Applications of genome mapping and marker-assisted selection (MAS) in crop improvement are reviewed. The following aspects are considered: a comparison of the choice of markers available for the generation of linkage maps (including amplified fragment length polymorphisms (AFLP); restriction fragment length polymorphisms (RFLP); randomly amplified polymorphic DNA (RAPD) and simple sequence repeats (SSR)); quantitative trait loci (QTL) analysis; use of molecular markers in the exploitation of hybrid vigour; physical genome mapping; map-based cloning and transposon tagging of agriculturally important genes; synteny in cereal genomes; and the use of MAS in breeding for disease and pest resistance.

Genome mapping, molecular markers and marker-assisted selection in crop plants

Calling female moths attract their mates late at night with intermittent release of a species-specific sex-pheromone blend Mean frequency of pheromone filaments encodes distance to the calling female In their zig-zagging upwind search male moths encounter turbulent pheromone blend filaments at highly variable concentrations and frequencies The male moth antennae are delicately designed to detect and distinguish even traces of these sex pheromones amongst the abundance of other odors Its olfactory receptor neurons sense even single pheromone molecules and track intermittent pheromone filaments of highly variable frequencies up to about 30 Hz over a wide concentration range In the hawkmoth Manduca sexta brief, weak pheromone stimuli as encountered during flight are detected via a metabotropic PLCβ-dependent signal transduction cascade which leads to transient changes in intracellular Ca2+ concentrations Strong or long pheromone stimuli, which are possibly perceived in direct contact with the female, activate receptor-guanylyl cyclases causing long-term adaptation In addition, depending on endogenous rhythms of the moth´s physiological state, hormones such as the stress hormone octopamine modulate second messenger levels in sensory neurons High octopamine levels during the activity phase maximize temporal resolution cAMP-dependently as a prerequisite to mate location Thus, I suggest that sliding adjustment of odor response threshold and kinetics is based upon relative concentration ratios of intracellular Ca2+ and cyclic nucleotide levels which gate different ion channels synergistically In addition, I propose a new hypothesis for the cyclic nucleotide-dependent ion channel formed by insect olfactory receptor/coreceptor complexes Instead of being employed for an ionotropic mechanism of odor detection it is proposed to control subthreshold membrane potential oscillation of sensory neurons, as a basis for temporal encoding of odors

/pdf/pheromone-transduction-in-moths-xgcz019ac8.pdf

Pheromone Transduction in Moths

Bitter gourd (Momordica charantia) is an important vegetable and medicinal plant in tropical and subtropical regions globally. In this study, the draft genome sequence of a monoecious bitter gourd inbred line, OHB3-1, was analyzed. Through Illumina sequencing and de novo assembly, scaffolds of 285.5 Mb in length were generated, corresponding to ∼84% of the estimated genome size of bitter gourd (339 Mb). In this draft genome sequence, 45,859 protein-coding gene loci were identified, and transposable elements accounted for 15.3% of the whole genome. According to synteny mapping and phylogenetic analysis of conserved genes, bitter gourd was more related to watermelon (Citrullus lanatus) than to cucumber (Cucumis sativus) or melon (C. melo). Using RAD-seq analysis, 1507 marker loci were genotyped in an F2 progeny of two bitter gourd lines, resulting in an improved linkage map, comprising 11 linkage groups. By anchoring RAD tag markers, 255 scaffolds were assigned to the linkage map. Comparative analysis of genome sequences and predicted genes determined that putative trypsin-inhibitor and ribosome-inactivating genes were distinctive in the bitter gourd genome. These genes could characterize the bitter gourd as a medicinal plant.

/pdf/draft-genome-sequence-of-bitter-gourd-momordica-charantia-a-37p503xyrr.pdf

Draft genome sequence of bitter gourd (Momordica charantia), a vegetable and medicinal plant in tropical and subtropical regions

Insect olfactory receptors are heteromeric ligand-gated ion channels composed of at least one common subunit (Orco) and at least one subunit that confers odorant specificity. Little is known about how individual subunits contribute to the structure and function of the olfactory receptor complex. We expressed insect olfactory receptors in Xenopus oocytes to investigate 2 functional features, ion channel block and odorant recognition. The sensitivity of Drosophila olfactory receptors to inhibition by ruthenium red, a cation channel blocker, varied widely when different specificity subunits were present, suggesting that the specificity subunits contribute to the structure of the ion pore. Olfactory receptors formed by Dmel\Or35a and Orco subunits from several different species displayed highly similar odorant response profiles, suggesting that the Orco subunit does not contribute to the structure of the odorant-binding site. We further explored odorant recognition by conducting a detailed examination of the odorant specificity Dmel\Or67a + Dmel\Orco, a receptor that responds to aromatic structures. This screen identified agonists, partial agonists, and an antagonist of Dmel\Or67a + Dmel\Orco. Our findings favor specific subunit arrangements within the olfactory receptor complex and provide a preliminary odorophore for an olfactory receptor, offering a useful foundation for future exploration of insect olfactory receptor structure.

