Allelic variation for broad‐spectrum resistance and susceptibility to bacterial pathogens identified in a rice <scp>MAGIC</scp> population

Bossa-Castro, A. M.; Tekete, C.; Raghavan, Chitra; Delorean, Emily; Dereeper, Alexis; Dagno, Karim; Koïta, Ousmane; Mosquera, Gloria; Leung, Hei; Verdier, Valérie; Leach, Jan E.

doi:10.1111/pbi.12895

Cited by 36 publications

(28 citation statements)

References 43 publications

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“…GWAS also identified SNP markers near known genes that are related to disease resistance and stress tolerance such as OsRLCK19 , OsLOL2 , and OsGLP8 , which are plausible candidate resistance genes on chromosomes 1 and 8. Similarly, a GWAS in a ulti-Parent Advanced Generation Inter-Cross (MAGIC) population identified several major and minor loci for BLB resistance [150]. Although major BLB resistance genes have been successfully introgressed using marker-assisted breeding, widespread use of these varieties narrows the genetic base, resulting in high selection pressure against the prevailing BLB strains, resulting in more virulent strains that could overcome the major R genes of rice.…”

Section: Discussionmentioning

confidence: 99%

Genetic Dissection of Grain Nutritional Traits and Leaf Blight Resistance in Rice

Descalsota-Empleo

Noraziyah

Navea

et al. 2019

Genes

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Colored rice is rich in nutrition and also a good source of valuable genes/quantitative trait loci (QTL) for nutrition, grain quality, and pest and disease resistance traits for use in rice breeding. Genome-wide association analysis using high-density single nucleotide polymorphism (SNP) is useful in precisely detecting QTLs and genes. We carried out genome-wide association analysis in 152 colored rice accessions, using 22,112 SNPs to map QTLs for nutritional, agronomic, and bacterial leaf blight (BLB) resistance traits. Wide variations and normal frequency distributions were observed for most of the traits except anthocyanin content and BLB resistance. The structural and principal component analysis revealed two subgroups. The linkage disequilibrium (LD) analysis showed 74.3% of the marker pairs in complete LD, with an average LD distance of 1000 kb and, interestingly, 36% of the LD pairs were less than 5 Kb, indicating high recombination in the panel. In total, 57 QTLs were identified for ten traits at p < 0.0001, and the phenotypic variance explained (PVE) by these QTLs varied from 9% to 18%. Interestingly, 30 (53%) QTLs were co-located with known or functionally-related genes. Some of the important candidate genes for grain Zinc (Zn) and BLB resistance were OsHMA9, OsMAPK6, OsNRAMP7, OsMADS13, and OsZFP252, and Xa1, Xa3, xa5, xa13 and xa26, respectively. Red rice genotype, Sayllebon, which is high in both Zn and anthocyanin content, could be a valuable material for a breeding program for nutritious rice. Overall, the QTLs identified in our study can be used for QTL pyramiding as well as genomic selection. Some of the novel QTLs can be further validated by fine mapping and functional characterization. The results show that pigmented rice is a valuable resource for mineral elements and antioxidant compounds; it can also provide novel alleles for disease resistance as well as for yield component traits. Therefore, large opportunities exist to further explore and exploit more colored rice accessions for use in breeding.

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Section: Discussionmentioning

confidence: 99%

Genetic Dissection of Grain Nutritional Traits and Leaf Blight Resistance in Rice

Descalsota-Empleo

Noraziyah

Navea

et al. 2019

Genes

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“…Of the 43 significantly associated SNP markers genome‐wide, 33 clustered on chromosome 5 (Figure 3; Table S6) and four of these were within the 95% confidence interval of qBB‐PXO99 A ‐5 (Table S4, S6). This QTL was previously detected in the indica MAGIC population in screenings for bacterial blight QTL (Bossa‐Castro et al ., 2018). The QTL and its associated SNP markers overlapped with the mapped bacterial blight susceptibility/resistance gene Xa5/xa5, a broad‐spectrum disease resistance gene that functions independently of TAL effector binding specificity through the naturally occurring recessive allele ( xa5) of the basal transcription factor TFIIA©5 ( Xa5 ) (Figures 3, 4a; Blair et al ., 2003; Huang et al ., 2016; Iyer and McCouch, 2004).…”

Section: Resultsmentioning

confidence: 99%

“…Genome-wide association studies GWAS was performed as described (Bossa-Castro et al, 2018). Briefly, a kinship matrix was generated for the MAGIC population, excluding parents, to account for population structure using TASSEL version 5.0.2 (Bradbury et al, 2007).…”

Section: Interval Mappingmentioning

confidence: 99%

Resistance and susceptibility QTL identified in a rice MAGIC population by screening with a minor‐effect virulence factor from Xanthomonas oryzae pv. oryzae

