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      An Overview of the Genetics and Genomics of the Urochloa Species Most Commonly Used in Pastures

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          Abstract

          Pastures based on perennial monocotyledonous plants are the principal source of nutrition for ruminant livestock in tropical and subtropical areas across the globe. The Urochloa genus comprises important species used in pastures, and these mainly include Urochloa brizantha, Urochloa decumbens, Urochloa humidicola, and Urochloa ruziziensis. Despite their economic relevance, there is an absence of genomic-level information for these species, and this lack is mainly due to genomic complexity, including polyploidy, high heterozygosity, and genomes with a high repeat content, which hinders advances in molecular approaches to genetic improvement. Next-generation sequencing techniques have enabled the recent release of reference genomes, genetic linkage maps, and transcriptome sequences, and this information helps improve our understanding of the genetic architecture and molecular mechanisms involved in relevant traits, such as the apomictic reproductive mode. However, more concerted research efforts are still needed to characterize germplasm resources and identify molecular markers and genes associated with target traits. In addition, the implementation of genomic selection and gene editing is needed to reduce the breeding time and expenditure. In this review, we highlight the importance and characteristics of the four main species of Urochloa used in pastures and discuss the current findings from genetic and genomic studies and research gaps that should be addressed in future research.

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          RNA-Seq: a revolutionary tool for transcriptomics.

          RNA-Seq is a recently developed approach to transcriptome profiling that uses deep-sequencing technologies. Studies using this method have already altered our view of the extent and complexity of eukaryotic transcriptomes. RNA-Seq also provides a far more precise measurement of levels of transcripts and their isoforms than other methods. This article describes the RNA-Seq approach, the challenges associated with its application, and the advances made so far in characterizing several eukaryote transcriptomes.
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            Phytozome: a comparative platform for green plant genomics

            The number of sequenced plant genomes and associated genomic resources is growing rapidly with the advent of both an increased focus on plant genomics from funding agencies, and the application of inexpensive next generation sequencing. To interact with this increasing body of data, we have developed Phytozome (http://www.phytozome.net), a comparative hub for plant genome and gene family data and analysis. Phytozome provides a view of the evolutionary history of every plant gene at the level of sequence, gene structure, gene family and genome organization, while at the same time providing access to the sequences and functional annotations of a growing number (currently 25) of complete plant genomes, including all the land plants and selected algae sequenced at the Joint Genome Institute, as well as selected species sequenced elsewhere. Through a comprehensive plant genome database and web portal, these data and analyses are available to the broader plant science research community, providing powerful comparative genomics tools that help to link model systems with other plants of economic and ecological importance.
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              Prediction of Total Genetic Value Using Genome-Wide Dense Marker Maps

              Recent advances in molecular genetic techniques will make dense marker maps available and genotyping many individuals for these markers feasible. Here we attempted to estimate the effects of ∼50,000 marker haplotypes simultaneously from a limited number of phenotypic records. A genome of 1000 cM was simulated with a marker spacing of 1 cM. The markers surrounding every 1-cM region were combined into marker haplotypes. Due to finite population size (Ne = 100), the marker haplotypes were in linkage disequilibrium with the QTL located between the markers. Using least squares, all haplotype effects could not be estimated simultaneously. When only the biggest effects were included, they were overestimated and the accuracy of predicting genetic values of the offspring of the recorded animals was only 0.32. Best linear unbiased prediction of haplotype effects assumed equal variances associated to each 1-cM chromosomal segment, which yielded an accuracy of 0.73, although this assumption was far from true. Bayesian methods that assumed a prior distribution of the variance associated with each chromosome segment increased this accuracy to 0.85, even when the prior was not correct. It was concluded that selection on genetic values predicted from markers could substantially increase the rate of genetic gain in animals and plants, especially if combined with reproductive techniques to shorten the generation interval.
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                Author and article information

                Contributors
                URI : https://loop.frontiersin.org/people/674390/overview
                URI : https://loop.frontiersin.org/people/829307/overview
                URI : https://loop.frontiersin.org/people/1268889/overview
                URI : https://loop.frontiersin.org/people/605435/overview
                URI : https://loop.frontiersin.org/people/335774/overview
                Journal
                Front Plant Sci
                Front Plant Sci
                Front. Plant Sci.
                Frontiers in Plant Science
                Frontiers Media S.A.
                1664-462X
                13 December 2021
                2021
                : 12
                : 770461
                Affiliations
                [1] 1Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP) , Campinas, Brazil
                [2] 2Embrapa Gado de Corte, Brazilian Agricultural Research Corporation , Campo Grande, Brazil
                [3] 3Embrapa Pecuária Sudeste, Brazilian Agricultural Research Corporation , São Carlos, Brazil
                [4] 4Department of Plant Biology, Biology Institute, University of Campinas (UNICAMP) , Campinas, Brazil
                Author notes

                Edited by: Byoung-Cheorl Kang, Seoul National University, South Korea

                Reviewed by: Margaret L. Worthington, University of Arkansas, United States; Milind B. Ratnaparkhe, ICAR Indian Institute of Soybean Research, India

                *Correspondence: Anete Pereira de Souza, anete@ 123456unicamp.br

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

                Article
                10.3389/fpls.2021.770461
                8710810
                0ce9aefe-ed5b-4642-88e8-a2778fce16d7
                Copyright © 2021 Ferreira, Moraes, Chiari, Simeão, Vigna and de Souza.

                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
                : 03 September 2021
                : 17 November 2021
                Page count
                Figures: 1, Tables: 6, Equations: 0, References: 224, Pages: 22, Words: 21944
                Funding
                Funded by: Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, doi 10.13039/501100002322;
                Funded by: Conselho Nacional de Desenvolvimento Científico e Tecnológico , doi 10.13039/501100003593;
                Categories
                Plant Science
                Review

                Plant science & Botany
                brachiaria,genetic studies,genomic tools,molecular breeding,tropical forage grasses

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