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Lazaridi E, Kapazoglou A, Gerakari M, Kleftogianni K, Passa K, Sarri E, Papasotiropoulos V, Tani E, Bebeli PJ. Crop Landraces and Indigenous Varieties: A Valuable Source of Genes for Plant Breeding. PLANTS (BASEL, SWITZERLAND) 2024; 13:758. [PMID: 38592762 PMCID: PMC10975389 DOI: 10.3390/plants13060758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 02/23/2024] [Accepted: 03/02/2024] [Indexed: 04/10/2024]
Abstract
Landraces and indigenous varieties comprise valuable sources of crop species diversity. Their utilization in plant breeding may lead to increased yield and enhanced quality traits, as well as resilience to various abiotic and biotic stresses. Recently, new approaches based on the rapid advancement of genomic technologies such as deciphering of pangenomes, multi-omics tools, marker-assisted selection (MAS), genome-wide association studies (GWAS), and CRISPR/Cas9 gene editing greatly facilitated the exploitation of landraces in modern plant breeding. In this paper, we present a comprehensive overview of the implementation of new genomic technologies and highlight their importance in pinpointing the genetic basis of desirable traits in landraces and indigenous varieties of annual, perennial herbaceous, and woody crop species cultivated in the Mediterranean region. The need for further employment of advanced -omic technologies to unravel the full potential of landraces and indigenous varieties underutilized genetic diversity is also indicated. Ultimately, the large amount of genomic data emerging from the investigation of landraces and indigenous varieties reveals their potential as a source of valuable genes and traits for breeding. The role of landraces and indigenous varieties in mitigating the ongoing risks posed by climate change in agriculture and food security is also highlighted.
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Affiliation(s)
- Efstathia Lazaridi
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Aliki Kapazoglou
- Institute of Olive Tree, Subtropical Crops and Viticulture (IOSV), Department of Vitis, Hellenic Agricultural Organization-Dimitra (ELGO-Dimitra), Sofokli Venizelou 1, Lykovrysi, 14123 Athens, Greece;
| | - Maria Gerakari
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Konstantina Kleftogianni
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Kondylia Passa
- Department of Agriculture, University of Patras, Nea Ktiria, 30200 Messolonghi, Greece;
| | - Efi Sarri
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Vasileios Papasotiropoulos
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Eleni Tani
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Penelope J. Bebeli
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
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Zenoni S, Savoi S, Busatto N, Tornielli GB, Costa F. Molecular regulation of apple and grape ripening: exploring common and distinct transcriptional aspects of representative climacteric and non-climacteric fruits. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6207-6223. [PMID: 37591311 PMCID: PMC10627160 DOI: 10.1093/jxb/erad324] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 08/14/2023] [Indexed: 08/19/2023]
Abstract
Fleshy fruits of angiosperms are organs specialized for promoting seed dispersal by attracting herbivores and enticing them to consume the organ and the seeds it contains. Ripening can be broadly defined as the processes serving as a plant strategy to make the fleshy fruit appealing to animals, consisting of a coordinated series of changes in color, texture, aroma, and flavor that result from an intricate interplay of genetically and epigenetically programmed events. The ripening of fruits can be categorized into two types: climacteric, which is characterized by a rapid increase in respiration rate typically accompanied by a burst of ethylene production, and non-climacteric, in which this pronounced peak in respiration is absent. Here we review current knowledge of transcriptomic changes taking place in apple (Malus × domestica, climacteric) and grapevine (Vitis vinifera, non-climacteric) fruit during ripening, with the aim of highlighting specific and common hormonal and molecular events governing the process in the two species. With this perspective, we found that specific NAC transcription factor members participate in ripening initiation in grape and are involved in restoring normal physiological ripening progression in impaired fruit ripening in apple. These elements suggest the existence of a common regulatory mechanism operated by NAC transcription factors and auxin in the two species.
