Publications by authors named "Phillip McClean"

55 Publications

Genome-Wide Association Mapping of and Reveals Candidate Genes and New Adjustments to the Host-Pathogen Interaction for Resistance to in Common Bean.

Front Plant Sci 2021 29;12:699569. Epub 2021 Jun 29.

Grain Legume Genetics and Physiology Research Unit, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), Prosser, WA, United States.

Bean common mosaic necrosis virus (BCMNV) is a major disease in common bean ( L.). Host plant resistance is the primary disease control. We sought to identify candidate genes to better understand the host-pathogen interaction and develop tools for marker-assisted selection (MAS). A genome-wide association study (GWAS) approach using 182 lines from a race Durango Diversity Panel (DDP) challenged by BCMNV isolates NL-8 [Pathogroup (PG)-III] and NL-3 (PG-VI), and genotyped with 1.26 million (SNPs), revealed significant peak regions on chromosomes Pv03 and Pv05, which correspond to and resistance gene loci, respectively. Three candidate genes were identified for NL-3 and NL-8 resistance. Side-by-side receptor-like protein kinases (RLKs), Phvul.003G038700 and Phvul.003G038800 were candidate genes for . These RLKs were orthologous to linked RLKs associated with virus resistance in soybean (). A basic Leucine Zipper (bZIP) transcription factor protein is the candidate gene for . bZIP protein gene Phvul.005G124100 carries a unique non-synonymous mutation at codon 14 in the first exon (Pv05: 36,114,516 bases), resulting in a premature termination codon that causes a nonfunctional protein. SNP markers for and and new markers for and genes were used to genotype the resistance genes underpinning BCMNV phenotypes in the DDP, host group (HG) differentials, and segregating F families. Results revealed major adjustments to the current host-pathogen interaction model: (i) there is only one resistance allele for the locus, and differential expression of the allele is based on presence vs. absence of ; (ii) exhibits dominance and incomplete dominance; (iii) alone confers resistance to NL-8; (iv) was absent from HGs 2, 4, 5, and 7 necessitating a new gene symbol to reflect this change; (v) alone delays susceptible symptoms, and when combined with enhanced resistance to NL-3; and (vi) is on Pv05, not Pv03 as previously thought. These candidate genes, markers, and adjustments to the host-pathogen interaction will facilitate breeding for resistance to BCMNV and related Bean common mosaic virus (BCMV) in common bean.
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http://dx.doi.org/10.3389/fpls.2021.699569DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8277298PMC
June 2021

The tepary bean genome provides insight into evolution and domestication under heat stress.

Nat Commun 2021 05 11;12(1):2638. Epub 2021 May 11.

Department of Plant Sciences and Genomics and Bioinformatics Program, North Dakota State University, Fargo, ND, USA.

Tepary bean (Phaseolus acutifolis A. Gray), native to the Sonoran Desert, is highly adapted to heat and drought. It is a sister species of common bean (Phaseolus vulgaris L.), the most important legume protein source for direct human consumption, and whose production is threatened by climate change. Here, we report on the tepary genome including exploration of possible mechanisms for resilience to moderate heat stress and a reduced disease resistance gene repertoire, consistent with adaptation to arid and hot environments. Extensive collinearity and shared gene content among these Phaseolus species will facilitate engineering climate adaptation in common bean, a key food security crop, and accelerate tepary bean improvement.
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http://dx.doi.org/10.1038/s41467-021-22858-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8113540PMC
May 2021

NAC Candidate Gene Marker for and Interaction With QTL for Resistance to in Common Bean.

Front Plant Sci 2021 25;12:628443. Epub 2021 Mar 25.

Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA, United States.

Genetic resistance is the primary means for control of (BGYMV) in common bean (). Breeding for resistance is difficult because of sporadic and uneven infection across field nurseries. We sought to facilitate breeding for BGYMV resistance by improving marker-assisted selection (MAS) for the recessive gene and identifying and developing MAS for quantitative trait loci (QTL) conditioning resistance. Genetic linkage mapping in two recombinant inbred line populations and genome-wide association study (GWAS) in a large breeding population and two diversity panels revealed a candidate gene for and three QTL BGY4.1, BGY7.1, and BGY8.1 on independent chromosomes. A mutation (5 bp deletion) in a NAC (No Apical Meristem) domain transcriptional regulator superfamily protein gene on chromosome Pv03 corresponded with the recessive resistance allele. The five bp deletion in exon 2 starting at 20 bp (Pv03: 2,601,582) is expected to cause a stop codon at codon 23 (Pv03: 2,601,625), disrupting further translation of the gene. A T -shift assay marker named PvNAC1 was developed to track . PvNAC1 corresponded with across ∼1,000 lines which trace back to a single landrace "Garrapato" from Mexico. BGY8.1 has no effect on its own but exhibited a major effect when combined with . BGY4.1 and BGY7.1 acted additively, and they enhanced the level of resistance when combined with . T -shift assay markers were generated for MAS of the QTL, but their effectiveness requires further validation.
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http://dx.doi.org/10.3389/fpls.2021.628443DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8027503PMC
March 2021

Using Breeding Populations With a Dual Purpose: Cultivar Development and Gene Mapping-A Case Study Using Resistance to Common Bacterial Blight in Dry Bean ( L.).

Front Plant Sci 2021 26;12:621097. Epub 2021 Feb 26.

Department of Plant Pathology, North Dakota State University, Fargo, ND, United States.

Dry bean ( L.) is an important worldwide legume crop with low to moderate levels of resistance to common bacterial blight (CBB) caused by pv. . A total of 852 genotypes (cultivars, preliminary and advanced breeding lines) from the North Dakota State University dry bean breeding program were tested for their effectiveness as populations for genome-wide association studies (GWAS) to identify genomic regions associated with resistance to CBB, to exploit the associated markers for marker-assisted breeding (MAB), and to identify candidate genes. The genotypes were evaluated in a growth chamber for disease resistance at both the unifoliate and trifoliate stages. At the unifoliate stage, 35% of genotypes were resistant, while 25% of genotypes were resistant at the trifoliate stage. Libraries generated from each genotype were sequenced using the Illumina platform. After filtering for sequence quality, read depth, and minor allele frequency, 41,998 single-nucleotide polymorphisms (SNPs) and 30,285 SNPs were used in GWAS for the Middle American and Andean gene pools, respectively. One region near the distal end of Pv10 near the SAP6 molecular marker from the Andean gene pool explained 26.7-36.4% of the resistance variation. Three to seven regions from the Middle American gene pool contributed to 25.8-27.7% of the resistance, with the most significant peak also near the SAP6 marker. Six of the eight total regions associated with CBB resistance are likely the physical locations of quantitative trait loci identified from previous genetic studies. The two new locations associated with CBB resistance are located at Pv10:22.91-23.36 and Pv11:52.4. A ortholog on Pv10 emerged as a candidate gene for CBB resistance. The state of one SNP on Pv07 was associated with susceptibility. Its subsequent use in MAB would reduce the current number of lines in preliminary and advanced field yield trial by up to 14% and eliminate only susceptible genotypes. These results provide a foundational SNP data set, improve our understanding of CBB resistance in dry bean, and impact resource allocation within breeding programs as breeding populations may be used for dual purposes: cultivar development as well as genetic studies.
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http://dx.doi.org/10.3389/fpls.2021.621097DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7953056PMC
February 2021

