ASSESSMENT OF MOLECULAR MARKER BASED GENETIC DIVERSITY

The characterization of genetically diverse germplasm is prerequisite in breeding programs for crop improvement strategies. This study will also be helpful to screen the elite clone for collection, maintenance, preservation, and utilization adequately. The characterization of germplasm serves essential link between the conservation and appropriate utilization of genetic resource (Paterson et al., 1991). Genetic diversity is usually analyzed by measurement of genetic distance, through which differences or similarities at the genetic level can be calculated efficiently. The analysis of molecular markers could be explored for genetic diversity analysis. The molecular marker- based genetic diversity analysis (MMGDA) play a pivotal role to identify different accessions of plants at the taxonomic level and evaluate diversity among species over different time point and geographic locations (Duwick 1984). The MMGDA including restriction fragment length polymorphism, random amplified polymorphic DNA (RAPD), simple sequence repeats (SSR), and amplified fragment length polymorphism (AFLP) are regularly being executed in analysis of genetic resources in different plant species

Region of study

No. of accessions

Capsicum species

Parameters

Range

References

Mexico

13

C. annuum

Capsaicinoids (pg-g"1 DW) Diliydrocapsaicin (pg-g"1 DW) Capsaicin (pg-g"1 DW) p-carotene (pg-g"1 DW) p-cryptoxanthin (pg g"1 DW) Zeaxantliin (pg g'1 DW) Violaxantliin (pg g"1 DW) Capsanthin (pg g'1 DW)

Total carotenoids (pg g"1 DW)

  • 250-1750
  • 146.7- 1024.9
  • 103.1- 719.5 5.0-22.0 29.9-87.8
  • 73.8- 169.0
  • 61.8- 125.8
  • 465.2- 1006.8
  • 1697.7- 3481.6

Rodriguez-Uribe et al. (2014)

Brazil

8

C. annuum, C. chinense, C. baccatum

Total carotenoids (pg/g) Vitamin C (mglOO g)

Total phenolics (uig/100 g) Total antliocyanins (mglOO g) DPPH* (g/g DP PH)

ABTS+ (pM trolox/g)

  • 59.86-1349.97
  • 82.55-264.13
  • 215.73-1103.20
  • 5.99-18.30
  • 1745.18-4905.06
  • 46.79-113.08

Carvalho et al. (2015)

World-wide

101

Capsicum sp.

Cliile pepper pungency (SHU) Vitamin A (IU/100 g pepper) Vitamin C (mg lOO g pepper) Folate (pg/100 g pepper)

  • 1053.5- 852404.6
  • 302.5- 20840.0 11.85-195.75 9.95-265.24

Kantar et al. (2016)

India

139

Capsicum sp.

Total capsaicinoid (mg/g) Pungency (SHU)

Capsaicin content (%) Diliydrocapsaicin content (%) Mean ratio of (Cap/Dhc)

  • 0.02-72.05
  • 317-1,152,832
  • 25.52-83.10
  • 16.9-74.48
  • 0.33-4.92

Islam etal. (2015)

Region of study

No. of accessions

Capsicum species

Parameters

Range

References

Spain

2

Capsicum frutescens

Betulin (mg/kg) Campesterol (mg/kg) Stigmasterol (mg/kg) p-Sitosterol (mg'kg) Organic acid (mg/kg) Ascorbic acid (mg'kg) Total fatty acid (mg/kg) SFA (mg/kg)

MUFA (mg/kg)

PUFA (mg/kg)

  • 138.2- 161.9
  • 42.3- 54.1
  • 6.3- 9.3 46.1-67.4
  • 8218.2- 8527.4 66.6-230.4 59104.9-59803.7
  • 30077.2- 28140.3 6381.7-9200.2 22646.0-22463.2

Silva et al. (2013)

Peru and Bolivia

186

Capsicum sp.

Antioxidant capacity (mmol/100 g) Extractable color (ASTA) Capsaicinoids (ing/100 g)

Fat (g/100 g)

Flavonoids (mg/100 g)

Polyphenols (g/100 g)

Quercetin (mg/100 g)

  • 2.1- 9.2 1-146 0.3-1244.3
  • 2.2- 32.8 0.4-46.8 1.09-3.69 0.4-42.6

Zonneveld et al. (2015)

Peni. Guatemala, and Ecuador

5

C. baccatum, C. pubescens, C. chinense

Total capsaicinoid (mg'kg) Pungency (SHU)

Capsaicin content (%) Diliydrocapsaicin content (%)

  • 13-1605
  • 200-23500
  • 33.6-83.0
  • 13.9-43.3

Kolhnannsbeiger et al. 2011

South Asia

6

С. annuum, C. chinense

Total capsaicinoid (SHU) Capsaicin content (SHU) Diliydrocapsaicin content (SHU)

