scholarly journals Genomic regions and candidate genes linked with Phytophthora capsici root rot resistance in chile pepper (Capsicum annuum L.)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Dennis N. Lozada ◽  
Guillermo Nunez ◽  
Phillip Lujan ◽  
Srijana Dura ◽  
Danise Coon ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Root Rot ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Phytophthora Capsici ◽  
Snp Markers ◽  
Chile Pepper ◽  
Phytophthora Root Rot ◽  
Genomic Regions

Abstract Background Phytophthora root rot, caused by Phytophthora capsici, is a major disease affecting Capsicum production worldwide. A recombinant inbred line (RIL) population derived from the hybridization between ‘Criollo de Morellos-334’ (CM-334), a resistant landrace from Mexico, and ‘Early Jalapeno’, a susceptible cultivar was genotyped using genotyping-by-sequencing (GBS)-derived single nucleotide polymorphism (SNP) markers. A GBS-SNP based genetic linkage map for the RIL population was constructed. Quantitative trait loci (QTL) mapping dissected the genetic architecture of P. capsici resistance and candidate genes linked to resistance for this important disease were identified. Results Development of a genetic linkage map using 1,973 GBS-derived polymorphic SNP markers identified 12 linkage groups corresponding to the 12 chromosomes of chile pepper, with a total length of 1,277.7 cM and a marker density of 1.5 SNP/cM. The maximum gaps between consecutive SNP markers ranged between 1.9 (LG7) and 13.5 cM (LG5). Collinearity between genetic and physical positions of markers reached a maximum of 0.92 for LG8. QTL mapping identified genomic regions associated with P. capsici resistance in chromosomes P5, P8, and P9 that explained between 19.7 and 30.4% of phenotypic variation for resistance. Additive interactions between QTL in chromosomes P5 and P8 were observed. The role of chromosome P5 as major genomic region containing P. capsici resistance QTL was established. Through candidate gene analysis, biological functions associated with response to pathogen infections, regulation of cyclin-dependent protein serine/threonine kinase activity, and epigenetic mechanisms such as DNA methylation were identified. Conclusions Results support the genetic complexity of the P. capsici–Capsicum pathosystem and the possible role of epigenetics in conferring resistance to Phytophthora root rot. Significant genomic regions and candidate genes associated with disease response and gene regulatory activity were identified which allows for a deeper understanding of the genomic landscape of Phytophthora root rot resistance in chile pepper.

scholarly journals Genetic Analysis of Phytophthora Root Rot Race-specific Resistance in Chile Pepper

2008 ◽  
Vol 133 (6) ◽  
pp. 825-829 ◽  
Author(s):  
Ariadna Monroy-Barbosa ◽  
Paul W. Bosland
Keyword(s):  
Root Rot ◽  
Recombinant Inbred Lines ◽  
Single Gene ◽  
Phytophthora Capsici ◽  
Segregation Ratio ◽  
Descent Method ◽  
Chile Pepper ◽  
Phytophthora Root Rot ◽  
Multiple Alleles ◽  
Seven Generations

Phytophthora capsici Leon., causal agent of phytophthora root rot, is one of the most devastating pathogens attacking chile pepper (Capsicum annuum L.) plants. Many studies have tried to better understand phytophthora resistance, but the genetic behavior is not completely understood. To determine if phytophthora root rot resistance in chile pepper is controlled by multiple alleles at a few loci, or multiple genes at different loci, five recombinant inbred lines (RILs) were evaluated. The resistant accession, Criollo de Morelos-334, and the susceptible cultivar, Early Jalapeno, were hybridized to develop multiple RILs. After seven generations of selfing using the single seed descent method, four RILs were selected based on their phenotypic response to inoculation by five P. capsici isolates. The RILs were hybridized to each other to obtain F1 and F2 populations. The F2 populations were inoculated with single and a pair of races of P. capsici. When the F2 populations were inoculated with a single race, ratios of three resistant:one susceptible were obtained in the majority of the populations, indicating the action of an independent single gene. When the F2 populations were inoculated with a combination of two races, segregation ratios of 15 resistant:one susceptible were observed in two populations out of the four populations. The presence of susceptible individuals in all of the F2 population indicates that the resistant genes for the different P. capsici races are located at different loci. However, the rejection of the segregation ratio in one of the F2 population under a single race inoculation and in two of the F2 populations challenged with a combination of two races suggest a linkage phenomenon between some of the R genes. None of the RILs evaluated in this study displayed allelism for phytophthora root rot resistance.

scholarly journals Candidate Genes for the High-Altitude Adaptations of Two Mountain Pine Taxa

2021 ◽  
Vol 22 (7) ◽  
pp. 3477
Author(s):  
Julia Zaborowska ◽  
Bartosz Łabiszak ◽  
Annika Perry ◽  
Stephen Cavers ◽  
Witold Wachowiak
Keyword(s):  
Population Structure ◽  
Candidate Genes ◽  
Genetic Basis ◽  
Redox Homeostasis ◽  
Snp Markers ◽  
Regulation Of Transcription ◽  
Single Nucleotide ◽  
Homeostasis Regulation ◽  
Genomic Regions ◽  
Mountain Plants

