A single nucleotide polymorphism in the alternative oxidase gene among rice varieties differing in low temperature tolerance

FEBS Letters ◽  
2002 ◽  
Vol 527 (1-3) ◽  
pp. 181-185 ◽  
Author(s):  
Fumitaka Abe ◽  
Koji Saito ◽  
Kiyoyuki Miura ◽  
Kinya Toriyama
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Low Temperature ◽  
Alternative Oxidase ◽  
Temperature Tolerance ◽  
Nucleotide Polymorphism ◽  
Rice Varieties ◽  
Single Nucleotide ◽  
Oxidase Gene ◽  
Low Temperature Tolerance

scholarly journals Genetic diversity of released Malaysian rice varieties based on single nucleotide polymorphism markers

2020 ◽  
Vol 56 (No. 2) ◽  
pp. 62-70 ◽  
Author(s):  
Shahril Ab Razak ◽  
Nor Helwa Ezzah Nor Azman ◽  
Rahiniza Kamaruzaman ◽  
Shamsul Amri Saidon ◽  
Muhammad Fairuz Mohd Yusof ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism ◽  
Crop Improvement ◽  
Snp Markers ◽  
Group Method ◽  
Chromosome 11 ◽  
Nucleotide Polymorphism ◽  
Rice Varieties ◽  
Single Nucleotide ◽  
K Value

Understanding genetic diversity is a main key for crop improvement and genetic resource management. In this study, we aim to evaluate the genetic diversity of the released Malaysian rice varieties using single nucleotide polymorphism (SNP) markers. A total of 46 released Malaysian rice varieties were genotyped using 1536 SNP markers to evaluate their diversity. Out of 1536 SNPs, only 932 SNPs (60.7%) represented high quality alleles, whereas the remainder either failed to amplify or had low call rates across the samples. Analysis of the 932 SNPs revealed that a total of 16 SNPs were monomorphic. The analysis of the SNPs per chromosome revealed that the average of the polymorphic information content (PIC) value ranged from 0.173 for chromosome 12 to 0.259 for chromosome 11, with an average of 0.213 per locus. The genetic analysis of the 46 released Malaysian rice varieties using an unweighted pair group method with arithmetic mean (UPGMA) dendrogram revealed the presence of two major groups. The analysis was supported by the findings from the STRUCTURE analysis which indicated the ∆K value to be at the highest peak at K = 2, followed by K = 4. The pairwise genetic distance of the shared alleles showed that the value ranged from 0.000 (MR159–MR167) to 0.723 (MRIA–Setanjung), which suggested that MR159 and MR167 were identical, and that the highest dissimilarity was detected between MRIA 1 and Setanjung. The results of the study will be very useful for the variety identification, the proper management and conservation of the genetic resources, and the exploitation and utilisation in future breeding programmes.

Cold tolerance in rice varieties at different growth stages

2009 ◽  
Vol 60 (4) ◽  
pp. 328 ◽  
Author(s):  
C. Ye ◽  
S. Fukai ◽  
I. Godwin ◽  
R. Reinke ◽  
P. Snell ◽  
...  
Keyword(s):  
Low Temperature ◽  
Cold Tolerance ◽  
High Elevation ◽  
Temperature Tolerance ◽  
Seedling Stage ◽  
Growth Stages ◽  
Rice Varieties ◽  
Low Temperature Tolerance ◽  
Wide Range ◽  
Different Growth Stages

Low temperature is a common production constraint in rice cultivation in temperate zones and high-elevation environments, with the potential to affect growth and development from germination to grain filling. There is a wide range of genotype-based differences in cold tolerance among rice varieties, these differences often reflecting growth conditions in the place of origin, as well as breeding history. However, improving low temperature tolerance of varieties has been difficult, due to a lack of clarity of the genetic basis to low temperature tolerance for different growth stages of the rice plant. Seeds or plants of 17 rice varieties of different origins were exposed to low temperature during germination (15°C), seedling, booting, and flowering stages (18.5°C), to assess their cold tolerance at different growth stages. Low temperature at the germination stage reduced both the percentage and speed of germination. Varieties from China (B55, Banjiemang, and Lijianghegu) and Hungary (HSC55) were more tolerant of low temperature than other varieties. Most of the varieties showed moderate levels of low temperature tolerance during the seedling stage, the exceptions being some varieties from Australia (Pelde, YRL39, and YRM64) and Africa (WAB160 and WAB38), which were susceptible to low temperature at the seedling stage. Low temperature at booting and flowering stages reduced plant growth and caused a significant decline in spikelet fertility. Some varieties from China (B55, Bangjiemang, Lijiangheigu), Japan (Jyoudeki), the USA (M103, M104), and Australia (Quest) were tolerant or moderately tolerant, while the remaining varieties were susceptible or moderately susceptible to low temperature at booting and flowering stages. Three varieties from China (B55, Lijianghegu, Banjiemang) and one from Hungary (HSC55) showed consistent tolerance to low temperature at all growth stages. These varieties are potentially important gene donors for breeding and genetic studies. The cold tolerance of the 17 rice varieties assessed at different growth stages was correlated. Screening for cold tolerance during early growth stages can therefore potentially be an effective way for assessing cold tolerance in breeding programs.

