Resequencing of Capsicum annuum parental lines (YCM334 and Taean) for the genetic analysis of bacterial wilt resistance

Development of a 45K pepper GBTS liquid-phase gene chip and its application in genome-wide association studies

Introduction

Pepper (Capsicum spp.) is a vegetable that is cultivated globally and has undergone extensive domestication, leading to a significant diversification in its agronomic traits. With the advancement of genomics in pepper and the reduction in sequencing costs, the high-throughput detection of single nucleotide polymorphisms (SNPs) and small insertions-deletions (indels) has become increasingly critical for analyzing pepper germplasms and improving breeding programs. As a result, there is a pressing need for a cost-effective, high-throughput, and versatile technique suitable for both foreground and background selection in pepper breeding.

Methods

In the present study, Python-based web scraping scripts were utilized to systematically extract data from published literatures and relevant sequence databases focusing on pepper genomes. Subsequent to data extraction, SNPs and indels were meticulously identified and filtered. This process culminated in the delineation of core polymorphic sites, which were instrumental in the development of specific probes. Following this, comprehensive phenotypic and genotypic analyses were conducted on a diverse collection of 420 pepper germplasms. Concurrently, a genome-wide association study (GWAS) was conducted to elucidate the genetic determinants of helical fruit shape in peppers.

Results

In this study, a 45K pepper Genotyping-By-Target-Sequencing (GBTS) liquid-phase gene chip was developed on the GenoBaits platform. This chip is composed of 45,389 probes, of which 42,535 are derived from core polymorphic sites (CPS) in the background genetic landscape, while 2,854 are associated with foreground agronomic traits, spanning across 43 traits. The CPS probes are spaced at an average interval of 68 Kb. We have assessed the performance of this chip on 420 pepper germplasms, with successful capture of target DNA fragments by 45,387 probes. Furthermore, the probe capture ratio surpassed 70% in 410 of the 420 germplasms tested. Using this chip, we have efficiently genotyped 273 germplasms for spiciness levels and elucidated the genetic relationships among 410 pepper germplasms. Our results allowed for precise clustering of sister lines and C. chinense germplasms. In addition, through a GWAS for helical fruit shape, we identified three quantitative trait loci (QTLs): heli2.1, heli11.1, and heli11.2. Within the heli11.1 QTL, a gene encoding the tubulin alpha chain was identified, suggesting its potential role in the helical growth pattern of pepper fruits.

Discussion

In summary, the 45K pepper GBTS liquid-phase gene chip offers robust detection of polymorphic sites and is a promising tool for advancing research into pepper germplasm and the breeding of new pepper varieties.

Development and validation of KASP markers for resistance to Phytophthora capsici in Capsicum annuum L

Resistance of Capsicum annuum to Phytophthora blight is dependent on the genetic background of the resistance source and the Phytophthora capsici isolate, which poses challenges for development of generally applicable molecular markers for marker-assisted selection. In this study, the resistance to P. capsici of C. annuum was genetically mapped to chromosome 5 within a 1.68-Mb interval by genome-wide association study analysis of 237 accessions. In this candidate region, 30 KASP markers were developed using genome resequencing data for a P. capsici-resistant line (0601 M) and a susceptible line (77,013). Seven of these KASP markers, located in the coding region of a probable leucine-rich repeats receptor-like serine/threonine-protein kinase gene (Capana05g000704), were validated in the 237 accessions, which showed an average accuracy of 82.7%. The genotyping of the seven KASP markers strongly corresponded with the phenotype of 42 individual plants in a pedigree family (PC83-163) developed from the P. capsici-resistant line CM334. This research provides a set of efficient and high-throughput KASP markers for marker-assisted selection of resistance to P. capsici in C. annuum.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01367-3.

Whole-genome resequencing reveals genomic footprints of Italian sweet and hot pepper heirlooms giving insight into genes underlying key agronomic and qualitative traits

BACKGROUND

Pepper is a major crop species of the Solanaceae family, largely appreciated for its high nutritional and healthy contribution to human diets. In the Mediterranean basin, the favorable pedoclimatic conditions enhanced the selection of several diversified landraces cultivated pepper (Capsicum annuum), for whom Italy can be considered a main pole of diversification. Hence, a survey of traditional C. annuum genetic resources is essential for deep understanding of such diversity and for applications in genomics assisted breeding. Here, we report whole-genome resequencing analyses of two sweet and two pungent genotypes highly diffused in South Italy and representative of the variability for shape, colour and nutritional properties.

