Mapping of a Novel Race Specific Resistance Gene to Phytophthora Root Rot of Pepper (Capsicum annuum) Using Bulked Segregant Analysis Combined with Specific Length Amplified Fragment Sequencing Strategy

Xu, Xinlan; Chao, Juan; Cheng, Xingwang; Wang, Rui; Sun, Baoshan; Wang, Hengming; Luo, Shuhong; Xu, Xiaogang; Wu, Tianbin; Liu, Ying

doi:10.1371/journal.pone.0151401

Cited by 62 publications

(53 citation statements)

References 45 publications

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“…In the same population was identified the gene CaDMR1 encoding for a homoserine kinase, as the candidate responsible for the major QTL on Chr 5 for resistance to P. capsici [71]. Recently, Bulk Segregant Analysis (BSA) combined with Specific locus amplified fragment sequencing (SLAF-seq) allowed to identify PhR10: a single dominant gene positioned on the long arm of Chr 10 and responsible for the resistance to race 3 (Byl4) [72]. Functional studies reported that cell death was mediated by the increased reactive oxidative species (ROS) production due to the silencing of the methionine sulfoxide reductase B2 gene (CaMsrB2), suggesting that the regulation of pathogen defense responses and oxidative stresses is controlled by ROS accumulation or reduction, respectively [73].…”

Section: Bacterial Spot Of Peppermentioning

confidence: 99%

“…A microsatellite marker (ZL6726) positioned at a distance of 1.5 cM from CaPhyto, was validated to be reliable for selecting phenotypes of resistance to the same P. capsici race. Several other molecular markers associated with resistance to P. capsici have been reported in chile pepper for more rapid selection [51,64,66,68,72,75].…”

Section: Bacterial Spot Of Peppermentioning

confidence: 99%

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Overview of Biotic Stresses in Pepper (Capsicum spp.): Sources of Genetic Resistance, Molecular Breeding and Genomics

Parisi¹,

Alioto

Tripodi³

2020

IJMS

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Pepper (Capsicum spp.) is one of the major vegetable crops grown worldwide largely appreciated for its economic importance and nutritional value. This crop belongs to the large Solanaceae family, which, among more than 90 genera and 2500 species of flowering plants, includes commercially important vegetables such as tomato and eggplant. The genus includes over 30 species, five of which (C. annuum, C. frutescens, C. chinense, C. baccatum, and C. pubescens) are domesticated and mainly grown for consumption as food and for non-food purposes (e.g., cosmetics). The main challenges for vegetable crop improvement are linked to the sustainable development of agriculture, food security, the growing consumers’ demand for food. Furthermore, demographic trends and changes to climate require more efficient use of plant genetic resources in breeding programs. Increases in pepper consumption have been observed in the past 20 years, and for maintaining this trend, the development of new resistant and high yielding varieties is demanded. The range of pathogens afflicting peppers is very broad and includes fungi, viruses, bacteria, and insects. In this context, the large number of accessions of domesticated and wild species stored in the world seed banks represents a valuable resource for breeding in order to transfer traits related to resistance mechanisms to various biotic stresses. In the present review, we report comprehensive information on sources of resistance to a broad range of pathogens in pepper, revisiting the classical genetic studies and showing the contribution of genomics for the understanding of the molecular basis of resistance.

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Section: Bacterial Spot Of Peppermentioning

confidence: 99%

Section: Bacterial Spot Of Peppermentioning

confidence: 99%

Overview of Biotic Stresses in Pepper (Capsicum spp.): Sources of Genetic Resistance, Molecular Breeding and Genomics

Parisi¹,

Alioto

Tripodi³

2020

IJMS

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“…We found two isolate-specific QTL, on chromosomes 10 and 11, associated with two isolates of P. capsici, PWB53 and PWB106, respectively (Table 1). Recently, an isolatespecific single, dominant gene conferring resistance to P. capsici was identified using bulk segregant analysis in a backcross population from CM334 as a resistant source (Xu et al, 2016). This locus was located at the end of long arm of chromosome 10, in a similar location as the QTL from PWB53.…”

Section: Discussionmentioning

confidence: 99%

Genetic Analysis of Resistance to Multiple Isolates of Phytophthora capsici and Linkage to Horticultural Traits in Bell Pepper

