Assessing the leaf shape dynamic through marker–trait association under drought stress in a rice germplasm panel

The flag leaf acts as a functional leaf in rice, Oryza sativa L., primarily supplying photosynthate to the developing grains and influencing yields to a certain extent. Drought stress damages the leaf physiology, severely affecting grain fertility. Autumn rice of northeast India is called locally as ‘ahu’ rice, and is known for its drought tolerance. Exploring diverse germplasm resources at the morphological level using an association mapping approach can aid in identifying the genomic regions influencing leaf shape dynamics. A marker–trait association (MTA) study was carried out using 95 polymorphic SSR markers and a panel of 273 ahu rice germplasm accessions in drought stress and irrigated conditions. The trials suggest that at the vegetative stage, drought stress significantly affects leaf morphology. The leaf physiology of some tolerant accessions was relatively little affected by stress and these can be considered as ideal varieties for drought conditions. The phenotypic coefficient of variance and genotypic coefficient of variance values implied moderate to high variability for the leaf traits studied. Analysis of molecular variance inferred that 11% of variation in the germplasm panel was due to differences between populations, while the remaining 89% may be attributed to a difference within subgroups formed through STRUCTURE analysis. Using the mixed linear model approach revealed 11 MTAs explaining between 4.5 and 20.0% of phenotypic variance at P > 0.001 for all the leaf traits. The study concludes that ahu rice germplasm is extremely diverse and can serve as a valuable resource for mining desirable alleles for drought tolerance.

Genetic diversity of yield related traits in a large subset of exotic and indigenous rice germplasm collection maintained at Tamil Nadu Agricultural University gene bank

The present investigation was carried out to explore the extent of genetic divergence in 95 rice germplasm accessions for twelve characters during kharif, 2018. In D2 analysis, the 95 genotypes were grouped into fifteen clusters. The clustering pattern indicated that there was no parallelism between genetic diversity and geographical origin as the genotypes from same origin were included in different clusters and vice versa. The highest intra cluster distance was registered in cluster V (215.183) followed by cluster IX (209.831), cluster VIII (204.057) and cluster XIV (202.623).The maximum inter cluster distance was observed between cluster II and cluster III (991.049) followed by cluster II and cluster X (974.960), cluster III and cluster XI (963.826), cluster II and XII (962.013), cluster X and cluster XI (932.469) and cluster XI and cluster XII (919.151). Genetically distant parents from those clusters could be able to produce higher heterosis in progenies on hybridization. Grain yield per plant, 100 grain weight and days to 50% flowering were the major contributors towards the total genetic divergence among the genotypes studied. Thus selection could be made based on grain yield per plant, hundred grain weight and days to 50%flowering for the progenies identified.

Agro-morphological characterization based genetic diversity of Indonesian local rice germplasm

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.

Morphological variability and genetic diversity of Aman rice germplasm of Bangladesh cultivated in Mymensingh region

Thirty-one Aman rice germplasm were evaluated to assess their morphological variability and genetic diversity considering ten quantitative and thirty one qualitative traits at the field experimental plot of Bangladesh Institute of Nuclear Agriculture, Mymensingh, following randomized complete block design. The germplasm showed significant differences for all the studied traits. The highest grain yield/plant was recorded in Sentu-16 whereas the lowest was found in Gaindha. The genotypic coefficient of variation (GCV) was lower than those of the corresponding phenotypic coefficient of variation (PCV) for all the traits. High PCV and GCV along with heritability, genetic advance (GA) and GA in percentage of mean were recorded for number of filled grains/panicle and number of unfilled grains/panicle. Grain yield/plant had positively significant correlation with plant height, number of total tillers/hill, number of effective tillers/hill, number of filled grains/panicle and thousand grain weight. Path co-efficient analysis suggested that grain yield/plant had positive direct effect in association with days to fifty percent flowering, number of effective tillers/hill, panicle length, number of filled grains/panicle and thousand grain weight. Principal component analysis revealed that the first three components accounted for 79.57% of cumulative variance. Cluster analyses were revealed that the studied rice germplasm organized into five clusters based on D2 values where maximum inter-cluster distance was observed between cluster II and V. Qualitative characterization by distinctness, uniformity and stability test revealed that a wide range of variation was observed among the genotypes. Therefore, this study would be useful for breeders to choose and identify the revival and preservation of beneficial genes for crop improvement.

