Construction of an interspecific genetic map based on InDel and SSR for mapping the QTLs affecting the initiation of flower primordia in pepper (Capsicum spp.)

A Compendium for Novel Marker-Based Breeding Strategies in Eggplant

The worldwide production of eggplant is estimated at about 58 Mt, with China, India and Egypt being the major producing countries. Breeding efforts in the species have mainly focused on increasing productivity, abiotic and biotic tolerance/resistance, shelf-life, the content of health-promoting metabolites in the fruit rather than decreasing the content of anti-nutritional compounds in the fruit. From the literature, we collected information on mapping quantitative trait loci (QTLs) affecting eggplant's traits following a biparental or multi-parent approach as well as genome-wide association (GWA) studies. The positions of QTLs were lifted according to the eggplant reference line (v4.1) and more than 700 QTLs were identified, here organized into 180 quantitative genomic regions (QGRs). Our findings thus provide a tool to: (i) determine the best donor genotypes for specific traits; (ii) narrow down QTL regions affecting a trait by combining information from different populations; (iii) pinpoint potential candidate genes.

Identification of Fruit Traits Related QTLs and a Candidate Gene, CaBRX, Controlling Locule Number in Pepper (Capsicum annuum L.)

Fruit traits are important in pepper (Capsicum annuum L.) and affect its quality and yield. These traits are controlled by quantitative trait loci (QTLs). In this study, we identified many major QTLs that control fruit length (Ftl), fruit diameter (Ftd), fruit shape (Fts), fruit weight (Ftw) and locule number (Lcn) in the F2 and F2:3 populations developed from the QTL mapping of GS6 (P1) and Qiemen (P2). A total of 111 simple sequence repeats and insertion/deletion markers were utilized to construct a linkage map with 12 linkage groups over a length of 1320.72 cM. An inclusive composite interval mapping analysis indicated that many QTLs were detected and included ftl2.1, ftd2.1, fts1.1, ftw2.1 and lcn1.1. As a novel QTL, lcn1.1 was located between HM1112 and EPMS709, and the genetic distance was 3.18 cM covering 60 predicted genes. Within the region, we identified Capana01g004285 as a candidate gene by functional annotation and expression analysis and found that it encodes the BREVIS RADIX (BRX) protein. Knockdown of CaBRX through the virus-induced gene silencing approach in GS6 reduced the number of locules and influenced the expressions of genes related to flower and locule development, suggesting that CaBRX plays an important function in the development of locules.

The APETALA2 homolog CaFFN regulates flowering time in pepper

Flowering time is an important agronomic trait that contributes to fitness in plants. However, the genetic basis of flowering time has not been extensively studied in pepper. To understand the genetics underlying flowering time, we constructed an F₂ population by crossing a spontaneous early flowering mutant and a late-flowering pepper line. Using bulked segregant RNA-seq, a major locus controlling flowering time in this population was mapped to the end of chromosome 2. An APETALA2 (AP2) homolog (CaFFN) cosegregated with flowering time in 297 individuals of the F₂ population. A comparison between the parents revealed a naturally occurring rare SNP (SNP2T > C) that resulted in the loss of a start codon in CaFFN in the early flowering mutant. Transgenic Nicotiana benthamiana plants with high CaFFN expression exhibited a delay in flowering time and floral patterning defects. On the other hand, pepper plants with CaFFN silencing flowered early. Therefore, the CaFFN gene acts as a flowering repressor in pepper. CaFFN may function as a transcriptional activator to activate the expression of CaAGL15 and miR156e and as a transcriptional repressor to repress the expression of CaAG, CaAP1, CaSEP3, CaSOC1, and miR172b based on a qRT-PCR assay. Direct activation of CaAGL15 by CaFFN was detected using yeast one-hybrid and dual-luciferase reporter assays, consistent with the hypothesis that CaFFN regulates flowering time. Moreover, the CaFFN gene association analysis revealed a significant association with flowering time in a natural pepper population, indicating that the CaFFN gene has a broad effect on flowering time in pepper. Finally, the phylogeny, evolutionary expansion and expression patterns of CaFFN/AP2 homologs were analyzed to provide valuable insight into CaFFN. This study increases our understanding of the involvement of CaFFN in controlling flowering time in pepper, thus making CaFFN a target gene for breeding early maturing pepper.

