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Bhavani P, Nandini C, Maharajan T, Ningaraju TM, Nandini B, Parveen SG, Pushpa K, Ravikumar RL, Nagaraja TE, Ceasar SA. Brown-top millet: an overview of breeding, genetic, and genomic resources development for crop improvement. PLANTA 2024; 260:10. [PMID: 38796805 DOI: 10.1007/s00425-024-04446-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 05/19/2024] [Indexed: 05/29/2024]
Abstract
MAIN CONCLUSION Brown-top millet is a lesser-known millet with a high grain nutrient value, early maturation, and drought tolerance that needs basic research to understand and conserve food security. Brown-top millet [Urochloa ramosa (L.)] is currently cultivated in some developing countries (especially in India) for food and fodder, although it is less known among the small millets. Like other millets, it contains macro- and micronutrients, vitamins, minerals, proteins, and fiber, all of which have rich health benefits. The nutritional importance and health benefits of brown-top millet are still unknown to many people due to a lack of awareness, wide cultivation, and research. Hence, this millet is currently overshadowed by other major cereals. This review article aims to present the nutritional, breeding, genetic, and genomic resources of brown-top millet to inform millet and other plant researchers. It is important to note that genetic and genomic resources have not yet been created for this millet. To date, there are no genomic and transcriptomic resources for brown-top millet to develop single nucleotide polymorphisms (SNP) and insertion/Deletions (InDels) for breeding studies. Furthermore, studies regarding nutritional significance and health benefits are required to investigate the exact nutritional contents and health benefits of the brown-top millet. The present review delves into the nutritional value and health advantages of brown-top millet, as supported by the available literature. The limitations of producing brown-top millet have been enumerated. We also cover the status of marker-assisted breeding and functional genomics research on closely related species. Lastly, we draw insights for further research such as developing omics resources and applying genome editing to study and improve brown-top millet. This review will help to start breeding and other molecular studies to increase the growth and development of this cereal.
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Affiliation(s)
- P Bhavani
- Department of Biotechnology, University of Agricultural Sciences, Bangalore, Karnataka, India.
| | - C Nandini
- Zonal Agricultural and Horticultural Research Station, Babbur Farm, Hiriyur, KSNUAHS, Shivamogga, Karnataka, India.
| | - Theivanayagam Maharajan
- Division of Plant Molecular Biology and Biotechnology, Department of Biosciences, Rajagiri College of Social Sciences, Cochin, 683104, Kerala, India
| | - T M Ningaraju
- Department of Biotechnology, University of Agricultural Sciences, Bangalore, Karnataka, India
| | - B Nandini
- College of Horticulture, Kolar, University of Horticultural Sciences, Bagalkot, Karnataka, India
| | - S Gazala Parveen
- AICRP on Small Millets, University of Agricultural Sciences, GKVK, Bengaluru, Karnataka, India
| | - K Pushpa
- Department of Agronomy, University of Agricultural Sciences, GKVK, Bengaluru, Karnataka, India
| | - R L Ravikumar
- Department of Biotechnology, University of Agricultural Sciences, Bangalore, Karnataka, India
| | - T E Nagaraja
- AICRP on Small Millets, University of Agricultural Sciences, GKVK, Bengaluru, Karnataka, India
| | - Stanislaus Antony Ceasar
- Division of Plant Molecular Biology and Biotechnology, Department of Biosciences, Rajagiri College of Social Sciences, Cochin, 683104, Kerala, India
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Njuguna JN, Clark LV, Lipka AE, Anzoua KG, Bagmet L, Chebukin P, Dwiyanti MS, Dzyubenko E, Dzyubenko N, Ghimire BK, Jin X, Johnson DA, Kjeldsen JB, Nagano H, de Bem Oliveira I, Peng J, Petersen KK, Sabitov A, Seong ES, Yamada T, Yoo JH, Yu CY, Zhao H, Munoz P, Long SP, Sacks EJ. Impact of genotype-calling methodologies on genome-wide association and genomic prediction in polyploids. THE PLANT GENOME 2023; 16:e20401. [PMID: 37903749 DOI: 10.1002/tpg2.20401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 09/17/2023] [Accepted: 09/23/2023] [Indexed: 11/01/2023]
Abstract
