Crop Breeding and Applied Biotechnology, Volume: 21, Issue: spe, Published: 2021
  • Genomics of grain quality in cereals Article

    Henry, Robert J

    Abstract in English:

    Abstract: Rapid advances in genomics are providing the tools to determine the genetic basis of quality (both nutritional and functional) in cereals. This promises to allow increased rates of genetic gain in breeding by reducing the need for extensive end-product testing of new varieties. Many quality traits are the result of relatively recent human selection and are thus likely to be controlled by only a few major genes. This makes identification of these genes for use in breeding selection an attractive target for breeders. Examples of the discovery of genes that are major contributors to key grain quality attributes include, fragrance and cooking temperature in rice (identified by re-sequencing) and loaf volume and milling yield in wheat (identified by transcriptome analysis). Extension of genomic tools to an analysis of the wider gene pool including wild relatives will enable the identification of alleles that may contribute to improved or novel grain quality in the future and may be critical to ensuring quality is retained in a changed climate. Completely new cereal species might be produced.
  • Technical nuances of machine learning: implementation and validation of supervised methods for genomic prediction in plant breeding Article

    Xavier, Alencar

    Abstract in English:

    Abstract The decision-making process in plant breeding is driven by data. The machine learning framework has powerful tools that can extract useful information from data. However, there is still a lack of understanding about the underlying algorithms of these methods, their strengths, and pitfalls. Machine learning has two main branches: supervised and unsupervised learning. In plant breeding, supervised learning is used for genomic prediction, where phenotypic traits are modeled as a function of molecular markers. The key supervised learning algorithms for genomic prediction are linear methods, kernel methods, neural networks, and tree ensembles. This manuscript provides an insight into the implementation of these algorithms and how cross-validations can be used to compare methods. Examples for genomic prediction come from plant breeding.
  • Plant breeding in Brazil: Retrospective of the past 50 years Article

    Ramalho, Magno Antonio Patto; Marques, Thaís Lima; Lemos, Roxane do Carmo

    Abstract in English:

    Abstract: The importance of plant breeding in Brazilian agriculture has grown a lot in the last 50 years. This occurred mainly because of the: increase in graduate programs, which qualified hundreds of professionals; creation of EMBRAPA and other research institutes or state companies, with an emphasis on the production of new cultivars and; promulgation of the cultivar protection law, which stimulates investments in seed production. The retrospective of what happened, enabling the country to move from being an importer of grains, fruits, and fibers to one of the largest exporters of these products worldwide, was the focus of this work. Taking as reference some agricultural products, this article highlights the significant contribution of plant breeding in recent years. Also, some of the enormous challenges that still have to be overcome, in which the participation of Brazilian breeders will be fundamental to continue the progress of agriculture in the coming years.
  • Biometry in plant breeding Article

    Cruz, Cosme Damião; Carneiro, Pedro Crescêncio Souza; Bhering, Leonardo Lopes

    Abstract in English:

    Abstract In this manuscript we discuss the purpose and scope of biometry and its interactions, complementation, and even overlap with several other areas of genetics. We emphasize that biometry is an area of genetics that enables researchers to analyze, process, and interpret biological phenomena from data, usually obtained from experimental tests, in an improved way to guide strategies and decision making for optimization of resources. We also highlight the importance of the biometry professional in the context of breeding and the need for continual training, due to new demands for and challenges from inclusion of different types of information for processing and analysis paradigms to better interpret these paradigms.
  • Recurrent selection in papaya: An effective strategy for the continuous development of new cultivars Article

    Pereira, Messias Gonzaga; Santa-Catarina, Renato

    Abstract in English:

    Abstract: Part of the success of a breeding program depends on the composition of the base population. Superior genotypes and unimproved dioecious varieties are sources of genes for traits of interest and excellent options for the formation of segregating populations. Here we describe the first cycle of recurrent selection (RS) in papaya and propose an effective strategy, unprecedented in the crop, to generate variability and new cultivars. Initially, the RS base population (UCP-C0) was developed with wide variability. Subsequently, 196 S1 progenies were obtained, evaluated in a trial, and the superior 40 S1 progenies were recombined. Among the traits of the selected progenies, high fruit yield (producing two to five fruits per axil) stands out. The S1 progenies were recombined and their seed bulk corresponds to the base population for the second cycle (UCP-C1). The results of the first cycle demonstrate the genetic potential of this population for the development of superior cultivars, and the breeding strategy applied is promising.
  • Germplasm enhancement and cultivar development: The need for sustainable breeding Article