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Affiliation(s)
- Sara Zenoni
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Stefania Savoi
- Department of Agricultural, Forest, and Food Sciences, University of Turin, Largo Paolo Braccini 2, 10095 Grugliasco (Torino), Italy
| | - Nicola Busatto
- Research and Innovation Centre, Fondazione Edmund Mach, Via Mach 1, 39098 San Michele all’Adige (Trento), Italy
| | | | - Fabrizio Costa
- Center Agriculture Food Environment (C3A), University of Trento, Via Mach 1, 39098 San Michele all’Adige (Trento), Italy
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Chen X, Cornille A, An N, Xing L, Ma J, Zhao C, Wang Y, Han M, Zhang D. The East Asian wild apples, Malus baccata (L.) Borkh and Malus hupehensis (Pamp.) Rehder., are additional contributors to the genomes of cultivated European and Chinese varieties. Mol Ecol 2023; 32:5125-5139. [PMID: 35510734 DOI: 10.1111/mec.16485] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 04/09/2022] [Accepted: 04/17/2022] [Indexed: 11/29/2022]
Abstract
The domestication process in long-lived plant perennials differs dramatically from that of annuals, with a huge amount of genetic exchange between crop and wild populations. Though apple is a major fruit crop grown worldwide, the contribution of wild apple species to the genetic makeup of the cultivated apple genome remains a topic of intense study. We used population genomics approaches to investigate the contributions of several wild apple species to European and Chinese rootstock and dessert genomes, with a focus on the extent of wild-crop gene flow. Population genetic structure inferences revealed that the East Asian wild apples, Malus baccata (L.) Borkh and M. hupehensis (Pamp.), form a single panmictic group, and that the European dessert and rootstock apples form a specific gene pool whereas the Chinese dessert and rootstock apples were a mixture of three wild gene pools, suggesting different evolutionary histories of European and Chinese apple varieties. Coalescent-based inferences and gene flow estimates indicated that M. baccata - M. hupehensis contributed to the genome of both European and Chinese cultivated apples through wild-to-crop introgressions, and not as an initial contributor as previously supposed. We also confirmed the contribution through wild-to-crop introgressions of Malus sylvestris Mill. to the cultivated apple genome. Apple tree domestication is therefore one example in woody perennials that involved gene flow from several wild species from multiple geographical areas. This study provides an example of a complex protracted process of domestication in long-lived plant perennials, and is a starting point for apple breeding programmes.
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Affiliation(s)
- Xilong Chen
- College of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, Northwest A&F University, Yangling, Shaanxi, China
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Gif-sur-Yvette, France
| | - Amandine Cornille
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Gif-sur-Yvette, France
| | - Na An
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Libo Xing
- College of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, Northwest A&F University, Yangling, Shaanxi, China
| | - Juanjuan Ma
- College of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, Northwest A&F University, Yangling, Shaanxi, China
| | - Caiping Zhao
- College of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, Northwest A&F University, Yangling, Shaanxi, China
| | - Yibin Wang
- College of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, Northwest A&F University, Yangling, Shaanxi, China
| | - Mingyu Han
- College of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, Northwest A&F University, Yangling, Shaanxi, China
| | - Dong Zhang
- College of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, Northwest A&F University, Yangling, Shaanxi, China
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Chen X, Avia K, Forler A, Remoué C, Venon A, Rousselet A, Lucas G, Kwarteng AO, Rover R, Le Guilloux M, Belcram H, Combes V, Corti H, Olverà-Vazquez S, Falque M, Alins G, Kirisits T, Ursu TM, Roman A, Volk GM, Bazot S, Cornille A. Ecological and evolutionary drivers of phenotypic and genetic variation in the European crabapple [Malus sylvestris (L.) Mill.], a wild relative of the cultivated apple. ANNALS OF BOTANY 2023; 131:1025-1037. [PMID: 37148364 PMCID: PMC10332392 DOI: 10.1093/aob/mcad061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 05/03/2023] [Indexed: 05/08/2023]
Abstract
BACKGROUND AND AIMS Studying the relationship between phenotypic and genetic variation in populations distributed across environmental gradients can help us to understand the ecological and evolutionary processes involved in population divergence. We investigated the patterns of genetic and phenotypic diversity in the European crabapple, Malus sylvestris, a wild relative of the cultivated apple (Malus domestica) that occurs naturally across Europe in areas subjected to different climatic conditions, to test for divergence among populations. METHODS Growth rates and traits related to carbon uptake in seedlings collected across Europe were measured in controlled conditions and associated with the genetic status of the seedlings, which was assessed using 13 microsatellite loci and the Bayesian clustering method. Isolation-by-distance, isolation-by-climate and isolation-by-adaptation patterns, which can explain genetic and phenotypic differentiation among M. sylvestris populations, were also tested. KEY RESULTS A total of 11.6 % of seedlings were introgressed by M. domestica, indicating that crop-wild gene flow is ongoing in Europe. The remaining seedlings (88.4 %) belonged to seven M. sylvestris populations. Significant phenotypic trait variation among M. sylvestris populations was observed. We did not observe significant isolation by adaptation; however, the significant association between genetic variation and the climate during the Last Glacial Maximum suggests that there has been local adaptation of M. sylvestris to past climates. CONCLUSIONS This study provides insight into the phenotypic and genetic differentiation among populations of a wild relative of the cultivated apple. This might help us to make better use of its diversity and provide options for mitigating the impact of climate change on the cultivated apple through breeding.
