Exploring the Genetic Diversity Among Weedy Rice Accessions Differing in Herbicide Tolerance and Allelopathic Potential

Increasing agricultural productivity is indispensable to meet future food demand. Crop im-provement programs rely heavily on genetic diversity. The success of weeds in the ecosystem can be attributed to genetic diversity and plasticity. Weedy rice, a major weed of rice, has diverse morphology and phenology, implying wide genetic diversity. Study was conducted to genotype weedy rice accessions (n =54) previously phenotyped for herbicide tolerance and allelopathic potential using 30 SSR markers. Cultivated rice (CL163, REX) and allelopathic rice (RONDO, PI312777, PI338047) were also included in the study. Nei’s genetic diversity among weedy rice (0.45) was found to be higher than cultivated rice (0.24) but less than allelopathic rice (0.56). The genetic relationship and population structure based on herbicide tolerance and allelopathic po-tential were evaluated. Herbicide-tolerant and susceptible accessions formed distinct clusters in the dendrogram, indicating their genetic variation, whereas no distinction was observed between allelopathic and non-allelopathic weedy rice accessions. Weedy rice accession B2, which was previously reported to have high allelopathy and herbicide tolerance, was genetically distinct from other weedy rice. Results from the study will help leverage weedy rice for rice improvement programs as both rice and weedy rice are closely related, thus having a low breeding barrier.

Extensively Current Activity of Transposable Elements in Natural Rice Accessions Revealed by Singleton Insertions

Active transposable elements (TEs) have drawn more attention as they continue to create new insertions and contribute to genetic diversity of the genome. However, only a few have been discovered in rice up to now, and their activities are mostly induced by artificial treatments (e.g., tissue culture, hybridization etc.) rather than under normal growth conditions. To systematically survey the current activity of TEs in natural rice accessions and identify rice accessions carrying highly active TEs, the transposon insertion polymorphisms (TIPs) profile was used to identify singleton insertions, which were unique to a single accession and represented the new insertion of TEs in the genome. As a result, 10,924 high-confidence singletons from 251 TE families were obtained, covering all investigated TE types. The number of singletons varied substantially among different superfamilies/families, perhaps reflecting distinct current activity. Particularly, eight TE families maintained potentially higher activity in 3,000 natural rice accessions. Sixty percent of rice accessions were detected to contain singletons, indicating the extensive activity of TEs in natural rice accessions. Thirty-five TE families exhibited potentially high activity in at least one rice accession, and the majority of them showed variable activity among different rice groups/subgroups. These naturally active TEs would be ideal candidates for elucidating the molecular mechanisms underlying the transposition and activation of TEs, as well as investigating the interactions between TEs and the host genome.

Proximate composition and aroma quality of five aromatic upland-rice accessions from Sumba Barat Daya District, East Nusa Tenggara Province, Indonesia

Arsa IGBA, Lalel HJD, Pollo R. 2019. Proximate composition and aroma quality of five aromatic upland-rice accessions from Sumba Barat Daya District, East Nusa Tenggara Province, Indonesia. Trop Drylands 3: 35-40. This research aimed to know the proximate composition and aroma quality of five aromatic upland-rice accessions from South West Sumba, East Nusa Tenggara Province and their correlation with the physical and chemical properties of the soil taken from the planting area of each accession. The five accessions are ACC-04, ACC-05, ACC-06, ACC-08, and ACC-09. Proximate composition analysis of each aromatic upland-rice accession was carried out by method recommended by AOAC (1970) to determine the water content, ash, fat, protein, carbohydrate, starch, amylose, and amylopectin contents of the rice. The rice aroma score was determined by a sensory test. Analysis of physical and chemical characters of soil was done on a composited soil taken from planting area of each aromatic upland-rice accession at the time of harvest. The results showed that ACC-04 had the highest ash content, AC-09 had the highest fat content and protein contents, and ACC-06 showed the highest carbohydrate content of rice. Furthermore, the best aroma quality of rice based on aroma score and 2-AP content was shown by, respectively, ACC-06 and ACC-05. There was no significant correlation between proximate composition and aroma quality with any component of environmental factors, thus, they were more likely to be determined by genetic factors.