Discovery and analysis of genetic variants underlying agriculturally important traits are key to molecular breeding of crops. Reduced representation approaches have provided cost-efficient genotyping using next-generation sequencing. However, accurate genotype calling from next-generation sequencing data is challenging, particularly in polyploid species due to their genome complexity. Recently developed Bayesian statistical methods implemented in available software packages, polyRAD, EBG, and updog, incorporate error rates and population parameters to accurately estimate allelic dosage across any ploidy. We used empirical and simulated data to evaluate the three Bayesian algorithms and demonstrated their impact on the power of genome-wide association study (GWAS) analysis and the accuracy of genomic prediction. We further incorporated uncertainty in allelic dosage estimation by testing continuous genotype calls and comparing their performance to discrete genotypes in GWAS and genomic prediction. We tested the genotype-calling methods using data from two autotetraploid species, Miscanthus sacchariflorus and Vaccinium corymbosum, and performed GWAS and genomic prediction. In the empirical study, the tested Bayesian genotype-calling algorithms differed in their downstream effects on GWAS and genomic prediction, with some showing advantages over others. Through subsequent simulation studies, we observed that at low read depth, polyRAD was advantageous in its effect on GWAS power and limit of false positives. Additionally, we found that continuous genotypes increased the accuracy of genomic prediction, by reducing genotyping error, particularly at low sequencing depth. Our results indicate that by using the Bayesian algorithm implemented in polyRAD and continuous genotypes, we can accurately and cost-efficiently implement GWAS and genomic prediction in polyploid crops.
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Affiliation(s)
- Joyce N Njuguna
- Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Lindsay V Clark
- Research Scientific Computing, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Alexander E Lipka
- Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Kossonou G Anzoua
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Japan
| | - Larisa Bagmet
- Vavilov All-Russian Institute of Plant Genetic Resources, St. Petersburg, Russian Federation
| | - Pavel Chebukin
- FSBSI "FSC of Agricultural Biotechnology of the Far East named after A.K. Chaiki", Ussuriysk, Russian Federation
| | - Maria S Dwiyanti
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Japan
| | - Elena Dzyubenko
- Vavilov All-Russian Institute of Plant Genetic Resources, St. Petersburg, Russian Federation
| | - Nicolay Dzyubenko
- Vavilov All-Russian Institute of Plant Genetic Resources, St. Petersburg, Russian Federation
| | - Bimal Kumar Ghimire
- Department of Crop Science, College of Sanghuh Life Science, Konkuk University, Seoul, South Korea
| | - Xiaoli Jin
- Agronomy Department, Key Laboratory of Crop Germplasm Research of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Douglas A Johnson
- USDA-ARS Forage and Range Research Lab, Utah State University, Logan, Utah, USA
| | | | - Hironori Nagano
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Japan
| | | | - Junhua Peng
- Spring Valley Agriscience Co. Ltd., Jinan, China
| | | | - Andrey Sabitov
- Vavilov All-Russian Institute of Plant Genetic Resources, St. Petersburg, Russian Federation
| | - Eun Soo Seong
- Division of Bioresource Sciences, Kangwon National University, Chuncheon, South Korea
| | - Toshihiko Yamada
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Japan
| | - Ji Hye Yoo
- Bioherb Research Institute, Kangwon National University, Chuncheon, South Korea
| | - Chang Yeon Yu
- Bioherb Research Institute, Kangwon National University, Chuncheon, South Korea
| | - Hua Zhao
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Patricio Munoz
- Horticultural Science Department, University of Florida, Gainesville, Florida, USA
| | - Stephen P Long
- Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Erik J Sacks
- Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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3
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da Costa Lima Moraes A, Mollinari M, Ferreira RCU, Aono A, de Castro Lara LA, Pessoa-Filho M, Barrios SCL, Garcia AAF, do Valle CB, de Souza AP, Vigna BBZ. Advances in genomic characterization of Urochloa humidicola: exploring polyploid inheritance and apomixis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:238. [PMID: 37919432 DOI: 10.1007/s00122-023-04485-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 10/11/2023] [Indexed: 11/04/2023]
Abstract
