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.

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

Horticulturae ◽  
2021 ◽  
Vol 7 (8) ◽  
pp. 227
Author(s):  
Dennis N. Lozada ◽  
Madelin Whelpley ◽  
Andrea Acuña-Galindo
Keyword(s):  
Qtl Analysis ◽  
Genetic Architecture ◽  
Meta Analysis ◽  
Phytophthora Capsici ◽  
Chile Pepper ◽  
Resistant Lines ◽  
Capsicum Spp ◽  
Allele Specific ◽  
Chile Peppers ◽  
Genomic Regions

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). Meta-QTL analysis for different traits in chile peppers (Capsicum spp.) 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 P5 meta-QTL revealed functions related to histone methylation and demethylation, indicating the potential role of epigenetics for P. capsici resistance. Allele-specific markers for the meta-QTL will be developed and validated 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.

scholarly journals Single Nucleotide Polymorphisms Reveal Genetic Diversity in New Mexican Chile Peppers (Capsicum Spp.) 

2021 ◽  
Author(s):  
Dennis N. Lozada ◽  
Madhav Bhatta ◽  
Danise Coon ◽  
Paul W. Bosland
Keyword(s):  
Genetic Diversity ◽  
New Mexico ◽  
Genetic Improvement ◽  
The United States ◽  
Snp Markers ◽  
Single Nucleotide ◽  
Chile Pepper ◽  
New Mexican ◽  
Selection For ◽  
Chile Peppers

Abstract Background: Chile peppers (Capsicum spp.) are among the most important horticultural crops in the world due to their number of uses. They are considered a major cultural and economic crop in the state of New Mexico in the United States. Evaluating genetic diversity in current New Mexican germplasm would facilitate genetic improvement for different traits. This study assessed genetic diversity, population structure, and linkage disequilibrium (LD) among 165 chile pepper genotypes using single nucleotide polymorphism (SNP) markers derived from genotyping-by-sequencing (GBS). Results: A GBS approach identified 66,750 high-quality SNP markers with known map positions distributed across the 12 chromosomes of Capsicum. Principal components analysis revealed four distinct clusters based on species. Neighbor-joining phylogenetic analysis among New Mexico State University (NMSU) chile pepper varieties showed two main clusters, where the C. annuum genotypes grouped together based on fruit or pod type. A Bayesian clustering approach for the Capsicum population inferred K= 2 as the optimal number of clusters, where the C. chinense and C. frutescens grouped in a single cluster. Analysis of molecular variance revealed majority of variation to be between the Capsicum species (76.08%). Extensive LD decay (~5.59 Mb) across the whole Capsicum population was observed, demonstrating that a lower number of markers would be required for implementing genomewide association studies for different traits in New Mexican type chile peppers. Tajima’s D values demonstrated positive selection, population bottleneck, and balancing selection for the New Mexico Capsicum population. Genetic diversity for the New Mexican chile peppers was relatively low, indicating the need to introduce new alleles in the breeding program to broaden the genetic base of current germplasm. Conclusions: Analysis of genetic diversity among New Mexican chile peppers were evaluated using GBS-derived SNP markers and genetic relatedness on the species level was observed. Introducing novel alleles from other breeding programs or from wild species could help increase diversity in current germplasm. We present valuable information for future association mapping and genomic selection for different traits for New Mexican chile peppers for genetic improvement through marker-assisted breeding.

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 Single nucleotide polymorphisms reveal genetic diversity in New Mexican chile peppers (Capsicum spp.)