  • 20867.4-187100.7
  • 14047.3-115532.8
  • 6820.0-74212.1

Gurung et al. (2012)

Region of study

No. of accessions

Capsicum species

Parameters

Range

References

Texas

7

C. aim mini, C. chin erne, C. ftvtescens

p-cryptoxanthin (pg/100 g) a-carotene (pg/100 g) p-carotene (pg/100 g) Retinol equiv (RE/100 g) Provitamin A (% RDA) Capsantliin (pg/100 g) Lutein (pg 100 g) Zeaxantliin (pg/100 g) Quercetin (mg/g)

Luteolin (mg/g)

Ascorbic Acid (mg/100 g)

  • 131-973
  • 222—2127
  • 2-1187
  • 0.33-336
  • 0.03-33.7
  • 984-20861
  • 61-955
  • 15-1958
  • 0.88-64.47
  • 1.75-81.30
  • 74.55-202.40

Howard et al. (2000)

Peru

147

Capsicum spp.

Capsaicinoids (mg/100 g) Nordiliydrocapsaicin (mg/100 g) Capsaicin (mg/100 g) Diliydrocapsaicin (mg/100 g) Total Polyphenols (g GAE/100 g) TEAC (imnol/100 g)

Ascorbic acid (mg/100 g)

Total Flavonoids (mg/100 g) Quercetin (mg/100 g)

Luteolin (mg/100 g)

Extractable color (ASTA)

Fat (g/100 g)

Moisture (g/100 g)

  • 0.4-1560.1
  • 0-81.5
  • 0.3-1074.3
  • 0.2-459.8
  • 1.22-3.69
  • 1.8-9.2
  • 0- 295 0.5-29.5 0.5-26.6 0.4-5.2
  • 1- 146 2.2-19.6 0.4-6.6

Meckelmann et al. (2013)

Region of study

No. of accessions

Capsicum species

Parameters

Range

References

Mexico

4

C. annuum

Total protein (g/100 g DW)

Total fat (g/100 gDW)

Total dietary fiber (g/100 g DW) Total polyphenols (ing/100 g DW) Total carotenoids (mg/100 g DW) FRAP (prnol TE/g DW)

ABTS (prnol TE-'g DW) p-carotene (mg/100 g DW) p-cryptoxanthin (mg/100 g DW) Zeaxantliin (mg/100 g DW)

  • 13.4- 15.5
  • 7.4- 13.2 27.9-41.7
  • 2325.4- 2843.5 87.6-373.3
  • 37.5- 66.5
  • 18.6- 36.4 7.3-85.7 2.0-10.6 0.9-10.3

Hervert-Hernandez et al. (2010)

Peru

50

Capsicum sp.

Total terpenoids (%) Copaene (%)

Limonene (%) O-cymene (%)

Total esters (%) n-hexyl hexanoate (%) Total hydrocarbons (%) 2-metliyl tridecane (%) Pentadecane (%) n-tetradecane (%)

Total aldehydes (%) Cumaldehyde (%) 2-hexenal (%)

Total ketones 2-nonanone

  • 4.3-47.6
  • 0.2-13.8
  • 0.3-17.4
  • 0.3-7.9
  • 1.6-72.0
  • 0.5-29.4
  • 1.9-71.8
  • 0.2-9.7
  • 0.4-37.0
  • 0.2-5.3
  • 0.1-12.9
  • 0.5-5.6
  • 0.2-5.8
  • 0.7-34.2
  • 0.4-23.8

Patel etal. (2016)

Region of study

No. of accessions

Capsicum species

Parameters

Range

References

Peru

23

Capsicum sp.

Capsaicinoids (ing/100 g) Capsaicin (ing/100 g) Diliydrocapsaicin (ing/100 g) Nordiliydrocapsaicin (ing/100 g) Total Polyphenols (g GAE /100 g) TEAC (mmol/100 g)

Total Flavonoids (ing/100 g) Quercetin (ing/100 g)

Luteolin (mg/100 g)

Tocopherols (mg/100 g) a-Tocopherol (ing/100 g) y-Tocopherol (ing/100 g) p-Tocopherol (ing/100 g) Extractable color (ASТА) Moisture (g/100 g)

  • 0.99-1515.53
  • 0.71-1199.10
  • 0.29-307.89
  • 0.55-159.96
  • 1.34-2.77
  • 2.0-7.0
  • 1.27- 13.77
  • 1.27- 13.77 0.57-3.33 0.23-29.09 1.09-26.36 0.23-5.29 0.03-0.78 3.50-94.23 0.43-2.60

Meckehnann et al. (2015a)

USA

90

Capsicum spp.