/pdf/subunit-contributions-to-insect-olfactory-receptor-function-16ymas8wk7.pdf

Subunit Contributions to Insect Olfactory Receptor Function: Channel Block and Odorant Recognition

Food prospects and nutraceutical attributes of Momordica species: A potential tropical bioresources – A review

A number of recent papers suggest that use of RFLPs as markers offers a clear advantage in breeding for improvement in quantitative traits (QTs). The concepts underlying establishment of linkage between RFLP markers and QT loci stem from three papers on tomato published during 1987–1991. Essentially, continuously varying QT phenotypes are assigned to RFLP genotype classes, which can be considered to be determined by a single, diallelic gene with codominant alleles. Linkage is inferred through statistical analysis. Similarly, interaction between markers and QT is also tested by an analysis of variance. Here, the statistical methods employed in these three papers to detect linkage are critically evaluated, especially because subsequent investigations take the concepts developed in these papers as proven. In this paper, we examine the three fundamental papersde novo. We scrutinize the methods employed and the inferences drawn to bring to light what we believe are conceptual drawbacks.

RFLP approach to breeding for quantitative traits in plants—a critique

We report novel findings on the cytogenetic location, functional complexity and maternal and germline roles of thestambh A locus ofDrosophila melanogaster. stmA is localized to polytene bands 44D1.2 on 2R.stmA mutations are of two types: temperature-sensitive (ts) adult and larval paralytic or unconditional embryonic or larval lethal. Twelve alleles reported in this study fall into two intragenic complementing groups suggesting thatstmA is a complex locus with more than one functional domain. Some unconditional embryonic lethal alleles show a ‘neurogenic’ phenotype of cuticle loss accompanied by neural hypertrophy. It is shown that embryos of ts paralytic alleles also show mild neural hypertrophy at permissive temperatures while short exposure to heat induces severe cuticle loss in these embryos.stmA exerts a maternal influence over heat-induced cuticle loss. Unconditional embryonic lethal alleles ofstmA are also germline lethal.

Effects of mutations at the stambh A locus of Drosophila melanogaster.

Crop Biotechnology and Developing Countries

The genome region represented byDeficiency (2L) E55 inDrosophila melanogaster has been implicated in maternal gene activity, based on high levels of F1 embryonic mortality in hemizygousDf(2L) E55/+female x+/+male matings Extensive mutagenesis screens were conducted to detect any maternal embryonic lethal loci in theDf (2L) E55, 37D2-38A1 cytological region Consequently, seven maternal effect embryonic lethal loci have been identified Five of them altered the ventral embryonic cuticle pattern in various ways In addition to these, a new ovarian tumour mutant has also been identified in the same region This demonstrates that maternal haplo insufficiency of theDf (2L) E55/+females, leading to embryonic mortality, is due to theen bloc removal of the wild type alleles of these mutants, whose activity is required in the female for ovarian organisation and embryonic development

https://link.springer.com/content/pdf/10.1007/BF02927971.pdf

Maternal effect embryonic lethal mutants identified in the 37D 2 -38A 1 region of chromosome 2 of Drosophila melanogaster

Maternal hemizygosity of the 21 B8C1-21 C8D1 aristaless region of chromosome 2L of Drosophila melanogaster leads to high levels of embryonic mortality from the cross of Df(2L) al/+ females x +/+ males The 21 B8C1-21 C8D1 polytene section therefore carries maternally active genes essential for embryogenesis Selective screening for female sterile mutants against Df(2L) al yielded six alleles of a new female sterile embryonic lethal This confirms the assumption that genomic regions that are maternally haplo-insufficient for normal embryogenesis house maternally active gene(s) It also demonstrates that mutational analysis of similar genomic regions can identify maternally acting embryonic lethal loci which escaped detection in spite of extensive screening experiments

https://www.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1601-5223.1995.00121.x

Shanti Chandrashekaran

Papers

RFLP approach to breeding for quantitative traits in plants—a critique

Effects of mutations at the stambh A locus of Drosophila melanogaster.

Crop Biotechnology and Developing Countries

Maternal effect embryonic lethal mutants identified in the 37D 2 -38A 1 region of chromosome 2 of Drosophila melanogaster

A Female Sterile Embryonic Lethal in the Maternally Haplo‐Insufficient 21 B8.C1‐21 C8.D1 Genomic Region of Drosophila melanogaster