Molecular characterization of peanut (Arahcis hypogaea L.) germplasms in Bangladesh

Abstract

Eleven varieties of peanut (Arachis hypogaea L.) were investigated cytogenetically and at the molecular level using Random Amplified Polymorphic DNA (RAPD) and Simple Sequence Repeat (SSR) primers for authentic characterization. All varieties were found to possess 2n= 40 chromosomes, except BARI Cheena Badam-7 and BARI Cheena Badam-8, where a small extra chromosome found in addition to 2n=40 chromosomes in several cells. The extra chromosome may be considered as B-chromosome and this is the first report of B-chromosome in Arachis hypogaea. One pair (XX) of small chromosomes was found in all varieties. The 11 varieties showed distinct centromeric formulae viz., i) 34m+6sm, ii) 36m+4sm, iii) 38m+2sm, iv) 32m+ 8sm and v) 40m. All varieties of peanut have distinct CMA- and DAPIbanding patterns. The number, location, intensity and percentage of GC- and AT-rich repeats were different in these varieties. Asymmetry banding pattern in homologue members indicated minute chromosomal alterations. Similar numbers of CMA and DAPI bands were observed in different stages of cell cycle revealed that the GC- and AT-rich repeats were very stable in each variety. Few chromosomes could be used as marker chromosomes of respective variety due to their unique banding pattern. Genetic diversity analysis among 11 peanut varieties was performed through polymerase chain reaction (PCR) using RAPD and SSR primers. Eight arbitrary oligonucleotide RAPD primer and four pairs of SSR primer were used for DNA fingerprinting. In case of RAPD, a total of 272 bands were produced in all the 11 peanut varieties with an average of 34 bands per primer. Based on the banding pattern 71.69% polymorphisms observed among the peanut varieties. The molecular size of the amplified DNA fragments ranged from 400 to 3000 bp. Eight unique bands were amplified from the genome of the 11 peanut varieties. 62.06% polymorphic fragments and a unique band of 50 bp were found in four SSR primer pairs. The size of the amplified bands ranged from 50 to 246 bp. The values of pair-wise genetic distances ranged from 0.1226 to 0.5500, indicating the presence of wide genetic diversity. The highest genetic distance (0.5500) was found between Dhaka-1 vs BARI Cheena Badam-8 while the lowest (0.1226) between BINA Cheena Badam-2 vs BINA Cheena Badam-3 and Tridana Badam (DM-1) vs Basanti Badam (DG-2). Dendrogram based on Nei’s (1972) genetic distance was constructed using Unweighted Pair Group Method of Arithmetic Means (UPGMA) segregating the 11 varieties of peanut into two major clusters C1 and C2. BARI Cheena Badam-7 and BARI Cheena Badam-8 were distinctly related from the rest. Therefore, each variety could be characterized by combined cytogenetical and molecular features which would be helpful for future breeding programme. en_