Assessment of genetic diversity among sugarcane cultivars using novel microsatellite markers

Abstract

Genetic diversity based on the characterization of genetic makeup, using molecular markers is of utmost importance for breeders in crop improvement programme. A total of 26 microsatellite primers were used to determine the genetic diversity among 40 sugarcane genotypes including their parents. The polymerase chain reaction (PCR) products were examined for both size and polymorphism using these primers. Overall alleles are amplified with an average of 2.3 per locus in this study. Of the total 26 simple sequence repeat (SSR) markers, only 10 (38.4%) displayed polymorphism, with polymorphism index contents (PIC) values ranging from 0.15 to 0.67. The observed homozygosity (Ho) and gene diversity (Nei's) for individual loci varied from 0.0000 to 0.277 and 0.129 to 0.473, respectively. Shannon's informative index (I) was found to be highest (0.661) in SKM04 while the lowest was 0.252 in SKM01 SSR loci with an average of 0.524. Fixation index was also calculated which was in the range of-0.074 to 1.00. A genetic relationship among cultivars and parental genotype was also analyzed by cluster analysis using unweighted pair group method with arithmetic mean (UPGMA), the averagelinkage method, with the similarity matrix as input data. The genetic relationship and genetic diversity among the cultivars depicted from this study can be used to select the parents in sugarcane breeding programme.

Development and Use of Simple Sequence Repeats (SSRs) Markers for Sugarcane Breeding and Genetic Studies

“…SSR markers are useful in screening of sugarcane cultivars and in pedigree analysis because they represent a single locus [72,73]. Because they represent multiple alleles, these markers are reliable across a wide range of genetic sources [74,75].…”

“…Nayak et al [73] screened out 36 SSR markers on 1002 genotypes of sugarcane and related grasses, and recorded 209 alleles for important agronomic traits. Sharma et al [74] measured genetic diversity across 40 sugarcane genotypes and their parents by using 26 SSR primers. Tena et al [75] used 22 SSR markers to amplify a total of 260 alleles in a study of introduced sugarcane accessions in Ethiopia to determine population relationships and differentiation.…”

ANALYSIS OF GENETIC STABILITY OF MICROPROPAGATED SUGARCANE IN DIFFERENT SUBCULTURE FREQUENCIES USING SSR MARKER / Analisis Kestabilan Genetik Tebu Hasil Mikropropagasi pada Beberapa Frekuensi Subkultur Menggunakan Marka SSR

“…A total of 20 SSR primer pairs (Abdullah et al 2013;Sharma et al 2014) were used to analyze the genetic stability of sugarcane varieties (Table 1). Polymorphic Information Content (PIC) values of each SSR marker were analyzed using PowerMarker 3.25 software following the method described by Liu and Muse (2005).…”

“…The PCR reaction was carried out in a total volume of 20 µL containing a 20 ng DNA template, 1X PCR reaction buffer, dNTPs of 0.2 mM each, primers (forward and reverse) of 20 μM each and 1 unit of DNA polymerase. The process of DNA amplification was carried out following the PCR profile described by Sharma et al (2014). PCR amplification was performed on a PCR machine (Biorad T100TM Thermal Cycler).…”

Genotype-Specific Microsatellite (SSR) Markers for the Sugarcane Germplasm from the Karst Region of Guizhou, China

“…Molecular breeding scientists have successfully developed sugarcane SSRs including 221 genomic-SSRs developed by the International Sugarcane Microsatellite Consortium (ISMC) [11], 402 expressed sequence tags (EST)-derived SSRs developed by da Silva [12], 837 EST-SSRs from SUCEST by Souza's group [25] [26] [27] [28] [29], and 702 SSRs mined from both genomic and expressed sequences by the Indian Agricultural Research Institute (IARI) [30]. Some of the sugarcane SSR markers were applied to paternity analysis [31], genetic diversity assessment [32] [33] [34], genetic linkage map construction [28] [35], germplasm evaluation and variety identity testing [13] [36]. In addition, SSR technology combined with capillary electrophoresis and fluorescence detection system shows better performance in genotyping analysis due to higher accuracy and detection power [36].…”