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Dennis N. Lozada ◽  
Madhav Bhatta ◽  
Danise Coon ◽  
Paul W. Bosland
Keyword(s):  
Genetic Diversity ◽  
New Mexico ◽  
Genetic Improvement ◽  
The United States ◽  
Snp Markers ◽  
Single Nucleotide ◽  
Chile Pepper ◽  
New Mexican ◽  
Selection For ◽  
Chile Peppers

Abstract Background Chile peppers (Capsicum spp.) are among the most important horticultural crops in the world due to their number of uses. They are considered a major cultural and economic crop in the state of New Mexico in the United States. Evaluating genetic diversity in current New Mexican germplasm would facilitate genetic improvement for different traits. This study assessed genetic diversity, population structure, and linkage disequilibrium (LD) among 165 chile pepper genotypes using single nucleotide polymorphism (SNP) markers derived from genotyping-by-sequencing (GBS). Results A GBS approach identified 66,750 high-quality SNP markers with known map positions distributed across the 12 chromosomes of Capsicum. Principal components analysis revealed four distinct clusters based on species. Neighbor-joining phylogenetic analysis among New Mexico State University (NMSU) chile pepper cultivars showed two main clusters, where the C. annuum genotypes grouped together based on fruit or pod type. A Bayesian clustering approach for the Capsicum population inferred K = 2 as the optimal number of clusters, where the C. chinense and C. frutescens grouped in a single cluster. Analysis of molecular variance revealed majority of variation to be between the Capsicum species (76.08 %). Extensive LD decay (~ 5.59 Mb) across the whole Capsicum population was observed, demonstrating that a lower number of markers would be required for implementing genome wide association studies for different traits in New Mexican type chile peppers. Tajima’s D values demonstrated positive selection, population bottleneck, and balancing selection for the New Mexico Capsicum population. Genetic diversity for the New Mexican chile peppers was relatively low, indicating the need to introduce new alleles in the breeding program to broaden the genetic base of current germplasm. Conclusions Genetic diversity among New Mexican chile peppers was evaluated using GBS-derived SNP markers and genetic relatedness on the species level was observed. Introducing novel alleles from other breeding programs or from wild species could help increase diversity in current germplasm. We present valuable information for future association mapping and genomic selection for different traits for New Mexican chile peppers for genetic improvement through marker-assisted breeding.

A field evaluation of jalapeño and non-jalapeño chile pepper resistance to Phytophthora blight caused by Phytophthora capsici

2021 ◽  
Author(s):  
Srijana Dura ◽  
Phillip A Lujan ◽  
Ivette Guzman ◽  
Robert Steiner ◽  
Soum Sanogo
Keyword(s):  
Disease Incidence ◽  
Phytophthora Capsici ◽  
Field Evaluation ◽  
Severity Index ◽  
Vegetable Crops ◽  
Phytophthora Blight ◽  
Inoculum Level ◽  
Chile Pepper ◽  
Progress Curve ◽  
Stage Disease

Phytophthora capsici is a destructive soilborne pathogen, which causes Phytophthora blight in many vegetable crops including chile pepper (Capsicum sp.). Our research was aimed at evaluating the resistance of jalapeño cultivars in field conditions and identifying the factors associated with reduction of Phytophthora blight caused by P. capsici. Six jalapeño (NuMex Orange Spice, NuMex Pumpkin Spice, NuMex Jalmundo, TAM Jalapeño, Early Jalapeño, and NuMex Vaquero) and two non-jalapeño (CM-334 and NM 6-4) cultivars were inoculated with P. capsici at the fruiting stage. Disease severity index (DSI), disease incidence (DI), and area under the disease progress curve (AUDPC) for each cultivar were measured. The most susceptible jalapeño cultivars with the highest DSI, DI, and AUDPC were NuMex Orange Spice, NuMex Jalmundo and NuMex Pumpkin Spice, whereas the least susceptible jalapeño cultivars were Early Jalapeño, TAM Jalapeño, and NuMex Vaquero, with the lowest DSI, DI, and AUDPC. The identified jalapeños with reduced susceptibility to Phytophthora blight can be planted in infested fields, combined with other control methods which may help in soil disinfestation by reducing the inoculum level in soil over time.

scholarly journals A meta-analysis of genome-wide association studies for average daily gain and lean meat percentage in two Duroc pig populations

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Shenping Zhou ◽  
Rongrong Ding ◽  
Fanming Meng ◽  
Xingwang Wang ◽  
Zhanwei Zhuang ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Growth And Development ◽  
Genetic Architecture ◽  
Association Studies ◽  
Meta Analysis ◽  
Average Daily Gain ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Daily Gain

