Iso-lines and inbred-lines confirmed loci that underlie resistance from cultivar 'Hartwig' to three soybean cyst nematode populations.

Soybean [Glycine max (L.) Merr.] cultivars varied in their resistance to different populations of the soybean cyst nematode (SCN), Heterodera glycines, called HG Types. The rhg1 locus on linkage group G was necessary for resistance to all HG types. However, the loci for resistance to H. glycines HG Type 1.3- (race 14) and HG Type 1.2.5- (race 2) of the soybean cyst nematode have varied in their reported locations. The aims were to compare the inheritance of resistance to three nematode HG Types in a population segregating for resistance to SCN and to identify the underlying quantitative trait loci (QTL). 'Hartwig', a soybean cultivar resistant to most SCN HG Types, was crossed with the susceptible cultivar 'Flyer'. A total of 92 F5-derived recombinant inbred lines (RILs; or inbred lines) and 144 molecular markers were used for map development. The rhg1 associated QTL found in earlier studies were confirmed and shown to underlie resistance to all three HG Types in RILs (Satt309; HG Type 0, P = 0.0001 R (2) = 22%; Satt275; HG Type 1.3, P = 0.001, R (2) = 14%) and near isogeneic lines (NILs; or iso-lines; Satt309; HG Type 1.2.5-, P = 0.001 R (2) = 24%). A new QTL underlying resistance to HG Type 1.2.5- was detected on LG D2 (Satt574; P = 0.001, R (2) = 11%) among 14 RILs resistant to the other HG types. The locus was confirmed in a small NIL population consisting of 60 plants of ten genotypes (P = 0.04). This QTL (cqSCN-005) is located in an interval previously associated with resistance to both SDS leaf scorch from 'Pyramid' and 'Ripley' (cqSDS-001) and SCN HG Type 1.3- from Hartwig and Pyramid. The QTL detected will allow marker assisted selection for multigenic resistance to complex nematode populations in combination with sudden death syndrome resistance (SDS) and other agronomic traits.

The development of BAC-end sequence-based microsatellite markers and placement in the physical and genetic maps of soybean.

The composite map of soybean shared among Soybase, LIS and SoyGD (March 2006) contained 3,073 DNA markers in the "Locus" class. Among the markers were 1,019 class I microsatellite markers with 2-3 bp simple sequence repeats (SSRs) of >10 iterations (BARC-SSR markers). However, there were few class II SSRs (2-5 bp repeats with <10 iterations; mostly SIUC-Satt markers). The aims here were to increase the number of classes I and II SSR markers and to integrate bacterial artificial chromosome (BAC) clones onto the soybean physical map using the markers. Used was 10 Mb of BAC-end sequence (BES) derived from 13,473 reads from 7,050 clones constituting minimum tile path 2 of the soybean physical map ( http://www.soybeangenome.siu.edu ; SoyGD). Identified were 1,053 1-6 bp motif, repeat sequences, 333 from class I (>10 repeats) and 720 from class II (<10 repeats). Potential markers were shown on the MTP_SSR track at Gbrowse. Primers were designed as 20-24 bp oligomers that had Tm of 55 +/- 1 C that would generate 100-500 bp amplicons. About 853 useful primer pairs were established. Motifs were not randomly distributed with biases toward AT rich motifs. Strong biases against the GC motif and all tetra-nucleotide repeats were found. The markers discovered were useful. Among the first 135 targeted for use in genetic map improvement about 60% of class II markers and 75% of class I markers were polymorphic among on the parents of four recombinant inbred line (RIL) populations. Many of the BES-based SSRs were located on the soybean genetic map in regions with few BARC-SSR markers. Therefore, BES-based SSRs represent useful tools for genetic map development in soybean. New members of a consortium to map the markers in additional populations are invited.

The Soybean Genome Database (SoyGD): a browser for display of duplicated, polyploid, regions and sequence tagged sites on the integrated physical and genetic maps of Glycine max.

Genomes that have been highly conserved following increases in ploidy (by duplication or hybridization) like Glycine max (soybean) present challenges during genome analysis. At http://soybeangenome.siu.edu the Soybean Genome Database (SoyGD) genome browser has, since 2002, integrated and served the publicly available soybean physical map, bacterial artificial chromosome (BAC) fingerprint database and genetic map associated genomic data. The browser shows both build 3 and build 4 contiguous sets of clones (contigs) of the soybean physical map. Build 4 consisted of 2854 contigs that encompassed 1.05 Gb and 404 high-quality DNA markers that anchored 742 contigs. Many DNA markers anchored sets of 2-8 different contigs. Each contig in the set represented a homologous region of related sequences. GBrowse was adapted to show sets of homologous contigs at all potential anchor points, spread laterally and prevented from overlapping. About 8064 minimum tiling path (MTP2) clones provided 13,473 BAC end sequences (BES) to decorate the physical map. Analyses of BES placed 2111 gene models, 40 marker anchors and 1053 new microsatellite markers on the map. Estimated sequence tag probes from 201 low-copy gene families located 613 paralogs. The genome browser portal showed each data type as a separate track. Tetraploid, octoploid, diploid and homologous regions are shown clearly in relation to an integrated genetic and physical map.