Identification of unique alleles and assessment of genetic diversity of rabi sorghum accessions using simple sequence repeat markers

Genetic diversity among 42 sorghum accessions representing landraces (19), advanced breeding lines (16), local cultivars (2) and release varieties (5) with 30 simple sequence repeat (SSR) markers revealed 7.6 mean number of alleles per locus showing 93.3% polymorphism and an average polymorphism information content of 0.78 which range from 0.22 (Xtxp12) and 0.91(Xtxp321). The average heterozygosity and effective number of alleles per locus were 0.8 and 6.65 respectively. Cluster analysis based on microsatellite allelic diversity clearly demarcated the accessions into ten clusters. A total of 24 unique alleles were obtained from seven SSR loci in 23 accessions in a size range of 110–380 bp; these unique alleles may serve as diagnostic tools for particular region of the genome of respective genotypes. Selected SSR markers from different linkage groups provided an accurate way of determining genetic diversity at the molecular leve

Dissection of genetic diversity present in eggplant populations using simple sequence repeat markers

Eggplant (Solanum melongena L.) is the third most important solanaceous vegetable and most diversified within species spread across the world-geographical area. A study was conducted to assess the genetic diversity among the selected fifty-four eggplant genotypes (sub-categorized into five sub-population) using twenty-three SSR markers. The Analysis of Molecular Variance among the five sub-population of eggplant revealed the existence of 90.67% variation within populations and 9.34% variation among populations. The SSR markers analysis revealed important locus-wise information like mean Observed-Heterozygosity (0.216), mean Expected-Heterozygosity (0.496), Shannon’s Information Index (0.879), mean number of different alleles (3.209), mean number of effective alleles (2.535), Fixation-Index (0.649). Further, Phylogenetic-analysis clearly categorize genetically distinct individuals in which the most diversified clusters was cluster-1 (C1) out of total of five clusters and especially, wild cultivars were grouped into cluster-5 (C5). The obtained results can be used in eggplant breeding and germplasm conservation in a resourceful manner

Analisis Spasial Distribusi Bulan Basah dan Bulan Kering di Jawa Timur

Makalah ini memaparkan distribusi spasial Bulan Basah (BB) dan Bulan Kering (BK) di Jawa Timur. Data hujan diperoleh dari 943 lokasi stasiun hujan yang tersebar merata di seluruh wilayah Provinsi Jawa Timur. Hujan bulanan dihitung dari kumulatif hujan harian. Selanjutnya, nilai BB dan BK ditentukan berdasarkan metode klasifikasi Iklim Oldeman. Analisa spasial dilakukan menggunakan tool ESDA (Exploratory Spatial Data Analysis) yang terdapat pada ArcGIS Geostatistical Analyst. Tool yang digunakan mencakup: Histogram, Voronoi Map, dan QQ-Plot. Hasil analisa menunjukkan grafik Histogram dan Normal QQPlot untuk Bulan Basah dan Bulan Kering (BK) mendekati distribusi normal. Nilai statistik BB yang diperoleh adalah: minimal = 1 bulan/tahun dan maksimal = 9 bulan/tahun. Nilai bulan basah (BB) rerata dari seluruh stasiun untuk semua periode adalah 3,67 bulan/tahun dan nilai median = 4 bulan/tahun. Histogram bulan basah menghasilkan nilai standar deviasi = 1,2; koefisien skewness = 0,05; dan koefisien curtosis sebesar (3,09). Histogram Bulan Kering, menghasilkan nilai minimal 2 bulan/tahun dan maksimal = 11 bulan/tahun. Sedangkan, nilai BK rerata dari seluruh stasiun untuk semua periode adalah 6,4 bulan/tahun dan nilai median = 6 bulan/tahun. Histogram juga menampilkan nilai standar deviasi = 1,21; koefisien skewness = 0,11; dan koefisien curtosis = (3,6). Penelitian menunjukkan bahwa analisa menggunakan : histogram, Voronoi Map, Normal QQ-Plot dapat menggambarkan lebih detail variabilitas spasial Bulan Basah dan Bulan Kering di Jawa Timur