Genome-Wide Discovery of InDel Markers in Sesame (Sesamum indicum L.) Using ddRADSeq

The development and validation of different types of molecular markers is crucial to conducting marker-assisted sesame breeding. Insertion-deletion (InDel) markers are highly polymorphic and suitable for low-cost gel-based genotyping. From this perspective, this study aimed to discover and develop InDel markers through bioinformatic analysis of double digest restriction site-associated DNA sequencing (ddRADSeq) data from 95 accessions belonging to the Mediterranean sesame core collection. Bioinformatic analysis indicated the presence of 7477 InDel positions genome wide. Deletions accounted for 61% of the InDels and short deletions (1-2 bp) were the most abundant type (94.9%). On average, InDels of at least 2 bp in length had a frequency of 2.99 InDels/Mb. The 86 InDel sites having length ≥8 bp were detected in genome-wide analysis. These regions can be used for the development of InDel markers considering low-cost genotyping with agarose gels. In order to validate these InDels, a total of 38 InDel regions were selected and primers were successfully amplified. About 13% of these InDels were in the coding sequences (CDSs) and in the 3'- and 5'- untranslated regions (UTRs). Furthermore, the efficiencies of these 16 InDel markers were assessed on 32 sesame accessions. The polymorphic information content (PIC) of these 16 markers ranged from 0.06 to 0.62 (average: 0.33). These results demonstrated the success of InDel identification and marker development for sesame with the use of ddRADSeq data. These agarose-resolvable InDel markers are expected to be useful for sesame breeders.

Fine mapping of restorer-of-fertility gene based on high-density genetic mapping and collinearity analysis in pepper (Capsicum annuum L.)

The pepper restorer-of-fertility (CaRf) gene was fine mapped based on conjoint analysis of recombinants and collinearity between the two pepper reference genomes. Capana06g003028, encoding an Rf-like PPR protein, was proposed as the strongest candidate for pepper CaRf based on sequence comparison and expression analysis. The cytoplasmic male sterility (CMS)/restorer-of-fertility (Rf) system not only provides an excellent model to dissect genetic interactions between the mitochondria and nucleus but also plays a vital role in high-efficiency hybrid seed production in crops including pepper (Capsicum spp.). Although two important CMS candidate genes, orf507 and Ψatp6-2, have previously been suggested, the pepper Rf gene (CaRf) has not yet been isolated. In this study, a high-density genetic map comprising 7566 SNP markers in 1944 bins was first constructed with the array genotyping results from 317 F₂ individuals. Based on this map, the CaRf gene was preliminarily mapped to a region of 1.15 Mb in length at the end of chromosome P6. Then, by means of a conjoint analysis of recombinants and collinearity between the two pepper reference genomes, an important candidate interval with 270.10 kb in length was delimited for CaRf. Finally, Capana06g003028, which encodes an Rf-like PPR protein, was proposed as the strongest candidate for CaRf based on sequence analysis and expression characteristics in sterile and fertile plants. The high-density genetic map and fine mapping results provided here lay a foundation for the application of molecular breeding, as well as cloning and functional analysis of CaRf, in pepper.

Target sequencing reveals genetic diversity, population structure, core-SNP markers, and fruit shape-associated loci in pepper varieties

BACKGROUND

The widely cultivated pepper (Capsicum spp.) is one of the most diverse vegetables; however, little research has focused on characterizing the genetic diversity and relatedness of commercial varieties grown in China. In this study, a panel of 92 perfect single-nucleotide polymorphisms (SNPs) was identified using re-sequencing data from 35 different C. annuum lines. Based on this panel, a Target SNP-seq genotyping method was designed, which combined multiplex amplification of perfect SNPs with Illumina sequencing, to detect polymorphisms across 271 commercial pepper varieties.

