Variety Specific Markers Research Articles

Non-targeted metabolomics of cooked cowpea (Vigna unguiculata) and pigeon pea (Cajanus cajan) from Ghana using two distinct and complementary analytical platforms

Legumes are global staple foods with multiple human health properties that merit detailed composition analysis in cooked forms. This study analyzed cowpea [Vigna unguiculata] (three varieties: Dagbantuya, Sangyi, and Tukara), pigeon pea [Cajanus cajan], and common bean [Phaseolus vulgaris] using two distinct ultra-performance liquid chromatography mass spectrometry (UPLC-MS) platforms and analytical workflows. Comparisons between cowpea and pigeon pea consumed in Ghana, and common bean (navy bean) from USA, revealed 75 metabolites that differentiated cowpeas. Metabolite fold-change comparisons resulted in 142 metabolites with significantly higher abundance in cowpea, and 154 higher in abundance from pigeon pea. 3-(all-trans-nonaprenyl)benzene-1,2-diol, N-tetracosanoylphytosphingosine, and sitoindoside II are novel identifications in cowpea, with notably higher abundance than other legumes tested. Cowpea variety specific markers were tonkinelin (Dagbantuya), pheophytin A (Sangyi), and linoleoyl ethanolamide (Tukara). This study identified novel cowpea and pigeon pea food metabolites that warrant continued investigation as bioactive food components following consumption in people.

Comparison of relative efficiency of genomic SSR and EST-SSR markers in estimating genetic diversity in sugarcane.

Twenty-five primer pairs developed from genomic simple sequence repeats (SSR) were compared with 25 expressed sequence tags (EST) SSRs to evaluate the efficiency of these two sets of primers using 59 sugarcane genetic stocks. The mean polymorphism information content (PIC) of genomic SSR was higher (0.72) compared to the PIC value recorded by EST-SSR marker (0.62). The relatively low level of polymorphism in EST-SSR markers may be due to the location of these markers in more conserved and expressed sequences compared to genomic sequences which are spread throughout the genome. Dendrogram based on the genomic SSR and EST-SSR marker data showed differences in grouping of genotypes. A total of 59 sugarcane accessions were grouped into 6 and 4 clusters using genomic SSR and EST-SSR, respectively. The highly efficient genomic SSR could subcluster the genotypes of some of the clusters formed by EST-SSR markers. The difference in dendrogram observed was probably due to the variation in number of markers produced by genomic SSR and EST-SSR and different portion of genome amplified by both the markers. The combined dendrogram (genomic SSR and EST-SSR) more clearly showed the genetic relationship among the sugarcane genotypes by forming four clusters. The mean genetic similarity (GS) value obtained using EST-SSR among 59 sugarcane accessions was 0.70, whereas the mean GS obtained using genomic SSR was 0.63. Although relatively lower level of polymorphism was displayed by the EST-SSR markers, genetic diversity shown by the EST-SSR was found to be promising as they were functional marker. High level of PIC and low genetic similarity values of genomic SSR may be more useful in DNA fingerprinting, selection of true hybrids, identification of variety specific markers and genetic diversity analysis. Identification of diverse parents based on cluster analysis can be effectively done with EST-SSR as the genetic similarity estimates are based on functional attributes related to morphological/agronomical traits.

Genetic Diversity Analysis of Coconut (Cocos nucifera L.) Genotypes and Hybrids Using Molecular Marker

The present investigation was carried out to study molecular diversity of different coconut genotypes and hybrids using PCR based molecular markers to find out the phylogenic relationship among them. In this study, 15 RAPD, 15 ISSR and 15 SSR primers were used to observe the relationship and polymorphism of coconut genotypes. Total 15 RAPD primers used for the study has generated 82 polymorphic bands having 80 shared and 2 unique bands with an average of 5.46 bands with 100% polymorphism per primer. The 15 ISSR primers engendered 82 bands in which 80 bands were polymorphic with 75 shared and 5 unique bands that were equal to 100% polymorphism with an average of 5.3 bands per primer. Total 15 SSR primers generated the 28 fragments in which 23 bands were polymorphic having 22 shared and 1 unique band with 75.55% polymorphism with an average of 1.5 bands per primer. The similarity coefficient of clusters analysis ranged from 22 to 83% for RAPD, 26 to 86% for ISSR and 50 to 97% for SSR. Dendrogram construction of all these the molecular markers showed that in RAPD, Nikobar variety of coconut was the most diversified variety observed having alone separate position. The pooled study of RAPD, ISSR and SSR generated clustering pattern appeared to be similar as RAPD clustering pattern. Based on the molecular markers associated with coconut genotypes, it was concluded that all molecular markers like RAPD, ISSR and SSR are most reliable to distinguish coconut genotypes. RAPD primers OPC-05 and OPF-05, ISSR primers UBC-818, UBC-825, UBC-843, UBC-847 and UBC-848, SSR primer WCYZ3554 gave variety specific markers in all coconut varieties.

