CAAT Box-derived Polymorphism Markers Research Articles

Exploring the efficacy of targeted fingerprinting marker techniques in genetic studies of the Indian poppy (Papaver somniferum L.): A comparative analysis

Targeted fingerprinting marker techniques have emerged as promising tools in plant sciences, particularly in plant breeding. To initiate an effective breeding program for a licit but industrially potential plant, the opium poppy, a comparative assessment of these markers was conducted. In this study, we compared the Start Codon Targeted polymorphism (SCoT), CAAT box-derived polymorphism (CBDP), and Expressed sequence tag-simple sequence repeats (EST-SSRs) markers for their competence and informativeness in revealing genetic identity, relatedness, and diversity among ten released varieties of the Indian opium poppy. Among the markers studied, EST-SSR markers demonstrated higher discriminating power, attributed to their ability to unveil comparatively higher polymorphic information content, marker index, and effective marker index. While all three marker systems effectively discriminated the poppy varieties, EST-SSR markers showed greater genetic diversity and a more informative ancestral history-based dendrogram topology. Significant correlation coefficients were observed between EST-SSR and CBDP markers, particularly in the combined marker dataset. Furthermore, the co-phenetic correlation was significant for three marker systems, with EST-SSR markers showing maximum correlation. Notably, the dendrograms constructed using EST-SSR markers and combined marker data displayed a significant and positive correlation with phenotypic traits assessed for the ten poppy varieties. Overall, the findings highlight the superiority of EST-SSR markers in deciphering genetic relationships among Indian opium poppy varieties and suggest their potential as valuable tools in breeding and genetic diversity studies.

Deciphering the level of genetic diversity in some aegilops species using CAAT box-derived polymorphism (CBDP) and start codon target polymorphism (SCoT) markers.

Maintaining genetic diversity is of the most essential principle for a long-term conservation of plant genetic resources and could play a crucial role in their management. The genus Aegilops is one important member of wheat germplasm, and there are evidences that novel genes of this genus' species can be studied/utilized as ideal sources for the wheat cultivar improvement. The objective of this study was to dissect the genetic diversity and population structure among a set of Iranian Aegilops using two gene-based molecular markers. This study investigated the level of genetic diversity among 157 Aegilops accessions consisting of Ae. tauschii Coss. (DD genome), Ae. crassa Boiss. (DDMM genome), and Ae. cylindrica Host. (CCDD genome) belonging to NPGBI using two sets of CBDP and SCoT markers. The SCoT and CBDP primers yielded 171 and 174 fragments, out of which 145 (90.23%) and 167 (97.66%) fragments were polymorphic, respectively. The average of polymorphism information content (PIC)/ marker index (MI)/resolving power (Rp) for SCoT and CBDP markers were 0.32/3.59/16.03 and 0.29/3.01/16.26, respectively. Results of AMOVA revealed the genetic variability within species was greater than the variation observed among them (SCoT: 88% vs. 12%; CBDP: 72% vs. 28%; SCoT + CBDP: 80% vs. 20%). Based on the information obtained from both markers, the higher level of genetic diversity was found in Ae. tauschii as compared to other species. The grouping patterns obtained by Neighbor-joining algorithms, principal coordinate analysis (PCoA), and Bayesian-model-based structure were consistent with each other and resulted in grouping all studied accessions according to their genomic constitutions. The results of this study revealed a high level of genetic diversity among Iranian Aegilops germplasm. Moreover, SCoT and CBDP marker systems were efficient in deciphering DNA polymorphism and classification of Aegilops germplasm.