RESULTS

The four genomes were reconstructed at a chromosomal scale using a reference-guided approach, based on a dataset of 2.6 billion paired-end reads, corresponding to 20× genome coverage and a mapping rate above 99% for a final genomes size of approximately 3 Gb. After five iterations of variant calling, a total of 29,258,818 single nucleotide polymorphisms (SNPs) and 1,879,112 InDels, were identified. Substantial differences were observed among the four genomes based on geographical origin, with chromosomes 9 and 11 showing more polymorphisms in the accessions with higher fruit weight and absence of pungency. Among the identified variants, a small private indel (T - > TA) shared between sweet and big fruits accessions induces a frameshift with the generation of a new stop codon in a gene annotated as extensin, whereas two private SNPs within hot types were identified in 1-aminocyclopropane-1-carboxylate oxidase (ACO), a key gene involved in fruit ripening. The estimation of repetitive elements highlights a preponderant presence of Long Terminal Repeats (LTRs), the majority of which belonged to Gypsy superfamily. By comparing the four genomes with publicly available references including 'CM334' and Zunla-1 highlight the presence of 49,475 shared gene families.

CONCLUSIONS

The new genomic sequences aim to enrich the whole genome information of pepper local varieties, providing a valuable tool for precision gene mapping, marker discovery, comparative studies. Such knowledge widens the frontiers to understand the selection history of Italian pepper landraces toward the recognition of specificity local agri-food products marks.

Whole-genome resequencing of Coffea arabica L. (Rubiaceae) genotypes identify SNP and unravels distinct groups showing a strong geographical pattern

BACKGROUND

Coffea arabica L. is an economically important agricultural crop and the most popular beverage worldwide. As a perennial crop with recalcitrant seed, conservation of the genetic resources of coffee can be achieved through the complementary approach of in-situ and ex-situ field genebank. In Ethiopia, a large collection of C. arabica L. germplasm is preserved in field gene banks. Here, we report the whole-genome resequencing of 90 accessions from Choche germplasm bank representing garden and forest-based coffee production systems using Illumina sequencing technology.

RESULTS

The genome sequencing generated 6.41 billion paired-end reads, with a mean of 71.19 million reads per sample. More than 93% of the clean reads were mapped onto the C. arabica L. reference genome. A total of 11.08 million variants were identified, among which 9.74 million (87.9%) were SNPs (Single nucleotide polymorphisms) and 1.34 million (12.1%) were InDels. In all accessions, genomic variants were unevenly distributed across the coffee genome. The phylogenetic analysis using the SNP markers displayed distinct groups.

CONCLUSIONS

Resequencing of the coffee accessions has allowed identification of genetic markers, such as SNPs and InDels. The SNPs discovered in this study might contribute to the variation in important pathways of genes for important agronomic traits such as caffeine content, yield, disease, and pest in coffee. Moreover, the genome resequencing data and the genetic markers identified from 90 accessions provide insight into the genetic variation of the coffee germplasm and facilitate a broad range of genetic studies.

QTL Mapping of Resistance to Bacterial Wilt in Pepper Plants (Capsicum annuum) Using Genotyping-by-Sequencing (GBS)

Bacterial wilt (BW) disease, which is caused by Ralstonia solanacearum, is one globally prevalent plant disease leading to significant losses of crop production and yield with the involvement of a diverse variety of monocot and dicot host plants. In particular, the BW of the soil-borne disease seriously influences solanaceous crops, including peppers (sweet and chili peppers), paprika, tomatoes, potatoes, and eggplants. Recent studies have explored genetic regions that are associated with BW resistance for pepper crops. However, owing to the complexity of BW resistance, the identification of the genomic regions controlling BW resistance is poorly understood and still remains to be unraveled in the pepper cultivars. In this study, we performed the quantitative trait loci (QTL) analysis to identify genomic loci and alleles, which play a critical role in the resistance to BW in pepper plants. The disease symptoms and resistance levels for BW were assessed by inoculation with R. solanacearum. Genotyping-by-sequencing (GBS) was utilized in 94 F2 segregating populations originated from a cross between a resistant line, KC352, and a susceptible line, 14F6002-14. A total of 628,437 single-nucleotide polymorphism (SNP) was obtained, and a pepper genetic linkage map was constructed with putative 1550 SNP markers via the filtering criteria. The linkage map exhibited 16 linkage groups (LG) with a total linkage distance of 828.449 cM. Notably, QTL analysis with CIM (composite interval mapping) method uncovered pBWR-1 QTL underlying on chromosome 01 and explained 20.13 to 25.16% by R2 (proportion of explained phenotyphic variance by the QTL) values. These results will be valuable for developing SNP markers associated with BW-resistant QTLs as well as for developing elite BW-resistant cultivars in pepper breeding programs.