S1199 Analysis of Non-Synonymous Single Nucleotide Polymorphism At Diamine Oxidase Gene (Refsnp ID: Rs1049793) in Patients with Crohn's Disease

2009 ◽  
Vol 136 (5) ◽  
pp. A-211
Author(s):  
Natalia López-Palacios ◽  
Jose A.G. Agundez ◽  
Juan Luis Mendoza ◽  
Elena Garcia-Martin ◽  
Carmen Martinez ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Crohn’S Disease ◽  
Crohn's Disease ◽  
Diamine Oxidase ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Oxidase Gene

scholarly journals SNP in DFR1 Coding Sequence Is Tightly Associated with Anthocyanin Accumulation in Cabbage (B. oleracea var. capitata f. alba) at Low Temperature

Agronomy ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 602 ◽  
Author(s):  
Hayoung Song ◽  
Jong-In Park ◽  
Byung-Ho Hwang ◽  
Hankuil Yi ◽  
HyeRan Kim ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Amino Acid ◽  
Low Temperature ◽  
Anthocyanin Accumulation ◽  
Nucleotide Polymorphism ◽  
High Level Expression ◽  
Single Nucleotide ◽  
Coding Sequence ◽  
Low Level ◽  
High Level

Keeping green leaf color at the time of harvest is one of the important traits for breeding of Brassica oleracea var. capitata f. alba, and this trait is related to low anthocyanin contents. To understand the differential accumulation of anthocyanins in cabbage, we selected high anthocyanin accumulators (HAAs) and low anthocyanin accumulator (LAAs) of cabbages and examined the anthocyanin content and the expression of anthocyanin biosynthesis-related genes. Among many genes investigated, BoDFR1 was found to be closely related to anthocyanin accumulation, even under low temperature (LT) conditions. BoDFR1 sequence analyses between HAAs and LAAs revealed that there is a single nucleotide polymorphism (SNP) (1118T/A) in the coding sequence, which substitutes one amino acid from Leu261 to His261; we named BoDFR1 with His261 substitution as BoDFR1v. This amino acid substitution did not affect dihydroflavonol 4-reductase (DFR) activity and substrate specificity, but the polymorphism showed tight association to the BoDFR1 expression, i.e., high level expression of BoDFR1 and low level expression of BoDFR1v under LT conditions. The high levels of BoDFR1 expression were due to the high levels of BoMYB114 and BobHLH expressions combined with low level expression of BoMYBL2, a repressor MYB. On the other hand, low levels of BoDFR1v expression seemed to be related to very low level expressions of BoMYB114 and BobHLH combined with a high level expression of BoMYBL2. It seems that different expression levels of these regulatory genes for MBW (MYB-bHLH-WD40) complex between HAAs and LAAs regulate BoDFR expression and anthocyanin accumulation. Using a single nucleotide polymorphism (SNP) between BoDFR1 and BoDFR1v, molecular markers for PCR and high resolution melt analyses were developed and validated to distinguish between HAAs and LAAs. Combined use of the BoDFR1 SNP marker with other stress markers, such as a cold tolerant marker, will greatly improve cabbage breeding.

scholarly journals Breeding for Low Temperature Germinability in Temperate Japonica Rice Varieties: Analysis of Candidate Genes in Associated QTLs

Agronomy ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 2125
Author(s):  
Ester Sales ◽  
Eva Miedes ◽  
Luis Marqués
Keyword(s):  
Low Temperature ◽  
Genome Wide Association Study ◽  
Recombinant Inbred Lines ◽  
Rice Chromosome ◽  
Temperature Tolerance ◽  
Chromosome 3 ◽  
Japonica Rice ◽  
Rice Cultivars ◽  
Rice Varieties ◽  
Low Temperature Tolerance

In temperate areas, rice deals with low temperatures that can affect plant growth and crop yield. Rapid germination is required for adequate plant establishment in the field, therefore obtaining cultivars that maintain this phenotype under suboptimal temperature conditions is a challenge for rice breeders. Our study aimed to investigate temperature-induced expression changes in genes underlying quantitative trait loci (QTLs) associated to this trait (low temperature germinability, LTG) that were detected in a previous genome wide association study (GWAS). In the context of a breeding program for japonica rice cultivars adapted to cultivation in Spain, we obtained two biparental families of lines derived from hybridization with two cold tolerant Italian cultivars, and we have studied the effect on the LTG phenotype of introgressing these QTLs. A wide region in chromosome 3 was related to significant increases in seedling growth rate at 15 °C, although the extent of the effect depended on the analyzed family. In parallel, we studied the pattern of expression during germination at different temperatures of 10 genes located in the LTG-associated QTLs, in five japonica rice cultivars and in a biparental family of recombinant inbred lines (RILs). Cold induced changes in the expression of the 10 analyzed genes, with significant differences among genotypes. Variation in LTG phenotype was consistently associated with changes in the pattern of expression of five genes from the tagged regions in rice chromosome 3, which encoded for enzymes implicated in phytohormone metabolism (OsFBK12, Os3Bglu6), oxidative stress (SPL35, OsSRO1c) and Mn homeostasis maintenance (OsMTP8.1). Differential expression induced by cold in two regulatory genes (Os02g0824000 and Os06g06400) also contributed to explain low temperature tolerance during rice germination. In conclusion, introgression in defective cultivars of favorable alleles for these genes would contribute to the genetic improvement of LTG in japonica rice varieties.

Sign in / Sign up

Export Citation Format

Share Document