Phytochemical and genetic marker (SCoT and CBDP) based study of genetic diversity and population structure in natural populations of Cannabis sativa L.: A high-value sustainable biodiversity of North-Indian Himalaya

Cannabis sativa is a versatile, sustainable cash crop grown in vast agro-climatic zones of India. The present study used comprehensive datasets involving phytochemical and molecular genotyping to characterize forty-two wild cannabis accessions collected from fourteen geographical locations of the North Indian Himalayas. Two gene-targeted dominant molecular markers, i.e., start codon targeted (SCoT) polymorphism and CAAT-box derived polymorphism (CBDP), were used for molecular genotyping to evaluate genetic assortment and interrelatedness among and within wild inhabitants of C.sativa. Multiple t-tests indicated significant differences among the studied cannabis populations for the phytochemical traits. Five major cannabinoids were identified in Indian Cannabis sativa germplasm, and most of the populations were of drug/marijuana types. The considerable diversity in drug types was observed at the chemical and genetic levels. Twenty-six SCoT and twenty-one CBDP markers generated a sum of 134, and 80 alleles averaged with 3.08 and 6.65 alleles per primer, respectively. The average polymorphic information content (PIC) and resolving power per primer indicated both SCoT and CBDP as ideal markers system for genetic diversity study in Cannabis sativa. The population diversity analysis based on SCoT, CBDP, and cumulative marker dataset revealed a high genetic differentiation (Gst>0.15), and a low estimated gene flow (Nm<1.0) between the studied populations. The highest gene diversity (H) and Shannon diversity Index (I) were observed for the population of Matiyal location (Pop3) using SCoT and cumulative marker dataset. However, Population 7 (Pop7) of location Kanatal was found to be highly diverse using the CBDP marker dataset. The multivariate analyses, i.e., Neighbour-joining tree based phenetic analysis, Principal Coordinate Analysis (PCoA), and Structure, revealed that there was no individual geographical location based grouping among the cannabis populations using both markers data set individually and their cumulative datasets. However, the allocation of accessions in common groups corresponding to their geographical locations was maximum in the case of Analysis with a cumulative marker data set. Analysis of molecular variance (AMOVA) also demonstrated a maximum percentage of molecular variation at the intra-population level (77–86%) rather than the inter-population level (14–23%). Altogether, our data suggest that both SCoT and CBDP markers are the ideal markers to study the genetic relationship among geographically different populations of C.sativa, and populations identified as highly diverse can be utilized as parents in Indian cannabis breeding programs.

Investigation of molecular variability in some Aegilops species using Start Codon Targeted Polymorphism (SCoT) and CAAT-Box Derived Polymorphism (CBDP) markers

Among wild relatives of wheat, Aegilops species are ideal genetic resources for the discovery of new characteristics such as resistance to environmental stresses and even grain quality for wheat improvement. Hence, knowledge of the population structure and genetic diversity of this germplasm is very important for their conservation and further utilization. In the present study, 80 accessions of the Aegilops including Ae. tauschii, Ae. cylindrica and Ae. triuncialis were investigated for genetic diversity using SCoT and CBDP markers. Eight SCOT and twelve CBDP primers amplified a total of 84 and 94 fragments with a mean of 10.50 and 7.83 fragments per primer, respectively. Resolving power (Rp) for SCoT and CBDP primers varied between 6.04 and 11.65, and 13.08 and 28.02, with the polymorphic information content (PIC) from 0.40 to 0.49 and 0.35 to 0.48, respectively. The results of analysis of molecular variance (AMOVA) indicated that the highest proportion of genetic variance referred to between species. SCoT primers indicated high values for all informativeness parameter (except resolving power) than CBDP primers across all tested accessions. However, CBDP primers indicated higher values of the genetic parameters than using SCoT primers. As a result, the maximum values for genetic parameters such as number of effective alleles (Ne), Nei?s gene diversity (H) and Shannon?s information index (I) were detected in Ae. cylindrica and Ae. triuncialis using SCoT and CBDP markers, respectively. Cluster analysis based on those molecular system grouped all accessions into three main clusters. The grouping pattern observed by CBDP primers indicated more clear phylogenetic relationship among some Aegilops species, so that PCoA?s results confirmed the grouping pattern. In conclusion, it was observed that SCoT and CBDP displayed good efficiency in depicting polymorphism among the tested accessions, however, CBDP markers provided a clear grouping pattern of evaluated accessions. Hence, the use of CBDP markers in determining population structure and estimating genetic diversity in other plant species is recommended.

