Aromatic Rice Germplasm Research Articles

Allele mining for Granule Bound Starch Synthase1 (GBSS1) gene governing amylose content in aromatic rice (Oryza sativa L.) germplasm

The current research investigated sequence polymorphism and allelic variation in the GBSS1 gene responsible for determining the apparent amylose content (AAC) in an aromatic rice germplasm panel. Analysis of 271 germplasm accessions from India revealed a wide range of variation in AAC, from 4.81% (Manipur Black Rice) to 35.88% (IGSR -3-1-5). Re-sequencing and sequence analysis of a representative subset of 28 accessions unveiled a nucleotide diversity (π) of 0.00374, identifying 72 sequence variants. Two novel non-synonymous SNPs were identified: a G/A transition in exon 2, resulting in the substitution of glutamic acid at the 91st position with lysine, and a C/T transition in exon 11, substituting alanine at the 468thposition with valine. Additionally, two previously reported SNPs were validated: A/C in exon 6 (Tyr224Ser) and C/T in exon 10 (Pro415Ser). Furthermore, a 23 bp exon 2 duplication was found in Manipur Black Rice (4.81%), Bhogali Bora (6.20%), and NJ-72 (7.36%), indicating the prevalence of this allele in the very low AAC category (3–9%) in addition to the glutinous or waxy rice category with 0–2% AAC. These findings are significant for manipulating starch content in aromatic rice germplasm.

Allele mining of Badh1 gene in aromatic rice germplasm

Allele mining of Badh1 gene in aromatic rice germplasm

Assessment of agro-morphological traits, grain physical and physico-chemical properties in the Indian aromatic rice (Oryza sativa) germplasm

Information on genetic diversity with respect to various agro-morphological traits and eating and cooking quality traits plays a key role in the improvement of rice (Oryza sativa L.). With this aim, we have characterized a set of 98 indigenous aromatic rice germplasm accessions for four agro-morphological, two physical and two physico-chemical traits. Significant variation was observed among the cultivars for all the traits. Correlation analysis showed negative correlation of DFF with KLBC (r= -0.29; p=0.022) and kernel L/W ratio (r= -0.25; p=0.003), while PL was significantly and positively correlated with KLBC (r=0.38; p=0.000) and kernel L/W ratio (r=0.43; p=0.0649). KLBC showed highly significant positive correlation with GC (r=0.22; p=0.614) while between AAC and GC a significant negative correlation was observed (r= -0.38; p=0.000).

Genetic diversity analysis of aromatic rice (Oryza sativa L.) germplasm based on agro-morphological characterization

Aromatic rice is a special class of rice known in the Indian subcontinent. A total of fifty-eight aromatic rice genotypes were evaluated on the basis of 12 agro-morphological traits at Agricultural Experimental Farm, University of Calcutta, Baruipur, West Bengal to characterize and estimate genetic diversity. Phenotypic coefficient of variation exhibited higher values but maintained close relation with genotypic coefficient of variation for all the traits. Additive gene action was prominent for traits like plant height, panicle length, number of filled grains per panicle and 1000 grain weight. A correlation study showed that grain yield per plant was positive and significantly correlated with tillers per plant, panicles per plant, number of filled grains per panicle, total number of filled grains per plant and 1000 grain weight. The principal component analysis revealed that total number of filled grains per plant had a strong relation with grain yield. Based on Manhattan clustering, fifty-eight genotypes were grouped into five distinct clusters. 24 genotypes in cluster III,17 in cluster I, 9 in cluster II,7 in Cluster IV and 1 genotype in Cluster V.

Molecular profiling of BADH2 locus reveals distinct functional allelic polymorphism associated with fragrance variation in Indian aromatic rice germplasm.

The online version contains supplementary material available at 10.1007/s12298-022-01181-9.

A novel LOX3-null allele (lox3-b) originated in the aromatic Basmati rice cultivars imparts storage stability to rice bran

Rapid deterioration of rice bran due to the LOX3 enzyme catalysed oxidation of PUFA is the major bottleneck for its utilization in various downstream applications. In the present study, we have identified a set of nine novel LOX3-null rice accessions carrying a deletion of C residue in the exon2 causing a frameshift mutation resulting in a truncated non-functional LOX3 protein. Our study, further manifested the predominance of C deletion based LOX3-null allele, named lox3-b, in the aromatic rice germplasm particularly in the Indian Basmati rice group. The LOX3-null genotypes exhibited significantly reduced rancidity, after six months of storage. They also showed significantly lower percentage reduction of linoleic acid (LA), higher γ-oryzanol content and lower hexanal content. A functional dCAPS marker designed based on the deletion polymorphism clearly differentiated LOX3 and lox3-b alleles, and has the potential application in marker assisted rice breeding programmes to develop cultivars with better bran storability.