Transcriptome-Based Identification and Functional Characterization of NAC Transcription Factors Responsive to Drought Stress in Capsicum annuum L

Capsicum annuum L. is one of the most cultivated Solanaceae species, and in the open field, water limitation leading to drought stress affects its fruit quality, fruit setting, fruit size and ultimately yield. We identified stage-specific and a common core set of differentially expressed genes, following RNA-seq transcriptome analyses of a breeding line subjected to acute drought stress followed by recovery (rewatering), at three stages of plant development. Among them, two NAC transcription factor (TF) genes, i.e., CaNAC072 and CaNAC104, were always upregulated after drought stress and downregulated after recovery. The two TF proteins were observed to be localized in the nucleus following their transient expression in Nicotiana benthamiana leaves. The expression of the two NACs was also induced by NaCl, polyethylene glycol (PEG) and abscisic acid (ABA) treatments, suggesting that CaNAC072 is an early, while CaNAC104 is a late abiotic stress-responsive gene. Virus-induced gene silencing (VIGS) of CaNAC104 did not affect the pepper plantlet’s tolerance to drought stress, while VIGS of CaNAC072 increased drought tolerance. Heterologous expression of CaNAC072 in Arabidopsis thaliana as well as in plants mutated for its homolog ANAC072 did not increase drought stress tolerance. This highlights a different role of the two NAC homologs in the two species. Here, we discuss the complex role of NACs as transcriptional switches in the response to drought stress in bell pepper.

Genetic Diversity and Genome-Wide Association Study of Seed Aspect Ratio Using a High-Density SNP Array in Peanut (Arachis hypogaea L.)

Peanut (Arachis hypogaea L.) is one of the important oil crops of the world. In this study, we aimed to evaluate the genetic diversity of 384 peanut germplasms including 100 Korean germplasms and 284 core collections from the United States Department of Agriculture (USDA) using an Axiom_Arachis array with 58K single-nucleotide polymorphisms (SNPs). We evaluated the evolutionary relationships among 384 peanut germplasms using a genome-wide association study (GWAS) of seed aspect ratio data processed by ImageJ software. In total, 14,030 filtered polymorphic SNPs were identified from the peanut 58K SNP array. We identified five SNPs with significant associations to seed aspect ratio on chromosomes Aradu.A09, Aradu.A10, Araip.B08, and Araip.B09. AX-177640219 on chromosome Araip.B08 was the most significantly associated marker in GAPIT and Regularization method. Phosphoenolpyruvate carboxylase (PEPC) was found among the eleven genes within a linkage disequilibrium (LD) of the significant SNPs on Araip.B08 and could have a strong causal effect in determining seed aspect ratio. The results of the present study provide information and methods that are useful for further genetic and genomic studies as well as molecular breeding programs in peanuts.

Recalibration of mapping quality scores in Illumina short-read alignments improves SNP detection results in low-coverage sequencing data

Background

Low-coverage sequencing is a cost-effective way to obtain reads spanning an entire genome. However, read depth at each locus is low, making sequencing error difficult to separate from actual variation. Prior to variant calling, sequencer reads are aligned to a reference genome, with alignments stored in Sequence Alignment/Map (SAM) files. Each alignment has a mapping quality (MAPQ) score indicating the probability a read is incorrectly aligned. This study investigated the recalibration of probability estimates used to compute MAPQ scores for improving variant calling performance in single-sample, low-coverage settings.