Elucidating genetic diversity and population structure in jamun [Syzygium cumini (L.) Skeels] using morpho-physiological traits and CAAT box-derived polymorphism

• Assessment of morpho-physiological and molecular diversity in Syzygium cumini . • Population structure analysis using CBDP markers. • CBDP markers were highly informative in detecting the polymorphism. • Evidence for high levels of gene flow and less genetic differentiation. The use of molecular markers has received little attention in jamun [ Syzygium cumini (L.) Skeels], an underutilized fruit crop highly valued for its medicinal and nutraceutical properties. In this study, 50 jamun accessions from four different populations were analyzed using 21 morpho-physiological traits and 22 polymorphic gene-targeted CAAT box-derived polymorphism (CBDP) markers. The morpho-physiological variability was fairly high among the jamun accessions. The UPGMA analysis based on morpho-physiological traits produced three clusters with a cophenetic correlation of 0.75, reflecting a good fit between the original matrix and the clustering algorithm. The average polymorphism of 91.17% and the wide-ranging heterozygosity values (0.282-0.499) for the CBDP markers revealed considerable genetic variation among jamun genotypes. The average PIC of 0.352 evinced a high discriminatory power of the CBDP markers in distinguishing the accessions. CDBP data-based UPGMA clustering and population structure analysis identified four distinct populations; albeit with overlaps among them. This, together with the existence of admixed types in all four populations, indicated a fairly high degree of gene flow within jamun populations sampled in this study. It is therefore likely that despite widely differing geographic origins, some accessions in all the populations have a shared ancestral origin. Analysis of Molecular Variance also supports this assumption, as an exceedingly higher within-population variance (84%) than among-population variance (16%) reflected a high degree of gene flow and low genetic differentiation for the Jamun populations examined. Our findings improve the existing understanding vis-à-vis genetic diversity and population structure in jamun, and are expected to increase the use of CBDP and similar marker techniques in cultivar development programs.

An Analysis of Genetic Variability and Population Structure in Wheat Germplasm Using Microsatellite and Gene-Based Markers

Knowledge of the natural patterns of genetic variation and their evolutionary basis is required for sustainable management and conservation of wheat germplasm. In the current study, the genetic diversity and population structure of 100 individuals from four Triticum and Aegilops species (including T. aestivum, Ae. tauschii, Ae. cylindrica, and Ae. crassa) were investigated using two gene-based markers (start codon targeted (SCoT) polymorphism and CAAT-box derived polymorphism (CBDP)) and simple-sequence repeats (SSRs). The SCoT, CBDP, and SSR markers yielded 76, 116, and 48 polymorphism fragments, respectively. The CBDP marker had greater efficiency than the SCoT and SSR markers due to its higher polymorphism content information (PIC), resolving power (Rp), and marker index (MI). Based on an analysis of molecular variance (AMOVA) performed using all marker systems and combined data, there was a higher distribution of genetic variation within species than among them. Ae. cylindrica and Ae. tauschii had the highest values for all genetic variation parameters. A cluster analysis using each marker system and combined data showed that the SSR marker had greater efficiency in grouping of tested accessions, such that the results of principal coordinate analysis (PCoA) and population structure confirmed the obtained clustering patterns. Hence, combining the SCoT and CBDP markers with polymorphic SSR markers may be useful in genetic fingerprinting and fine mapping and for association analysis in wheat and its germplasm for various agronomic traits or tolerance mechanisms to environmental stresses.

Molecular diversity analysis in hexaploid wheat (Triticum aestivum L.) and two Aegilops species (Aegilops crassa and Aegilops cylindrica) using CBDP and SCoT markers