Capsaicin (rng/g) Diliydrocapsaicin (rng/g)

  • 0.00-2.89
  • 0.00-1.71

Antonious and Janet (2006)

Peru

32

C. pubescens

Capsaicinoids (ing/100 g)

Capsaicin (ing/100 g) Diliydrocapsaicin (ing/100 g) Nordiliydrocapsaicin (ing/100 g) Total Polyphenols (g GAE/100 g) TEAC (nunol/lOO g)

  • 55-410
  • 13-128 25-207 9-122 0.7-1.5 1.8-2.4

Meckehnann et al. (2015b)

Region of study

No. of accessions

Capsicum species

Parameters

Range

References

Total Flavonoids (rng/TOO g) Quercetin (mg/100 g) Tocopherols (mg/100 g) a-Tocopherol (mg/100 g) y-Tocopherol (mg/100 g)

(3-Tocopherol (mg/100 g) Extractable color (ASTA) Moisture (g/100 g)

  • 2.4- 4.6
  • 6.8- 16.9
  • 5.9- 18.2 0.1-1.8 0.0-0.2 2.8-9.3 2-66
  • 1.4- 3.4

India

136

C. annuum, C. frute- scens, C. chinense

Capsaicinoids (pg/g DW)

SHU

Capsaicin (pg/g DW) Dihydrocapsaicin (pg/g DW) Nordihydrocapsaicin (pg/g DW) Nonivamide (pg/g DW) Antioxdant activity (%)

  • 168.5-64333.0
  • 3188.4-1037305.0
  • 101.18-54543.0
  • 5011.66-26455.189
  • 0.035-914.1
  • 0.006-816.7
  • 3.52-81.78

Sarpras et al. (2016)

Netherlands

24

C. annuum

Glucose (g/100 g fw) Fructose (g/100 g fw)

Malic acid (mg/100 g fw) Citric acid (mg/100 g fw) Ascorbic acid (mg/100 g fw)

1.79-3.81

I. 89-3.75

II. 71-159.27 185.7-609.7 137.9-247.1

Eggink et al. (2012)

India

30

C. annuum

Capsaicin content (%) Ascorbic acid (mg/lOOg) Chlorophyll content (mg/g)

  • 0.42-2.06
  • 175.23-328.26
  • 0.16-0.59

Yatung et al. (2014)

Region of study

No. of accessions

Capsicum species

Parameters

Range

References

Texas

12

C. annuum

Total Flavonoids (ing/100 g) Quercetin (mg/100 g) Luteolin (mg/100 g)

Ascorbic acid (mg/lOOg) Total Polyphenols (mg/100 g) Antioxidant activity (%)

Heat index

  • 27.37-851.53
  • 17.60-783.83
  • 6.07-103.50
  • 48.9-168.4
  • 178.2-384.9
  • 50.1-81.5
  • 1-8

Lee et al. (1995)

Poland

4

C. annuum

Vitamin C (mg/100 g)

(3-carotene (mg/100 g) Xanthophylls (mg/100 g) Phenolic compounds (mg/100 g)

  • 101.19-167.54
  • 0.058-0.460
  • 0.500-4.658
  • 37.54-67.35

Perucka and Materska (2007)

World-wide

Capsicum sp.

Vitamin C (mg/100 g) Vitamin E (pg/ g)

  • 76.1-243.1
  • 322-883

Palevitch and Craker (1996)

Poland

4

C. annuum

Capsaicin (mg/g) Dihydrocapsaicin (mg/g)

  • 0.035-0.530
  • 0.350-0.015

Materska and Perucka (2005)

Alabama

19

C. annuum

Ascorbic acid (mg/ lOOg FW) Provitamin A (RE1 lOOg FW) Sodium (mg/ lOOg DW) Potassium (mg/ lOOg DW) Calcium (mg/ lOOg DW) Phosphorus (mg/ lOOg DW) Nitrogen (mg/ lOOg DW)

  • 62-124
  • 29-127
  • 7-12
  • 80-139
  • 3-6
  • 9-18
  • 335-743

Simonne et al. (1997)

Cote d’Ivoire

5

Capsicum sp.

Beta carotene (pg/100 g FW) Ascorbic acid (mg/100 g FW)

  • 68.47-535.98
  • 86.38-96.62

Kouassi et al. (2012)

