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Minamikawa MF, Kunihisa M, Moriya S, Shimizu T, Inamori M, Iwata H. Genomic prediction and genome-wide association study using combined genotypic data from different genotyping systems: application to apple fruit quality traits. HORTICULTURE RESEARCH 2024; 11:uhae131. [PMID: 38979105 PMCID: PMC11228094 DOI: 10.1093/hr/uhae131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 04/25/2024] [Indexed: 07/10/2024]
Abstract
With advances in next-generation sequencing technologies, various marker genotyping systems have been developed for genomics-based approaches such as genomic selection (GS) and genome-wide association study (GWAS). As new genotyping platforms are developed, data from different genotyping platforms must be combined. However, the potential use of combined data for GS and GWAS has not yet been clarified. In this study, the accuracy of genomic prediction (GP) and the detection power of GWAS increased for most fruit quality traits of apples when using combined data from different genotyping systems, Illumina Infinium single-nucleotide polymorphism array and genotyping by random amplicon sequencing-direct (GRAS-Di) systems. In addition, the GP model, which considered the inbreeding effect, further improved the accuracy of the seven fruit traits. Runs of homozygosity (ROH) islands overlapped with the significantly associated regions detected by the GWAS for several fruit traits. Breeders may have exploited these regions to select promising apples by breeders, increasing homozygosity. These results suggest that combining genotypic data from different genotyping platforms benefits the GS and GWAS of fruit quality traits in apples. Information on inbreeding could be beneficial for improving the accuracy of GS for fruit traits of apples; however, further analysis is required to elucidate the relationship between the fruit traits and inbreeding depression (e.g. decreased vigor).
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Affiliation(s)
- Mai F Minamikawa
- Institute for Advanced Academic Research (IAAR), Chiba University, 1-33 Yayoi, Inage, Chiba, Chiba 263-8522, Japan
- Laboratory of Biometry and Bioinformatics, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Miyuki Kunihisa
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605, Japan
| | - Shigeki Moriya
- Institute of Fruit Tree and Tea Science, NARO, 92-24 Shimokuriyagawa Nabeyashiki, Morioka, Iwate 020-0123, Japan
| | - Tokurou Shimizu
- Institute of Fruit Tree and Tea Science, NARO, Okitsu Nakacho, Shimizu, Shizuoka 424-0292, Japan
| | - Minoru Inamori
- Laboratory of Biometry and Bioinformatics, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Hiroyoshi Iwata
- Laboratory of Biometry and Bioinformatics, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
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2
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Hiraoka Y, Ferrante SP, Wu GA, Federici CT, Roose ML. Development and Assessment of SNP Genotyping Arrays for Citrus and Its Close Relatives. PLANTS (BASEL, SWITZERLAND) 2024; 13:691. [PMID: 38475537 DOI: 10.3390/plants13050691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/13/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024]
Abstract
Rapid advancements in technologies provide various tools to analyze fruit crop genomes to better understand genetic diversity and relationships and aid in breeding. Genome-wide single nucleotide polymorphism (SNP) genotyping arrays offer highly multiplexed assays at a relatively low cost per data point. We report the development and validation of 1.4M SNP Axiom® Citrus HD Genotyping Array (Citrus 15AX 1 and Citrus 15AX 2) and 58K SNP Axiom® Citrus Genotyping Arrays for Citrus and close relatives. SNPs represented were chosen from a citrus variant discovery panel consisting of 41 diverse whole-genome re-sequenced accessions of Citrus and close relatives, including eight progenitor citrus species. SNPs chosen mainly target putative genic regions of the genome and are accurately called in both Citrus and its closely related genera while providing good coverage of the nuclear and chloroplast genomes. Reproducibility of the arrays was nearly 100%, with a large majority of the SNPs classified as the most stringent class of markers, "PolyHighResolution" (PHR) polymorphisms. Concordance between SNP calls in sequence data and array data average 98%. Phylogenies generated with array data were similar to those with comparable sequence data and little affected by 3 to 5% genotyping error. Both arrays are publicly available.
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Affiliation(s)
- Yoko Hiraoka
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Sergio Pietro Ferrante
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Guohong Albert Wu
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Claire T Federici
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Mikeal L Roose
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
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Kerr SC, Shehnaz S, Paudel L, Manivannan MS, Shaw LM, Johnson A, Velasquez JTJ, Tanurdžić M, Cazzonelli CI, Varkonyi-Gasic E, Prentis PJ. Advancing tree genomics to future proof next generation orchard production. FRONTIERS IN PLANT SCIENCE 2024; 14:1321555. [PMID: 38312357 PMCID: PMC10834703 DOI: 10.3389/fpls.2023.1321555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 12/26/2023] [Indexed: 02/06/2024]
Abstract
The challenges facing tree orchard production in the coming years will be largely driven by changes in the climate affecting the sustainability of farming practices in specific geographical regions. Identifying key traits that enable tree crops to modify their growth to varying environmental conditions and taking advantage of new crop improvement opportunities and technologies will ensure the tree crop industry remains viable and profitable into the future. In this review article we 1) outline climate and sustainability challenges relevant to horticultural tree crop industries, 2) describe key tree crop traits targeted for improvement in agroecosystem productivity and resilience to environmental change, and 3) discuss existing and emerging genomic technologies that provide opportunities for industries to future proof the next generation of orchards.
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Affiliation(s)
- Stephanie C Kerr
- School of Biology and Environmental Science, Queensland University of Technology (QUT), Brisbane, QLD, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Saiyara Shehnaz
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Lucky Paudel
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Mekaladevi S Manivannan
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Lindsay M Shaw
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
- School of Agriculture and Food Sustainability, The University of Queensland, Brisbane, QLD, Australia
| | - Amanda Johnson
- School of Biology and Environmental Science, Queensland University of Technology (QUT), Brisbane, QLD, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Jose Teodoro J Velasquez
- School of Biology and Environmental Science, Queensland University of Technology (QUT), Brisbane, QLD, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Miloš Tanurdžić
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | | | - Erika Varkonyi-Gasic
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Peter J Prentis
- School of Biology and Environmental Science, Queensland University of Technology (QUT), Brisbane, QLD, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, QLD, Australia
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Soto-Cerda BJ, Larama G, Cloutier S, Fofana B, Inostroza-Blancheteau C, Aravena G. The Genetic Dissection of Nitrogen Use-Related Traits in Flax ( Linum usitatissimum L.) at the Seedling Stage through the Integration of Multi-Locus GWAS, RNA-seq and Genomic Selection. Int J Mol Sci 2023; 24:17624. [PMID: 38139451 PMCID: PMC10743809 DOI: 10.3390/ijms242417624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/10/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Nitrogen (N), the most important macro-nutrient for plant growth and development, is a key factor that determines crop yield. Yet its excessive applications pollute the environment and are expensive. Hence, studying nitrogen use efficiency (NUE) in crops is fundamental for sustainable agriculture. Here, an association panel consisting of 123 flax accessions was evaluated for 21 NUE-related traits at the seedling stage under optimum N (N+) and N deficiency (N-) treatments to dissect the genetic architecture of NUE-related traits using a multi-omics approach integrating genome-wide association studies (GWAS), transcriptome analysis and genomic selection (GS). Root traits exhibited significant and positive correlations with NUE under N- conditions (r = 0.33 to 0.43, p < 0.05). A total of 359 QTLs were identified, accounting for 0.11% to 23.1% of the phenotypic variation in NUE-related traits. Transcriptomic analysis identified 1034 differentially expressed genes (DEGs) under contrasting N conditions. DEGs involved in N metabolism, root development, amino acid transport and catabolism and others, were found near the QTLs. GS models to predict NUE stress tolerance index (NUE_STI) trait were tested using a random genome-wide SNP dataset and a GWAS-derived QTLs dataset. The latter produced superior prediction accuracy (r = 0.62 to 0.79) compared to the genome-wide SNP marker dataset (r = 0.11) for NUE_STI. Our results provide insights into the QTL architecture of NUE-related traits, identify candidate genes for further studies, and propose genomic breeding tools to achieve superior NUE in flax under low N input.
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Affiliation(s)
- Braulio J. Soto-Cerda
- Departamento de Ciencias Agropecuarias y Acuícolas, Universidad Católica de Temuco, Rudecindo Ortega 02950, Temuco 4781312, Chile; (C.I.-B.); (G.A.)
- Núcleo de Investigación en Producción Alimentaria, Facultad de Recursos Naturales, Universidad Católica de Temuco, Rudecindo Ortega 02950, Temuco 4781312, Chile
| | - Giovanni Larama
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile;
- Biocontrol Research Laboratory, Universidad de La Frontera, Temuco 4811230, Chile
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada;
| | - Bourlaye Fofana
- Charlottetown Research and Development Centre, Agriculture and Agri-Food Canada, 440 University Avenue, Charlottetown, PE C1A 4N6, Canada
| | - Claudio Inostroza-Blancheteau
- Departamento de Ciencias Agropecuarias y Acuícolas, Universidad Católica de Temuco, Rudecindo Ortega 02950, Temuco 4781312, Chile; (C.I.-B.); (G.A.)
- Núcleo de Investigación en Producción Alimentaria, Facultad de Recursos Naturales, Universidad Católica de Temuco, Rudecindo Ortega 02950, Temuco 4781312, Chile
| | - Gabriela Aravena
- Departamento de Ciencias Agropecuarias y Acuícolas, Universidad Católica de Temuco, Rudecindo Ortega 02950, Temuco 4781312, Chile; (C.I.-B.); (G.A.)
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Magon G, De Rosa V, Martina M, Falchi R, Acquadro A, Barcaccia G, Portis E, Vannozzi A, De Paoli E. Boosting grapevine breeding for climate-smart viticulture: from genetic resources to predictive genomics. FRONTIERS IN PLANT SCIENCE 2023; 14:1293186. [PMID: 38148866 PMCID: PMC10750425 DOI: 10.3389/fpls.2023.1293186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 11/27/2023] [Indexed: 12/28/2023]
Abstract
The multifaceted nature of climate change is increasing the urgency to select resilient grapevine varieties, or generate new, fitter cultivars, to withstand a multitude of new challenging conditions. The attainment of this goal is hindered by the limiting pace of traditional breeding approaches, which require decades to result in new selections. On the other hand, marker-assisted breeding has proved useful when it comes to traits governed by one or few genes with great effects on the phenotype, but its efficacy is still restricted for complex traits controlled by many loci. On these premises, innovative strategies are emerging which could help guide selection, taking advantage of the genetic diversity within the Vitis genus in its entirety. Multiple germplasm collections are also available as a source of genetic material for the introgression of alleles of interest via adapted and pioneering transformation protocols, which present themselves as promising tools for future applications on a notably recalcitrant species such as grapevine. Genome editing intersects both these strategies, not only by being an alternative to obtain focused changes in a relatively rapid way, but also by supporting a fine-tuning of new genotypes developed with other methods. A review on the state of the art concerning the available genetic resources and the possibilities of use of innovative techniques in aid of selection is presented here to support the production of climate-smart grapevine genotypes.
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Affiliation(s)
- Gabriele Magon
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padova, Agripolis, Viale dell’Università 16, Legnaro, Italy
| | - Valeria De Rosa
- Department of Agricultural, Food, Environmental and Animal Sciences (DI4A), University of Udine, Via delle Scienze, 206, Udine, Italy
| | - Matteo Martina
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Largo P. Braccini 2, Grugliasco, Italy
| | - Rachele Falchi
- Department of Agricultural, Food, Environmental and Animal Sciences (DI4A), University of Udine, Via delle Scienze, 206, Udine, Italy
| | - Alberto Acquadro
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Largo P. Braccini 2, Grugliasco, Italy
| | - Gianni Barcaccia
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padova, Agripolis, Viale dell’Università 16, Legnaro, Italy
| | - Ezio Portis
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Largo P. Braccini 2, Grugliasco, Italy
| | - Alessandro Vannozzi
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padova, Agripolis, Viale dell’Università 16, Legnaro, Italy
| | - Emanuele De Paoli
- Department of Agricultural, Food, Environmental and Animal Sciences (DI4A), University of Udine, Via delle Scienze, 206, Udine, Italy
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6
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Numaguchi K, Kitamura Y, Kashiwamoto T, Morimoto T, Oe T. Genomic region and origin for selected traits during differentiation of small-fruit cultivars in Japanese apricot (Prunus mume). Mol Genet Genomics 2023; 298:1365-1375. [PMID: 37632570 DOI: 10.1007/s00438-023-02062-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/14/2023] [Indexed: 08/28/2023]
Abstract
The Japanese apricot (Prunus mume) is a popular fruit tree in Japan. However, the genetic factors associated with fruit trait variations are poorly understood. In this study, we investigated nine fruit-associated traits, including harvesting time, fruit diameter, fruit shape, fruit weight, stone (endocarp) weight, ratio of stone weight to fruit weight, and rate of fruit gumming, using 110 Japanese apricot accessions over four years. A genome-wide association study (GWAS) was performed for these traits and strong signals were detected on chromosome 6 for harvesting time and fruit diameters. These peaks were shown to undergo strong artificial selection during the differentiation of small-fruit cultivars. The genomic region defined by the GWAS and XP-nSL analyses harbored several candidate genes associated with plant hormone regulation. Furthermore, the alleles of small-fruit cultivars in this region were shown to have genetic proximity to some Chinese cultivars of P. mume. These results indicate that the small-fruit trait originated in China; after being introduced into Japan, it was preferred and selected by the Japanese people, resulting in the differentiation of small-fruit cultivars.
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Affiliation(s)
- Koji Numaguchi
- Japanese Apricot Laboratory, Wakayama Fruit Tree Experiment Station, 1416-7 Higashi-Honjo, Minabe-cho, Hidaka-gun, Wakayama, 645-0021, Japan.
- Wakayama Fruit Tree Experiment Station, 751-1, Oki, Aridagawa-cho, Arida-gun, Wakayama, 643-0022, Japan.
| | - Yuto Kitamura
- Japanese Apricot Laboratory, Wakayama Fruit Tree Experiment Station, 1416-7 Higashi-Honjo, Minabe-cho, Hidaka-gun, Wakayama, 645-0021, Japan
- Faculty of Agriculture, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, Osaka, 573-0101, Japan
| | - Tomoaki Kashiwamoto
- Japanese Apricot Laboratory, Wakayama Fruit Tree Experiment Station, 1416-7 Higashi-Honjo, Minabe-cho, Hidaka-gun, Wakayama, 645-0021, Japan
| | - Takuya Morimoto
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 74 Kitainayazuma, Seika-cho, Soraku-gun, Kyoto, 619-0244, Japan
| | - Takaaki Oe
- Japanese Apricot Laboratory, Wakayama Fruit Tree Experiment Station, 1416-7 Higashi-Honjo, Minabe-cho, Hidaka-gun, Wakayama, 645-0021, Japan
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Singh J, Sharma A, Sharma V, Gaikwad PN, Sidhu GS, Kaur G, Kaur N, Jindal T, Chhuneja P, Rattanpal HS. Comprehensive genome-wide identification and transferability of chromosome-specific highly variable microsatellite markers from citrus species. Sci Rep 2023; 13:10919. [PMID: 37407627 DOI: 10.1038/s41598-023-37024-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 06/14/2023] [Indexed: 07/07/2023] Open
Abstract
Citrus species among the most important and widely consumed fruit in the world due to Vitamin C, essential oil glands, and flavonoids. Highly variable simple sequence repeats (SSR) markers are one of the most informative and versatile molecular markers used in perennial tree genetic research. SSR survey of Citrus sinensis and Citrus maxima were identified perfect SSRs spanning nine chromosomes. Furthermore, we categorized all SSR motifs into three major classes based on their tract lengths. We designed and validated a class I SSRs in the C. sinensis and C. maxima genome through electronic polymerase chain reaction (ePCR) and found 83.89% in C. sinensis and 78.52% in C. maxima SSRs producing a single amplicon. Then, we selected extremely variable SSRs (> 40 nt) from the ePCR-verified class I SSRs and in silico validated across seven draft genomes of citrus, which provided us a subset of 84.74% in C. sinensis and 77.53% in C. maxima highly polymorphic SSRs. Out of these, 129 primers were validated on 24 citrus genotypes through wet-lab experiment. We found 127 (98.45%) polymorphic HvSSRs on 24 genotypes. The utility of the developed HvSSRs was demonstrated by analysing genetic diversity of 181 citrus genotypes using 17 HvSSRs spanning nine citrus chromosomes and were divided into 11 main groups through 17 HvSSRs. These chromosome-specific SSRs will serve as a powerful genomic tool used for future QTL mapping, molecular breeding, investigation of population genetic diversity, comparative mapping, and evolutionary studies among citrus and other relative genera/species.
