Genetic relationships among improved varieties of rice (Oryza sativa L.) in Indonesia over the last 60 years as revealed by morphological traits and DNA markers (original) (raw)
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Morphological variability of Indonesian rice germplasm and the associated SNP markers
Emirates Journal of Food and Agriculture, 2016
Morphological and molecular characterization of rice genotypes with varied genetic background is highly considerable to be carried out to their utilization and to genetic variability incorporation into rice breeding program. In this study, the diversity within 60 rice genotypes from different subspecies of indica, japonica and tropical japonica was analyzed for 19 morphological traits and 384-plex SNPs with GoldenGate assay. Principal component analysis (PCA) clustered the germplasm into three main groups (indica, indica/tropical japonica/ japonica and indica/tropical japonica). PCA axes 1 and 2 and morphological traits with eigenvalue at arbitrary above 0.2, explained 24.60% of total variation in the rice germplasm. Seven traits (leaf color, leaf sheats color, ligule color, diameter of basal internode, culm color, ligule length, and flag leaf angle) could be the potential traits as descriptors for further characterization and conservation studies in Indonesian rice germplasm. Based on total morphological traits and 384 SNPs, two major clades were generated and differentiated most genotypes into subspecies/cultivar group according to their individual genetic background. Of total 154 SNPs associated with 15 morphological traits, approximately 48 SNPs were highly significant associated with quantitative and quantitative traits. The associated SNPs which were located inside or very near to genes of interest/QTLs would be potential as genetic markers. These alleles could provide breeders to effectively identify, track and incorporate regions of chromosomes governing the desired morphological traits to improve rice varieties in Indonesia.
Mau YS, Markus JER, Shirly, Oematan S, Ndiwa ASS, Handoko DD, Nasution A, Makbul K. 2017. Genetic diversity of red and black upland rice accessions from East Nusa Tenggara, Indonesia as revealed by agro-morphological characters. Biodiversitas 18: 197-211. A number of upland red and black rice accessions were collected from various locations of East Nusa Tenggara Province, Indonesia. This germplasm collection is invaluable genetic resource that can be utilized to generate new improved varieties. The objective of the present study was to elucidate genetic diversity of the rice germplasm based on agro-morphological characters. The study was carried out in the Glasshouse involving 40 upland red and black rice accessions. Observed variables included qualitative and quantitative agro-morphological characters. A total of 26 qualitative and 16 quantitative characters were observed. Qualitative characters were descriptively analyzed while quantitative characters were subjected to analysis of variance. Both data were also subjected to cluster analysis. Research results revealed a significant difference among rice accessions in both qualitative and quantitative characters. The tested rice accessions exhibited substantial differences in most of the observed qualitative and quantitative variables. Cluster analysis employing qualitative variables classified the rice accessions into 4 clusters and 15 sub-clusters. The same analysis using quantitative characters placed the 40 rice accessions into 5 clusters and 8 sub-clusters. Evaluation of agro-morphological characters demonstrated that the rice germplasm under the present study possessed a high genetic diversity.
Biodiversitas Journal of Biological Diversity
For rice plants in Indonesia, stagnation in increasing crop yields due to a reduction in genetic diversity is a significant issue. The issue of using the same parents in breeding programs and consumer preferences for a single main variety are among the causes of the narrowing of rice plants' genetic diversity. The purpose of this study is to figure out which ancestors are significant and how the genetic diversity of improved Indonesian rice cultivars has changed over time. Changes in the genetic background of the Indonesian rice gene pool were decided using pedigree analysis by calculating the coefficient of parentage (COP) among varieties. There are 280 ancestors in the rice gene pool. The pedigree map exemplifies the complexities of rice breeding in Indonesia. The four classical ancestors of DGWG, Taichung Native1, China, and Latisail had a noteworthy influence on all irrigated rice plant types (11.22%) and upland rice plant types (8.30%) in the gene pool. The dominance of the phenomenal variety IR64 has been continued by Inpari 32, which is a direct derivative of Ciherang. In the meantime, Inpago9, Luhur 2, and UPLRI ancestors set the foundation for the upland rice plant type. Inpara7 and Inpara9, along with their IRRIintroduced parents (IRRIpara4 and IRRIpara5), had a significant impact on Indonesian tidal rice plants. The A1, Hipa7, and Hipa3 varieties are heavily influenced by the hybrid rice plants of Indonesia.
Theoretical and Applied Genetics, 2007
The archipelago of Indonesia has a long history of rice production across a broad range of rice-growing environments resulting in a diverse array of local Indonesian rice varieties. Although some have been incorporated into modern breeding programs, the vast majority of these landraces remain untapped. To better understand this rich source of genetic diversity we have characterized 330 rice accessions, including 246 Indonesian landraces and 63 Indonesian improved cultivars, using 30 fluorescently-labeled microsatellite markers. The landraces were selected across 21 provinces and include representatives of the classical subpopulations of cere, bulu, and gundil rices. A total of 394 alleles were detected at the 30 simple sequence repeat loci, with an average number of 13 alleles per locus across all accessions, and an average polymorphism information content value of 0.66. Genetic diversity analysis characterized the Indonesian landraces as 68% indica and 32% tropical japonica, with an indica gene diversity of 0.53 and a tropical japonica gene diversity of 0.56, and a F st of 0.38 between the two groups. All of the improved varieties sampled were indica, and had an average gene diversity of 0.46. A set of high quality Indonesian varieties, including Rojolele, formed a separate cluster within the tropical japonicas. This germplasm presents a valuable source of diversity for future breeding and association mapping efforts.