RESULTS

The perfect SNPs panel had a high discriminating capacity due to the average value of polymorphism information content, observed heterozygosity, expected heterozygosity, and minor allele frequency, which were 0.31, 0.28, 0.4, and 0.31, respectively. Notably, the studied pepper varieties were morphologically categorized based on fruit shape as blocky-, long horn-, short horn-, and linear-fruited. The long horn-fruited population exhibited the most genetic diversity followed by the short horn-, linear-, and blocky-fruited populations. A set of 35 core SNPs were then used as kompetitive allele-specific PCR (KASPar) markers, another robust genotyping technique for variety identification. Analysis of genetic relatedness using principal component analysis and phylogenetic tree construction indicated that the four fruit shape populations clustered separately with limited overlaps. Based on STRUCTURE clustering, it was possible to divide the varieties into five subpopulations, which correlated with fruit shape. Further, the subpopulations were statistically different according to a randomization test and F_st statistics. Nine loci, located on chromosomes 1, 2, 3, 4, 6, and 12, were identified to be significantly associated with the fruit shape index (p < 0.0001).

CONCLUSIONS

Target SNP-seq developed in this study appears as an efficient power tool to detect the genetic diversity, population relatedness and molecular breeding in pepper. Moreover, this study demonstrates that the genetic structure of Chinese pepper varieties is significantly influenced by breeding programs focused on fruit shape.

High-density genetic map construction and QTL mapping of first flower node in pepper (Capsicum annuum L.)

BACKGROUND

First flower node (FFN) is an important trait for evaluating fruit earliness in pepper (Capsicum annuum L.). The trait is controlled by quantitative trait loci (QTL); however, studies have been limited on QTL mapping and genes contributing to the trait.

RESULTS

In this study, we developed a high density genetic map using specific-locus amplified fragment sequencing (SLAF-seq), a high-throughput strategy for de novo single nucleotide polymorphism discovery, based on 146 recombinant inbred lines (RILs) derived from an intraspecific cross between PM702 and FS871. The map contained 9328 SLAF markers on 12 linkage groups (LGs), and spanned a total genetic distance of 2009.69 centimorgan (cM) with an average distance of 0.22 cM. The sequencing depth for the map was 72.39-fold in the male parent, 57.04-fold in the female parent, and 15.65-fold in offspring. Using the genetic map, two major QTLs, named Ffn2.1 and Ffn2.2, identified on LG02 were strongly associated with FFN, with a phenotypic variance explanation of 28.62 and 19.56%, respectively. On the basis of the current annotation of C. annuum cv. Criollo de Morelos (CM334), 59 candidate genes were found within the Ffn2.1 and Ffn2.2 region, but only 3 of 59 genes were differentially expressed according to the RNA-seq results. Eventually we identified one gene associated with the FFN based on the function through GO, KEGG, and Swiss-prot analysis.

CONCLUSIONS

Our research showed that the construction of high-density genetic map using SLAF-seq is a valuable tool for fine QTL mapping. The map we constructed is by far the most saturated complete genetic map of pepper, and using it we conducted fine QTL mapping for the important trait, FFN. QTLs and candidate genes obtained in this study lay a good foundation for the further research on FFN-related genes and other genetic applications in pepper.

Development and Application of InDel Markers for Capsicum spp. Based on Whole-Genome Re-Sequencing

Genome-wide identification of Insertion/Deletion polymorphisms (InDels) in Capsicum spp. was performed through comparing whole-genome re-sequencing data from two Capsicum accessions, C. annuum cv. G29 and C. frutescens cv. PBC688, with the reference genome sequence of C. annuum cv. CM334. In total, we identified 1,664,770 InDels between CM334 and PBC688, 533,523 between CM334 and G29, and 1,651,856 between PBC688 and G29. From these InDels, 1605 markers of 3-49 bp in length difference between PBC688 and G29 were selected for experimental validation: 1262 (78.6%) showed polymorphisms, 90 (5.6%) failed to amplify, and 298 (18.6%) were monomorphic. For further validation of these InDels, 288 markers were screened across five accessions representing five domesticated species. Of these assayed markers, 194 (67.4%) were polymorphic, 87 (30.2%) monomorphic and 7 (2.4%) failed. We developed three interspecific InDels, which associated with three genes and showed specific amplification in five domesticated species and clearly differentiated the interspecific hybrids. Thus, our novel PCR-based InDel markers provide high application value in germplasm classification, genetic research and marker-assisted breeding in Capsicum species.