Assessment of diversity of Indian aromatic rice germplasm collections for morphological, agronomical, quality traits and molecular characters to identify a core set for crop improvement

BackgroundBesides the Basmati, the aromatic rice germplasm (ARG) accessions are treasured for quality, medicinal value and aroma. The demand for aromatic rice is ever increasing. Genetic diversity is the source of variability to identify superior alleles controlling morphological, agronomic and quality traits, and molecular attributes. This study reports on the characterization of traits in ARG to identify a core set for breeding high-yielding varieties.MethodsThe genetic diversity was measured on the distinctness, uniformity and stability (DUS) of 46 traits in 208 Indian ARG in field, greenhouse and laboratory tests. We performed individual and combined analysis of DUS traits and molecular data generated using 55 SSR markers. The genetic distances between genotypes were estimated using Mahalanobis D2 analysis and clustering by standardized Euclidean2 distances, Ward Minimum variance, Gowers’ similarity index and PowerMarker. The aim was to derive a core set of non-Basmati ARG using PowerCore to deploy in crop improvement.ResultsEighty-two alleles were detected. Alleles per marker ranged from 2 (RM505) to 5 (RM276) with an average of 3.04 alleles. The markers are informative in analyzing the diversity as the PIC values estimated varied from 0.17 (RM577 on chromosome 1) to 0.72 (RM276 on chromosome 6) with an average of 0.54 per locus. RM276 with repeat motif of (AG)8A3(GA) 33 on chromosome 6 was the most informative (amplified 5 alleles). The combined analysis had shown genotypes in a few clusters to be more diverse than others. SSR markers RM289, RM505, RM577 and RM22866 were identified as genotype specific markers. With PowerCore, 46 genotypes (22%) were identified as a core set of ARG that represent all the alleles detected in the entire set investigated. 2-Acetyl-1-pyrroline is considered to impart aroma; it was not detected by GC–MS tests in many ARG.ConclusionsForty-six genotypes in the core set have different maturity periods, plant statures, grain types and grain quality traits. A parent can be selected from the core set to improve aromatic rice depending on the breeding objective. The olfactory sensing of strong aroma emitted by cooked kernels of all ARG was found more decisive than the costly GC–MS tests.

Mapping QTLs underpin nutrition components in aromatic rice germplasm

As rice is an important staple food globally, research for development and enhancement of its nutritional value it is an imperative task. Identification of nutrient enriched rice germplasm and exploiting them for breeding programme is the easiest way to develop better quality rice. In this study, we analyzed 113 aromatic rice germplasm in order to identify quantitative trait loci (QTL) underpinning nutrition components and determined by measuring the normal frequency distribution for Fe, Zn, amylose, and protein content in those rice germplasm. Comparatively, the germplasm Radhuni pagal, Kalobakri, Thakurbhog (26.6 ppm) and Hatisail exhibited the highest mean values for Fe (16.9 ppm), Zn (34.1 ppm), amylose (26.6 ppm) and protein content (11.0 ppm), respectively. Moreover, a significant linear relationship (R2 = 0.693) was observed between Fe and Zn contents. Cluster analysis based on Mahalanobis D2 distances revealed four major clusters of 113 rice germplasm, with cluster III containing a maximum 37 germplasm and a maximum inter-cluster distance between clusters III and IV. The 45 polymorphic SSRs and four trait associations exhibited eight significant quantitative trait loci (QTL) located on eight different chromosomes using composite interval mapping (CIM). The highly significant QTL (variance 7.89%, LOD 2.02) for protein content (QTL.pro.1) was observed on chromosome 1 at 94.9cM position. Also, four QTLs for amylose content were observed with the highly significant QTL.amy.8 located on chromosome 8 exhibiting 7.2% variance with LOD 1.83. Only one QTL (QTL.Fe.9) for Fe content was located on chromosome 9 (LOD 1.24), and two (QTL.Zn.4 and QTL.Zn.5) for Zn on chromosome 4 (LOD 1.71) and 5 (LOD 1.18), respectively. Overall, germplasm from clusters III and IV might offer higher heterotic response with the identified QTLs playing a significant role in any rice biofortification breeding program and released with development of new varieties.

