Density-Enhanced Genetic Linkage Map of RIL Population NJRIKY and Its Impacts on Mapping Genes and QTLs in Soybean

A high-density genetic linkage map with informative markers is essential for plant genome analysis,including gene mapping,identification of quantitative trait locus (QTL),map-based cloning,and physical map construction.Though four genetic linkage maps for the recombinant inbred line population NJRIKY derived from (Kefeng 1×Nannong 1138-2) have been established already,there are still problems of precision and accuracy in mapping genes and QTLs due to insufficiency of genetic information and number of markers.A total of 401 polymorphic SSR markers were screened out from 967 ones for density-enhancement of the previous maps.Along with other marker data,a new genetic linkage map was constructed by using Mapmaker/Exp 3.0b,with 553 markers,including 316 SSR,197 RFLP,39 EST and one morphologic markers,spanning 25 linkage groups,covering total length 2 071.6 cM of the soybean genome,with an average marker interval distance of 3.70 cM.In comparison with the old map,the number of gaps larger than 20 cM decreased from forty-two to two on the enhanced map.Using this map to relocate the seven SMV resistant genes,Rsc-3,Rsc-7,Rsc-9,Rsc-13,Rsa,Rn1,and Rn3 were mapped on LG D1b again with distances to the flanking markers all less than 6 cM,among them,Rsc-9,Rn1,and Rsa less than 1 cM and Rsc-13 co-segregating with EST-SSR marker GMKF168a.After re-mapping the QTLs for eight agronomic traits,42 QTLs were detected on 12 linkage groups,with 20 of them accounted for more than 10% of the total variation,respectively,and their marker intervals obviously shortened.