Brian W. Diers

Bio: Brian W. Diers is an academic researcher from University of Illinois at Urbana–Champaign. The author has contributed to research in topics: Population & Quantitative trait locus. The author has an hindex of 52, co-authored 155 publications receiving 8373 citations. Previous affiliations of Brian W. Diers include Michigan State University & University of Wisconsin-Madison.

RNA-Seq Atlas of Glycine max: a guide to the soybean transcriptome.

Abstract: Next generation sequencing is transforming our understanding of transcriptomes. It can determine the expression level of transcripts with a dynamic range of over six orders of magnitude from multiple tissues, developmental stages or conditions. Patterns of gene expression provide insight into functions of genes with unknown annotation. The RNA Seq-Atlas presented here provides a record of high-resolution gene expression in a set of fourteen diverse tissues. Hierarchical clustering of transcriptional profiles for these tissues suggests three clades with similar profiles: aerial, underground and seed tissues. We also investigate the relationship between gene structure and gene expression and find a correlation between gene length and expression. Additionally, we find dramatic tissue-specific gene expression of both the most highly-expressed genes and the genes specific to legumes in seed development and nodule tissues. Analysis of the gene expression profiles of over 2,000 genes with preferential gene expression in seed suggests there are more than 177 genes with functional roles that are involved in the economically important seed filling process. Finally, the Seq-atlas also provides a means of evaluating existing gene model annotations for the Glycine max genome. This RNA-Seq atlas extends the analyses of previous gene expression atlases performed using Affymetrix GeneChip technology and provides an example of new methods to accommodate the increase in transcriptome data obtained from next generation sequencing. Data contained within this RNA-Seq atlas of Glycine max can be explored at http://www.soybase.org/soyseq .

Copy Number Variation of Multiple Genes at Rhg1 Mediates Nematode Resistance in Soybean

Abstract: The rhg1-b allele of soybean is widely used for resistance against soybean cyst nematode (SCN), the most economically damaging pathogen of soybeans in the United States. Gene silencing showed that genes in a 31-kilobase segment at rhg1-b, encoding an amino acid transporter, an α-SNAP protein, and a WI12 (wound-inducible domain) protein, each contribute to resistance. There is one copy of the 31-kilobase segment per haploid genome in susceptible varieties, but 10 tandem copies are present in an rhg1-b haplotype. Overexpression of the individual genes in roots was ineffective, but overexpression of the genes together conferred enhanced SCN resistance. Hence, SCN resistance mediated by the soybean quantitative trait locus Rhg1 is conferred by copy number variation that increases the expression of a set of dissimilar genes in a repeated multigene segment.

RFLP Mapping in Soybean: Association between Marker Loci and Variation in Quantitative Traits

Abstract: We have constructed a genetic map for soybean and identified associations between genetic markers and quantitative trait loci. One-hundred-fifty restriction fragment length polymorphisms (RFLPs) were used to identify genetic linkages in an F2 segregating population from an interspecific cross (Glycine max x Glycine soja). Twenty-six genetic linkage groups containing ca. 1200 recombination units are reported. Progeny-testing of F2-derived families allowed quantitative traits to be evaluated in replicated field trials. Genomic regions, which accounted for a portion of the genetic variation (R2 = 16 to 24%) in several reproductive and morphological traits, were linked to RFLP markers. Significant associations between RFLP markers and quantitative trait loci were detected for eight of nine traits evaluated. The ability to identify genes within a continuously varying trait has important consequences for plant breeding and for understanding evolutionary processes.

A Decade of QTL Mapping for Cyst Nematode Resistance in Soybean

Abstract: Soybean cyst nematode (SCN) (Heterodera glycines Ichinohe), the most destructive pest of soybean [Glycine max (L.) Merrill], is estimated to be responsible for almost nine million megagrams in annual yield loss worldwide. Host plant resistance is the most cost-effective and environmentally friendly method of controlling SCN. Resistance is present among soybean plant introductions (PIs) and related wild species, such as Glycine soja Sieb. and Zucc. Molecular marker technology has ushered in a decade devoted to the identification and characterization of quantitative trait loci (QTL) underlying SCN. These genetic mapping efforts uncovered numerous locations of SCN resistance QTL in many PIs. In more than a decade of mapping SCN resistance QTL, there is some consistency in the results. In almost all studies involving various sources of resistance, the QTL conferring the greatest level of resistance mapped to the region containing rhg1 on linkage group (LG) G. In addition, a major resistance QTL was mapped in many sources to the region containing Rhg4 on LG A2. The mapping of QTL to these regions from many sources suggests that these sources may have resistance genes in common, which has caused concern over the possible dependence on a few resistance genes. Recently, two independent research groups reported cloning candidate genes for rhg1 and Rhg4. Despite these advances, there is some degree of trepidation, especially in the public sector, on the use of rhg1 and Rhg4 genetic mapping and cloning information in SCN resistance breeding because of intellectual property issues.

