Candidate effectors contribute to race differentiation and virulence of the lentil anthracnose pathogen Colletotrichum lentis

RT-qPCR primers used to quantify expression of Colletotrichum lentis candidate effectors in an infection time-course on lentil cultivar Eston. (XLSX 10 kb

One-Year Research Experience for Associate’s Degree Students Impacts Graduation, STEM Retention, and Transfer Patterns

The CUNY Research Scholars Program (CRSP) provides a yearlong faculty-mentored research experience to associate’s degree students. The program takes place at all 10 associate’s degree–granting colleges within the City University of New York system. We report on a mixed-methods study of 500 students who participated in the program during its initial 3 years. Quantitative longitudinal assessments revealed that students who en-gaged in CRSP were more likely to be retained in a science, technology, engineering, and mathematics (STEM) discipline or to graduate with a STEM degree than their counterparts in a matched comparison group. Furthermore, students who participated in CRSP demon-strated an increased likelihood of transferring to the more research-intensive 4-year schools within the CUNY system and to R1 universities outside the CUNY system. CRSP students reported an increased sense of belonging in college based on survey data, and focus groups with their mentors provided insight into the factors that led to the gains listed above. These combined results—of student data analysis, student surveys, and mentor focus groups—provide evidence that early research experiences for associate’s degree students contribute to their academic success

Review of two-photon exchange in electron scattering

We review the role of two-photon exchange (TPE) in electron-hadron scattering, focusing in particular on hadronic frameworks suitable for describing the low and moderate Q^2 region relevant to most experimental studies. We discuss the effects of TPE on the extraction of nucleon form factors and their role in the resolution of the proton electric to magnetic form factor ratio puzzle. The implications of TPE on various other observables, including neutron form factors, electroproduction of resonances and pions, and nuclear form factors, are summarized. Measurements seeking to directly identify TPE effects, such as through the angular dependence of polarization measurements, nonlinear epsilon contributions to the cross sections, and via e+ p to e- p cross section ratios, are also outlined. In the weak sector, we describe the role of TPE and gamma-Z interference in parity-violating electron scattering, and assess their impact on the extraction of the strange form factors of the nucleon and the weak charge of the proton.Comment: 73 pages, 40 figures, review article for Prog. Part. Nucl. Phys. (dedicated to the memory of John A. Tjon

A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes

BACKGROUND: Bread wheat is an allopolyploid species with a large, highly repetitive genome. To investigate the impact of selection on variants distributed among homoeologous wheat genomes and to build a foundation for understanding genotype-phenotype relationships, we performed population-scale re-sequencing of a diverse panel of wheat lines. RESULTS: A sample of 62 diverse lines was re-sequenced using the whole exome capture and genotyping-by-sequencing approaches. We describe the allele frequency, functional significance, and chromosomal distribution of 1.57 million single nucleotide polymorphisms and 161,719 small indels. Our results suggest that duplicated homoeologous genes are under purifying selection. We find contrasting patterns of variation and inter-variant associations among wheat genomes; this, in addition to demographic factors, could be explained by differences in the effect of directional selection on duplicated homoeologs. Only a small fraction of the homoeologous regions harboring selected variants overlapped among the wheat genomes in any given wheat line. These selected regions are enriched for loci associated with agronomic traits detected in genome-wide association studies. CONCLUSIONS: Evidence suggests that directional selection in allopolyploids rarely acted on multiple parallel advantageous mutations across homoeologous regions, likely indicating that a fitness benefit could be obtained by a mutation at any one of the homoeologs. Additional advantageous variants in other homoelogs probably either contributed little benefit, or were unavailable in populations subjected to directional selection. We hypothesize that allopolyploidy may have increased the likelihood of beneficial allele recovery by broadening the set of possible selection targets

Shifting the limits in wheat research and breeding using a fully annotated reference genome

Introduction: Wheat (Triticum aestivum L.) is the most widely cultivated crop on Earth, contributing about a fifth of the total calories consumed by humans. Consequently, wheat yields and production affect the global economy, and failed harvests can lead to social unrest. Breeders continuously strive to develop improved varieties by fine-tuning genetically complex yield and end-use quality parameters while maintaining stable yields and adapting the crop to regionally specific biotic and abiotic stresses. Rationale: Breeding efforts are limited by insufficient knowledge and understanding of wheat biology and the molecular basis of central agronomic traits. To meet the demands of human population growth, there is an urgent need for wheat research and breeding to accelerate genetic gain as well as to increase and protect wheat yield and quality traits. In other plant and animal species, access to a fully annotated and ordered genome sequence, including regulatory sequences and genome-diversity information, has promoted the development of systematic and more time-efficient approaches for the selection and understanding of important traits. Wheat has lagged behind, primarily owing to the challenges of assembling a genome that is more than five times as large as the human genome, polyploid, and complex, containing more than 85% repetitive DNA. To provide a foundation for improvement through molecular breeding, in 2005, the International Wheat Genome Sequencing Consortium set out to deliver a high-quality annotated reference genome sequence of bread wheat. Results: An annotated reference sequence representing the hexaploid bread wheat genome in the form of 21 chromosome-like sequence assemblies has now been delivered, giving access to 107,891 high-confidence genes, including their genomic context of regulatory sequences. This assembly enabled the discovery of tissue- and developmental stage–related gene coexpression networks using a transcriptome atlas representing all stages of wheat development. The dynamics of change in complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. Aspects of the future value of the annotated assembly for molecular breeding and research were exemplarily illustrated by resolving the genetic basis of a quantitative trait locus conferring resistance to abiotic stress and insect damage as well as by serving as the basis for genome editing of the flowering-time trait. Conclusion: This annotated reference sequence of wheat is a resource that can now drive disruptive innovation in wheat improvement, as this community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding. Importantly, the bioinformatics capacity developed for model-organism genomes will facilitate a better understanding of the wheat genome as a result of the high-quality chromosome-based genome assembly. By necessity, breeders work with the genome at the whole chromosome level, as each new cross involves the modification of genome-wide gene networks that control the expression of complex traits such as yield. With the annotated and ordered reference genome sequence in place, researchers and breeders can now easily access sequence-level information to precisely define the necessary changes in the genomes for breeding programs. This will be realized through the implementation of new DNA marker platforms and targeted breeding technologies, including genome editing