BackgroundEvaluation of genetic diversity and relationships among crop wild relatives is an important task in crop improvement. The main objective of the current study was to estimate molecular variability within the set of 91 samples from Triticum aestivum, Aegilops cylindrica, and Aegilops crassa species using 30 CAAT box–derived polymorphism (CBDP) and start codon targeted (SCoT) markers. ResultsFifteen SCoT and Fifteen CBDP primers produced 262 and 298 fragments which all of them were polymorphic, respectively. The number of polymorphic bands (NPB), polymorphic information content (PIC), resolving power (Rp), and marker index (MI) for SCoT primers ranged from 14 to 23, 0.31 to 0.39, 2.55 to 7.49, and 7.56 to 14.46 with an average of 17.47, 0.34, 10.44, and 5.69, respectively, whereas these values for CBDP primers were 15 to 26, 0.28 to 0.36, 3.82 to 6.94, and 4.74 to 7.96 with a mean of 19.87, 0.31, 5.35, and 6.24, respectively. Based on both marker systems, analysis of molecular variance (AMOVA) indicated that the portion of genetic diversity within species was more than among them. In both analyses, the highest values of the number of observed (Na) and effective alleles (Ne), Nei’s gene diversity (He), and Shannon’s information index (I) were estimated for Ae. cylindrica species. ConclusionThe results of cluster analysis and population structure showed that SCoT and CBDP markers grouped all samples based on their genomic constitutions. In conclusion, the used markers are very effective techniques for the evaluation of the genetic diversity in wild relatives of wheat.

Assessment of genetic diversity among Iranian Aegilops triuncialis accessions using ISSR, SCoT, and CBDP markers

BackgroundCrop wild relatives (CWRs) are commonly used as a suitable genetic reservoir for plant breeding. They can be used for enhancing the tolerance of plant varieties to biotic and abiotic stresses. Studying the genetic diversity of related wheat species in Iran could be useful to improve different traits of bread wheat, since the country is one of the major centers of genetic diversity and distribution of Aegilops species. Therefore, the aim of the present study was to determine the relationship among 48 Aegilops triuncialis accessions using three DNA marker systems, including start codon targeted (SCoT), CAAT box-derived polymorphism (CBDP), and inter-simple sequence repeat (ISSR) markers. ResultsA total of 359 amplified DNA fragments were generated using 13 CBDP, 14 SCoT, and 16 ISSR primers that produced 96, 147, and 152 bands, respectively. The discriminating power of the three markers was assessed using polymorphism information content (PIC), marker index (MI), and resolving power (Rp). The mean values of PIC for ISSR, SCoT, and CBDP markers were 0.3, 0.26, and 0.34, respectively, indicating the efficiency of the three markers in detecting polymorphism among the studied accessions. ISSR markers had the highest values of MI, Rp, and polymorphism percentage as compared to SCoT and CBDP markers. Based on the Shannon index and heterozygosity values, genetic diversity in the Alborz population was more than in other populations. The accessions were classified into six, five, and five groups based on ISSR, SCoT, and CBDP using the UPGMA method. According to the results of cluster and PCoA analyses, the variation patterns corresponded with the geographical distribution of the Ae. triuncialis accessions. ConclusionsThe three markers provided a comprehensive pattern of the genetic diversity among the Iranian Ae. triuncialis accessions. This information could allow for a future insight into wheat breeding programs.

Genetic Diversity and Population Structure Analysis of Landrace and Wild Relatives of Lentil Germplasm Using CBDP Marker

Assessment of genetic diversity and population structure of germplasm collections provides an opportunity for plant breeders to develop new and improved cultivars. In this study, genotypic variation of 90 lentil genotypes was evaluated using 10 CAAT Box Derived Polymorphism (CBDP) markers. The polymorphism percentage was 100% with an average of 100% indicating a high polymorphism level. A total of 117 alleles were identified for different genetic locations and with an average of 13 alleles per primer. Among CBDP markers used, the highest allele amplified belonged to CBDP22 marker with 21 bands and the lowest allele amplified corresponded to CBDP3, CBDP6 and CBDP13 markers with 11 bands. The Polymorphic information content (PIC) ranged from 0.413 to 0.471 with an average of 0.448. Marker Index (MI) ranged from 4.85 to 9.90. The highest index for genetic diversity (PIC and MI) belonged to the CBDP22 indicating a high resolution for this marker as compared to other markers. Based on neighbor joining clustering for molecular data, genotypes were grouped into five distinct groups. Population structure analysis showed that the highest peak was at K = 3, indicating the presence of three major clusters. The results of this study showed that CBDP markers can be used as a useful tool for studying the genetic diversity of lentil germplasm.

