Assessment of Genetic Relationship and Diversity among Chinese Sugarcane Parental Clones using SCoT and ISSR Markers

Abstract

Sugarcane is an allopolyploid crop with ≥120 or more chromosomes, of which~5.0-10% are Saccharum spontaneum and 90-95% are S. officinarum. The genetic characteristics of sugarcane provides a complex genetic background. The objective of this study was to use two molecular marker systems, start codon targeted (SCoT) and inter-simple sequence repeat (ISSR), to assess the genetic relationship and diversity of 75 sugarcane parental clones from Chinese sugarcane breeding program. Twenty-four SCoT primers produced 227 loci, of which 200 (88.11%) were polymorphic, whereas 15 ISSR primers resulted in a total of 146 loci, with 123 (84.25%) being polymorphic. Mean polymorphism information content values of 0.8152 and 0.8361 were detected using SCoT and ISSR primers, respectively. The genetic similarity coefficients ranged from 0.542 between ROC22 and HoCP95-988 to 0.831 between ROC25 and ROC20, with a mean value of 0.687 based on SCoT+ISSR data set. The unweighted pair group method of arithmetic averages (UPGMA) clusters and principal coordinate analysis (PCA) gave similar results. The 75 Chinese sugarcane parental clones were clustered into two main groups (A and B). Group A was primarily comprised of 42 clones from all Q-series, all CP-, HoCP-, or LCP-series, all YT-series and three Erianthus arundinaceus F4 innovative parental clones, etc., while 33 parental clones of Group B contained all TT-series, all GT-series, three Saccharum officinarum species, etc. The genetic similarity was high among the Q-series, CP-series, HoCP-series and YT-series. The genetic relationship was close among TT-series, GT-series and three S. officinarum species, while the genetic similarity between YT-series and TT-series or GT-series was low. There was an abundant genetic diversity among these sugarcane parental clones however the parental clones bred by the same breeding organization have a narrow genetic basis. This information was useful for selecting crossing parents and combinations. Correlation detection between SCoT and ISSR was not significant, but highly complementary, indicating that the combination of the two marker systems could avoid biases based on a single marker.

Microsatellite Genetic Markers of Saccharrum spp., and Erianthus sp. on Their Hybrids

“…Many study also reported that in many sugarcane crossing program around the world, the parents that used for crosses originated from inter-and intraspecific hybridization and its progenies. They results progenies with the same and share genetic makeup with parents (Stevenson, 1965;Zhang et al, 2001;Perera et al, 2012;Filho et al, 2010;Pan et al, 2003;Hapsoro et al, 2015;Chen et al, 2017). In contrast to previous result, in crosses between Erianthus sp.…”

“…This term based on the appearance of progenies at the early stage of selection (Sukarso, 1986in Budhisantoso, 2012. Therfore, the choice of parents and parents set is the crucial aspect in sugarcane breeding programe (Skinner, 1971in Budhisantoso, 2012Hapsoro et al, 2015;Chen et al, 2017). The choice of pricise parents and parents set will determine the success of the crossing by the appearance of progenies better than the average or the best parent value (heterosis).…”

Development of a SCAR Marker Based on SCoT Polymorphisms for Sugarcane Smut Resistance

“…The SCoT primers that generated polymorphic fragments in two bulk pools were first screened using the established SCoT-PCR (Chen et al 2017). Then, further testing of the selected primers using 10 lines (individuals in pools) was performed, and 34 control cultivars were assessed for primer polymorphisms and the specific fragment was obtained that was amplified only in the smut-resistant or susceptible materials.…”

“…The identification of smut resistance is an important part of sugarcane breeding, and the traditional identification method of sugarcane smut resistance involves phenotypic identification by artificial inoculation. However, this method is generally time and energy consuming, and it is difficult to evaluate disease resistance of the sample on a large scale, and the identification results are also affected by environmental interaction effects (Chen et al 2017). Marker assisted selection (MAS) is not affected by genotype and environment interactions and can significantly improve the selection efficiency and accuracy of disease-resistant breeding when combined with routine identification methods, although selection accuracy requires molecular markers that are closely linked to target traits (Lee 1995;Collard and Mackill 2007).…”

“…Due to its simplicity of operation, low cost, rich polymorphism, and good repeatability, this technology has been successfully applied to various investigations such as genetic diversity (Shen et al 2016;Shekhawat et al 2018), population structure analysis (Tiwari et al 2016;Golkar and Nourbakhsh 2019) and disease resistance (Zeng et al 2014;Li et al 2019). In addition, the primer length of SCoT is 18 bp, with the same reaction conditions as conventional PCR, although with higher stability (Shen et al 2016;Chen et al 2017). No study on the development of sugarcane smut resistance markers based on SCoT molecular marker technology combined with BSA analysis population has been conducted to date.…”