Identification of Parental Lines and Hybrid using Molecular Techniques in CGMS based Chilli (Capsicum annuum L.) Hybrid UARChH42 (JCH42)

Background: Molecular markers are the landmarks on DNA that identifies a particular sequence of base pairs coding for a character. SCAR (Sequenced Characterized Amplified Region) markers are proving to be more effective in identification of genotypes as they are PCR based co-dominant markers. In view of plant variety registration under PPV and FRA, 2001 molecular characterization/ identification of the variety is essential to ascertain the trueness of the variety, hence present studies have been planned and executed. Methods: In present investigation CGMS based chilli hybrid UARChH42 and its parental lines were identified using molecular techniques. A line, B line, R line and hybrid seedlings were used for DNA extraction and characterized on the basis of polymorphism with respect to sterility or fertility by using SCAR markers. Result: P1 and P2 and coxII-SCAR which are sterility specific markers could amplify A line and hybrid showing a definite band. CRF-SCAR 870 is a fertility specific marker amplified R line and hybrid. Also CMS-SCAR 130 and CMS-SCAR 130/140 were able to identified A line, B line, R line and hybrid. Two of the markers viz. orf-456-SCAR atp6-SCAR and were not able to specify any case of parental lines or hybrid identification. Hybridity of UARChH42 (JCH42) chilli hybrid was determined by any similarity in the banding pattern with any of its parent. This study would help in the fulfillment of the requirements of protection of plant varieties and farmers’ rights authority (PPVFRA), New Delhi for registration purpose.

Morphological and molecular characterization of recombinant inbred lines for dormancy related traits in rice (Oryza sativa L.)

The study was carried out to assess the genetic relatedness of 119 recombinant inbred lines along with their parents BPT 2231and MTU 1001 based on morphological and molecular characterization. Data recorded for 10 morphological characters was used for grouping genotypes into different clusters by using Tocher’s and UPGMA dendrogram methods. Under D2analysis, the genotypes were grouped into 6 clusters and out of 10 characters studied, free amino acids contributed maximum divergence followed by days to 50% flowering and test weight. The genotypes grouped in cluster III recorded strong dormancy both at 5 days and 10 days after harvesting whereas the genotypes of cluster IV recorded maximum grain yield/plant. Four polymorphic markers were used for genotyping of the RIL population and the lines viz.,SD 3, SD 12, SD 15, SD 68, SD 72, SD 87 and SD 113 which were categorized as strongly dormant upto 10 days after harvesting also exhibited similar banding pattern with the dormant parent MTU 1001 when amplified with more than two markers. Among the 119 RIL population studied, SD 12 manifested banding pattern as that of the dormant parent MTU 1001 with all the four polymorphic markers viz., RM346, RM22565, RM7051 and RM10793 under study and also exhibited <10% germination at 10 days after harvesting. The number of alleles detected for each of the 4 polymorphic markers ranged from 2 to 4 per loci with mean value of 2.75 alleles per locus. The dendrogram analysis divided the entire population into two distinct clusters at the distance of 2.25. The RILs viz., SD11, SD12, SD15, SD27, SD30, SD63, SD65, SD68, SD74, SD75, SD80 along with the dormant parent MTU 1001(SD 121) which recorded less than 50% germination and categorized as strongly dormant under phenotyping were grouped in cluster IB2 in molecular analysis thus revealing the similarity between the two methods.

Chromosome Banding and Mechanism of Chromosome Aberrations

Chromosome identification depends on the morphological features of the chromosome and therefore karyotype and its banding pattern analyses are the most suitable technique to identify each and every chromosome of a chromosome complement. Moreover, aberrations caused by breaks play an important role in the evolution of a chromosome set and chromosome complement by decreasing or increasing the chromosome number. Therefore, both the aspects are discussed in detail in the present chapter. At present, the chapter will highlight the karyotype and its components, karyotype trends, evolution and its role in speciation, banding pattern and techniques, chromosome differentiation and linearization, banding applications and their uses, detection and analysis of chromosomal aberrations, chromosome and chromatid types of aberrations and mechanism of the formation of chromosome aberrations and breaks for karyotype evolutionary trends.

GC and Repeats Profiling along Chromosomes—The Future of Fish Compositional Cytogenomics

The study of fish cytogenetics has been impeded by the inability to produce G-bands that could assign chromosomes to their homologous pairs. Thus, the majority of karyotypes published have been estimated based on morphological similarities of chromosomes. The reason why chromosome G-banding does not work in fish remains elusive. However, the recent increase in the number of fish genomes assembled to the chromosome level provides a way to analyse this issue. We have developed a Python tool to visualize and quantify GC percentage (GC%) of both repeats and unique DNA along chromosomes using a non-overlapping sliding window approach. Our tool profiles GC% and simultaneously plots the proportion of repeats (rep%) in a color scale (or vice versa). Hence, it is possible to assess the contribution of repeats to the total GC%. The main differences are the GC% of repeats homogenizing the overall GC% along fish chromosomes and a greater range of GC% scattered along fish chromosomes. This may explain the inability to produce G-banding in fish. We also show an occasional banding pattern along the chromosomes in some fish that probably cannot be detected with traditional qualitative cytogenetic methods.

Multivariate Analysis and Its Application for Characterizing Cowpea Landraces

Background: Several major crops have been genetically eroded due to introduction of new material but cowpea have great potential and wide genetic base of novel significance. A new strategy of cowpea evaluation was adopted to investigate the potential of 71 landraces representing 31 districts of Pakistan through multivariate analysis to devise future plan for germplasm conservation. Methods: Cowpea 71 landraces collected from 31 districts were planted under field conditions in an augmented design. Plant descriptors qualitative traits (plant color, leaf shape, plant type, twining tendency, anthocynin pigment and fodder types) and agronomic traits (plant height, branches, pods, grain yield, biomass and harvest index) were recorded. Protein banding pattern was established. Similarity index, variance were calculated and phylogenetic trees were constructed by software “Statistica”.Result: Four cowpea landraces showed tremendous performance to phenotypic as well as protein banding pattern variation viz., Pk-27154 (Jhang), Pk-27047 (Vehari), Pk-27029 (Sialkot) and Pk-27107 (Bahawalpur). High inter and intra variation suggested further genotype x environmental interaction trials at multi-locations. Sampling from the neglected areas especially Sindh and Baluchistan parts are hereby recommended to gather unique landraces and accessions before the genetic resources might be depleted through various environmental stresses.