Khwaja Hossain

Synteny perturbations between wheat homoeologous chromosomes caused by locus duplications and deletions correlate with recombination rates

Loci detected by Southern blot hybridization of 3,977 expressed sequence tag unigenes were mapped into 159 chromosome bins delineated by breakpoints of a series of overlapping deletions. These data were used to assess synteny levels along homoeologous chromosomes of the wheat A, B, and D genomes, in relation to both bin position on the centromere-telomere axis and the gradient of recombination rates along chromosome arms. Synteny level decreased with the distance of a chromosome region from the centromere. It also decreased with an increase in recombination rates along the average chromosome arm. There were twice as many unique loci in the B genome than in the A and D genomes, and synteny levels between the B genome chromosomes and the A and D genome homoeologues were lower than those between the A and D genome homoeologues. These differences among the wheat genomes were attributed to differences in the mating systems of wheat diploid ancestors. Synteny perturbations were characterized in 31 paralogous sets of loci with perturbed synteny. Both insertions and deletions of loci were detected and both preferentially occurred in high recombination regions of chromosomes.

An integrated high-density linkage map of soybean with RFLP, SSR, STS, and AFLP markers using A single F2 population.

Abstract Soybean [Glycine max (L.) Merrill] is the most important leguminous crop in the world due to its high contents of high-quality protein and oil for human and animal consumption as well as for industrial uses. An accurate and saturated genetic linkage map of soybean is an essential tool for studies on modern soybean genomics. In order to update the linkage map of a F2 population derived from a cross between Misuzudaizu and Moshidou Gong 503 and to make it more informative and useful to the soybean genome research community, a total of 318 AFLP, 121 SSR, 108 RFLP, and 126 STS markers were newly developed and integrated into the framework of the previously described linkage map. The updated genetic map is composed of 509 RFLP, 318 SSR, 318 AFLP, 97 AFLP-derived STS, 29 BAC-end or EST-derived STS, 1 RAPD, and five morphological markers, covering a map distance of 3080 cM (Kosambi function) in 20 linkage groups (LGs). To our knowledge, this is presently the densest linkage map developed from a single F2 population in soybean. The average intermarker distance was reduced to 2.41 from 5.78 cM in the earlier version of the linkage map. Most SSR and RFLP markers were relatively evenly distributed among different LGs in contrast to the moderately clustered AFLP markers. The number of gaps of more than 25 cM was reduced to 6 from 19 in the earlier version of the linkage map. The coverage of the linkage map was extended since 17 markers were mapped beyond the distal ends of the previous linkage map. In particular, 17 markers were tagged in a 5.7 cM interval between CE47M5a and Satt100 on LG C2, where several important QTLs were clustered. This newly updated soybean linkage map will enable to streamline positional cloning of agronomically important trait locus genes, and promote the development of physical maps, genome sequencing, and other genomic research activities.

High-Resolution Radiation Hybrid Map of Wheat Chromosome 1D

Physical mapping methods that do not rely on meiotic recombination are necessary for complex polyploid genomes such as wheat (Triticum aestivum L.). This need is due to the uneven distribution of recombination and significant variation in genetic to physical distance ratios. One method that has proven valuable in a number of nonplant and plant systems is radiation hybrid (RH) mapping. This work presents, for the first time, a high-resolution radiation hybrid map of wheat chromosome 1D (D genome) in a tetraploid durum wheat (T. turgidum L., AB genomes) background. An RH panel of 87 lines was used to map 378 molecular markers, which detected 2312 chromosome breaks. The total map distance ranged from ∼3,341 cR35,000 for five major linkage groups to 11,773 cR35,000 for a comprehensive map. The mapping resolution was estimated to be ∼199 kb/break and provided the starting point for BAC contig alignment. To date, this is the highest resolution that has been obtained by plant RH mapping and serves as a first step for the development of RH resources in wheat.

Analyses of Methylomes Derived from Meso-American Common Bean (Phaseolus vulgaris L.) Using MeDIP-Seq and Whole Genome Sodium Bisulfite-Sequencing

Common bean (Phaseolus vulgaris L.) is economically important for its high protein, fiber, and micronutrient contents, with a relatively small genome size of ∼587 Mb. Common bean is genetically diverse with two major gene pools, Meso-American and Andean. The phenotypic variability within common bean is partly attributed to the genetic diversity and epigenetic changes that are largely influenced by environmental factors. It is well established that an important epigenetic regulator of gene expression is DNA methylation. Here, we present results generated from two high-throughput sequencing technologies, methylated DNA immunoprecipitation-sequencing (MeDIP-seq) and whole genome bisulfite-sequencing (BS-Seq). Our analyses revealed that this Meso-American common bean displays similar methylation patterns as other previously published plant methylomes, with CG ∼50%, CHG ∼30%, and CHH ∼2.7% methylation, however, these differ from the common bean reference methylome of Andean origin. We identified higher CG methylation levels in both promoter and genic regions than CHG and CHH contexts. Moreover, we found relatively higher CG methylation levels in genes than in promoters. Conversely, the CHG and CHH methylation levels were highest in promoters than in genes. This is the first genome-wide DNA methylation profiling study in a Meso-American common bean cultivar (“Sierra”) using NGS approaches. Our long-term goal is to generate genome-wide epigenomic maps in common bean focusing on chromatin accessibility, histone modifications, and DNA methylation.

