
Lalith Suriyagoda ◽  
...  
Keyword(s):  
Resistance Gene ◽  
High Throughput ◽  
Rice Chromosome ◽  
Leaf Blight ◽  
Bacterial Leaf Blight ◽  
Economic Losses ◽  
Linkage Drag ◽  
Resistance Allele ◽  
Chromosome 11 ◽  
Susceptible Allele

Abstract Background Among the diseases in rice (Oryza sativa L.), bacterial leaf blight (BLB) caused by Xanthomonas oryzae pv. oryzae results in devastating economic losses, both in terms of yield and quality. The Xa21 mapped to the rice chromosome 11, is known to convey resistance against BLB by its involvement in plant pathogen recognition and immunity responses. The closely-linked sequence-tagged site marker pTA248 is frequently used for marker-assisted selection (MAS) of Xa21. However, lower precision and linkage drag of linked-markers hinders the reliability and effectiveness in MAS compared to the use of flanking or intergenic markers. Results In the current study, a diagnostic intragenic marker was developed for MAS of Xa21 in rice. The new marker ABUOP0001 targets a 19-bp insertion/deletion (InDel) on the ectodomain of the Xa21, and amplifies a 200-bp amplicon from the rice line IRBB 62, which is known-to-carry the ‘resistance allele’, and a 181-bp amplicon from IRBB 7, which is known-to-carry the ‘susceptible allele’. The resistance allele was identified in ten IRBB lines, and five newly improved Sri Lankan rice accessions through ABUOP0001 marker assay. In a field study, 14 of these accessions conveyed highly resistant BLB disease responses, and one conveyed an intermediate response. While carrying the susceptible allele at Xa21, 30 accessions conveyed a resistance response to BLB, and it could be due to the contribution of other Xa resistance alleles in their genetic background. Further, the Xa21 resistance allele was identified in 1,675 rice accessions through an in silico analysis of genomic sequences available through the 3K Rice Genomes Project. The intragenic marker ABUOP0001 performs equally to that of the linked-marker pTA248 anchored 224 kbp upstream of Xa21, in detecting resistant and susceptible BLB phenotypes. The marker ABUOP0001 is compatible for high-throughput screening with high resolution melting (HRM) and can be multiplexed effectively with an intragenic marker of BLB resistance gene Xa4. Conclusion The marker ABUOP0001 is a diagnostic intragenic marker that can be recommended for MAS of Xa21 in rice. The marker can be assayed as a high-throughput marker using HRM and multiplexed PCR.

scholarly journals Identification of Rice Genotypes Resistant To Bacterial Leaf Blight Disease Using Ssr Markers

2018 ◽  
Vol 35 (1) ◽  
pp. 113-120
Author(s):  
A. Acharya ◽  
N. R. Adhikari ◽  
R. B. Amgain ◽  
A. Poudel ◽  
R. Yadav ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Resistance Gene ◽  
Bacterial Blight ◽  
Gene Pyramiding ◽  
Bacterial Pathogen ◽  
Leaf Blight ◽  
Bacterial Leaf Blight ◽  
Resistant Varieties ◽  
Blight Disease ◽  
Almost All

 Bacterial blight disease of rice is a growing and challenging concern in Nepal. Since bacterial pathogen (Xanthomonas oryzae pv. oryzae) is difficult to manage by other means effectively, development of host plant resistance is the most effective mean to control this disease. This study was carried out to identify the bacterial leaf blight resistant genotypes of rice by using of molecular markers linked with bacterial blight resistant genes. Sixty genotypes of rice were screened at glass house for BB resistance and they were tested for the presence of Xa4, Xa5, Xa7 and Xa21 genes using markers MP, RM122, M5 and pTA248 respectively. IRBB 60 and Jumli Marshi were used as resistant and susceptible check respectively. Twenty five genotypes of rice were detected with presence of Xa4 gene, 24 genotypes with Xa5 gene and fourteen genotypes with Xa7 gene. Twenty four genotypes did not showed presence of any gene. Twenty four genotypes showed the presence of more than one gene with the specific molecular markers. Almost all genotypes that did not show presence of any gene were found highly susceptible in greenhouse conditions with both inoculums. Genotypes having more than one BB resistance gene were found resistant in greenhouse conditions with both inoculums suggesting combination of BB resistance gene through gene pyramiding will provide BB resistant varieties in rice breeding.

scholarly journals Phenotype and genotype variability of interspecific rice lines related to bacterial leaf blight resistance (Xanthomonas oryzae pv. oryzae) character

