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India is blessed with an abundance of diverse rice landraces in its traditional cultivated areas. Two marker systems (simple sequence repeats (SSR) and single nucleotide polymorphism (SNP)) were used to study a set of 298 rice landrace accessions collected from six different regions of India (Andaman and Nicobar Islands, Chhattisgarh, Jharkhand, Uttar Pradesh, Uttarakhand, and West Bengal). Thirty hyper-variable simple sequence repeats (HvSSRs) and 32,782 single nucleotide polymorphisms (SNPs) were used in inferring genetic structure and geographical isolation. Rice landraces from Uttar Pradesh were the most diverse, with a gene diversity value of 0.42 and 0.49 with SSR and SNP markers, respectively. Neighbor-joining trees classified the rice landraces into two major groups with SSR and SNP markers, and complete geographical isolation was observed with SSR markers. Fast STRUCTURE analysis revealed four populations for SSR markers and three populations for SNP markers. The population structure with SSR markers showed that few individuals from Uttarakhand and Andaman and Nicobar Islands were grouped in small clusters. Population structure analysis with SNP markers showed not very distinct region-wise clustering among the rice landraces. Discriminant analysis of principal components (DAPC) and minimum spanning network (MSN) using SSR markers showed region-wise grouping of landraces with some intermixing, but DAPC and MSN with SNP markers showed very clear region-wise clustering. Genetic differentiation of rice landraces between the regions was significant with both SSR (Fst 0.094–0.487) and SNP markers (Fst 0.047–0.285). A Mantel test revealed a positive correlation between the genetic and geographic distance of rice landraces. The present study concludes that rice landraces investigated in this study were very diverse, and unlinked SSR markers show better geographical isolation than a large set of SNP markers. [ABSTRACT FROM AUTHOR]

Genetic diversity assessment is prerequisite for future crop improvement programme therefore in the present study, morphological and molecular diversity among the 12 Indian drumstick (Moringa oleifera Lam.) populations were assessed. A total of 300 genotypes belonging to 12 populations of drumstick (M. oleifera Lam.) were collected from northern (Himachal Pradesh) and southern (Tamil Nadu) parts of India. Under field condition 14 qualitative and 11 quantitative morphological characters were recorded to assess the diversity at morphological level. Correlation studies showed significant correlation between the quantitative characters. At molecular level, 19 SSR primers that produced clear and reproducible bands were selected for diversity study. A total of 35 bands were amplified of which 29 (82.86%) were polymorphic with an average of 1.84 bands per primer. Polymorphic information content (PIC) value for SSR primers ranged from 0.01 for primer MO64 to 0.37 for primer MO1 with an average of 0.15. The gene diversity ranged from 0.01 to 0.49 with an average of 0.18. Cluster analysis based on morphological characters (qualitative and quantitative) divided populations into two groups whereas; SSR makers divided it into three groups. Population MO9 (PKM1) form Periyakulum, Tamil Nadu was ungrouped based on quantitative characters. Principal coordinate analysis (PCoA) with SSR markers showed that large diversity existed in Indian drumsticks collection. The percentage of variation explained by the first 3 axes was 31.69% (axis1 - 14.35%, axis2 - 9.39% and axis3 - 7.95%). Analysis of molecular variance (AMOVA) indicated that 2% diversity was attributed to differences among regions, 3% at the level of populations and 95% contributed by the genotypes within the populations. Model based population structure were tested using K values from 1 to 20, but there was no clear population structure, therefore Ln(PD) derived Δk was plotted against the K to determine the number of populations. Based on population structure analysis five clear populations were obtained instead of 12 natural populations. Cluster analysis and structure based population study showed that, no geographical isolation exists between genotypes collected from northern and southern part of India. Principal coordinate analysis showed large genetic diversity exists in Indian drumstick collection which can be utilised for crop improvement programme particularly traits related to oil yield. [ABSTRACT FROM AUTHOR]