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. 2021 Mar 10;10(3):518.
doi: 10.3390/plants10030518.

Identification of Bacterial Blight Resistance Loci in Rice (Oryza sativa L.) against Diverse Xoo Thai Strains by Genome-Wide Association Study

Siriporn Korinsak  1 , Clive T Darwell  1 , Samart Wanchana  1 , Lawan Praphaisal  1 , Siripar Korinsak  1 , Burin Thunnom  1 , Sujin Patarapuwadol  2 , Theerayut Toojinda  1
Affiliations

Identification of Bacterial Blight Resistance Loci in Rice (Oryza sativa L.) against Diverse Xoo Thai Strains by Genome-Wide Association Study

Siriporn Korinsak et al. Plants (Basel). .

Abstract

Bacterial leaf blight (BLB) is a serious disease affecting global rice agriculture caused by Xanthomonas oryzae pv. oryzae (Xoo). Most resistant rice lines are dependent on single genes that are vulnerable to resistance breakdown caused by pathogen mutation. Here we describe a genome-wide association study of 222 predominantly Thai rice accessions assayed by phenotypic screening against 20 Xoo isolates. Loci corresponding to BLB resistance were detected using >142,000 SNPs. We identified 147 genes according to employed significance thresholds across chromosomes 1-6, 8, 9 and 11. Moreover, 127 of identified genes are located on chromosomal regions outside estimated Linkage Disequilibrium influences of known resistance genes, potentially indicating novel BLB resistance markers. However, significantly associated SNPs only occurred across a maximum of six Xoo isolates indicating that the development of broad-spectrum Xoo strain varieties may prove challenging. Analyses indicated a range of gene functions likely underpinning BLB resistance. In accordance with previous studies of accession panels focusing on indica varieties, our germplasm displays large numbers of SNPs associated with resistance. Despite encouraging data suggesting that many loci contribute to resistance, our findings corroborate previous inferences that multi-strain resistant varieties may not be easily realised in breeding programs without resorting to multi-locus strategies.

Keywords: GWAS; Xanthomonas oryzae pv. oryzae; bacterial leaf blight; rice.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Percentage of susceptible versus resistant lines across 20 focal Xoo isolates (x-axis). Most rice accessions are predominantly susceptible to all but one Xoo isolate.
Figure 2
Figure 2
Leaf lesion length scores for BLB damage for rice panel cultivars across 20 focal Xoo isolates. Most Xoo isolates cause serious leaf damage.
Figure 3
Figure 3
Principal component analysis of 222 accessions from our rice panel. Grey colour (PC1 <= 100) are indica varieties with a handful of japonica (blue) and aus/aro varieties (orange).
Figure 4
Figure 4
Linkage disequilibrium decay across 12 chromosomes in 222 O. sativa accessions. Mean LD decay ranges between 61–210 Kb.
Figure 5
Figure 5
QQ and Manhattan plots from GWAS analyses highlighting significantly associated SNPs associating with bacterial leaf blight resistance for representative Xoo isolates. Figures (a–i), Xoo isolates: (a) 2XORE1-14; (b) 2XOST2-2; (c) 3XOBR2-6; (d) 4XORB4-5; (e) 59XOCRMS9-4; (f) 59XOCRMSO3-1-1; (g) 59XOCRPA20-10; (h) SP1-1; and (i) XONS3-2. Dot-dash and dashed lines represent FDR and bootstrap significance thresholds, respectively.
Figure 5
Figure 5
QQ and Manhattan plots from GWAS analyses highlighting significantly associated SNPs associating with bacterial leaf blight resistance for representative Xoo isolates. Figures (a–i), Xoo isolates: (a) 2XORE1-14; (b) 2XOST2-2; (c) 3XOBR2-6; (d) 4XORB4-5; (e) 59XOCRMS9-4; (f) 59XOCRMSO3-1-1; (g) 59XOCRPA20-10; (h) SP1-1; and (i) XONS3-2. Dot-dash and dashed lines represent FDR and bootstrap significance thresholds, respectively.
Figure 6
Figure 6
Linkage disequilibrium (LD) heatmap for chromosome 11 (region 17–29Mb) indicating chromosomal locations of six previously mapped R (Xa) genes and ten MSU annotated genes (LOC_Os prefix) that contain significantly associated SNPs highlighted by GWAS that are: (i) greater than LD decay threshold (61 Kb) away from R genes; and (ii) described by Go categorizations as having stress response functionality. A lack of red areas on the heatmap indicates the generally low levels of LD for this chromosome. Red triangles indicate densely clustered regions of significantly associated SNPs. Pointers show map positions (bottom) and relative position on chromosome within the region (top).
Figure 7
Figure 7
Tabular representation of alternative haplotypes determined by occurrence of significantly associated SNPs identified by GWAS analysis. (a–j) indicates specified MSU annotated genes.
Figure 8
Figure 8
Boxplots indicating phenotypic responses in BLB resistance among rice accessions featuring alternative haplotypes determined by occurrence of significantly associated SNPs identified by GWAS analysis. (a) LOC_Os11g31620; (b) LOC_Os11g32210; (c) LOC_Os11g40840; (d) LOC_Os11g45620; (e) LOC_Os11g37860; (f) LOC_Os11g37870; (g) LOC_Os11g37960; (h) LOC_Os11g38870; (i) LOC_Os11g31620; and (j) LOC_Os11g31620.
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