Reliability and comparison of the polymorphism revealed in amaranth by amplified fragment length polymorphisms (AFLPs) and inters simple sequence repeats (ISSRs)

Abstract

The present study reported the effectiveness of two PCR-based molecular techniques, inters simple sequence repeats (ISSRs) and amplified fragment length polymorphisms (AFLPs), for genetic assessment of amaranth. The polymorphic loci ranged from 110 among A. caudatus to 228 among A. cruentus and 16 among A. tricolor to 56 among A. hypochondriacus for AFLP primer combinations and ISSR primers, respectively. Among the two marker systems used, ISSR fingerprinting detected the highest number of alleles per locus (1.83) compared to AFLPs (1.63). However, the assay efficiency index for AFLP was 14.49, more than five-fold higher than ISSR (1.75). The study also revealed that ISSR primers with di-nucleotide repeats gave a good fingerprint, indicating that di-nucleotide repeats are more frequent in amaranth genome. The reproducibility of the two marker systems was confirmed by the narrow gene diversity (0.03 ± 0.11 to 0.07 ± 0.17) observed between the controls. Bayesian consensus and neighbor-joining trees were constructed to describe the cluster arrangement among the Amaranthus spp. The cluster pattern was similar for both markers, though the cluster order in the trees was slightly different. The results of this study confirm the usefulness of AFLPs and ISSRs for the genetic assessment of amaranth.

Genetic diversity analysis and molecular characterization of grain amaranth genotypes using inter simple sequence repeat (ISSR) markers

“…In the present investigation, average bands per primer were 10.36. Raut et al (2014) and Oduwaye et al (2014) reported 4.41 and 6.57 average bands per ISSR primers in amaranth genotypes, respectively, which are very lower than the results of the present study. However, Ray and Roy (2007) and Žiarovská et al (2013) found 11.36 and 16.00 bands per primer, respectively, which is higher than the findings of the present investigation.…”

“…Overall, primers used in the present study gave the good amplification and can be used in the diversity analysis in grain amaranth. The average percent polymorphism among Amaranthus genotypes detected by the ISSR primers in the present investigation was 87.15%, which is higher than the findings of the previous reports, viz., 86.88% (Raut et al 2014) and 80.4% (Xu and Sun 2001), whereas it is lower than the findings of few previous reports, viz., 93% (Oduwaye et al, 2014) and 98.4% (Ray and Roy, 2007). Hence, it is concluded that the primers used in the present study possessed good power to differentiate the genotypes used in the study.…”

“…The average PIC value of all the 11 ISSR primers was 0.853, which indicates good selection of primers in the present study for the assessment of genetic diversity. Most of the previous studies were lacking of PIC calculation in diversity analysis of grain Amaranthus by ISSR; however, very low PIC values (0.48) was found in one of the past studies (Oduwaye et al 2014). As the primers used in the present study possessed very high PIC values, they have a high promising efficiency to be used in the genetic diversity analysis in grain amaranth.…”

CARACTERIZACIÓN DE LA DIVERSIDAD GENÉTICA DE UNA COLECCIÓN DE QUINUA (Chenopodium quinoa Willd)

“…El número de bandas por cebador varió entre 20 para el CGA y 35 para ACA, con pesos moleculares entre 300 y 1300 Kb, lo cual se considera adecuado para la estimación de los parámetros genéticos [9,19]. El porcentaje de loci polimórficos para los siete cebadores estuvieron en un rango comprendido entre el 86,36% al 100% (CCA y AG-CCA, respectivamente), con valores de heterocigosidad entre 0,28 para el cebador CT y 0,39 para CGA.…”

“…Asimismo se identificaron que las repeticiones CA, CGA y TG son las secuencias repetidas más frecuentes en el genoma de la quinua a comparación de CCA y AG las cuales parecen estar en uma menor frecuencia en los genotipos evaluados y está relacionado con los procesos evolutivos que ha sufrido la especie; resultados similares a los encontrados por Jarvis et al, 2008 [22], quienes desarrollaron un mapa de ligamiento usando marcadores SSR, AFLPs, la región de almacenamiento de proteína en la semilla (11S) y la región organizadora nucleolar (NOR) y en otras especies relacionadas como el amaranto [19].…”