Orthology and synteny analysis of receptor-like kinases "RLK" and receptor-like proteins "RLP" in legumes.

BMC Genomics 2021 Feb 10;22(1):113. Epub 2021 Feb 10.

Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108-6050, USA.

Background: Legume species are an important plant model because of their protein-rich physiology. The adaptability and productivity of legumes are limited by major biotic and abiotic stresses. Responses to these stresses directly involve plasma membrane receptor proteins known as receptor-like kinases and receptor-like proteins. Evaluating the homology relations among RLK and RLP for seven legume species, and exploring their presence among synteny blocks allow an increased understanding of evolutionary relations, physical position, and chromosomal distribution in related species and their shared roles in stress responses.

Results: Typically, a high proportion of RLK and RLP legume proteins belong to orthologous clusters, which is confirmed in this study, where between 66 to 90% of the RLKs and RLPs per legume species were classified in orthologous clusters. One-third of the evaluated syntenic blocks had shared RLK/RLP genes among both legumes and non-legumes. Among the legumes, between 75 and 98% of the RLK/RLP were present in syntenic blocks. The distribution of chromosomal segments between Phaseolus vulgaris and Vigna unguiculata, two species that diverged ~ 8 mya, were highly similar. Among the RLK/RLP synteny clusters, seven experimentally validated resistance RLK/RLP genes were identified in syntenic blocks. The RLK resistant genes FLS2, BIR2, ERECTA, IOS1, and AtSERK1 from Arabidopsis and SLSERK1 from Solanum lycopersicum were present in different pairwise syntenic blocks among the legume species. Meanwhile, only the LYM1- RLP resistant gene from Arabidopsis shared a syntenic blocks with Glycine max.

Conclusions: The orthology analysis of the RLK and RLP suggests a dynamic evolution in the legume family, with between 66 to 85% of RLK and 83 to 88% of RLP belonging to orthologous clusters among the species evaluated. In fact, for the 10-species comparison, a lower number of singleton proteins were reported among RLP compared to RLK, suggesting that RLP positions are more physically conserved compared to RLK. The identification of RLK and RLP genes among the synteny blocks in legumes revealed multiple highly conserved syntenic blocks on multiple chromosomes. Additionally, the analysis suggests that P. vulgaris is an appropriate anchor species for comparative genomics among legumes.
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http://dx.doi.org/10.1186/s12864-021-07384-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7874474PMC
February 2021

The genetics and physiology of seed dormancy, a crucial trait in common bean domestication.

BMC Plant Biol 2021 Jan 22;21(1):58. Epub 2021 Jan 22.

Plant Resilience Institute, Michigan State University, East Lansing, MI, USA.

Background: Physical seed dormancy is an important trait in legume domestication. Although seed dormancy is beneficial in wild ecosystems, it is generally considered to be an undesirable trait in crops due to reduction in yield and / or quality. The physiological mechanism and underlying genetic factor(s) of seed dormancy is largely unknown in several legume species. Here we employed an integrative approach to understand the mechanisms controlling physical seed dormancy in common bean (Phaseolus vulgaris L.).

Results: Using an innovative CT scan imaging system, we were able to track water movements inside the seed coat. We found that water uptake initiates from the bean seed lens. Using a scanning electron microscopy (SEM) we further identified several micro-cracks on the lens surface of non-dormant bean genotypes. Bulked segregant analysis (BSA) was conducted on a bi-parental RIL (recombinant inbred line) population, segregating for seed dormancy. This analysis revealed that the seed water uptake is associated with a single major QTL on Pv03. The QTL region was fine-mapped to a 118 Kb interval possessing 11 genes. Coding sequence analysis of candidate genes revealed a 5-bp insertion in an ortholog of pectin acetylesterase 8 that causes a frame shift, loss-of-function mutation in non-dormant genotype. Gene expression analysis of the candidate genes in the seed coat of contrasting genotypes indicated 21-fold lower expression of pectin acetylesterase 8 in non-dormant genotype. An analysis of mutational polymorphism was conducted among wild and domesticated beans. Although all the wild beans possessed the functional allele of pectin acetylesterase 8, the majority (77%) of domesticated beans had the non-functional allele suggesting that this variant was under strong selection pressure through domestication.

Conclusions: In this study, we identified the physiological mechanism of physical seed dormancy and have identified a candidate allele causing variation in this trait. Our findings suggest that a 5-bp insertion in an ortholog of pectin acetylesterase 8 is likely a major causative mutation underlying the loss of seed dormancy during domestication. Although the results of current study provide strong evidences for the role of pectin acetylesterase 8 in seed dormancy, further confirmations seem necessary by employing transgenic approaches.
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http://dx.doi.org/10.1186/s12870-021-02837-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7821524PMC
January 2021

Genetic Factors Associated With Nodulation and Nitrogen Derived From Atmosphere in a Middle American Common Bean Panel.

Front Plant Sci 2020 15;11:576078. Epub 2020 Dec 15.

Department of Plant Sciences, North Dakota State University, Fargo, ND, United States.

