Specific patterns of genetic diversity among aromatic rice varieties in Myanmar

Myint, Khin Myo; Courtois, B.; Risterucci, Ange-Marie; Frouin, Julien; Soe, Khin; Thet, Khin Maung; Vanavichit, Apichart; Glaszmann, Jean-Christophe

doi:10.1186/1939-8433-5-20

Cited by 25 publications

(19 citation statements)

References 27 publications

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“…The numbers of alleles detected in this study are comparable to those observed by [18] using Basmati and non-Basmati rice varieties from Pakistan which had allelic richness of 2-4 alleles with an average of 2.75 alleles per SSR locus. In contrast, the average number of alleles detected in this study was comparatively higher than the values obtained using Indian aromatic rice varieties which had an average of 2.08 and 2.5 alleles per locus [19] and [5]. The average number of alleles per locus detected in this study was lower than the values obtained using a different set of rice germplasm from India, Portugal and Venezuela which had 4.5, 7.7 and 13.0 alleles per locus for various classes of SSR markers [20][21][22].…”

Section: Resultscontrasting

confidence: 82%

“…Therefore, characterization and varietal identification of available landraces and improved varieties have become important in modern day crop improvement [4]. There are more than 100,000 rice varieties worldwide but the major categories include; indica, japonica, basmati and glutinous [5]. This study was carried out using 13 randomly selected rice landraces and improved varieties largely grown in Kenya and Tanzania.…”

Section: Introductionmentioning

confidence: 99%

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Genetic Diversity Studies on Selected Rice (Oryza sativa L) Populations Based on Aroma and Cooked Kernel Elongation

Kioko¹,

Musyoki²,

Ngugi³

2015

J Phylogenetics Evol Biol

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Rice (Oryza sativa L.) is the main staple food for more than half of the world's population. Improving cooking and eating quality of rice is one of the important objectives of many plant breeding programs. Aroma and cooked kernel elongation are two critical parameters that determine the market value, cooking and eating qualities of rice. The objective of this study was to evaluate the genetic diversity of thirteen (13) Oryza sativa L. populations from Kenyan and Tanzanian. Genetic diversity was determined using 8 simple sequence repeats (SSR) markers. Diversity data was analyzed using POWERMARKER version 3.25 and GENALEX v 6.5 software packages. The number of alleles per locus ranged from 2 to 4 alleles with an average of 3.12 across 8 loci. The polymorphic information content (pic) ranged from 0.2920 (RM 282) to 0.6409 (RM 339) in all loci with an average of 0.4821. Pair-wise genetic dissimilarity coefficients ranged from 0.1125 to 0.9003 with an average of 0.5312. The average gene diversity over all SSR loci for the 13 rice varieties was 0.6036, ranging from 0.3550 to 0.6391. Maximum genetic similarity was observed between Kilombero and Supa, BS 370 and BS 217. Minimum genetic similarity was observed between Kahogo and BS 217. Cluster analysis was used to group varieties by constructing dendrograms based on SSR data and morphological characterization of grains. The dendrogram based on SSR data formed two distinct clusters of the 13 rice varieties. RM 339 and RM 241 were the most informative markers and could be used for differentiating rice varieties from diverse geographical origins. Results obtained from this study demonstrated that use of trait specific SSR markers can be relied upon in diversity studies among diverse and closely related genotypes. RM 339 and RM 241 markers are recommended for use in diversity studies and in quality assurance for grading of rice varieties. Further analysis should be carried out using a larger number of samples and markers to come up a more conclusive report on the discriminating power of microsatellite markers based on rice grain quality traits.

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Section: Resultscontrasting

confidence: 82%

Section: Introductionmentioning

confidence: 99%

Genetic Diversity Studies on Selected Rice (Oryza sativa L) Populations Based on Aroma and Cooked Kernel Elongation

Kioko¹,

Musyoki²,

Ngugi³

2015

J Phylogenetics Evol Biol

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“…On the other hand, the loss of function of BADH2 allows an accumulation of the precursor and triggers the synthesis of 2-AP (Bradbury et al 2008a), and thus several haplotypes have been identified based on SNP (Jin et al 2003) and microsatellite markers associated with loss of BADH2 function (Cordeiro et al 2002). Studies have mapped insertions, deletions, and polymorphisms resulting in the discovery of multiple alleles of badh2 across the different subpopulations of rice (Amarawathi et al 2008;Bourgis et al 2008;Bradbury et al 2005;Kovach et al 2009;Myint et al 2012;Niu et al 2008;Shao et al 2011;Shi et al 2008). Studies have mapped insertions, deletions, and polymorphisms resulting in the discovery of multiple alleles of badh2 across the different subpopulations of rice (Amarawathi et al 2008;Bourgis et al 2008;Bradbury et al 2005;Kovach et al 2009;Myint et al 2012;Niu et al 2008;Shao et al 2011;Shi et al 2008).…”