Genetic Diversity and Identification of Variety-specific RAPD and ISSR Markers in Foeniculum vulgare

Inter simple sequence repeats (ISSRs) and random amplification of polymorphic DNA (RAPD) were used to determine genetic relationships and variety specific markers in fennel varieties grown in Rajasthan. In this study, the percentage polymorphism revealed by RAPD and ISSR was 50 and 39.1%, respectively. Dendrogram constructed from unweighted pair group method with arithmetic mean cluster analysis based on RAPD and ISSR data showed clear genetic relationships among these germplasms. Similar clustering was obtained when another software DARwin 5 was used to construct tree plot from factorial analysis based on RAPD and ISSR data. Besides, from the bands amplified, there were three independent ways to identify the fennel varieties, such as unique RAPD and ISSR markers, unique band patterns and a combination of the band patterns provided by different primers. Finally, the molecular fingerprints have been generated for five fennel varieties, namely FNL-41, 46, RF-125, 143 and 178. These could be distinguished by using specific 10 RAPD and four ISSR markers, which showed either presence or absence of bands generated by seven RAPD and four ISSR primers.

Comparative Analysis of RAPD and ISSR Markers for Characterization of Sesame (Sesamum indicum L) Genotypes

The determination of genetic differences among crop genotypes has become the primary need to grant patent and the protection of Plant Breeder Rights (PBR). In the present study RAPD and ISSR markers were employed for the characterization of 16 sesame genotypes. Twenty six RAPD and 17 ISSR primers that generated clear and reproducible banding patterns amplified 194 and 163 bands, respectively among 16 sesame genotypes. Both RAPD and ISSR primers showed maximum discrimination power, and produced putative variety specific bands, which could be used for the identification of all the sesame genotypes, individually. However, only AG and CA based ISSR primers were found effective in the discrimination of genotypes. A poor correlation was observed between the matrices produced by RAPD and ISSR primers, which might be due to the array of different sites of the genome. Though, there was greater similarity among sesame genotypes (0.78 for RAPD and 0.71 for ISSR), the observed genetic diversity (0.22 for RAPD and 0.29 for ISSR), was found effective for the characterization of sesame genotypes. It is suggested that putative variety specific RAPD and ISSR markers could be converted to Codominant sequence characterized amplified region/sequence tagged site (SCAR /STS) markers to develop robust variety specific markers.

Application of RAPD and SI-typing techniques to confirm genetic integrity of radish ( Raphanus sativus L.) varieties

The random amplified polymorphic DNA (RAPD) and self-incompatibility (SI) typing techniques were applied to settle a lawsuit between a Seed Company and a farmer concerning seed impurity in radish ( Raphanus sativus L.). After sowing “Halra Woldong” (HW) a winter radish variety, two morphologically different radish plants grew. Genomic DNA from each of the two types were prepared and analyzed using ninety-six RAPD markers and four variety-specific markers were found. The polymorphic RAPD band patterns were compared with those of the twenty Korean radish varieties. The genetic integrity of the two varieties in question was identified and further confirmed by SI-typing of S-locus glycoprotein ( SLG) and S-locus receptor kinase ( SRK) genes.

Genetic Erosion from Modern Varieties into Traditional Upland Rice Cultivars (Oryza sativa L.) in Northern Thailand

The purpose of this study was to assess the extent of genetic erosion of traditional upland germplasm in northern Thailand as a result of gene-flow from distinct strains carrying different genotypes. Even modern variety specific markers have not been developed, there is a comparative population in Laos. Thus, both populations were compared with various characters to evaluate gene-flow from modern variety to landraces. Glutinous and glabrous strains are predominated in Laos. However, such strains were drastically decreased in north–east Thailand. Gene diversity is higher in Thailand, compared to Laos at seven isozyme loci. This was a result of the higher frequencies of Indica strains and heterozygotes in Thailand. Plastid type was also determined by using an INDEL marker. Nearly half of Indica strains carried the Japonica plastid. Heterozygotes also tended to carry Japonica cytoplasm. Such nuclear–cytoplasm substituted strains and heterozygotes were probably generated by natural hybridization. Japonica strains tended to be a maternal donor rather than Indica ones. Or Indica strains would easily release pollens, which grow outside of upland fields.

Genetic relationships and discrimination of ten influential Upland cotton varieties using RAPD markers.

Influential Upland cotton ( Gossypium hirsutum L.) varieties are those that have the higher genetic contributions to modern Upland cultivars than other germplasms. Our previous research has shown significant differences in general combining ability (GCA) effects for yield, yield components, and fiber properties among ten influential cotton varieties. In this study, we used random amplified polymorphic DNA (RAPD) data to evaluate DNA variation of these ten varieties. Of 86 random decamer primers screened for their capability of amplifying DNA via the polymerase chain reaction (PCR), 63 generated a total of 312 DNA fragments. Forty two bands were polymorphic, which showed a low percentage (13.5%) of DNA variation among these influential varieties. Genetic similarities among the ten varieties based on RAPD data were from 92.7% to 97.6%. All of the varieties were individually identified by variety specific markers in genetic fingerprinting. One primer, UBC-149, amplified a 1,430-bp DNA fragment that was absent in five varieties and present in the other five varieties. This RAPD marker had significant negative relationships with GCA-effect estimates for seed cotton yield, lint yield, number of bolls per plant and micronaire, and significant positive relationships with GCA effects for boll size and seed index. This finding, for the first time, identifies a DNA fragment in cotton that is a potential DNA marker linked to a yield gene(s) or a yield-related gene(s).