Molecular Characterization and Evaluation of Genetic Relationship in Temperate Rice (Oryza sativa L.) Germplasm

Abstract

Nature and magnitude of genetic variability, genetic diversity (D2 statistic) at the phenotypic level and genetic distance (GD) at the molecular level (using SSR primers) was estimated in 116 rice genotypes (42 landraces and 74 cultivars) of Kashmir valley. These rice cultivars/landraces were grown in replicated trial during the kharif season of 2008 and 2009 at the Experimental Farm of the Division of Plant Breeding and Genetics, SKUAST-K, Shalimar, Srinagar. Morphological traits viz. leaf blade colour, collar colour, auricle colour, ligule colour, flag leaf angle, panicle type, awning pattern, palea and lemme pubescence, seed coat colour and panicle threshability was characterised using standard procedure of IRRI on the basis of scales (scores 0 to 9). Leaf blade colour and collar colour was predominantly green in more than 80.0 per cent genotypes, while auricle colour, ligule colour and seed coat colour was desirable in most of the genotypes (54 to 90%). Flag leaf angle was erect/intermediate in nearly 60 per cent genotypes. Panicle type was compact/intermediate in nearly 85 per cent population with its threshability as intermediate to easy in about 77 per cent. Estimates of coefficient of variation (phenotypic and genotypic) was moderate (10-30%) for plant height, panicle length, 100-grain weight, days to 50 per cent flowering, grain length and its width and leaf length. It was high (>30%) for leaf width, tillers plant-1 and grain yield (q ha-1). Heritability estimates (broad sense) were high (>60%) for all the 10 quantitative traits studied. Expected genetic gain (% of the mean) was high (>30%) for all the traits except plant height and leaf length (data pooled over years). Genetic diversity at the phenotypic level, based on 10 quantitative traits, revealed presence of significant diversity (Wilk’s test) among the genotypes. A total of 19 clusters were formed with 26 genotypes in cluster-1; 10 (cluster-2); 36 (cluster-3), 23 (cluter-5) and 7 (cluster-13). Remaining clusters had one genotype each. Majority of landraces got grouped in the cluster-3, while few like Zager, Meer zag, Hapat China, Prene never and Rehman Batt-1 formed single genotype clusters. SKAU-105 also formed a single genotype cluster. Most of the genotypes for cold and short duration agro-ecosystem got grouped in the cluster-1 while most of the released high yielding varieties for valley basin agro-ecosystem got grouped in the cluster-2. Maximum inter-cluster distance (D2) of 35201.15 was observed between the single genotypes clusters viz. cluster-14 (Prene never) and cluster-17 (SKAU-105) followed by D2 value of 33363.13 between the cluster-II (Hapat China) and cluster-17 (SKAU-105). Intra-cluster distance was maximum (2653.36) in the cluster-13. Highest contribution towards total divergence in the present set of genotypes came from grain yield (55.85%), days to 50 per cent flowering (19.66%) and plant height (13.18%), contributing a total of 88.7 per cent diversity. Preliminary screening of these cultivars/landraces for their kernel aroma on cooking revealed that majority (71.6%) had no aroma, 25.0 per cent were having slight aroma while 4 landraces viz. Tilazag, Mushka budji, Larbeol and Kamad had presence of good kernel aroma on cooking. Screening of the genotypes for their field reaction to brown spot (Cochlio bolus miyabeanus) and blast (Magnaporthe grisea) at seedling and tillering stages of growth revealed that 73.3 per cent showed moderate to high resistance against brown spot at the seedling stage and 75.86 per cent at the tillering stage. Similarly, the blast disease revealed that 90.52 per cent genotypes had moderate to high resistance at the seedling stage, while at the tillering stage it was only 65.52 per cent. For the molecular characterisation 42 genotypes (21 landraces and 21 cultivars) from amongst the 116 genotypes were studied. Nine SSR primers were used, which identified a total of 62 alleles across these genotypes with a range of 2 - 11 alleles per locus and a mean of 6.89 alleles per locus. The PIC values, measuring allelic diversity and polymorphism ranged from 0.490 (RM2592) on chromosome-1 to 0.806 (RM585) on the chromosome-6, with a mean PIC value of 0.719 per locus. Similarity coefficients (measuring relatedness) were used to construct the dendogram and clustering pattern. Pairwise similarity coefficients ranged from 0.10 to 0.89, with the average similarity coefficient around 0.40. the wide range and lower mean. Similarity coefficient value revealed presence of good genetic diversity among these genotypes at the molecular level. Clustering pattern revealed grouping of these genotypes into 5 clusters. All the landraces got grouped into 2 clusters viz. cluster-I (13) and cluster-II (7) except Rehman Batt-1 which got grouped in the cluster which mostly contained genotypes for higher altitude conditions. High yielding varieties for valley basin conditions formed cluster-V (5 cultivars), while cluster-III contained mostly pre-release exotic varieties. Dendogram revealed formation of 2 major groups with all the landraces except Rehman Batt-1 in the group-I and remaining cultivars with exotic genetic background in the group - II