Omics techniques in crop research: an overview

Omics is a collective, broad discipline largely referring to analysis of the interactions of biological information obtained from the profiling of the genome, transcriptome, proteome, metabolome, and several other relevant -omes. While phase one of omics technologies aims at nontargeted identification of transcripts, proteins, and metabolites (essentially gene products) in a given biological sample, phase two deals with a very challenging analysis of data eventually leading to the dissection of the qualitative and quantitative dynamics of biological systems

Assessment of growth and yield parameters in recombinant inbred line populations of tomato (Solanum lycopersicum L.) through correlation and path analysis

Tomato (Solanum lycopersicum L.) is high value crop, also called as protective food due to its high nutritional and biochemical compounds. Correlation and path analysis was carried out for 147 tomato recombinant inbred line population. Correlation studies suggested that the association of fruit yield per plant was positive and significant with plant height (0.595), branches per plant (0.657), fruits per cluster (0.500), clusters per plant (0.717), average fruit weight (0.244) and fruits per plant (0.891). Path analysis revealed that among eleven characters studied only two characters viz., average fruit weight (0.415) and fruits per plant (0.817) showed very high positive and direct effect on yield per plant. This study helps to understand the mutual relationship among various traits thereby assist in selecting the character contributing to the yield

Molecular dissection of genetic diversity in pigeonpea [Cajanus cajan (L) Millsp.] minicore collection

The present investigation was carried out using 191genotypes as mini core collections of pigeonpea along with 5 check varieties to know the genetic diversity at molecular level. Significant variation was observed by the way of analysis of variance for nine characters viz., days to 50% flowering, days to maturity, plant height, number of branches per plant, pod bearing length, number of pods per plant, number of seeds per pod, seed yield per plant and hundred seed weight. Molecular diversity using 18 polymorphic simple sequence repeat (SSR) markers divided genotypes into 15 clusters, of which ICP11059 and AK-101 were solitary, indicating their distinctiveness among all genotypes. Similarly, BSMR-533, JKM-7, RVK-285, ICP-1126, ICP-348, ICP-6859 and ICP-7869 were found distinct among the genotypes. Geographical origin based diversity separated Indian and non Indian genotypes. The Un weighted Pair Group Method with Arithmetic mean (UPGMA) based dendrogram indicated distinctiveness of ICP-13633 and Bennur local, as they formed solitary cluster. The SSR marker CcM 602, as it could differentiate 4 genotypes at different base pair size can be used for identification and finger printing of genotypes

Genetic variability of the bollworm, Helicoverpa armigera, occurring on different host plants

The bollworm, Helicoverpa armigera Hübner (Lepidoptera: Noctuidae) is a polyphagous pest of worldwide occurrence inflicting annual crop damage in India worth US$ 1billion. In India this insect occurs as a major pest in many economically important crops, including cotton, pigeonpea, chickpea, tomato, okra, and blackgram. Understanding the genetic variation among the H. armigera populations occurring on host plants has become essential to understand the variation in their susceptibility to different insecticides, including Bacillus thuringiensis. This preliminary study uses 10 microsatellite simple sequence repeat (SSR) markers, to provide insight into the genetic variability of H. armigera populations from six different host plants. Nine of the SSR primers indicated high variability across the different host associated populations with polymorphism ranging from 75 to 100 per cent. Using the un-weighted pair-group method analysis, H. armigera collected and reared from cotton stood out as unique in one cluster while the insects collected and reared on all other hosts grouped separately

Analysis of relative nuclear DNA content in carnation (Dianthus caryophyllus) accessions reveals ploidy levels by flow cytometry

