Association of waxy gene single nucleotide polymorphisms with starch characteristics in rice (Oryza sativa L.)

Larkin, Patrick; Park, William D.

doi:10.1023/b:molb.0000006797.51786.92

Cited by 136 publications

(123 citation statements)

References 9 publications

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“…Currently, the AC of most rice varieties in China is either high or low, and breeding rice varieties with intermediate AC will be of great worth. Of the haplotypes of Wx In1-Ex6 in the Chinese mini core collection of Oryza sativa L., the SNP Ex6C genotype was detected exclusively in the haplotype of the intermediate-AC gene Wx-in (In1G-Ex6C) in non-waxy rice, which was consistent with previous studies (Chen et al 2008, Larkin andPark 2003). Therefore, the co-dominant marker for functional SNP Ex6C developed in this study can be used to screen the intermediate-AC gene Wx-in in non-waxy rice.…”

Section: Discussionsupporting

confidence: 90%

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A perfect functional marker for the gene of intermediate amylose content Wx-in in rice (Oryza sativa L.)

Zhou

Chen

Yang

et al. 2018

Crop Breed. Appl. Biotechnol.

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Section: Discussionsupporting

confidence: 90%

“…Moreover, two main functional single-nucleotide polymorphisms (SNPs) in the Wx gene have been identified, strongly associated with the AC and pasting properties of starch (Chen et al 2010, Larkin and Park 2003, Ayres et al 1997. The first SNP is the G/T SNP at the 5' splice site of the first intron (WxIn1).…”

Section: Introductionmentioning

confidence: 99%

A perfect functional marker for the gene of intermediate amylose content Wx-in in rice (Oryza sativa L.)

Zhou

Chen

Yang

et al. 2018

Crop Breed. Appl. Biotechnol.

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“…What is known so far is that the amount of amylose in rice grain is primarily due to allelic variations in the structural gene of GBSSI, its transcriptional regulation by cis-regulatory elements, the level of transcripts after alternative mRNA splicing, and the enzymatic activity of its protein product GBSSI (Sano, 1984;Shimada et al, 1993;Bligh et al, 1995;Ayres et al, 1997;Hirano et al, 1998;Larkin and Park, 2003;Mikami et al, 2008;Zhu et al, 2011). Any mutations influencing the synthesis and regulation of GBSSI lead to significant alterations in the proportion of amylose and long-chain amylopectin with a concomitant impact on the ratio of medium-and short-chain amylopectin.…”

Section: Discussion Starch Structure Implication To Tweak Cooking Quamentioning

confidence: 99%

“…This aberrant splicing results in decreased concentration of functional GBSSI enzymes, which explains the glutinous to lowamylose phenotypes commonly observed in japonica lines. Lastly, two exonic SNPs can differentiate between intermediate-and high-amylose rice grains: one is present on exon 6 (A/C) and the other on exon 10 (C/T; Larkin and Park, 2003;Dobo et al, 2010;KharabianMasouleh et al, 2011). Although not functionally validated, these two nonsynonymous SNP mutations are believed to change the polarity and therefore enzymatic activity of GBSSI.…”

Section: Discussion Starch Structure Implication To Tweak Cooking Quamentioning

confidence: 99%

Systems Genetics Identifies a Novel Regulatory Domain of Amylose Synthesis

et al. 2016

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A deeper understanding of the regulation of starch biosynthesis in rice (Oryza sativa) endosperm is crucial in tailoring digestibility without sacrificing grain quality. In this study, significant association peaks on chromosomes 6 and 7 were identified through a genomewide association study (GWAS) of debranched starch structure from grains of a 320 indica rice diversity panel using genotyping data from the high-density rice array. A systems genetics approach that interrelates starch structure data from GWAS to functional pathways from a gene regulatory network identified known genes with high correlation to the proportion of amylose and amylopectin. An SNP in the promoter region of Granule Bound Starch Synthase I was identified along with seven other SNPs to form haplotypes that discriminate samples into different phenotypic ranges of amylose. A GWAS peak on chromosome 7 between LOC_Os07g11020 and LOC_Os07g11520 indexed by a nonsynonymous SNP mutation on exon 5 of a bHLH transcription factor was found to elevate the proportion of amylose at the expense of reduced short-chain amylopectin. Linking starch structure with starch digestibility by determining the kinetics of cooked grain amylolysis of selected haplotypes revealed strong association of starch structure with estimated digestibility kinetics. Combining all results from grain quality genomics, systems genetics, and digestibility phenotyping, we propose target haplotypes for fine-tuning starch structure in rice through marker-assisted breeding that can be used to alter the digestibility of rice grain, thus offering rice consumers a new diet-based intervention to mitigate the impact of nutrition-related noncommunicable diseases.

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“…Larkin and Park (2003) found that the Wx gene is one of the many genes that play a part in starch synthesis in the endosperm of rice. Furthermore, Wanchana et al (2003) found two alleles of the Wx gene (Wxa and Wxb) that regulated the enhancement of the protein and amylose contents of the starch.…”

Section: Waxy Gene Markersmentioning

confidence: 99%

Sago Palm Genetic Resource Diversity in Indonesia

Abbas

2018

Sago Palm

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Information of genetic diversity is very important in supporting the implementation of genetic resource conservation and plant breeding. This study aims to determine the genetic diversity of 11 sago palm accessions that have been collected by the Sago Research Consortium (SRC), University of Papua (UNIPA). Methods of research were divided into three steps.Step 1 was DNA extraction by using Geneaid DNA plant Mini Kit.Step 2 was PCR amplification fragments DNA by using KAPA2G Robust HotStart polymerases and performed by using Bio-Rad PCR instrument.Step 3 was purified and sequenced DNA by Macrogen Inc. Seoul, Korea. Data analyses were performed by using a MEGA6.06 software. Morphological characteristics in the rosette stage of 11 sago palm accessions were divided into 4 phenotypes only, and several accessions showed the same phenotypes. Based on atp6-2 gene markers, the 11 sago palm accessions had a different genetic characteristic among the others. Genetic distances among 11 sago palm accessions were in the range among 0.22 and 3.01 with an average 1.21 pairwise distant. Phylogenetic construction showed that the genetic relationship of 11 sago palm accessions was clustered into 6 groups. The accession numbers SP001 and SP002 are in group 1, the accession numbers SP003 and SP011 group 2, the accession numbers SP005 and SP007 group 3, the accession number SP009 group 4, the accession numbers SP008 and SP010 group 5, and the accession numbers SP004 and SP006 group 6. Nucleotide sequence alignments of mitochondrial atp6-2 gene and introns were different from each other in 11 accessions.

show abstract

Association of waxy gene single nucleotide polymorphisms with starch characteristics in rice (Oryza sativa L.)

Cited by 136 publications

References 9 publications

A perfect functional marker for the gene of intermediate amylose content Wx-in in rice (Oryza sativa L.)

A perfect functional marker for the gene of intermediate amylose content Wx-in in rice (Oryza sativa L.)

Systems Genetics Identifies a Novel Regulatory Domain of Amylose Synthesis

Sago Palm Genetic Resource Diversity in Indonesia

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