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Affiliation(s)
- X Chen
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - K Avia
- Université de Strasbourg, INRAE, SVQV UMR-A 1131, F-68000 Colmar, France
| | - A Forler
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - C Remoué
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - A Venon
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - A Rousselet
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - G Lucas
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - A O Kwarteng
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - R Rover
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - M Le Guilloux
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - H Belcram
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - V Combes
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - H Corti
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - S Olverà-Vazquez
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - M Falque
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - G Alins
- Institut de Recerca i Tecnologia Agroalimentàries, IRTA-Fruit Production, PCiTAL, Parc 21 de Gardeny, edifici Fruitcentre, 25003 Lleida, Spain
| | - T Kirisits
- Institute of Forest Entomology, Forest Pathology and Forest Protection (IFFF), Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences, Vienna (BOKU), Peter-Jordan-Straße 82 (Franz Schwackhöfer-Haus), A-1190 Vienna, Austria
| | - T M Ursu
- NIRDBS, Institute of Biological Research Cluj-Napoca, 48 Republicii St., Cluj-Napoca, Romania
| | - A Roman
- NIRDBS, Institute of Biological Research Cluj-Napoca, 48 Republicii St., Cluj-Napoca, Romania
| | - G M Volk
- USDA-ARS National Laboratory for Genetic Resources Preservation, 1111 South Mason Street, Fort Collins, CO 80521, USA
| | - S Bazot
- Ecologie Systématique et Evolution, CNRS, AgroParisTech, Ecologie Systématique Evolution, Université Paris‐Saclay, Orsay, France
| | - A Cornille
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
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Cong L, Ling H, Liu S, Wang A, Zhai R, Yang C, Wang Z, Xu L. 'Yunnan' quince rootstock promoted flower bud formation of 'Abbé Fetel' pear by altering hormone levels and PbAGL9 expression. JOURNAL OF PLANT PHYSIOLOGY 2023; 282:153924. [PMID: 36805518 DOI: 10.1016/j.jplph.2023.153924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 12/21/2022] [Accepted: 01/11/2023] [Indexed: 06/18/2023]
Abstract
Flower busd formation is an important plant growth process. It has been reported that dwarfing rootstocks can significantly affect the flower bud formation of scions. In this study, we found the dwarfing rootstock 'Yunnan' quince could significantly increase the flowering rate of 'Abbé Fetel' pear scions. The RNA-sequencing data revealed significant changes in the expression of genes related to hormone pathways. Furthermore, hormone analyses indicated that 'Yunnan' quince significantly decreased the GA3 content and increased the cytokinin/auxin ratio in 'Abbé Fetel' pear apical buds. The hormone contents were consistent with the RNA-sequencing data. Moreover, we found the flower development-related genes PbAGL9 and PbCAL-A1 were significantly upregulated and PbTFL1 was significantly downregulated in 'Abbé Fetel'/'Yunnan' quince apical buds. To further clarify the relationship between hormones and flowering-related genes, a hormone response assay was carried out. We found the expression levels of PbCAl-A1, PbTFL1 and PbAGL9 were regulated by hormones including GA3, CPPU and NAA. Y1H and dual-luciferase assays indicated that PbAGL9 significantly decreased the promoter activity of PbTFL1. In summary, 'Yunnan' quince upregulated PbCAL-A1 and PbAGL9, and downregulated PbTFL1 expression by decreasing the GA3 content and increasing the cytokinin/auxin ratio in 'Abbé Fetel' pear apical buds. Additionally, 'Yunnan' quince down-regulate PbTFL1 by upregulating the expression of PbAGL9, and eventually promoted floral induction in 'Abbé Fetel' pear.
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Affiliation(s)
- Liu Cong
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province, 712100, China.
| | - Hutian Ling
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province, 712100, China.
| | - Shanshan Liu
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province, 712100, China.
| | - Azheng Wang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province, 712100, China.
| | - Rui Zhai
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province, 712100, China.
| | - Chengquan Yang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province, 712100, China.
| | - Zhigang Wang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province, 712100, China.
| | - Lingfei Xu
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province, 712100, China.
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Sestras RE, Sestras AF. Quantitative Traits of Interest in Apple Breeding and Their Implications for Selection. PLANTS (BASEL, SWITZERLAND) 2023; 12:903. [PMID: 36840249 PMCID: PMC9964287 DOI: 10.3390/plants12040903] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
Apple breeding is a laborious and long-lasting process that requires qualified resources, land, time, and funds. In this study, more than 5000 F1 apple hybrids from direct and testcrosses were analyzed. The results revealed how the phenotypic expression of the main quantitative traits of interest assessed in five half-sib families was controlled by the additive genetic effects and by non-additive effects of dominance and epistasis. The statistical number of hybrids required to ensure efficient selection increased exponentially with the number of desirable traits. The minimum number of progenies required to obtain a hybrid with associated quantitative traits of agronomic interest was highly variable. For two independent traits essential in selection (fruit size and quality), but incorporated together in the same hybrid, the statistical number was between about 30 and 300. If three more cumulative traits were added (a large number of fruits per tree, resistance/tolerance to apple scab, and powdery mildew attack), the limits increased to between 1500 and 18,000. The study highlighted the need for new apple varieties due to the narrowing of the genetic diversity of the cultivated species and how the choice of parents used in hybridizations (as well as the objectives pursued in the selection) can increase the efficiency of apple breeding.
