Amplified Fragment Length Polymorphism: Applications and Recent Developments

AFLP or amplified fragment length polymorphism is a PCR-based molecular technique that uses selective amplification of a subset of digested DNA fragments from any source to generate and compare unique fingerprints of genomes. It is more efficient in terms of time, economy, reproducibility, informativeness, resolution, and sensitivity, compared to other popular DNA markers. Besides, it requires very small quantities of DNA and no prior genome information. This technique is widely used in plants for taxonomy, genetic diversity, phylogenetic analysis, construction of high-resolution genetic maps, and positional cloning of genes, to determine relatedness among cultivars and varietal identity, etc. The review encompasses in detail the various applications of AFLP in plants and the major advantages and disadvantages. The review also considers various modifications of this technique and novel developments in detection of polymorphism. A wet-lab protocol is also provided.

Diversity analysis in Indian genotypes of linseed (Linum usitatissimum L.) using AFLP markers

AFLP fingerprinting of 45 Indian genotypes of linseed was carried out to determine the genetic relationship among them. Sixteen primer combinations produced 1142 fragments with 1129 as polymorphic and 13 as monomorphic fragments. Polymorphic fragments varied from 44 (E-ACA/M-CTA) to 94 (E-AGC/M-CAC) with an average of 70.6 fragments per primer combination. The frequency of polymorphism varied from 93.7% to 100% with an average of 98.8% across all the genotypes. The PIC value ranged from 0.19 to 0.31 with an average of 0.23 per primer combination. The primer pair E-AGC/M-CAC showed the maximum PIC value (0.31) followed by E-AGC/M-CAG (0.29), E-AAC/M-CAG (0.26) and E-AGC/M-CTA (0.25). Resolving power (RP) and marker index (MI) varied from 13.73 to 43.50 and 8.81 to 28.91 respectively. The Jaccard's similarity coefficient varied from 0.16 to 0.57 with an average of 0.26 ± 0.05. The maximum genetic similarities (57%) were detected between genotypes Him Alsi-1 and Him Alsi-2, followed by Him Alsi-1 and GS41 and GS41 and LC-54. The genotypes R-552, Himani, RKY-14, Meera, Indira Alsi-32 and Suyog were found to be more divergent genotypes. The NJ clustering grouped all the 45 genotypes into three major clusters. In general the genotypes of cluster III had high oil content and those of cluster I had low oil content. At the population level, within population variance was much higher than between populations variance.

Assessment of molecular diversity in landraces of bread wheat (Triticum aestivum L.) held in an ex situ collection with Diversity Arrays Technology (DArT™)

Diversity Arrays Technology (DArT™) was evaluated as a tool for determining molecular diversity of wheat landraces held within the Australian Winter Cereals Collection (AWCC). Initially, a set of 44 wheat landraces was evaluated with 256 DArT markers. The dataset was compared with the results obtained using 16 amplified fragment length polymorphism (AFLP) primer combinations and 63 simple sequence repeat (SSR) markers, mapped on the 21 chromosomes, from a previous study. The DArT markers exhibited a strong positive correlation with AFLP and SSR, with each marker type distinguishing similar relationships among the 44 landrace accessions. The DArT markers exhibited a higher polymorphic information content than AFLP, and were comparable with that obtained with SSR. Three hundred and fifty-five DArT markers were then used to evaluate genetic diversity among 705 wheat landrace accessions from within the AWCC, chosen to represent 5 world regions. DArT analysis was capable of distinguishing accessions from different geographic regions, and suggested that accessions originating from Nepal represent a unique gene pool within the collection. A statistical resampling of DArT loci indicated that 10–20 loci were enough to distinguish the maximum molecular diversity present within the collection. This research demonstrates the efficacy of the DArT platform as a tool for efficient examination of wheat diversity. As an ex situ germplasm repository, the AWCC contains wheat accessions of high genetic diversity, from genetically differentiated collection sites, even though diversity was under-represented in some countries represented in the repository.