Among grain legume crops, common beans ( L.) are considered to have poor biological nitrogen (N) fixation (BNF) capabilities although variation in N fixing capabilities exists within the species. The availability of genetic panel varying in BNF capacity and a large-scale single nucleotide polymorphism (SNP) data set for common bean provided an opportunity to discover genetic factors associated with N fixation among genotypes in the Middle American gene pool. Using nodulation and percentage of N-derived from atmosphere (%NDFA) data collected from field trials, at least 11 genotypes with higher levels of BNF capacity were identified. Genome-wide association studies (GWASs) detected both major and minor effects that control these traits. A major nodulation interval at Pv06:28.0-28.27 Mbp was discovered. In this interval, the peak SNP was located within a small GTPase that positively regulates cellular polarity and growth of root hair tips. Located 20 kb upstream of this peak SNP is an auxin-responsive factor AUX/indole acetic auxin (IAA)-related gene involved in auxin transportation during root nodulation. For %NDFA, nitrate (NO ) transporters, and (Pv02:8.64), squamosa promoter binding transcriptome factor (Pv08:28.42), and multi-antimicrobial extrusion protein (MATE) efflux family protein (Pv06:10.91) were identified as candidate genes. Three additional QTLs were identified on chromosomes Pv03:5.24, Pv09:25.89, and Pv11: 32.89 Mbp. These key candidate genes from both traits were integrated with previous results on N fixation to describe a BNF pathway.
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http://dx.doi.org/10.3389/fpls.2020.576078DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7769817PMC
December 2020

Computational identification of receptor-like kinases "RLK" and receptor-like proteins "RLP" in legumes.

BMC Genomics 2020 Jul 3;21(1):459. Epub 2020 Jul 3.

Department of Plant Sciences, North Dakota State University, Fargo, ND, USA.

Background: In plants, the plasma membrane is enclosed by the cell wall and anchors RLK and RLP proteins, which play a fundamental role in perception of developmental and environmental cues and are crucial in plant development and immunity. These plasma membrane receptors belong to large gene/protein families that are not easily classified computationally. This detailed analysis of these plasma membrane proteins brings a new source of information to the legume genetic, physiology and breeding research communities.

Results: A computational approach to identify and classify RLK and RLP proteins is presented. The strategy was evaluated using experimentally-validated RLK and RLP proteins and was determined to have a sensitivity of over 0.85, a specificity of 1.00, and a Matthews correlation coefficient of 0.91. The computational approach can be used to develop a detailed catalog of plasma membrane receptors (by type and domains) in several legume/crop species. The exclusive domains identified in legumes for RLKs are WaaY, APH Pkinase_C, LRR_2, and EGF, and for RLP are L-lectin LPRY and PAN_4. The RLK-nonRD and RLCK subclasses are also discovered by the methodology. In both classes, less than 20% of the total RLK predicted for each species belong to this class. Among the 10-species evaluated ~ 40% of the proteins in the kinome are RLKs. The exclusive legume domain combinations identified are B-Lectin/PR5K domains in G. max, M. truncatula, V. angularis, and V. unguiculata and a three-domain combination B-lectin/S-locus/WAK in C. cajan, M. truncatula, P. vulgaris, V. angularis. and V. unguiculata.

Conclusions: The analysis suggests that about 2% of the proteins of each genome belong to the RLK family and less than 1% belong to RLP family. Domain diversity combinations are greater for RLKs compared with the RLP proteins and LRR domains, and the dual domain combination LRR/Malectin were the most frequent domain for both groups of plasma membrane receptors among legume and non-legume species. Legumes exclusively show Pkinase extracellular domains, and atypical domain combinations in RLK and RLP compared with the non-legumes evaluated. The computational logic approach is statistically well supported and can be used with the proteomes of other plant species.
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http://dx.doi.org/10.1186/s12864-020-06844-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7333395PMC
July 2020

Sources of Resistance to and Associated Genomic Regions in Common Bean Diversity Panels.

Front Genet 2020 16;11:475. Epub 2020 Jun 16.

Department of Plant Pathology, North Dakota State University, Fargo, ND, United States.

Common bean ( L.) production worldwide is hampered by Fusarium root rot (FRR), which is caused by . Screening for FRR resistance on a large scale is notoriously difficult and often yields inconsistent results due to variability within the environment and pathogen biology. A greenhouse screening assay was developed incorporating multiple isolates of to improve assay reproducibility. The Andean (ADP; = 270) and Middle American (MDP; = 280) Diversity Panels were screened in the greenhouse to identify genetic factors associated with FRR resistance. Forty-seven MDP and 34 ADP lines from multiple market classes were identified as resistant to FRR. Greenhouse phenotyping repeatability was confirmed via five control lines. Genome-wide association mapping using ∼200k SNPs was performed on standard phenotyping score 1-9, as well as binary and polynomial transformation of score data. Sixteen and seven significant genomic regions were identified for ADP and MDP, respectively, using all three classes of phenotypic data. Most candidate genes were associated with plant immune/defense mechanisms. For the ADP population, ortholog of glucan synthase-like enzyme, senescence-associated genes, and NAC domain protein, associated with peak genomic region Pv08:0.04-0.18 Mbp, were the most significant candidate genes. For the MDP population, the peak SNPs Pv07:15.29 Mbp and Pv01:51 Mbp mapped within gene models associated with ethylene response factor 1 and MAC/Perforin domain-containing gene respectively. The research provides a basis for bean improvement through the use of resistant genotypes and genomic regions for more durable root rot resistance.
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http://dx.doi.org/10.3389/fgene.2020.00475DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7308507PMC
June 2020

Genetic Associations in Four Decades of Multienvironment Trials Reveal Agronomic Trait Evolution in Common Bean.

Genetics 2020 05 23;215(1):267-284. Epub 2020 Mar 23.

Integrative Biology, The University of Texas at Austin, Texas 78712.

Multienvironment trials (METs) are widely used to assess the performance of promising crop germplasm. Though seldom designed to elucidate genetic mechanisms, MET data sets are often much larger than could be duplicated for genetic research and, given proper interpretation, may offer valuable insights into the genetics of adaptation across time and space. The Cooperative Dry Bean Nursery (CDBN) is a MET for common bean () grown for > 70 years in the United States and Canada, consisting of 20-50 entries each year at 10-20 locations. The CDBN provides a rich source of phenotypic data across entries, years, and locations that is amenable to genetic analysis. To study stable genetic effects segregating in this MET, we conducted genome-wide association studies (GWAS) using best linear unbiased predictions derived across years and locations for 21 CDBN phenotypes and genotypic data (1.2 million SNPs) for 327 CDBN genotypes. The value of this approach was confirmed by the discovery of three candidate genes and genomic regions previously identified in balanced GWAS. Multivariate adaptive shrinkage (mash) analysis, which increased our power to detect significant correlated effects, found significant effects for all phenotypes. Mash found two large genomic regions with effects on multiple phenotypes, supporting a hypothesis of pleiotropic or linked effects that were likely selected on in pursuit of a crop ideotype. Overall, our results demonstrate that statistical genomics approaches can be used on MET phenotypic data to discover significant genetic effects and to define genomic regions associated with crop improvement.
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http://dx.doi.org/10.1534/genetics.120.303038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7198278PMC
May 2020

Improving the Health Benefits of Snap Bean: Genome-Wide Association Studies of Total Phenolic Content.

