scholarly journals Genetic Diversity of Shanlan Upland Rice (Oryza sativa L.) and Association Analysis of SSR Markers Linked to Agronomic Traits

2021 ◽  
Vol 2021 ◽  
pp. 1-11
Author(s):  
Guofeng Yang ◽  
Yong Yang ◽  
Yali Guan ◽  
Zhixia Xu ◽  
Junyu Wang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Plant Height ◽  
Ssr Markers ◽  
Agronomic Traits ◽  
Upland Rice ◽  
Diversity Index ◽  
Oryza Sativa L ◽  
Grain Number ◽  
Rice Germplasm ◽  
Panicle Number

Shanlan upland rice, a kind of unique rice germplasm in Hainan Island, was used to evaluate genetic diversity and association between SSR markers and agronomic traits. A total of 239 alleles were detected in 57 Hainan upland rice varieties using 35 SSR markers, and the number of alleles per locus was 2-19. The observed heterozygosity was 0.0655-0.3115. The Shannon diversity index was 0.1352-0.4827. The genetic similarity coefficient was 0.6736-0.9707, and 46 varieties were clustered into one group, indicating that the genetic base of the Shanlan upland rice germplasm was narrow. A total of 25 SSR markers significantly related to plant height, effective panicle number per plant, panicle length, total grain number, filled grain number, seed rating rate, and 1000-grain weight were obtained ( P < 0.01 ), with the percentage of the total variations explained ranging from 0.12% to 42.62%. RM208 explained 42.62% of the total variations in plant height of Shanlan upland rice. RM493 was significantly associated with 6 agronomic traits. We can speculate that RM208 may flank QTLs responsible for plant height and RM493 may flank QTLs playing a fundamental role in the intertwined regulatory network of agronomic traits of Shanlan upland rice.

Genetic Diversity of Local Upland Rice (Oryza sativa L.) Genotypes Based on Agronomic Traits and Yield Potential in North Buton, Indonesia

2017 ◽  
Vol 9 (4) ◽  
pp. 109-117 ◽  
Author(s):  
Budianti Kadidaa ◽  
Gusti Ray Sadimantar ◽  
Suaib . ◽  
La Ode Safuan ◽  
Muhidin .
Keyword(s):  
Genetic Diversity ◽  
Oryza Sativa ◽  
Agronomic Traits ◽  
Upland Rice ◽  
Oryza Sativa L ◽  
Yield Potential

scholarly journals GENETIC DIVERSITY OF UPLAND RICE LANDRACES FROM JAVA ISLAND AS REVEALED BY SSR MARKERS

2015 ◽  
Vol 16 (1) ◽  
pp. 1
Author(s):  
Sutoro Sutoro ◽  
Puji Lestari ◽  
Hakim Kurniawan
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Ssr Markers ◽  
Upland Rice ◽  
Diversity Index ◽  
Crop Improvement ◽  
Conservation Strategy ◽  
Genetic Diversity Index ◽  
Rice Landraces ◽  
Glutinous Rice

Java Island is one of origins of a large number of indigenous upland rice accessions, which may serve as valuable plant genetic resources for future crop improvement in Indonesia. However, these landraces especially non-glutinous and glutinous rice are rapidly being lost because of land-use, agricultural practices and other factors. A better understanding of genetic diversity of local upland rice is important for crop improvement program, crop management and conservation strategy. This study aimed to evaluate the genetic diversity of upland rice landraces originating from Java Island. A total of 82 upland rice accessions comprising of 55 non-glutinous rice and 27 glutinous type were genotyped using the 16 simple sequence repeat (SSR) markers. The result showed that a total of 74 alleles were found with major allele frequency found on RM431 (0.96). Most of the SSR markers (56.3%) showed high discriminating power as represented by polymorphic informa-tion content (PIC) value higher than 0.5. A moderate genetic diversity index was detected in all landraces, which was 0.55. Genetic diversity index of non-glutinous and glutinous rice were 0.54 and 0.53, respectively. Their genetic distance was about 0.057. The phylogenetic tree generated two main clusters that demonstrated discrimination among landraces according to the individual genetic properties rather than their geographical origins and grain types (non-glutinous and glutinous type). The levels of genetic diversity were varied across rice types and geographical origins. According to the regions, the closest genetic distance was found between upland rice landraces from Central Java and West Java (0.040). The information derived from this study is important, in combination with phenotypic data, to identify desired useful traits came from different origins of the gene pool to be used for breeding purposes.

scholarly journals Assessment of Genetic Diversity in Rice Germplasm (Oryza sativa L.) using SSR Markers

2020 ◽  
Vol 9 (5) ◽  
pp. 3346-3355
Author(s):  
Akhand Pratap ◽  
Prashant Bisen ◽  
Bapsila Loitongbam ◽  
Sanket R. Rathi ◽  
Pragya Parmita ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Oryza Sativa ◽  
Ssr Markers ◽  
Oryza Sativa L ◽  
Rice Germplasm

scholarly journals Genetic Diversity of Aromatic Rice Germplasm Revealed By SSR Markers