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Affiliation(s)
- Jagveer Singh
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India
- Department of Fruit Science, College of Horticulture & Forestry, Acharya Narendra Deva University of Agricultural & Technology, Kumarganj, 224229, India
| | - Ankush Sharma
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA
| | - Vishal Sharma
- National Agri-Food Biotechnology Institute, Sector-81, SAS Nagar, Mohali, Punjab, 140308, India
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, 173229, India
| | - Popat Nanaso Gaikwad
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India
| | - Gurupkar Singh Sidhu
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India.
| | - Gurwinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India
| | - Nimarpreet Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India
| | - Taveena Jindal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India
| | - H S Rattanpal
- Department of Fruit Science, Punjab Agricultural University, Ludhiana, 141004, India
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Li X, Wang J, Su M, Zhang M, Hu Y, Du J, Zhou H, Yang X, Zhang X, Jia H, Gao Z, Ye Z. Multiple-statistical genome-wide association analysis and genomic prediction of fruit aroma and agronomic traits in peaches. HORTICULTURE RESEARCH 2023; 10:uhad117. [PMID: 37577398 PMCID: PMC10419450 DOI: 10.1093/hr/uhad117] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 05/21/2023] [Indexed: 08/15/2023]
Abstract
'Chinese Cling' is an important founder in peach breeding history due to the pleasant flavor. Genome-wide association studies (GWAS) combined with genomic selection are promising tools in fruit tree breeding, as there is a considerable time lapse between crossing and release of a cultivar. In this study, 242 peaches from Shanghai germplasm were genotyped with 145 456 single-nucleotide polymorphisms (SNPs). The six agronomic traits of fruit flesh color, fruit shape, fruit hairiness, flower type, pollen sterility, and soluble solids content, along with 14 key volatile odor compounds (VOCs), were recorded for multiple-statistical GWAS. Except the reported candidate genes, six novel genes were identified as associated with these traits. Thirty-nine significant SNPs were associated with eight VOCs. The putative candidate genes were confirmed for VOCs by RNA-seq, including three genes in the biosynthesis pathway found to be associated with linalool, soluble solids content, and cis-3-hexenyl acetate. Multiple-trait genomic prediction enhanced the predictive ability for γ-decalactone to 0.7415 compared with the single-trait model value of 0.1017. One PTS1-SSR marker was designed to predict the linalool content, and the favorable genotype 187/187 was confirmed, mainly existing in the 'Shanghai Shuimi' landrace. Overall, our findings will be helpful in determining peach accessions with the ideal phenotype and show the potential of multiple-trait genomic prediction to improve accuracy for highly correlated genetic traits. The diagnostic marker will be valuable for the breeder to bridge the gap between quantitative trait loci and marker-assisted selection for developing strong-aroma cultivars.
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Affiliation(s)
- Xiongwei Li
- Peach Research Department of Forest & Fruit Tree Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Jiabo Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization (Southwest Minzu University, Ministry of Education), Chengdu, Sichuan 610041, China
| | - Mingshen Su
- Peach Research Department of Forest & Fruit Tree Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Minghao Zhang
- Peach Research Department of Forest & Fruit Tree Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Yang Hu
- Peach Research Department of Forest & Fruit Tree Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Jihong Du
- Peach Research Department of Forest & Fruit Tree Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Huijuan Zhou
- Peach Research Department of Forest & Fruit Tree Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Xiaofeng Yang
- Peach Group of Shanghai Runzhuang Agricultural Science and Technology Institute, Shanghai 201415, China
| | - Xianan Zhang
- Peach Research Department of Forest & Fruit Tree Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Huijuan Jia
- Department of Horticulture, Key Laboratory for Horticultural Plant Growth, Development and Quality Improvement of State Agriculture Ministry, Zhejiang Unihversity, Hangzhou 310058, China
| | - Zhongshan Gao
- Department of Horticulture, Key Laboratory for Horticultural Plant Growth, Development and Quality Improvement of State Agriculture Ministry, Zhejiang Unihversity, Hangzhou 310058, China
| | - Zhengwen Ye
- Peach Research Department of Forest & Fruit Tree Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
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9
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Gao Y, Xu J, Li Z, Zhang Y, Riera N, Xiong Z, Ouyang Z, Liu X, Lu Z, Seymour D, Zhong B, Wang N. Citrus genomic resources unravel putative genetic determinants of Huanglongbing pathogenicity. iScience 2023; 26:106024. [PMID: 36824272 PMCID: PMC9941208 DOI: 10.1016/j.isci.2023.106024] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 11/08/2022] [Accepted: 01/17/2023] [Indexed: 01/24/2023] Open
Abstract
Citrus HLB caused by Candidatus Liberibacter asiaticus is a pathogen-triggered immune disease. Here, we identified putative genetic determinants of HLB pathogenicity by integrating citrus genomic resources to characterize the pan-genome of accessions that differ in their response to HLB. Genome-wide association mapping and analysis of allele-specific expression between susceptible, tolerant, and resistant accessions further refined candidates underlying the response to HLB. We first developed a phased diploid assembly of Citrus sinensis 'Newhall' genome and produced resequencing data for 91 citrus accessions that differ in their response to HLB. These data were combined with previous resequencing data from 356 accessions for genome-wide association mapping of the HLB response. Genes determinants for HLB pathogenicity were associated with host immune response, ROS production, and antioxidants. Overall, this study has provided a significant resource of citrus genomic data and identified candidate genes to be further explored to understand the genetic determinants of HLB pathogenicity.
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Affiliation(s)
- Yuxia Gao
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Jin Xu
- Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, FL, USA
| | - Zhilong Li
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Yunzeng Zhang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, FL, USA
| | - Nadia Riera
- Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, FL, USA
| | - Zhiwei Xiong
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Zhigang Ouyang
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Xinjun Liu
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Zhanjun Lu
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, China
| | | | - Balian Zhong
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, FL, USA
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10
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Bowman KD, McCollum G, Seymour DK. Genetic modulation of Valencia sweet orange field performance by 50 rootstocks under huanglongbing-endemic conditions. FRONTIERS IN PLANT SCIENCE 2023; 14:1061663. [PMID: 36844073 PMCID: PMC9945190 DOI: 10.3389/fpls.2023.1061663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Although the citrus scion cultivar primarily determines the characteristics of the fruit, the rootstock cultivar of the graft combination has a major role in determining the horticultural performance of the tree. The disease huanglongbing (HLB) is particularly devastating to citrus, and the rootstock has been demonstrated to modulate tree tolerance. However, no existing rootstock is entirely suitable in the HLB-endemic environment, and citrus rootstocks are particularly challenging to breed because of a long life cycle and several biological characteristics that interfere with breeding and commercial use. This study with Valencia sweet orange scion documents the multi-season performance of 50 new hybrid rootstocks and commercial standards in one trial that forms the first wave of a new breeding strategy, with the aim of identifying superior rootstocks for commercial use now, and mapping important traits to be used in selection for the next generation of outstanding rootstocks. A large assortment of traits were quantified for all trees in the study, including traits associated with tree size, health, cropping, and fruit quality. Among the quantitative traits compared between rootstock clones, all except one were observed to have significant rootstock influence. Multiple progeny from eight different parental combinations were included in the trial study, and significant differences between parental combinations of the rootstocks were observed for 27 of the 32 traits compared. Pedigree information was integrated with quantitative trait measurements to dissect the genetic components of rootstock-mediated tree performance. Results suggest there is a significant genetic component underlying rootstock-mediated tolerance to HLB and other critical traits, and that integration of pedigree-based genetic information with quantitative phenotypic data from trials should enable marker-based breeding approaches for the rapid selection of next-generation rootstocks with superior combinations of traits that are needed for commercial success. The current generation of new rootstocks included in this trial is a step toward this goal. Based on results from this trial, the new hybrids US-1649, US-1688, US-1709, and US-2338 were considered the four most promising new rootstocks. Release of these rootstocks for commercial use is being considered, pending the evaluation of continuing performance in this trial and the results from other trials.
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Affiliation(s)
- Kim D. Bowman
- U.S. Horticultural Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Ft. Pierce, FL, United States
| | - Greg McCollum
- U.S. Horticultural Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Ft. Pierce, FL, United States
| | - Danelle K. Seymour
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
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11
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Moret M, Ramírez-Tejero JA, Serrano A, Ramírez-Yera E, Cueva-López MD, Belaj A, León L, de la Rosa R, Bombarely A, Luque F. Identification of Genetic Markers and Genes Putatively Involved in Determining Olive Fruit Weight. PLANTS (BASEL, SWITZERLAND) 2022; 12:155. [PMID: 36616284 PMCID: PMC9823435 DOI: 10.3390/plants12010155] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
The fruit size of a cultivated olive tree is consistently larger than its corresponding wild relatives because fruit size is one of the main traits associated with olive tree domestication. Additionally, large fruit size is one of the main objectives of modern olive breeding programs. However, as the long juvenile period is one main hindrance in classic breeding approaches, obtaining genetic markers associated with this trait is a highly desirable tool. For this reason, GWAS analysis of both genetic markers and the genes associated with fruit size determination, measured as fruit weight, was herein carried out in 50 genotypes, of which 40 corresponded to cultivated and 10 to wild olive trees. As a result, 113 genetic markers were identified, which showed a very high statistically significant correlation with fruit weight variability, p < 10−10. These genetic markers corresponded to 39 clusters of genes in linkage disequilibrium. The analysis of a segregating progeny of the cross of “Frantoio” and “Picual” cultivars allowed us to confirm 10 of the 18 analyzed clusters. The annotation of the genes in each cluster and the expression pattern of the samples taken throughout fruit development by RNAseq enabled us to suggest that some studied genes are involved in olive fruit weight determination.
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Affiliation(s)
- Martín Moret
- Departamento de Biología Experimental, Instituto Universitario de Investigación en Olivar y Aceites de Oliva, Universidad de Jaén, 23071 Jaén, Spain
| | - Jorge A. Ramírez-Tejero
- Departamento de Biología Experimental, Instituto Universitario de Investigación en Olivar y Aceites de Oliva, Universidad de Jaén, 23071 Jaén, Spain
| | - Alicia Serrano
- Departamento de Biología Experimental, Instituto Universitario de Investigación en Olivar y Aceites de Oliva, Universidad de Jaén, 23071 Jaén, Spain
| | - Elena Ramírez-Yera
- Departamento de Biología Experimental, Instituto Universitario de Investigación en Olivar y Aceites de Oliva, Universidad de Jaén, 23071 Jaén, Spain
| | - María D. Cueva-López
- Departamento de Biología Experimental, Instituto Universitario de Investigación en Olivar y Aceites de Oliva, Universidad de Jaén, 23071 Jaén, Spain
| | - Angjelina Belaj
- Centro de Investigación y Formación Agraria de Alameda del Obispo, Instituto de Investigación y Formación Agraria y Pesquera (IFAPA), 14004 Córdoba, Spain
| | - Lorenzo León
- Centro de Investigación y Formación Agraria de Alameda del Obispo, Instituto de Investigación y Formación Agraria y Pesquera (IFAPA), 14004 Córdoba, Spain
| | - Raúl de la Rosa
- Centro de Investigación y Formación Agraria de Alameda del Obispo, Instituto de Investigación y Formación Agraria y Pesquera (IFAPA), 14004 Córdoba, Spain
| | - Aureliano Bombarely
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC and Universitat Politécnica de Valencia, 46011 Valencia, Spain
| | - Francisco Luque
- Departamento de Biología Experimental, Instituto Universitario de Investigación en Olivar y Aceites de Oliva, Universidad de Jaén, 23071 Jaén, Spain
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12
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Seyum EG, Bille NH, Abtew WG, Munyengwa N, Bell JM, Cros D. Genomic selection in tropical perennial crops and plantation trees: a review. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:58. [PMID: 37313015 PMCID: PMC10248687 DOI: 10.1007/s11032-022-01326-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 09/06/2022] [Indexed: 06/15/2023]
Abstract
To overcome the multiple challenges currently faced by agriculture, such as climate change and soil deterioration, more efficient plant breeding strategies are required. Genomic selection (GS) is crucial for the genetic improvement of quantitative traits, as it can increase selection intensity, shorten the generation interval, and improve selection accuracy for traits that are difficult to phenotype. Tropical perennial crops and plantation trees are of major economic importance and have consequently been the subject of many GS articles. In this review, we discuss the factors that affect GS accuracy (statistical models, linkage disequilibrium, information concerning markers, relatedness between training and target populations, the size of the training population, and trait heritability) and the genetic gain expected in these species. The impact of GS will be particularly strong in tropical perennial crops and plantation trees as they have long breeding cycles and constrained selection intensity. Future GS prospects are also discussed. High-throughput phenotyping will allow constructing of large training populations and implementing of phenomic selection. Optimized modeling is needed for longitudinal traits and multi-environment trials. The use of multi-omics, haploblocks, and structural variants will enable going beyond single-locus genotype data. Innovative statistical approaches, like artificial neural networks, are expected to efficiently handle the increasing amounts of heterogeneous multi-scale data. Targeted recombinations on sites identified from profiles of marker effects have the potential to further increase genetic gain. GS can also aid re-domestication and introgression breeding. Finally, GS consortia will play an important role in making the best of these opportunities. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01326-4.
