Genetic Diversity and Allelic Frequency of Selected Thai and Exotic Rice Germplasm Using SSR Markers

Pathaichindachote, Wanwarang; Panyawut, Natjaree; Sikaewtung, Kannika; Patarapuwadol, Sujin; Muangprom, Amorntip

doi:10.1016/j.rsci.2018.11.002

Cited by 38 publications

(27 citation statements)

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“…In Thai and exotic rice germplasm, 110 alleles were detected with an average of 8.46 alleles per locus using 13 markers distributed over 12 rice chromosomes. The averages of gene diversity, heterozygosity and polymorphic information content were 0.59, 0.02 and 0.56, respectively (Pathaichindachote et al 2019). The allelic diversity and relationship among 48 aus rice landraces determined through 11 SSR markers showed 3 alleles (RM234 and RM277) to 15 alleles (RM493) (Ahmed et al 2019).…”

Section: Discussionmentioning

confidence: 97%

“…In each genotype, leaves from 25 plants were bulked for DNA isolation. Limited sets of SSR markers have been demonstrated as adequate to discriminate even the most closely related genotypes in cereals; they varied from 11 (Plaschke et al 1995) to 13 (Pathaichindachote et al 2019), 15 (Struss and Plieske 1998), 23 (Russell et al 1997), 32 (Aljumaili et al 2018 or 63 (Nachimuthu et al 2015). We used 55 SSR markers that were dispersed across the 12 rice chromosomes and were hyper polymorphic to estimate the diversity in ARG ( Table 1).…”

Section: Molecular Analysis With Ssr Markersmentioning

confidence: 99%

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Assessment of diversity of Indian aromatic rice germplasm collections for morphological, agronomical, quality traits and molecular characters to identify a core set for crop improvement

et al. 2020

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Background Besides the Basmati, the aromatic rice germplasm (ARG) accessions are treasured for quality, medicinal value and aroma. The demand for aromatic rice is ever increasing. Genetic diversity is the source of variability to identify superior alleles controlling morphological, agronomic and quality traits, and molecular attributes. This study reports on the characterization of traits in ARG to identify a core set for breeding high-yielding varieties. Methods The genetic diversity was measured on the distinctness, uniformity and stability (DUS) of 46 traits in 208 Indian ARG in field, greenhouse and laboratory tests. We performed individual and combined analysis of DUS traits and molecular data generated using 55 SSR markers. The genetic distances between genotypes were estimated using Mahalanobis D2 analysis and clustering by standardized Euclidean2 distances, Ward Minimum variance, Gowers’ similarity index and PowerMarker. The aim was to derive a core set of non-Basmati ARG using PowerCore to deploy in crop improvement. Results Eighty-two alleles were detected. Alleles per marker ranged from 2 (RM505) to 5 (RM276) with an average of 3.04 alleles. The markers are informative in analyzing the diversity as the PIC values estimated varied from 0.17 (RM577 on chromosome 1) to 0.72 (RM276 on chromosome 6) with an average of 0.54 per locus. RM276 with repeat motif of (AG)8A3(GA) 33 on chromosome 6 was the most informative (amplified 5 alleles). The combined analysis had shown genotypes in a few clusters to be more diverse than others. SSR markers RM289, RM505, RM577 and RM22866 were identified as genotype specific markers. With PowerCore, 46 genotypes (22%) were identified as a core set of ARG that represent all the alleles detected in the entire set investigated. 2-Acetyl-1-pyrroline is considered to impart aroma; it was not detected by GC–MS tests in many ARG. Conclusions Forty-six genotypes in the core set have different maturity periods, plant statures, grain types and grain quality traits. A parent can be selected from the core set to improve aromatic rice depending on the breeding objective. The olfactory sensing of strong aroma emitted by cooked kernels of all ARG was found more decisive than the costly GC–MS tests.

