Genetic diversity analysis of colored and white rice genotypes using Microsatellite (SSR) and Insertion-Deletion (INDEL) markers

Patel, Sachin; Ravikiran, Rallapalli; Chakraborty, Sudeshna; Macwana, Sneha; Sasidharan, N.; Trivedi, Ruchi; Aher, B. M.

doi:10.9755/ejfa.v26i6.15722

Cited by 15 publications

(22 citation statements)

References 17 publications

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“…Of 99 InDel markers, 44 (44.44%) were polymorphic and identified a total of 88 bands and on average 2 bands per marker (Table 2). Our result was similar to that reported by Patel et al (2014), with an average number of 4.42 DNA bands for colored and white rice. The InDel PIC scores ranged from 0.06 to 0.50, with an average of 0.30 and the genetic similarity values ranged from 0.64 to 1.00 ( Table 2).…”

Section: Indel Marker Polymorphismsupporting

confidence: 92%

“…Because of their high abundance, reproducibility, co-dominant inheritance, and extensive genome coverage, InDels have been applied successfully for the analysis of genetic diversity and population structure in many plant species (García-Lor et al 2012, Wu et al 2013. They have also been widely applied for genotyping, QTLs mapping, mapbased cloning, and even marker-assisted selection, including Arabidopsis (Hou et al 2010), rice (Patel et al 2014), wheat (Raman et al 2006) and citrus (García-Lor et al 2012). Our objective in this study was to use InDel markers distributed throughout the 12 rice chromosomes so as to analyze the genetic diversity and relationships of improved Thai rice cultivars.…”

Section: Introductionmentioning

confidence: 99%

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Assessment of genetic variation of 15 Thai elite rice cultivars using InDel markers

Moonsap

Laksanavilat

Tasanasuwan

et al. 2019

Crop Breed. Appl. Biotechnol.

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Many elite rice varieties have been developed in the last decades by Thai rice breeders. No information about the genetic gene pool of these elite rice varieties is available. This study evaluated the genetic relationship of 15 elite Thai rice cultivars using Indel markers. Of the 133 markers screened, 44 were polymorphic. The PIC scores ranged from 0.06 to-0.50. By the UPGMA clustering method, they were separated into three major groups. Several markers identified specific DNA bands to certain rice cultivars, e.g., RD0305 and Rd0806 detected DNA bands specific for four photoperiod-sensitive rice cultivars. The gene pool of 15 elite Thai rice cultivars was moderately wide, and some closely related rice varieties were observed. The clustering result was consistent with the breeding pedigree. The data of this study can be used for the sustainable development of elite rice varieties in the future.

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Section: Indel Marker Polymorphismsupporting

confidence: 92%

Section: Introductionmentioning

confidence: 99%

Assessment of genetic variation of 15 Thai elite rice cultivars using InDel markers

Moonsap

Laksanavilat

Tasanasuwan

et al. 2019

Crop Breed. Appl. Biotechnol.

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“…Pemanfaatan penanda SSR untuk analisis keragaman genetik beras berwarna telah dilaporkan, seperti beras merah lokal (Utami et al, 2009), beras berwarna (Patel et al, 2014), dan beras cokelat (Suzuki et al, 2004). Penanda SSR juga memiliki kemampuan dalam membedakan varietas padi sehingga dapat direkomendasikan untuk digunakan dalam perlindungan varietas tanaman (Moeljopawiro, 2010).…”

Section: Pendahuluanunclassified

Keragaman Genetik Kultivar Padi Beras Hitam Lokal Berdasarkan Penanda Mikrosatelit

