Sequence-related amplified polymorphism (SRAP) markers for assessing genetic relationships and diversity in sugarcane germplasm collections

Abstract

Characterization of wild germplasm provides essential information on genetic diversity that breeders utilize for crop improvement. The potential of the sequence-related amplified polymorphism (SRAP) technique, which preferentially amplifies gene-rich regions, was evaluated to assess the genetic relationships among members of the Saccharum species. A panel of 31 SRAP primer combinations were used to score 30 genotypes of Saccharum officinarum, Saccharum spontaneum, Saccharum robustum, Saccharum sinense, Saccharum barberi and sugarcane hybrids, with Miscanthus and Erianthus included as outgroups. The amplifications produced 1364 DNA fragments for an average of 44 per primer combination, with 83% (1135) being polymorphic and 8.7% (119) being species specific. Based on the Dice index, all 30 genotypes were differentiated from each other with genetic similarity (GS) estimates ranging from 0.60 to 0.96 (mean ¼ 0.79). Both the dendrogram [obtained by the unweighted pairgroup method with arithmetic mean or (UPGMA)] and the non-metric multidimensional scaling method grouped the genotypes according to their phylogenetic relationships. Erianthus and Miscanthus were separated as two outgroups (at GS levels of 0.56 and 0.72, respectively) into two major clusters: cluster I separated the S. robustum, S. sinense, S. barberi and hybrids as different subgroups with each one including some S. officinarum clones, while cluster II included the S. spontaneum clones, exclusively. A S. officinarum -S. spontaneum sequence comparison of some of the monomorphic and polymorphic bands revealed 65 -90% homology with rice, corn or sugarcane sequences deposited in databases. The high discriminatory power coupled with the possibility that most of the amplicons may be amplifying gene-rich regions of the genome makes SRAP a potentially robust tool for genetic mapping aimed at markerassisted introgression in sugarcane.

Molecular Diversity Among Members of the Saccharum Complex Assessed Using TRAP Markers Based on Lignin-Related Genes

“…The PIC value is often used to measure the discriminatory power of a genetic marker system and the theoretical maximum PIC value for a dominant marker is 0.5 [27]. The PIC values reported in this study are comparable to those in previous studies that also used TRAP markers [14,16,27].…”

“…From the biplot, it is evident that a total of 324 polymorphic TRAP markers would be adequate to give a CV value of 5% as recommended value from earlier studies [28,29]. These values are comparable to what has been reported in previous studies involving Saccharum species using TRAP [15] and SRAP [27] markers.…”

“…Silver staining of the gel, and excision and elution of polymorphic bands were performed as described earlier [25]. The fragments were cloned into pGEMT-easy vector (Promega) and 39 positive clones were single-pass sequenced using T7 primer in a 3130xl genetic [14,26,27]. We previously reported a slightly lower number of polymorphic fragments on an almost identical set of genetic materials using TRAP markers based on sucrose, cold tolerance, and/or drought related genes [14].…”

“…S. barberi and S. sinense were more closely associated with each other in this study. These two species are known to be inter-specific hybrids of S. officinarum and S. spontaneum as has been established in several previous studies using RAPD [38], RFLP [39,40], AFLP [26], and SRAP [27] markers. While errors during plant sampling, labeling, and genotyping cannot be ruled out toward the misclassification of IS 76-184 (S. robustum) and China (S. sinense) in this study, such misclassification errors and their reasons were discussed in detail elsewhere [41].…”

Musa Genetic Diversity Revealed by SRAP and AFLP

“…It has several advantages over other molecular marker systems such as simplicity, reasonable throughput rate, disclosure of numerous co-dominant markers, ease of isolation of bands for sequencing and, most importantly, targeting of open reading frames (ORFs) [13]. SRAP has been used in other plant species, e.g., in Cucurbita pepo L. [14], Bixa orellana L. [15], sugarcane [16], or wheat [17]. Phothipan et al [18] used SRAP and RAPD molecular markers to study the genetic relationship amongst M. acuminata, M. balbisiana and plantains.…”