An optimized analysis of 2‐acetyl‐1‐pyrroline content diversity in the core collection of aromatic rice germplasm (Oryza sativa L.)

AbstractBackground and objectivesAromatic rice constitutes a small but a special group of rice varieties, considered as the best in quality. A headspace solid‐phase micro‐extraction (HS‐SPME) method, combined with a gas chromatography–mass spectrometry (GC‐MS) assay, was developed to enable the rapid, simple, and reliable quantification of 2‐acetyl‐1‐pyrroline (2AP) in rice.FindingsThe most effective release of 2AP was obtained using a divinylbenzene/carboxen/polydimethylsiloxane (DVB/CAR/PDMS) fiber and extracting brown flour or single whole brown grain at 80°C for 30 min. By the optimized protocol, the limit of detection (LOD) and limit of quantification (LOQ) for 2AP was 1.0 µg/kg of 2AP and 4.0 µg/kg of brown rice flour, respectively. The reproducibility and interday repeatability were <5.00% RSD (n = 10) and 12.5% RSD (n = 27), respectively. A good linearity was observed from 5 to 80 ng with a good correlation coefficient (R2) value of 0.9892. When the method was applied to a collection of aromatic rice germplasm, the 2AP content in 34 entries appeared to be below the limit of detection. The mean 2AP content in the set was 0.45 mg/kg, and the range was from undetectable to 2.73 mg/kg. Most entries contained 0.09–0.46 mg/kg 2AP.ConclusionsA rapid 2AP assay of brown flour or single brown whole grain, based on HS‐SPME combined with GC‐MS, was shown to generate reproducible and reliable outputs. When applied to a set of 228 aromatic rice entries, it was able to reveal the existence of substantial variation for 2AP content.Significance and noveltyThe results of this study produced an accurate, rapid, and highly reproducible assay, which are suitable for the screening of large numbers of samples and the helping of aromatic rice breeding.

DNA fingerprint and diversity in aromatic rice by Gn1 gene linked SSR markers

Number of grains per panicle is a limiting factor for the yield of aromatic rice. Toovercome this limitation, itmight behelpful to screenaromatic rice using markers linked to grain number.In this study, an elementary DNA fingerprinting database of the nine aromatic rice cultivars was built using four SSR primer pairs linked to Gn1 gene responsible for grain number in rice. For genotyping of aromatic rice cultivars, DNA was extracted from leaf samples using IRRI standard protocol. Allele scoring was done by using a computer based program Alpha Ease FC 4.0 and data were analyzed by Power Marker version 3.25 software. Nei’s genetic distance value and similarity werecomputed. From the analysis, it was found that a total of 21 alleles were detected with an average number of 5.25 alleles per locus having PIC values ranging from 0.3402 (RM5493) to 0.7883 (RM3452) and the average value 0.6629. The highest gene diversity (0.8148) was observed in loci RM3452,and the lowest gene diversity (0.3404) was observed in loci RM5493.From the study, it can be stated that all of the aromatic rice germplasm have bands of the gene that influence the grain but they showed genetic variability.Information obtained from genotyping of varieties helped to analyze the genetic diversity within and among closely related crop varieties which has the potential for crop improvement and to meet the diverse goals like producing cultivars with increased yield of aromatic rice.
 Progressive Agriculture 29 (4): 336-344, 2018

Documentation of the grain morphological variation within some traditional aromatic rice (Oryza sativa L.) varieties of West Bengal

With the introduction of high-yielding varieties, price incentives and research inclinations towards modern varieties of non-aromatic rice to achieve self reliance, cultivation of several indigenous scented rice varieties have been neglected. A large number of traditional scented rice has already been lost and many are on the verge of extinction. It is more so for the small and medium-grained non Basmati aromatic rice than the long-grained Basmati types which form the bulk of rice export. Even though the cultivation of traditional aromatic rice varieties in prime areas is fast declining, their aroma and grain quality is highly appreciated by local communities and they are used in several rituals and customs. Future progress in the improvement of scented rice largely depends on immediate documentation, evaluation, conservation of the extant scented rice genetic resources and their effective utilization. The present study is on the documentation and evaluation of some of the aromatic rice germplasm of West Bengal.

