Marker-trait Association for Resistance to Sugarcane Mosaic Virus (SCMV) in a Sugarcane (Saccharum spp.) Panel

Burbano, Roberto Carlos Villavicencio; Silva, Marcel Fernando da; Coutinho, Alisson Esdras; Gonçalves, Marcos César; Anjos, Ivan Antônio dos; Anjos, Luciana Oliveira Souza; Pérecin, Dilermando; Pinto, Luciana Rossini

doi:10.1007/s12355-022-01131-5

Cited by 4 publications

(6 citation statements)

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“…However, they fit in the upper range of those of other mapping studies in sugarcane; with the exceptions of resistance to brown and orange rust (Daugrois et al ., 1996; Yang et al ., 2018), markers explaining 10% or less of the phenotypic variation in traits of agronomic importance are common in this crop (Gouy et al ., 2015; Fickett et al ., 2019). Specifically, for resistance to SCMV, previous studies identified markers explaining 5-14% of the variance observed individually (Pinto et al ., 2013; Burbano et al ., 2022) or up to ∼40% together (Barnes et al ., 1997). The apparent quantitative nature of resistance to SCMV in sugarcane attests to the limitations of traditional marker-assisted breeding in this crop and demonstrates the need for the deployment of high-throughput genotyping and specific methodologies for association analyses in sugarcane.…”

Section: Discussionmentioning

confidence: 99%

“…Each row contained two plants, totaling six plants of each genotype per plot. Infection by SCMV isolate RIB-2 (Burbano et al ., 2022) was allowed to occur under natural conditions in conjunction with high inoculum pressure and a high incidence of aphid vectors.…”

Section: Methodsmentioning

confidence: 99%

“…A few phenotypic studies have been performed in Brazil: specifically, researchers have evaluated the genotypic correlation of this disease incidence in sugarcane families (Xavier et al ., 2013) and screened diverse genotypes for resistance (da Silva et al ., 2015a, b). In addition, three marker– trait association studies have been carried out targeting SCMV resistance in this crop (Barnes et al ., 1997; Pinto et al ., 2013; Burbano et al ., 2022); however, most included very few genotypes (≤50), and all employed dominantly scored markers. This apparent disparity between the information on SCMV resistance available for sugarcane and maize can be partially explained by the larger economic importance of the latter species in several countries; however, another important factor, i.e., sugarcane’s genomic complexity, has an effect.…”

Section: Introductionmentioning

confidence: 99%

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Multiomic investigation of sugarcane mosaic virus resistance in sugarcane

Pimenta

Aono

Burbano

et al. 2022

Preprint

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Sugarcane mosaic virus (SCMV) is the main etiological agent of sugarcane mosaic disease, which affects sugarcane, maize and other economically important grass species. Despite the extensive characterization of quantitative trait loci controlling resistance to SCMV in maize, the genetic basis of this trait is largely unexplored in sugarcane. Here, a genome-wide association study was performed and machine learning coupled to feature selection was used for the genomic prediction of resistance to SCMV in a diverse panel of sugarcane accessions. This ultimately led to the identification of nine single nucleotide polymorphisms (SNPs) explaining up to 29.9% of the phenotypic variance and a 73-SNP set that predicted resistance with high accuracy, precision, recall, and F1 scores. Both marker sets were validated in additional sugarcane genotypes, in which the SNPs explained up to 23.6% of the phenotypic variation and predicted resistance with a maximum accuracy of 69.1%. Synteny analyses showed that the gene responsible for the major SCMV resistance in maize is probably absent in sugarcane, explaining why such a major resistance source is thus far unknown in this crop. Lastly, using sugarcane RNA sequencing data, markers associated with the resistance to SCMV in sugarcane were annotated and a gene coexpression network was constructed to identify the predicted biological processes involved in SCMV resistance. This allowed the identification of candidate resistance genes and confirmed the involvement of stress responses, photosynthesis and regulation of transcription and translation in the resistance to this virus. These results provide a viable marker-assisted breeding approach for sugarcane and identify target genes for future molecular studies on resistance to SCMV.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Multiomic investigation of sugarcane mosaic virus resistance in sugarcane

Pimenta

Aono

Burbano

et al. 2022

Preprint

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“…For instance, a QTL locus qMdr9.02 was found to be associated with resistance to southern leaf blight, northern leaf blight, and gray leaf spot in maize . However, to date, only four SCMV resistanceassociated markers (AFLP-346, AFLP-372, AFLP-538, and CV29.13), each accounting for 5.51 to 14.02% of PVE, were reported by Burbano et al (2022). The objectives of this study were to construct a genetic mapping population, to evaluate the SMD response of the mapping population, and to develop SMD resistance-associated QTL markers and suggest candidate genes for the improvement of the efficiency and accuracy of sugarcane breeding.…”

Section: Introductionmentioning

confidence: 99%

“…For instance, a QTL locus qMdr9.02 was found to be associated with resistance to southern leaf blight, northern leaf blight, and gray leaf spot in maize ( Yang et al., 2017 ). However, to date, only four SCMV resistance-associated markers ( AFLP-346 , AFLP-372 , AFLP-538 , and CV29.13 ), each accounting for 5.51 to 14.02% of PVE, were reported by Burbano et al. (2022) .…”

Section: Introductionmentioning

confidence: 99%

Identification of QTLs and critical genes related to sugarcane mosaic disease resistance

Wang²,

Pan³

et al. 2023

Front. Plant Sci.

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Mosaic viral diseases affect sugarcane productivity worldwide. Mining disease resistance-associated molecular markers or genes is a key component of disease resistance breeding programs. In the present study, 285 F1 progeny were produced from a cross between Yuetang 93-159, a moderately resistant variety, and ROC22, a highly susceptible variety. The mosaic disease symptoms of these progenies, with ROC22 as the control, were surveyed by natural infection under 11 different environmental conditions in the field and by artificial infections with a mixed sugarcane mosaic virus (SCMV) and sorghum mosaic virus (SrMV) inoculum. Analysis of consolidated survey data enabled the identification of 29 immune, 55 highly resistant, 70 moderately resistant, 62 susceptible, and 40 highly susceptible progenies. The disease response data and a high-quality SNP genetic map were used in quantitative trait locus (QTL) mapping. The results showed that the correlation coefficients (0.26~0.91) between mosaic disease resistance and test environments were significant (p< 0.001), and that mosaic disease resistance was a highly heritable quantitative trait (H2 = 0.85). Seven mosaic resistance QTLs were located to the SNP genetic map, each QTL accounted for 3.57% ~ 17.10% of the phenotypic variation explained (PVE). Furthermore, 110 pathogen response genes and 69 transcription factors were identified in the QTLs interval. The expression levels of nine genes (Soffic.07G0015370-1P, Soffic.09G0015410-2T, Soffic.09G0016460-1T, Soffic.09G0016460-1P, Soffic.09G0017080-3C, Soffic.09G0018730-3P, Soffic.09G0018730-3C, Soffic.09G0019920-3C and Soffic.03G0019710-2C) were significantly different between resistant and susceptible progenies, indicating their key roles in sugarcane resistance to SCMV and SrMV infection. The seven QTLs and nine genes can provide a certain scientific reference to help sugarcane breeders develop varieties resistant to mosaic diseases.

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