cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20038569.v1
title: Spray-induced gene silencing: an innovative strategy for plant trait improvement and disease control

description: Abstract Modern plant breeding is still a time-consuming and costly process, even with the most advanced technologies such as gene editing. Hence, there is an urgent need to develop alternative means for plant trait manipulation and plant protection. RNA interference (RNAi) is a conserved cellular mechanism mediated by naturally occurring double-stranded RNA (dsRNA) and small RNAs (sRNAs) that can target mRNAs for destruction or transcript reduction. Here, we review the potential of technology based on RNAi, called spray-induced gene silencing (SIGS), as an alternative or adjunct to breeding for manipulation of endogenous gene expression in plants or pathogen control. SIGS based on exogenous application of RNA molecules in plants may be especially useful in reducing pest or pathogen impacts, thereby ameliorating biotic stresses and increasing the agronomic performance of crops.
DOI: 10.6084/m9.figshare.20038572
title: Enviromics: bridging different sources of data, building one framework

description: Abstract: Enviromics is the field of applied data science that integrates databases of environmental factors into biostatistics and quantitative genetics. It can leverage plant ecophysiology knowledge to bridge the gaps about environment interactions with systems biology (genes, transcripts, proteins, and metabolites), which also boosts the ability to understand and model the phenotypic plasticity of the main agronomic traits. Recently, the plant breeding community has experienced reduced costs for acquiring environmental sensors to be installed in the field trials while increasing the reliability and resolution of the remote sensing techniques. The combination of those two factors has started the spring of enviromics-aided breeding in recent years. However, the use of environmental information in plant breeding is not a novelty approach developed a few years ago, but a core of efforts originated in the last 60 years, yet some basic ideas traced back to early 20th century attempts to establish a relationship between phenotypic and environmental variation. This review highlights the main concepts surrounding the construction of the “modern enviromics science”, tracing back to its origins in the last decades. Finally, we present how this field has helped integrate different data sources in prediction-based models or build one framework.
DOI: 10.6084/m9.figshare.20038572.v1
title: Enviromics: bridging different sources of data, building one framework

description: Abstract: Enviromics is the field of applied data science that integrates databases of environmental factors into biostatistics and quantitative genetics. It can leverage plant ecophysiology knowledge to bridge the gaps about environment interactions with systems biology (genes, transcripts, proteins, and metabolites), which also boosts the ability to understand and model the phenotypic plasticity of the main agronomic traits. Recently, the plant breeding community has experienced reduced costs for acquiring environmental sensors to be installed in the field trials while increasing the reliability and resolution of the remote sensing techniques. The combination of those two factors has started the spring of enviromics-aided breeding in recent years. However, the use of environmental information in plant breeding is not a novelty approach developed a few years ago, but a core of efforts originated in the last 60 years, yet some basic ideas traced back to early 20th century attempts to establish a relationship between phenotypic and environmental variation. This review highlights the main concepts surrounding the construction of the “modern enviromics science”, tracing back to its origins in the last decades. Finally, we present how this field has helped integrate different data sources in prediction-based models or build one framework.
DOI: 10.6084/m9.figshare.20038573
title: How to write and publish articles in plant breeding: What do we need to know?

description: Abstract: Social, economic, and cultural globalization and the consumer society have enabled science to definitively participate in people’s daily lives. Human knowledge has advanced at an extraordinary rate; science has become present and imperative; and never has more been expected from scientific advances than now. Here I addressed answers to the following questions: What is the importance of science? How can science be correctly communicated? What can we learn from comparing articles from Mendel and from Watson & Crick? How is a scientific paper to be written? How are target journals for publishing articles to be chosen? What is the impact factor of a journal and the h-index of a researcher, and what importance do they have? What is the role of authors, editors, and reviewers in the publication process? What are the main scientific databases? What are predatory journals/publishers and their consequences for science? What are particular features of articles in the area of plant breeding? Finally, in what directions is science moving, considering that it has come to stay?
DOI: 10.6084/m9.figshare.20038575
title: Genomic selection with rapid cyclingcycling: Current insights and future prospects