2018 ◽  
Vol 2018 ◽  
pp. 1-11 ◽  
Author(s):  
Saba Jasim Aljumaili ◽  
M. Y. Rafii ◽  
M. A. Latif ◽  
Siti Zaharah Sakimin ◽  
Ibrahim Wasiu Arolu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Diversity Index ◽  
Gene Diversity ◽  
Allelic Diversity ◽  
Peninsular Malaysia ◽  
Breeding Program ◽  
Aromatic Rice ◽  
Information Index ◽  
Rice Germplasm

Aromatic rice cultivars constitute a small but special group of rice and are considered the best in terms of quality and aroma. Aroma is one of the most significant quality traits of rice, and variety with aroma has a higher price in the market. This research was carried out to study the genetic diversity among the 50 aromatic rice accessions from three regions (Peninsular Malaysia, Sabah, and Sarawak) with 3 released varieties as a control using the 32 simple sequence repeat (SSR) markers. The objectives of this research were to quantify the genetic divergence of aromatic rice accessions using SSR markers and to identify the potential accessions for introgression into the existing rice breeding program. Genetic diversity index among the three populations such as Shannon information index (I) ranged from 0.25 in control to 0.98 in Sabah population. The mean numbers of effective alleles and Shannon’s information index were 0.36 and 64.90%, respectively. Similarly, the allelic diversity was very high with mean expected heterozygosity (He) of 0.60 and mean Nei’s gene diversity index of 0.36. The dendrogram based on UPGMA and Nei’s genetic distance classified the 53 rice accessions into 10 clusters. Analysis of molecular variance (AMOVA) revealed that 89% of the total variation observed in this germplasm came from within the populations, while 11% of the variation emanated among the populations. These results reflect the high genetic differentiation existing in this aromatic rice germplasm. Using all these criteria and indices, seven accessions (Acc9993, Acc6288, Acc6893, Acc7580, Acc6009, Acc9956, and Acc11816) from three populations have been identified and selected for further evaluation before introgression into the existing breeding program and for future aromatic rice varietal development.

scholarly journals GENETIC DIVERSITY OF UPLAND RICE LANDRACES FROM JAVA ISLAND AS REVEALED BY SSR MARKERS

2015 ◽  
Vol 16 (1) ◽  
pp. 1 ◽  
Author(s):  
Sutoro Sutoro ◽  
Puji Lestari ◽  
Hakim Kurniawan
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Ssr Markers ◽  
Upland Rice ◽  
Diversity Index ◽  
Crop Improvement ◽  
Conservation Strategy ◽  
Genetic Diversity Index ◽  
Rice Landraces ◽  
Glutinous Rice

Java Island is one of origins of a large number of indigenous upland rice accessions, which may serve as valuable plant genetic resources for future crop improvement in Indonesia. However, these landraces especially non-glutinous and glutinous rice are rapidly being lost because of land-use, agricultural practices and other factors. A better understanding of genetic diversity of local upland rice is important for crop improvement program, crop management and conservation strategy. This study aimed to evaluate the genetic diversity of upland rice landraces originating from Java Island. A total of 82 upland rice accessions comprising of 55 non-glutinous rice and 27 glutinous type were genotyped using the 16 simple sequence repeat (SSR) markers. The result showed that a total of 74 alleles were found with major allele frequency found on RM431 (0.96). Most of the SSR markers (56.3%) showed high discriminating power as represented by polymorphic informa-tion content (PIC) value higher than 0.5. A moderate genetic diversity index was detected in all landraces, which was 0.55. Genetic diversity index of non-glutinous and glutinous rice were 0.54 and 0.53, respectively. Their genetic distance was about 0.057. The phylogenetic tree generated two main clusters that demonstrated discrimination among landraces according to the individual genetic properties rather than their geographical origins and grain types (non-glutinous and glutinous type). The levels of genetic diversity were varied across rice types and geographical origins. According to the regions, the closest genetic distance was found between upland rice landraces from Central Java and West Java (0.040). The information derived from this study is important, in combination with phenotypic data, to identify desired useful traits came from different origins of the gene pool to be used for breeding purposes.

scholarly journals Analysis of Population Structure and Genetic Diversity in Rice Germplasm Using SSR Markers: An Initiative Towards Association Mapping of Agronomic Traits in Oryza Sativa

Rice ◽  
2015 ◽  
Vol 8 (1) ◽  
Author(s):  
Vishnu Varthini Nachimuthu ◽  
Raveendran Muthurajan ◽  
Sudhakar Duraialaguraja ◽  
Rajeswari Sivakami ◽  
Balaji Aravindhan Pandian ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Oryza Sativa ◽  
Association Mapping ◽  
Ssr Markers ◽  
Agronomic Traits ◽  
Rice Germplasm

scholarly journals Genetic Diversity in Vietnamese Upland Rice Germplasm Revealed by SSR Markers