Huerta

Delorean

Bossa-Castro

et al. 2020

Plant Biotechnology Journal

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Effective and durable disease resistance for bacterial blight (BB) of rice is a continuous challenge due to the evolution and adaptation of the pathogen, Xanthomonas oryzae pv. oryzae (Xoo), on cultivated rice varieties. Fundamental to this pathogens' virulence is transcription activator-like (TAL) effectors that activate transcription of host genes and contribute differently to pathogen virulence, fitness or both. Host plant resistance is predicted to be more durable if directed at strategic virulence factors that impact both pathogen virulence and fitness. We characterized Tal7b, a minor-effect virulence factor that contributes incrementally to pathogen virulence in rice, is a fitness factor to the pathogen and is widely present in geographically diverse strains of Xoo. To identify sources of resistance to this conserved effector, we used a highly virulent strain carrying a plasmid borne copy of Tal7b to screen an indica multi-parent advanced generation inter-cross (MAGIC) population. Of 18 QTL revealed by genome-wide association studies and interval mapping analysis, six were specific to Tal7b (qBB-tal7b). Overall, 150 predicted Tal7b gene targets overlapped with qBB-tal7b QTL. Of these, 21 showed polymorphisms in the predicted effector binding element (EBE) site and 23 lost the EBE sequence altogether. Inoculation and bioinformatics studies suggest that the Tal7b target in one of the Tal7b-specific QTL, qBB-tal7b-8, is a disease susceptibility gene and that the resistance mechanism for this locus may be through loss of susceptibility. Our work demonstrates that minor-effect virulence factors significantly contribute to disease and provide a potential new approach to identify effective disease resistance.

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“…In a MAGIC rice population of over 1316 RILs, the mapping intervals were~700 Kbp on average (Raghavan et al 2017). However, as discussed above, empirical (Descalsota et al 2018) Bacterial leaf streak and bacterial leaf blight (Bossa-Castro et al 2018) Grain shape Grain quality, cooking and taste attributes (Ponce et al 2018) Yield, plant height, heading date, grain quality and biofortification (Zaw et al 2019) Grain length, grain width, grain thickness, and thousand grain weight (Ponce et al 2020) Heading date (Han et al 2020) Sorghum Plant height (Ongom and Ejeta 2018) Strawberry Fruit quality-related traits (Wada et al 2017) Tomato Fruit weight (Pascual et al 2015) Fruit weight and flowering time plasticity in response to water, salinity and heat stress (Diouf et al 2020) mapping resolution may be determined by the QTL effect size and population size. The wheat MAGIC populations developed at CSIRO (four Australian spring wheat founders, Huang et al 2012) and NIAB (eight UK winter wheat founders, Mackay et al 2014) are examples of MPPs that have been used to map genes controlling important yield related traits.…”

Section: Applications Of Mppsmentioning

confidence: 98%

Multi-parent populations in crops: a toolbox integrating genomics and genetic mapping with breeding

Scott¹,

Ladejobi²,

et al. 2020

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Crop populations derived from experimental crosses enable the genetic dissection of complex traits and support modern plant breeding. Among these, multi-parent populations now play a central role. By mixing and recombining the genomes of multiple founders, multi-parent populations combine many commonly sought beneficial properties of genetic mapping populations. For example, they have high power and resolution for mapping quantitative trait loci, high genetic diversity and minimal population structure. Many multi-parent populations have been constructed in crop species, and their inbred germplasm and associated phenotypic and genotypic data serve as enduring resources. Their utility has grown from being a tool for mapping quantitative trait loci to a means of providing germplasm for breeding programmes. Genomics approaches, including de novo genome assemblies and gene annotations for the population founders, have allowed the imputation of rich sequence information into the descendent population, expanding the breadth of research and breeding applications of multi-parent populations. Here, we report recent successes from crop multi-parent populations in crops. We also propose an ideal genotypic, phenotypic and germplasm 'package' that multi-parent populations should feature to optimise their use as powerful community resources for crop research, development and breeding. Over recent years, numerous multi-parent populations (MPPs) have been successfully developed in crops (Huang et al. 2015; Cockram and Mackay 2018). MPPs bring together key genomic, phenotypic and germplasm resources to form a

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Allelic variation for broad‐spectrum resistance and susceptibility to bacterial pathogens identified in a rice MAGIC population

Cited by 36 publications

References 43 publications

Genetic Dissection of Grain Nutritional Traits and Leaf Blight Resistance in Rice

Genetic Dissection of Grain Nutritional Traits and Leaf Blight Resistance in Rice

Resistance and susceptibility QTL identified in a rice MAGIC population by screening with a minor‐effect virulence factor from Xanthomonas oryzae pv. oryzae

Multi-parent populations in crops: a toolbox integrating genomics and genetic mapping with breeding

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