**5. Genome organization**

Genome sequence information of hot pepper revealed 37,989 scaffolds with an estimated size of 3.48 Gb [68]. The GC content was 35.03%, and there were 34,903 genes with an average exon and intron length of 286.5 pb and 541.6 bp, respectively [68]. These protein-coding genes of *Capsicum* were relatively the same as other Solanaceae species—tomato (34,771 genes) and potato (39,031 genes) [69–71].

The genetic maps of tomato and pepper are nearly comparable in length, with 1275 cm in tomato and 1246 cm in pepper [72]. However, it was determined that the average recombination rate/unit of physical distance in pepper and tomato is not the same [72]. This would happen if recombination were limited to homologous genes, as demonstrated in maize [73–83].

Regarding the number of homologous and segregating loci found by a probe, tomato, and pepper genomes differ, with pepper having a higher copy number [84]. The significant number of probes detecting multiple loci in pepper than in tomato might be related to the detection of more loci per probe in pepper, or it could be suggestive of a higher degree of interspecific polymorphism in *Capsicum* than in the interspecific cross used to generate the tomato map [84–86].

In plants, an increase in the amount of repetitive DNA has been identified as a cause of genome expansion [68, 87]. Retrotransposons distributed uniformly across gene-rich and gene-poor sections of the genome are likely to explain differences in nuclear DNA content among Solanaceae species [68, 81, 87]. Concerning transposable elements (TEs), *Capsicum's* TEs were predominantly composed of long terminal repeats (LTR). Specifically, most of the LTRs were Gypsy elements [68].

AFLP, SSR, RAPD, isozymes, inter-simple sequence repeat (ISSR), restrictions fragment length polymorphism (RFLP), gene-based makers, expressed sequence tag-simple sequence repeat (SCoT and EST SSR), and single nucleotide polymorphism (SNP) have all been used in the study and characterization of genetic diversity, phylogenetic relationships, genotypic variations, selection of parentals and progenies, cultivar identity, phenotypic characteristics, purity, population studies, and resistance to disease in *Capsicum* species [88, 89].

Chili peppers have been identified, and their germplasm diversity was evaluated using various molecular markers [90, 91]. Rodriguez discovered diagnostic RAPD (randomly amplified polymorphic DNA) producers for four domesticated species (including *C. chacoense*) but not for *C. frutescens* in a review [92]. Primarily, isozymes have been used to measure genetic diversity and define their genetic relationships within the genus [93].

Studies in the Solanaceae family linking the genetic maps of tomato and potato, respectively, sparked the discipline of comparative plant genomics in 1998 [94, 95]. The initial analysis discovered that the main difference between the tomato and

potato genomes was paracentric inversions, and further investigations revealed that five inversions separated the two species [69, 86, 96]. It was shown that no map of *Capsicum* has yet been developed that accomplishes the aim of thoroughly defining and saturating the pepper chromosomes [72].

About 655 of the 1007 markers produced could be examined for divergence from single-locus Mendelian ratios [72]. Slightly more than half of the tested subgroup (337 = 50.7%) indicated variation from predicted ratios (p = 0.01), with p values as low as 2.69 × 10–25 in 81 of them (12.2%) [72].

The pepper tomato comparative map can be used in conjunction with the *Capsicum*, Lycopersicon, and Solanum phylogeny. It can also be used to identify conserved linkage blocks, reconstruct portions of the genome of these species' most recent ancestor, and, in some cases, determine lineage rearrangements that occurred [69, 71, 72, 97]. Because the number of ad hoc hypotheses utilizing either condition as the ancestral state is the same for pepper and tomato/potato, only two different arrangements can be provided [72]. It was noted that paracentric, as well as pericentric inversions and translocations, were the most common structural changes [72]. Interestingly, all tomato clones examined were hybridized to pepper DNA [72].

There were differences in tomato and pepper genomes regarding the amount of homologous and segregating loci, with pepper having a larger copy number [72]. The increased number of probes identifying multiple loci in pepper compared to tomato might be due to the detection of more loci per probe in pepper or indicative of a higher degree of interspecific polymorphism with *Capsicum* [72]. Regardless, the discrepancies in copy numbers across the specifics lacked the patterns consistent with systemic duplication [72].

Increases in the quantity of repetitive DNA have been identified as a source of genome extension in plants. A recent study in the Gramineae has revealed a pattern of retroelement increases between the genes of large-genome species compared to smaller-genome species analysis of repetitive DNA in the pepper genome indicated that 5% of the pepper genome was made up of elements with copy numbers >10,000, 26% with copy numbers >150, and 65% single-copy sequences [81, 85, 98–100]. The blocks of constitutive heterochromatin (7% of total karyotypic length) detected primarily at the telomers of *C. annum* cannot explain all of the additional DNA in pepper compared to tomato chromosomes [101]. As a result, differences in nuclear DNA content between tomato and pepper are likely to be explained by retrotransposons interspersed evenly across both gene-rich and gene-poor areas of the genome, as shown in the Gramineae [102].

The genetic maps of tomato and pepper are nearly comparable in length, with 1275 cm in tomato and 1246 cm in pepper [73–76]. Because of the comparable lengths of the genetic maps and the difference in DNA content, the recombination rate per unit of physical distance in pepper and tomato is not the same [73–76]. This would happen if recombination were limited to homologous genes, as predicted and demonstrated in maize [73–83].

A map of *Capsicum* has yet to be established that achieves the goal of properly identifying and saturating the pepper chromosomes [72]. Pepper has similar genetic content to tomato in the tomato-pepper investigation [72]. The fundamental difference between the tomato and potato genomes was identified as paracentric inversions, and subsequent research indicated that five inversions separated the two species [71, 72]. The tomato-pepper study also discovered that pepper and tomato had similar genomic content, as evidenced by the presence of pepper sequences that were complementary to all tomato cDNA tested [86]. However, the pepper genome had been significantly

*Genetics and Genomics of Capsicum: Valuable Resources for Capsicum Development DOI: http://dx.doi.org/10.5772/intechopen.110407*

rearranged, with numerous pepper chromosomes that contain discrete tomato segments [72]. It was further discovered that the pepper genome had lost parts homologous to the tomato genome, but this did not change the fact that the homoeologous linkage blocks in the pepper genome had been considerably broken [72].

The number of homologous and segregating loci of tomato and pepper genomes differ, with pepper having a higher copy number [72]. The larger number of probes detecting multiple loci in pepper than in tomato might be related to the detection of more loci per probe in pepper, or it could be suggestive of a higher degree of interspecific polymorphism in *Capsicum* than in the interspecific cross used to generate the tomato map [72, 103]. The differences in copy quantity across the specificity, on the other hand, lack the patterns associated with systemic duplications [72].

In plants, an increase in the amount of repetitive DNA has been identified as a cause of genome expansion [72]. Retrotransposons are distributed uniformly across both gene-rich and gene-poor sections of the genome and may explain the differences in pepper and tomato nuclear DNA content [72]. Tomato and pepper genetic maps are approximately identical in length, with 1275 cm in tomato and 1246 cm in pepper [72]. The difference in the average recombination rate in pepper and tomato may be due to variable lengths of their genetic maps and differences in DNA content [72].
