Identification of Variant Transcripts of Waxy Gene in Non-glutinous Rice (O. sativa L.) With Different Amylose Content

Prathepha, Preecha

doi:10.3923/pjbs.2007.2500.2504

Cited by 7 publications

(7 citation statements)

References 11 publications

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“…As a consequence, the total amount of translatable Wx mRNA, and therefore the Wx protein and consequently amylose content, are reduced (Wang et al 1995;Cai et al 1998). Later studies further confirmed the importance of specific sequences in Wx intron 1 associated to the correct splicing of the pre-mRNA (Ayres et al 1997;Larkin and Park 1999;Isshiki et al 2000;Mikami et al 2000;Larkin and Park 2003;Bao et al 2006a;Prathepha 2007).…”

Section: Post-transcriptional Regulation Of Genes Involved In Grain Dmentioning

confidence: 85%

“…The most well-studied molecular marker in the first intron of Wx gene is a single-nucleotide polymorphism (SNP), which is involved in the proper splicing of Wx mRNA. This SNP represents a naturally occurring G to T change resulting into two alleles named Wxa and Wxb which determine a significantly different amylose content resulting in the change of cooking properties and taste of rice (Wang et al 1995;Ayres et al 1997;Cai et al 1998;Mikami et al 2000;Larkin and Park 2003;Han et al 2004;Bao et al 2006a;Prathepha 2007;Chen et al 2008a,b). Besides this, also other SNPs were found in the Wx gene which are associated with variations in amylose content and viscosity characteristics (Sato et al 2002;Larkin and Park 2003;Chen et al 2008a,b;Tran et al 2011).…”

Section: Genetic Diversity In Starch Synthetase Genes Is Related To Tmentioning

confidence: 99%

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Molecular and environmental factors determining grain quality in rice

Chen

Wang

Ouwerkerk

2012

Food and Energy Security

143

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Rice among other cereals is key to food security for at least half the world population. Since the 1960s, productivity of rice has largely been improved during the Green Revolution, which included development of new cultivars, irrigation infrastructure, new management techniques, and synthetic fertilizers and pesticides. Nowadays, scientists and breeders are more and more focused on improving the quality of rice for different purposes and markets. For instance, people in the Far East prefer sticky and soft rice, while in India, a non-sticky type is preferred. Consumers from developed countries ask mainly for grain with good cooking quality and eating characteristics, but in many developing regions, nutritional value is crucial as rice is the most consumed staple food. Grain quality is a general concept which covers many characteristics ranging from physical to biochemical and physiological properties. Starch and protein are the two main components of rice endosperm and therefore are key to quality. The knowledge of how starch and protein are synthesized, sorted, and stored in starch granules and protein bodies (PB) is important for rice breeding. Besides that, grain quality has been shown to be affected significantly by growing and environmental conditions, such as water availability, temperature, fertilizer application, drought, and salinity stresses. However, the signal transduction pathways controlling grain quality still remain largely unclear. In the following sections, we first briefly review the four main aspects of grain quality, followed by a discussion of the molecular and genetic basis of starch and seedstorage protein biosynthesis and the effects of environmental factors. Obviously, rice grain is also an important source of mineral micronutrients, as well as important vitamins. Storage of these also plays crucial roles in grain quality and nutritional value, but we will only discuss these aspects briefly in this review. Grain Quality Traits in Rice Major traits of grain qualityThe traits and parameters used to evaluate grain quality in rice vary across countries. However, four main quality traits are widely used to assess quality, namely milling properties, appearance, nutritional value, and cooking quality. After harvesting, rice seeds are milled to remove the outer husk and bran layers in order to produce different types of edible rice based on the requirements of the consumers. Thus, milling quality of the grain determines the final yield and the broken kernel rate of the milled rice, which is of concern for both breeders and farmers. Appearance is one of the crucial properties appealing consumers after milling. Cooking quality determines the easiness of cooking, as well as the firmness and stickiness of the cooked rice which is associated with eating properties. As one of the most important staple food in the world, nutritional value is also valued by consumers.Some criteria for the main quality traits are widely shared among the different rice-consuming regions. The

