Integrated physical mapping of the soybean genome: A tool for rapid
Authors:
Jeffry Shultz 1, Chad LaMontagne 1 Kimbely Zobrist 1, Khalid Meksem 1, Chengcang Wu2, Quanzhou Tao2, Padmavathi Nimmakayala 2, Filip Santos 2, Hongbin Zhang 2, David A. Lightfoot 1
Abstract:
The complex genomes of crops like soybean are rich in highly repeated sequences (55%) that block chromosome walking from linked DNA markers to target genes (Danesh et al., 1998) and confound shotgun approaches to complete genome sequencing (Boysen et al., 1999). In addition, much of the rest of the soybean genome is moderately repeated (25%) or unique but duplicated in two homeologous loci (20%)(Grant et al., 2000). Success of map-based cloning in crop plants depends on the target gene being localized to such a short genetic interval (0.01-0.1 cM) that the markers and target gene are separated from regions rich in repeated sequences (Meksem et al., 2000; 2001). Fine mapping to this degree can be accomplished 10-50 fold more efficiently with a physical map that encompasses the whole genome than by marker saturation and chromosome walking or landing (Zhang and Wing, 1997; Meksem et al., 2001a).
Users Guide to the Soybean Physical Map at the Website http://hbz.tamu.edu/.
Authors:
Jeffry Shultz 1, David A. Lightfoot 1
Abstract:
To develop the physical map of soybean, we have developed three large-insert soybean DNA libraries from 'Forrest' (Meksem et al., 2000). Texas A&M has generated restriction enzyme fragment fingerprints for 90,000 of 112,600 clones. About 50,000 clone fingerprints have been posted at at Physical Mapping sections of http://hbz.tamu.edu/. Each clone was tested for the content of known genetic markers and some ESTs (Wu et al., 2001) and SNPs (Zobrist et al., 2000; Meksem et al., 2001; Shultz et al., 2001). We have shown that fingerprints of BACs from other cultivars can be integrated with this data set (Shultz et al., 2001). The integrated genetic and physical map will inexpensively and rapidly enable identification of a number of genes underlying QTL of economic importance. Here we report methods of use for the genetic and physical map. This guide should allow soybean researchers to use the website at which data can be retrieved, clones submitted for fingerprinting and clones requested.
Theoretical and empirical studies of selection limits have provided a way to use estimates of genetic gain and effective population size to calculate the plateau (selection limit) beyond which further gains are impossible. Literature pertinent to genetic gain for soybean yield in North America was surveyed for this purpose. Most results indicate that the highest-yielding existing cultivars are far from the calculated selection limit. Selection limits are not an imminent threat to North American soybean breeders, but this does not imply that efforts to broaden the germplasm base are wasted.