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      Genomic Selection in Tropical Forage Grasses: Current Status and Future Applications

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          Abstract

          The world population is expected to be larger and wealthier over the next few decades and will require more animal products, such as milk and beef. Tropical regions have great potential to meet this growing global demand, where pasturelands play a major role in supporting increased animal production. Better forage is required in consonance with improved sustainability as the planted area should not increase and larger areas cultivated with one or a few forage species should be avoided. Although, conventional tropical forage breeding has successfully released well-adapted and high-yielding cultivars over the last few decades, genetic gains from these programs have been low in view of the growing food demand worldwide. To guarantee their future impact on livestock production, breeding programs should leverage genotyping, phenotyping, and envirotyping strategies to increase genetic gains. Genomic selection (GS) and genome-wide association studies play a primary role in this process, with the advantage of increasing genetic gain due to greater selection accuracy, reduced cycle time, and increased number of individuals that can be evaluated. This strategy provides solutions to bottlenecks faced by conventional breeding methods, including long breeding cycles and difficulties to evaluate complex traits. Initial results from implementing GS in tropical forage grasses (TFGs) are promising with notable improvements over phenotypic selection alone. However, the practical impact of GS in TFG breeding programs remains unclear. The development of appropriately sized training populations is essential for the evaluation and validation of selection markers based on estimated breeding values. Large panels of single-nucleotide polymorphism markers in different tropical forage species are required for multiple application targets at a reduced cost. In this context, this review highlights the current challenges, achievements, availability, and development of genomic resources and statistical methods for the implementation of GS in TFGs. Additionally, the prediction accuracies from recent experiments and the potential to harness diversity from genebanks are discussed. Although, GS in TFGs is still incipient, the advances in genomic tools and statistical models will speed up its implementation in the foreseeable future. All TFG breeding programs should be prepared for these changes.

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          Most cited references141

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          The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.

          Next-generation DNA sequencing (NGS) projects, such as the 1000 Genomes Project, are already revolutionizing our understanding of genetic variation among individuals. However, the massive data sets generated by NGS--the 1000 Genome pilot alone includes nearly five terabases--make writing feature-rich, efficient, and robust analysis tools difficult for even computationally sophisticated individuals. Indeed, many professionals are limited in the scope and the ease with which they can answer scientific questions by the complexity of accessing and manipulating the data produced by these machines. Here, we discuss our Genome Analysis Toolkit (GATK), a structured programming framework designed to ease the development of efficient and robust analysis tools for next-generation DNA sequencers using the functional programming philosophy of MapReduce. The GATK provides a small but rich set of data access patterns that encompass the majority of analysis tool needs. Separating specific analysis calculations from common data management infrastructure enables us to optimize the GATK framework for correctness, stability, and CPU and memory efficiency and to enable distributed and shared memory parallelization. We highlight the capabilities of the GATK by describing the implementation and application of robust, scale-tolerant tools like coverage calculators and single nucleotide polymorphism (SNP) calling. We conclude that the GATK programming framework enables developers and analysts to quickly and easily write efficient and robust NGS tools, many of which have already been incorporated into large-scale sequencing projects like the 1000 Genomes Project and The Cancer Genome Atlas.
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            Efficient methods to compute genomic predictions.

            P VanRaden (2008)
            Efficient methods for processing genomic data were developed to increase reliability of estimated breeding values and to estimate thousands of marker effects simultaneously. Algorithms were derived and computer programs tested with simulated data for 2,967 bulls and 50,000 markers distributed randomly across 30 chromosomes. Estimation of genomic inbreeding coefficients required accurate estimates of allele frequencies in the base population. Linear model predictions of breeding values were computed by 3 equivalent methods: 1) iteration for individual allele effects followed by summation across loci to obtain estimated breeding values, 2) selection index including a genomic relationship matrix, and 3) mixed model equations including the inverse of genomic relationships. A blend of first- and second-order Jacobi iteration using 2 separate relaxation factors converged well for allele frequencies and effects. Reliability of predicted net merit for young bulls was 63% compared with 32% using the traditional relationship matrix. Nonlinear predictions were also computed using iteration on data and nonlinear regression on marker deviations; an additional (about 3%) gain in reliability for young bulls increased average reliability to 66%. Computing times increased linearly with number of genotypes. Estimation of allele frequencies required 2 processor days, and genomic predictions required <1 d per trait, and traits were processed in parallel. Information from genotyping was equivalent to about 20 daughters with phenotypic records. Actual gains may differ because the simulation did not account for linkage disequilibrium in the base population or selection in subsequent generations.
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              A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

