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Background   ALK  is the key gene controlling rice gelatinization temperature (GT), which is closely associated with the eating and cooking quality (ECQ) in rice ( Oryza sativa  L.). To date, at least three  ALK  alleles are thought to be responsible for the diversity of GT among rice cultivars. The  ALK   c   /SSIIa   i   allele with high activity of the soluble starch synthase IIa (SSIIa) controls high GT, but the accurate functional difference between  ALK   a   and  ALK   b   alleles, both controlling low GT, is not clearly elucidated. Thus, we generated rice near-isogenic lines (NILs) by introducing different  ALK  alleles into the  japonica  cultivar Nipponbare (Nip) to clarify the discrepant effects of the two low-GT  ALK  alleles.    Results  The results showed that the function of two low-GT alleles ( ALK   a   and  ALK   b  ) was different, and a much lower GT was observed in NIL( ALK   b  ) rice grains compared with that of Nip( ALK   a  ). Moreover, the starches of NIL( ALK   b  ) grains had a higher degree of branching, higher setback, consistence and higher cool pasting viscosity than those of Nip( ALK   a  ). The lower expression level of  ALK   b  , compared with  ALK   a  , resulted in depleted intermediate chains and increased short chains of amylopectin, thus affected the thermal and pasting properties of NILs’ grains. Also, the data revealed both low-GT alleles were mainly found in temperate  japonica , but more  ALK   b   was found in other subpopulations such as  indica  as compared to  ALK   a  .    Conclusions  Overall, all the results suggested that the function between two low-GT alleles was different, and the distribution of  ALK   b   was much wider than that of  ALK   a   among the subpopulations of cultivated rice.

rice

Genetic Dissection and Functional Differentiation of ALKa and ALKb, Two Natural Alleles of the ALK/SSIIa Gene, Responding to Low Gelatinization Temperature in Rice