Amplified fragment length polymorphism (AFLP) in genomic DNA analysis of soybean (Glycine max (L.) Merr.)

Amplified Fragment Length Polymorphism (AFLP) is a PCR-based system that can detect large numbers of polymorphic bands. AFLP was applied to genomic analysis of soybean in an effort to identify quantitative trait loci (QTLs) linked with an economically important trait and to quantify the diversity within a collection of cultivars of diverse geographical origin. The two specific objectives were to: identify AFLP markers associated with soybean cyst nematode (SCN) race-3 resistance and characterize the genetic diversity within 190 Asian and North American soybean lines, identifying Asian cultivars; with maximum genetic difference from North American cultivars. AFLP and bulk segregant analysis (BSA) techniques were applied to 88 F_4:5 recombinant inbred lines (RILs) derived from the cross Hartwig x SL89-314. The cyst nematode assay identified 13 resistant and 75 susceptible lines. Fifty-nine EcoRI and MseI primer pairs identified 369 polymorphic loci between the parents. BSA screening reduced the 369 polymorphic loci to 3 potential AFLP markers, which were screened for their segregation pattern in the 88 RILs. The markers, AFLP8, AFLP16, and AFLP17, were linked to a QTL associated with resistance to SCN race-3 and were 26.5, 6.6 and 16.7 cM from the QTL, respectively. Satt309, an SSR locus in soybean linkage group G, mapped 7.1 cM from the QTL suggesting that the QTL is located in soybean linkage group G. Five primer pairs in the diversity studies generated 90 polymorphic and 242 monomorphic bands. A dendrogram and principal coordinate analysis scatter-plot, based on the similarity coefficient matrix, distinguished the three geographical origins of the germplasm. Average genetic distances (AGD) within each group were 7.3, 7.1, 7.5 and 6.3% for North American ancestors, North American, Chinese and Japanese cultivars, respectively. AGD between all possible pairs of the 190 genotypes was 8.1%. AGD for all possible pairing of the 66 North American cultivars, with all Chinese and Japanese cultivars was 8.5 (range 3.61–13.86) and 8.9% (range 4.82–14.5), respectively. A cluster of 45 Chinese cultivars was well isolated from the U.S. germplasm suggesting that cultivars in this cluster may serve as sources of new genes for U.S. soybean improvement.