KEY MESSAGE We present the highest-density genetic map for the hexaploid Urochloa humidicola. SNP markers expose genetic organization, reproduction, and species origin, aiding polyploid and tropical forage research. Tropical forage grasses are an important food source for animal feeding, with Urochloa humidicola, also known as Koronivia grass, being one of the main pasture grasses for poorly drained soils in the tropics. However, genetic and genomic resources for this species are lacking due to its genomic complexity, including high heterozygosity, evidence of segmental allopolyploidy, and reproduction by apomixis. These complexities hinder the application of marker-assisted selection (MAS) in breeding programs. Here, we developed the highest-density linkage map currently available for the hexaploid tropical forage grass U. humidicola. This map was constructed using a biparental F1 population generated from a cross between the female parent H031 (CIAT 26146), the only known sexual genotype for the species, and the apomictic male parent H016 (BRS cv. Tupi). The linkage analysis included 4873 single nucleotide polymorphism (SNP) markers with allele dosage information. It allowed mapping of the ASGR locus and apospory phenotype to linkage group 3, in a region syntenic with chromosome 3 of Urochloa ruziziensis and chromosome 1 of Setaria italica. We also identified hexaploid haplotypes for all individuals, assessed the meiotic configuration, and estimated the level of preferential pairing in parents during the meiotic process, which revealed the autopolyploid origin of sexual H031 in contrast to apomictic H016, which presented allopolyploid behavior in preferential pairing analysis. These results provide new information regarding the genetic organization, mode of reproduction, and allopolyploid origin of U. humidicola, potential SNPs markers associated with apomixis for MAS and resources for research on polyploids and tropical forage grasses.
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Affiliation(s)
- Aline da Costa Lima Moraes
- Department of Plant Biology, Biology Institute, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Marcelo Mollinari
- Department of Horticultural Science, Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | | | - Alexandre Aono
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | | | | | | | | | | | - Anete Pereira de Souza
- Department of Plant Biology, Biology Institute, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
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4
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Polyploid SNP Genotyping Using the MassARRAY System. Methods Mol Biol 2023; 2638:93-113. [PMID: 36781637 DOI: 10.1007/978-1-0716-3024-2_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Molecular marker discovery and genotyping are major challenges in polyploid breeding programs incorporating molecular biology tools. In this context, this work describes a method for single nucleotide polymorphism (SNP) genotyping in polyploid crops using matrix-assisted laser desorption ionization (MALDI) time-of-flight (TOF) mass spectrometry, the MassARRAY System.
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5
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A joint learning approach for genomic prediction in polyploid grasses. Sci Rep 2022; 12:12499. [PMID: 35864135 PMCID: PMC9304331 DOI: 10.1038/s41598-022-16417-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/11/2022] [Indexed: 12/20/2022] Open
Abstract
Poaceae, among the most abundant plant families, includes many economically important polyploid species, such as forage grasses and sugarcane (Saccharum spp.). These species have elevated genomic complexities and limited genetic resources, hindering the application of marker-assisted selection strategies. Currently, the most promising approach for increasing genetic gains in plant breeding is genomic selection. However, due to the polyploidy nature of these polyploid species, more accurate models for incorporating genomic selection into breeding schemes are needed. This study aims to develop a machine learning method by using a joint learning approach to predict complex traits from genotypic data. Biparental populations of sugarcane and two species of forage grasses (Urochloa decumbens, Megathyrsus maximus) were genotyped, and several quantitative traits were measured. High-quality markers were used to predict several traits in different cross-validation scenarios. By combining classification and regression strategies, we developed a predictive system with promising results. Compared with traditional genomic prediction methods, the proposed strategy achieved accuracy improvements exceeding 50%. Our results suggest that the developed methodology could be implemented in breeding programs, helping reduce breeding cycles and increase genetic gains.