description: Abstract: Enhancing the rate of genetic gain in plant breeding program is critical to address global food security in the face of climate change and a growing population. Rapid cycling genomic selection offers a powerful breeding strategy to reduce the breeding cycle and obtain rapid genetic gains in plant breeding programs. In this paper, we discuss theoretical and empirical approaches to deploy and optimize rapid cycling genomic selection in crop improvement programs. We highlight major advantages and challenges associated with rapid cycling genomic selection and provide example to overcome these issues. Finally, we discuss the trends and general conclusion on this breeding strategy and provide recommendations for future discussions and continued adoption in plant breeding programs.
DOI: 10.6084/m9.figshare.20038575.v1
title: Genomic selection with rapid cyclingcycling: Current insights and future prospects

description: Abstract: Enhancing the rate of genetic gain in plant breeding program is critical to address global food security in the face of climate change and a growing population. Rapid cycling genomic selection offers a powerful breeding strategy to reduce the breeding cycle and obtain rapid genetic gains in plant breeding programs. In this paper, we discuss theoretical and empirical approaches to deploy and optimize rapid cycling genomic selection in crop improvement programs. We highlight major advantages and challenges associated with rapid cycling genomic selection and provide example to overcome these issues. Finally, we discuss the trends and general conclusion on this breeding strategy and provide recommendations for future discussions and continued adoption in plant breeding programs.
DOI: 10.6084/m9.figshare.20038576
title: Implementation of genomic selection in public-sector plant breeding programs: Current status and opportunities

description: Abstract: The usefulness of genomic selection (GS) for improvement of complex traits has been demonstrated in plant and animal breeding. While fully adopted in the livestock sector and commercial plant breeding, the implementation of GS in public-sector plant breeding programs lags. The goal of this review is to discuss advancements in GS implementation and opportunities for near-term and long-term adoption in public-sector plant breeding programs. We also highlighted specific applications of GS for cultivar development ordered by what we believe to be their feasibility, where feasibility is defined by cost, disruption to current breeding practices, and risk.
DOI: 10.6084/m9.figshare.20038576.v1
title: Implementation of genomic selection in public-sector plant breeding programs: Current status and opportunities

description: Abstract: The usefulness of genomic selection (GS) for improvement of complex traits has been demonstrated in plant and animal breeding. While fully adopted in the livestock sector and commercial plant breeding, the implementation of GS in public-sector plant breeding programs lags. The goal of this review is to discuss advancements in GS implementation and opportunities for near-term and long-term adoption in public-sector plant breeding programs. We also highlighted specific applications of GS for cultivar development ordered by what we believe to be their feasibility, where feasibility is defined by cost, disruption to current breeding practices, and risk.
DOI: 10.6084/m9.figshare.20038579.v1
title: Karyotype polymorphism of GC-rich constitutive heterochromatin in Capsicum L. pepper accessions

description: Abstract Capsicum is represented by peppers and sweet peppers and comprises a group with remarkable genetic variability. Different cultivated Capsicum peppers of Brazil were evaluated by using CMA3 and DAPI specific fluorochromes. There was high polymorphism of highly GC-rich CMA heterochromatic bands among the analyzed species, ranging from six (BAGC 114; C. annuum) to 26 blocks (BAGC 81; C. baccatum). Heterochromatin percentage ranged from 3.14% (BAGC 114; C. annuum) to 8.72% (BAGC 81; C. baccatum), corroborating the variation in the number of heterochromatic bands, particularly those distributed in the terminal and subterminal regions of the chromosomes. The information reported in this paper supports the cytogenetic characterization of the domesticated peppers accessions belonging to the Capsicum Germplasm Active Bank of the Federal University of Piauí (BAGC-UFPI). Moreover, the present data helped to better understand the karyotype features of peppers and provide additional information that could contribute to the improvement and maintenance of Capsicum genetic breeding programs.
DOI: 10.6084/m9.figshare.20038579
title: Karyotype polymorphism of GC-rich constitutive heterochromatin in Capsicum L. pepper accessions

