Indel polymorphism in sugar translocation and transport genes associated with grain filling of rice (Oryza sativa L.)

Depending on the position on the panicle, grain filling differs for spikelets on primary branches and secondary branches of upper and lower portions in rice (Oryza sativa L.). With the objective of identifying candidate genes associated with the grain-filling process across the panicle, a candidate gene (CG)-based mapping approach was attempted in an F2 population derived from the cross between Rasi, a rice variety known for its good grain filling, and IC114927, a local landrace. The grain filling (%) was characterized for 444 F2 individual plants across the panicle. Within the F2 population, thirteen plants were identified with >90% grain filling across the panicle. For 120 markers designed from 1 kb upstream and within the candidate genes reported to be involved in translocation process of sugars, 18.3% polymorphism was observed. Using a selective genotyping approach comprising 24 individuals from eight groups based on their filling and position, two associated CG markers were identified. Further analysis of the mapping population showed a CG marker based on the sucrose phosphate synthase gene on chromosome 2 to be significantly associated with filling of grains on primary branches of the upper half of the panicle and another CG marker based on the transporter gene on chromosome 11 to be associated with filling of grains on primary branches of the lower half; secondary branches of the upper half and lower half of the panicle. Both the positive alleles were contributed by the variety Rasi. With a candidate gene-based marker mapping approach, two genes involved in sugar translocation and transport were identified to be directly associated with grain filling in rice.