    Carena, Marcelo J

    Abstract in English:

    Abstract: Farmers need sustainable cultivars to increase food supply and value with less production land, animals, and inputs. Next generation plant and animal breeders face climate change adaptation and mitigation challenges. These challenges need to be addressed with opportunities for significant reduction of environmental impact developing cultivars less addicted to fertilizers and soil moisture needs. Sustainable breeding can help balance agriculture with the environment. Sustainable breeders need to integrate long-term pre-breeding activities with cultivar development efforts providing farmers options to comply with environmental regulations. Good choice of germplasm is still the most important decision. The most sophisticated tools will have limited success if poor choices of germplasm are made. Seed companies need capable breeders developing the next generation of sustainable cultivars while public institutions need to mentor sustainable breeders capable to not only broadening and improving unique germplasm but also developing new cultivars carrying desirable traits. Graduates mentored in breeding programs integrating these needs will be selected for industry jobs without need for re-training. Sustainable breeders will need to operate in new breeding centers located in strategic environments for faster genetic improvement ahead of climate changes. Key factors for developing useful and unique sustainable cultivars will be the adaptation of exotic germplasm and the maximization of its genetic improvement before cultivar development through public and private partnerships. Inbreeding, genetic divergence, and reciprocal recurrent selection programs will continue to be essential to purify cultivars and exploit heterosis in economically important species.
  • The use of high-throughput phenotyping in genomic selection context Article

    Persa, Reyna; Ribeiro, Pedro Cesar de Oliveira; Jarquin, Diego

    Abstract in English:

    Abstract: One of the biggest challenges that breeders face is the development of improved cultivars in changing climate conditions posing extra challenges to their labor. On the other hand, the availability of data generated with automated systems offers an opportunity to characterize genetically and phenotypically genotypes with high detail. Modern sequencing technologies delivering hundreds of thousands of molecular makers, offered the opportunity of selecting genotypes without the need of observing these in fields and this methodology was coined as Genomic Selection (GS). More recently, sophisticated automated phenotyping platforms depending on sensors able to measure a large number of plant features were also developed and have shown potential in plant breeding applications. These modern phenotyping systems that attempt to efficiently deliver phenotypic information on secondary traits are also know as high-throughput phenotyping platforms (HTPPs). The integration of HTPP with GS models opened a new research front to improve the efficiency of the selection methods based on genomic data only, specially of those traits depending on a large number of genes with small effects (complex traits). However, there are still remaining some issues to solve for developing a robust methodology able to combine in an efficient and informed way these two high dimensional data types. In this document, we provide an overview of the statistical analysis of the data derived of the HTTPs for improving the predictive ability of conventional GS models. We provide a brief introduction showing the utility of genomic data in plant breeding applications. After, we provide an overview of the field-based HTPPs considering the light detection and ranging and the unmanned aerial vehicles and how the image data derived from these platforms can be used to accelerate genetic gains. After that, we discuss about the extension of the conventional GS models to allow the incorporation of data derived of the HTPPs as main effects and also in interaction with environmental factors. The availability of several sources of information have opened a venue to investigate besides the univariate or single trait model, models based on multiple traits and also models that consider multiple time measures allowing longitudinal GS studies. Finally, we provide some conclusions as well as we mention some the current issues that do not allow to fully exploit the potential of HTTPs in plant breeding applications.
  • Contribution of breeding to agriculture in the Brazilian Amazon. I. Açaí palm and oil palm Article

    Chaves, Saulo Fabrício da Silva; Alves, Rafael Moysés; Dias, Luiz Antônio dos Santos

    Abstract in English:

    Abstract Sustainable development in the Amazon involves moderate actions that combine technology-based agriculture with forest conservation. One of these actions is the genetic breeding of native species, which promotes cultural appreciation of the local society, and enables the opening of new markets. As an example, two breeding programs with solid results will be mentioned in this review: açaí palm (Euterpe oleracea Mart.) and oil palm (Elaeis guineensis Jacq. and E. oleifera (Kunth.) Cortés). Despite its importance, the prospects for breeding programs on Amazon are not optimistic. Factors intrinsic to plants, such as their incipient domestication, as well as their perennial nature and the difficulty linked to the improvement of plants in this category; and extrinsic factors, such as the lack of resources and specialized labour, in addition to the deficiency in logistics, are growing challenges that make it difficult to implementation of new programs and expansion of existing ones.
  • The numbers game of soybean breeding in the United States Article

