Microsatellites, single nucleotide polymorphisms and a sequence tagged site in starch-synthesizing genes in relation to starch physicochemical properties in nonwaxy rice (Oryza sativa L.)

The starch synthase IIa (SSIIa) gene of rice (Oryza sativa L.) has been shown to be the alk gene that controls alkali disintegration of rice grains, although the effects of naturally occurring alk mutant alleles on enzyme function have yet to be determined. We genotyped 60 rice cultivars for two single-nucleotide polymorphisms (SNPs) in rice SSIIa, including one that results in an amino acid substitution. Incorporating data for three other SNPs previously genotyped in rice SSIIa, five haplotypes were found. We analysed the association of these SSIIa haplotypes with the chain-length distribution of amylopectin, the gelatinisation temperature of rice flour, the alkali spreading score, and the starch association of the enzyme. It was determined that two SNPs resulting in amino acid changes close to the C-terminus most likely alter SSIIa both in terms of activity and starch granule association. This in turn alters the branch-length distribution of amylopectin and the gelatinisation properties of starch.

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Characterization of Indonesian pigmented rice (Oryza sativa) based on morphology and Single Nucleotide Polymorphisms

Biodiversitas Journal of Biological Diversity ◽

10.13057/biodiv/d200437 ◽

2019 ◽

Vol 20 (4) ◽

pp. 1208-1214 ◽

Cited By ~ 2

Author(s):

NUR SITI KURNIASIH ◽

RATNA SUSANDARINI ◽

FEBRI ADI SUSANTO ◽

TRI RINI NURINGTYAS ◽

GLYN JENKINS ◽

...

Keyword(s):

Oryza Sativa ◽

Single Nucleotide Polymorphisms ◽

Morphological Characters ◽

Snp Markers ◽

Hybrid Vigor ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Pigmented Rice ◽

Indica And Japonica Subspecies

Abstract. Kurniasih NS, Susandarini R, Susanto FA, Nuringtyas TR, Jenkins G, Purwestri YA. 2019. Characterization of Indonesian pigmented rice (Oryza sativa) based on morphology and Single Nucleotide Polymorphisms. Biodiversitas 20: 1208-1214. Indonesia has many cultivars of pigmented rice, but many variants have not been characterized using morphological characters and molecular markers. SNPs (Single Nucleotide polymorphisms) have been used in previous studies to identify the Indica and Japonica subspecies. Characterization of whether a line belongs to the Indica or Japonica subspecies is useful information for rice breeders, especially to generate line exhibiting the strong hybrid vigor. Morphological characters are used to determine the relationship between cultivars using cluster analysis. The SNP markers were amplified by PCR, sequenced and compared with sequences in the GenBank. Based on morphological characters, ten cultivars divide into two clusters. SNPs distinguish Indica and Japonica subspecies, and show that Hitam Lampung, Aek Sibundong, Melik, Hitam Toraja, Merah Kalimantan, and Merah Sumbawa belong to the Indica subspecies while Cempo Ireng and Pare Eja belong to Japonica. Abang Segreng and Hitam Toraja could not be clearly assigned to either the Indica or Japonica subspecies.

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