DNA fingerprinting and genetic diversities in some Bangladeshi aus rice (Oryza sativa L.) genotypes

Islam, M. S.; Begum, HA; Ali, Sajid; Kamruzzaman, Md.; Hoque, Sirajul; Hoque, MI

doi:10.3329/sja.v15i1.33162

Cited by 5 publications

(5 citation statements)

References 8 publications

(8 reference statements)

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“…Very few studies, however, have investigated the genetic diversity of Aus rice in Bangladesh [ 6 – 8 ]. While more comprehensive research into genetic variability, as well as the population configuration, of Aus varieties would inform germplasm utilization for rice breeding, research into morphological and agronomic variation will also be needed for any future breeding program.…”

Section: Introductionmentioning

confidence: 99%

Diversity and population structure of red rice germplasm in Bangladesh

et al. 2018

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While the functionality and healthy food value of red rice have increased its popularity, such that market demand for it is expected to rise, most strains suffer from low grain yield. To perform diversity and population structure analyses of red rice germplasm, therefore, becomes essential for improving yields for commercial production. In this study, fifty red rice germplasm from the Bangladesh Rice Research Institute (BRRI) genebank were characterized both morphologically and genetically using fifty simple sequence repeat (SSR) markers. Overall, 162 alleles were detected by the markers with the detected allele number varying from two to seven. Additionally, 22 unique alleles were identified for use as a germplasm diagnostic tool. The highest and lowest polymorphic information content (PIC) indices were 0.75 and 0.04 found in markers RM282 and RM304, respectively, and genetic diversity was moderate, varying from 0.05 to 0.78 (average: 0.35). While phylogenetic cluster analysis of the fifteen distance-based agro-morphological traits divided the germplasm into five clusters (I, II, III, IV and V), a similar SSR analysis yielded only three major groups (I, II, and III), and a model-based population structure analysis yielded four (A, B, C and D). Both principal component and neighbors joining tree analysis from the population structure method showed the tested germplasm as highly diverse in structure. Moreover, an analysis of molecular variance (AMOVA), as well as a pairwise FST analysis, both indicated significant differentiation (ranging from 0.108 to 0.207) among all pairs of populations, suggesting that all four population structure groups differed significantly. Populations A and D were the most differentiated from each other by FST. Findings from this study suggest that the diverse germplasm and polymorphic trait-linked SSR markers of red rice are suitable for the detection of economically desirable trait loci/genes for use in future molecular breeding programs.

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Section: Introductionmentioning

confidence: 99%

Diversity and population structure of red rice germplasm in Bangladesh

et al. 2018

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“…Few studies regarding the characterisation of Bangladeshi Aus rice, and some landraces have been reported thus far using SSR markers (Islam et al 2017(Islam et al , 2018. A majority of studies are either only limited to the molecular marker or to the biochemical or morphological markers for the characterisation.…”

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confidence: 99%

Morpho-molecular diversity study of rice cultivars in Bangladesh

Akter¹,

Mosab-Bin²,

Kamruzzaman³

et al. 2022

CZECH J GENET PLANT

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Rice is one of the frontline cereals in the world and the major cultivated crop in Bangladesh. A total of eleven simple sequence repeats (SSRs) and thirteen sequence-tagged site (STS) markers were used to characterize twenty-four rice cultivars in Bangladesh. Twenty-four markers generated 60 alleles with 2.5 alleles per locus. The average polymorphism information content (PIC) value was 0.40, while the mean value of heterozygosity, gene diversity, and major allele frequency were recorded as 0.10, 0.48 and 0.62, respectively. However, the SSR markers showed more specificity and a higher discrimination power than the STS markers. The cluster analysis displayed four major clusters with a genetic similarity coefficient value of 0.73. The morphological analyses of the grain identified that Binadhan-20 and BRRI dhan34 had the longest and the shortest seed size, respectively, with a variable correlation between the seed length, width and length/width ratio. The phenol reaction test distinguished seven cultivars as japonica and seventeen cultivars as indica or an intermediate type. All these results regarding the phenotypic data and marker information will be useful for parental selection in modern rice breeding programmes.

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“…In another study, Siddique et al (2016) found a PIC value of 0.90 among 96 Bangladeshi Aman rice employing 8 SSR markers. Islam et al (2017) studied genetic diversity in 120 Aus rice genotypes of Bangladesh and observed a PIC value of 0.8217. Other studies conducted using SSR markers reveled a polymorphism information content of 0.697 (Rashid et al, 2018), 0.6533 (Shakil et al, 2015), 0.36 (Syed et al, 2019) and 0.51 (Verma et al, 2019).…”

Section: Discussionmentioning

confidence: 99%

“…(2016) found a PIC value of 0.90 among 96 Bangladeshi Aman rice employing 8 SSR markers. Islam et al. (2017) studied genetic diversity in 120 Aus rice genotypes of Bangladesh and observed a PIC value of 0.8217.…”

Section: Discussionmentioning

confidence: 99%

Genetic variability analysis of partially salt tolerant local and inbred rice (Oryza sativa L.) through molecular markers

Mazumder

Hoque

Sinha

et al. 2020

Heliyon

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Random Amplified Polymorphic DNA (RAPD) analysis was performed to assess the genetic variability in sixteen selected germplasms of rice, Oryza sativa L. using eight decamer RAPD primers. The data obtained from this investigation reveals a high level of polymorphism between cultivars. The primers produced a total of 255 bands of which all 255 bands were polymorphic indicating 100% polymorphism. The size of the amplified bands ranged from 220 bp to 2290 bp. The number of polymorphic fragments ranged from 24 to 49 with an average of 32 polymorphic fragments for each primer. The primer OPX04 produced the maximum number (49) of polymorphic bands while the OPB04 and OPB17 produced the minimum number (24) of polymorphic bands. The polymorphic information content (PIC) values ranged from 0.6616 to 0.8845 with an average of 0.832. The highest PIC value (0.8845) was obtained for primer OPL03. The RAPD data was analyzed to determine the pair-wise genetic similarity coefficients which ranged from 0.00 to 0.83. The BRRIdhan 23 and the BRRIdhan 41 varieties were the closest genotypes with the highest similarity index of 83%. This was followed by 77% similarity between a pair of cultivars Kalamona and Horkuch. On the other hand, 100% dissimilarity was seen between BRRIdhan 53, BRRIdhan 50, BRRIdhan 10, BRRIdhan 70, BRRIdhan 54, BRRIdhan 40, BRRIdhan 23, BRRIdhan 47, BRRIdhan 41 and Dadsail respectively and between BRRIdhan 53 and Horkuch; indicating a high level of variability between paired genotypes. Cluster analysis was performed using Unweighted Paired Group of Arithmetic Means (UPGMA). The UPGMA dendrogram resolved the selected rice cultivars into four clusters.

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DNA fingerprinting and genetic diversities in some Bangladeshi aus rice (Oryza sativa L.) genotypes

Cited by 5 publications

References 8 publications

Diversity and population structure of red rice germplasm in Bangladesh

Diversity and population structure of red rice germplasm in Bangladesh

Morpho-molecular diversity study of rice cultivars in Bangladesh

Genetic variability analysis of partially salt tolerant local and inbred rice (Oryza sativa L.) through molecular markers

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