10.5109/25195 ◽  
2012 ◽  
Vol 57 (2) ◽  
pp. 383-391
Author(s):  
Thuy T. T. Nguyen ◽  
Nguyet M. T. Nguyen ◽  
Long H. Hoang ◽  
Naruto Furuya ◽  
Kenichi Tsuchiya
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Upland Rice ◽  
Rice Germplasm

scholarly journals KERAGAMAN GENETIK 24 VARIETAS PADI SAWAH DAN PADI GOGO (Oryza sativa L.) INDONESIA BERDASARKAN MARKA SSR

2017 ◽  
Vol 4 (1) ◽  
Author(s):  
Kristianto Nugroho ◽  
Slamet Slamet ◽  
Puji Lestari
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Upland Rice ◽  
Oryza Sativa L ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Rice Varieties ◽  
Major Allele Frequency ◽  
Biological Studies ◽  
Major Allele

The using of molecular marker is an efficient approach to analyze the genetic diversity and it can be used widely in biological studies. The characterization of rice germplasms  by using molecular markers is more precise because it is not influenced by environmental factors. The purpose of this study was to analyze the genetic diversity of 24 varieties of lowland and upland rice by using 15 SSR markers. The results showed as many as 86 alleles were detected in 24 rice varieties by using 15 SSR markers, with the average number of alleles per marker was 5,73 and the range of  alleles per locus was 2-10. The average of major allele frequency was 43% with the lowest score was 26% on RM6997 and RM536 markers and the highest score was 65% on RM60 marker. A total of 14 SSR markers were able to discriminate heterozygous alleles within a range between 0,17 (RM105) to 1,00 (RM201, RM263, RM416, RM518 and RM223). The value of gene diversity ranged from 0,48 (RM60) to 0,81 (RM536) with an average of 0,70. The value of PIC (Polymorphic Information Content) ranged from 0,38 (RM105) to 0,78 (RM536) with an average of 0,65. The phylogenetic analysis showed that 24 rice varieties separate into two main clusters in the coefficient of 0,63. The first cluster consists of 12 lowland varieties and the second cluster consists of 12 upland varieties. The genetic diversity  data  in this study were expected could be a valuable information in the rice plant breeding activities in the future.

scholarly journals Diversity Assessment of Some Sesame (Sesamum indicum L.) Genotypes Cultivated in Northern Ghana Using Morphological and Simple Sequence Repeat (SSR) Markers

2019 ◽  
Vol 2019 ◽  
pp. 1-10 ◽  
Author(s):  
Raphael Adu-Gyamfi ◽  
Ruth Prempeh ◽  
Issahaku Zakaria
Keyword(s):  
Genetic Diversity ◽  
Plant Height ◽  
Ssr Markers ◽  
Analysis Of Variance ◽  
Morphological Data ◽  
Northern Ghana ◽  
Land Races ◽  
Diversity Assessment ◽  
Parental Lines ◽  
Number Of Seeds

In Ghana, sesame is cultivated in some districts of northern Ghana. Genotypes cultivated are land races that are low yielding leading to decline in production. There is the need for improvement of these land races to generate high yielding cultivars. Characterization of genetic diversity of the sesame land races will be of great value in assisting in parental lines selection for sesame breeding programmes in Ghana. Twenty-five sesame land races were collected from five districts in northern Ghana noted for sesame cultivation. Seeds collected were planted in three replicates in randomized complete block design and were evaluated for a number of morphological characters. Data collected were subjected to Principal Component Analysis (PCA) and a dendrogram showing similarity between the accessions were drawn. Data on number of capsules per plant, number of seeds per capsule, and plant height at flowering were subjected to analysis of variance using GenStat Discovery Edition 4. Molecular genetic diversity was assessed by using thirty eight SSR markers widely distributed across sesame genome to characterize the materials. Twenty-one out of the 38 primers were polymorphic. Cluster analyses using the Euclidean similarity test and a complete link clustering method were used to make a dendrogram out of the morphological data. Analysis of variance showed that capsule number was significantly different; a range of 54.9 and 146.7 was produced. The number of seeds per capsule varied significantly and the variation between highest and lowest accession in seed production was 33%. Plant height was also significantly different ranging from 60.6 to 94.1 cm. Using morphological traits the accessions clustered into two major groups and two minor groups and variation among accessions were 10-61%. On the other hand, SSR marker-based dendrogram revealed five major and two minor groups. It showed that variation among the accessions was low, 10-20%. Heterozygosity was 0.52, total alleles produced were 410, and average allele per locus was 19.52. Six accessions, C3, C4, S5, W1, W3, and W5 fell in five different clusters in the SSR dendrogram and in six clusters in the morphomolecular based dendrogram. These accessions were noted for high capsule number per plant and seeds number per capsule and are recommended for consideration as potential parental lines for breeding programme for high yield.

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