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Ferreira RCU, da Costa Lima Moraes A, Chiari L, Simeão RM, Vigna BBZ, de Souza AP. An Overview of the Genetics and Genomics of the Urochloa Species Most Commonly Used in Pastures. FRONTIERS IN PLANT SCIENCE 2021; 12:770461. [PMID: 34966402 PMCID: PMC8710810 DOI: 10.3389/fpls.2021.770461] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/17/2021] [Indexed: 06/14/2023]
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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Affiliation(s)
| | - Aline da Costa Lima Moraes
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Lucimara Chiari
- Embrapa Gado de Corte, Brazilian Agricultural Research Corporation, Campo Grande, Brazil
| | - Rosangela Maria Simeão
- Embrapa Gado de Corte, Brazilian Agricultural Research Corporation, Campo Grande, Brazil
| | | | - Anete Pereira de Souza
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
- Department of Plant Biology, Biology Institute, University of Campinas (UNICAMP), Campinas, Brazil
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7
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Hanley SJ, Pellny TK, de Vega JJ, Castiblanco V, Arango J, Eastmond PJ, Heslop-Harrison JS(P, Mitchell RAC. Allele mining in diverse accessions of tropical grasses to improve forage quality and reduce environmental impact. ANNALS OF BOTANY 2021; 128:627-637. [PMID: 34320174 PMCID: PMC8422886 DOI: 10.1093/aob/mcab101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND AND AIMS The C4Urochloa species (syn. Brachiaria) and Megathyrsus maximus (syn. Panicum maximum) are used as pasture for cattle across vast areas in tropical agriculture systems in Africa and South America. A key target for variety improvement is forage quality: enhanced digestibility could decrease the amount of land required per unit production, and enhanced lipid content could decrease methane emissions from cattle. For these traits, loss-of-function (LOF) alleles in known gene targets are predicted to improve them, making a reverse genetics approach of allele mining feasible. We therefore set out to look for such alleles in diverse accessions of Urochloa species and Megathyrsus maximus from the genebank collection held at the CIAT. METHODS We studied allelic diversity of 20 target genes (11 for digestibility, nine for lipid content) in 104 accessions selected to represent genetic diversity and ploidy levels of U. brizantha, U. decumbens, U. humidicola, U. ruziziensis and M. maximum. We used RNA sequencing and then bait capture DNA sequencing to improve gene models in a U. ruziziensis reference genome to assign polymorphisms with high confidence. KEY RESULTS We found 953 non-synonymous polymorphisms across all genes and accessions; within these, we identified seven putative LOF alleles with high confidence, including those in the non-redundant SDP1 and BAHD01 genes present in diploid and tetraploid accessions. These LOF alleles could respectively confer increased lipid content and digestibility if incorporated into a breeding programme. CONCLUSIONS We demonstrated a novel, effective approach to allele discovery in diverse accessions using a draft reference genome from a single species. We used this to find gene variants in a collection of tropical grasses that could help reduce the environmental impact of cattle production.
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Affiliation(s)
| | | | | | | | - Jacobo Arango
- International Center for Tropical Agriculture (CIAT), Cali, Colombia
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8
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Simeão RM, Resende MDV, Alves RS, Pessoa-Filho M, Azevedo ALS, Jones CS, Pereira JF, Machado JC. Genomic Selection in Tropical Forage Grasses: Current Status and Future Applications. FRONTIERS IN PLANT SCIENCE 2021; 12:665195. [PMID: 33995461 PMCID: PMC8120112 DOI: 10.3389/fpls.2021.665195] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 04/06/2021] [Indexed: 05/06/2023]
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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Affiliation(s)
| | | | - Rodrigo S. Alves
- Instituto Nacional de Ciência e Tecnologia do Café, Universidade Federal de Viçosa, Viçosa, Brazil
| | | | | | - Chris S. Jones
- International Livestock Research Institute, Nairobi, Kenya
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Congio GFS, de Almeida PC, Barreto TR, Tinazo VA, da Silva TACC, Costa DFA, Corsi M. Spittlebug damage on tropical grass and its impact in pasture-based beef production systems. Sci Rep 2020; 10:10758. [PMID: 32612122 PMCID: PMC7329844 DOI: 10.1038/s41598-020-67490-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 06/05/2020] [Indexed: 11/20/2022] Open
Abstract
Spittlebugs are the main pest of tropical pastures and Marandu palisade grass (Urochloa brizantha cv. Marandu) is the most representative cultivated pasture in the tropics. Our objective was to characterize Marandu palisade grass responses subjected to Mahanarva (Hemiptera: Cercopidae) attack and to estimate the losses in terms of beef production from pasture-based systems. A set of five experiments were carried out. Three consecutive years of monitoring showed that Mahanarva spittlebugs increased their abundance after first rains with three to four peaks throughout the wet season. A decrease of 66% on herbage yield was observed in the greenhouse trial, with an average decrease of 61% on pools of calcium, magnesium, phosphorus, sulfur, potassium, crude protein, neutral-detergent fiber and in vitro digestible dry matter of Marandu palisade grass. Results from field experiments corroborated with greenhouse trial showing decreases on herbage yield varying from 31 to 43% depending on level of fertilization and grazing severity of Marandu palisade grass. Finally, an unprecedented 154-ha field experiment indicated that Mahanarva decreases 74% the beef productivity (i.e. kg body weight ha−1) of Nellore heifers grazing Marandu palisade grass.
