Wheat Breeding through Genetic and Physical Mapping 2

Following the success of the first topic, the special issue of “Wheat breeding through genetic and physical mapping 2” has been re-proposed in order to keep current the recent advancement in research on genetic and physical mapping of candidate genes for agronomically important traits, in studies of the regulatory sequence for biotic and abiotic stress resistance [...]

Charting the Identity of Shimla

Identity of a place changes due to rapid modern alterations in a city. There are various factors leading to these changes in the identity of a place. This research article investigates those factors through the physical mapping technique through the case study of the city, Shimla. The article delves into how the city of Shimla was formed as a British summer capital of India and has evolved its character and identity into a state capital. Components of identity of a place are explored and those components are applied to find the identity of Shimla on the basis of three major nodes of the city with important government offices. The components used to find the identity of the city are—historical layers of the structures, take of social community towards them, the components of the built form of the major nodes and activities performed at the nodes. The identity of a place is investigated by integrating all the aspects of the physical components associated with the major activity nodes extracted from the history and evolution of the city. Multiple ways of looking into physical spatial components of the nodes led to define the predominant factors to form the identity of the city.

Chromosome characterization and physical mapping of 18S rDNA in Lilium longiflorum originated interspecific hybrids using combined genomic and fluorescent in situ hybridization

This study was aimed at differentiating parental genomes, examining intergenomic composition, and mapping mitotic metaphase chromosomes by localizing parental and 18S rDNA probes in seven interspecific hybrid progenies that originated from Lilium longiflorum. Since in situ hybridization has not been previously used in lily breeding, flow cytometry was used in conjunction with genomic and fluorescent in situ hybridization to determine the genomic contribution of each parent to the interspecific progenies. A significant variation was observed in the DNA content, chromosome length, and 18S loci in F1 as compared to the female and male parents. L. longiflorum showed nearly two times higher DNA content than the male parents and L. longiflorum × Asiatic progenies, but eight times higher than L. longiflorum × L. hansonii. Genomic in situ hybridization results revealed that both female and male parents contributed an equal number of chromosomes to their interspecific F1 offspring. Fluorescent in situ hybridization mapping revealed that 18S rDNA had 8, 6 and 7 loci in L. longiflorum parents, i.e., White heaven, Bright tower, and White tower, respectively, whereas each Asiatic cultivar and L. hansonii used as male showed 8 and 12 loci respectively. Interspecific progenies showed 8 and 7 loci in LA, and 10–11 in LM hybrids. These cytogenetic results implied equal genetic and chromosomal contribution from both parents to their intergenomic progenies. Therefore, this combined (Schwarzacher et al., 1992)cytogenetic method has the potential to be an affordable and time-saving approach in lily breeding that could determine the status of hybrids and their genomic origin while achieving physical mapping and detecting genes in different genomes.

Pemetaan Batas Lahan Pondok Pesantren Entrepreneur Muhammadiyah Gondanglegi Kabupaten Malang

Modern Islamic boarding schools are a combination of Islamic boarding school curriculum with the national education curriculum. Therefore though the format is a boarding school, boarding education, students also acquire knowledge and graduation standards as students who attend public schools. The Entrepreneur Muhammadiyah Islamic Boarding School (PPEM) is a charity business unit managed by the Muhammadiyah Branch Leader (PCM) Gondanglegi, Malang Regency. The land used by the lodge is certified charity land. Along with the construction of housing on the side of cottage land, land boundaries have become a new problem between the border of cottage and housing developers. There is a difference in stake and land boundary, claimed by the housing developer next to the cottage. The target and output of this service program are that PPEM administrators can make an inventory of land through physical mapping. The product of this activity is the result of land mapping, which is applied directly in the form of a topographical mockup of the Islamic boarding school land that follows the mapping results and strengthens the land certificate.ABSTRAKSistem pondok pesantren yang modern adalah perpaduan antara kurikulum pendidikan nasional dengan kurikulum pesantren, sehingga walaupun bentuknya adalah sebuah pondok pesantren, santri juga memperoleh ilmu dan standar kelulusan seperti pelajar sekolah pada sekolah umum. Pondok Pesantren Entrepreneur Muhammadiyah (PPEM) adalah salah satu unit amal usaha di bawah pengelolaan Pimpinan Cabang Muhammadiyah (PCM) Gondanglegi, Kabupaten Malang. Lahan yang digunakan oleh pondok merupakan lahan wakaf bersertifikat. Seiring dengan pembangunan perumahan di sisi lahan pondok, batas lahan menjadi satu masalah baru, antara pengurus pondok, dengan pihak pengembang perumahan. Terdapat selisih patok dan batas lahan, yang diklaim oleh pengembang perumahan di sebelah pondok. Target dan luaran dari program pengabdian ini yaitu pengurus PPEM dapat menginventarisir lahan melalui pemetaan fisik. Produk kegiatan pengabdian masyarakat ini berupa hasil pemetaan lahan yang teraplikasikan langsung dalam bentuk maket topografi lahan pondok yang telah sesuai dengan hasil pemetaan dan memperkuat sertifikat pondok.