RFLP analysis of soybean seed protein and oil content

Abstract: The objectives of this study were to present an expanded soybean RFLP map and to identify quantitative trait loci (QTL) in soybean [Glycine max (L.) Merr.] for seed protein and oil content. The study population was formed from a cross between a G. max experimental line (A81-356022) and a G. soja Sieb. and Zucc. plant introduction (PI 468916). A total of 252 markers was mapped in the population, forming 31 linkage groups. Protein and oil content were measured on seed harvested from a replicated trial of 60 F2-derived lines in the F3 generation (F2∶3 lines). Each F2∶3 line was genotyped with 243 RFLP, five isozyme, one storage protein, and three morphological markers. Significant (P<0.01) associations were found between the segregation of markers and seed protein and oil content. Segregation of individual markers explained up to 43% of the total variation for specific traits. All G. max alleles at significant loci for oil content were associated with greater oil content than G. soja alleles. All G. soja alleles at significant loci for protein content were associated with greater protein content than G. max alleles.

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

Human biochemical genetics

Abstract: So far in this course we have dealt entirely with the evolution of characters that are controlled by simple Mendelian inheritance at a single locus. There are notes on the course website about gametic disequilibrium and how allele frequencies change at two loci simultaneously, but we didn’t discuss them. In every example we’ve considered we’ve imagined that we could understand something about evolution by examining the evolution of a single gene. That’s the domain of classical population genetics. For the next few weeks we’re going to be exploring a field that’s actually older than classical population genetics, although the approach we’ll be taking to it involves the use of population genetic machinery. If you know a little about the history of evolutionary biology, you may know that after the rediscovery of Mendel’s work in 1900 there was a heated debate between the “biometricians” (e.g., Galton and Pearson) and the “Mendelians” (e.g., de Vries, Correns, Bateson, and Morgan). Biometricians asserted that the really important variation in evolution didn’t follow Mendelian rules. Height, weight, skin color, and similar traits seemed to

An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: The basic concepts

Abstract: Recognizing the enormous potential of DNA markers in plant breeding, many agricultural research centers and plant breeding institutes have adopted the capacity for marker development and marker-assisted selection (MAS). However, due to rapid developments in marker technology, statistical methodology for identifying quantitative trait loci (QTLs) and the jargon used by molecular biologists, the utility of DNA markers in plant breeding may not be clearly understood by non-molecular biologists. This review provides an introduction to DNA markers and the concept of polymorphism, linkage analysis and map construction, the principles of QTL analysis and how markers may be applied in breeding programs using MAS. This review has been specifically written for readers who have only a basic knowledge of molecular biology and/or plant genetics. Its format is therefore ideal for conventional plant breeders, physiologists, pathologists, other plant scientists and students.

An introgression line population of Lycopersicon pennellii in the cultivated tomato enables the identification and fine mapping of yield-associated QTL

Abstract: Methodologies for mapping of genes underlying quantitative traits have advanced considerably but have not been accompanied by a parallel development of new population structures. We present a novel population consisting of 50 introgression lines (ILs) originating from a cross between the green-fruited species Lycopersicon pennellii and the cultivated tomato (cv M82). Each of the lines contains a single homozygous restriction fragment length polymorphism-defined L. pennellii chromosome segment, and together the lines provide complete coverage of the genome and a set of lines nearly isogenic to M82. A field trial of the ILs and their hybrids revealed at least 23 quantitative trait loci (QTL) for total soluble solids content and 18 for fruit mass; these estimates are twice as high as previously reported estimates based on traditional mapping populations. For finer mapping of a QTL affecting fruit mass, the introgressed segment was recombined into smaller fragments that allowed the identification of three linked loci. At least 16 QTL for plant weight, 22 for percentage green fruit weight, 11 for total yield and 14 for total soluble solids yield were identified. Gene action for fruit and plant characteristics was mainly additive, while overdominance (or pseudo-overdominance) of wild species introgressions was detected for yield.