description: Abstract Capsicum is represented by peppers and sweet peppers and comprises a group with remarkable genetic variability. Different cultivated Capsicum peppers of Brazil were evaluated by using CMA3 and DAPI specific fluorochromes. There was high polymorphism of highly GC-rich CMA heterochromatic bands among the analyzed species, ranging from six (BAGC 114; C. annuum) to 26 blocks (BAGC 81; C. baccatum). Heterochromatin percentage ranged from 3.14% (BAGC 114; C. annuum) to 8.72% (BAGC 81; C. baccatum), corroborating the variation in the number of heterochromatic bands, particularly those distributed in the terminal and subterminal regions of the chromosomes. The information reported in this paper supports the cytogenetic characterization of the domesticated peppers accessions belonging to the Capsicum Germplasm Active Bank of the Federal University of Piauí (BAGC-UFPI). Moreover, the present data helped to better understand the karyotype features of peppers and provide additional information that could contribute to the improvement and maintenance of Capsicum genetic breeding programs.
DOI: 10.6084/m9.figshare.20038582
title: Identification of sources of resistance to race 63-63 of Pseudocercospora griseola in common bean lines

description: Abstract Angular leaf spot (ALS), caused by the fungus Pseudocercospora griseola, is one of the most important foliar fungal diseases in common bean (Phaseolus vulgaris L.). The search for new sources of resistance to ALS is a promising activity in common bean breeding programs. In this study, the reaction of 416 germplasm accessions from the Universidade Federal de Lavras (UFLA) to P. griseola (race 63-63, the most important and most aggressive race) was assessed under greenhouse conditions (plants in the V2 stage, fully developed unifoliolate leaves). We identified 102 (24.5%) resistant and 314 (75.5%) susceptible accessions. Among the resistant lines, more than half are Carioca grain type lines. This study characterizes the resistance of a wide collection of common bean genotypes. The identification of new accessions resistant to P. griseola is an important step in common bean breeding programs. These lines can continually be incorporated in backcrosses to obtain cultivars resistant to ALS.
DOI: 10.6084/m9.figshare.20038582.v1
title: Identification of sources of resistance to race 63-63 of Pseudocercospora griseola in common bean lines

description: Abstract Angular leaf spot (ALS), caused by the fungus Pseudocercospora griseola, is one of the most important foliar fungal diseases in common bean (Phaseolus vulgaris L.). The search for new sources of resistance to ALS is a promising activity in common bean breeding programs. In this study, the reaction of 416 germplasm accessions from the Universidade Federal de Lavras (UFLA) to P. griseola (race 63-63, the most important and most aggressive race) was assessed under greenhouse conditions (plants in the V2 stage, fully developed unifoliolate leaves). We identified 102 (24.5%) resistant and 314 (75.5%) susceptible accessions. Among the resistant lines, more than half are Carioca grain type lines. This study characterizes the resistance of a wide collection of common bean genotypes. The identification of new accessions resistant to P. griseola is an important step in common bean breeding programs. These lines can continually be incorporated in backcrosses to obtain cultivars resistant to ALS.
DOI: 10.6084/m9.figshare.20038584
title: A simple and inexpensive procedure to more quickly obtain new varieties in soybean

description: Abstract Soybean (Glycine max L.) is one of the four most important crops in the world. The creation of new commercial varieties is a long-term activity that requires from seven to eight years from the beginning of the cross design up to registration for commercialization of cultivars. Rapid generation advance (RGA) is a technique that consists of controlling external factors that affect plant growth with the aim of shortening the sowing to harvest cycle. In the present study, an optimized method is described that can accelerate soybean breeding by means of RGA using inexpensive facilities and that can be easily applied by breeders. Our breeding method uses a modified cold storage chamber fitted with fluorescent lamps delivering a 12/24 h light photoperiod, while temperature is set at 24 °C. This method allows development of up to 5 generations per year instead of the 1-2 generations currently possible under field or greenhouse conditions.
DOI: 10.6084/m9.figshare.20038584.v1
title: A simple and inexpensive procedure to more quickly obtain new varieties in soybean

