Genetic analysis of immunity to Soybean cyst nematode race 3 in elite line Zhongpin 03-5373

Soybean cyst nematode (SCN) race 3, one of the eight races identified in China, is widely distributed and severely reduced soybean yield. Zhongpin 03-5373 (ZP03-5373) is an elite line immune to SCN race 3. In this study, a recombinant inbred line (RIL) population was developed from a cross between ZP03-5373 and Zhonghuang 13 (ZH13). A genetic linkage map was constructed using a total of 506 molecular markers, including SSRs, EST-SSRs, InDel, and SNP. The total length of the genetic map was 2651.90 cM with an average marker spacing of 5.24 cM. Based on the phenotyping data, we detected three QTL intervals to dominate SCN3, including SCN3-7 (Gm07), SCN3-11 (Gm11), and SCN3-18 (Gm11). Main effect QTL, SCN3-18 could explain 29.5% of resistant variation. Two minor effect QTLs, SCN3-7 and SCN3-11, explained 6.2% and 5.5% of resistant variation, respectively. And it further showed there was significant epistatic interaction between SCN3-7 and SCN3-18 for resistance to SCN3. Both SCN3-7 and SCN3-11 were confirmed to be resistant to SCN3 by tracking flanking marker in the ancestors of ZP03-5373. These markers will be helpful for developing SCN resistant cultivars and cloning resistant genes by marker assisted selection.