Physical mapping of repetitive oligonucleotides facilitates the establishment of a genome map-based karyotype to identify chromosomal variations in peanut

Background Chromosomal variants play important roles in crop breeding and genetic research. The development of single-stranded oligonucleotide (oligo) probes simplifies the process of fluorescence in situ hybridization (FISH) and facilitates chromosomal identification in many species. Genome sequencing provides rich resources for the development of oligo probes. However, little progress has been made in peanut due to the lack of efficient chromosomal markers. Until now, the identification of chromosomal variants in peanut has remained a challenge. Results A total of 114 new oligo probes were developed based on the genome-wide tandem repeats (TRs) identified from the reference sequences of the peanut variety Tifrunner (AABB, 2n = 4x = 40) and the diploid species Arachis ipaensis (BB, 2n = 2x = 20). These oligo probes were classified into 28 types based on their positions and overlapping signals in chromosomes. For each type, a representative oligo was selected and modified with green fluorescein 6-carboxyfluorescein (FAM) or red fluorescein 6-carboxytetramethylrhodamine (TAMRA). Two cocktails, Multiplex #3 and Multiplex #4, were developed by pooling the fluorophore conjugated probes. Multiplex #3 included FAM-modified oligo TIF-439, oligo TIF-185-1, oligo TIF-134-3 and oligo TIF-165. Multiplex #4 included TAMRA-modified oligo Ipa-1162, oligo Ipa-1137, oligo DP-1 and oligo DP-5. Each cocktail enabled the establishment of a genome map-based karyotype after sequential FISH/genomic in situ hybridization (GISH) and in silico mapping. Furthermore, we identified 14 chromosomal variants of the peanut induced by radiation exposure. A total of 28 representative probes were further chromosomally mapped onto the new karyotype. Among the probes, eight were mapped in the secondary constrictions, intercalary and terminal regions; four were B genome-specific; one was chromosome-specific; and the remaining 15 were extensively mapped in the pericentric regions of the chromosomes. Conclusions The development of new oligo probes provides an effective set of tools which can be used to distinguish the various chromosomes of the peanut. Physical mapping by FISH reveals the genomic organization of repetitive oligos in peanut chromosomes. A genome map-based karyotype was established and used for the identification of chromosome variations in peanut following comparisons with their reference sequence positions.

Physical Mapping of the Anopheles (Nyssorhynchus) darlingi Genomic Scaffolds

The genome assembly of Anopheles darlingi consists of 2221 scaffolds (N50 = 115,072 bp) and has a size spanning 136.94 Mbp. This assembly represents one of the smallest genomes among Anopheles species. Anopheles darlingi genomic DNA fragments of ~37 Kb were cloned, end-sequenced, and used as probes for fluorescence in situ hybridization (FISH) with salivary gland polytene chromosomes. In total, we mapped nine DNA probes to scaffolds and autosomal arms. Comparative analysis of the An. darlingi scaffolds with homologous sequences of the Anopheles albimanus and Anopheles gambiae genomes identified chromosomal rearrangements among these species. Our results confirmed that physical mapping is a useful tool for anchoring genome assemblies to mosquito chromosomes.