description: Abstract Soybean (Glycine max L.) is one of the four most important crops in the world. The creation of new commercial varieties is a long-term activity that requires from seven to eight years from the beginning of the cross design up to registration for commercialization of cultivars. Rapid generation advance (RGA) is a technique that consists of controlling external factors that affect plant growth with the aim of shortening the sowing to harvest cycle. In the present study, an optimized method is described that can accelerate soybean breeding by means of RGA using inexpensive facilities and that can be easily applied by breeders. Our breeding method uses a modified cold storage chamber fitted with fluorescent lamps delivering a 12/24 h light photoperiod, while temperature is set at 24 °C. This method allows development of up to 5 generations per year instead of the 1-2 generations currently possible under field or greenhouse conditions.
DOI: 10.6084/m9.figshare.20038585
title: Causal variant loci and protein-coding genes for soybean bacterial pustule resistance in the flowering stage

description: Abstract Bacterial pustule is an important soybean disease caused by Xanthomonas citri pv. glycines, but information about genetic resistance to this pathogen is scarce. This study aimed to investigate soybean genetic resistance to bacterial pustule in the flowering stage through association analysis, characterization of candidate SNP markers, and identification of protein-coding genes potentially regulating defense processes. Therefore, 109 soybean cultivars genotyped with a 6k Illumina platform were assessed for disease severity. A genome-wide analysis revealed a total of 13 SNPs significantly associated. Through protein annotation, we identified three markers located inside the coding regions of uncharacterized protein LOC100779077, histone-lysine N-methyltransferase SUVR4, and ABC-transporter B family member-9. Nucleotide polymorphism on the first two of these markers produces a non-synonymous polymorphism with polarity shift from hydrophobic to polar amino acid. It is convenient to prioritize these three candidate markers for validation procedures with the purpose of using them in marker-assisted soybean breeding programs.
DOI: 10.25773/mqqx-ny62
title:   Storm Surge Simulation from the 2009 Nor’easter on the Virginia Shoreline
DOI: 10.6084/m9.figshare.20038585.v1
title: Causal variant loci and protein-coding genes for soybean bacterial pustule resistance in the flowering stage

description: Abstract Bacterial pustule is an important soybean disease caused by Xanthomonas citri pv. glycines, but information about genetic resistance to this pathogen is scarce. This study aimed to investigate soybean genetic resistance to bacterial pustule in the flowering stage through association analysis, characterization of candidate SNP markers, and identification of protein-coding genes potentially regulating defense processes. Therefore, 109 soybean cultivars genotyped with a 6k Illumina platform were assessed for disease severity. A genome-wide analysis revealed a total of 13 SNPs significantly associated. Through protein annotation, we identified three markers located inside the coding regions of uncharacterized protein LOC100779077, histone-lysine N-methyltransferase SUVR4, and ABC-transporter B family member-9. Nucleotide polymorphism on the first two of these markers produces a non-synonymous polymorphism with polarity shift from hydrophobic to polar amino acid. It is convenient to prioritize these three candidate markers for validation procedures with the purpose of using them in marker-assisted soybean breeding programs.
DOI: 10.6084/m9.figshare.20038590
title: Improvement of vegetable soybean: genetic diversity and correlations of traits between immature and mature plants