2021 ◽  
Vol 22 (10) ◽  
Author(s):  
SITI YURIYAH ◽  
DEDY DARNAEDI ◽  
TATANG MITRA SETIA ◽  
GUT WINDARSIH ◽  
Dwinita Wikan Utami
Keyword(s):  
Resistance Gene ◽  
Wild Rice ◽  
Leaf Blight ◽  
Oryza Rufipogon ◽  
Xanthomonas Oryzae ◽  
Bacterial Leaf Blight ◽  
Yield Potential ◽  
Interspecific Crosses ◽  
Blight Resistance ◽  
Wild Rice Species

Abstract. Yuriyah S, Darnaedi D, Setia TM, Windarsih G, Utami DW. 2021. Phenotype and genotype variability of interspecific rice lines related to bacterial leaf blight resistance (Xanthomonas oryzae pv. oryzae) character. Biodiversitas 22: 4123-4130. Wild rice species are the source of the gene pool for rice genetic diversity. The cross-species crosses (interspecific crosses) play an important role in breeding, namely in terms of expanding the diversity of desirable characters, such as disease resistance and improvement in yield potential. Currently, the genes from wild rice species have been successfully introgressed into cultivated rice so that they can overcome the rice production constraints, including the introgression of genes for the bacterial leaf blight (BLB) resistance. The purpose of this study was to analyze the variability of phenotype and genotype performance of lines derived from wild rice species for the character of resistance to BLB disease. A total of 33 selected backcross lines derived from wild rice species of O. rufipogon and O. glaberrima as the donor parents and 2 control varieties (resistant and susceptible to BLB disease), were used in this study. The evaluation of phenotype and genotype of resistance characters to BLB disease was carried out during a vegetative phase of the plant. The resistance evaluation was carried out in a greenhouse, while the genotype performance was analyzed using 4 STS markers linked to Xa4, Xa7, and Xa13 genes. The result of the phenotype evaluation showed that there were variations among the resistance of the tested lines. Three lines derived from a Situ Bagendit/Oryza rufipogon cross were resistant to all BLB races used in the testing. Those three lines indicated to have the allele of the Xa7 resistance gene based on the genotype performance which grouped with the Code variety that had the Xa7 resistance gene.

scholarly journals Close linkage of a blast resistance gene, Pias(t), with a bacterial leaf blight resistance gene, Xa1-as(t), in a rice cultivar ‘Asominori’

2012 ◽  
Vol 62 (4) ◽  
pp. 334-339 ◽  
Author(s):  
Takashi Endo ◽  
Masayuki Yamaguchi ◽  
Ryota Kaji ◽  
Koji Nakagomi ◽  
Tomomori Kataoka ◽  
...  
Keyword(s):  
Resistance Gene ◽  
Blast Resistance ◽  
Rice Cultivar ◽  
Leaf Blight ◽  
Close Linkage ◽  
Bacterial Leaf Blight ◽  
Blight Resistance ◽  
Blast Resistance Gene

scholarly journals Marker Assisted Screening of Nepalese rice for bacterial leaf blight (BLB) resistance

2015 ◽  
Vol 3 (1) ◽  
pp. 35-39 ◽  
Author(s):  
Resham Babu Amgai ◽  
Raj Kumar Niroula ◽  
Sumitra Pantha ◽  
Shreya Singh Hamal ◽  
Bishal Gole Tamang ◽  
...  
Keyword(s):  
Resistance Gene ◽  
Leaf Blight ◽  
Bacterial Leaf Blight ◽  
Limiting Factor ◽  
Rice Varieties ◽  
Resistant Gene ◽  
Rice Landraces ◽  
Sequence Tagged Sites ◽  
Check Variety ◽  
Simple Sequence

Bacterial Leaf Blight (BLB) is the most important yield limiting factor in Nepalese rice. BLB resistance rice varieties are highly demanding in the country. Breeding efforts for developing disease resistant depends on availability and use of resistant gene donors. Nepalese rice landraces could be the source of resistant gene. Therefore, ninety six Nepalese rice accessions were screened using eight Simple Sequence Repeats (SSR) markers and one Sequence Tagged Sites (STS) marker for presence and absence of BLB resistance gene. We have detected BLB resistance gene Xa-10 on five accessions, Xa-13 on six accessions, Xa-7 on 23 accessions, Xa-3 and Xa-4 on 52 accessions, Xa-5 on 25 accessions, Xa-8 on 30 rice accessions. No any rice accessions tested have Xa-21. Similarly, 17 rice accessions showed three and more than three BLB resistance genes. Presence of Xa-13 on susceptible check variety CNTRL-85033 confirmed that this resistant gene is not working in Nepalese rice field. Therefore, Nepal need to pyramide the BLB resistant genes for durable resistance.Nepal Journal of Biotechnology. Dec. 2015 Vol. 3, No. 1: 35-39

scholarly journals Bacterial Leaf Blight on shrunken-2 Sweet Corn

Plant Disease ◽  
1997 ◽  
Vol 81 (11) ◽  
pp. 1293-1298 ◽  
Author(s):  
J. K. Pataky ◽  
L. J. du Toit ◽  
M. R. Kerns
Keyword(s):  
Sweet Corn ◽  
Inbred Lines ◽  
Leaf Blight ◽  
Bacterial Leaf Blight ◽  
Economic Losses ◽  
Corn Hybrids ◽  
Slope Coefficient ◽  
Foliar Symptoms

