Soybean [Glycine max (L.) Merr.] is one of the most important crops worldwide. As the largest soybean producer, the United States produces $40.2 billion US dollar worth soybeans in 2011. Biotic stresses such as soybean cyst nematode (SCN), Phytophthora root rot (PRR), sudden death syndromes (SDS) and soybean aphids are threatening soybean production and plant health. Three independent projects were performed to identify genetic resistance against PRR, caused by Phytophthora sojae; to identify genetic resistance against soybean aphid, Aphis glycines Matsumura; and to develop breeder-friendly simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers to facilitate marker-assisted selection (MAS) in breeding for PRR resistance and aphid resistance. In the first project, a major locus Rps1 was identified for resistance to PRR in Michigan elite soybean E00003 (Glycine max) through a genetic mapping approach. A bi-parental mapping population was evaluated in the greenhouse for PRR resistance against P. sojae races 1, 4, and 7, in 2009 and 2010 using a modified rice grain inoculation method. The heritability of the PRR resistance ranged from 83% to 94%. A major locus contributing 50% to 76% of the phenotypic variation was detected within a 3 cM interval in the Rps1 region. Based on the specific responses to the tested races, this locus was determined to be Rps1k. Two SSRs and three SNPs were found located within the predicted functional gene and are highly associated with PRR resistance in the mapping population. In the second project, two major quantitative trait loci (QTLs) for soybean aphid resistance were detected and confirmed in E08934, derived from a wild type soybean, Glycine soja. Aphid resistance phenotyping was conducted one season in the greenhouse and three seasons in field cages. The broad-sense heritability of aphid resistance from field trials was 0.84. After genotyping with SNPs and SSRs, two major QTLs were detected (P < 0.001) in intervals of 13.5 cM between Sat_382 and Satt455 on Chr. 8, and 3.5 cM between Satt693 and Sat_370 on Chr. 16. The locus on Chr. 8 explained 40.8% of the phenotypic variation in the greenhouse trial, and 46.4, 19.5 and 39.1% of the 2009, 2010 and 2011 field trials, respectively. The locus on Chr. 16 explained 12.5 to 22.9% of the phenotypic variation. Further, these two loci were both confirmed in a validation population. The no-choice test indicated both loci confer antibiotic resistant to aphids. The novel locus on Chr. 8 (LG A2) is denoted as Rag6, since it showed significant partially dominant effect in the validation population (P < 0.05). In the third project, nearly 4,000 F2 plants from bi-parental populations were employed to fine map partially dominant locus Rag3 derived from PI 567543C. A major locus explaining 44.7% of the phenotype variance was detected in QTL analysis of 376 F2 lines and confirmed as Rag3 between markers MSUSNP16-10 (Gm16_6262227) and MSUSNP16-12 (Gm16_6423098) on chr.16. After genotyping all 3802 F2 progeny and 983 F3 progeny of 102 F2 recombinants, two F3 recombinants with crossovers between 6.26 and 6.47 Mbp were identified and confirmed according to their F4 progeny. Rag3 was fine mapped to 207 Kbp between MSUSNP16-10 (Gm16_6262227) and SNP at Gm16_6469551
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