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Affiliation(s)
- Guilhermo Francklin Souza Congio
- Colombian Corporation for Agricultural Research, Agrosavia, Km 14 via Mosquera, Bogota, Cundinamarca, 250047, Colombia. .,Animal Science Department, "Luiz de Queiroz" College of Agriculture (USP/ESALQ), University of Sao Paulo, Av. Padua Dias, 11, Piracicaba, Sao Paulo, 13418-900, Brazil.
| | - Pedro Castro de Almeida
- Animal Science Department, "Luiz de Queiroz" College of Agriculture (USP/ESALQ), University of Sao Paulo, Av. Padua Dias, 11, Piracicaba, Sao Paulo, 13418-900, Brazil
| | - Tadeu Ruzza Barreto
- Animal Science Department, "Luiz de Queiroz" College of Agriculture (USP/ESALQ), University of Sao Paulo, Av. Padua Dias, 11, Piracicaba, Sao Paulo, 13418-900, Brazil
| | - Vitor Afonso Tinazo
- Animal Science Department, "Luiz de Queiroz" College of Agriculture (USP/ESALQ), University of Sao Paulo, Av. Padua Dias, 11, Piracicaba, Sao Paulo, 13418-900, Brazil
| | | | - Diogo Fleury Azevedo Costa
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Gatton, QLD, 4343, Australia
| | - Moacyr Corsi
- Animal Science Department, "Luiz de Queiroz" College of Agriculture (USP/ESALQ), University of Sao Paulo, Av. Padua Dias, 11, Piracicaba, Sao Paulo, 13418-900, Brazil
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10
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Gerard D, Ferrão LFV. Priors for genotyping polyploids. BIOINFORMATICS (OXFORD, ENGLAND) 2020; 36:1795-1800. [PMID: 32176767 DOI: 10.1101/751784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/01/2019] [Accepted: 11/12/2019] [Indexed: 05/29/2023]
Abstract
MOTIVATION Empirical Bayes techniques to genotype polyploid organisms usually either (i) assume technical artifacts are known a priori or (ii) estimate technical artifacts simultaneously with the prior genotype distribution. Case (i) is unappealing as it places the onus on the researcher to estimate these artifacts, or to ensure that there are no systematic biases in the data. However, as we demonstrate with a few empirical examples, case (ii) makes choosing the class of prior genotype distributions extremely important. Choosing a class is either too flexible or too restrictive results in poor genotyping performance. RESULTS We propose two classes of prior genotype distributions that are of intermediate levels of flexibility: the class of proportional normal distributions and the class of unimodal distributions. We provide a complete characterization of and optimization details for the class of unimodal distributions. We demonstrate, using both simulated and real data that using these classes results in superior genotyping performance. AVAILABILITY AND IMPLEMENTATION Genotyping methods that use these priors are implemented in the updog R package available on the Comprehensive R Archive Network: https://cran.r-project.org/package=updog. All code needed to reproduce the results of this article is available on GitHub: https://github.com/dcgerard/reproduce_prior_sims. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- David Gerard
- Department of Mathematics and Statistics, American University, Washington, DC 20016, USA
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11
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Deo TG, Ferreira RCU, Lara LAC, Moraes ACL, Alves-Pereira A, de Oliveira FA, Garcia AAF, Santos MF, Jank L, de Souza AP. High-Resolution Linkage Map With Allele Dosage Allows the Identification of Regions Governing Complex Traits and Apospory in Guinea Grass ( Megathyrsus maximus). FRONTIERS IN PLANT SCIENCE 2020; 11:15. [PMID: 32161603 PMCID: PMC7054243 DOI: 10.3389/fpls.2020.00015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 01/08/2020] [Indexed: 05/11/2023]
Abstract
