Genetic Dissection and Functional Differentiation of ALK(a) and ALK(b), Two Natural Alleles of the ALK/SSIIa Gene, Responding to Low Gelatinization Temperature in Rice

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.