Abstract Background Average daily gain (ADG) and lean meat percentage (LMP) are the main production performance indicators of pigs. Nevertheless, the genetic architecture of ADG and LMP is still elusive. Here, we conducted genome-wide association studies (GWAS) and meta-analysis for ADG and LMP in 3770 American and 2090 Canadian Duroc pigs. Results In the American Duroc pigs, one novel pleiotropic quantitative trait locus (QTL) on Sus scrofa chromosome 1 (SSC1) was identified to be associated with ADG and LMP, which spans 2.53 Mb (from 159.66 to 162.19 Mb). In the Canadian Duroc pigs, two novel QTLs on SSC1 were detected for LMP, which were situated in 3.86 Mb (from 157.99 to 161.85 Mb) and 555 kb (from 37.63 to 38.19 Mb) regions. The meta-analysis identified ten and 20 additional SNPs for ADG and LMP, respectively. Finally, four genes (PHLPP1, STC1, DYRK1B, and PIK3C2A) were detected to be associated with ADG and/or LMP. Further bioinformatics analysis showed that the candidate genes for ADG are mainly involved in bone growth and development, whereas the candidate genes for LMP mainly participated in adipose tissue and muscle tissue growth and development. Conclusions We performed GWAS and meta-analysis for ADG and LMP based on a large sample size consisting of two Duroc pig populations. One pleiotropic QTL that shared a 2.19 Mb haplotype block from 159.66 to 161.85 Mb on SSC1 was found to affect ADG and LMP in the two Duroc pig populations. Furthermore, the combination of single-population and meta-analysis of GWAS improved the efficiency of detecting additional SNPs for the analyzed traits. Our results provide new insights into the genetic architecture of ADG and LMP traits in pigs. Moreover, some significant SNPs associated with ADG and/or LMP in this study may be useful for marker-assisted selection in pig breeding.

scholarly journals Exome Chip Meta-analysis Fine Maps Causal Variants and Elucidates the Genetic Architecture of Rare Coding Variants in Smoking and Alcohol Use

2019 ◽  
Vol 85 (11) ◽  
pp. 946-955 ◽  
Author(s):  
David M. Brazel ◽  
Yu Jiang ◽  
Jordan M. Hughey ◽  
Valérie Turcot ◽  
Xiaowei Zhan ◽  
...  
Keyword(s):  
Alcohol Use ◽  
Genetic Architecture ◽  
Meta Analysis ◽  
Causal Variants ◽  
Coding Variants ◽  
Exome Chip

scholarly journals Genetic markers of ADHD-related variations in intracranial volume

2017 ◽  
Author(s):  
Marieke Klein ◽  
Raymond K. Walters ◽  
Ditte Demontis ◽  
Jason L. Stein ◽  
Derrek P. Hibar ◽  
...  
Keyword(s):  
Genetic Architecture ◽  
Meta Analysis ◽  
Neurodevelopmental Disorder ◽  
Structure And Function ◽  
Intracranial Volume ◽  
Biological Mechanisms ◽  
Brain Volumes ◽  
Hyperactivity Disorder ◽  
Genetic Overlap ◽  
And Function

ABSTRACTAttention-Deficit/Hyperactivity Disorder (ADHD) is a common and highly heritable neurodevelopmental disorder with a complex pathophysiology, where genetic risk is hypothesized to be mediated by alterations in structure and function of diverse brain networks. We tested one aspect of this hypothesis by investigating the genetic overlap between ADHD (n=55,374) and (mainly subcortical) brain volumes (n=11,221-24,704), using the largest publicly available studies. At the level of common variant genetic architecture, we discovered a significant negative genetic correlation between ADHD and intracranial volume (ICV). Meta-analysis of individual variants found significant loci associated with both ADHD risk and ICV; additional loci were identified for ADHD and amygdala, caudate nucleus, and putamen volumes. Gene-set analysis in the ADHD-ICV meta-analytic data showed significant association with variation in neurite outgrowth-related genes. In summary, our results suggest new hypotheses about biological mechanisms involved in ADHD etiology and highlight the need to study additional brain parameters.

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