The effect of genetic background on QTL mapping in rice (Oryza sativa L.) for traits related to cooking quality

In order to map the QTLs for cooking quality in rice، two populations of BC2F5 lines، derived from indica rice varieties IR64 and Teqing (TQ) as recurrent parents and an Iranian rice variety، Tarom molaeii (TM) as donor، studied in International Rice Research Institute. Traits amylose content (AMY)، gelatinization temperature (GT)، and gel consistency (GC) were used to evaluate cooking quality. Two-hundred thirty five SSR markers on all 12 rice linkage groups were tested on parents to identify polymorphic markers potentially linked to QTLs controlling studied traits. One-hundred fourteen markers showed polymorphism and assigned for genotyping of the populations. The map length in IR64/TM and TQ/TM populations were 1692. 6 cM and 1743. 3 cM، respectively with an average interval size of 16. 3 cM and 15. 3 cM.، respectively. Transgressive segregation observed for all traits in population IR64/TM while in population TQ/TM، it was onley observed for AMY. Seventeen QTLs were identified in the population IR64/TM، including one for AMY، 3 for GC، and 13 for GT. QTLs identified in the population Teqing/TM were twenty six as one for AMY، 15 for GC، and 10 for GT. However، of the 43 QTLs detected in both backgrounds، only one (2%) were common and mapped to the same genomic regions in both genetic backgrounds. Our results indicated that expression of QTLs involved in cooking quality are affected by different genetic backgrounds and should be specially considered in marker-aided breeding programms of cooking quality in rice.