Identification of Promising Genotypes Through Systematic Evaluation for Arsenic Tolerance and Exclusion in Rice (Oryza sativa L.)

Rice remains a major staple food source for the rapidly growing world population. However, regular occurrences of carcinogenic arsenic (As) minerals in waterlogged paddy topsoil pose a great threat to rice production and consumers across the globe. Although As contamination in rice has been well recognized over the past two decades, no suitable rice germplasm had been identified to exploit in adaptive breeding programs. Therefore, this current study identified suitable rice germplasm for As tolerance and exclusion based on a variety of traits and investigated the interlinkages of favorable traits during different growth stages. Fifty-three different genotypes were systematically evaluated for As tolerance and accumulation. A germination screening assay was carried out to identify the ability of individual germplasm to germinate under varying As stress. Seedling-stage screening was conducted in hydroponics under varying As stress to identify tolerant and excluder genotypes, and a field experiment was carried out to identify genotypes accumulating less As in grain. Irrespective of the rice genotypes, plant health declined significantly with increasing As in the treatment. However, genotype-dependent variation in germination, tolerance, and As accumulation was observed among the genotypes. Some genotypes (WTR1-BRRI dhan69, NPT-IR68552-55-3-2, OM997, and GSR IR1-5-Y4-S1-Y1) showed high tolerance by excluding As in the shoot system. Arsenic content in grain ranged from 0.12 mg kg−1 in Huang-Hua-Zhan (indica) from China to 0.48 mg kg−1 in IRAT 109 (japonica) from Brazil. This current study provides novel insights into the performance of rice genotypes under varying As stress during different growth stages for further use in ongoing breeding programs for the development of As-excluding rice varieties for As-polluted environments.

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

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 Evaluation and Conservation of Kam Fragrant Glutinous Rice (Oryza sativa L.) Germplasm in Southeast Guizhou, China

The genetic diversity of rice germplasm is the basis for increases in rice yield and quality. The collection, assessment, and protection of the genetic diversity of rice germplasm is important for achieving sustainable agriculture and assuring food security. Many underdeveloped indigenous areas have abundant and valuable rice germplasm resources. However, in-depth assessments of the genetic diversity of rice germplasm from these areas and studies related to protecting these traditional cultures are not available. In this study, from 2005 to 2016, the authors have conducted in-depth evaluation of the genetic diversity of Kam fragrant glutinous rice germplasm resources in southeast Guizhou by using multidisciplinary comprehensive methods such as ethnobotany, cultural anthropology, and modern molecular markers. In total, 376 Kam fragrant glutinous rice samples from 42 villages in the Dong community in southeast Guizhou were collected. Agronomic traits of panicles were complex and exhibited diversity. Some varieties had good disease resistance and adaptation to cold and wet climates. The Dong people named the Kam fragrant glutinous rice varieties by using seven elements, including diverse traits, growth environment, and origin. Traditional folk classification, in addition to morphology and biological analysis using molecular markers, indicates that Kam fragrant glutinous rice includes 91 varieties. Kam fragrant glutinous rice comprises a very high number of varieties, most of which are japonica-type and exhibit a high level of genetic diversity. The traditional folk classification of Kam fragrant glutinous rice by the Dong community is consistent with the biological classification. The traditional naming of Kam fragrant glutinous rice provides an important reference for understanding its genetic diversity. The high level of genetic diversity in Kam fragrant glutinous rice is not only related to the natural environment of the area but also tightly linked with the abundant and diverse Dong ethnic traditional cultures, which has led to protection of Kam fragrant glutinous rice’s genetic diversity.