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Affiliation(s)
- Essubalew Getachew Seyum
- Department of Plant Biology and Physiology, Faculty of Sciences, University of Yaoundé I, Yaoundé, Cameroon
- Department of Horticulture and Plant Sciences, College of Agriculture and Veterinary Medicine, Jimma University, P.O. Box 307, Jimma, Ethiopia
| | - Ngalle Hermine Bille
- Department of Plant Biology and Physiology, Faculty of Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | - Wosene Gebreselassie Abtew
- Department of Horticulture and Plant Sciences, College of Agriculture and Veterinary Medicine, Jimma University, P.O. Box 307, Jimma, Ethiopia
| | - Norman Munyengwa
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072 Australia
| | - Joseph Martin Bell
- Department of Plant Biology and Physiology, Faculty of Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | - David Cros
- CIRAD, UMR AGAP Institut, 34398 Montpellier, France
- UMR AGAP Institut, CIRAD, INRAE, Univ. Montpellier, Institut Agro, 34398 Montpellier, France
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13
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Noda T, Daiou K, Mihara T, Murakami H, Nagano Y. Efficient method for generating citrus hybrids with polyembryonic Satsuma mandarin as the female parent. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:51. [PMID: 37313420 PMCID: PMC10248698 DOI: 10.1007/s11032-022-01324-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 08/21/2022] [Indexed: 06/15/2023]
Abstract
Many citrus fruits have polyembryonic traits, and their seeds contain many nucellar embryos along with a single zygotic embryo, affecting the crossbreeding process. Generally, nucellar embryos are considered to have more vigorous growth than zygotic embryos. Therefore, the in vitro method using an embryo rescue culture is often chosen to obtain zygotic embryo-derived individuals. Nevertheless, hybrids can be obtained with a certain probability from the seeds sown in the soil. The in-soil method, which sows seeds in the soil, has distinct advantages over the in vitro method, including lower cost and simpler technology. However, the efficiency of obtaining hybrids from these methods has not been compared in detail. The current study evaluates the effectiveness of these methods for obtaining hybrids using polyembryonic Satsuma mandarin as the female parent. The number of mature embryos per seed using the in-soil method was less than one-third of that produced using the in vitro method. Although the in vitro method produced more hybrids than the in-soil method, the ratio of the hybrids to the resulting population was significantly higher in the in-soil method. Thus, the in-soil method was more efficient and practical than the in vitro method for selecting hybrids from polyembryonic Satsuma mandarin seeds. The observations of the individuals obtained using the in-soil method suggest that zygotic embryos were not poorer in growth than nucellar embryos when using our selected parental combinations. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01324-6.
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Affiliation(s)
- Takahiro Noda
- Kumamoto Prefectural Agricultural Research Center, 3801, Sakae, Koshi-shi, Kumamoto, 861-1113 Japan
| | - Kaoru Daiou
- Kumamoto Prefectural Agriculture College, 3805, Sakae, Koshi-shi, Kumamoto, 861-1113 Japan
| | - Takashi Mihara
- Agriculture and Horticulture Division, Kumamoto Prefectural Government, 6-18-1, Suizenji, Chuo-ku, Kumamoto-shi, Kumamoto, 862-8570 Japan
| | - Hisao Murakami
- Kumamoto Prefectural Agricultural Research Center, 3801, Sakae, Koshi-shi, Kumamoto, 861-1113 Japan
| | - Yukio Nagano
- Analytical Research Center for Experimental Sciences, Saga University, 1 Honjo-machi, Saga, 840-8502 Japan
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14
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Cheng W, Ramachandran S, Crawford L. Uncertainty quantification in variable selection for genetic fine-mapping using bayesian neural networks. iScience 2022; 25:104553. [PMID: 35769876 PMCID: PMC9234235 DOI: 10.1016/j.isci.2022.104553] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/09/2022] [Accepted: 06/01/2022] [Indexed: 02/07/2023] Open
Abstract
In this paper, we propose a new approach for variable selection using a collection of Bayesian neural networks with a focus on quantifying uncertainty over which variables are selected. Motivated by fine-mapping applications in statistical genetics, we refer to our framework as an "ensemble of single-effect neural networks" (ESNN) which generalizes the "sum of single effects" regression framework by both accounting for nonlinear structure in genotypic data (e.g., dominance effects) and having the capability to model discrete phenotypes (e.g., case-control studies). Through extensive simulations, we demonstrate our method's ability to produce calibrated posterior summaries such as credible sets and posterior inclusion probabilities, particularly for traits with genetic architectures that have significant proportions of non-additive variation driven by correlated variants. Lastly, we use real data to demonstrate that the ESNN framework improves upon the state of the art for identifying true effect variables underlying various complex traits.
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Affiliation(s)
- Wei Cheng
- Department of Computer Science, Brown University, Providence, RI, USA.,Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, USA.,Center for Computational Molecular Biology, Brown University, Providence, RI, USA
| | - Sohini Ramachandran
- Department of Computer Science, Brown University, Providence, RI, USA.,Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, USA.,Center for Computational Molecular Biology, Brown University, Providence, RI, USA
| | - Lorin Crawford
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA.,Department of Biostatistics, Brown University, Providence, RI, USA.,Microsoft Research New England, Cambridge, MA, USA
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15
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Flutre T, Le Cunff L, Fodor A, Launay A, Romieu C, Berger G, Bertrand Y, Terrier N, Beccavin I, Bouckenooghe V, Roques M, Pinasseau L, Verbaere A, Sommerer N, Cheynier V, Bacilieri R, Boursiquot JM, Lacombe T, Laucou V, This P, Péros JP, Doligez A. A genome-wide association and prediction study in grapevine deciphers the genetic architecture of multiple traits and identifies genes under many new QTLs. G3 (BETHESDA, MD.) 2022; 12:6575896. [PMID: 35485948 PMCID: PMC9258538 DOI: 10.1093/g3journal/jkac103] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/21/2022] [Indexed: 12/11/2022]
Abstract
To cope with the challenges facing agriculture, speeding-up breeding programs is a worthy endeavor, especially for perennial species such as grapevine, but requires understanding the genetic architecture of target traits. To go beyond the mapping of quantitative trait loci in bi-parental crosses, we exploited a diversity panel of 279 Vitis vinifera L. cultivars planted in 5 blocks in the vineyard. This panel was phenotyped over several years for 127 traits including yield components, organic acids, aroma precursors, polyphenols, and a water stress indicator. The panel was genotyped for 63k single nucleotide polymorphisms by combining an 18K microarray and genotyping-by-sequencing. The experimental design allowed to reliably assess the genotypic values for most traits. Marker densification via genotyping-by-sequencing markedly increased the proportion of genetic variance explained by single nucleotide polymorphisms, and 2 multi-single nucleotide polymorphism models identified quantitative trait loci not found by a single nucleotide polymorphism-by-single nucleotide polymorphism model. Overall, 489 reliable quantitative trait loci were detected for 41% more response variables than by a single nucleotide polymorphism-by-single nucleotide polymorphism model with microarray-only single nucleotide polymorphisms, many new ones compared with the results from bi-parental crosses. A prediction accuracy higher than 0.42 was obtained for 50% of the response variables. Our overall approach as well as quantitative trait locus and prediction results provide insights into the genetic architecture of target traits. New candidate genes and the application into breeding are discussed.
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Affiliation(s)
- Timothée Flutre
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France.,Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, 91190 Gif-sur-Yvette, France
| | - Loïc Le Cunff
- UMT Géno-Vigne, 34398 Montpellier, France.,IFV, 30240 Le Grau-du-Roi, France
| | - Agota Fodor
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Amandine Launay
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Charles Romieu
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Gilles Berger
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Yves Bertrand
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Nancy Terrier
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France
| | | | | | - Maryline Roques
- UMT Géno-Vigne, 34398 Montpellier, France.,IFV, 30240 Le Grau-du-Roi, France
| | - Lucie Pinasseau
- SPO, Univ Montpellier, INRAE, Institut Agro, 34060 Montpellier, France
| | - Arnaud Verbaere
- SPO, Univ Montpellier, INRAE, Institut Agro, 34060 Montpellier, France
| | - Nicolas Sommerer
- SPO, Univ Montpellier, INRAE, Institut Agro, 34060 Montpellier, France
| | | | - Roberto Bacilieri
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Jean-Michel Boursiquot
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Thierry Lacombe
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Valérie Laucou
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Patrice This
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Jean-Pierre Péros
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Agnès Doligez
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
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16
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Shen F, Bianco L, Wu B, Tian Z, Wang Y, Wu T, Xu X, Han Z, Velasco R, Fontana P, Zhang X. A bulked segregant analysis tool for out-crossing species (BSATOS) and QTL-based genomics-assisted prediction of complex traits in apple. J Adv Res 2022; 42:149-162. [PMID: 36513410 PMCID: PMC9788957 DOI: 10.1016/j.jare.2022.03.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/06/2022] [Accepted: 03/22/2022] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION Genomic heterozygosity, self-incompatibility, and rich-in somatic mutations hinder the molecular breeding efficiency of outcrossing plants. OBJECTIVES We attempted to develop an efficient integrated strategy to identify quantitative trait loci (QTLs) and trait-associated genes, to develop gene markers, and to construct genomics-assisted prediction (GAP) modes. METHODS A novel protocol, bulked segregant analysis tool for out-crossing species (BSATOS), is presented here, which is characterized by taking full advantage of all segregation patterns (including AB × AB markers) and haplotype information. To verify the effectiveness of the protocol in dealing with the complex traits of outbreeding species, three apple cross populations with 9,654 individuals were adopted. RESULTS By using BSATOS, 90, 60, and 77 significant QTLs were identified successfully and candidate genes were predicted for apple fruit weight (FW), fruit ripening date (FRD), and fruit soluble solid content (SSC), respectively. The gene-based markers were developed and genotyped for 1,396 individuals in a training population, including 145 Malus accessions and 1,251 F1 plants of the three full-sib families. GAP models were trained using marker genotype effect estimates of the training population. The prediction accuracy was 0.7658, 0.6455, and 0.3758 for FW, FRD, and SSC, respectively. CONCLUSION The BSATOS and GAP models provided a convenient and efficient methodology for candidate gene mining and molecular breeding in out-crossing plant species. The BSATOS pipeline can be freely downloaded from: https://github.com/maypoleflyn/BSATOS.
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Affiliation(s)
- Fei Shen
- College of Horticulture, China Agricultural University, Beijing 100193, China,Research and Innovation Center, Edmund Mach Foundation, 38010 S. Michele all’Adige, Italy,Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Luca Bianco
- Research and Innovation Center, Edmund Mach Foundation, 38010 S. Michele all’Adige, Italy
| | - Bei Wu
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Zhendong Tian
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Yi Wang
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Ting Wu
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Xuefeng Xu
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Zhenhai Han
- College of Horticulture, China Agricultural University, Beijing 100193, China,Corresponding authors.
| | - Riccardo Velasco
- Research Centre for Viticulture and Enology, CREA, Conegliano, Italy
| | - Paolo Fontana
- Research and Innovation Center, Edmund Mach Foundation, 38010 S. Michele all’Adige, Italy,Corresponding authors.
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, Beijing 100193, China,Corresponding authors.
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17
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Borredá C, Perez-Roman E, Talon M, Terol J. Comparative transcriptomics of wild and commercial Citrus during early ripening reveals how domestication shaped fruit gene expression. BMC PLANT BIOLOGY 2022; 22:123. [PMID: 35300613 PMCID: PMC8928680 DOI: 10.1186/s12870-022-03509-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/03/2022] [Indexed: 05/03/2023]
Abstract
BACKGROUND Interspecific hybridizations and admixtures were key in Citrus domestication, but very little is known about their impact at the transcriptomic level. To determine the effects of genome introgressions on gene expression, the transcriptomes of the pulp and flavedo of three pure species (citron, pure mandarin and pummelo) and four derived domesticated genetic admixtures (sour orange, sweet orange, lemon and domesticated mandarin) have been analyzed at color break. RESULTS Many genes involved in relevant physiological processes for domestication, such sugar/acid metabolism and carotenoid/flavonoid synthesis, were differentially expressed among samples. In the low-sugar, highly acidic species lemon and citron, many genes involved in sugar metabolism, the TCA cycle and GABA shunt displayed a reduced expression, while the P-type ATPase CitPH5 and most subunits of the vacuolar ATPase were overexpressed. The red-colored species and admixtures were generally characterized by the overexpression in the flavedo of specific pivotal genes involved in the carotenoid biosynthesis, including phytoene synthase, ζ-carotene desaturase, β-lycopene cyclase and CCD4b, a carotenoid cleavage dioxygenase. The expression patterns of many genes involved in flavonoid modifications, especially the flavonoid and phenylpropanoid O-methyltransferases showed extreme diversity. However, the most noticeable differential expression was shown by a chalcone synthase gene, which catalyzes a key step in the biosynthesis of flavonoids. This chalcone synthase was exclusively expressed in mandarins and their admixed species, which only expressed the mandarin allele. In addition, comparisons between wild and domesticated mandarins revealed that the major differences between their transcriptomes concentrate in the admixed regions. CONCLUSION In this work we present a first study providing broad evidence that the genome introgressions that took place during citrus domestication largely shaped gene expression in their fruits.
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Affiliation(s)
- Carles Borredá
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113, Moncada, Valencia, Spain
| | - Estela Perez-Roman
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113, Moncada, Valencia, Spain
| | - Manuel Talon
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113, Moncada, Valencia, Spain
| | - Javier Terol
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113, Moncada, Valencia, Spain.
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18
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Metabolic Profiling of Organic Acids Reveals the Involvement of HuIPMS2 in Citramalic Acid Synthesis in Pitaya. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8020167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Pitayas are rich in organic acids, especially citramalic acid, which is significantly higher than the plants. However, the mechanism of citramalic acid biosynthesis remains to be fully elucidated. In this study, organic acid compositions and contents, as well as expression patterns of key genes related to organic acid metabolism were analyzed during fruit maturation of four different pitaya cultivars i.e., ‘Guanhuabai’ (GHB), ‘Guanhuahong’ (GHH), ‘Wucihuanglong’ (WCHL), and ‘Youcihuanglong’ (YCHL). The total organic acid contents increased first and then declined during fruit maturation. The main organic acids were citramalic acid during the early stages of GHB, GHH, and WCHL pitayas, and dominated by malic acid as fruit maturation. In comparison, citric acid and malic acid were main organic acid for ‘YCHL’ pitaya. Citramalate synthase (IPMS) was involved in the synthesis of citramalic acid, and three types of HuIPMS i.e., HuIPMS1, HuIPMS2, and HuIPMS3, were obtained in our study. Highest expression levels of HuIPMS1 were detected in sepals, while HuIPMS2 and HuIPMS3 exhibited preferential expression in tender stems and ovaries. The expression levels of HuIPMS2 and HuIPMS3 were positively correlated with the content of citramalic acid in the four pitaya cultivars. HuIPMS2 was a chloroplast-localized protein, while HuIPMS3 presented a cytoplasmic-like and nuclear subcellular localization. These findings provide an important basis for further understanding of the molecular mechanism that leads to citramalic acid metabolism during pitaya fruit maturation.
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19
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Minamikawa MF, Nonaka K, Hamada H, Shimizu T, Iwata H. Dissecting Breeders' Sense via Explainable Machine Learning Approach: Application to Fruit Peelability and Hardness in Citrus. FRONTIERS IN PLANT SCIENCE 2022; 13:832749. [PMID: 35222489 PMCID: PMC8867066 DOI: 10.3389/fpls.2022.832749] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
"Genomics-assisted breeding", which utilizes genomics-based methods, e.g., genome-wide association study (GWAS) and genomic selection (GS), has been attracting attention, especially in the field of fruit breeding. Low-cost genotyping technologies that support genome-assisted breeding have already been established. However, efficient collection of large amounts of high-quality phenotypic data is essential for the success of such breeding. Most of the fruit quality traits have been sensorily and visually evaluated by professional breeders. However, the fruit morphological features that serve as the basis for such sensory and visual judgments are unclear. This makes it difficult to collect efficient phenotypic data on fruit quality traits using image analysis. In this study, we developed a method to automatically measure the morphological features of citrus fruits by the image analysis of cross-sectional images of citrus fruits. We applied explainable machine learning methods and Bayesian networks to determine the relationship between fruit morphological features and two sensorily evaluated fruit quality traits: easiness of peeling (Peeling) and fruit hardness (FruH). In each of all the methods applied in this study, the degradation area of the central core of the fruit was significantly and directly associated with both Peeling and FruH, while the seed area was significantly and directly related to FruH alone. The degradation area of albedo and the area of flavedo were also significantly and directly related to Peeling and FruH, respectively, except in one or two methods. These results suggest that an approach that combines explainable machine learning methods, Bayesian networks, and image analysis can be effective in dissecting the experienced sense of a breeder. In breeding programs, collecting fruit images and efficiently measuring and documenting fruit morphological features that are related to fruit quality traits may increase the size of data for the analysis and improvement of the accuracy of GWAS and GS on the quality traits of the citrus fruits.
