Study of genetic diversity in rice (Oryza sativa L.) cultivars of Central and Western Asia using microsatellite markers tightly linked to important quality and yield related traits

Tarang, Alireza; Kordrostami, Mojtaba; Kumleh, A Shahdi; Chaleshtori, Maryam Hosseini; Saravani, Amir Forghani; Ghanbarzadeh, Milad; Sattari, Majid

doi:10.1007/s10722-020-00927-2

Cited by 12 publications

(5 citation statements)

References 35 publications

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“…The highest PIC value of 0.76 at RM481 was shown to be the best marker for differentiating across rice cultivars. A number of other researchers have conducted similar investigations (Tarang et al, 2020).…”

Section: Discussionmentioning

confidence: 92%

Molecular diversity of rice (Oryza sativa L.) genotypes in Malaysia based on SSR markers

Anisuzzaman

Islam

Khatun

et al. 2022

AAS

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<p class="042abstractstekst"><span lang="EN-US">Rice crop improvement is determined by the degree of genetic variability and the heritability of favorable genes. A total of twenty-five SSR markers were used to measure the level of polymorphism and genetic variation among the 65 rice genotypes. Twenty-one of the twenty-five SSRs were discovered to be polymorphic, whereas the rest were determined to be monomorphic. A total of 91 alleles were found in 21 SSR markers, with an average of 4.00 alleles which ranged from 3 (RM335, RM551, RM538 RM190, RM242 and RM270) to 7 (RM263). The average PIC value was 0.62 ranging from 0.28 (RM 270) to 0.76 (RM 481). The rice genotypes were divided into nine primary clusters by a dendrogram based on NTSYS software’s UPGMA analysis. The cluster analysis revealed that these genotypes were divided into nine clusters where cluster IB-1a has the most genotypes (31) followed by cluster IB-1b (24).The genotype BR24 and Utri as well as Pukhi and WANGI PUTEH had the highest dissimilarity coefficient values indicating genotype diversity. These accessions have a lot of genetic diversity among the constituents; thus, they could be used directly in a hybridization program to improve yield-related parameters.</span></p>

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Section: Discussionmentioning

confidence: 92%

Molecular diversity of rice (Oryza sativa L.) genotypes in Malaysia based on SSR markers

Anisuzzaman

Islam

Khatun

et al. 2022

AAS

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“…A mean PIC value of 0.61 has been reported by Suvi et al (2020 ) while they were accessing the genetic diversity and population structure of 54 rice accessions using 14 SSR markers. Tarang et al (2020 ) reported a PIC value of 0.92 with 60 microsatellite markers of 63 rice genotypes in Central and West Asia. PIC values and expected heterozygosity (He, also called gene diversity) are both indices of genetic diversity among genotypes in breeding populations.…”

Section: Discussionmentioning

confidence: 99%

Identification of a Diverse Core Set Panel of Rice From the East Coast Region of India Using SNP Markers

Choudhury

Kumar

et al. 2021

Front. Genet.

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In India, rice (Oryza sativa L.) is cultivated under a variety of climatic conditions. Due to the fragility of the coastal ecosystem, rice farming in these areas has lagged behind. Salinity coupled with floods has added to this trend. Hence, to prevent genetic erosion, conserving and characterizing the coastal rice, is the need of the hour. This work accessed the genetic variation and population structure among 2,242 rice accessions originating from India’s east coast comprising Andhra Pradesh, Orissa, and Tamil Nadu, using 36 SNP markers, and have generated a core set (247 accessions) as well as a mini-core set (30 accessions) of rice germplasm. All the 36 SNP loci were biallelic and 72 alleles found with average two alleles per locus. The genetic relatedness of the total collection was inferred using the un-rooted neighbor-joining tree, which grouped all the genotypes (2,242) into three major clusters. Two groups were obtained with a core set and three groups obtained with a mini core set. The mean PIC value of total collection was 0.24, and those of the core collection and mini core collection were 0.27 and 0.32, respectively. The mean heterozygosity and gene diversity of the overall collection were 0.07 and 0.29, respectively, and the core set and mini core set revealed 0.12 and 0.34, 0.20 and 0.40 values, respectively, representing 99% of distinctiveness in the core and mini core sets. Population structure analysis showed maximum population at K = 4 for total collection and core collection. Accessions were distributed according to their population structure confirmed by PCoA and AMOVA analysis. The identified small and diverse core set panel will be useful in allele mining for biotic and abiotic traits and managing the genetic diversity of the coastal rice collection. Validation of the 36-plex SNP assay was done by comparing the genetic diversity parameters across two different rice core collections, i.e., east coast and northeast rice collection. The same set of SNP markers was found very effective in deciphering diversity at different genetic parameters in both the collections; hence, these marker sets can be utilized for core development and diversity analysis studies.

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“…However, there are very few studies on the grain quality and yield characteristics of rice from the North East Hill region. Therefore, to create better rice varieties, these landraces must be preserved and utilized by wisely choosing among local cultivars based on genetic diversity and structure (Tarang et al 2020).…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity and marker trait association analysis for grain quality, yield and yield attributes in hilly rice of North-Eastern Himalayan region

Verma

Theunuo

Das

et al. 2023

Preprint

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Background: The demand for quality rice is increasing due to the influence of population growth and rising living standards. North eastern region of India is considered as centre of origin of rice and has diversified rice landraces with unique cooking quality and yield attributing traits. The studies on genetic diversity and marker-trait association analysis of north-eastern hilly rice for grain quality and yield attributes are of enormous importance for the identification of promising rice genotypes with better grain and cooking quality vis a vis markers associated with grain quality and yield attributes. This will assist in development of high-yielding cultivars. Results: Genetic diversity among 130 rice genotypes of North East India and marker-trait association was assessed using genotypic data of 90 SSR markers and phenotypic data. The phenotypic diversity analysis showed considerable variation across genotypes for grain quality, yield and yield-attributing traits. The principal component analysis revealed that plant height, panicle length, spikelet fertility, decorticated grain length and width, days to maturity, days to 50% flowering, and grain yield govern the diversity. Population structure analysis, distance-based neighbour joining cluster and principal coordinate analysis using genotypic data grouped the genotypes into two sub-populations. Analysis of molecular variance and pairwise FST values showed significant differentiation among all the pairs of sub-population. Marker trait association analysis using the mixed linear model revealed a total of six associations at P < 0.0001 for grain quality and yield attributing traits with R2 ranging from 3.55 to 11.91% under the upland ecosystem. The present study validated the association of RM240 marker with Gel consistency for use in MAS and existence of plant height gene on chromosome 3. The study indicated the presence of novel QTLs for days to maturity with RM210 and RM105 and days to flowering with RM101 under consideration. Conclusions: The present study suggests that the diverse germplasm of NE India and identified markers could be used in rice breeding programs for the improvement of grain quality and yield attributes.

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Study of genetic diversity in rice (Oryza sativa L.) cultivars of Central and Western Asia using microsatellite markers tightly linked to important quality and yield related traits

Cited by 12 publications

References 35 publications

Molecular diversity of rice (Oryza sativa L.) genotypes in Malaysia based on SSR markers

Molecular diversity of rice (Oryza sativa L.) genotypes in Malaysia based on SSR markers

Identification of a Diverse Core Set Panel of Rice From the East Coast Region of India Using SNP Markers

Genetic diversity and marker trait association analysis for grain quality, yield and yield attributes in hilly rice of North-Eastern Himalayan region

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