(Williams et al., 1990; Vos et al., 1995; Meudt and Clarke, 2007; Agarwal et al., 2008). The studies of variation in phenotypic traits are essential for diversity analysis; they need to be corroborated with molecular markers to provide robust genetic diversity evaluations. A plethora of DNA markers has been developed and utilized for diversity analysis in capsicum germplasm from different geographic locations. Among the molecular markers, AFLP was first executed among 25 accessions in pepper from different locations of Mexico (Prince et al., 1992). In this pioneer work, principal component analysis combined with cluster analysis have revealed the significant correlation between genetic distance calculated through AFLP and distance measured through isozyme analysis. Subsequent to the above analysis, AFLP markers have been used in different chili germplasm for genetic diversity analysis (Aktas et al. 2009; Thul et al., 2006; Krishnamurthy et al., 2015; Islam et al., 2016; Prince et al. 1995; Wahyuni et al., 2013). The morphological classification of different Capsicum species was validated with germplasm analysis using RAPD and AFLP markers and these markers were also found to be helpful in identifications of different species of an accession. A comparative PCR-based molecular marker analysis was executed between 34 pepper cultivars of different geographic origin to assess the effectiveness between RAPD and AFLP markers (Paran et al., 1998). They have reported the higher efficiency of AFLP marker over RAPD and highlighted the divergence between the large-fruited sweet cultivars from the small-fruited pungent peppers using dendrogram based study. The AFLP markers combined with morphological traits were utilized to cluster different genotypes of Capsicum (Geleta et al., 2005). In another study, 134 accessions from six Capsicum species were genetically characterized using >100 RAPD markers at the Asian Vegetable Research and Development Center (Rodriguez et al., 1999). Due to the difficulty in scoring of major morphological traits used in the identification, they have deployed the diagnostic markers for better taxonomic characterization of Capsicum accessions. Lately, several studies have been executed by researchers throughout the world to assess genetic homology or diversity along with phylogenetic analysis using RAPD markers (Adetula 2006; Costa et al., 2006; Finger et al., 2010; Bhadragoudar and Patil 2011; Sitthiwong et al., 2005; Rad et al., 2009; Sanatombi et al., 2010; Thul et al., 2012). Among these different types of molecular markers, sequence-tagged microsatellite sites (STMS) based on microsatellite DNA loci have emerged as an important tool in molecular marker analysis. The variation in these microsatellite loci, termed as SSRs, have been comprehensively employed in plant genetics over the years due to their stability, codominance, multiallele genetic markers detection, as well as for better sensitivity (Mason 2015). However, single nucleotide polymorphisms (SNPs) analysis is an additional attractive molecular marker in breeding program. The SNPs are enormously abundant, mostly biallelic, easily scored and can be coupled with differences in phenotypic traits. The genetic diversity, along with structure of population of different accessions, was examined through a transcriptome-based SNPs marker and it was observed that C. annuum exhibited maximum diversity (Lee et al., 2016). The establishment of SNPs for genetic mapping, as well as for diversity analysis, were also executed by another group of researchers (Cheng et al., 2016). They have recognized SNP markers, constructed high- density genetic map, explored the genetic diversity of different capsicum species for the study of pepper molecular genetics and advanced breeding program. The pioneer work to develop polymorphic microsatellite markers of Capsicum, as well as molecular map, were executed in 2004 by a group of researchers (Lee et al., 2004). The investigators were able to successfully identify 32 microsatellite markers through screening of entire capsicum genome. Through EST-nricrosatellites analysis, polymorphism was detected between C. annuum cv TF68 and C. chinense cv Habanero. Consequently, SSR-based libraries were constructed from the C. annum genome and over six hundred unique SSR were detected (Minamiyama et al., 2006). Efficient breeding, as well as marker-assisted selection, could be executed through the construction of linkage map. In subsequent years, several groups of researchers have worked on pepper microsatellites markers to explore high- density linkage map in intra- and interspecific populations of Capsicum collected from different geographic locations (Ince et al., 2010; Mimura et al., 2012; Nagy et al., 2007; Patel et al., 2011; Rodrigues and Tam, 2010; Sugita et al., 2013; Huang et al. 2000; Yumnam et al., 2012; Alin et al., 2013; Rana et al., 2014; Rivera et al., 2016). The genetic characterization along with interactions among different capsicum germplasm was analyzed through high-throughput genome-wide markers. Pepper GeneChip® array (Affymetrix) for analysis of genome-wide transcript-based markers was developed to evaluate capsicum’s genetic polymorphism (Hill et al., 2013). The designed array offered maximum redundancy to detect single position polymorphism and more than 33,000 SSP markers were detected from 40 diverse C. annuum lines. The ‘state-of-the-art’ technology including next-generation sequencing was successfully deployed to the three pepper genotypes to identify SNPs and SSRs (Ashrafi et al., 2012). A large collection of transcriptomic data were analyzed through bioinformatics tools and thousands of SSRs and SNPs were detected among 65 Capsicum genotypes (Cheng et al., 2015). In order to explore genetic diversity among different pepper genotypes, SSRs combined with random amplified microsatellite polymorphism (RAMPO) markers were successfully deployed (Rai et ah, 2013). Among them, 25 polymorphic SSR markers and seventeen RAMPO markers with better polymorphic information content were detected. The PCR-based molecular markers corroborated with EST-based markers has explored the genetic diversity in Capsicum germplasm and exposed the avenue towards mapping the populations. The comprehensive research work on the development of different types of molecular markers in Capsicum and their applications in genetic diversity analysis is represented in Table 16.3.

 
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