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Affiliation(s)
- Mai F. Minamikawa
- Laboratory of Biometry and Bioinformatics, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Keisuke Nonaka
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), Shizuoka, Japan
| | - Hiroko Hamada
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), Shizuoka, Japan
| | - Tokurou Shimizu
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), Shizuoka, Japan
| | - Hiroyoshi Iwata
- Laboratory of Biometry and Bioinformatics, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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20
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Budhlakoti N, Kushwaha AK, Rai A, Chaturvedi KK, Kumar A, Pradhan AK, Kumar U, Kumar RR, Juliana P, Mishra DC, Kumar S. Genomic Selection: A Tool for Accelerating the Efficiency of Molecular Breeding for Development of Climate-Resilient Crops. Front Genet 2022; 13:832153. [PMID: 35222548 PMCID: PMC8864149 DOI: 10.3389/fgene.2022.832153] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 01/10/2022] [Indexed: 12/17/2022] Open
Abstract
Since the inception of the theory and conceptual framework of genomic selection (GS), extensive research has been done on evaluating its efficiency for utilization in crop improvement. Though, the marker-assisted selection has proven its potential for improvement of qualitative traits controlled by one to few genes with large effects. Its role in improving quantitative traits controlled by several genes with small effects is limited. In this regard, GS that utilizes genomic-estimated breeding values of individuals obtained from genome-wide markers to choose candidates for the next breeding cycle is a powerful approach to improve quantitative traits. In the last two decades, GS has been widely adopted in animal breeding programs globally because of its potential to improve selection accuracy, minimize phenotyping, reduce cycle time, and increase genetic gains. In addition, given the promising initial evaluation outcomes of GS for the improvement of yield, biotic and abiotic stress tolerance, and quality in cereal crops like wheat, maize, and rice, prospects of integrating it in breeding crops are also being explored. Improved statistical models that leverage the genomic information to increase the prediction accuracies are critical for the effectiveness of GS-enabled breeding programs. Study on genetic architecture under drought and heat stress helps in developing production markers that can significantly accelerate the development of stress-resilient crop varieties through GS. This review focuses on the transition from traditional selection methods to GS, underlying statistical methods and tools used for this purpose, current status of GS studies in crop plants, and perspectives for its successful implementation in the development of climate-resilient crops.
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Affiliation(s)
- Neeraj Budhlakoti
- ICAR- Indian Agricultural Statistics Research Institute, New Delhi, India
| | | | - Anil Rai
- ICAR- Indian Agricultural Statistics Research Institute, New Delhi, India
| | - K K Chaturvedi
- ICAR- Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Anuj Kumar
- ICAR- Indian Agricultural Statistics Research Institute, New Delhi, India
| | | | - Uttam Kumar
- Borlaug Institute for South Asia (BISA), Ludhiana, India
| | | | | | - D C Mishra
- ICAR- Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sundeep Kumar
- ICAR- National Bureau of Plant Genetic Resources, New Delhi, India
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21
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Mattia MR, Du D, Yu Q, Kahn T, Roose M, Hiraoka Y, Wang Y, Munoz P, Gmitter FG. Genome-Wide Association Study of Healthful Flavonoids among Diverse Mandarin Accessions. PLANTS 2022; 11:plants11030317. [PMID: 35161299 PMCID: PMC8839032 DOI: 10.3390/plants11030317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 11/16/2022]
Abstract
Mandarins have many unique flavonoids with documented health benefits and that help to prevent chronic human diseases. Flavonoids are difficult to measure and cannot be phenotyped without the use of specialized equipment; consequently, citrus breeders have not used flavonoid contents as selection criteria to develop cultivars with increased benefits for human health or increased tolerance to diseases. In this study, peel, pulp, and seed samples collected from many mandarin accessions and their hybrids were analyzed for the presence of selected flavonoids with documented human health benefits. A genome-wide association study (GWAS) was used to identify SNPs associated with biosynthesis of flavonoids in these mandarin accessions, and there were 420 significant SNPs were found to be associated with 28 compounds in peel, pulp, or seed samples. Four candidate genes involved in flavonoid biosynthesis were identified by enrichment analysis. SNPs that were found to be associated with compounds in pulp samples have the potential to be used as markers to select mandarins with improved phytonutrient content to benefit human health. Mandarin cultivars bred with increased flavonoid content may provide value to growers and consumers.
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Affiliation(s)
- Matthew R. Mattia
- Citrus Research and Education Center, Department of Horticultural Sciences, University of Florida, Lake Alfred, FL 33850, USA; (M.R.M.); (D.D.); (Q.Y.); (Y.W.)
| | - Dongliang Du
- Citrus Research and Education Center, Department of Horticultural Sciences, University of Florida, Lake Alfred, FL 33850, USA; (M.R.M.); (D.D.); (Q.Y.); (Y.W.)
| | - Qibin Yu
- Citrus Research and Education Center, Department of Horticultural Sciences, University of Florida, Lake Alfred, FL 33850, USA; (M.R.M.); (D.D.); (Q.Y.); (Y.W.)
| | - Tracy Kahn
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA; (T.K.); (M.R.); (Y.H.)
| | - Mikeal Roose
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA; (T.K.); (M.R.); (Y.H.)
| | - Yoko Hiraoka
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA; (T.K.); (M.R.); (Y.H.)
| | - Yu Wang
- Citrus Research and Education Center, Department of Horticultural Sciences, University of Florida, Lake Alfred, FL 33850, USA; (M.R.M.); (D.D.); (Q.Y.); (Y.W.)
| | - Patricio Munoz
- Department of Horticultural Sciences, University of Florida, Gainesville, FL 32611, USA;
| | - Fred G. Gmitter
- Citrus Research and Education Center, Department of Horticultural Sciences, University of Florida, Lake Alfred, FL 33850, USA; (M.R.M.); (D.D.); (Q.Y.); (Y.W.)
- Correspondence:
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22
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Zahid G, Aka Kaçar Y, Dönmez D, Küden A, Giordani T. Perspectives and recent progress of genome-wide association studies (GWAS) in fruits. Mol Biol Rep 2022; 49:5341-5352. [PMID: 35064403 DOI: 10.1007/s11033-021-07055-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/06/2021] [Indexed: 11/25/2022]
Abstract
BACKGROUND Earlier next-generation sequencing technologies are being vastly used to explore, administer, and investigate the gene space with accurate profiling of nucleotide variations in the germplasm. OVERVIEW AND PROGRESS: Recently, novel advancements in high-throughput sequencing technologies allow a genotyping-by-sequencing approach that has opened up new horizons for extensive genotyping exploiting single-nucleotide-polymorphisms (SNPs). This method acts as a bridge to support and minimize a genotype to phenotype gap allowing genetic selection at the genome-wide level, named genomic selection that could facilitate the selection of traits also in the pomology sector. In addition to this, genome-wide genotyping is a prerequisite for genome-wide association studies that have been used successfully to discover the genes, which control polygenic traits including the genetic loci, associated with the trait of interest in fruit crops. AIMS AND PROSPECTS This review article emphasizes the role of genome-wide approaches to unlock and explore the genetic potential along with the detection of SNPs affecting the phenotype of fruit crops and highlights the prospects of genome-wide association studies in fruits.
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Affiliation(s)
- Ghassan Zahid
- Department of Biotechnology, Institute of Natural and Applied Sciences, Çukurova University, 01330, Adana, Turkey.
| | - Yıldız Aka Kaçar
- Department of Horticulture, Faculty of Agriculture, Çukurova University, 01330, Adana, Turkey
| | - Dicle Dönmez
- Biotechnology Research and Application Center, Çukurova University, 01330, Adana, Turkey
| | - Ayzin Küden
- Department of Horticulture, Faculty of Agriculture, Çukurova University, 01330, Adana, Turkey
| | - Tommaso Giordani
- Department of Agriculture, Food and Environment, University of Pisa, 56124, Pisa, Italy
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23
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Perry A, Wachowiak W, Beaton J, Iason G, Cottrell J, Cavers S. Identifying and testing marker‐trait associations for growth and phenology in three pine species: implications for genomic prediction. Evol Appl 2022; 15:330-348. [PMID: 35233251 PMCID: PMC8867712 DOI: 10.1111/eva.13345] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 12/02/2022] Open
Abstract
In tree species, genomic prediction offers the potential to forecast mature trait values in early growth stages, if robust marker–trait associations can be identified. Here we apply a novel multispecies approach using genotypes from a new genotyping array, based on 20,795 single nucleotide polymorphisms (SNPs) from three closely related pine species (Pinus sylvestris, Pinus uncinata and Pinus mugo), to test for associations with growth and phenology data from a common garden study. Predictive models constructed using significantly associated SNPs were then tested and applied to an independent multisite field trial of P. sylvestris and the capability to predict trait values was evaluated. One hundred and eighteen SNPs showed significant associations with the traits in the pine species. Common SNPs (MAF > 0.05) associated with bud set were only found in genes putatively involved in growth and development, whereas those associated with growth and budburst were also located in genes putatively involved in response to environment and, to a lesser extent, reproduction. At one of the two independent sites, the model we developed produced highly significant correlations between predicted values and observed height data (YA, height 2020: r = 0.376, p < 0.001). Predicted values estimated with our budburst model were weakly but positively correlated with duration of budburst at one of the sites (GS, 2015: r = 0.204, p = 0.034; 2018: r = 0.205, p = 0.034–0.037) and negatively associated with budburst timing at the other (YA: r = −0.202, p = 0.046). Genomic prediction resulted in the selection of sets of trees whose mean height was taller than the average for each site. Our results provide tentative support for the capability of prediction models to forecast trait values in trees, while highlighting the need for caution in applying them to trees grown in different environments.
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Affiliation(s)
- Annika Perry
- UK Centre for Ecology & Hydrology Edinburgh Penicuik Midlothian EH26 0QB UK
| | - Witold Wachowiak
- Institute of Environmental Biology Faculty of Biology Adam Mickiewicz University Poznań Poland
| | - Joan Beaton
- James Hutton Institute Craigiebuckler, Aberdeen AB15 8QH UK
| | - Glenn Iason
- James Hutton Institute Craigiebuckler, Aberdeen AB15 8QH UK
| | - Joan Cottrell
- Northern Research Station, Forest Research Roslin EH25 9SY UK
| | - Stephen Cavers
- UK Centre for Ecology & Hydrology Edinburgh Penicuik Midlothian EH26 0QB UK
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24
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Guo L, Hunag W, Zheng W, Chen F, Wang W, Zhang D, Hu Z, Chu Y. Indirect quantitative analysis of soluble solid content in citrus by the leaves using hyperspectral imaging combined with machine learning. APPLIED OPTICS 2022; 61:491-497. [PMID: 35200888 DOI: 10.1364/ao.440669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
Due to the effect of bagging on fruit growth, non-destructive and in situ soluble solid content (SSC) in citrus detection remains a challenge. In this work, a new method for accurately quantifying SSC in citrus using hyperspectral imaging of citrus leaves was proposed. Sixty-five Ehime Kashi No. 28 citruses with surrounding leaves picked at two different times were picked for the experiment. Using the principal components analysis combined with Gaussian process regression model, the correlation coefficients of prediction-real value by citrus and its leaves in cross-validation were 0.972 and 0.986, respectively. In addition, the relationship between citrus leaves and SSC content was further explored, and the possible relationship between chlorophyll in leaves and SSC of citrus was analyzed. Comparing the quantitative analysis results by citrus and its leaves, the results show that the proposed method is a non-destructive and reliable method for determining the SSC by citrus leaves and has broad application prospects in indirect detection of citrus.
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25
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Mathiazhagan M, Chidambara B, Hunashikatti LR, Ravishankar KV. Genomic Approaches for Improvement of Tropical Fruits: Fruit Quality, Shelf Life and Nutrient Content. Genes (Basel) 2021; 12:1881. [PMID: 34946829 PMCID: PMC8701245 DOI: 10.3390/genes12121881] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/23/2021] [Accepted: 11/16/2021] [Indexed: 12/17/2022] Open
Abstract
The breeding of tropical fruit trees for improving fruit traits is complicated, due to the long juvenile phase, generation cycle, parthenocarpy, polyploidy, polyembryony, heterozygosity and biotic and abiotic factors, as well as a lack of good genomic resources. Many molecular techniques have recently evolved to assist and hasten conventional breeding efforts. Molecular markers linked to fruit development and fruit quality traits such as fruit shape, size, texture, aroma, peel and pulp colour were identified in tropical fruit crops, facilitating Marker-assisted breeding (MAB). An increase in the availability of genome sequences of tropical fruits further aided in the discovery of SNP variants/Indels, QTLs and genes that can ascertain the genetic determinants of fruit characters. Through multi-omics approaches such as genomics, transcriptomics, metabolomics and proteomics, the identification and quantification of transcripts, including non-coding RNAs, involved in sugar metabolism, fruit development and ripening, shelf life, and the biotic and abiotic stress that impacts fruit quality were made possible. Utilizing genomic assisted breeding methods such as genome wide association (GWAS), genomic selection (GS) and genetic modifications using CRISPR/Cas9 and transgenics has paved the way to studying gene function and developing cultivars with desirable fruit traits by overcoming long breeding cycles. Such comprehensive multi-omics approaches related to fruit characters in tropical fruits and their applications in breeding strategies and crop improvement are reviewed, discussed and presented here.
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Affiliation(s)
| | | | | | - Kundapura V. Ravishankar
- Division of Basic Sciences, ICAR Indian Institute of Horticultural Research, Hessaraghatta Lake Post, Bengaluru 560089, India; (M.M.); (B.C.); (L.R.H.)
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26
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Nayak SN, Aravind B, Malavalli SS, Sukanth BS, Poornima R, Bharati P, Hefferon K, Kole C, Puppala N. Omics Technologies to Enhance Plant Based Functional Foods: An Overview. Front Genet 2021; 12:742095. [PMID: 34858472 PMCID: PMC8631721 DOI: 10.3389/fgene.2021.742095] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/13/2021] [Indexed: 11/25/2022] Open
Abstract
Functional foods are natural products of plants that have health benefits beyond necessary nutrition. Functional foods are abundant in fruits, vegetables, spices, beverages and some are found in cereals, millets, pulses and oilseeds. Efforts to identify functional foods in our diet and their beneficial aspects are limited to few crops. Advances in sequencing and availability of different omics technologies have given opportunity to utilize these tools to enhance the functional components of the foods, thus ensuring the nutritional security. Integrated omics approaches including genomics, transcriptomics, proteomics, metabolomics coupled with artificial intelligence and machine learning approaches can be used to improve the crops. This review provides insights into omics studies that are carried out to find the active components and crop improvement by enhancing the functional compounds in different plants including cereals, millets, pulses, oilseeds, fruits, vegetables, spices, beverages and medicinal plants. There is a need to characterize functional foods that are being used in traditional medicines, as well as utilization of this knowledge to improve the staple foods in order to tackle malnutrition and hunger more effectively.