Identification of candidate genes, regions and markers for pre-harvest sprouting resistance in wheat (Triticum aestivum L.)

Background: Pre-harvest sprouting (PHS) of wheat grain leads to a reduction in grain yield and quality. The availability of markers for marker-assisted selection (MAS) of PHS resistance will serve to enhance breeding selection and advancement of lines for cultivar development. The aim of this study was to identify candidate regions and develop molecular markers for PHS resistance in wheat. This was achieved via high density mapping of single nucleotide polymorphism (SNP) markers from an Illumina 90 K Infinium Custom Beadchip in a doubled haploid (DH) population derived from a RL4452/'AC Domain' cross and subsequent detection of quantitative trait loci (QTL) for PHS related traits (falling number [FN], germination index [GI] and sprouting index [SI]). SNP marker sequences flanking QTL were used to locate colinear regions in Brachypodium and rice, and identify genic markers associated with PHS resistance that can be utilized for MAS in wheat. Results: A linkage map spanning 2569.4 cM was constructed with a total of 12,201 SNP, simple sequence repeat (SSR), diversity arrays technology (DArT) and expressed sequence tag (EST) markers. QTL analyses using Multiple Interval Mapping (MIM) identified four QTL for PHS resistance traits on chromosomes 3B, 4A, 7B and 7D. Sequences of SNPs flanking these QTL were subject to a BLASTN search on the International Wheat Genome Sequencing Consortium (IWGSC) database (http://wheat-urgi.versailles.inra.fr/Seq-Repository). Best survey sequence hits were subject to a BLASTN search on Gramene (www.gramene.org) against both Brachypodium and rice databases, and candidate genes and regions for PHS resistance were identified. A total of 18 SNP flanking sequences on chromosomes 3B, 4A, 7B and 7D were converted to KASP markers and validated with matching genotype calls of Infinium SNP data. Conclusions: Our study identified candidate genes involved in abscissic acid (ABA) and gibberellin (GA) metabolism, and flowering time in four genomic regions of Brachypodium and rice respectively, in addition to 18 KASP markers for PHS resistance in wheat. These markers can be deployed in future genetic studies of PHS resistance and might also be useful in the evaluation of PHS in germplasm and breeding material.Peer reviewed: YesNRC publication: Ye

High density mapping and haplotype analysis of the major stem-solidness locus <i>SSt1</i> in durum and common wheat

<div><p>Breeding for solid-stemmed durum <i>(Triticum turgidum</i> L. var <i>durum</i>) and common wheat (<i>Triticum aestivum</i> L.) cultivars is one strategy to minimize yield losses caused by the wheat stem sawfly (<i>Cephus cinctus</i> Norton). Major stem-solidness QTL have been localized to the long arm of chromosome 3B in both wheat species, but it is unclear if these QTL span a common genetic interval. In this study, we have improved the resolution of the QTL on chromosome 3B in a durum (Kofa/W9262-260D3) and common wheat (Lillian/Vesper) mapping population. Coincident QTL (LOD = 94–127, <i>R</i>^<i>2</i> = 78–92%) were localized near the telomere of chromosome 3BL in both mapping populations, which we designate <i>SSt1</i>. We further examined the <i>SSt1</i> interval by using available consensus maps for durum and common wheat and compared genetic to physical intervals by anchoring markers to the current version of the wild emmer wheat (WEW) reference sequence. These results suggest that the <i>SSt1</i> interval spans a physical distance of 1.6 Mb in WEW (positions 833.4–835.0 Mb). In addition, minor QTL were identified on chromosomes 2A, 2D, 4A, and 5A that were found to synergistically enhance expression of <i>SSt1</i> to increase stem-solidness. These results suggest that developing new wheat cultivars with improved stem-solidness is possible by combining <i>SSt1</i> with favorable alleles at minor loci within both wheat species.</p></div