Severity of bacterial leaf blight (BLB, caused by Acidovorax avenae subsp. avenae) on shrunken-2 (sh2) sweet corn hybrids grown in BLB-conducive environments and sporadic outbreaks of BLB in recent years warranted evaluations of the potential for this disease to cause economic losses. BLB symptoms on 122 sh2 hybrids, 30 sh2 inbred lines, and 29 crosses of the inbreds and the effects of BLB on yield (ear weight and marketable ears) were evaluated in 1994 and 1996. BLB severity ratings for 122 hybrids averaged 3.3 and 3.7 (on a scale of 1 to 9) in 1994 and 1996, respectively. Hybrid means ranged from 1.8 to 5.5 in 1994 and from 1.9 to 5.7 in 1996, with Bayesian LSD values of 1.20 and 1.22, respectively. There were no differences in BLB ratings among hybrids with yellow, white, or bicolored kernels. Severity of symptoms on 30 sh2 inbreds ranged from 1.5 to 5.7, whereas the reactions of 29 crosses of the inbreds ranged from 1.9 to 5. The slope coefficient of the regression of crosses on mid-parent values was not different from 1. Thus, mid-parent values gave a good indication of severity of BLB symptoms on crosses, with the exception of a few crosses that tended to be more severely infected than expected based on mid-parent values. Ear weights and number of marketable ears differed among hybrids in the 1994 trial, but there was no significant effect of BLB treatments on either of these measures of yield. In 1996, ear weights in inoculated plots were 10 and 15% lower than those from noninoculated plots for 2 of 12 hybrids. Despite moderately severe foliar symptoms, BLB did not affect yield substantially in these trials even among hybrids with the most susceptible reactions.

scholarly journals Characterization of New Races of Xanthomonas oryzae pv. oryzae in Mali Informs Resistance Gene Deployment

2020 ◽  
Vol 110 (2) ◽  
pp. 267-277
Author(s):  
C. Tekete ◽  
S. Cunnac ◽  
H. Doucouré ◽  
M. Dembele ◽  
I. Keita ◽  
...  
Keyword(s):  
Resistance Gene ◽  
Rice Variety ◽  
Leaf Blight ◽  
Rice Cultivation ◽  
Xanthomonas Oryzae ◽  
Bacterial Leaf Blight ◽  
Local Source ◽  
Sources Of Resistance ◽  
Rice Varieties ◽  
New Races

Bacterial leaf blight caused by Xanthomonas oryzae pv. oryzae represents a severe threat to rice cultivation in Mali. Characterizing the pathotypic diversity of bacterial populations is key to the management of pathogen-resistant varieties. Forty-one X. oryzae pv. oryzae isolates were collected between 2010 and 2013 in the major rice growing regions in Mali. All isolates were virulent on the susceptible rice variety Azucena; evaluation of the isolates on 12 near isogenic rice lines, each carrying a single resistance gene, identified six new races (A4 to A9) and confirmed race A3 that was previously reported in Mali. Races A5 and A6, isolated in Office du Niger and Sélingué, were the most prevalent races in Mali. Race A9 was the most virulent, circumventing all of the resistance genes tested. Xa3 controlled six of seven races (i.e., 89% of the isolates tested). The expansion of race A9 represents a major risk to rice cultivation and highlights the urgent need to identify a local source of resistance. We selected 14 isolates of X. oryzae pv. oryzae representative of the most prevalent races to evaluate 29 rice varieties grown by farmers in Mali. Six isolates showed a high level of resistance to X. oryzae pv. oryzae and were then screened with a larger collection of isolates. Based on the interactions among the six varieties and the X. oryzae pv. oryzae isolates, we characterized eight different pathotypes (P1 to P8). Two rice varieties, SK20-28 and Gigante, effectively controlled all of the isolates tested. The low association observed among races and pathotypes of X. oryzae pv. oryzae suggests that the resistance observed in the local rice varieties does not simply rely on single known Xa genes. X. oryzae pv. oryzae is pathogenically and geographically diverse. Both the races of X. oryzae pv. oryzae characterized in this study and the identification of sources of resistance in local rice varieties provide useful information to inform the design of effective breeding programs for resistance to bacterial leaf blight in Mali.

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