Forage grasses are mainly used in animal feed to fatten cattle and dairy herds, and guinea grass (Megathyrsus maximus) is considered one of the most productive of the tropical forage crops that reproduce by seeds. Due to the recent process of domestication, this species has several genomic complexities, such as autotetraploidy and aposporous apomixis. Consequently, approaches that relate phenotypic and genotypic data are incipient. In this context, we built a linkage map with allele dosage and generated novel information of the genetic architecture of traits that are important for the breeding of M. maximus. From a full-sib progeny, a linkage map containing 858 single nucleotide polymorphism (SNP) markers with allele dosage information expected for an autotetraploid was obtained. The high genetic variability of the progeny allowed us to map 10 quantitative trait loci (QTLs) related to agronomic traits, such as regrowth capacity and total dry matter, and 36 QTLs related to nutritional quality, which were distributed among all homology groups (HGs). Various overlapping regions associated with the quantitative traits suggested QTL hotspots. In addition, we were able to map one locus that controls apospory (apo-locus) in HG II. A total of 55 different gene families involved in cellular metabolism and plant growth were identified from markers adjacent to the QTLs and APOSPORY locus using the Panicum virgatum genome as a reference in comparisons with the genomes of Arabidopsis thaliana and Oryza sativa. Our results provide a better understanding of the genetic basis of reproduction by apomixis and traits important for breeding programs that considerably influence animal productivity as well as the quality of meat and milk.
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Affiliation(s)
- Thamiris G. Deo
- Center for Molecular Biology and Genetic Engineering, University of Campinas, Campinas, Brazil
| | - Rebecca C. U. Ferreira
- Center for Molecular Biology and Genetic Engineering, University of Campinas, Campinas, Brazil
| | - Letícia A. C. Lara
- Genetics Department, Escola Superior de Agricultura “Luiz de Queiroz,” University of São Paulo, Piracicaba, Brazil
| | - Aline C. L. Moraes
- Plant Biology Department, Biology Institute, University of Campinas, Campinas, Brazil
| | | | - Fernanda A. de Oliveira
- Center for Molecular Biology and Genetic Engineering, University of Campinas, Campinas, Brazil
| | - Antonio A. F. Garcia
- Genetics Department, Escola Superior de Agricultura “Luiz de Queiroz,” University of São Paulo, Piracicaba, Brazil
| | - Mateus F. Santos
- Embrapa Beef Cattle, Brazilian Agricultural Research Corporation, Campo Grande, Brazil
| | - Liana Jank
- Embrapa Beef Cattle, Brazilian Agricultural Research Corporation, Campo Grande, Brazil
| | - Anete P. de Souza
- Center for Molecular Biology and Genetic Engineering, University of Campinas, Campinas, Brazil
- Plant Biology Department, Biology Institute, University of Campinas, Campinas, Brazil
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Cappai F, Amadeu RR, Benevenuto J, Cullen R, Garcia A, Grossman A, Ferrão LFV, Munoz P. High-Resolution Linkage Map and QTL Analyses of Fruit Firmness in Autotetraploid Blueberry. FRONTIERS IN PLANT SCIENCE 2020; 11:562171. [PMID: 33304360 PMCID: PMC7701094 DOI: 10.3389/fpls.2020.562171] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 10/21/2020] [Indexed: 05/21/2023]
Abstract
Blueberry (Vaccinium corymbosum and hybrids) is an autotetraploid crop whose commercial relevance has been growing steadily during the last 20 years. However, the ever-increasing cost of labor for hand-picking blueberry is one main constraint in competitive marketing of the fruit. Machine harvestability is, therefore, a key trait for the blueberry industry. Understanding the genetic architecture of traits related to machine harvestability through Quantitative Trait Loci (QTL) mapping is the first step toward implementation of molecular breeding for faster genetic gains. Despite recent advances in software development for autotetraploid genetic mapping, a high-resolution map is still not available for blueberry. In this study, we crafted a map for autotetraploid low-chill highbush blueberry containing 11,292 SNP markers and a total size of 1,953.97 cM (average density of 5.78 markers/cM). This map was subsequently used to perform QTL analyses in 2-year field trials for a trait crucial to machine harvesting: fruit firmness. Preliminary insights were also sought for single evaluations of firmness retention after cold storage, and fruit detachment force traits. Significant QTL peaks were identified for all the traits and overlapping QTL intervals were detected for firmness across the years. We found low-to-moderate QTL effects explaining the phenotypic variance, which suggest a quantitative nature of these traits. The QTL intervals were further speculated for putative gene repertoire. Altogether, our findings provide the basis for future fine-mapping and molecular breeding efforts for machine harvesting in blueberry.