Materials and Methods

Simulated tomato, hot pepper and rice genomes were implanted with known variants. From these, simulated paired-end reads were generated at low coverage and aligned to the original reference genomes. Features extracted from the SAM formatted alignment files for tomato were used to train machine learning models to detect incorrectly aligned reads and output estimates of the probability of misalignment for each read in all three data sets. MAPQ scores were then re-computed from these estimates. Next, the SAM files were updated with new MAPQ scores. Finally, Variant calling was performed on the original and recalibrated alignments and the results compared.

Results

Incorrectly aligned reads comprised only 0.16% of the reads in the training set. This severe class imbalance required special consideration for model training. The F1 score for detecting misaligned reads ranged from 0.76 to 0.82. The best performing model was used to compute new MAPQ scores. Single Nucleotide Polymorphism (SNP) detection was improved after mapping score recalibration. In rice, recall for called SNPs increased by 5.2%, while for tomato and pepper it increased by 3.1% and 1.5%, respectively. For all three data sets the precision of SNP calls ranged from 0.91 to 0.95, and was largely unchanged both before and after mapping score recalibration.

Conclusion

Recalibrating MAPQ scores delivers modest improvements in single-sample variant calling results. Some variant callers operate on multiple samples simultaneously. They exploit every sample’s reads to compensate for the low read-depth of individual samples. This improves polymorphism detection and genotype inference. It may be that small improvements in single-sample settings translate to larger gains in a multi-sample experiment. A study to investigate this is ongoing.

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

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.

Construction, characteristics and high throughput molecular screening methodologies in some special breeding populations: a horticultural perspective

Advanced marker technologies are widely used for evaluation of genetic diversity in cultivated crops, wild ancestors, landraces or any special plant genotypes. Developing agricultural cultivars requires the following steps: (i) determining desired characteristics to be improved, (ii) screening genetic resources to help find a superior cultivar, (iii) intercrossing selected individuals, (iv) generating genetically hybrid populations and screening them for agro-morphological or molecular traits, (v) evaluating the superior cultivar candidates, (vi) testing field performance at different locations, and (vii) certifying. In the cultivar development process valuable genes can be identified by creating special biparental or multiparental populations and analysing their association using suitable markers in given populations. These special populations and advanced marker technologies give us a deeper knowledge about the inherited agronomic characteristics. Unaffected by the changing environmental conditions, these provide a higher understanding of genome dynamics in plants. The last decade witnessed new applications for advanced molecular techniques in the area of breeding,with low costs per sample. These, especially, include next-generation sequencing technologies like reduced representation genome sequencing (genotyping by sequencing, restriction site-associated DNA). These enabled researchers to develop new markers, such as simple sequence repeat and single- nucleotide polymorphism, for expanding the qualitative and quantitative information onpopulation dynamics. Thus, the knowledge acquired from novel technologies is a valuable asset for the breeding process and to better understand the population dynamics, their properties, and analysis methods.

A MYB transcription factor is a candidate to control pungency in Capsicum annuum

Identification of a novel pungency-controlling gene Pun3, which acts as a master regulator of capsaicinoid biosynthetic genes in Capsicum annuum. Capsaicinoid is a unique compound that gives hot peppers (Capsicum spp.) their spicy taste. The Pun1 and Pun2 loci are known to control pungency in Capsicum species. Whereas Pun1 encodes an acyltransferase, the identity of Pun2 is currently unknown. Here, we used recombinant inbred lines and F₂ plants derived from a cross between the non-pungent C. annuum accession 'YCM334' and the pungent C. annuum cultivar 'Tean' to identify a novel non-pungency locus. Inheritance studies showed that non-pungency in C. annuum 'YCM334' is controlled by a single recessive gene, which we named Pun3. Using a high-density SNP map derived from genotyping-by-sequencing, Pun3 was mapped to chromosome 7. By comparing physical information about the Pun3 region in the C. annuum 'Zunla-1' and C. chinense 'PI159236' reference genomes, we identified candidate genes in this target region. One cDNA sequence from 'PI159236' was homologous to an unannotated gene in 'Zunla-1.' This sequence was also homologous to CaMYB31, which is expressed only in 'Tean' and harbors one stop codon in the non-pungent accession 'YCM334.' RNA-Seq analysis showed that major structural genes in the capsaicinoid biosynthetic pathway were significantly downregulated in 'YCM334' compared to pungent pepper. Therefore, CaMYB31 is a candidate gene for Pun3, which may act as a master regulator of capsaicinoid biosynthetic genes in pepper.