Chapter 6 Radiation Hybrid Mapping in Crop Plants

Abstract A number of recombination‐based and physical mapping methods have been developed in order to study and understand the genomic organization of plant species. Of these methods, physical mapping methods provide the best correlation between position on a map and actual physical location on the chromosome. In this review, we discuss differences between maps developed on the basis of recombination and those developed independent of recombination. In the latter method, termed commonly as physical mapping, we discuss methods that have been employed in a number of agriculturally important plant species including rice, the legume model Medicago , tomato, soybean, barley and wheat, and then focus on the radiation hybrid method of physical mapping. After a brief overview of the radiation hybrid methods employed in mammalian species, we discuss radiation hybrid mapping for maize, barley, cotton and wheat in detail.

Genome Structure and Chromosome Function

Aneuploidy refers to the loss or gain of individual chromosomes or loss of a portion of an individual chromosome from the normal chromosome set. The resulting gene-dosage imbalance may or may not noticeably affect phenotype. Although its phenotypic manifestations are usually apparent, information about the underlying alterations in structure, expression, and interphase organization of unbalanced chromosome sets is still sparse. Aneuploidy is the most common chromosomal aberration in plants, and aneuploids are valuable for the study of chromosome evolution, phenotypic manifestation of chromosome loss or gain, and mapping genes and genome. Breeding programs intended to transfer desirable genes from one species to another produce addition lines as intermediate crossing products. Such aneuploids can be used for further introgression, but their abnormal recombination and segregation interfere with production of stable introgression lines. They can have specific morphological characteristics, but more often additional confirmation is needed. Their genetic and cytogenetic properties make them powerful tools for fundamental research on regulation of homeologous recombination, distribution of chromosome-specific markers and repetitive DNA sequences, and regulation of heterologous gene expression. Recent advancements and availability of genomic resources have widened the scope for their use. They make possible assignment of individual linkage groups to specific chromosomes and can improve identification of quantitative trait loci (QTLs) and underlying DNA components/sequences.

Practical laboratory exercises for plant molecular cytogenetics

Practical laboratory work parallel with a lecture topic is one way to improve understanding of the subject matter. Cytogenetics deals mainly with chromosome behavior and biology. The key concepts of cytogenetics can be attached to actual experimental observations that can help students visualize the relationship of the concepts to chromosomes in practice. Many new technological developments are available to aid understanding of chromosome behavior, biology, and manipulation for plant and animal improvement. We present here a series of exercises designed to help students understand chromosome behavior during cellular divisions, chromosomal aberrations, and chromosome preparations for molecular cytogenetics, such as fluorescence in situ hybridization (FISH), genomic in situ hybridization (GISH), and even fiber-FISH. These exercises are used in several undergraduate and graduate courses. If they are to be incorporated into a cytogenetics course, we recommend that the instructor choose those that fit the course time-table and available resources.

Characterization and Expression Analysis of Common Bean Histone Deacetylase 6 during Development and Cold Stress Response

Histone deacetylases (HDACs) are important regulators of gene transcription thus controlling multiple cellular processes. Despite its essential role in plants, HDA6 is yet to be validated in common bean. In this study, we show that HDA6 is involved in plant development and stress response. Differential expression of HDA6 was determined in various tissues and the expression was seen to be upregulated with plant age (seedling < flowering < maturity). Higher expression was observed in flowers and pods than in stem, leaf, and root. Upregulation of HDA6 gene during cold stress implies its prominent role in abiotic stress. Furthermore, the HDA6 gene was isolated from three common bean genotypes and sequence analyses revealed homology with functionally characterized homologs in model species. The 53 kDa translated product was detected using an HDA6 specific antibody and recombinant protein overexpressed in Escherichia coli showed HDAC activity in vitro. To our knowledge, this is the first report in the agriculturally important crop common bean describing the functional characterization and biological role of HDA6.

Pretreatment of Wheat Bran for Suitable Reinforcement in Biocomposites

Wheat bran, abundant but underutilized, was investigated for its potential as a reinforcement in biocomposites through different pretreatment methods. Pretreatment methods included were dilute sodium hydroxide (NaOH), dilute sulfuric acid (H2SO4), liquid hot water (LHW), calcium hydroxide (CaOH), organosolv such as aqueous ethanol (EtOH), and methyl isobutyl ketone (MIBK). Changes in chemical composition and fiber characteristics of the treated bran were studied using scanning electron microscopy (SEM) and Fourier transform infrared spectroscopy (FTIR). Cellulose content increased to 35.1% and 29.6% in brans treated with H2SO4 and NaOH, respectively. The SEM micrographs showed surface cleaning of treated bran while maintaining sufficient surface roughness for the H2SO4, NaOH, and MIBK treated brans. Crystallinity index increased slightly for all treatments except H2SO4. NaOH and H2SO4 pretreated brans achieved important fiber characteristics, which could be useful for making thermoplastic biocomposites. Innovative use of bran in thermoplastic will create more opportunities for growers while enhancing biodegradability.