Ideotype breeding for submergence tolerance and cooking quality by marker-assisted selection in rice

Submergence tolerance and jasmine-like cooking quality are desirable for rice varieties grown in rainfed and irrigated lowland ecosystems in the Mekong region of Southeast Asia. Hybridization between varieties IR57514 and Kao Dawk Mali 105 (KDML105) was initiated with the goal of producing an ideotype that combines submergence tolerance and jasmine-like cooking quality. Through the single seed descent (SSD) method, a large population of recombinant inbred lines (RILs) was developed, and we demonstrated the potential of using marker-assisted selection (MAS) in the identification of the ideotype from the offspring. Four markers, R10783Indel, Waxy, Aromarker and GT11, were used to select the favored alleles of the Sub1, Wx, badh2 and SSIIa loci, respectively. The ideotype was classified into two groups: ideotype1 (ID1), carrying the Sub1IR, badh2KD, WxKD and SSIIaKD alleles and consisting of 66 RILs and ideotype2 (ID2), carrying the Sub1IR, badh2KD, WxKD and SSIIaIR alleles and consisting of 31 RILs. Submergence tolerance, cooking quality, grain quality and agronomic characteristics of the IDs were evaluated and compared with those of the parents. All of the ID1 lines exhibited submergence tolerance and jasmine-like cooking quality and displayed a low amylose content, a fragrance and a high alkali spreading value, whereas the ID2s showed the same characteristics as ID1, except for a low alkali spreading value, which was inherited from IR57514. A wide range of agronomic characteristics was observed in both of the ID groups, and some of the IDs were superior in the yield component, as compared to their parents. This study provides further support that the precision of markers used in MAS can enhance the development of ideotypes in rice.

► Recombinant inbred line (RIL) populations derived from a single cross between the parental varieties, IR57514 and KDML105, were developed by single seed descent.
► Marker-assisted selection was successfully applied to identify the RILs that possess combinations of submergence tolerance inherited from IR57514 and good cooking quality inherited from KDML 105.
► The selected RILs exhibited submergence tolerance, low amylose content, fragrance and high gel consistency were considered ideotype.
► The ideotype was classified into two groups based on the alkali spreading value (ASV).
► Ideotype1 had a high ASV and ideotype2 had a low ASV.