Diversity and Population Structure of Local Rice Varieties from Indonesia Revealed by SSR Markers
HAYATI Journal of Biosciences
Indonesia's local rice varieties (Oryza sativa L.) have a wide range of diversity that can be valuable sources for crop improvement with molecular markers. This study investigated local rice varieties' genetic diversity and population structure using simple sequence repeat (SSR) markers. The SSR markers demonstrated their informativeness for genotypic characterization as represented by the gene diversity indices and polymorphic information content. The UPGMA dendrogram divided 63 varieties into two distinct clusters with different levels of sub-grouping and the tendency according to their origins, as supported by PCoA. In contrast, PCA of these varieties according to agro-morphological traits was scattered in all quadrants. Thus, DNA level variation analyzed by SSR seems to complement the phenotypic traits, which were not well structured and revealed significant genetic diversity among varieties, within, and among populations (P<0.01). The pattern of grouping structure an...
International Journal on Advanced Science, Engineering and Information Technology
The genetic diversity of crops in West Sumatra Province is very high. One of the potentials of plant genetic resources that are well conserved is brown rice. However, the development of new rice varieties has threatened the existence of brown rice. Therefore, conservation efforts are needed to preserve West Sumatra brown-rice-landrace through several stages. The first step is exploration and collection of brown rice genotypes that are still cultivated in West Sumatra Province. The next step is to identify and characterize the brown rice to determine the character of each genotype. The purpose of this study was to explore and characterize brown rice landrace in West Sumatra. The exploration resulted in 31 brown rice genotypes. Variation in quantitative and qualitative traits was observed according to grain morphology. Analysis of relatedness base on morphological grain markers resulted in three groups of brown rice with the degree of similarity of 0.70 and with slight differences in each group. Furthermore, DNA markers categorized the relatedness of brown rice landrace into six groups with 0.70 similarities.
PloS one, 2015
Coloured rice genotypes have greater nutritious value and consumer demand for these varieties is now greater than ever. The documentation of these genotypes is important for the improvement of the rice plant. In this study, 42 coloured rice genotypes were selected for determination of their genetic divergence using 25 simple sequence repeat (SSR) primers and 15 agro-morphological traits. Twenty-one out of the 25 SSR primers showed distinct, reproducible polymorphism. A dendrogram constructed using the SSR primers clustered the 42 coloured rice genotypes into 7 groups. Further, principle component analysis showed 75.28% of total variations were explained by the first-three components. All agro-morphological traits showed significant difference at the (p≤0.05) and (p≤0.01) levels. From the dendrogram constructed using the agro-morphological traits, all the genotypes were clustered into four distinct groups. Pearson's correlation coefficient showed that among the 15 agro-morphologi...
Biodiversitas Journal of Biological Diversity
Indonesia has many cultivars of pigmented rice, but many variants have not been characterized using morphological characters and molecular markers. SNPs (Single Nucleotide polymorphisms) have been used in previous studies to identify the Indica and Japonica subspecies. Characterization of wheter a line belongs to the Indica or Japonica subspecies is useful information for rice breeders, especially to generate line exhibiting the strong hybrid vigor. Morphological characters are used to determine the relationship between cultivars using cluster analysis. The SNP markers were amplified by PCR, sequenced and compared with sequences in the GenBank. Based on morphological characters, ten cultivars divide into two clusters. SNPs distinguish Indica and Japonica subspecies, and show that Hitam Lampung, Aek Sibundong, Melik, Hitam Toraja, Merah Kalimantan, and Merah Sumbawa belong to the Indica subspecies while Cempo Ireng and Pare Eja belong to Japonica. Abang Segreng and Hitam Toraja could not be clearly assigned to either the Indica or Japonica subspecies.
Agro-morphological characterization based genetic diversity of Indonesian local rice germplasm
IOP conference series, 2021
The present study was carried out to characterize 103 Indonesian local rice germplasm on the basis of 20 agro-morphological traits. The local rice germplasm originated from Riau and Jambi province in Sumatera island. Principal Component Analysis (PCA) was used to analyzed 11 quantitative data. PCA explained the genetic diversity of the rice germplasm accession. Most of the morphological characters showed variation in different accession. PC1 and PC2 explained about 32.5% and 22.1% of the variability, respectively. PCI and PC2 mostly related with traits such as productive tiller number (PTN), vegetative tiller number (VTN), plant height (PH), and culm length (CL). PCA-Biplot showed accession from Jambi and Riau manage to be separated, even though the PCA percent is only 54.6%. Accession originated from Riau marked by number of tillers (PTN, VTN), and grain weight (GW) traits. Based on cluster analysis, rice germplasm grouped in to 4 main clusters. Most of the accession from Jambi and Riau grouped in the same cluster, which is cluster I. Whereas eight local accessions from Riau grouped in the same cluster separately (cluster II). Two accession which are Padi Jarum (Acc 2711) and Ketan Hitam (Acc 9300) are individually, separated from others.
Akta Agrosia
Rice (Oryza sativa L.) is the most important crops commodity in Indonesia because it is the main staple for the people of Indonesia but currently, in Indonesia, the production of rice is still not maximal so it can not meet the demand of Indonesian people for national food needs. Therefore, it is necessary for rice plants that have high production and tolerant to various stresses. Plant breeding is one of the ways that can be done to increase the production of rice, one of which is the method of cross-recurring selection. Genetic diversity is a variation of characteristics that are inherited in the same species population. This study aims to obtain information about genetic diversity and agro-morphological characters of 50 genotypes rice derived from the recurrent selection. This research was conducted from August until December 2017 in Rawa Makmur Village, Bengkulu Province with the height of place from sea level ± 2 m. The study used a Completely Randomized Block Design (RAK) wi...