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Affiliation(s)
- Spurthi N. Nayak
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - B. Aravind
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - Sachin S. Malavalli
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - B. S. Sukanth
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - R. Poornima
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - Pushpa Bharati
- Department of Food Science and Nutrition, University of Agricultural Sciences, Dharwad, India
| | - Kathleen Hefferon
- Department of Microbiology, Cornell University, Ithaca, NY, United States
| | - Chittaranjan Kole
- President, International Phytomedomics and Nutriomics Consortium (ipnc.info), Daejeon, South Korea
| | - Naveen Puppala
- New Mexico State University-Agricultural Science Center at Clovis, New Mexico, NM, United States
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27
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Rabier CE, Berry V, Stoltz M, Santos JD, Wang W, Glaszmann JC, Pardi F, Scornavacca C. On the inference of complex phylogenetic networks by Markov Chain Monte-Carlo. PLoS Comput Biol 2021; 17:e1008380. [PMID: 34478440 PMCID: PMC8445492 DOI: 10.1371/journal.pcbi.1008380] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 09/16/2021] [Accepted: 07/13/2021] [Indexed: 11/19/2022] Open
Abstract
For various species, high quality sequences and complete genomes are nowadays available for many individuals. This makes data analysis challenging, as methods need not only to be accurate, but also time efficient given the tremendous amount of data to process. In this article, we introduce an efficient method to infer the evolutionary history of individuals under the multispecies coalescent model in networks (MSNC). Phylogenetic networks are an extension of phylogenetic trees that can contain reticulate nodes, which allow to model complex biological events such as horizontal gene transfer, hybridization and introgression. We present a novel way to compute the likelihood of biallelic markers sampled along genomes whose evolution involved such events. This likelihood computation is at the heart of a Bayesian network inference method called SnappNet, as it extends the Snapp method inferring evolutionary trees under the multispecies coalescent model, to networks. SnappNet is available as a package of the well-known beast 2 software. Recently, the MCMC_BiMarkers method, implemented in PhyloNet, also extended Snapp to networks. Both methods take biallelic markers as input, rely on the same model of evolution and sample networks in a Bayesian framework, though using different methods for computing priors. However, SnappNet relies on algorithms that are exponentially more time-efficient on non-trivial networks. Using simulations, we compare performances of SnappNet and MCMC_BiMarkers. We show that both methods enjoy similar abilities to recover simple networks, but SnappNet is more accurate than MCMC_BiMarkers on more complex network scenarios. Also, on complex networks, SnappNet is found to be extremely faster than MCMC_BiMarkers in terms of time required for the likelihood computation. We finally illustrate SnappNet performances on a rice data set. SnappNet infers a scenario that is consistent with previous results and provides additional understanding of rice evolution.
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Affiliation(s)
- Charles-Elie Rabier
- Institut des Sciences de l’Evolution (ISEM), Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
- Laboratoire d’Informatique, de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier, CNRS, Montpellier, France
- Institut Montpelliérain Alexander Grothendieck (IMAG), Université de Montpellier, CNRS, Montpellier, France
| | - Vincent Berry
- Laboratoire d’Informatique, de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier, CNRS, Montpellier, France
| | - Marnus Stoltz
- Institut des Sciences de l’Evolution (ISEM), Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - João D. Santos
- CIRAD, UMR AGAP, Montpellier, France
- Amélioration Génétique et Adaptation des Plantes méditerranéennes et tropicales (AGAP), Université de Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Wensheng Wang
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jean-Christophe Glaszmann
- CIRAD, UMR AGAP, Montpellier, France
- Amélioration Génétique et Adaptation des Plantes méditerranéennes et tropicales (AGAP), Université de Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Fabio Pardi
- Laboratoire d’Informatique, de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier, CNRS, Montpellier, France
| | - Celine Scornavacca
- Institut des Sciences de l’Evolution (ISEM), Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
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28
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O'Connor KM, Hayes BJ, Hardner CM, Alam M, Henry RJ, Topp BL. Genomic selection and genetic gain for nut yield in an Australian macadamia breeding population. BMC Genomics 2021; 22:370. [PMID: 34016055 PMCID: PMC8139092 DOI: 10.1186/s12864-021-07694-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 05/10/2021] [Indexed: 02/06/2023] Open
Abstract
Background Improving yield prediction and selection efficiency is critical for tree breeding. This is vital for macadamia trees with the time from crossing to production of new cultivars being almost a quarter of a century. Genomic selection (GS) is a useful tool in plant breeding, particularly with perennial trees, contributing to an increased rate of genetic gain and reducing the length of the breeding cycle. We investigated the potential of using GS methods to increase genetic gain and accelerate selection efficiency in the Australian macadamia breeding program with comparison to traditional breeding methods. This study evaluated the prediction accuracy of GS in a macadamia breeding population of 295 full-sib progeny from 32 families (29 parents, reciprocals combined), along with a subset of parents. Historical yield data for tree ages 5 to 8years were used in the study, along with a set of 4113 SNP markers. The traits of focus were average nut yield from tree ages 5 to 8years and yield stability, measured as the standard deviation of yield over these 4 years. GBLUP GS models were used to obtain genomic estimated breeding values for each genotype, with a five-fold cross-validation method and two techniques: prediction across related populations and prediction across unrelated populations. Results Narrow-sense heritability of yield and yield stability was low (h2=0.30 and 0.04, respectively). Prediction accuracy for yield was 0.57 for predictions across related populations and 0.14 when predicted across unrelated populations. Accuracy of prediction of yield stability was high (r=0.79) for predictions across related populations. Predicted genetic gain of yield using GS in related populations was 474g/year, more than double that of traditional breeding methods (226g/year), due to the halving of generation length from 8 to 4years. Conclusions The results of this study indicate that the incorporation of GS for yield into the Australian macadamia breeding program may accelerate genetic gain due to reduction in generation length, though the cost of genotyping appears to be a constraint at present. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07694-z.
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Affiliation(s)
- Katie M O'Connor
- Queensland Department of Agriculture and Fisheries, Maroochy Research Facility, 47 Mayers Road, Nambour, QLD, 4560, Australia. .,Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Maroochy Research Facility, 47 Mayers Road, Nambour, QLD, 4560, Australia.
| | - Ben J Hayes
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD, 4072, Australia
| | - Craig M Hardner
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD, 4072, Australia
| | - Mobashwer Alam
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Maroochy Research Facility, 47 Mayers Road, Nambour, QLD, 4560, Australia
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD, 4072, Australia
| | - Bruce L Topp
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Maroochy Research Facility, 47 Mayers Road, Nambour, QLD, 4560, Australia
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29
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Catalano C, Di Guardo M, Distefano G, Caruso M, Nicolosi E, Deng Z, Gentile A, La Malfa SG. Biotechnological Approaches for Genetic Improvement of Lemon ( Citrus limon (L.) Burm. f.) against Mal Secco Disease. PLANTS 2021; 10:plants10051002. [PMID: 34067841 PMCID: PMC8157051 DOI: 10.3390/plants10051002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/12/2021] [Accepted: 05/13/2021] [Indexed: 12/17/2022]
Abstract
Among Citrus species, lemon is one of the most susceptible to mal secco disease, a tracheomycosis caused by the mitosporic fungus Plenodomus tracheiphilus, which induces chlorosis followed by leaf drop and progressive desiccation of twigs and branches. Severe infection can cause the death of the plant. Since no effective control strategies are available to efficiently control the pathogen spread, host tolerance is the most desirable goal in the struggle against mal secco disease. To date, both traditional breeding programs and biotechnological techniques were not efficient in developing novel varieties coupling tolerance to mal secco with optimal fruit quality. Furthermore, the genetic basis of host resistance has not been fully deciphered yet, hampering the set-up of marker-assisted selection (MAS) schemes. This paper provides an overview of the biotechnological approaches adopted so far for the selection of mal secco tolerant lemon varieties and emphasizes the promising contribution of marker-trait association analysis techniques for both unraveling the genetic determinism of the resistance to mal secco and detecting molecular markers that can be readily used for MAS. Such an approach has already proved its efficiency in several crops and could represent a valuable tool to select novel lemon varieties coupling superior fruit quality traits and resistance to mal secco.
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Affiliation(s)
- Chiara Catalano
- Department of Agriculture, Food and Environment (Di3A), University of Catania, via Valdisavoia 5, 95123 Catania, Italy; (C.C.); (M.D.G.); (G.D.); (E.N.); (S.G.L.M.)
| | - Mario Di Guardo
- Department of Agriculture, Food and Environment (Di3A), University of Catania, via Valdisavoia 5, 95123 Catania, Italy; (C.C.); (M.D.G.); (G.D.); (E.N.); (S.G.L.M.)
| | - Gaetano Distefano
- Department of Agriculture, Food and Environment (Di3A), University of Catania, via Valdisavoia 5, 95123 Catania, Italy; (C.C.); (M.D.G.); (G.D.); (E.N.); (S.G.L.M.)
| | - Marco Caruso
- CREA, Research Centre for Olive, Fruit and Citrus Crops, Corso Savoia 190, 95024 Acireale, Italy;
| | - Elisabetta Nicolosi
- Department of Agriculture, Food and Environment (Di3A), University of Catania, via Valdisavoia 5, 95123 Catania, Italy; (C.C.); (M.D.G.); (G.D.); (E.N.); (S.G.L.M.)
| | - Ziniu Deng
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha 410128, China;
| | - Alessandra Gentile
- Department of Agriculture, Food and Environment (Di3A), University of Catania, via Valdisavoia 5, 95123 Catania, Italy; (C.C.); (M.D.G.); (G.D.); (E.N.); (S.G.L.M.)
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha 410128, China;
- Correspondence:
| | - Stefano Giovanni La Malfa
- Department of Agriculture, Food and Environment (Di3A), University of Catania, via Valdisavoia 5, 95123 Catania, Italy; (C.C.); (M.D.G.); (G.D.); (E.N.); (S.G.L.M.)
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Minamikawa MF, Kunihisa M, Noshita K, Moriya S, Abe K, Hayashi T, Katayose Y, Matsumoto T, Nishitani C, Terakami S, Yamamoto T, Iwata H. Tracing founder haplotypes of Japanese apple varieties: application in genomic prediction and genome-wide association study. HORTICULTURE RESEARCH 2021; 8:49. [PMID: 33642580 PMCID: PMC7917097 DOI: 10.1038/s41438-021-00485-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/28/2020] [Accepted: 01/03/2021] [Indexed: 05/21/2023]
Abstract
Haplotypes provide useful information for genomics-based approaches, genomic prediction, and genome-wide association study. As a small number of superior founders have contributed largely to the breeding history of fruit trees, the information of founder haplotypes may be relevant for performing the genomics-based approaches in these plants. In this study, we proposed a method to estimate 14 haplotypes from 7 founders and automatically trace the haplotypes forward to apple parental (185 varieties) and breeding (659 F1 individuals from 16 full-sib families) populations based on 11,786 single-nucleotide polymorphisms, by combining multiple algorithms. Overall, 92% of the single-nucleotide polymorphisms information in the parental and breeding populations was characterized by the 14 founder haplotypes. The use of founder haplotype information improved the accuracy of genomic prediction in 7 traits and the resolution of genome-wide association study in 13 out of 27 fruit quality traits analyzed in this study. We also visualized the significant propagation of the founder haplotype with the largest genetic effect in genome-wide association study over the pedigree tree of the parental population. These results suggest that the information of founder haplotypes can be useful for not only genetic improvement of fruit quality traits in apples but also for understanding the selection history of founder haplotypes in the breeding program of Japanese apple varieties.
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Affiliation(s)
- Mai F Minamikawa
- Laboratory of Biometry and Bioinformatics, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Miyuki Kunihisa
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), 2-1 Fujimoto, Tsukuba, Ibaraki, 305-8605, Japan
| | - Koji Noshita
- Laboratory of Biometry and Bioinformatics, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Shigeki Moriya
- Division of Apple Research, Institute of Fruit Tree and Tea Science, NARO, 92-24 Shimokuriyagawa Nabeyashiki, Morioka, Iwate, 020-0123, Japan
| | - Kazuyuki Abe
- Division of Apple Research, Institute of Fruit Tree and Tea Science, NARO, 92-24 Shimokuriyagawa Nabeyashiki, Morioka, Iwate, 020-0123, Japan
| | - Takeshi Hayashi
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Yuichi Katayose
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Toshimi Matsumoto
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
- Institute of Agrobiological Sciences, NARO, 1-2 Owashi, Tsukuba, Ibaraki, 305-8634, Japan
| | - Chikako Nishitani
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), 2-1 Fujimoto, Tsukuba, Ibaraki, 305-8605, Japan
| | - Shingo Terakami
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), 2-1 Fujimoto, Tsukuba, Ibaraki, 305-8605, Japan
| | - Toshiya Yamamoto
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), 2-1 Fujimoto, Tsukuba, Ibaraki, 305-8605, Japan
| | - Hiroyoshi Iwata
- Laboratory of Biometry and Bioinformatics, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan.
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Recent Large-Scale Genotyping and Phenotyping of Plant Genetic Resources of Vegetatively Propagated Crops. PLANTS 2021; 10:plants10020415. [PMID: 33672381 PMCID: PMC7926561 DOI: 10.3390/plants10020415] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/19/2021] [Accepted: 02/19/2021] [Indexed: 12/12/2022]
Abstract
Several recent national and international projects have focused on large-scale genotyping of plant genetic resources in vegetatively propagated crops like fruit and berries, potatoes and woody ornamentals. The primary goal is usually to identify true-to-type plant material, detect possible synonyms, and investigate genetic diversity and relatedness among accessions. A secondary goal may be to create sustainable databases that can be utilized in research and breeding for several years ahead. Commonly applied DNA markers (like microsatellite DNA and SNPs) and next-generation sequencing each have their pros and cons for these purposes. Methods for large-scale phenotyping have lagged behind, which is unfortunate since many commercially important traits (yield, growth habit, storability, and disease resistance) are difficult to score. Nevertheless, the analysis of gene action and development of robust DNA markers depends on environmentally controlled screening of very large sets of plant material. Although more time-consuming, co-operative projects with broad-scale data collection are likely to produce more reliable results. In this review, we will describe some of the approaches taken in genotyping and/or phenotyping projects concerning a wide variety of vegetatively propagated crops.