Mountain plants, challenged by vegetation time contractions and dynamic changes in environmental conditions, developed adaptations that help them to balance their growth, reproduction, survival, and regeneration. However, knowledge regarding the genetic basis of species adaptation to higher altitudes remain scarce for most plant species. Here, we attempted to identify such corresponding genomic regions of high evolutionary importance in two closely related European pines, Pinus mugo and P. uncinata, contrasting them with a reference lowland relative—P. sylvestris. We genotyped 438 samples at thousands of single nucleotide polymorphism (SNP) markers, tested their genetic differentiation and population structure followed by outlier detection and gene ontology annotations. Markers clearly differentiated the species and uncovered patterns of population structure in two of them. In P. uncinata three Pyrenean sites were grouped together, while two outlying populations constituted a separate cluster. In P. sylvestris, Spanish population appeared distinct from the remaining four European sites. Between mountain pines and the reference species, 35 candidate genes for altitude-dependent selection were identified, including such encoding proteins responsible for photosynthesis, photorespiration and cell redox homeostasis, regulation of transcription, and mRNA processing. In comparison between two mountain pines, 75 outlier SNPs were found in proteins involved mainly in the gene expression and metabolism.

scholarly journals A high-density SNP-based genetic map and several economic traits-related loci in Pelteobagrus vachelli

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Guosong Zhang ◽  
Jie Li ◽  
Jiajia Zhang ◽  
Xia Liang ◽  
Tao Wang ◽  
...  
Keyword(s):  
Sex Determination ◽  
Linkage Map ◽  
Candidate Genes ◽  
Genetic Map ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
High Density ◽  
Hypoxia Tolerance ◽  
Genome Wide ◽  
Pelteobagrus Vachelli

Abstract Background A high-density genetic linkage map is essential for QTL fine mapping, comparative genome analysis, identification of candidate genes and marker-assisted selection in aquaculture species. Pelteobagrus vachelli is a very popular commercial species in Asia. However, some specific characters hindered achievement of the traditional selective breeding based on phenotypes, such as lack of large-scale genomic resource and short of markers tightly associated with growth, sex determination and hypoxia tolerance related traits. Results By making use of 5059 ddRAD markers in P. vachelli, a high-resolution genetic linkage map was successfully constructed. The map’ length was 4047.01 cM by using an interval of 0.11 cm, which is an average marker standard. Comparative genome mapping revealed that a high proportion (83.2%) of markers with a one-to-one correspondence were observed between P. vachelli and P. fulvidraco. Based on the genetic map, 8 significant genome-wide QTLs for 4 weight, 1 body proportion, 2 sex determination, and 1 hypoxia tolerance related traits were detected on 4 LGs. Some SNPs from these significant genome-wide QTLs were observably associated with these phenotypic traits in other individuals by Kompetitive Allele Specific PCR. In addition, two candidate genes for weight, Sipa1 and HSD11B2, were differentially expressed between fast-, medium- and slow-growing P. vachelli. Sema7a, associated with hypoxia tolerance, was induced after hypoxia exposure and reoxygenation. Conclusions We mapped a set of suggestive and significant QTLs as well as candidate genes for 12 growth, 1 sex determination and 1 hypoxia tolerance related traits based on a high-density genetic linkage map by making use of SNP markers for P. fulvidraco. Our results have offered a valuable method about the much more efficient production of all-male, fast growth and hypoxia tolerance P. vachelli for the aquaculture industry.

A microsatellite-based genetic linkage map and putative sex-determining genomic regions in Lake Victoria cichlids

Gene ◽  
2015 ◽  
Vol 560 (2) ◽  
pp. 156-164 ◽  
Author(s):  
Yu Kudo ◽  
Masato Nikaido ◽  
Azusa Kondo ◽  
Hikoyu Suzuki ◽  
Kohta Yoshida ◽  
...  
Keyword(s):  
Linkage Map ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Lake Victoria ◽  
Genomic Regions

scholarly journals A SNP-Based Genetic Linkage Map of Soybean Using the SoySNP6K Illumina Infinium BeadChip Genotyping Array

2017 ◽  
Vol 1 (3) ◽  
pp. 80-89 ◽  
Author(s):  
Masum Akond ◽  
Shiming Liu ◽  
Lauren Schoener ◽  
James A. Anderson ◽  
Stella K. Kantartzi ◽  
...  
Keyword(s):  
Linkage Map ◽  
Genetic Linkage ◽  
Goodness Of Fit ◽  
Genetic Linkage Map ◽  
Agronomic Traits ◽  
Snp Markers ◽  
High Density ◽  
Genotyping Array ◽  
Glycine Max L ◽  
Average Marker Density

