**4. Genetic diversity and QTLs**

Genetic diversity is crucial for *Capsicum* development and management. Genetic diversity is correlated with average fitness across populations [18, 32]. The robust genetic diversity of *Capsicum* populations will enable them to adapt to ever-changing environments, be a resource of valuable alleles and genes in the population, and contribute to ecosystem diversity [18, 32]. To date, there are various estimates as to the number of *Capsicum* species [20–24, 33–35].

Capsicum fruits are diverse and vary in form and characteristics. Fruit form has been examined extensively in the Solanaceae family, including tomato, pepper, and eggplant [36–38]. On chromosomes 2, 3, 7, 8, and 10, allelic variations in the Sun, Ovate, Fascinated (FAS), and Locule Number (LC) genes determine the form of the

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

tomato fruit [36, 39–46]. Individual alleles of these genes might account for up to 71% of the particular shape variance in a population [46]. Individual alleles of these genes accounted for up to 71% of the particular shape variation in a broad sample of 368 wild and cultivated tomatoes [46]. Fruit weight was strongly co-localized across tomato and pepper QTLs, and a single fruit shape QTL was co-localized, suggesting that conserved components contribute to one, if not both, of the traits [38, 39, 44–51]. Multiple QTLs for fruit length, width, and the fruit shape ratio (length: width) have been discovered on chromosomes 1–4, 8, 10, and 11 [39, 44, 48, 50]. Two essential fruit QTLs, fs 3.1 (fruit shape) and fe 10.1 (fruit elongation), were linked to chromosome 3 and 10, respectively, in a BC4F2 population segregating for fruit-shaped [44]. These QTLs accounted for 67, and 44% of the variance in fruit form and elongation found in the population, respectively [44]. Fruit trait inheritance in connection to pericarp form, color thickness, and total soluble solids was also investigated [52].

The round form characteristic was governed by a single gene based on segregation ratios. Five QTLs contributing to fruit form and one QTL for pericarp thickness on chromosomes 1, 2, 4, 10, and 3 were determined. This explains the 4 to 26% of the diversity in the Jalapeno recombinant inbred lines [50]. The expression of a gene that resembled the tomato gene Ovate and discovered substantial variations between round and elongated pepper cultivars was compared [51]. Further study was carried out on five domesticated species [53].

Another QTL analysis in 2012 found that two dominant genes regulated fruit mass length, diameter, form ratio, and flesh thickness, with heritability ranging from 38 to 88% [45, 54]. Fruit width was highly heritable, and fruit weight and width were positively associated while examining a pepper germplasm collection from the Caribbean, which was consistent with the QTL study [44, 48, 54]. The heritability of fruit form and flesh thickness was 80% in another mapping investigation [48]. The INRA characterized the phenotype of almost 1300 pepper accessions in their collection for 12 fruit traits; form and color varied across domesticated species, but wild species often featured tiny, elongated fruit [55]. Despite the large number of studies examining pepper fruit form, the use of subjective visual (e.g., elongate, triangular, square, heart) or manual (length/width ratio) measures to define fruit shape was a shortcoming in all of them [55]. With this, software has been created that allows for more objective and reliable assessments of fruit attributes [33, 41].

Disease resistance is also crucial, even if fruit form is one of the most critical features of a cultivar [30]. Cultivated cultivars frequently lack disease resistance due to breeding bottlenecks [30]. Resistance is frequently found in small-fruited wild species and then adopted into larger-fruited commercial cultivars [56, 57]. Through linkage drag or pleiotropic effects, negative horticultural features such as disease resistance can be passed together with beneficial traits like disease resistance [56, 57]. Recent research on tomatoes found a relationship between resistance to the late blight pathogen (*Phytophthora infestans*) and unfavorable impacts on maturity, fruit size, yield, and plant architecture [58, 59]. In pepper, a link between fruit features and disease resistance for a single strain of *P. capsici*, a destructive fungus that causes fruit, foliar, and root rot [50, 55]. In an eggplant germplasm population, fruit form was positively linked with disease susceptibility to *P. capsica* [48, 50]. Negative associations were found between resistance to the bacterium pathogen *Pseudomonas syringae* (PV) in Kiwi [60]. When transferring disease resistance into commercial cultivars, it is critical to look for possible correlations, linkage drag, and pleiotropic effects [60].

Since their introduction in Mexico, peppers have been subjected to a substantial selection for fruit forms and sizes [61, 62]. Domesticated pepper fruit has an unlimited variety of phenotypic variability [63–66]. While cousins and landrace peppers are typically tiny and very pungent, domesticated pepper fruit has an endless array of phenotypic diversity [64–66]. Various regional preferences exist for pepper consumed in most nations and marketplaces [64]. Regional choices have increased morphological variability among market classes [64].

In addition to Capsicum's genetic diversity, we also analyzed the phylogenetic relationships of 22 Nicotinamide Adenine Dinucleotide Dehydrogenase (NADH dehydrogenase) sequences of Capsicum from 19 different species. NADH dehydrogenase is a flavoprotein-containing oxidoreductase that catalyzes the conversion of NADH to NAD. The enzyme may be found in eukaryotes as a part of the mitochondrial electron transport complex I and in transferring electrons from photoproduced stromal reductants like NADPH and ferredoxin to the intersystem plastoquinone pool. NADH dehydrogenase is the primary enzyme complex in the electron transport chain in mitochondria. Nicotinamide adenine dinucleotide (NAD) is transformed from its reduced form, NADH, to its oxidized form, NAD+ [67].

Phylogenetic analysis using UPGMA Maximum Composite Likelihood with 1000 bootstrap replications revealed that the *C. ciliatum, C. lanceolatum, C. lycianthoides,* and *C. geminifolium* grouped together. More so, *C. minutiflorum and C. ceratocalyx* were strongly clustered together, the same with *C. chinensis and C. frutescens* (**Figure 1**).

*C. pubescens, C. galapagoence, C. chacoense*, and *C. cardenasi* formed a cluster adjacent to *C. annuum* on top and *C. baccatum* species below (**Figure 1**). Other *Capsicum*

species like *C. eximium, C. coccineum, C. flexuosum,* and *C. hunzikerianum* had distinct branches and separated from other *Capsicum* taxa (**Figure 1**).

The phylogenetic study on the waxy gene [2] indicated that *C. chinense* and *C. frutescens* were grouped together. More so, a study on the trnC-rpoB intron, trnHpsbA intron, and waxy gene sequence data from seven *Capsicum spp*. also revealed that *C. chinense, C. annuum, and C. frutescens* grouped in the same cluster [2]. The above grouping supported our *Capsicum's* phylogenetic analysis based on NADH Dehydrogenase (**Figure 1**).