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Fujii H, Nonaka K, Minamikawa MF, Endo T, Sugiyama A, Hamazaki K, Iwata H, Omura M, Shimada T. Allelic composition of carotenoid metabolic genes in 13 founders influences carotenoid composition in juice sac tissues of fruits among Japanese citrus breeding population. PLoS One 2021; 16:e0246468. [PMID: 33539435 PMCID: PMC7861536 DOI: 10.1371/journal.pone.0246468] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 01/19/2021] [Indexed: 11/24/2022] Open
Abstract
To enrich carotenoids, especially β-cryptoxanthin, in juice sac tissues of fruits via molecular breeding in citrus, allele mining was utilized to dissect allelic variation of carotenoid metabolic genes and identify an optimum allele on the target loci characterized by expression quantitative trait (eQTL) analysis. SNPs of target carotenoid metabolic genes in 13 founders of the Japanese citrus breeding population were explored using the SureSelect target enrichment method. An independent allele was determined based on the presence or absence of reliable SNPs, using trio analysis to confirm inheritability between parent and offspring. Among the 13 founders, there were 7 PSY alleles, 7 HYb alleles, 11 ZEP alleles, 5 NCED alleles, and 4 alleles for the eQTL that control the transcription levels of PDS and ZDS among the ancestral species, indicating that some founders acquired those alleles from them. The carotenoid composition data of 263 breeding pedigrees in juice sac tissues revealed that the phenotypic variance of carotenoid composition was similar to that in the 13 founders, whereas the mean of total carotenoid content increased. This increase in total carotenoid content correlated with the increase in either or both β-cryptoxanthin and violaxanthin in juice sac tissues. Bayesian statistical analysis between allelic composition of target genes and carotenoid composition in 263 breeding pedigrees indicated that PSY-a and ZEP-e alleles at PSY and ZEP loci had strong positive effects on increasing the total carotenoid content, including β-cryptoxanthin and violaxanthin, in juice sac tissues. Moreover, the pyramiding of these alleles also increased the β-cryptoxanthin content. Interestingly, the offset interaction between the alleles with increasing and decreasing effects on carotenoid content and the epistatic interaction among carotenoid metabolic genes were observed and these interactions complexed carotenoid profiles in breeding population. These results revealed that allele composition would highly influence the carotenoid composition in citrus fruits. The allelic genotype information for the examined carotenoid metabolic genes in major citrus varieties and the trio-tagged SNPs to discriminate the optimum alleles (PSY-a and ZEP-e) from the rest would promise citrus breeders carotenoid enrichment in fruit via molecular breeding.
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Affiliation(s)
- Hiroshi Fujii
- National Agriculture and Food Research Organization Institute of Fruit and Tea Tree Science, Shimizu, Shizuoka, Japan
| | - Keisuke Nonaka
- National Agriculture and Food Research Organization Institute of Fruit and Tea Tree Science, Shimizu, Shizuoka, Japan
| | - Mai F. Minamikawa
- Laboratory of Biometry and Bioinformatics, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Tomoko Endo
- National Agriculture and Food Research Organization Institute of Fruit and Tea Tree Science, Shimizu, Shizuoka, Japan
| | - Aiko Sugiyama
- Faculty of Agriculture, Shizuoka University, Suruga, Shizuoka, Japan
| | - Kosuke Hamazaki
- Laboratory of Biometry and Bioinformatics, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Hiroyoshi Iwata
- Laboratory of Biometry and Bioinformatics, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Mitsuo Omura
- Faculty of Agriculture, Shizuoka University, Suruga, Shizuoka, Japan
| | - Takehiko Shimada
- National Agriculture and Food Research Organization Institute of Fruit and Tea Tree Science, Shimizu, Shizuoka, Japan
- * E-mail:
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Reyes-Herrera PH, Muñoz-Baena L, Velásquez-Zapata V, Patiño L, Delgado-Paz OA, Díaz-Diez CA, Navas-Arboleda AA, Cortés AJ. Inheritance of Rootstock Effects in Avocado ( Persea americana Mill.) cv. Hass. FRONTIERS IN PLANT SCIENCE 2020; 11:555071. [PMID: 33424874 PMCID: PMC7785968 DOI: 10.3389/fpls.2020.555071] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 11/17/2020] [Indexed: 05/16/2023]
Abstract
Grafting is typically utilized to merge adapted seedling rootstocks with highly productive clonal scions. This process implies the interaction of multiple genomes to produce a unique tree phenotype. However, the interconnection of both genotypes obscures individual contributions to phenotypic variation (rootstock-mediated heritability), hampering tree breeding. Therefore, our goal was to quantify the inheritance of seedling rootstock effects on scion traits using avocado (Persea americana Mill.) cv. Hass as a model fruit tree. We characterized 240 diverse rootstocks from 8 avocado cv. Hass orchards with similar management in three regions of the province of Antioquia, northwest Andes of Colombia, using 13 microsatellite markers simple sequence repeats (SSRs). Parallel to this, we recorded 20 phenotypic traits (including morphological, biomass/reproductive, and fruit yield and quality traits) in the scions for 3 years (2015-2017). Relatedness among rootstocks was inferred through the genetic markers and inputted in a "genetic prediction" model to calculate narrow-sense heritabilities (h 2) on scion traits. We used three different randomization tests to highlight traits with consistently significant heritability estimates. This strategy allowed us to capture five traits with significant heritability values that ranged from 0.33 to 0.45 and model fits (r) that oscillated between 0.58 and 0.73 across orchards. The results showed significance in the rootstock effects for four complex harvest and quality traits (i.e., total number of fruits, number of fruits with exportation quality, and number of fruits discarded because of low weight or thrips damage), whereas the only morphological trait that had a significant heritability value was overall trunk height (an emergent property of the rootstock-scion interaction). These findings suggest the inheritance of rootstock effects, beyond root phenotype, on a surprisingly wide spectrum of scion traits in "Hass" avocado. They also reinforce the utility of polymorphic SSRs for relatedness reconstruction and genetic prediction of complex traits. This research is, up to date, the most cohesive evidence of narrow-sense inheritance of rootstock effects in a tropical fruit tree crop. Ultimately, our work highlights the importance of considering the rootstock-scion interaction to broaden the genetic basis of fruit tree breeding programs while enhancing our understanding of the consequences of grafting.
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Affiliation(s)
- Paula H. Reyes-Herrera
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA)—CI Tibaitatá, Mosquera, Colombia
| | - Laura Muñoz-Baena
- Department of Microbiology and Immunology, Western University, London, ON, Canada
| | - Valeria Velásquez-Zapata
- Department of Plant Pathology and Microbiology, Interdepartmental Bioinformatics and Computational Biology, Iowa State University, Ames, IA, United States
| | - Laura Patiño
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA)—CI La Selva, Rionegro, Colombia
| | - Oscar A. Delgado-Paz
- Facultad de Ingenierías, Universidad Católica de Oriente—UCO, Rionegro, Antioquia
| | - Cipriano A. Díaz-Diez
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA)—CI La Selva, Rionegro, Colombia
| | | | - Andrés J. Cortés
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA)—CI La Selva, Rionegro, Colombia
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Adoption and Optimization of Genomic Selection To Sustain Breeding for Apricot Fruit Quality. G3-GENES GENOMES GENETICS 2020; 10:4513-4529. [PMID: 33067307 PMCID: PMC7718743 DOI: 10.1534/g3.120.401452] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Genomic selection (GS) is a breeding approach which exploits genome-wide information and whose unprecedented success has shaped several animal and plant breeding schemes through delivering their genetic progress. This is the first study assessing the potential of GS in apricot (Prunus armeniaca) to enhance postharvest fruit quality attributes. Genomic predictions were based on a F1 pseudo-testcross population, comprising 153 individuals with contrasting fruit quality traits. They were phenotyped for physical and biochemical fruit metrics in contrasting climatic conditions over two years. Prediction accuracy (PA) varied from 0.31 for glucose content with the Bayesian LASSO (BL) to 0.78 for ethylene production with RR-BLUP, which yielded the most accurate predictions in comparison to Bayesian models and only 10% out of 61,030 SNPs were sufficient to reach accurate predictions. Useful insights were provided on the genetic architecture of apricot fruit quality whose integration in prediction models improved their performance, notably for traits governed by major QTL. Furthermore, multivariate modeling yielded promising outcomes in terms of PA within training partitions partially phenotyped for target traits. This provides a useful framework for the implementation of indirect selection based on easy-to-measure traits. Thus, we highlighted the main levers to take into account for the implementation of GS for fruit quality in apricot, but also to improve the genetic gain in perennial species.
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Zheng W, Shen F, Wang W, Wu B, Wang X, Xiao C, Tian Z, Yang X, Yang J, Wang Y, Wu T, Xu X, Han Z, Zhang X. Quantitative trait loci-based genomics-assisted prediction for the degree of apple fruit cover color. THE PLANT GENOME 2020; 13:e20047. [PMID: 33217219 DOI: 10.1002/tpg2.20047] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 06/22/2020] [Indexed: 06/11/2023]
Abstract
Apple fruit cover color is an important appearance trait determining fruit quality, high degree of fruit cover color or completely red fruit skin is also the ultimate breeding goal. MdMYB1 has repeatedly been reported as a major gene controlling apple fruit cover color. There are also multiple minor-effect genes affecting degree of fruit cover color (DFC). This study was to identify genome-wide quantitative trait loci (QTLs) and to develop genomics-assisted prediction for apple DFC. The DFC phenotype data of 9,422 hybrids from five full-sib families of Malus asiatica 'Zisai Pearl', M. domestica 'Red Fuji', 'Golden Delicious', and 'Jonathan' were collected in 2014-2017. The phenotype varied considerably among hybrids with the same MdMYB1 genotype. Ten QTLs for DFC were identified using MapQTL and bulked segregant analysis via sequencing. From these QTLs, ten candidate genes were predicted, including MdMYB1 from a year-stable QTL on chromosome 9 of 'Zisai Pearl' and 'Red Fuji'. Then, kompetitive allele-specific polymerase chain reaction (KASP) markers were designed on these candidate genes and 821 randomly selected hybrids were genotyped. The genotype effects of the markers were estimated. MdMYB1-1 (represented by marker H162) exhibited a partial dominant allelic effect on MdMYB1-2 and showed non-allelic epistasis on markers H1245 and G6. Finally, a non-additive QTL-based genomics assisted prediction model was established for DFC. The Pearson's correlation coefficient between the genomic predicted value and the observed phenotype value was 0.5690. These results can be beneficial for apple genomics-assisted breeding and may provide insights for understanding the mechanism of fruit coloration.
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Affiliation(s)
- Wenyan Zheng
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, China, 100193
| | - Fei Shen
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, China, 100193
| | - Wuqian Wang
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, China, 100193
| | - Bei Wu
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, China, 100193
| | - Xuan Wang
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, China, 100193
| | - Chen Xiao
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, China, 100193
| | - Zhendong Tian
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, China, 100193
| | - Xianglong Yang
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, China, 100193
| | - Jing Yang
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, China, 100193
| | - Yi Wang
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, China, 100193
| | - Ting Wu
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, China, 100193
| | - Xuefeng Xu
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, China, 100193
| | - Zhenhai Han
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, China, 100193
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, China, 100193
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Yamashita H, Uchida T, Tanaka Y, Katai H, Nagano AJ, Morita A, Ikka T. Genomic predictions and genome-wide association studies based on RAD-seq of quality-related metabolites for the genomics-assisted breeding of tea plants. Sci Rep 2020; 10:17480. [PMID: 33060786 PMCID: PMC7562905 DOI: 10.1038/s41598-020-74623-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 09/14/2020] [Indexed: 12/01/2022] Open
Abstract
Effectively using genomic information greatly accelerates conventional breeding and applying it to long-lived crops promotes the conversion to genomic breeding. Because tea plants are bred using conventional methods, we evaluated the potential of genomic predictions (GPs) and genome-wide association studies (GWASs) for the genetic breeding of tea quality-related metabolites using genome-wide single nucleotide polymorphisms (SNPs) detected from restriction site-associated DNA sequencing of 150 tea accessions. The present GP, based on genome-wide SNPs, and six models produced moderate prediction accuracy values (r) for the levels of most catechins, represented by ( -)-epigallocatechin gallate (r = 0.32-0.41) and caffeine (r = 0.44-0.51), but low r values for free amino acids and chlorophylls. Integrated analysis of GWAS and GP detected potential candidate genes for each metabolite using 80-160 top-ranked SNPs that resulted in the maximum cumulative prediction value. Applying GPs and GWASs to tea accession traits will contribute to genomics-assisted tea breeding.
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Affiliation(s)
- Hiroto Yamashita
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
- United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagito, Gifu, 501-1193, Japan
| | - Tomoki Uchida
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Yasuno Tanaka
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
- United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagito, Gifu, 501-1193, Japan
| | - Hideyuki Katai
- Shizuoka Prefectural Research Institute of Agriculture and Forestry, Tea Research Center, 1706-11 Kurasawa, Kikugawa, Shizuoka, 439-0002, Japan
- Shizuoka Prefecture Chubu Agriculture and Forestry Office, 2-20 Ariake-cho, Suruga-ku, Shizuoka, 422-8031, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu, Shiga, 520-2194, Japan
| | - Akio Morita
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
- Institute for Tea Science, Shizuoka University, 836 Ohya, Shizuoka, 422-8529, Japan
| | - Takashi Ikka
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan.
- Institute for Tea Science, Shizuoka University, 836 Ohya, Shizuoka, 422-8529, Japan.
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Roth M, Muranty H, Di Guardo M, Guerra W, Patocchi A, Costa F. Genomic prediction of fruit texture and training population optimization towards the application of genomic selection in apple. HORTICULTURE RESEARCH 2020; 7:148. [PMID: 32922820 PMCID: PMC7459338 DOI: 10.1038/s41438-020-00370-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 07/18/2020] [Accepted: 07/24/2020] [Indexed: 05/11/2023]
Abstract
Texture is a complex trait and a major component of fruit quality in apple. While the major effect of MdPG1, a gene controlling firmness, has already been exploited in elite cultivars, the genetic basis of crispness remains poorly understood. To further improve fruit texture, harnessing loci with minor effects via genomic selection is therefore necessary. In this study, we measured acoustic and mechanical features in 537 genotypes to dissect the firmness and crispness components of fruit texture. Predictions of across-year phenotypic values for these components were calculated using a model calibrated with 8,294 SNP markers. The best prediction accuracies following cross-validations within the training set of 259 genotypes were obtained for the acoustic linear distance (0.64). Predictions for biparental families using the entire training set varied from low to high accuracy, depending on the family considered. While adding siblings or half-siblings into the training set did not clearly improve predictions, we performed an optimization of the training set size and composition for each validation set. This allowed us to increase prediction accuracies by 0.17 on average, with a maximal accuracy of 0.81 when predicting firmness in the 'Gala' × 'Pink Lady' family. Our results therefore identified key genetic parameters to consider when deploying genomic selection for texture in apple. In particular, we advise to rely on a large training population, with high phenotypic variability from which a 'tailored training population' can be extracted using a priori information on genetic relatedness, in order to predict a specific target population.