Genome diversity and population structure analysis of Iranian landrace and improved barley (Hordeum vulgare L.) genotypes using arbitrary functional gene-based molecular markers

Barley (Hordeum vulgare L. subsp. vulgare) is one of the earliest domesticated crop plants, which originated in Fertile Crescent. Genetic diversity analysis in primary gene pool and landraces is an effective strategy for germplasm conservation and utilization in breeding programs. In this study, Eighty-two barley genotypes comprised 22 Iranian improved cultivars and 60 landrace accessions collected from different zones of Iran were assumed for genetic diversity analysis using three gene targeted markers, start codon targeted (SCoT) polymorphism, conserved DNA-derived polymorphism (CDDP) and CAAT box-derived polymorphism (CBDP) in comparison with sequence-related amplified polymorphism (SRAP) markers. A total of 40 primers (10 primers from each marker) detected genetic polymorphism among barley genotypes. Four different marker types showed high level of polymorphism and SRAP markers produced higher number of polymorphic bands (67) in comparisons with SCoT, CDDP and CBDP. Average PIC values for SCoT, CDDP, CBDP and SRAP were 0.33, 0.37, 0.37 and 0.31, respectively. Marker index (MI) in SRAP and CBDP markers was higher than SCoT and CDDP markers. Cluster analysis using CDDP, CBDP and SRAP markers grouped barley genotypes in three distinct groups, while SCoT markers divided genotypes in four clusters. There were positive correlations between similarity matrixes obtained by each marker types. The results from cluster analysis and STRUCTURE analysis using combined data grouped barley genotypes in three clusters and the grouping of genotypes was strongly in agreement with their origins. Results showed that genotypes from west and north-west of Iran grouped in distinct clusters from those originated from north-east and center of Iran. To our knowledge, this is the first detailed report of using gene targeted molecular marker for genetic diversity analysis in barley. Our results showed the efficiency of these markers for genetic diversity analysis in barley and their potential for genome diversity and germplasm conservation.

The study of genetic diversity in a minicore collection of durum wheat genotypes using agro-morphological traits and molecular markers

The evaluation of genetic diversity in a gene pool contributes to the effective selection of genotypes and truncates the breeding time. In the present study, 96 durum wheat genotypes were evaluated for (1) genotypic diversity using two DNA marker systems: CAAT box-derived polymorphism (CBDP) and inter-simple sequence repeats (ISSR) markers and (2) phenotypic diversity using several drought-adaptive traits under rainfed conditions for two cropping seasons. Our results revealed that the ISSR primers produced 99 bands across the genotypes, the average of which was 6 fragments per primer, whereas CBDP primers generated 70 polymorphic bands, with an average of 5.3 fragments per primer. The values of marker index (MI) and polymorphism information content (PIC) indicated that CBDP markers were more efficient than ISSR markers for detection of genetic diversity in durum wheat. The average of PIC values for the CBDP and ISSR markers were 0.40 and 0.23, respectively. Based on the values of Shannon index (I) ICARDA population had a higher than CIMMYT population and the heterozygosis values confirmed these results. Dendrogram was created with a neighbor-joining clustering method. The studied genotypes were divided into five and seven groups based on data from the CBDP and ISSR markers, respectively, which was supported by principal coordinate analyses. The results of genotype by trait biplot analysis showed different patterns of interaction accessions and traits across years. High level of diversity among the studied accessions based on each studies trait was observed.