This study reports a high density genetic linkage map based on the ‘Maryland 96-5722’ by ‘Spencer’ recombinant inbred line (RIL) population of soybean [Glycine max (L.) Merr.] and constructed exclusively with single nucleotide polymorphism (SNP) markers. The Illumina Infinium SoySNP6K BeadChip genotyping array produced 5,376 SNPs in the mapping population, with a 96.75% success rate. Significant level of goodness-of-fit for each locus was tested based on the observed vs. expected ratio (1:1). Out of 5,376 markers, 1,465 SNPs fit the 1:1 segregation rate having ≤20% missing data plus heterozygosity among the RILs. Among this 1,456 just 657 were polymorphic between the parents DNAs tested. These 657 SNPs were mapped using the JoinMap 4.0 software and 550 SNPs were distributed on 16 linkage groups (LGs) among the 20 chromosomes of the soybean genome. The total map length was just 201.57 centiMorgans (cM) with an average marker density of 0.37 cM. This is one of the high density SNP-based genetic linkage maps of soybean that will be used by the scientific community to map quantitative trait loci (QTL) and identify candidate genes for important agronomic traits in soybean.

scholarly journals A Rapid Technique for Multiple-race Disease Screening of Phytophthora Foliar Blight on Single Capsicum annuum L. Plants

HortScience ◽  
2010 ◽  
Vol 45 (10) ◽  
pp. 1563-1566 ◽  
Author(s):  
Ariadna Monroy-Barbosa ◽  
Paul W. Bosland
Keyword(s):  
Capsicum Annuum ◽  
Root Rot ◽  
Recombinant Inbred Lines ◽  
Phytophthora Capsici ◽  
Pepper Plant ◽  
Phytophthora Blight ◽  
Chile Pepper ◽  
Physiological Races ◽  
Foliar Blight

Phytophthora blight, caused by the oomycete Phytophthora capsici Leon., is a major disease that threatens production and long-term viability of the chile pepper (Capsicum annuum L.) industry. For each phytophthora disease syndrome such as root rot, foliar blight, and stem blight separate and independent resistant systems have evolved in the host. In addition, several physiological races of the pathogen have been identified. A novel, effective, and accurate screening technique is described that allows for multiple races to be evaluated on a single plant of C. annuum. The P. capsici resistant line Criollo de Morelos-334, a susceptible cultivar, Camelot, and three New Mexico Recombinant Inbred Lines, -F, -I, -S, were used to evaluate the new technique for phytophthora foliar blight multiple-race screening. Using three P. capsici physiological races, no interaction among the physiological races was observed with this technique. This novel technique provided a rapid disease screen evaluating multiple physiological races for phytophthora foliar blight resistance in a single chile pepper plant and can assist plant breeders in selecting for disease-resistant plants.

A fine‐scale genetic linkage map reveals genomic regions associated with economic traits in walnut ( Juglans regia )

2019 ◽  
Vol 138 (5) ◽  
pp. 635-646 ◽  
Author(s):  
Mallikarjuna K. Aradhya ◽  
Dianne Velasco ◽  
Ji‐Rui Wang ◽  
Ramesh Ramasamy ◽  
Frank M. You ◽  
...  
Keyword(s):  
Linkage Map ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Juglans Regia ◽  
Fine Scale ◽  
Economic Traits ◽  
Genomic Regions

Genetic Architecture of Chile Pepper (Capsicum Spp.) QTLome Revealed Using Meta-QTL Analysis

2021 ◽  
Author(s):  
Dennis N. Lozada ◽  
Lanie Whelpley ◽  
Andrea Acuña-Galindo
Keyword(s):  
Qtl Analysis ◽  
Genetic Architecture ◽  
Meta Analysis ◽  
Phytophthora Capsici ◽  
Snp Markers ◽  
Vegetable Crops ◽  
Chile Pepper ◽  
Breeding Populations ◽  
Capsicum Spp ◽  
Chile Peppers

Abstract Chile peppers (Capsicum spp.) are among the most important vegetable crops in the world due to their health-related, economic, and industrial uses. In recent years, quantitative trait loci (QTL) mapping approaches have been widely implemented to identify genomic regions affecting variation for different traits for marker-assisted selection (MAS) in peppers. Meta-QTL analysis for different traits in Capsicum remains lacking, and therefore it would be necessary to re-evaluate identified QTL for a more precise MAS for genetic improvement. We report the first known meta-QTL analysis for diverse traits in the chile pepper QTLome. A literature survey using 29 published linkage mapping studies identified 766 individual QTL from five different trait classes. A total of 311 QTL were projected into a consensus map. Meta-analysis identified 30 meta-QTL regions distributed across the 12 chromosomes of Capsicum. MQTL5.1 and MQTL5.2 related to Phytophthora capsici fruit and root rot resistance were delimited to < 1.0 cM confidence intervals in chromosome P5. Candidate gene analysis for the flanking sequences for the P5 meta-QTL revealed biological functions related to DNA repair and transcription regulation. Moreover, epigenetic mechanisms such as histone and RNA methylation and demethylation were predicted, indicating the potential role of epigenetics for P. capsici resistance. Allele specific SNP markers for the meta-QTL will be developed and validated using different breeding populations of Capsicum for MAS of P. capsici resistant lines. Altogether, results from meta-QTL analysis for chile pepper QTLome rendered further insights into the genetic architecture of different traits for this valuable horticultural crop.

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