Nutrients 2019 Oct 18;11(10). Epub 2019 Oct 18.

Department of Plant Science, North Dakota State University, Fargo, ND 58105, USA.

Snap beans are a significant source of micronutrients in the human diet. Among the micronutrients present in snap beans are phenolic compounds with known beneficial effects on human health, potentially via their metabolism by the gut-associated microbiome. The genetic pathways leading to the production of phenolics in snap bean pods remain uncertain. In this study, we quantified the level of total phenolic content (TPC) in the Bean Coordinated Agriculture Program (CAP) snap bean diversity panel of 149 accessions. The panel was characterized spectrophotometrically for phenolic content with a Folin-Ciocalteu colorimetric assay. Flower, seed and pod color were also quantified, as red, purple, yellow and brown colors are associated with anthocyanins and flavonols in common bean. Genotyping was performed through an Illumina Infinium Genechip BARCBEAN6K_3 single nucleotide polymorphism (SNP) array. Genome-Wide Association Studies (GWAS) analysis identified 11 quantitative trait nucleotides (QTN) associated with TPC. An SNP was identified for TPC on Pv07 located near the gene, which is a major switch in the flavonoid biosynthetic pathway. Candidate genes were identified for seven of the 11 TPC QTN. Five regulatory genes were identified and represent novel sources of variation for exploitation in developing snap beans with higher phenolic levels for greater health benefits to the consumer.
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http://dx.doi.org/10.3390/nu11102509DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6835575PMC
October 2019

Mapping and characterization of two stem rust resistance genes derived from cultivated emmer wheat accession PI 193883.

Theor Appl Genet 2019 Nov 7;132(11):3177-3189. Epub 2019 Sep 7.

USDA-ARS, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, 1616 Albrecht Blvd. North, Fargo, ND, 58102-2765, USA.

Key Message: Two stem rust resistance genes identified on chromosome arms 2BL and 6AL of the cultivated emmer wheat accession PI 193883 can be used for protecting modern varieties against Ug99 strains. The wheat research community consistently strives to identify new genes that confer resistance to stem rust caused by the fungal pathogen Puccinia graminis f. sp. tritici Eriks & E. Henn (Pgt). In the current study, our objective was to identify and genetically characterize the stem rust resistance derived from the cultivated emmer accession PI 193883. A recombinant inbred line population developed from a cross between the susceptible durum wheat line Rusty and PI 193883 was genotyped and evaluated for reaction to Pgt races TTKSK, TRTTF, and TMLKC. Two QTLs conferring resistance were identified on chromosome arms 2BL (QSr.fcu-2B) and 6AL (QSr.fcu-6A). The stem rust resistance gene (Sr883-2B) underlying QSr.fcu-2B was recessive, and based on its physical location it is located proximal to the Sr9 region. QSr.fcu-6A was located in the Sr13 region, but PI 193883 is known to carry the susceptible haplotype S4 for Sr13, indicating that the gene underlying QSr.fcu-6A (Sr883-6A) is likely a new allele of Sr13 or a gene residing close to Sr13. Three IWGSC scaffold-based simple sequence repeat (SSR) and two SNP-based semi-thermal asymmetric reverse PCR (STARP) markers were developed for the Sr883-2B region, and one STARP marker was developed for Sr883-6A. Sr883-2B was epistatic to Sr883-6A for reaction to TTKSK and TRTTF, and the two genes had additive effects for TMLKC. These two genes and the markers developed in this research provide additional resources and tools for the improvement in stem rust resistance in durum and common wheat breeding programs.
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http://dx.doi.org/10.1007/s00122-019-03417-xDOI Listing
November 2019

Genotypes and Genomic Regions Associated With Resistance in Common Bean.

Front Plant Sci 2019 24;10:956. Epub 2019 Jul 24.

Department of Plant Pathology, North Dakota State University, Fargo, ND, United States.

Kühn (teleomorph ) is an important root rot pathogen of common bean ( L.). To uncover genetic factors associated with resistance to the pathogen, the Andean (ADP; = 273) and Middle American (MDP; = 279) diversity panels, which represent much of the genetic diversity known in cultivated common bean, were screened in the greenhouse using anastomosis group 2-2. Repeatability of the assay was confirmed by the response of five control genotypes. The phenotypic data for both panels were normally distributed. The resistance responses of ∼10% of the ADP ( = 28) and ∼6% of the MDP ( = 18) genotypes were similar or higher than that of the resistant control line VAX 3. A genome-wide association study (GWAS) was performed using ∼200k single nucleotide polymorphisms to discover genomic regions associated with resistance in each panel, For GWAS, the raw phenotypic score, and polynomial and binary transformation of the scores, were individually used as the input data. A major QTL peak was observed on Pv02 in the ADP, while a major QTL was observed on Pv01 with the MDP. These regions were associated with clusters of TIR-NB_ARC-LRR (TNL) gene models encoding proteins similar to known disease resistance genes. Other QTL, unique to each panel, were mapped within or adjacent to a gene model or cluster of related genes associated with disease resistance. This is a first case study that provides evidence for major as well as minor genes involved in resistance to in common bean. This information will be useful to integrate more durable root rot resistance in common bean breeding programs and to study the genetic mechanisms associated with root diseases in this important societal legume.
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http://dx.doi.org/10.3389/fpls.2019.00956DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6667560PMC
July 2019

Single and Multi-trait GWAS Identify Genetic Factors Associated with Production Traits in Common Bean Under Abiotic Stress Environments.

G3 (Bethesda) 2019 06 5;9(6):1881-1892. Epub 2019 Jun 5.

Department of Plant Sciences, North Dakota State University, Fargo, ND, 58102.

