Molecular characterization of secaloindoline genes in introduced CIMMYT primary hexaploid triticale

In order to widen gene germplasm for kernel hardness in triticale, 60 synthetic hexaploid triticales were tested by the single kernel characterization system (SKCS) and secaloindoline alleles were identified by sequencing. Phenotyping showed that frequencies of soft, mixed and hard genotypes were 43.3%, 48.3%, and 8.4%, respectively. Genotyping identified three known secaloindoline-a alleles and four known secaloindoline-b alleles. Three new Sina-R1 alleles were designated Sina-R1d, Sina-R1e and Sina-R1f. Compared to Sina-D1c, Sina-R1d showed four point mutations causing changes in four amino acids, Sina-R1e had one point mutation causing an alanine to glycine substitution, and Sina-R1f possessed five point mutations but produced the same amino acid sequence as Sina-R1d. Two new Sinb-R1 alleles were discovered and designated Sinb-R1e and Sinb-R1f. Compared to Sinb-R1a, Sinb-R1e possessed a triplet-code insertion and four point mutations causing a cysteine insertion and two amino acid substitutions, and Sinb-R1f possessed three point mutations causing a cysteine insertion and a change of arginine to glycine. Association of hardness index with secaloindoline alleles indicated that SKCS of the Sina-R1d genotype was significantly lower than that of Sina-R1e, and Sinb-R1e was significantly lower than that of the Sinb-R1d genotype. A total of eight allelic combinations of secaloindoline genes were identified; Sina-R1d/Sinb-R1e and Sina-R1e/Sinb-R1d were relatively prevalent in the triticales surveyed. The results provide valuable information for further use of these germplasms in triticale breeding program due to the diverse polymorphism in secaloindoline genes.