Construction of a high density genetic map of an interspecific cross of Capsicum chinense and Capsicum annuum and QTL analysis of floral traits

The yield of pepper plants (Capsicum spp.) is their most important trait and is affected by the flower number and flowering time. Capsicum annuum produces a single flower per node and has an early flowering habit. By contrast, Capsicum chinense yields multiple flowers per node and has a late flowering character. However, the genetic mechanism underlying the control of these floral traits remains largely unknown. In this study, 150 F₂ populations from an interspecific cross between the inbred lines 740 (C. chinense) and CA1 (C. annuum) and their parents were used to construct a molecular genetic linkage map using the specific length amplified fragment sequencing (SLAF-seq) technique. This linkage map, spanning 1,586.78 cM in length, contained 9,038 markers on 12 chromosomes, with a mean marker distance of 0.18 cM. Phenotypic data on the flowering time and flower number per node were collected over multiple years, and QTL analysis identified 6 QTLs for the flowering time and flower number per node by composite interval mapping (CIM) and genome-wide composite interval mapping (GCIM) methods at least in two environments. The candidate genes within the major QTL were predicted. In the major flowering time QTL, the candidate gene Capana02g000700, which encodes the homeotic protein APETALA2, was identified. Quantitative reverse-transcription PCR (qRT-PCR) analysis indicated that its expression level in 740 was higher than that in CA1. Gene expression analysis indicated that the expression of Capana02g000700 was significantly upregulated in flowers, and many floral development-related genes were found to be coexpressed with Capana02g000700, supporting the function of this gene in association with flowering time in C. chinense and C. annuum species.

Candidate genes for first flower node identified in pepper using combined SLAF-seq and BSA

First flower node (FFN) is an important trait for evaluating fruit earliness in pepper (Capsicum annuum L.), but the genetic mechanisms that control FFN are still poorly understood. In the present study, we developed 249 F₂ plants derived from an intraspecific cross between the inbred pepper lines Z4 and Z5. Thirty plants with the highest FFN and 30 plants with the lowest FFN were chosen and their DNAs were pooled according to phenotype to construct two bulked DNA pools. Specific-locus amplified fragment sequencing (SLAF-seq) was combined with bulked segregant analysis (BSA) to identify candidate regions related to FFN. According to our genetic analysis, the FFN trait is quantitatively inherited. A total of 106,848 high-quality single nucleotide polymorphism (SNP) markers were obtained, and 393 high-quality SNP markers associated with FFN were detected. Ten candidate regions within an interval of 3.98 Mb on chromosome 12 harboring 23 candidate genes were identified as closely correlated with FFN. Five genes (CA12g15130, CA12g15160, CA12g15370, CA12g15360, and CA12g15390) are predicted based on their annotations to be associated with expression of the FFN trait. The present study demonstrates an efficient genetic mapping strategy and lays a good foundation for molecular marker-assisted breeding using SNP markers linked to FFN and for cloning and functional analysis of the key genes controlling FFN.

Transcriptome analysis and development of simple sequence repeat (SSR) markers in Zingiber striolatum Diels

Illumina-based paired-end sequencing technology was used for the high-throughput transcriptome sequencing of combined Zingiber striolatum Diels tissues (i.e., root, stem, leaf, flower, and fruit tissues). More than 130 million sequencing reads were generated, and a de novo assembly yielded 287,959 contigs and 112,107 unigenes with an average length of 1029 and 28,891 bp, respectively. Similarity searches with known sequences led to the identification of 51,804 (46.21%) genes. Of the annotated unigenes, 6867 and 51,987 were assigned to Gene Ontology and Clusters of Orthologous Groups categories, respectively. Additionally, 8384 simple sequence repeats (SSRs) were identified as potential molecular markers in the unigenes. Thirty pairs of polymerase chain reaction primers were designed and used to validate the unigenes and assess the associated genomic polymorphism. The PCR amplification products for 25 primer pairs were of the expected size. These primers may represent usable molecular markers. The thousands of SSR markers identified in the present study may be useful for analyses of genetic diversity, genetic linkage mapping, and the identification and improvement of varieties during the breeding of Z. striolatum Diels. The unigene sequences and SSR markers described herein may serve as valuable resources for future investigations of Z. striolatum Diels.

