Genome-wide indel markers shared by diverse Asian rice cultivars compared to Japanese rice cultivar ‘Koshihikari’

Insertion-deletion (indel) polymorphisms, such as simple sequence repeats, have been widely used as DNA markers to identify QTLs and genes and to facilitate rice breeding. Recently, next-generation sequencing has produced deep sequences that allow genome-wide detection of indels. These polymorphisms can potentially be used to develop high-accuracy polymerase chain reaction (PCR)-based markers. Here, re-sequencing of 5 indica, 2 aus, and 3 tropical japonica cultivars and Japanese elite cultivar ‘Koshihikari’ was performed to extract regions containing large indels (10–51 bp) shared by diverse cultivars. To design indel markers for the discrimination of genomic regions between ‘Koshihikari’ and other diverse cultivars, we subtracted the indel regions detected in ‘Koshihikari’ from those shared in other cultivars. Two sets of indel markers, KNJ8-indel (shared in eight or more cultivars, including ‘Khao Nam Jen’ as a representative tropical japonica cultivar) and C5-indel (shared in five to eight cultivars), were established, with 915 and 9,899 indel regions, respectively. Validation of the two marker sets by using 23 diverse cultivars showed a high PCR success rate (≥95%) for 83.3% of the KNJ8-indel markers and 73.9% of the C5-indel markers. The marker sets will therefore be useful for the effective breeding of Japanese rice cultivars.     

Fine Structures of Amylose and Amylopectin from Large,Medium, and Small Waxy Barley Starch Granules

Amylose and amylopectin were prepared from large, medium, and small granule starches of classified waxy barley flour, and their fine structures were investigated. The amylose content had a wide distribution range (≈1.4–9.4%). Number‐average degrees of polymerization (DP_n) of the amyloses were similar among the samples (≈1,200–1,300). But number of chains per molecule (NC) decreased from the surface to the center (≈6–10 chains). DP_n of the amylopectins varied from 4,657 to 14,604; decreased in the order of large, medium, and small granules in same fractions of the grain; and increased from the surface layer to the center. Longest chains (LC) were not found in any of the amylopectin molecules. The large amylopectin molecule had more long chains and fewer A chains than the small molecule. The amylose content had definite effects on the transition temperature range and crystal formation of the starch granules. There were positive correlations between DP_n of the amylopectin and relative crystallinity (γ = +0.69) and enthalpy value (γ = +0.80), respectively. These findings may help to elucidate biosynthesis mechanism of starch.