The genetic improvement of economically important production traits of dry bean ( L.), for geographic regions where production is threatened by drought and high temperature stress, is challenging because of the complex genetic nature of these traits. Large scale SNP data sets for the two major gene pools of bean, Andean and Middle American, were developed by mapping multiple pools of genotype-by-sequencing reads and identifying over 200k SNPs for each gene pool against the most recent assembly of the genome sequence. Moderately sized ean biotic tress valuation (BASE) panels, consisting of genotypes appropriate for production in Central America and Africa, were assembled. Phylogenetic analyses demonstrated the BASE populations represented broad genetic diversity for the appropriate races within the two gene pools. Joint mixed linear model genome-wide association studies with data from multiple locations discovered genetic factors associated with four production traits in both heat and drought stress environments using the BASE panels. Pleiotropic genetic factors were discovered using a multi-trait mixed model analysis. SNPs within or near candidate genes associated with hormone signaling, epigenetic regulation, and ROS detoxification under stress conditions were identified and can be used as genetic markers in dry bean breeding programs.
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http://dx.doi.org/10.1534/g3.119.400072DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6553540PMC
June 2019

Shovelomics for phenotyping root architectural traits of rapeseed/canola (Brassica napus L.) and genome-wide association mapping.

Mol Genet Genomics 2019 Aug 9;294(4):985-1000. Epub 2019 Apr 9.

Departemnt of Plant Sciences, North Dakota State University, Fargo, ND, USA.

Root system in plants plays an important role in mining moisture and nutrients from the soil and is positively correlated to yield in many crops including rapeseed/canola (Brassica napus L.). Substantial phenotypic diversity in root architectural traits among the B. napus growth types leads to a scope of root system improvement in breeding populations. In this study, 216 diverse genotypes were phenotyped for five different root architectural traits following shovelomics approach in the field condition during 2015 and 2016. A single nucleotide polymorphism (SNP) marker panel consisting of 30,262 SNPs was used to conduct genome-wide association study to detect marker/trait association. A total of 31 significant marker loci were identified at 0.01 percentile tail P value cutoff for different root traits. Six marker loci for soil-level taproot diameter (RDia), six loci for belowground taproot diameter (RDia), seven loci for number of primary root branches (PRB), eight loci for root angle, and eight loci for root score (RS) were detected in this study. Several markers associated with root diameters RDia and RDia were also associated with PRB and RS. Significant phenotypic correlation between these traits was observed in both environments. Therefore, taproot diameter appears to be a major determinant of the canola root system architecture and can be used as proxy for other root traits. Fifteen candidate genes related to root traits and root development were detected within 100 kbp upstream and downstream of different significant markers. The identified markers associated with different root architectural traits can be considered for marker-assisted selection for root traits in canola in future.
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http://dx.doi.org/10.1007/s00438-019-01563-xDOI Listing
August 2019

Genetic analysis of threshability and other spike traits in the evolution of cultivated emmer to fully domesticated durum wheat.

Mol Genet Genomics 2019 Jun 18;294(3):757-771. Epub 2019 Mar 18.

USDA-ARS, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Northern Crop Science Laboratory, 1605 Albrecht Blvd. North, Fargo, ND, 58102-2765, USA.

Genetic mutations in genes governing wheat threshability were critical for domestication. Knowing when these genes mutated during wheat evolution will provide more insight into the domestication process and lead to further exploitation of primitive alleles for wheat improvement. We evaluated a population of recombinant inbred lines derived from a cross between the durum variety Rusty and the cultivated emmer accession PI 193883 for threshability, rachis fragility, and other spike-related traits. Quantitative trait loci (QTL) associated with spike length, spikelets per spike, and spike compactness were primarily associated with known genes such as the pleiotropic domestication gene Q. Interestingly, rachis fragility was not associated with the Q locus, suggesting that this trait, usually a pleiotropic effect of the q allele, can be influenced by the genetic background. Threshability QTL were identified on chromosome arms 2AS, 2BS, and 5AL corresponding to the tenacious glume genes Tg and Tg as well as the Q gene, respectively, further demonstrating that cultivated emmer harbors the primitive non-free-threshing alleles at all three loci. Genetic analysis indicated that the effects of the three genes are mostly additive, with Q having the most profound effects on threshability, and that free-threshing alleles are necessary at all three loci to attain a completely free-threshing phenotype. These findings provide further insight into the timeline and possible pathways of wheat domestication and evolution that led to the formation of modern day domesticated wheats.
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http://dx.doi.org/10.1007/s00438-019-01544-0DOI Listing
June 2019

Genome wide association study discovers genomic regions involved in resistance to soybean cyst nematode (Heterodera glycines) in common bean.

PLoS One 2019 7;14(2):e0212140. Epub 2019 Feb 7.

Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, United States of America.

Common bean (Phaseolus vulgaris L.) is an important high protein crop grown worldwide. North Dakota and Minnesota are the largest producers of common beans in the USA, but crop production is threatened by soybean cyst nematode (SCN; Heterodera glycines Ichinohe) because most current cultivars are susceptible. Greenhouse screening data using SCN HG type 0 from 317 plant introductions (PI's) from the USDA core collection was used to conduct a genome wide association study (GWAS). These lines were divided into two subpopulations based on principal component analysis (Middle American vs. Andean). Phenotypic results based on the female index showed that accessions could be classified as highly resistant (21% and 27%), moderately resistant (51% and 48%), moderately susceptible (27% and 22%) and highly susceptible (1% and 3%) for Middle American and Andean gene pools, respectively. Mixed models with two principal components (PCs) and kinship matrix for Middle American genotypes and Andean genotypes were used in the GWAS analysis using 3,985 and 4,811 single nucleotide polymorphic (SNP) markers, respectively which were evenly distributed across all 11 chromosomes. Significant peaks on Pv07, and Pv11 in Middle American and on Pv07, Pv08, Pv09 and Pv11 in Andean group were found to be associated with SCN resistance. Homologs of soybean rhg1, a locus which confers resistance to SCN in soybean, were identified on chromosomes Pv01 and Pv08 in the Middle American and Andean gene pools, respectively. These genomic regions may be the key to develop SCN-resistant common bean cultivars.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0212140PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6366866PMC
November 2019

Investigation of a Stand-Alone Online Learning Module for Cellular Respiration Instruction.

J Microbiol Biol Educ 2018 29;19(2). Epub 2018 Jun 29.

Department of Biological Sciences, University of South Carolina, Columbia, SC 29208.

With the recent rise of alternative instructional methodologies such as flipped classrooms and active learning, many core concepts are being introduced outside of the classroom prior to scheduled class meeting times. One popular means for external concept introduction in many undergraduate biology courses is the use of stand-alone online learning modules. Using a group of four large introductory biology course sections, we investigate the use of a stand-alone online learning module developed using animations from Virtual Cell Animation Collection as a resource for the introduction of cellular respiration concepts outside of the classroom. Results from four sections of introductory biology ( = 629) randomized to treatments show that students who interacted with the stand-alone online learning module had significantly higher normalized gain scores on a cellular respiration assessment than students who only attended a traditional lecture as a means of concept introduction ( < 0.001, = 0.59). These findings suggest a superior ability to convey certain introductory cellular respiration topics in a stand-alone manner outside of the classroom than in a more traditional lecture-based classroom setting.
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http://dx.doi.org/10.1128/jmbe.v19i2.1460DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6022776PMC
June 2018

Genetic Analysis of Flooding Tolerance in an Andean Diversity Panel of Dry Bean ( L.).

