Exploring the genetic makeup and population structure among Capsicum accessions for crop improvement and breeding curriculum insights

Abstract

Background Capsicum or chilli is an important crop in India which exhibits immense structural and genetic variations reflecting their intra- and inter-specific relationships. The aim of this study was to establish relationships amongst 54 Capsicum accessions through analysis of genetic and population structure using ISSR markers. Results Out of 19, successful DNA amplifications were shown by 7 ISSR primers and a total of 80 bands were identified ranging between 8 and 14 with an average of 11.43 bands/primer. A significant degree of polymorphic information content (PIC), discriminating power (DP), resolving power (RP), effective multiplex ratio (EMR), and marker index (MI) were identified as 0.39, 0.70, 6.40, 5.88, and 2.30, respectively, using ISSR markers in chillies. The cross-transferability ranged from 8.0 to 72.15% with an average of 52.63% among chillies. Amongst genetic information, grand mean values were 0.264, 0.180, 0.376, 0.296, and 0.180, which correspond to Shannon’s information index (I), expected heterozygosity (He), Nei’s gene diversity, total diversity among species (Ht), diversity within species (Hs), respectively. Further, the coefficients of gene differentiation (Gst) and gene flow (Nm) were 0.393 and 0.773, representing higher genetic variation among the population which was confirmed by analysis of molecular variance (AMOVA). Conclusion ISSR markers represented a potent system for the estimation of relationships or variation studies and generated information useful for planning crop management and improvement strategies in chilli breeding.

Metabolic pathway responsive gene encoding enzyme anchored EST–SSR markers based genetic and population assessment among Capsicum accessions

“…In a similar study, an average primer polymorphism was 81.52%, ranging from 50-100% in Capsicum accessions using SCoT (Start Codon Targeted polymorphism) markers(Gupta et al 2019). In the present study, observed cross transferability ranged from 6.0-76% with an average of 44.52% among 48 different chilli accessions which are quite comparable with different chilli accessions using other marker systems(Nagy et al 2007;Portis et al 2007;Rai et al 2013;Gupta et al 2019;Haq et al 2022). Thus, results of primer polymorphism and cross transferability displayed competency of chosen primers and exhibited inter accessions polymorphism and allelic conservation among chillies.…”

Genetic variation of Amaranthus retroflexus L. and Chenopodium album L. (Amaranthaceae) suggests multiple independent introductions into Iran

“…Moreover based on PIC values, it can be concluded that the capacity of the marker system to detect polymorphic loci in a single amplification was very efficient; the average value of this coefficient amounted 0.78 for A. retroflexus L. and 0.71 for C. album L.. These results demonstrate this technique can be conveniently used for the genetic characterization of these populations of A. retroflexus L. and C. album L. Use of ISSR markers are also recently reported as a functional markers elsewhere (Sivaprakash et al, 2004;Yan et al, 2019;Kwiecińska-Poppe et al, 2020;Alotaibi and Abd-Elgawad, 2022;Flihi et al, 2022;Ghanbari et al, 2022;Haq et al, 2022).…”

“…ISSR markers are highly reproducible and accurate tools that generate highly reproducible banding patterns from a single polymerase chain reaction (PCR) amplification (Raut et al, 2014;Stefunova et al, 2014). Although newer technique are available, ISRR makers have historically (Wolfe et al, 1998) and recently (Yan et al, 2019;Kwiecińska-Poppe et al, 2020;Tang and Ma, 2020;Liu et al, 2021;Alotaibi and Abd-Elgawad, 2022;Flihi et al, 2022;Ghanbari et al, 2022;Haq et al, 2022) been used successfully for diversity studies and structuring of natural populations. Genomic DNA was isolated from the young leaves of plants according to the cetyltrimethylammonium bromide (CTAB) method described by Saghai-Maroof et al (1984).…”