Use of SSR, RAPD markers and protein profiles based analysis to differentiate Eleusine coracana genotypes differing in their protein content

Abstract

Fifty-two genotypes of Eleusine coracana collected from Uttarakhand hills were subjected to simple sequence repeat (SSR), random amplified polymorphic DNA (RAPD)-PCR and protein profiling analysis to investigate the variation in protein content. The main objective of the present study was to detect variability among E. coracana and also assess the discriminating ability of these three molecular methods. A total of 21 RAPD and 24 SSR primers were assayed for their specificity in detecting genetic variability in E. coracana, of which 20 RAPD and 21 SSR primers were highly reproducible and were found suitable for use in PCR analysis. Assessing genetic diversity among E. coracana genotypes by RAPD-PCR using 20 polymorphic primers yielded 56 different RAPD markers which clustered the genotypes into different groups on the basis of protein content. Similarly, SSR-PCR with 21 polymorphic primers clustered the genotypes into different groups. On the other hand, biochemical typing of E. coracana using whole seed proteins generated profiles that showed no major difference indicating the technique to be not useful in typing genotypes of this crop. However, a few of the genotypes showed the presence of a unique band of 32 kDa that needs to be further investigated to understand the role of the protein from nutritional point of view, if any. In the present study, significant negative correlation (r = -0.69*) was found between the protein and calcium content of finger millet genotypes. Sodium Dodecyl Sulphate Polyacrylamide Gel Electrophoresis based seed storage proteins generated profiles showed no major differences in banding pattern among 52 finger millet genotypes while quantitative estimation of seed storage protein fractions using Lowry method revealed that glutelin was highest followed by prolamin, globulin and albumin.

Gene Discovery and Advances in Finger Millet [Eleusine coracana (L.) Gaertn.] Genomics—An Important Nutri-Cereal of Future

“…In addition, the seeds contain on an average 7% protein, which varies from 4.88 to 15.58% (Singh and Srivastava, 2006), and contains 44.7% of the essential amino acids (Mbithi-Mwikya et al, 2000). A significant negative correlation between calcium and protein content was observed by Kumar et al (2012) indicating that protein and calcium content improvement programmes cannot be simultaneously taken up in finger millet. Various proteins, including calmodulin, calcineurin-B like proteins, Ca-dependent protein kinases, calreticulin and calsequestrin have been found to regulate the calcium transporters, sensors and responders.…”

“…In all subsequent studies on genetic diversity, the genomic SSRs developed by Dida et al (2007) were repeatedly used. Most of these studies were limited to a small set of germplasm collections (Arya et al, 2013; De Villiers et al, 2015), local germplasm of a restricted area (Panwar et al, 2010a,b; Kumar et al, 2012) or the number of markers used were limited where large germplasm sets were analyzed (Bharathi, 2011; Kalyana Babu et al, 2014a, 2016; Ramakrishnan et al, 2016). In one such study using a set of 14 polymorphic genomic SSRs and three genic SSRs (Arya et al, 2013), greater magnitude of diversity in African as compared to Indian finger millet accessions was reported.…”

Comparative Genomics and Association Mapping Approaches for Blast Resistant Genes in Finger Millet Using SSRs

“…A considerable amount of molecular work has been carried out since the establishment of molecular biology techniques [9], [10]. Dida et al [11] generated the first ever genetic map of the finger millet genome using different types of markers like RFLP, AFLP, EST and SSR markers.…”

Genetic Linkage Map Construction and QTL Mapping of Salt Tolerance Traits in Zoysiagrass (Zoysia japonica)

“…These benefits justify the frequent application of the technique. It has been developed and used extensively to assess genetic diversity, phylogenetic relationships, construct genetic maps and identify QTLs [36], [38]–[41]. Some genetic linkage maps of zoysiagrass have been constructed using AFLP, RFLP and SSR molecular markers [7], [16]–[18], [42].…”