Isolation and Molecular Marker Detection of Badh2 Gene from Aromatic Rice Germplasm Resources in Southern Henan

The production of aroma in aromatic rice is due to the increase of 2-acetyl-1-pyrroline (2-AP) precursor substances caused by the functional deletion of Badh2 gene on chromosome 8, and the accumulation of 2AP makes rice produce aroma. In this study, Badh2 gene was isolated and cloned from 18 representative aromatic rice cultivars in Southern Henan, and the bioinformatics analysis of Badh2 gene was carried out. Meanwhile, seven functional molecular markers developed by Badh2 gene were used to detect and analyze Badh2 gene in 18 aromatic rice varieties from Southern Henan. The results showed that the coding region of Badh2 gene was 1509 bp in length. It contained 15 exons and 14 introns, and encoded 503 amino acids. There are many types of variation of the Badh2 gene in the 18 aromatic rice varieties. According to the variation of Badh2 gene, the tested aromatic rice varieties could be divided into three groups, among which Xinxianggeng 1, Xiangnuo 25, Heixiangdao 193 and Xiangbao 2 were concentrated in group Ⅰ, while the other 14 kinds of aromatic rice were concentrated in group II. Seven functional molecular markers of Badh2 gene were used to detect different varieties mutation types in exon 2, exon 4~5, exon 7 and exon 13 of Badh2 gene. No aromatic rice varieties with different mutation types were found in promoter region, exon 12 and exon 14 of Badh2 gene. Therefore, our results provide important information for understanding the genetic basis of fragrant genes in aromatic rice germplasm resources in Southern Henan and breeding new varieties of high-quality aromatic rice using molecular marker-assisted selection.

Molecular Characterization and Genetic Divergence Analysis of Traditional and Improved Aromatic Rice Varieties Using Microsatellite Markers

Microsatellite profiling was employed to analyze the nature and extent of differentiation and divergence among eighteen traditional and improved varieties of aromatic rice. Analysis of 18 primers dependent genetic polymorphism revealed 89 shared and 91 unique allelic variants generated in the form of amplified products amongst 18 varieties. Polymorphic information content of the primers ranged from 0.60 to 0.88 with an average of 0.80. Ample genetic differentiation and divergence amongst entries was deduced by a comparison of similarity coefficients. Broadly, the entries were distinctly divided into three multi-genotypic groups, each of which accommodated traditional and improved varieties. However, the first and second groups were dominated by traditional varieties, whereas the third group was dominated by improved varieties. With maximum similarity in respect of targeted genomic regions, Champaran Basmati and Sanwal Basmati (0.45) were accommodated into the first group along with Jeerabati and Rajendra Kasturi (0.45), in addition to Baharni, Birsamati and Kasturi. Spatial distribution pattern of two dimensional ordinations of microsatellite primers specific genetic profiles from traditional and improved varieties completely validated the hierarchical classification pattern exhibited by sequential agglomerative clustering based dendrogram. The varieties from different groups could be utilized in breeding programs for genetic enhancement of aromatic rice germplasm base and molecular profiles could be helpful in preserving the integrity of these valuable aromatic rice varieties.

Assessment of genetic diversity in aromatic rice (Oryza sativa L.) germplasm using PCA and cluster analysis

A total of 67 aromatic rice germplasm lines were evaluated for nine traits by PCA and cluster analysis for determining the pattern of variation, relationship among individuals and their characteristics. Out of nine PCs, four exhibited more than 1.0 eigen values and showed 70.14 per cent total variability among the characters. PC1 showed high proportion of total variation 25.9 per cent and PC2, PC3 and PC4 contributed 16.96 per cent, 15.06 per cent and 12.22 per cent of the total variance, respectively. Highest positive eigen vector was observed in grain width (0.46) followed by plant height (0.34) in PC1 indicated the large effect in the overall variation of the genotypes. From the cluster analysis, clusters I, II and III had desirable mean values for days to 50 per cent flowering, plant height, number of productive tillers/plant, grain length, grain width, 100 grain weight, panicle length and single plant yield. The genotypes in these clusters would be utilized for aromatic rice improvement breeding.

Variability Assessment of Aromatic Rice Germplasm by Pheno-Genomic traits and Population Structure Analysis

While the pleasant scent of aromatic rice is making it more popular, with demand for aromatic rice expected to rise in future, varieties of this have low yield potential. Genetic diversity and population structure of aromatic germplasm provide valuable information for yield improvement which has potential market value and farm profit. Here, we show diversity and population structure of 113 rice germplasm based on phenotypic and genotypic traits. Phenotypic traits showed that considerable variation existed across the germplasm. Based on Shannon–Weaver index, the most variable phenotypic trait was lemma-palea color. Detecting 140 alleles, 11 were unique and suitable as a germplasm diagnostic tool. Phylogenetic cluster analysis using genotypic traits classified germplasm into three major groups. Moreover, model-based population structure analysis divided all germplasm into three groups, confirmed by principal component and neighbors joining tree analyses. An analysis of molecular variance (AMOVA) and pairwise FST test showed significant differentiation among all population pairs, ranging from 0.023 to 0.068, suggesting that all three groups differed. Significant correlation coefficient was detected between phenotypic and genotypic traits which could be valuable to select further improvement of germplasm. Findings from this study have the potential for future use in aromatic rice molecular breeding programs.