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Affiliation(s)
- Morgane Roth
- Plant Breeding Research Division, Agroscope, Wädenswil, Zurich, Switzerland
- Present Address: GAFL, INRAE, 84140 Montfavet, France
| | - Hélène Muranty
- IRHS, INRAE, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Mario Di Guardo
- Department of Genomics and Biology of Fruit Crops, Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38010 San Michele all’Adige, Italy
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
| | - Walter Guerra
- Research Centre Laimburg, Laimburg 6, 39040 Auer, Italy
| | - Andrea Patocchi
- Plant Breeding Research Division, Agroscope, Wädenswil, Zurich, Switzerland
| | - Fabrizio Costa
- Department of Genomics and Biology of Fruit Crops, Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38010 San Michele all’Adige, Italy
- Center Agriculture Food Environment, University of Trento, Via Mach 1, 38010 San Michele all’Adige, Italy
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Feldmann MJ, Hardigan MA, Famula RA, López CM, Tabb A, Cole GS, Knapp SJ. Multi-dimensional machine learning approaches for fruit shape phenotyping in strawberry. Gigascience 2020; 9:giaa030. [PMID: 32352533 PMCID: PMC7191992 DOI: 10.1093/gigascience/giaa030] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 02/06/2020] [Accepted: 03/10/2020] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Shape is a critical element of the visual appeal of strawberry fruit and is influenced by both genetic and non-genetic determinants. Current fruit phenotyping approaches for external characteristics in strawberry often rely on the human eye to make categorical assessments. However, fruit shape is an inherently multi-dimensional, continuously variable trait and not adequately described by a single categorical or quantitative feature. Morphometric approaches enable the study of complex, multi-dimensional forms but are often abstract and difficult to interpret. In this study, we developed a mathematical approach for transforming fruit shape classifications from digital images onto an ordinal scale called the Principal Progression of k Clusters (PPKC). We use these human-recognizable shape categories to select quantitative features extracted from multiple morphometric analyses that are best fit for genetic dissection and analysis. RESULTS We transformed images of strawberry fruit into human-recognizable categories using unsupervised machine learning, discovered 4 principal shape categories, and inferred progression using PPKC. We extracted 68 quantitative features from digital images of strawberries using a suite of morphometric analyses and multivariate statistical approaches. These analyses defined informative feature sets that effectively captured quantitative differences between shape classes. Classification accuracy ranged from 68% to 99% for the newly created phenotypic variables for describing a shape. CONCLUSIONS Our results demonstrated that strawberry fruit shapes could be robustly quantified, accurately classified, and empirically ordered using image analyses, machine learning, and PPKC. We generated a dictionary of quantitative traits for studying and predicting shape classes and identifying genetic factors underlying phenotypic variability for fruit shape in strawberry. The methods and approaches that we applied in strawberry should apply to other fruits, vegetables, and specialty crops.
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Affiliation(s)
- Mitchell J Feldmann
- Department of Plant Sciences, University of California, Davis, 1 Shields Ave, Davis, CA 95616, USA
| | - Michael A Hardigan
- Department of Plant Sciences, University of California, Davis, 1 Shields Ave, Davis, CA 95616, USA
| | - Randi A Famula
- Department of Plant Sciences, University of California, Davis, 1 Shields Ave, Davis, CA 95616, USA
| | - Cindy M López
- Department of Plant Sciences, University of California, Davis, 1 Shields Ave, Davis, CA 95616, USA
| | - Amy Tabb
- USDA-ARS-AFRS, 2217 Wiltshire Rd, Kearneysville, WV 25430, USA
| | - Glenn S Cole
- Department of Plant Sciences, University of California, Davis, 1 Shields Ave, Davis, CA 95616, USA
| | - Steven J Knapp
- Department of Plant Sciences, University of California, Davis, 1 Shields Ave, Davis, CA 95616, USA
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Kawahara Y, Endo T, Omura M, Teramoto Y, Itoh T, Fujii H, Shimada T. Mikan Genome Database (MiGD): integrated database of genome annotation, genomic diversity, and CAPS marker information for mandarin molecular breeding. BREEDING SCIENCE 2020; 70:200-211. [PMID: 32523402 PMCID: PMC7272249 DOI: 10.1270/jsbbs.19097] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 10/16/2019] [Indexed: 06/11/2023]
Abstract
Citrus species are some of the most valuable and widely consumed fruits globally. The genome sequences of representative citrus (e.g., Citrus clementina, C. sinensis, C. grandis) species have been released but the research base for mandarin molecular breeding is still poor. We assembled the genomes of Citrus unshiu and Poncirus trifoliata, two important species for citrus industry in Japan, using hybrid de novo assembly of Illumina and PacBio sequence data, and developed the Mikan Genome Database (MiGD). The assembled genome sizes of C. unshiu and P. trifoliata are 346 and 292 Mb, respectively, similar to those of citrus species in public databases; they are predicted to possess 41,489 and 34,333 protein-coding genes in their draft genome sequences, with 9,642 and 8,377 specific genes when compared to C. clementina, respectively. MiGD is an integrated database of genome annotation, genetic diversity, and Cleaved Amplified Polymorphic Sequence (CAPS) marker information, with these contents being mutually linked by genes. MiGD facilitates access to genome sequences of interest from previously reported linkage maps through CAPS markers and obtains polymorphism information through the multiple genome browser TASUKE. The genomic resources in MiGD (https://mikan.dna.affrc.go.jp) could provide valuable information for mandarin molecular breeding in Japan.
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Affiliation(s)
- Yoshihiro Kawahara
- National Agriculture and Food Research Organization Advanced Analysis Center, Tsukuba, Ibaraki 305-8602, Japan
- National Agriculture and Food Research Organization Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan
| | - Tomoko Endo
- National Agriculture and Food Research Organization Institute of Fruit and Tea Tree Science, Shimizu, Shizuoka 424-0292, Japan
| | - Mitsuo Omura
- Faculty of Agriculture, Shizuoka University, Suruga, Shizuoka 422-8529, Japan
| | - Yumiko Teramoto
- IMSBIO Co., Ltd., Owl Tower 6F, 4-21-1, Higashi-ikebukuro, Toshima-ku, Tokyo 170-0013, Japan
| | - Takeshi Itoh
- National Agriculture and Food Research Organization Advanced Analysis Center, Tsukuba, Ibaraki 305-8602, Japan
| | - Hiroshi Fujii
- National Agriculture and Food Research Organization Institute of Fruit and Tea Tree Science, Shimizu, Shizuoka 424-0292, Japan
| | - Takehiko Shimada
- National Agriculture and Food Research Organization Institute of Fruit and Tea Tree Science, Shimizu, Shizuoka 424-0292, Japan
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O'Connor K, Hayes B, Hardner C, Nock C, Baten A, Alam M, Henry R, Topp B. Genome-wide association studies for yield component traits in a macadamia breeding population. BMC Genomics 2020; 21:199. [PMID: 32131725 PMCID: PMC7057592 DOI: 10.1186/s12864-020-6575-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 02/10/2020] [Indexed: 11/12/2022] Open
Abstract
Background Breeding for new macadamia cultivars with high nut yield is expensive in terms of time, labour and cost. Most trees set nuts after four to five years, and candidate varieties for breeding are evaluated for at least eight years for various traits. Genome-wide association studies (GWAS) are promising methods to reduce evaluation and selection cycles by identifying genetic markers linked with key traits, potentially enabling early selection through marker-assisted selection. This study used 295 progeny from 32 full-sib families and 29 parents (18 phenotyped) which were planted across four sites, with each tree genotyped for 4113 SNPs. ASReml-R was used to perform association analyses with linear mixed models including a genomic relationship matrix to account for population structure. Traits investigated were: nut weight (NW), kernel weight (KW), kernel recovery (KR), percentage of whole kernels (WK), tree trunk circumference (TC), percentage of racemes that survived from flowering through to nut set, and number of nuts per raceme. Results Seven SNPs were significantly associated with NW (at a genome-wide false discovery rate of < 0.05), and four with WK. Multiple regression, as well as mapping of markers to genome assembly scaffolds suggested that some SNPs were detecting the same QTL. There were 44 significant SNPs identified for TC although multiple regression suggested detection of 16 separate QTLs. Conclusions These findings have important implications for macadamia breeding, and highlight the difficulties of heterozygous populations with rapid LD decay. By coupling validated marker-trait associations detected through GWAS with MAS, genetic gain could be increased by reducing the selection time for economically important nut characteristics. Genomic selection may be a more appropriate method to predict complex traits like tree size and yield.
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Affiliation(s)
- Katie O'Connor
- Queensland Department of Agriculture and Fisheries, Maroochy Research Facility, Nambour, Qld, Australia. .,Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, Qld, Australia.
| | - Ben Hayes
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, Qld, Australia
| | - Craig Hardner
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, Qld, Australia
| | - Catherine Nock
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia
| | - Abdul Baten
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia.,AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | - Mobashwer Alam
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, Qld, Australia
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, Qld, Australia
| | - Bruce Topp
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, Qld, Australia
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Diaz S, Ariza-Suarez D, Ramdeen R, Aparicio J, Arunachalam N, Hernandez C, Diaz H, Ruiz H, Piepho HP, Raatz B. Genetic Architecture and Genomic Prediction of Cooking Time in Common Bean ( Phaseolus vulgaris L.). FRONTIERS IN PLANT SCIENCE 2020; 11:622213. [PMID: 33643335 PMCID: PMC7905357 DOI: 10.3389/fpls.2020.622213] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 12/21/2020] [Indexed: 05/21/2023]
Abstract
Cooking time of the common bean is an important trait for consumer preference, with implications for nutrition, health, and environment. For efficient germplasm improvement, breeders need more information on the genetics to identify fast cooking sources with good agronomic properties and molecular breeding tools. In this study, we investigated a broad genetic variation among tropical germplasm from both Andean and Mesoamerican genepools. Four populations were evaluated for cooking time (CKT), water absorption capacity (WAC), and seed weight (SdW): a bi-parental RIL population (DxG), an eight-parental Mesoamerican MAGIC population, an Andean (VEF), and a Mesoamerican (MIP) breeding line panel. A total of 922 lines were evaluated in this study. Significant genetic variation was found in all populations with high heritabilities, ranging from 0.64 to 0.89 for CKT. CKT was related to the color of the seed coat, with the white colored seeds being the ones that cooked the fastest. Marker trait associations were investigated by QTL analysis and GWAS, resulting in the identification of 10 QTL. In populations with Andean germplasm, an inverse correlation of CKT and WAC, and also a QTL on Pv03 that inversely controls CKT and WAC (CKT3.2/WAC3.1) were observed. WAC7.1 was found in both Mesoamerican populations. QTL only explained a small part of the variance, and phenotypic distributions support a more quantitative mode of inheritance. For this reason, we evaluated how genomic prediction (GP) models can capture the genetic variation. GP accuracies for CKT varied, ranging from good results for the MAGIC population (0.55) to lower accuracies in the MIP panel (0.22). The phenotypic characterization of parental material will allow for the cooking time trait to be implemented in the active germplasm improvement programs. Molecular breeding tools can be developed to employ marker-assisted selection or genomic selection, which looks to be a promising tool in some populations to increase the efficiency of breeding activities.
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Affiliation(s)
- Santiago Diaz
- Bean Program, Agrobiodiversity Area, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Daniel Ariza-Suarez
- Bean Program, Agrobiodiversity Area, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Raisa Ramdeen
- Institute of Crop Science, University of Hohenheim, Hohenheim, Germany
| | - Johan Aparicio
- Bean Program, Agrobiodiversity Area, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Nirmala Arunachalam
- Bean Program, Agrobiodiversity Area, International Center for Tropical Agriculture (CIAT), Cali, Colombia
- Departamento de Agronomía, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Bogotá, Colombia
| | | | - Harold Diaz
- Bean Program, Agrobiodiversity Area, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Henry Ruiz
- Bean Program, Agrobiodiversity Area, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Hans-Peter Piepho
- Institute of Crop Science, University of Hohenheim, Hohenheim, Germany
| | - Bodo Raatz
- Bean Program, Agrobiodiversity Area, International Center for Tropical Agriculture (CIAT), Cali, Colombia
- *Correspondence: Bodo Raatz,
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Liu Q, Hobbs HA, Domier LL. Genome-wide association study of the seed transmission rate of soybean mosaic virus and associated traits using two diverse population panels. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:3413-3424. [PMID: 31630210 DOI: 10.1007/s00122-019-03434-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 09/17/2019] [Indexed: 06/10/2023]
Abstract
KEY MESSAGE Genome-wide association analyses identified candidates for genes involved in restricting virus movement into embryonic tissues, suppressing virus-induced seed coat mottling and preserving yield in soybean plants infected with soybean mosaic virus. Soybean mosaic virus (SMV) causes significant reductions in soybean yield and seed quality. Because seedborne infections can serve as primary sources of inoculum for SMV infections, resistance to SMV seed transmission provides a means to limit the impacts of SMV. In this study, two diverse population panels, Pop1 and Pop2, composed of 409 and 199 soybean plant introductions, respectively, were evaluated for SMV seed transmission rate, seed coat mottling, and seed yield from SMV-infected plants. The phenotypic data and genotypic data from the SoySNP50K dataset were analyzed using GAPIT and rrBLUP. For SMV seed transmission rate, a single locus was identified on chromosome 9 in Pop1. For SMV-induced seed coat mottling, loci were identified on chromosome 9 in Pop1 and on chromosome 3 in Pop2. For seed yield from SMV-infected plants, a single locus was identified on chromosome 3 in Pop2 that was within the map interval of a previously described quantitative trait locus for seed number. The high linkage disequilibrium regions surrounding the markers on chromosomes 3 and 9 contained a predicted nonsense-mediated RNA decay gene, multiple pectin methylesterase inhibitor genes (involved in restricting virus movement), two chalcone synthase genes, and a homolog of the yeast Rtf1 gene (involved in RNA-mediated transcriptional gene silencing). The results of this study provided additional insight into the genetic architecture of these three important traits, suggested candidate genes for downstream functional validation, and suggested that genomic prediction would outperform marker-assisted selection for two of the four trait-marker associations.
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Affiliation(s)
- Qiong Liu
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA
| | - Houston A Hobbs
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA
| | - Leslie L Domier
- Soybean/Maize Germplasm, Pathology, and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Urbana, IL, 61801, USA.
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Imai A, Kuniga T, Yoshioka T, Nonaka K, Mitani N, Fukamachi H, Hiehata N, Yamamoto M, Hayashi T. Single-step genomic prediction of fruit-quality traits using phenotypic records of non-genotyped relatives in citrus. PLoS One 2019; 14:e0221880. [PMID: 31465502 PMCID: PMC6715226 DOI: 10.1371/journal.pone.0221880] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 08/17/2019] [Indexed: 11/24/2022] Open
Abstract
The potential of genomic selection (GS) is currently being evaluated for fruit breeding. GS models are usually constructed based on information from both the genotype and phenotype of population. However, information from phenotyped but non-genotyped relatives can also be used to construct GS models, and this additional information can improve their accuracy. In the present study, we evaluated the utility of single-step genomic best linear unbiased prediction (ssGBLUP) in citrus breeding, which is a genomic prediction method that combines the kinship information from genotyped and non-genotyped relatives into a single relationship matrix for a mixed model to apply GS. Fruit weight, sugar content, and acid content of 1,935 citrus individuals, of which 483 had genotype data of 2,354 genome-wide single nucleotide polymorphisms, were evaluated from 2009–2012. The prediction accuracy of ssGBLUP for genotyped individuals was similar to or higher than that of usual genomic best linear unbiased prediction method using only genotyped individuals, especially for sugar content. Therefore, ssGBLUP could yield higher accuracy in genotyped individuals by adding information from non-genotyped relatives. The prediction accuracy of ssGBLUP for non-genotyped individuals was also slightly higher than that of conventional best linear unbiased prediction method using pedigree information. This indicates that ssGBLUP can enhance prediction accuracy of breeding values for non-genotyped individuals using genomic information of genotyped relatives. These results demonstrate the potential of ssGBLUP for fruit breeding, including citrus.