Section: Genetic Variations In Rice Grain Aroma and Its Contribution mentioning

confidence: 99%

Prospects of breeding high-quality rice using post-genomic tools

et al. 2015

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The holistic understanding derived from integrating grain quality and sensory research outcomes in breeding high-quality rice in the light of post-genomics resources has been synthesized. Acceptance of new rice genotypes by producers and consumers hinges not only on their potential for higher yield but recent emphasis has also been on premium-value genotypes that have the ability to satisfy consumer preferences for grain quality. This review article provides insights into how to link grain quality attributes and sensory perception to support breeding superior rice varieties. Recent advances in quality profiling and omics technologies have provided efficient approaches to identify the key genes and biochemical markers involved in rice quality traits. Emphasis has been given to the upcoming area of holistic understanding of grain quality and attributes derived from sensory evaluation to leverage integrative gene discovery strategies that enable breeding programs to efficiently tap the huge genetic diversity in rice for novel genes that enhance rice food quality.

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“…Naturally, genetic diversity within species can be identified using microsatellite DNA in fragrance rice [2][3][4][5][6][7][8][9][10], also identification of germplasm collection of basmati rice cultivar from India, they are genetic variability among these cultivars [11][12][13]. According to myint et al, [14] that Myanmar's aromatic rice difference with indica or japonica type and Badh2 allele showed three base pair insertion.…”

Section: Introduction mentioning

confidence: 99%

“…Several molecular markers can be used for identification of genes linked to fragrance in rice [12], such as SSR markers [5][6][7][8][9][10][11][12][13][14][15]. The DNA marker reported by Bradburry et al [21] can clearly show the difference between aromatic rice and non-aromatic rice, but fails to differentiate the Indonesian local aromatic rice variety derived from cv.…”

Section: Introduction mentioning

confidence: 99%

Identification of the Second Mutation of BADH2 Gene Derived from Rice Mutant Lines Induced by Gamma Rays

Ishak

2016

Atom Indo.

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The BADH2 gene acts as suppressor of 2-acetyl-1-pyrolline (2AP) biosynthesis in plants. 2AP is the volatile compound which provides fragrance in rice. Biosynthesis of 2AP occurs when BADH2 loses its function as suppressor gene. Aromatic rice cultivars naturally incur mutation of BADH2 gene at 8 bp. In this experiment, aromatic mutant rice lines derived from irradiation of Sintanur cultivar by gamma rays with dose of 100 Gy were studied in molecular level. These mutant lines were characterized at the M 10 plantgeneration under the assumption that genetically these aromatic mutant rice lines were homozygotic. Several primers related to aroma in rice have been used for polymerase chain reaction (PCR) in a thermal cycler instrument. Gel electrophoreses were carried out using 1.5% agarose in TAE buffer. DNA fragments at 254 bp and 355 bp (base pair) were taken and amplified by primer for nucleotide sequencing of these fragments. Molecular identification and characterization after electrophoresis showed that the mutant line from AR1020 can be differentiated from AR.1080 at 254 bp. Nucleotide sequence data from of these DNA fragments showed that point mutations (deletions and substitutions) occurred at the BADH2 gene in exon 7; those are called second mutation and were caused by gamma rays effects. The Sintanur variety was used as check cultivar and its DNA sequence was compared to that of the AR.1020 mutant line. The results from both DNA sequences (from cv. Sintanur and AR.1020) derived from fragments at 254 bp show that point mutations occurred within exon 7 and earlier stop codon occurred in the AR.1020 mutant rice line. Further, the use of EA primer in PCR resulted in detection of deletion and substitution of nucleotides in the AR.1020 mutant line.

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Specific patterns of genetic diversity among aromatic rice varieties in Myanmar

Cited by 25 publications

References 27 publications

Genetic Diversity Studies on Selected Rice (Oryza sativa L) Populations Based on Aroma and Cooked Kernel Elongation

Genetic Diversity Studies on Selected Rice (Oryza sativa L) Populations Based on Aroma and Cooked Kernel Elongation

Prospects of breeding high-quality rice using post-genomic tools

Identification of the Second Mutation of BADH2 Gene Derived from Rice Mutant Lines Induced by Gamma Rays

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