Carnation (Dianthus caryophyllus L.) is one of the fifth most important ornamental species worldwide. Many desirable plant characteristics such as big size flower, adaptation to stress, and intra or interspecific hybridization capability are dependent on plant ploidy level. We optimized a quick flow cytometry method for DNA content determination in carnation accession samples that allowed a systematic evaluation of ploidy levels. To verify the actual ploidy levels, we counted chromosome numbers in the root tips of representative cultivar for each ploidy level. The relative nuclear DNA content was distributed into four kinds of discontinuous groups: 1.32 to 1.95 pg (group 1), 2.03 to 2.72 pg (group 2), 2.98 to 4.65 pg (group 3) and 5.33 pg (group 4) which might correspond to the following ploidy levels; diploid, triploid, tetraploid and hexaploid. The results showed that out of 60 carnation accessions, 33 were diploid, 5 were triploid, 21 were tetraploid and 1 was hexaploid

Mining of gene-based SNPs from publicly available ESTs and their conversion to cost-effective genotyping assay in sorghum [Sorghum bicolor (L.) Moench]

Single Nucleotide Polymorphisms (SNPs) are the commonest type of nucleotide variation distributed throughout the genome and have enormous potential to saturate genetic maps. However, their identification is constrained by the huge investment required for their detection. In this study, we used publicly available EST (Expressed Sequence Tag) sequences to identify SNPs in Sorghum bicolor. A total of 12,421 putative SNPs were identified from 2,921 contiguous transcripts leading to an average SNP interval of one putative SNP for every 275.26 bp. The proportion of transition type mutations (0.598) was larger than transversion types conforming to biological expectations. In order to demonstrate the utility of the SNPs for development of markers with relatively cheap assays, we experimentally validated SNPs using Single Strand Conformation Polymorphism (SSCP) technique in sorghum accessions, which are used as parents for development mapping populations. Genotyping these parents of mapping populations with SSCP markers showed up to 33% polymorphism in the markers suggesting that the SNPs can be used as potential resource for S. bicolor crop improvement programs

Identification of Coupling and Repulsion Phase DNA Marker Associated With an Allele of a Gene Conferring Host Plant Resistance to Pigeonpea sterility mosaic virus (PPSMV) in Pigeonpea (Cajanus cajan L. Millsp.)

Pigeonpea Sterility Mosaic Disease (PSMD) is an important foliar disease caused by Pigeonpea sterility mosaic virus (PPSMV) which is transmitted by eriophyid mites (Aceria cajani Channabasavanna). In present study, a F₂ mapping population comprising 325 individuals was developed by crossing PSMD susceptible genotype (Gullyal white) and PSMD resistant genotype (BSMR 736). We identified a set of 32 out of 300 short decamer random DNA markers that showed polymorphism between Gullyal white and BSMR 736 parents. Among them, eleven DNA markers showed polymorphism including coupling and repulsion phase type of polymorphism across the parents. Bulked Segregant Analysis (BSA), revealed that the DNA marker, IABTPPN7, produced a single coupling phase marker (IABTPPN7₄₁₄) and a repulsion phase marker (IABTPPN7₉₈₃) co-segregating with PSMD reaction. Screening of 325 F₂ population using IABTPPN7 revealed that the repulsion phase marker, IABTPPN7₉₈₃, was co-segregating with the PSMD responsive SV1 at a distance of 23.9 cM for Bidar PPSMV isolate. On the other hand, the coupling phase marker IABTPPN7₄₁₄ did not show any linkage with PSMD resistance. Additionally, single marker analysis both IABTPPN7983 (P<0.0001) and IABTPPN 7₄₁₄ (P<0.0001) recorded a significant association with the PSMD resistance and explained a phenotypic variance of 31 and 36% respectively in F₂ population. The repulsion phase marker, IABTPPN7₉₈₃, could be of use in Marker-Assisted Selection (MAS) in the PPSMV resistance breeding programmes of pigeonpea