Characterization of Induced High Yielding Cowpea Mutant Lines Using Physiological, Biochemical and Molecular Markers

Cowpea, Vigna unguiculata (L.) Walp. is an important grain legume grown in the dry agro-ecologies of the tropics with considerably low yield due to lack of improved varieties, aggravated by prevalent narrow genetic base. Thus, induced mutagenesis was employed using sodium azide and gamma rays to increase genetic variability in cowpea genotypes that resulted in isolation of eleven high yielding mutant lines at the M4 generation from the genetic background of cowpea varieties Gomati VU-89 and Pusa-578. In order to analyze the induced genetic divergence among the mutant lines and parent genotypes, biochemical and molecular characterization was carried out with sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), simple sequence repeat (SSR) and CAAT box derived polymorphism (CBDP) markers. Activity of nitrate reductase (NR) and content of chlorophyll, carotenoid, protein and mineral were found to be significantly high in the selected mutant lines compared to their respective parent genotypes. SDS-PAGE profile of seed proteins generated 54 and 28 polymorphic bands and a total polymorphism of 62.06 and 41.17% in Gomati VU-89 and Pusa-578, respectively. SSR primers amplified a total of 16 and 24 polymorphic bands with an average polymorphism of 20.69 and 50.74% in Gomati VU-89 and Pusa-578, respectively. CBDP markers, used for the first time in mutagenized population, generated 175 bands with 77 bands being polymorphic in Gomati VU-89 and 121 bands with 59 bands being polymorphic in Pusa-578. Physiological, biochemical and molecular profiling of the selected promising mutants lines showed that Gomati VU-89-G and Pusa-578-C are genetically most diverged high yielding genotypes with significant increase in protein and micronutrient content, therefore, could be recommended for further research considerations. Thus, the favorable combination of genes induced in the novel cowpea mutants selected through the present study are valuable to correspond farmers requirements for new improved cultivars (direct or hybrids).

Assessment of genetic diversity and relationships among Salvia species using gene targeted CAAT box-derived polymorphism markers

To detect the genetic variation and relationships among different Salvia ecotypes/species, the gene targeted CAAT box derived polymorphism (CBDP) markers were employed in terms of their efficiency. In this study, 25 CBDP primers amplified a total of 323 different polymorphic fragments that discriminate all 26 Salvia ecotypes/species and produced an informative and differentiated dendrogram and population structure. The CBDP markers were found to be effective in Salvia genetic diversity estimation with regard to the averages polymorphism (100%), polymorphism information content (PIC = 0.89), marker index (MI = 4.5) and the effective multiplex ratio (EMR = 5.01) which were higher than other reported markers on Salvia. The extent of heterozygosity (0.034≤H≤0.223) and Shannon index (0.042≤I≤0.278) indicated a high level of genetic variation among Salvia species. The species containing the highest basic chromosome number (X = 12) revealed the highest values for the number of different (Na) and effective (N e) alleles, Shannon index (I), and heterozygosity (H). Additionally, the tetraploid species showed high values of N a, Ne, I and H compared to the diploid species. Mean of gene differentiation (Gst) among Salvia species was 0.792, and the estimation of gene flow (Nm) was 0.13, indicating high genetic differentiation. Remarkably, similar results were obtained from the principal co-ordinate analysis (PCoA) as compared with the cluster analysis, in which all different Salvia species formed individual groups. In conclusion, because the CBDP markers are derived from the gene containing regions of the genome, consequently, the high genetic diversity among studied Salvia species would be more useful for crop improvement programmes, such as hybridization between species and QTL mapping. The potential of CBDPs for analysing the phylogeny and genetic diversity of Salvia species is another key result with practical implications.

Genetic diversity and population structure analysis of landrace and improved safflower (Cartamus tinctorious L.) germplasm using arbitrary functional gene-based molecular markers

The genetic diversity and relationships among 48 landrace and improved safflower (Carthamus tinctorius L.) genotypes were analyzed using three gene-targeted markers, start codon-targeted (SCoT) polymorphism, conserved DNA-derived polymorphism (CDDP) and CAAT box-derived polymorphism (CBDP). A total of 30 primers (10 primers from each marker) detected genetic polymorphism among the safflower genotypes. Three different marker types showed high level of polymorphism and the CDDP markers produced a higher number of polymorphic bands (74) in comparisons with SCoT and CBDP. The average PIC values for SCoT, CDDP, and CBDP were 0.39, 0.43, and 0.41, respectively. The marker index (MI) in CDDP markers was higher than that in SCoT and CBDP markers. Cluster analysis using SCoT and CDDP markers grouped the safflower genotypes into three distinct groups, whereas the CBDP markers divided the genotypes into two clusters. There were positive correlations between the similarity matrices obtained by each marker type. The results from the cluster analysis and STRUCTURE analysis using combined data grouped the genotypes into two clusters, generally in agreement with their origins. To our knowledge, this is the first detailed report of using gene-targeted molecular markers for genetic diversity analysis in safflower. Our results showed the efficiency of these markers for genetic diversity analysis in safflower and their potential for genome diversity and germplasm conservation.