Front Plant Sci 2018 6;9:767. Epub 2018 Jun 6.

Department of Plant Sciences, North Dakota State University, Fargo, ND, United States.

Climate change models predict temporal and spatial shifts in precipitation resulting in more frequent incidents of flooding, particularly in regions with poor soil drainage. In these flooding conditions, crop losses are inevitable due to exposure of plants to hypoxia and the spread of root rot diseases. Improving the tolerance of bean cultivars to flooding is crucial to minimize crop losses. In this experiment, we evaluated the phenotypic responses of 277 genotypes from the Andean Diversity Panel to flooding at germination and seedling stages. A randomized complete block design, with a split plot arrangement, was employed for phenotyping germination rate, total weight, shoot weight, root weight, hypocotyl length, SPAD index, adventitious root rate, and survival score. A subset of genotypes ( = 20) were further evaluated under field conditions to assess correlations between field and greenhouse data and to identify the most tolerant genotypes. A genome-wide association study (GWAS) was performed using ~203 K SNP markers to understand the genetic architecture of flooding tolerance in this panel. Survival scores between field and greenhouse data were significantly correlated ( = 0.55, = 0.01). Subsequently, a subset of the most tolerant and susceptible genotypes were evaluated under pathogenic spp. pressure. This experiment revealed a potential link between flooding tolerance and spp. resistance. Several tolerant genotypes were identified that could be used as donor parents in breeding pipelines, especially ADP-429 and ADP-604. Based on the population structure analysis, a subpopulation consisting of 20 genotypes from the Middle American gene pool was detected that also possessed the highest root weight, hypocotyl length, and adventitious root development under flooding conditions. Genomic regions associated with flooding tolerance were identified including a region on Pv08/3.2 Mb, which is associated with germination rate and resides in vicinity of , a central gene involved in response of plants to hypoxia. Furthermore, a QTL at Pv07/4.7 Mb was detected that controls survival score of seedlings under flooding conditions. The association of these QTL with the survivability traits including germination rate and survival score, indicates that these loci can be used in marker-assisted selection breeding to improve flooding tolerance in the Andean germplasm.
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http://dx.doi.org/10.3389/fpls.2018.00767DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5997968PMC
June 2018

White seed color in common bean (Phaseolus vulgaris) results from convergent evolution in the P (pigment) gene.

New Phytol 2018 08 13;219(3):1112-1123. Epub 2018 Jun 13.

Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA.

The presence of seed color in common bean (Phaseolus vulgaris) requires the dominant-acting P (pigment) gene, and white seed is a recessive phenotype in all domesticated races of the species. P was classically associated with seed size, thus describing it as the first genetic marker for a quantitative trait. The molecular structure of P was characterized to understand the selection of white seeds during bean diversification and the relationship of P to seed weight. P was identified by homology searches, a genome-wide association study (GWAS) and gene remodeling, and confirmed by gene silencing. Allelic variation was assessed by a combination of resequencing and marker development, and the relationship between P and seed weight was assessed by a GWAS study. P is a member of clade B of subclass IIIf of plant basic helix-loop-helix (bHLH) proteins. Ten race-specific P alleles conditioned the white seed phenotype, and each causative mutation affected at least one bHLH domain required for color expression. GWAS analysis confirmed the classic association of P with seed weight. In common bean, white seeds are the result of convergent evolution and, among plant species, orthologous convergence on a single transcription factor gene was observed.
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http://dx.doi.org/10.1111/nph.15259DOI Listing
August 2018

Genetic Architecture of Dietary Fiber and Oligosaccharide Content in a Middle American Panel of Edible Dry Bean.

Plant Genome 2018 03;11(1)

Common bean ( L.) is the most consumed edible grain legume worldwide and contains a wide range of nutrients for human health including dietary fiber. Diets high in beans are associated with lower rates of chronic diseases such as obesity and type 2 diabetes, and the content of dietary fibers varies among different market classes of dry bean. In this study, we evaluated the dietary fiber content in a Middle American diversity panel (MDP) of common bean and evaluated the genetic architecture of the various dietary fiber components. The dietary fiber components included insoluble and soluble dietary fibers as well as the antinutritional raffinose family of oligosaccharides (RFOs; raffinose, stachyose, and verbascose). All variables measured differed among market classes and entries. Colored bean seeds had higher levels of insoluble dietary fibers with the black market class showing also the highest raffinose and stachyose content. Cultivars and lines released since 1997 had higher insoluble dietary fibers and RFO content in race Durango. Higher levels of RFOs were also observed in cultivars with type II growth habit that was a recent breeding target in Durango race germplasm. Candidate genes for dietary fiber traits, especially homologs to two main genes in the RFO biosynthesis pathway, were identified. The knowledge of diversity of dietary fibers in the MDP accompanied with the identification of candidate genes could effectively improve dietary fiber components in common bean.
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http://dx.doi.org/10.3835/plantgenome2017.08.0074DOI Listing
March 2018

Genetic Architecture of Flooding Tolerance in the Dry Bean Middle-American Diversity Panel.

Front Plant Sci 2017 6;8:1183. Epub 2017 Jul 6.

Department of Plant Sciences, North Dakota State UniversityFargo, ND, United States.