description: Abstract Human consumption of vegetable soybeans is increasing, and consequently, breeding programs need to be encouraged and optimized. Therefore, there is a need to understand the relationship between the traits evaluated in the R6 (full seed) and R8 (full maturity) stages and estimate genetic divergence. At two sites and two crop seasons, we evaluated 42 progenies (F6 generation) from crosses between vegetable soybean genotypes and three commercial cultivars. In general, we found significant coincident correlations between environments. Positive and significant correlations between pod width (PWR6) and hundred-seed weight (HSW) and between PWR6 and hundred-pod weight (HPW) suggest the possibility of replacing the labor-intensive process of obtaining HSW and HPW by estimating PWR6, which is faster and easier to apply. The unweighted pair-group method arithmetic average analysis allocated soybean genotypes into six major clusters. Furthermore, information from the present work may guide practical actions in breeding programs.
DOI: 10.6084/m9.figshare.20038590.v1
title: Improvement of vegetable soybean: genetic diversity and correlations of traits between immature and mature plants

description: Abstract Human consumption of vegetable soybeans is increasing, and consequently, breeding programs need to be encouraged and optimized. Therefore, there is a need to understand the relationship between the traits evaluated in the R6 (full seed) and R8 (full maturity) stages and estimate genetic divergence. At two sites and two crop seasons, we evaluated 42 progenies (F6 generation) from crosses between vegetable soybean genotypes and three commercial cultivars. In general, we found significant coincident correlations between environments. Positive and significant correlations between pod width (PWR6) and hundred-seed weight (HSW) and between PWR6 and hundred-pod weight (HPW) suggest the possibility of replacing the labor-intensive process of obtaining HSW and HPW by estimating PWR6, which is faster and easier to apply. The unweighted pair-group method arithmetic average analysis allocated soybean genotypes into six major clusters. Furthermore, information from the present work may guide practical actions in breeding programs.
DOI: 10.6084/m9.figshare.20038591
title: Analysis of heterosis components and prediction of hybrid means based on intergroup topcrosses in maize

description: Abstract Diallel designs are widely used in plant breeding to select parents and to study trait inheritance. The present work aimed to present a method to evaluate two divergent groups of parents, in which one group is used as a tester of the contrasting group. Each parent is crossed with a balanced mixture of seeds from the parents of the other group, and the parents and topcrosses are experimentally evaluated. Two groups of ten inbred maize lines were used to obtain intergroup topcrosses and biparental crosses in a diallel scheme. The data were subjected to analysis of variance and parameter estimation using the two models. The results showed the reliability of the method for the evaluation of lines and prediction of means of hybrid populations and can be recommended when the number of parents to be evaluated is large, making it difficult to evaluate biparental crosses in a diallel scheme.
DOI: 10.6084/m9.figshare.20038591.v1
title: Analysis of heterosis components and prediction of hybrid means based on intergroup topcrosses in maize

description: Abstract Diallel designs are widely used in plant breeding to select parents and to study trait inheritance. The present work aimed to present a method to evaluate two divergent groups of parents, in which one group is used as a tester of the contrasting group. Each parent is crossed with a balanced mixture of seeds from the parents of the other group, and the parents and topcrosses are experimentally evaluated. Two groups of ten inbred maize lines were used to obtain intergroup topcrosses and biparental crosses in a diallel scheme. The data were subjected to analysis of variance and parameter estimation using the two models. The results showed the reliability of the method for the evaluation of lines and prediction of means of hybrid populations and can be recommended when the number of parents to be evaluated is large, making it difficult to evaluate biparental crosses in a diallel scheme.
DOI: 10.6084/m9.figshare.20038594
title: BRS Deni - Super-sweet corn open-pollinated variety

description: Abstract BRS Deni is a super-sweet corn open-pollinated variety, developed and released by the Brazilian Agricultural Research Corporation (Embrapa) that combines high yield and good ear and grain quality and lower production costs. The grain can be consumed fresh or canned.
DOI: 10.6084/m9.figshare.20038594.v1
title: BRS Deni - Super-sweet corn open-pollinated variety

description: Abstract BRS Deni is a super-sweet corn open-pollinated variety, developed and released by the Brazilian Agricultural Research Corporation (Embrapa) that combines high yield and good ear and grain quality and lower production costs. The grain can be consumed fresh or canned.