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Section: Discussionmentioning

confidence: 97%

Section: Molecular Analysis With Ssr Markersmentioning

confidence: 99%

Assessment of diversity of Indian aromatic rice germplasm collections for morphological, agronomical, quality traits and molecular characters to identify a core set for crop improvement

et al. 2020

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“…SSRs are highly useful in assessing diversity among closely related rice cultivars (Singh et al, 2013;Yadav et al, 2013) as they provide better resolvability, are multi-allelic, provide genomewide coverage, are highly reproducible, are easy to score, and are cost-effective (Akagi et al, 1997;Singh and Singh, 2015). There are several studies that used SSR markers for finding the genetic structure of the rice germplasm, as one of the most widely used molecular markers for genetic diversity studies (Nachimuthu et al, 2015;Singh et al, 2016;Aljumaili et al, 2018;Islam et al, 2018a,b;Pathaichindachote et al, 2019;Suvi et al, 2019;Verma et al, 2019). Further, SSR markers are also proven to be efficient in delineating major genetic groups of rice, namely, indica, temperate japonica, tropical japonica, aus, and aromatic (Roy et al, 2015(Roy et al, , 2016Wang et al, 2014).…”

Section: Discussionmentioning

confidence: 99%

Genetic Architecture and Anthocyanin Profiling of Aromatic Rice From Manipur Reveals Divergence of Chakhao Landraces

et al. 2020

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Aromatic rice of Manipur popularly known as Chakhao is a speciality glutinous rice, for which protection under geographical indication in India has been granted recently. The agronomic and nutraceutical variability of the Chakhao rice germplasm is yet to be genetically characterized. To address this gap, characterization of ninety-three landraces for agro-morphological traits, grain pigmentation, antioxidant properties, and molecular genetic variation was carried out to unravel their population genetic structure. Two major groups were identified based on pericarp color, namely, purple and non-purple, which showed a significant variation for plant height, panicle length, and grain yield. Molecular marker analysis revealed three subpopulations that could be associated with pericarp pigmentation. Deep purple genotypes formed POP3, japonica genotypes adapted to hill environment formed POP1, while POP2 comprised of both indica and aus types. Liquid chromatography-mass spectrometry (LC-MS) analysis revealed two major anthocyanin compounds in pigmented rices, namely, cyanidin-3-O-glucoside (C3G) and peonidin-3-O-glucoside (P3G). The total anthocyanin content among pigmented genotypes ranged from 29.8 to 275.8 mg.100g −1 DW. Total phenolics ranged from 66.5 to 700.3 mg GAE.100g −1 DW with radical scavenging activity (RSA) varying between 17.7 and 65.7%. Anthocyanins and phenolics showed a direct relationship with RSA implying the nutraceutical benefits of deep pigmented rice such as Manipur black rice. Aromatic rices from Manipur were found to be genetically diverse. Therefore, efforts need to be made for maintaining the geographic identity of these rice and utilization in breeding for region-specific cultivar improvement.

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“…Two species, Oryza glaberrima Steud. (in Africa) and Oryza sativa L. (in Asia), are commonly cultivated [4]. However, rice consumption can pose problems because of the arsenic (As) accumulation in rice and thus serves a vital source of As exposure in humans [5].…”

Section: Introductionmentioning

confidence: 99%

Arsenic Uptake and Accumulation Mechanisms in Rice Species

Abedi

Mojiri

2020

Plants

100

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Rice consumption is a source of arsenic (As) exposure, which poses serious health risks. In this study, the accumulation of As in rice was studied. Research shows that As accumulation in rice in Taiwan and Bangladesh is higher than that in other countries. In addition, the critical factors influencing the uptake of As into rice crops are defined. Furthermore, determining the feasibility of using effective ways to reduce the accumulation of As in rice was studied. AsV and AsIII are transported to the root through phosphate transporters and nodulin 26-like intrinsic channels. The silicic acid transporter may have a vital role in the entry of methylated As, dimethylarsinic acid (DMA) and monomethylarsonic acid (MMA), into the root. Amongst As species, DMA(V) is particularly mobile in plants and can easily transfer from root to shoot. The OsPTR7 gene has a key role in moving DMA in the xylem or phloem. Soil properties can affect the uptake of As by plants. An increase in organic matter and in the concentrations of sulphur, iron, and manganese reduces the uptake of As by plants. Amongst the agronomic strategies in diminishing the uptake and accumulation of As in rice, using microalgae and bacteria is the most efficient.

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Genetic Diversity and Allelic Frequency of Selected Thai and Exotic Rice Germplasm Using SSR Markers

Cited by 38 publications

References 50 publications

Assessment of diversity of Indian aromatic rice germplasm collections for morphological, agronomical, quality traits and molecular characters to identify a core set for crop improvement

Assessment of diversity of Indian aromatic rice germplasm collections for morphological, agronomical, quality traits and molecular characters to identify a core set for crop improvement

Genetic Architecture and Anthocyanin Profiling of Aromatic Rice From Manipur Reveals Divergence of Chakhao Landraces

Arsenic Uptake and Accumulation Mechanisms in Rice Species

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