et al. 2016

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Genetic Diversity of Local Black Rice Cultivars Based on Microsatellite Markers. Kristamtini, Taryono, Panjisakti Basunanda, and Rudi H. Murti. Indonesia has diverse accessions of local black rice, which are important sources of germplasm. However, some of the local black rice cultivars have different names, leading a need to be identified to determine their genetic diversity using molecular marker. This study aimed to identify genetic diversity of eleven cultivars of local black rice, collection of the Assessment Institute for Agricultural Technology, Yogyakarta and compared them with two white rice varieties using four microsatellite markers. Detection of microsatellite alleles polymorphism was carried out by visualization of PCR amplicons by electrophoresis on agarose gel. To estimate their genetic diversity, phylogenetic tree and principal coordinate analysis were performed using binary data of SSR alleles. The results revealed that total markers enabled to differentiate black rice cultivars as reflected by high value of polymorphic information content (PIC) mean (0.695). This value was consistent with the high genetic diversity of black rice (genetic diversity index, h = 0.283) in comparison with white rice cultivars (h = 0.020). The phylogenetic and main coordinate analyses suggested that black rice cultivars genetically differed from white rice. The local black rice cultivars were preferentially grouped based on their genetic those were distributed in three coordinates and did not represent their local geographic origin. Genetic diversity analysis in this study will be useful as an initial basis for proper identification and selection for appropriate parents to assist breeding program of black rice in Indonesia.Keywords: Genetic diversity, local cultivar, black rice, microsatellite markers. ABSTRAK PENDAHULUANBeras hitam merupakan salah satu jenis beras yang ada di dunia, di samping beras putih, beras cokelat, dan beras merah. Akhir-akhir ini beras hitam mulai populer dan dikonsumsi oleh sebagian masyarakat sebagai bahan pangan fungsional karena secara alami atau melalui proses tertentu mengandung satu atau lebih senyawa yang dianggap mempunyai fungsi fisiologis yang bermanfaat bagi kesehatan. Beras hitam memiliki kandungan antosianin tinggi yang terletak pada lapisan perikarp, yang memberikan warna ungu gelap (Ryu et al., 1998;Takashi et al., 2001). Antosianin telah diakui sebagai bahan pangan fungsional kesehatan karena aktivitas antioksidan

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“…Previous nding of(Kumar et al 2010) also supported the present study that similarity coe cient varied from 0.40-0.96 among genotypes of rice. Similarity index varied from 0.56-0.95 among red and white rice genotypes for SSRs markers that described by(Patel et al 2014). According to nding of (Kumar and Bhagat 2012), similarity index was 35% as establishment of genetic diversity among dwarf mutant genotypes.…”

mentioning

confidence: 88%

Detection of genetic divergence among Putative Ethyl Methane Sulfonate Mutants of Super Basmati using Microsatellite Markers

Hameed¹,

Sadia²,

Habib³

et al. 2020

Preprint

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Mutation is a resource of generating genetic diversity in crop plant for breeding as well as genetic analysis. Ethyl Methane Sulphonate (EMS) is frequently applied chemical agents in plants. The present study was completed to investigate the mutagenic effects of different concentration of EMS on yield contributing traits of super basmati. The seeds of rice cultivar (Super basmati) were mutagenized with different doses from 0-2% v/v of EMS with difference of 0.25% for determination LD50. The treated and non-treated plants were observed under different agronomic parameters. A total of 48 putative EMS mutants of super basmati were selected randomly to analyze genetic diversity using 25 SSR primers. These markers were located on twelve chromosomes of rice. SSRs analysis revealed that abroad level of genetic diversity was existed among mutants of super basmati. A sum of 91 alleles was identified of which 82 alleles were originated to be polymorphic and the rest of nine alleles were discovered as monomorphic. The range of allele number was 2-10 with mean of 3.64 alleles/locus. The value of polymorphic information content (PIC) was from 0.039 (RM5) to 0.878 (RM44) with mean of 0.439 for each locus. All mutants differentiated from each other in more than two set of primers due to presence or absence of unique bands on chromosomes at definite base pair. The size base pair range was 75-1000bp. Dendrogram located mutant indices into four major groups. Phylogenic analyses exposed 40-96% similarity. It is concluded that EMS induced genetic variability and SSRs markers (RM44, RM154, RM1, RM252, RM334, RM487, RM110 and RM257) could be employed for the selection of rice mutants throughout molecular breeding program.

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Genetic diversity analysis of colored and white rice genotypes using Microsatellite (SSR) and Insertion-Deletion (INDEL) markers

Cited by 15 publications

References 17 publications

Assessment of genetic variation of 15 Thai elite rice cultivars using InDel markers

Assessment of genetic variation of 15 Thai elite rice cultivars using InDel markers

Keragaman Genetik Kultivar Padi Beras Hitam Lokal Berdasarkan Penanda Mikrosatelit

Detection of genetic divergence among Putative Ethyl Methane Sulfonate Mutants of Super Basmati using Microsatellite Markers

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