Flooding is a devastating abiotic stress that endangers crop production in the twenty-first century. Because of the severe susceptibility of common bean ( L.) to flooding, an understanding of the genetic architecture and physiological responses of this crop will set the stage for further improvement. However, challenging phenotyping methods hinder a large-scale genetic study of flooding tolerance in common bean and other economically important crops. A greenhouse phenotyping protocol was developed to evaluate the flooding conditions at early stages. The Middle-American diversity panel ( = 272) of common bean was developed to capture most of the diversity exits in North American germplasm. This panel was evaluated for seven traits under both flooded and non-flooded conditions at two early developmental stages. A subset of contrasting genotypes was further evaluated in the field to assess the relationship between greenhouse and field data under flooding condition. A genome-wide association study using ~150 K SNPs was performed to discover genomic regions associated with multiple physiological responses. The results indicate a significant strong correlation ( > 0.77) between greenhouse and field data, highlighting the reliability of greenhouse phenotyping method. Black and small red beans were the least affected by excess water at germination stage. At the seedling stage, pinto and great northern genotypes were the most tolerant. Root weight reduction due to flooding was greatest in pink and small red cultivars. Flooding reduced the chlorophyll content to the greatest extent in the navy bean cultivars compared with other market classes. Races of Durango/Jalisco and Mesoamerica were separated by both genotypic and phenotypic data indicating the potential effect of eco-geographical variations. Furthermore, several loci were identified that potentially represent the antagonistic pleiotropy. The GWAS analysis revealed peaks at Pv08/1.6 Mb and Pv02/41 Mb that are associated with root weight and germination rate, respectively. These regions are syntenic with two QTL reported in soybean ( L.) that contribute to flooding tolerance, suggesting a conserved evolutionary pathway involved in flooding tolerance for these related legumes.
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http://dx.doi.org/10.3389/fpls.2017.01183DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5498472PMC
July 2017

Marker-Assisted Molecular Profiling, Deletion Mutant Analysis, and RNA-Seq Reveal a Disease Resistance Cluster Associated with Uromyces appendiculatus Infection in Common Bean Phaseolus vulgaris L.

Int J Mol Sci 2017 May 23;18(6). Epub 2017 May 23.

Department of Agriculture and Natural Resources, Delaware State University, Dover, DE 19901, USA.

Common bean ( L.) is an important legume, useful for its high protein and dietary fiber. The fungal pathogen (Pers.) Unger can cause major loss in susceptible varieties of the common bean. The locus provides race specific resistance to virulent strains or races of the bean rust pathogen along with , (Complements resistance gene), which is required for -mediated rust resistance. In this study, we inoculated two common bean genotypes (resistant "Sierra" and susceptible crg) with rust race 53 of , isolated leaf RNA at specific time points, and sequenced their transcriptomes. First, molecular markers were used to locate and identify a 250 kb deletion on chromosome 10 in mutant crg (which carries a deletion at the locus). Next, we identified differential expression of several disease resistance genes between Mock Inoculated (MI) and Inoculated (I) samples of "Sierra" leaf RNA within the 250 kb delineated region. Both marker assisted molecular profiling and RNA-seq were used to identify possible transcriptomic locations of interest regarding the resistance in the common bean to race 53. Identification of differential expression among samples in disease resistance clusters in the bean genome may elucidate significant genes underlying rust resistance. Along with preserving favorable traits in the crop, the current research may also aid in global sustainability of food stocks necessary for many populations.
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http://dx.doi.org/10.3390/ijms18061109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5485933PMC
May 2017

Learning about Chemiosmosis and ATP Synthesis with Animations Outside of the Classroom.

J Microbiol Biol Educ 2017 Apr 21;18(1). Epub 2017 Apr 21.

Department of Biological Sciences, University of South Carolina, Columbia, SC 29208.

Many undergraduate biology courses have begun to implement instructional strategies aimed at increasing student interaction with course material outside of the classroom. Two examples of such practices are introducing students to concepts as preparation prior to instruction, and as conceptual reinforcement after the instructional period. Using a three-group design, we investigate the impact of an animation developed as part of the Virtual Cell Animation Collection on the topic of concentration gradients and their role in the actions of ATP synthase as a means of pre-class preparation or post-class reinforcement compared with a no-intervention control group. Results from seven sections of introductory biology ( = 732) randomized to treatments over two semesters show that students who viewed animation as preparation ( = 0.44, < 0.001) or as reinforcement ( = 0.53, < 0.001) both outperformed students in the control group on a follow-up assessment. Direct comparison of the preparation and reinforcement treatments shows no significant difference in student outcomes between the two treatment groups ( = 0.87). Results suggest that while student interaction with animations on the topic of concentration gradients outside of the classroom may lead to greater learning outcomes than the control group, in the traditional lecture-based course the timing of such interactions may not be as important.
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http://dx.doi.org/10.1128/jmbe.v18i1.1223DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5410753PMC
April 2017

Efficacy of a Meiosis Learning Module Developed for the Virtual Cell Animation Collection.

CBE Life Sci Educ 2017 ;16(1)

Department of Biological Sciences, University of South Carolina, Columbia, SC 29208

Recent reports calling for change in undergraduate biology education have resulted in the redesign of many introductory biology courses. Reports on one common change to course structure, the active-learning environment, have placed an emphasis on student preparation, noting that the positive outcomes of active learning in the classroom depend greatly on how well the student prepares before class. As a possible preparatory resource, we test the efficacy of a learning module developed for the Virtual Cell Animation Collection. This module presents the concepts of meiosis in an interactive, dynamic environment that has previously been shown to facilitate learning in introductory biology students. Participants ( = 534) were enrolled in an introductory biology course and were presented the concepts of meiosis in one of two treatments: the interactive-learning module or a traditional lecture session. Analysis of student achievement shows that students who viewed the learning module as their only means of conceptual presentation scored significantly higher ( = 0.40, < 0.001) than students who only attended a traditional lecture on the topic. Our results show the animation-based learning module effectively conveyed meiosis conceptual understanding, which suggests that it may facilitate student learning outside the classroom. Moreover, these results have implications for instructors seeking to expand their arsenal of tools for "flipping" undergraduate biology courses.
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http://dx.doi.org/10.1187/cbe.16-03-0141DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5332052PMC
June 2018

High Level of Nonsynonymous Changes in Common Bean Suggests That Selection under Domestication Increased Functional Diversity at Target Traits.

Front Plant Sci 2016 6;7:2005. Epub 2017 Jan 6.

Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche Ancona, Italy.

Crop species have been deeply affected by the domestication process, and there have been many efforts to identify selection signatures at the genome level. This knowledge will help geneticists to better understand the evolution of organisms, and at the same time, help breeders to implement successful breeding strategies. Here, we focused on domestication in the Mesoamerican gene pool of by sequencing 49 gene fragments from a sample of 45 wild and domesticated accessions, and as controls, two accessions each of the closely related species and . An excess of nonsynonymous mutations within the domesticated germplasm was found. Our data suggest that the cost of domestication alone cannot explain fully this finding. Indeed, the significantly higher frequency of polymorphisms in the coding regions observed only in the domesticated plants (compared to noncoding regions), the fact that these mutations were mostly nonsynonymous and appear to be recently derived mutations, and the investigations into the functions of their relative genes (responses to biotic and abiotic stresses), support a scenario that involves new functional mutations selected for adaptation during domestication. Moreover, consistent with this hypothesis, selection analysis and the possibility to compare data obtained for the same genes in different studies of varying sizes, data types, and methodologies allowed us to identify four genes that were strongly selected during domestication. Each selection candidate is involved in plant resistance/tolerance to abiotic stresses, such as heat, drought, and salinity. Overall, our study suggests that domestication acted to increase functional diversity at target loci, which probably controlled traits related to expansion and adaptation to new agro-ecological growing conditions.
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http://dx.doi.org/10.3389/fpls.2016.02005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5216878PMC
January 2017

Variation in external representations as part of the classroom lecture:An investigation of virtual cell animations in introductory photosynthesis instruction.