Variability Assessment for Root and Drought Tolerance Traits and Genetic Diversity Analysis of Rice Germplasm using SSR Markers

The studies on genetic variation, diversity and population structure of rice germplasm of North East India could be an important step for improvements of abiotic and biotic stress tolerance in rice. Genetic diversity and genetic relatedness among 114 rice genotypes of North East India were assessed using genotypic data of 65 SSR markers and phenotypic data. The phenotypic diversity analysis showed the considerable variation across genotypes for root, shoot and drought tolerance traits. The principal component analysis (PCA) revealed the fresh shoot weight, root volume, dry shoot weight, fresh root weight and drought score as a major contributor to diversity. Genotyping of 114 rice genotypes using 65 SSR markers detected 147 alleles with the average polymorphic information content (PIC) value of 0.51. Population structure analysis using the Bayesian clustering model approach, distance-based neighbor-joining cluster and principal coordinate analysis using genotypic data grouped the accession into three sub-populations. Population structure analysis revealed that rice accession was moderately structured based on FST value estimates. Analysis of molecular variance (AMOVA) and pairwise FST values showed significant differentiation among all the pairs of sub-population ranging from 0.152 to 0.222 suggesting that all the three subpopulations were significantly different from each other. AMOVA revealed that most of the variation in rice accession mainly occurred among individuals. The present study suggests that diverse germplasm of NE India could be used for the improvement of root and drought tolerance in rice breeding programmes.

KERAGAMAN GENETIK 22 AKSESI PADI LOKAL TORAJA UTARA BERBASIS MARKA SIMPLE SEQUENCE REPEATS (SSR)

Genetic Diversity of 22 Local Rice Accessions from North Toraja Based on Simple Sequence Repeats (SSR) MarkersABSTRACTOne way to explore the potential of local rice is by the characterization that could obtain genetic diversity of that plants. The aim of this study was to obtain the genetic diversity of 22 local rice accession from North Toraja. Twenty-two of local rice accessions from North Toraja were characterized by 30 SSR markers and using NTSYS pc 2.1 program to analyze genetic diversity. The results showed that twenty-six SSR markers that had been analyzed produced some alelles with a size between 106.75-311 bp, the average number of alleles were 3 and the polymorphism rate was 0.53. On coefficient genetic similarity at 0.38, the population formed three clusters. Cluster I and II were dominated by rice that had no hair on the tip of the grain and cluster III were dominated by rice that had hair on the tip of the grain. There were 105 opportunities to crossing between accessions when the genetic distance was above 0.7.Keywords: genetic diversity, local rice, North Toraja, polymorphism rate, SSR markers ABSTRAKSalah satu cara untuk menggali potensi padi lokal adalah dengan karakterisasi. Dengan adanya kegiatan karakterisasi tersebut maka dapat diketahui bagaimana keragaman genetik dari suatu tanaman. Penelitian ini bertujuan untuk mengetahui keragaman genetik dari 22 aksesi padi lokal Toraja Utara. Duapuluh dua aksesi padi lokal Toraja Utara dikarakterisasi menggunakan 30 marka SSR dan dianalisis keragaman genetiknya menggunakan program NTSYS pc 2.1. Hasil penelitian menunjukkan bahwa duapuluh enam marka SSR yang dianalisis memiliki kisaran ukuran alel antara 106.75-311 bp, dengan jumlah alel rata-rata 3 dan tingkat polimorfisme sebesar 0,53. Koefisien kemiripan genetik 0,38 dan terbentuk 3 klaster. Pada klaster I dan klaster II didominasi oleh padi yang tidak memiliki rambut pada ujung gabahnya, dan pada klaster III didominasi oleh padi yang memiliki rambut pada ujung gabahnya. Selain itu, pada jarak genetik diatas 0,7 terdapat 105 peluang persilangan.Kata Kunci: keragaman genetik, marka SSR, padi lokal, tingkat polimorfisme, Toraja Utara

Selection of Bangka Local Rice Accession by Variability and Heritability Test

Selection of parent plant is the first step in hybridization activities. The parent plant usually come from germplasms because it has a high diversity and good potential. Testing the potential of germplasm can be done by variability and heritability test. The purpose of this research was to selection of parent plant for plant breeding activity based on the value of variability and heritability. The research was conducted at the Experimental Garden of Faculty of Agriculture, Fisheries, and Biology, Bangka Belitung University. The research used experimental methods by was Randomized Block Design (RBD) with 3 blocks. The treatment are 7 accessions is Grintil, Balok Runti, Mukud Besak, Mayang Curui, Payang Tebing, Balok Lutong and Balok Lukan Jintan. The results showed that there were character differences between 7 local rice accessions of Bangka. The 7 local rice accessions of Bangka have high heritabilities value on The results showed that there were character differences between 7 local rice accessions of Bangka. The 7 local rice accessions of Bangka have high heritabilities values for plant height, flowering time, long panicle, total empty grain, harvest time, long seed, seed width, weight of 1000 seeds, total seeds, and weight seed/plant. Wide variability was found in long seed character. Balok Runti and Payak Tebing were recommended as the parent plants for further breeding activities.