Simple and Rapid Molecular Techniques for Identification of Amylose Levels in Rice Varieties

Abstract

The polymorphisms of Waxy (Wx) microsatellite and G-T single-nucleotide polymorphism (SNP) in the Wx gene region were analyzed using simplified techniques in fifteen rice varieties. A rapid and reliable electrophoresis method, MetaPhor agarose gel electrophoresis (MAGE), was effectively employed as an alternative to polyacrylamide gel electrophoresis (PAGE) for separating Wx microsatellite alleles. The amplified products containing the Wx microsatellite ranged from 100 to 130 bp in length. Five Wx microsatellite alleles, namely (CT)10, (CT)11, (CT)16, (CT)17, and (CT)18 were identified. Of these, (CT)11 and (CT)17 were the predominant classes among the tested varieties. All varieties with an apparent amylose content higher than 24% were associated with the shorter repeat alleles; (CT)10 and (CT)11, while varieties with 24% or less amylose were associated with the longer repeat alleles. All varieties with intermediate and high amylose content had the sequence AGGTATA at the 5′-leader intron splice site, while varieties with low amylose content had the sequence AGTTATA. The G-T polymorphism was further verified by the PCR-AccI cleaved amplified polymorphic sequence (CAPS) method, in which only genotypes containing the AGGTATA sequence were cleaved by AccI. Hence, varieties with desirable amylose levels can be developed rapidly using the Wx microsatellite and G-T SNP, along with MAGE.

Rice grain nutritional traits and their enhancement using relevant genes and QTLs through advanced approaches

“…Conversely, Cheng et al (2012) identified intron1 is insufficient to explain the genetic variations of AC in rice. Therefore, the study based on the AC and molecular analysis would be helpful for the selection of appropriate nutritional quality rice for diabetic.…”

Rapid and targeted introgression of fgr gene through marker-assisted backcrossing in rice (Oryza sativa L.)

“…and 5 min at 72 °C for the final extension. PCR products from fgr-SNP for foreground selection 140 D r a f t were separated on standard 1% agarose gel at 100 V for 1 h, while products from the SSR 141 markers for background selection were separated on high resolution 3% MetaPhor agarose gel at 142 80 V for 3.5 h. The 3% MetaPhor agarose gel was prepared following the protocol described by 143 Cheng et al (2012). The resolved PCR bands were detected by staining the agarose or MetaPhor 144 agarose gels for 30 s with ethidium bromide (EtBr), followed by destaining for 30 min in 145 distilled water and visualisation with a UV gel imager (Alpha Innotech, USA).…”

Identification of Important Physical Properties and Amylose Content in Commercially Available Improved and Traditional Rice Varieties in Sri Lanka

“…Amylose content is often contributed, to the differences in cooking and eating qualities of rice about 65 % (Juliano, 1971). Cheng et al (2012) reveal, higher amylose tends to absorb more water during the cooking process and resulting higher volume expansion of rice. After cooking, it receives dry and fluffy texture and grains can be separated easily.…”