Molecular characterization of the wild relatives of wheat using CAAT-box derived polymorphism

A molecular assessment of genetic diversity was performed on a set of 228 selected accessions belonging to the different Aegilops and Triticum species using CAAT-box derived polymorphism (CBDP) markers. Fifteen CBDP primers generated 141 polymorphic fragments with an average of 9.40 per primer. The average of polymorphic information content and resolving power revealed a high efficiency of CBDP markers in analyzing genetic diversity among different wheat genotypes. The diversity indexes including polymorphic loci percent, number of observed and effective alleles, Shannon’s index and gene diversity among different populations were 76.24%, 1.67, 1.49, 0.42 and 0.28, respectively. These essentially coincided with the analysis of molecular variance results, indicating that 86, 68, and 59.46% of genetic variation were found within two Aegilops and Triticum genera and their populations, respectively. Genetic relationships inferred from cluster analysis was matched with STRUCTURE analysis, disclosing the accessions were grouped based on their genomic constitution. Furthermore, these results were confirmed by principal coordinate analysis (PCoA). Taken together, our results suggest that CBDP markers will be useful for genetic diversity assessment in the domesticated and wild relatives of wheat.

Genetic diversity analysis among male and female Jojoba genotypes employing gene targeted molecular markers, start codon targeted (SCoT) polymorphism and CAAT box-derived polymorphism (CBDP) markers

To detect genetic variations among different Simmondsia chinensis genotypes, two gene targeted markers, start codon targeted (SCoT) polymorphism and CAAT box-derived polymorphism (CBDP) were employed in terms of their informativeness and efficiency in analyzing genetic relationships among different genotypes. A total of 15 SCoT and 17 CBDP primers detected genetic polymorphism among 39 Jojoba genotypes (22 females and 17 males). Comparatively, CBDP markers proved to be more effective than SCoT markers in terms of percentage polymorphism as the former detecting an average of 53.4% and the latter as 49.4%. The Polymorphic information content (PIC) value and marker index (MI) of CBPD were 0.43 and 1.10, respectively which were higher than those of SCoT where the respective values of PIC and MI were 0.38 and 1.09. While comparing male and female genotype populations, the former showed higher variation in respect of polymorphic percentage and PIC, MI and Rp values over female populations. Nei's diversity (h) and Shannon index (I) were calculated for each genotype and found that the genotype “MS F” (in both markers) was highly diverse and genotypes “Q104 F” (SCoT) and “82–18 F” (CBDP) were least diverse among the female genotype populations. Among male genotypes, “32 M” (CBDP) and “MS M” (SCoT) revealed highest h and I values while “58-5 M” (both markers) was the least diverse. Jaccard's similarity co-efficient of SCoT markers ranged from 0.733 to 0.922 in female genotypes and 0.941 to 0.746 in male genotype population. Likewise, CBDP data analysis also revealed similarity ranging from 0.751 to 0.958 within female genotypes and 0.754 to 0.976 within male genotype populations thereby, indicating genetically diverse Jojoba population. Employing the NTSYS (Numerical taxonomy and multivariate analysis system) Version 2.1 software, both the markers generated dendrograms which revealed that all the Jojoba genotypes were clustered into two major groups, one group consisting of all female genotypes and another group comprising of all male genotypes. During the present investigation, CBDP markers proved more informative in studying genetic diversity among Jojoba. Such genetically diverse genotypes would thus be of great significance for breeding, management and conservation of elite (high yielding) Jojoba germplasm.