              Advances in next generation technologies have driven the costs of DNA sequencing down to the point that genotyping-by-sequencing (GBS) is now feasible for high diversity, large genome species. Here, we report a procedure for constructing GBS libraries based on reducing genome complexity with restriction enzymes (REs). This approach is simple, quick, extremely specific, highly reproducible, and may reach important regions of the genome that are inaccessible to sequence capture approaches. By using methylation-sensitive REs, repetitive regions of genomes can be avoided and lower copy regions targeted with two to three fold higher efficiency. This tremendously simplifies computationally challenging alignment problems in species with high levels of genetic diversity. The GBS procedure is demonstrated with maize (IBM) and barley (Oregon Wolfe Barley) recombinant inbred populations where roughly 200,000 and 25,000 sequence tags were mapped, respectively. An advantage in species like barley that lack a complete genome sequence is that a reference map need only be developed around the restriction sites, and this can be done in the process of sample genotyping. In such cases, the consensus of the read clusters across the sequence tagged sites becomes the reference. Alternatively, for kinship analyses in the absence of a reference genome, the sequence tags can simply be treated as dominant markers. Future application of GBS to breeding, conservation, and global species and population surveys may allow plant breeders to conduct genomic selection on a novel germplasm or species without first having to develop any prior molecular tools, or conservation biologists to determine population structure without prior knowledge of the genome or diversity in the species.
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                Author and article information

                Contributors
                Journal
                Front Plant Sci
                Front Plant Sci
                Front. Plant Sci.
                Frontiers in Plant Science
                Frontiers Media S.A.
                1664-462X
                30 April 2021
                2021
                : 12
                : 665195
                Affiliations
                [1] 1Embrapa Gado de Corte , Campo Grande, Brazil
                [2] 2Embrapa Café, Universidade Federal de Viçosa , Viçosa, Brazil
                [3] 3Instituto Nacional de Ciência e Tecnologia do Café, Universidade Federal de Viçosa , Viçosa, Brazil
                [4] 4Embrapa Cerrados , Brasília, Brazil
                [5] 5Embrapa Gado de Leite , Juiz de Fora, Brazil
                [6] 6International Livestock Research Institute , Nairobi, Kenya
                Author notes

                Edited by: Fernando H. Toledo, International Maize and Wheat Improvement Center, Mexico

                Reviewed by: Russell Jessup, Texas A & M University, United States; Filipe Matias, University of Wisconsin-Madison, United States; Jose Crossa, International Maize and Wheat Improvement Center, Mexico

                *Correspondence: Juarez C. Machado, juarez.machado@ 123456embrapa.br

                ORCID: Rosangela M. Simeão, orcid.org/0000-0001-8351-846X; Marcos D. V. Resende, orcid.org/0000-0002-3087-3588; Rodrigo S. Alves, orcid.org/0000-0002-3038-6210; Marco Pessoa-Filho, orcid.org/0000-0002-7333-4429; Ana Luisa S. Azevedo, orcid.org/0000-0003-1939-0339; Chris S. Jones, orcid.org/0000-0001-9096-9728; Jorge F. Pereira, orcid.org/0000-0001-9340-065X; Juarez C. Machado, orcid.org/0000-0003-2551-2080

                This article was submitted to Plant Breeding, a section of the journal Frontiers in Plant Science

                Article
                10.3389/fpls.2021.665195
                8120112
                56b1c61f-d7a0-4ac6-a1bd-f92ce382204f
                Copyright © 2021 Simeão, Resende, Alves, Pessoa-Filho, Azevedo, Jones, Pereira and Machado.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 07 February 2021
                : 06 April 2021
                Page count
                Figures: 7, Tables: 2, Equations: 2, References: 141, Pages: 22, Words: 0
                Funding
                Funded by: Empresa Brasileira de Pesquisa Agropecuária 10.13039/501100003046
                Funded by: Conselho Nacional de Desenvolvimento Científico e Tecnológico 10.13039/501100003593
                Funded by: Fundação de Amparo à Pesquisa do Estado de Minas Gerais 10.13039/501100004901
                Funded by: Instituto Nacional de Ciência e Tecnologia do Café 10.13039/501100011667
                Funded by: Associação para o Fomento à Pesquisa de Melhoramento de Forrageiras 10.13039/501100011106
                Categories
                Plant Science
                Review

                Plant science & Botany
                apomixis,brachiaria,elephant grass,forage breeding,guinea grass,marker-assisted selection,polyploidy

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