Genetic Diversity of Aromatic Rice Germplasm Revealed By SSR Markers.

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.

국내 육성된 향미 품종의이앙시기별 이화학적 특성 및 향기성분 비교 분석

국내 육성된 향미 품종의이앙시기별 이화학적 특성 및 향기성분 비교 분석

Study of genetic diversity for agro-morphological and quality characters in diverse aromatic rice germplasm

Grain quality has always been an important consideration in rice variety selection and development. Fine grained aromatic rice fetch higher demand than the normal variety in national as well as international market. Indian sub continent has rich diversity of short grain aromatic rice grown in various parts of country while long grain basmati types are confined to the north-western region. Knowledge of genetics of aroma would help in deciding the breeding procedure to evolve the scented varieties. In the present study 81 aromatic rice germplasm, collected from different locations of Chhattisgarh were evaluated for divergence analysis. Observations were recorded on five randomly selected plants for 16 agro-morphological and quality characters. Based on relative magnitude of D2 estimates 81 genotypes which were grouped into nine clusters. A wide range of variation was observed in cluster means for all the characters studied. The genotypes from cluster II having desired mean value for quality characters like hulling, milling and head rice recovery percentage and panicle length; cluster VII having high value for kernel length and length breadth ratio and cluster V for earliness and high yield could be incorporated in hybridization for developing high yielding, early maturing with good quality aromatic rice variety.

Agro-morphological and quality characterization of indigenous and exotic aromatic rice (Oryza sativa L.) germplasm

For establishment of the distinctness among 64 aromatic rice germplasm, 35 agro-morphological and quality traits were used. Most of the studied traits showed wide variation among the germplasm. Purple colour of auricles and ligule was found in only one genotype, while light purple colour of auricles was recorded in four genotypes. White colour of stigma was recorded in 57 accessions, whereas purple stigma was observed in six accessions. Awns present in 31 accessions. The weight of 1000 grains, which is one of the most important yield attributing traits showed wide variation among accessions, and ranges from very low to very high weight. Grain: length and decorticated grain: length showed high variation and ranges from very short to long type, while grain: width and decorticated grain: width showed somewhat little variation among the genotypes. Extra long slender type grain shape was observed in 27 accessions. White type of decorticated grain colour was found in 55 genotypes, while light red and red colour was observed in only three genotypes. The present study concluded that all sixty four accessions were found to be distinct on the basis of thirty one agro-morphological and quality traits. Accessions having short stem length, very long panicle length, more number of panicle per plant, and extra long slender grain may be used as potential donor in hybridization programmes. This study will be useful for breeders, researchers and farmers toidentify and choose the restoration and conservation of beneficial genes for crop improvement.

Genetic Variability in Bangladeshi Aromatic Rice through RAPD Analysis

Genetic polymorphism and relationships among 30 commercial varieties of Bangladeshi aromatic rice (Oryza sativa L.) were established using random amplified polymorphic DNA (RAPD) primers. Out of fifty 10-mer RAPD primers screened initially, four were chosen and used in a comparative analysis of different varieties of indigenous Bangladeshi aromatic rice. Of the 33 total RAPD fragments amplified, 7 (21.21%) were found to be shared by individuals of all eight varieties. The remaining 26 fragments were found to be polymorphic (78.79%). Pair-wise estimates of similarity ranged from 0.101 to 0.911. Highest genetic diversity was determined between Radhunipagol and Dubsail varieties (0.911). The amount of genetic diversity within aromatic rice germplasm was quite high as determined by the genetic similarity coefficients between varieties. Genetic similarities obtained from RAPD data were also used to create a cluster diagram. Cluster analysis using an un-weighted pair-group method with arithmetic averages (UPGMA) was used to group the varieties and the 30 aromatic rice varieties were grouped into 6 clusters where cluster I includes the maximum number of varieties (9). Cluster VI includes minimum number of varieties (2). This Study offered a rapid and reliable method for the estimation of variability between different varieties which could be utilized by the breeders for further improvement of the local aromatic rice varieties.