Translational genomics and multi-omics integrated approaches as a useful strategy for crop breeding

Recent next generation sequencing-driven mass production of genomic data and multi-omics-integrated approaches have significantly contributed to broadening and deepening our knowledge on the molecular system of living organisms. Accordingly, translational genomics (TG) approach can play a pivotal role in creating an informational bridge between model systems and relatively less studied plants. This review focuses mainly on addressing recent advancement in omics-related technologies, a diverse array of bioinformatic resources and potential applications of TG for the crop breeding. To accomplish above objectives, information on omics data production, various DBs and high throughput technologies was collected, integrated, and used to analyze current status and future perspectives towards omics-assisted crop breeding. Various omics data and resources have been organized and integrated into the databases and/or bioinformatic infrastructures, and thereby serve as the ome's information center for cross-genome translation of biological data. Although the size of accumulated omics data and availability of reference genomes are different among plant families, translational approaches have been actively progressing to access particular biological characteristics. When multi-layered omics data are integrated in a synthetic manner, it will allow providing a stereoscopic view of dynamic molecular behavior and interacting networks of genes occurring in plants. Consequently, TG approach will lead us to broader and deeper insights into target traits for the plant breeding. Furthermore, such systems approach will renovate conventional breeding programs and accelerate precision crop breeding in the future.

RNA-Seq-derived identification of differential transcription in the eggplant (Solanum melongena) following inoculation with bacterial wilt

Eggplant (Solanum melongena) is a major vegetable crop worldwide. However, it is susceptible to bacterial wilt (BW) caused by Ralstonia solanacearum, which has become an important factor limiting eggplant yield and quality. The underlying mechanism of BW remains unknown. Here, RNA-sequencing was used to characterize the transcriptomes of resistant (R) and susceptible (S) strains before (R0, S0) and after (R1, S1) R. solanacearum inoculation. After the removal of low-quality sequences and assembly, 125,852 contigs, 122,508 transcripts, and 68,792 unigenes were identified, with 51,165 non-redundant unigenes annotated. Functional annotations were provided for 11,039 unigenes using four databases (NCBI Nr, Swissprot, KEGG and COG database). A total of 1137 and 9048 genes were found to be up- and down-regulated, respectively, in R0 relative to R1 samples, with 738 and 217 up- and down-regulated in S0 relative to R0 samples, 6087 and 5832 up- and down-regulated in S0 relative to S1 samples, and 4712 and 12,523 up- and down-regulated in S1 relative to R1 samples, respectively. In conclusion, our results provide useful insights into the potential mechanism of BW and are an important basis for further analysis.

Mapping and screening of the tomato Stemphylium lycopersici resistance gene, Sm, based on bulked segregant analysis in combination with genome resequencing

BACKGROUND

Tomato gray leaf spot disease caused by Stemphylium lycopersici (S. lycopersici) is considered one of the major diseases of cultivated tomatoes. The only S. lycopersici resistance gene, Sm, was derived from the wild tomato species S. pimpinellifolium. Sm has been identified as an effective source of gray leaf spot resistance in tomatoes and has been mapped to tomato chromosome 11. In this study, the first bulked segregant analysis (BSA) combined with genome resequencing for the mapping and screening of the Sm candidate gene was performed.

RESULTS

Based on the resequencing results, we identified 50,968 Diff-markers, most of which were distributed on chromosome 11. A total of 37 genes were located in the interval of 0.26-Mb. The gene loci of resistant and susceptible lines were sequenced successfully using PCR products. The relative expression levels of candidate genes in resistant and susceptible lines were confirmed via qRT-PCR, Solyc11g011870.1.1 and Solyc11g011880.1.1 were identified through qRT-PCR. A marker, D5, which was cosegregated with the resistant locus, was identified according to the mutation of the Solyc11g011880.1.1 trait in the resistant line.

CONCLUSIONS

The Sm gene was mapped to the short arm of chromosome 11. The candidate genes Solyc11g011870.1.1 and Solyc11g011880.1.1 displayed expression patterns related to the resistance response. This study will be valuable for Sm cloning and Sm gene breeding in tomato.