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Section: Post-transcriptional Regulation Of Genes Involved In Grain Dmentioning

confidence: 85%

Section: Genetic Diversity In Starch Synthetase Genes Is Related To Tmentioning

confidence: 99%

Molecular and environmental factors determining grain quality in rice

Chen

Wang

Ouwerkerk

2012

Food and Energy Security

143

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“…EST sequencing has suggested that at least 20% of both Arabidopsis thaliana and rice genes are affected by AS (Buell et al 2006). In rice, traits and processes as diverse as the abiotic stress responses (Koo et al 2009;Matsukura et al 2010;Shi et al 2005), grain quality (Prathepha 2007), grain aroma Niu et al 2007) and photosynthetic rate (Isshiki et al 2000;To et al 1999) have all been shown to involve AS. The co-existence of both full-length and truncated transcripts is a welldocumented phenomenon, exactly as occurred for qFLW4/ NAL1 in cv.…”

Section: Discussionmentioning

confidence: 98%

Fine mapping of a major QTL for flag leaf width in rice, qFLW4, which might be caused by alternative splicing of NAL1

et al. 2011

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Leaf width is an important agricultural trait in rice. QTL mapping in a recombinant inbred line population derived from the cross between the javanica cultivar D50 (narrow-leaved) and the indica cultivar HB277 (wide-leaved) identified five QTLs controlling flag leaf width. Fine mapping of the major QTL qFLW4 narrowed its location to a 74.8 kb interval between the SSR loci RM17483 and RM17486, a region which also contains the gene NAL1 (Narrow leaf 1). There was no difference in the level of NAL1 expression between cvs. D50 and HB277, but an analysis of the NAL1 transcripts showed that while most (if not all) of those produced in cv. D50 were full-length, two-thirds of those in HB277 were non-functional due to either loss or gain of sequence. The inference was that NAL1 is probably synonymous with qFLW4, and that the functional difference between the two alleles was due to alternative splicing. The analysis of expression of other known genes involved in the determination of leaf width provided no evidence of their having any clear functional association with qFLW4/NAL1.

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“…RT-PCR with primers specific for unspliced variant of Wx transcript (Liu et al, 2009) confirmedthe absence of intron 1 containing 1.1 kb fragment in all of the selected Beruincultivars (Fig. 4B).A second set of RT-PCR primers previously described by Prathepha (2007) was used to re-confirm the absence of G/T SNP at intron1 splice donor site of Wx gene of these selected cultivars (Fig. 4C).…”

Section: 5wx Gene Expression In Selected Beruin Cultivars Without mentioning

confidence: 65%

Variability in amylose content of Bangladeshi rice cultivars due to unique SNPs in Waxy allele

Shahid¹,

Begum²,

Razzaque³

et al. 2016

Journal of Cereal Science

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Waxy gene (Granule Bound Starch Synthase I) is responsible for amylose synthesis in the rice endosperm.Several mutations in this gene have been shown to be responsible for variable amylose content (AC) phenotypes. The G/T mutation in 5′ splice site of Waxy intron 1 has been traced as the origin of the glutinous rice phenotype and differentiates low AC fromnon-glutinous intermediate/high AC rice. Sequencing of Waxypromoter and 5′ noncoding regions from 22 rice cultivars showed that the evolutionary pattern of all Bangladeshi non-glutinous and most glutinous rice accessions are in line with the general patternsof South and Southeast Asia. However, three cultivars Khara Beruin, Modhu Beruin White and Kathali Beruin Red with low to very low amylose lackedthe G/T splice site mutation. These were more closely related to non-glutinous cultivars based on their SNP patterns in promoter and noncoding regions. Further sequencing revealed a unique C deletion at a pyrimidine tract of intron 5 of these three cultivars that may cause slippage of intron splicing. Additional SNPs at intron 9 and 10 were also identified among these cultivars. These Bangladeshi-genotype-specific mutations could be the cause of waxy or low amylose phenotypes in theseglutinous accessions.

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Identification of Variant Transcripts of Waxy Gene in Non-glutinous Rice (O. sativa L.) With Different Amylose Content

Cited by 7 publications

References 11 publications

Molecular and environmental factors determining grain quality in rice

Molecular and environmental factors determining grain quality in rice

Fine mapping of a major QTL for flag leaf width in rice, qFLW4, which might be caused by alternative splicing of NAL1

Variability in amylose content of Bangladeshi rice cultivars due to unique SNPs in Waxy allele

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