Development of a SNP array and its application to genetic mapping and diversity assessment in pepper (Capsicum spp.)

The development and application of single nucleotide polymorphisms (SNPs) is in its infancy for pepper. Here, a set of 15,000 SNPs were chosen from the resequencing data to develop an array for pepper with 12,720 loci being ultimately synthesized. Of these, 8,199 (~64.46%) SNPs were found to be scorable and covered ~81.18% of the whole genome. With this array, a high-density interspecific genetic map with 5,569 SNPs was constructed using 297 F2 individuals, and genetic diversity of a panel of 399 pepper elite/landrace lines was successfully characterized. Based on the genetic map, one major QTL, named Up12.1, was detected for the fruit orientation trait. A total of 65 protein-coding genes were predicted within this QTL region based on the current annotation of the Zunla-1 genome. In summary, the thousands of well-validated SNP markers, high-density genetic map and genetic diversity information will be useful for molecular genetics and innovative breeding in pepper. Furthermore, the mapping results lay foundation for isolating the genes underlying variation in fruit orientation of Capsicum.

Transcriptome Characterization and Functional Marker Development in Sorghum Sudanense

Sudangrass, Sorghum sudanense, is an important forage in warm regions. But little is known about its genome. In this study, the transcriptomes of sudangrass S722 and sorghum Tx623B were sequenced by Illumina sequencing. More than 4Gb bases were sequenced for each library. For Tx623B and S722, 88.79% and 83.88% reads, respectively were matched to the Sorghum bicolor genome. A total of 2,397 differentially expressed genes (DEGs) were detected by RNA-Seq between the two libraries, including 849 up-regulated genes and 1,548 down-regulated genes. These DEGs could be divided into three groups by annotation analysis. A total of 44,495 single nucleotide polymorphisms (SNPs) were discovered by aligning S722 reads to the sorghum reference genome. Of these SNPs, 61.37% were transition, and this value did not differ much between different chromosomes. In addition, 16,928 insertion and deletion (indel) loci were identified between the two genomes. A total of 5,344 indel markers were designed, 15 of which were selected to construct the genetic map derived from the cross of Tx623A and Sa. It was indicated that the indel markers were useful and versatile between sorghum and sudangrass. Comparison of synonymous base substitutions (Ks) and non-synonymous base substitutions (Ka) between the two libraries showed that 95% orthologous pairs exhibited Ka/Ks<1.0, indicating that these genes were influenced by purifying selection. The results from this study provide important information for molecular genetic research and a rich resource for marker development in sudangrass and other Sorghum species.

A comprehensive characterization of simple sequence repeats in pepper genomes provides valuable resources for marker development in Capsicum

The sequences of the full set of pepper genomes including nuclear, mitochondrial and chloroplast are now available for use. However, the overall of simple sequence repeats (SSR) distribution in these genomes and their practical implications for molecular marker development in Capsicum have not yet been described. Here, an average of 868,047.50, 45.50 and 30.00 SSR loci were identified in the nuclear, mitochondrial and chloroplast genomes of pepper, respectively. Subsequently, systematic comparisons of various species, genome types, motif lengths, repeat numbers and classified types were executed and discussed. In addition, a local database composed of 113,500 in silico unique SSR primer pairs was built using a homemade bioinformatics workflow. As a pilot study, 65 polymorphic markers were validated among a wide collection of 21 Capsicum genotypes with allele number and polymorphic information content value per marker raging from 2 to 6 and 0.05 to 0.64, respectively. Finally, a comparison of the clustering results with those of a previous study indicated the usability of the newly developed SSR markers. In summary, this first report on the comprehensive characterization of SSR motifs in pepper genomes and the very large set of SSR primer pairs will benefit various genetic studies in Capsicum.