    Vieira, Caio Canella; Chen, Pengyin

    Abstract in English:

    Abstract: Soybean [Glycine max (L.) Merr.] represents one of the most essential crops to the world’s economy and food security due to its unique seed composition. Public soybean breeding programs in the United States played an important role in developing the genetic basis of American soybean and discovering many economically important traits. After the passage of the Plant Variety Protection Act (PVP) in 1970 and the authorization to patent living matter in 1980, private companies have dominated the market share of commercial soybean varieties and public breeding programs shifted the efforts towards basic and applied research and education of the next generation of plant breeders. The short history of soybean breeding combined with a very narrow genetic basis derived from few ancestors can only make us reflect on all the innovations yet to be unveiled and the multiple possibilities to explore the unique traits that the golden miracle bean offers.
  • Rice blast: strategies and challenges for improving genetic resistance Article

    Nizolli, Valéria Oliveira; Pegoraro, Camila; Oliveira, Antonio Costa de

    Abstract in English:

    Abstract: Rice blast, caused by the fungus Pyricularia oryzae L., is considered one of the main threats to world rice production. The development of resistant cultivars is one of the best and sustainable control alternatives. Plant breeding efforts have been accelerated by genetic mapping (linkage and associative) and marker assisted selection. On the other hand, genomic editing techniques, such as meganucleases (MNs), Zinc-finger nucleases (ZFNs), Transcription Activator-like Effector Nucleases (TALENs) and Clustered Regularly Interspaced Short Palindrome Repeats/CRISPR-associated protein 9 (CRISPR/Cas9), can be used to promote specific genetic modifications. Likewise, transgenics can also be used to manipulate specific genes. In this sense, this work aims to characterize rice blast and elucidate available biotechnological alternatives to accelerate the development of improved rice cultivars resistant to rice blast.
  • Spray-induced gene silencing: an innovative strategy for plant trait improvement and disease control Article

    Vetukuri, Ramesh R.; Dubey, Mukesh; Kalyandurg, Pruthvi B.; Carlsson, Anders S.; Whisson, Stephen C.; Ortiz, Rodomiro

    Abstract in English:

    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.
  • How to write and publish articles in plant breeding: What do we need to know? Article

    Dias, Luiz Antônio dos Santos

    Abstract in English:

    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?
  • Enviromics: bridging different sources of data, building one framework Article

    Costa-Neto, Germano; Fritsche-Neto, Roberto

    Abstract in English:

    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.
  • Next generation breeding in pulses: Present status and future directions Article

    Kumar, Ashish; Bohra, Abhishek; Mir, Reyazul Rouf; Sharma, Radheshyam; Tiwari, Abha; Khan, Mohd Anwar; Varshney, Rajeev K.

    Abstract in English:

    Abstract: Human population growth in combination with changing patterns of global food consumption under climate change is posing formidable challenge to attaining sustainable global food security. Besides being economically viable sources of plant based protein for human consumption, pulses are also beneficial for the environment owing to their inherent capacity of nitrogen fixation. Hence, further development of pulses has become imperative in the vigorously transitional global scenario where flourishing anthropogenic activities are triggering irreplaceable depletion of natural resources. During past years, considerable attention has been given on the use of next generation sequencing for enriching the genomic resources in pulse crops including high-throughput DNA markers, candidate gene(s) and QTLs for predicting plant phenotypes, and whole genome sequences. With refinements in DNA sequencing technologies and computational analytical tools, the rapidly grown numbers of sequenced pulse genomes offer novel insights on crop evolution and breeding history. Integration of new-generation genomic and phenomic tools with generation acceleration procedures like genomic selection and speed breeding could greatly accelerate progress in pulses genetic improvement. The present review discusses current status and future scope of using next-generation breeding approaches in pulses that will cause not only an increase in the rate of developing climate-resilient superior cultivars but also help to reach to goal of global food security.
  • Implementation of genomic selection in public-sector plant breeding programs: Current status and opportunities Article

    Wartha, Cleiton Antonio; Lorenz, Aaron Joel

    Abstract in English:

    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.
  • Genomic selection with rapid cyclingcycling: Current insights and future prospects Article

    Volpato, Leonardo; Bernardeli, Arthur; Gomez, Francisco

    Abstract in English:

    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.
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