Biochem Mol Biol Educ 2017 05 28;45(3):226-234. Epub 2016 Dec 28.

Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, 29208.

The use of external representations (ERs) to introduce concepts in undergraduate biology has become increasingly common. Two of the most prevalent are static images and dynamic animations. While previous studies comparing static images and dynamic animations have resulted in somewhat conflicting findings in regards to learning outcomes, the benefits of each have been shown individually. Using ERs developed by the Virtual Cell Animation project, we aim to further investigate student learning using different ERs as part of an introductory biology lecture. We focus our study on the topic of photosynthesis as reports have noted that students struggle with a number of basic photosynthesis concepts. Students (n = 167) in ten sections of introductory biology laboratory were introduced to photosynthesis concepts by instructional lectures differing only in the format of the embedded ERs. Normalized gain scores were calculated, showing that students who learned with dynamic animations outperformed students who learned from static images on the posttest. The results of this study provide possible instructional guidelines for those delivering photosynthesis instruction in the introductory biology classroom. © 2016 by The International Union of Biochemistry and Molecular Biology, 45(3):226-234, 2017.
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http://dx.doi.org/10.1002/bmb.21032DOI Listing
May 2017

Genome-Wide Association Study Identifies Candidate Loci Underlying Agronomic Traits in a Middle American Diversity Panel of Common Bean.

Plant Genome 2016 11;9(3)

Common bean ( L.) breeding programs aim to improve both agronomic and seed characteristics traits. However, the genetic architecture of the many traits that affect common bean production are not completely understood. Genome-wide association studies (GWAS) provide an experimental approach to identify genomic regions where important candidate genes are located. A panel of 280 modern bean genotypes from race Mesoamerica, referred to as the Middle American Diversity Panel (MDP), were grown in four US locations, and a GWAS using >150,000 single-nucleotide polymorphisms (SNPs) (minor allele frequency [MAF] ≥ 5%) was conducted for six agronomic traits. The degree of inter- and intrachromosomal linkage disequilibrium (LD) was estimated after accounting for population structure and relatedness. The LD varied between chromosomes for the entire MDP and among race Mesoamerica and Durango-Jalisco genotypes within the panel. The LD patterns reflected the breeding history of common bean. Genome-wide association studies led to the discovery of new and known genomic regions affecting the agronomic traits at the entire population, race, and location levels. We observed strong colocalized signals in a narrow genomic interval for three interrelated traits: growth habit, lodging, and canopy height. Overall, this study detected ∼30 candidate genes based on a priori and candidate gene search strategies centered on the 100-kb region surrounding a significant SNP. These results provide a framework from which further research can begin to understand the actual genes controlling important agronomic production traits in common bean.
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http://dx.doi.org/10.3835/plantgenome2016.02.0012DOI Listing
November 2016

Sequence-Based Introgression Mapping Identifies Candidate White Mold Tolerance Genes in Common Bean.

Plant Genome 2016 07;9(2)

White mold, caused by the necrotrophic fungus (Lib.) de Bary, is a major disease of common bean ( L.). WM7.1 and WM8.3 are two quantitative trait loci (QTL) with major effects on tolerance to the pathogen. Advanced backcross populations segregating individually for either of the two QTL, and a recombinant inbred (RI) population segregating for both QTL were used to fine map and confirm the genetic location of the QTL. The QTL intervals were physically mapped using the reference common bean genome sequence, and the physical intervals for each QTL were further confirmed by sequence-based introgression mapping. Using whole-genome sequence data from susceptible and tolerant DNA pools, introgressed regions were identified as those with significantly higher numbers of single-nucleotide polymorphisms (SNPs) relative to the whole genome. By combining the QTL and SNP data, WM7.1 was located to a 660-kb region that contained 41 gene models on the proximal end of chromosome Pv07, while the WM8.3 introgression was narrowed to a 1.36-Mb region containing 70 gene models. The most polymorphic candidate gene in the WM7.1 region encodes a BEACH-domain protein associated with apoptosis. Within the WM8.3 interval, a receptor-like protein with the potential to recognize pathogen effectors was the most polymorphic gene. The use of gene and sequence-based mapping identified two candidate genes whose putative functions are consistent with the current model of pathogenicity.
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http://dx.doi.org/10.3835/plantgenome2015.09.0092DOI Listing
July 2016

Transcriptome Analysis of Piperlongumine-Treated Human Pancreatic Cancer Cells Reveals Involvement of Oxidative Stress and Endoplasmic Reticulum Stress Pathways.

J Med Food 2016 Jun 27;19(6):578-85. Epub 2016 Apr 27.

1 Department of Biological Sciences North Dakota State University , Fargo, North Dakota, USA .

Piperlongumine (PL), an alkaloid obtained from long peppers, displays antitumorigenic properties for a variety of human cell- and animal-based models. The aim of this study was to identify the underlying molecular mechanisms for PL anticancer effects on human pancreatic cancer cells. RNA sequencing (RNA-seq) was used to identify the effects of PL on the transcriptome of MIA PaCa-2 human pancreatic cancer cells. PL treatment of pancreatic cancer cells resulted in differential expression of 683 mRNA transcripts with known protein functions, 351 of which were upregulated and 332 of which were downregulated compared to control-treated cells. Transcripts associated with oxidative stress, endoplasmic reticulum (ER) stress, and unfolded protein response pathways were significantly overexpressed with PL treatment. Reverse transcription-quantitative polymerase chain reaction and western blotting were used to validate the RNA-seq results, which included upregulation of HO-1, IRE1α, cytochrome c, and ASNS. The results provide key insight into the mechanisms by which PL alters cancer cell physiology and identify that activation of oxidative stress and ER stress pathways is a critical avenue for PL anticancer effects.
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http://dx.doi.org/10.1089/jmf.2015.0152DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4904158PMC
June 2016
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