Chunthawodtiporn¹,

Hill²,

Stoffel³

et al. 2019

horts

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Phytophthora capsici is one of the major pathogens found in pepper production, especially in bell pepper. Due to the high level of genetic diversity of the pathogen, bell pepper varieties with broad genetic resistance are essential for disease management. Criollo de Morelos – 334 (CM334), a landrace that has a high level of genetic resistance to P. capsici, has been used as the resistant source for P. capsici to generate a recombinant inbred line (RIL) population with the susceptible bell pepper cultivar Maor. From the resulting population, quantitative trait locus (QTL) models explaining resistance to each of four isolates of P. capsici were derived from QTL regions on three chromosomes using stepwiseqtl in R/qtl. A single region of chromosome 5 contained major QTL for resistance to each of the four isolates. Two isolate-specific QTL conferring resistance to isolates PWB53 and PWB106 were located on chromosomes 10 and 11, respectively. Both isolate-specific QTL had epistatic interactions with a major QTL on chromosome 5. Using the pepper reference genome and gene annotation, candidate genes for P. capsici resistance within 1.5-logarithm of odds (LOD) interval were identified. Based on functional annotations derived from Arabidopsis thaliana and solanaceous crop databases, multiple candidate genes related to resistance (R) gene complexes or to plant immune system were found under the QTL on all three chromosomes. A comparison of the locations of resistance QTL and previously identified horticultural QTL using the same population revealed tight linkage between resistance to P. capsici and a stem pubescence QTL o chromosome 10. Both candidate genes for P. capsici resistance and the linkages between resistance and horticultural traits could be applied for selection to broad resistance to P. capsici in bell pepper–breeding programs.

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“…For example, the use of BSA with next-generation sequencing technology, a novel resistance gene Pi65(t) conferring a broad-spectrum resistance to the fungus Magnaporthe oryzae was fine mapped within an interval of 1 Mb [20]. Using BSA combined with the specific-locus amplified fragment sequencing (SLAF-seq) strategy, a single dominant gene PhR10 conferring resistance to the isolate Byl4 ( race 3 ) was fine mapped into an interval of 2.57 Mb [19]. BSA has also been combined with RNA sequencing to rapidly and precisely detect genetic determinants underlying traits of interest [18].…”

Section: Introductionmentioning

confidence: 99%

Genetic architecture of the maize kernel row number revealed by combining QTL mapping using a high-density genetic map and bulked segregant RNA sequencing

et al. 2016

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BackgroundThe maize kernel row number (KRN) is a key component that contributes to grain yield and has high broad-sense heritability (H 2). Quantitative trait locus/loci (QTL) mapping using a high-density genetic map is a powerful approach to detecting loci that are responsible for traits of interest. Bulked segregant ribonucleic acid (RNA) sequencing (BSR-seq) is another rapid and cost-effective strategy to identify QTL. Combining QTL mapping using a high-density genetic map and BSR-seq may dissect comprehensively the genetic architecture underlying the maize KRN.ResultsA panel of 300 F2 individuals derived from inbred lines abe2 and B73 were genotyped using the specific-locus amplified fragment sequencing (SLAF-seq) method. A total of 4,579 high-quality polymorphic SLAF markers were obtained and used to construct a high-density genetic map with a total length of 2,123 centimorgan (cM) and an average distance between adjacent markers of 0.46 cM. Combining the genetic map and KRN of F2 individuals, four QTL (qKRN1, qKRN2, qKRN5, and qKRN8-1) were identified on chromosomes 1, 2, 5, and 8, respectively. The physical intervals of these four QTL ranged from 4.36 Mb for qKRN8-1 to 7.11 Mb for qKRN1 with an average value of 6.08 Mb. Based on high-throughput sequencing of two RNA pools bulked from leaves of plants with extremely high and low KRNs, two QTL were detected on chromosome 8 in the 10–25 Mb (BSR_QTL1) and 60–150 Mb (BSR_QTL2) intervals. According to the physical positions of these QTL, qKRN8-1 was included by BSR_QTL2. In addition, qKRN8-1 was validated using QTL mapping with a recombinant inbred lines population that was derived from inbred lines abe2 and B73.ConclusionsIn this study, we proved that combining QTL mapping using a high-density genetic map and BSR-seq is a powerful and cost-effective approach to comprehensively revealing genetic architecture underlying traits of interest. The QTL for the KRN detected in this study, especially qKRN8-1, can be used for performing fine mapping experiments and marker-assisted selection in maize breeding.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3240-y) contains supplementary material, which is available to authorized users.

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Mapping of a Novel Race Specific Resistance Gene to Phytophthora Root Rot of Pepper (Capsicum annuum) Using Bulked Segregant Analysis Combined with Specific Length Amplified Fragment Sequencing Strategy

Cited by 62 publications

References 45 publications

Overview of Biotic Stresses in Pepper (Capsicum spp.): Sources of Genetic Resistance, Molecular Breeding and Genomics

Overview of Biotic Stresses in Pepper (Capsicum spp.): Sources of Genetic Resistance, Molecular Breeding and Genomics

Genetic Analysis of Resistance to Multiple Isolates of Phytophthora capsici and Linkage to Horticultural Traits in Bell Pepper

Genetic architecture of the maize kernel row number revealed by combining QTL mapping using a high-density genetic map and bulked segregant RNA sequencing

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