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Affiliation(s)
- Atsushi Imai
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization, Fujimoto, Tsukuba, Ibaraki, Japan
- Graduate School of Life and Environmental Science, University of Tsukuba, Tennodai, Tsukuba, Ibaraki, Japan
| | - Takeshi Kuniga
- Western Region Agricultural Research Center, National Agriculture and Food Research Organization, Senyucho, Zentsuji, Kagawa, Japan
| | - Terutaka Yoshioka
- Western Region Agricultural Research Center, National Agriculture and Food Research Organization, Senyucho, Zentsuji, Kagawa, Japan
| | - Keisuke Nonaka
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization, Okitsunakacho, Shimizu, Shizuoka, Japan
| | - Nobuhito Mitani
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization, Fujimoto, Tsukuba, Ibaraki, Japan
| | - Hiroshi Fukamachi
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization, Okitsunakacho, Shimizu, Shizuoka, Japan
| | - Naofumi Hiehata
- Nagasaki Agricultural and Forestry Technical Development Center, Nagasaki Prefectural Government, Kaizumachi, Isahaya, Nagasaki, Japan
| | - Masashi Yamamoto
- Faculty of Agriculture, Kagoshima University, Korimoto, Kagoshima, Kagoshima, Japan
| | - Takeshi Hayashi
- Graduate School of Life and Environmental Science, University of Tsukuba, Tennodai, Tsukuba, Ibaraki, Japan
- Institute of Crop Science, National Agriculture and Food Research Organization, Kannondai, Tsukuba, Ibaraki, Japan
- * E-mail:
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Wang DR, Guadagno CR, Mao X, Mackay DS, Pleban JR, Baker RL, Weinig C, Jannink JL, Ewers BE. A framework for genomics-informed ecophysiological modeling in plants. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2561-2574. [PMID: 30825375 PMCID: PMC6487588 DOI: 10.1093/jxb/erz090] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 02/18/2019] [Indexed: 05/06/2023]
Abstract
Dynamic process-based plant models capture complex physiological response across time, carrying the potential to extend simulations out to novel environments and lend mechanistic insight to observed phenotypes. Despite the translational opportunities for varietal crop improvement that could be unlocked by linking natural genetic variation to first principles-based modeling, these models are challenging to apply to large populations of related individuals. Here we use a combination of model development, experimental evaluation, and genomic prediction in Brassica rapa L. to set the stage for future large-scale process-based modeling of intraspecific variation. We develop a new canopy growth submodel for B. rapa within the process-based model Terrestrial Regional Ecosystem Exchange Simulator (TREES), test input parameters for feasibility of direct estimation with observed phenotypes across cultivated morphotypes and indirect estimation using genomic prediction on a recombinant inbred line population, and explore model performance on an in silico population under non-stressed and mild water-stressed conditions. We find evidence that the updated whole-plant model has the capacity to distill genotype by environment interaction (G×E) into tractable components. The framework presented offers a means to link genetic variation with environment-modulated plant response and serves as a stepping stone towards large-scale prediction of unphenotyped, genetically related individuals under untested environmental scenarios.
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Affiliation(s)
- Diane R Wang
- Geography Department, University at Buffalo, Buffalo, NY, USA
| | | | - Xiaowei Mao
- Plant Breeding and Genetics Section, Cornell University, Ithaca, NY, USA
| | - D Scott Mackay
- Geography Department, University at Buffalo, Buffalo, NY, USA
| | | | | | - Cynthia Weinig
- Botany Department, University of Wyoming, Laramie, WY, USA
| | - Jean-Luc Jannink
- Plant Breeding and Genetics Section, Cornell University, Ithaca, NY, USA
- USDA-ARS, Ithaca, NY, USA
| | - Brent E Ewers
- Botany Department, University of Wyoming, Laramie, WY, USA
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De Ollas C, Morillón R, Fotopoulos V, Puértolas J, Ollitrault P, Gómez-Cadenas A, Arbona V. Facing Climate Change: Biotechnology of Iconic Mediterranean Woody Crops. FRONTIERS IN PLANT SCIENCE 2019; 10:427. [PMID: 31057569 PMCID: PMC6477659 DOI: 10.3389/fpls.2019.00427] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 03/21/2019] [Indexed: 05/03/2023]
Abstract
The Mediterranean basin is especially sensitive to the adverse outcomes of climate change and especially to variations in rainfall patterns and the incidence of extremely high temperatures. These two concurring adverse environmental conditions will surely have a detrimental effect on crop performance and productivity that will be particularly severe on woody crops such as citrus, olive and grapevine that define the backbone of traditional Mediterranean agriculture. These woody species have been traditionally selected for traits such as improved fruit yield and quality or alteration in harvesting periods, leaving out traits related to plant field performance. This is currently a crucial aspect due to the progressive and imminent effects of global climate change. Although complete genome sequence exists for sweet orange (Citrus sinensis) and clementine (Citrus clementina), olive tree (Olea europaea) and grapevine (Vitis vinifera), the development of biotechnological tools to improve stress tolerance still relies on the study of the available genetic resources including interspecific hybrids, naturally occurring (or induced) polyploids and wild relatives under field conditions. To this respect, post-genomic era studies including transcriptomics, metabolomics and proteomics provide a wide and unbiased view of plant physiology and biochemistry under adverse environmental conditions that, along with high-throughput phenotyping, could contribute to the characterization of plant genotypes exhibiting physiological and/or genetic traits that are correlated to abiotic stress tolerance. The ultimate goal of precision agriculture is to improve crop productivity, in terms of yield and quality, making a sustainable use of land and water resources under adverse environmental conditions using all available biotechnological tools and high-throughput phenotyping. This review focuses on the current state-of-the-art of biotechnological tools such as high throughput -omics and phenotyping on grapevine, citrus and olive and their contribution to plant breeding programs.
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Affiliation(s)
- Carlos De Ollas
- Departament de Ciències Agràries i del Medi Natural, Universitat Jaume I, Castellón de la Plana, Spain
| | - Raphaël Morillón
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Petit-Bourg, France
| | - Vasileios Fotopoulos
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Limassol, Cyprus
| | - Jaime Puértolas
- Lancaster Environment Centre, Lancaster University, Lancaster, United Kingdom
| | - Patrick Ollitrault
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), San-Giuliano, France
| | - Aurelio Gómez-Cadenas
- Departament de Ciències Agràries i del Medi Natural, Universitat Jaume I, Castellón de la Plana, Spain
| | - Vicent Arbona
- Departament de Ciències Agràries i del Medi Natural, Universitat Jaume I, Castellón de la Plana, Spain
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Onogi A. Comparison of F-tests for Univariate and Multivariate Mixed-Effect Models in Genome-Wide Association Mapping. Front Genet 2019; 10:30. [PMID: 30778369 PMCID: PMC6369166 DOI: 10.3389/fgene.2019.00030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 01/17/2019] [Indexed: 01/24/2023] Open
Abstract
Genome-wide association mapping (GWA) has been widely applied to a variety of species to identify genomic regions responsible for quantitative traits. The use of multivariate information could enhance the detection power of GWA. Although mixed-effect models are frequently used for GWA, the utility of F-tests for multivariate mixed-effect models is not well-recognized. Thus, we compared the F-tests for univariate and multivariate mixed-effect models with simulations. The superiority of the multivariate F-test over the univariate test varied depending on three parameters: phenotypic correlation between variates (r), relative size of quantitative trait locus effects between variates (ad), and missing proportion of phenotypic records (mprop). Simulation results showed that, when mprop was low, the multivariate F-test outperformed the univariate test as r and ad differ, and as mprop increased, the multivariate F-test outperformed as ad increased. These observations were consistent with results of the analytical evaluation of the F-value. When mprop was at the maximum, i.e., when no individual had phenotypic values for multiple variates, as in the case of meta-analysis, the multivariate F-test gained more detection power as ad increased. Although using multivariate information in mixed-effect model contexts did not always ensure more detection power than with univariate tests, the multivariate F-test will be a method applied when multivariate data are available because it does not show inflation of signals and could lead to new findings.
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Affiliation(s)
- Akio Onogi
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Japan.,Japan Science and Technology Agency PRESTO, Kawaguchi, Japan
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Choi HK. Translational genomics and multi-omics integrated approaches as a useful strategy for crop breeding. Genes Genomics 2019; 41:133-146. [PMID: 30353370 PMCID: PMC6394800 DOI: 10.1007/s13258-018-0751-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/01/2018] [Indexed: 01/25/2023]
Abstract
Recent next generation sequencing-driven mass production of genomic data and multi-omics-integrated approaches have significantly contributed to broadening and deepening our knowledge on the molecular system of living organisms. Accordingly, translational genomics (TG) approach can play a pivotal role in creating an informational bridge between model systems and relatively less studied plants. This review focuses mainly on addressing recent advancement in omics-related technologies, a diverse array of bioinformatic resources and potential applications of TG for the crop breeding. To accomplish above objectives, information on omics data production, various DBs and high throughput technologies was collected, integrated, and used to analyze current status and future perspectives towards omics-assisted crop breeding. Various omics data and resources have been organized and integrated into the databases and/or bioinformatic infrastructures, and thereby serve as the ome's information center for cross-genome translation of biological data. Although the size of accumulated omics data and availability of reference genomes are different among plant families, translational approaches have been actively progressing to access particular biological characteristics. When multi-layered omics data are integrated in a synthetic manner, it will allow providing a stereoscopic view of dynamic molecular behavior and interacting networks of genes occurring in plants. Consequently, TG approach will lead us to broader and deeper insights into target traits for the plant breeding. Furthermore, such systems approach will renovate conventional breeding programs and accelerate precision crop breeding in the future.
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Affiliation(s)
- Hong-Kyu Choi
- Department of Molecular Genetics, College of Natural Resources and Life Science, Dong-A University, Nakdong-Daero 550-Beongil 37, Saha-Gu, Busan, 49315, Republic of Korea.
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48
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Zaidem ML, Groen SC, Purugganan MD. Evolutionary and ecological functional genomics, from lab to the wild. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:40-55. [PMID: 30444573 DOI: 10.1111/tpj.14167] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 11/10/2018] [Accepted: 11/13/2018] [Indexed: 05/12/2023]
Abstract
Plant phenotypes are the result of both genetic and environmental forces that act to modulate trait expression. Over the last few years, numerous approaches in functional genomics and systems biology have led to a greater understanding of plant phenotypic variation and plant responses to the environment. These approaches, and the questions that they can address, have been loosely termed evolutionary and ecological functional genomics (EEFG), and have been providing key insights on how plants adapt and evolve. In particular, by bringing these studies from the laboratory to the field, EEFG studies allow us to gain greater knowledge of how plants function in their natural contexts.
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Affiliation(s)
- Maricris L Zaidem
- Department of Biology, Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, NY, 10003, USA
| | - Simon C Groen
- Department of Biology, Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, NY, 10003, USA
| | - Michael D Purugganan
- Department of Biology, Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, NY, 10003, USA
- Center for Genomics and Systems Biology, NYU Abu Dhabi Research Institute, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
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49
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Yabe S, Yoshida H, Kajiya-Kanegae H, Yamasaki M, Iwata H, Ebana K, Hayashi T, Nakagawa H. Description of grain weight distribution leading to genomic selection for grain-filling characteristics in rice. PLoS One 2018; 13:e0207627. [PMID: 30458025 PMCID: PMC6245794 DOI: 10.1371/journal.pone.0207627] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 11/02/2018] [Indexed: 01/10/2023] Open
Abstract
Grain-filling ability is one of the factors that controls grain yield in rice (Oryza sativa L.). We developed a method for describing grain weight distribution, which is the probability density function of single grain weight in a panicle, using 128 Japanese rice varieties. With this method, we quantitively analyzed genotypic differences in grain-filling ability and used the grain weight distribution parameters for genomic prediction subject to genetic improvement in grain yield in rice. The novel description method could represent the observed grain weight distribution with five genotype-specific parameters of a mixture of two gamma distributions. The estimated genotype-specific parameters representing the proportion of filled grains had applicability to explain the grain filling ability of genotypes comparable to that of sink-filling rate and the conventionally measured proportion of filled grains, which suggested the efficiency and flexibility of grain weight distribution parameters to handle several genotypes. We revealed that perfectly filled grains have to be prioritized over partially filled grains for the optimum allocation of the source of yield in a panicle, from the analysis for obtaining an ideal shape of grain weight distribution. We conducted genomic prediction of grain weight distribution considering five genotype-specific parameters of the distribution as phenotypes relating to grain filling ability. The proportion of filled grains, average weight of filled grains, and variance of filled grain weight, which were considered to control grain yield to a certain degree, were predicted with accuracies of 0.30, 0.28, and 0.53, respectively. The proposed description method of grain weight distribution facilitated not only the investigation of the optimum allocation of nutrients in a panicle for realizing high grain-filling ability, but also allowed genomic selection of grain weight distribution.
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Affiliation(s)
- Shiori Yabe
- Institute of Crop Science, NARO, Tsukuba, Ibaraki, Japan
- PRESTO, JST, Kawaguchi, Saitama, Japan
| | - Hiroe Yoshida
- Institute for Agro-Environmental Sciences, NARO, Tsukuba, Ibaraki, Japan
| | - Hiromi Kajiya-Kanegae
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo, Japan
| | - Masanori Yamasaki
- Food Resources Education and Research Center, Graduate School of Agricultural Science, Kobe University, Kasai, Hyogo, Japan
| | - Hiroyoshi Iwata
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo, Japan
| | - Kaworu Ebana
- Genetic Resources Center, NARO, Tsukuba, Ibaraki, Japan
| | | | - Hiroshi Nakagawa
- Institute for Agro-Environmental Sciences, NARO, Tsukuba, Ibaraki, Japan
- * E-mail:
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50
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Hiraoka Y, Fukatsu E, Mishima K, Hirao T, Teshima KM, Tamura M, Tsubomura M, Iki T, Kurita M, Takahashi M, Watanabe A. Potential of Genome-Wide Studies in Unrelated Plus Trees of a Coniferous Species, Cryptomeria japonica (Japanese Cedar). FRONTIERS IN PLANT SCIENCE 2018; 9:1322. [PMID: 30254658 PMCID: PMC6141754 DOI: 10.3389/fpls.2018.01322] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 08/22/2018] [Indexed: 06/08/2023]
Abstract
A genome-wide association study (GWAS) was conducted on more than 30,000 single nucleotide polymorphisms (SNPs) in unrelated first-generation plus tree genotypes from three populations of Japanese cedar Cryptomeria japonica D. Don with genomic prediction for traits of growth, wood properties and male fecundity. Among the assessed populations, genetic characteristics including the extent of linkage disequilibrium (LD) and genetic structure differed and these differences are considered to be due to differences in genetic background. Through population-independent GWAS, several significant SNPs found close to the regions associated with each of these traits and shared in common across the populations were identified. The accuracies of genomic predictions were dependent on the traits and populations and reflected the genetic architecture of traits and genetic characteristics. Prediction accuracies using SNPs selected based on GWAS results were similar to those using all SNPs for several combinations of traits and populations. We discussed the application of genome-wide studies for C. japonica improvement.
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Affiliation(s)
- Yuichiro Hiraoka
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Hitachi, Japan
| | - Eitaro Fukatsu
- Kyushu Regional Breeding Office, Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Kumamoto, Japan
| | - Kentaro Mishima
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Hitachi, Japan
| | - Tomonori Hirao
- Forest Bio-Research Center, Forestry and Forest Products Research Institute, Hitachi, Japan
| | | | - Miho Tamura
- Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Miyoko Tsubomura
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Hitachi, Japan
| | - Taiichi Iki
- Tohoku Regional Breeding Office, Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Takizawa, Japan
| | - Manabu Kurita
- Kyushu Regional Breeding Office, Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Kumamoto, Japan
| | - Makoto Takahashi
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Hitachi, Japan
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