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Affiliation(s)
- Francesco Cappai
- Blueberry Breeding and Genomics Lab, Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Rodrigo R. Amadeu
- Blueberry Breeding and Genomics Lab, Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Juliana Benevenuto
- Blueberry Breeding and Genomics Lab, Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Ryan Cullen
- Blueberry Breeding and Genomics Lab, Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Alexandria Garcia
- Blueberry Breeding and Genomics Lab, Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Adina Grossman
- Forage Breeding and Genetics Lab, Agronomy Department, University of Florida, Gainesville, FL, United States
| | - Luís Felipe V. Ferrão
- Blueberry Breeding and Genomics Lab, Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Patricio Munoz
- Blueberry Breeding and Genomics Lab, Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
- *Correspondence: Patricio Munoz
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Matias FI, Xavier Meireles KG, Nagamatsu ST, Lima Barrios SC, Borges do Valle C, Carazzolle MF, Fritsche-Neto R, Endelman JB. Expected Genotype Quality and Diploidized Marker Data from Genotyping-by-Sequencing of Urochloa spp. Tetraploids. THE PLANT GENOME 2019; 12:1-9. [PMID: 33016594 DOI: 10.3835/plantgenome2019.01.0002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 04/29/2019] [Indexed: 05/08/2023]
Abstract
Introduced concept of expected genotype quality (EGQ) and software to calculate it Provided read depth guidelines for GBS in tetraploids Developed software to generate diploidized genotype calls from VCF files Demonstrated value of aligning GBS reads to a mock reference genome for SNP discovery Recommend filtering based on GQ and read depth to prevent genotype bias Although genotyping-by-sequencing (GBS) is a well-established marker technology in diploids, the development of best practices for tetraploid species is a topic of current research. We determined the theoretical relationship between read depth and the phred-scaled probability of genotype misclassification conditioned on the true genotype, which we call expected genotype quality (EGQ). If the GBS method has 0.5% allelic error, then 17 reads are needed to classify simplex tetraploids as heterozygous with 95% accuracy (EGQ = 13) vs. 61 reads to determine allele dosage. We developed an R script to convert tetraploid GBS data in variant call format (VCF) into diploidized genotype calls and applied it to 267 interspecific hybrids of the tetraploid forage grass Urochloa. When reads were aligned to a mock reference genome created from GBS data of the Urochloa brizantha (Hochst. ex A. Rich.) R. D. Webster cultivar Marandu, 25,678 biallelic single nucleotide polymorphism (SNPs) were discovered, compared with ∼3000 SNPs when aligning to the closest true reference genomes, Setaria viridis (L.) P. Beauv. and S. italica (L.) P. Beauv. Cross-validation revealed that missing genotypes were imputed by the random forest method with a median accuracy of 0.85 regardless of heterozygote frequency. Using the Urochloa spp. hybrids, we illustrated how filtering samples based only on genotype quality (GQ) creates genotype bias; a depth threshold based on EGQ is also needed regardless of whether genotypes are called using a diploidized or allele dosage model.
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Affiliation(s)
- Filipe Inácio Matias
- Genetics Dep., Luiz de Queiroz College of Agriculture, Univ. of São Paulo, Av. Pádua Dias, 11, C. P. 9, 13.418-900, Piracicaba, São Paulo, Brazil
| | | | - Sheila Tiemi Nagamatsu
- Genetics and Evolution Dep., Univ. of Campinas, Cidade Univ. Zeferino Vaz, 13.083-970, Campinas, São Paulo, Brazil
| | | | - Cacilda Borges do Valle
- Embrapa Beef Cattle, Av. Rádio Maia, 830, Zona Rural, 79.106-550, Campo Grande, Mato Grosso do Sul, Brazil
| | | | - Roberto Fritsche-Neto
- Genetics Dep., Luiz de Queiroz College of Agriculture, Univ. of São Paulo, Av. Pádua Dias, 11, C. P. 9, 13.418-900, Piracicaba, São Paulo, Brazil
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