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Affiliation(s)
- Radu E. Sestras
- Department of Horticulture and Landscape, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, 3–5 Manastur Street, 400372 Cluj-Napoca, Romania
| | - Adriana F. Sestras
- Department of Forestry, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, 3–5 Manastur Street, 400372 Cluj-Napoca, Romania
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Schaller A, Vanderzande S, Peace C. Deducing genotypes for loci of interest from SNP array data via haplotype sharing, demonstrated for apple and cherry. PLoS One 2023; 18:e0272888. [PMID: 36749762 PMCID: PMC9904487 DOI: 10.1371/journal.pone.0272888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 01/24/2023] [Indexed: 02/08/2023] Open
Abstract
Breeders, collection curators, and other germplasm users require genetic information, both genome-wide and locus-specific, to effectively manage their genetically diverse plant material. SNP arrays have become the preferred platform to provide genome-wide genetic profiles for elite germplasm and could also provide locus-specific genotypic information. However, genotypic information for loci of interest such as those within PCR-based DNA fingerprinting panels and trait-predictive DNA tests is not readily extracted from SNP array data, thus creating a disconnect between historic and new data sets. This study aimed to establish a method for deducing genotypes at loci of interest from their associated SNP haplotypes, demonstrated for two fruit crops and three locus types: quantitative trait loci Ma and Ma3 for acidity in apple, apple fingerprinting microsatellite marker GD12, and Mendelian trait locus Rf for sweet cherry fruit color. Using phased data from an apple 8K SNP array and sweet cherry 6K SNP array, unique haplotypes spanning each target locus were associated with alleles of important breeding parents. These haplotypes were compared via identity-by-descent (IBD) or identity-by-state (IBS) to haplotypes present in germplasm important to U.S. apple and cherry breeding programs to deduce target locus alleles in this germplasm. While IBD segments were confidently tracked through pedigrees, confidence in allele identity among IBS segments used a shared length threshold. At least one allele per locus was deduced for 64-93% of the 181 individuals. Successful validation compared deduced Rf and GD12 genotypes with reported and newly obtained genotypes. Our approach can efficiently merge and expand genotypic data sets, deducing missing data and identifying errors, and is appropriate for any crop with SNP array data and historic genotypic data sets, especially where linkage disequilibrium is high. Locus-specific genotypic information extracted from genome-wide SNP data is expected to enhance confidence in management of genetic resources.
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Affiliation(s)
- Alexander Schaller
- Department of Horticulture, Washington State University, Pullman, WA, United States of America
| | - Stijn Vanderzande
- Department of Horticulture, Washington State University, Pullman, WA, United States of America
| | - Cameron Peace
- Department of Horticulture, Washington State University, Pullman, WA, United States of America
- * E-mail:
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Manzoor I, Samantara K, Bhat MS, Farooq I, Bhat KM, Mir MA, Wani SH. Advances in genomics for diversity studies and trait improvement in temperate fruit and nut crops under changing climatic scenarios. FRONTIERS IN PLANT SCIENCE 2023; 13:1048217. [PMID: 36743560 PMCID: PMC9893892 DOI: 10.3389/fpls.2022.1048217] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/09/2022] [Indexed: 06/18/2023]
Abstract
Genetic improvement of temperate fruit and nut crops through conventional breeding methods is not sufficient alone due to its extreme time-consuming, cost-intensive, and hard-to-handle approach. Again, few other constraints that are associated with these species, viz., their long juvenile period, high heterozygosity, sterility, presence of sexual incompatibility, polyploidy, etc., make their selection and improvement process more complicated. Therefore, to promote precise and accurate selection of plants based on their genotypes, supplement of advanced biotechnological tools, viz., molecular marker approaches along with traditional breeding methods, is highly required in these species. Different markers, especially the molecular ones, enable direct selection of genomic regions governing the trait of interest such as high quality, yield, and resistance to abiotic and biotic stresses instead of the trait itself, thus saving the overall time and space and helping screen fruit quality and other related desired traits at early stages. The availability of molecular markers like SNP (single-nucleotide polymorphism), DArT (Diversity Arrays Technology) markers, and dense molecular genetic maps in crop plants, including fruit and nut crops, led to a revelation of facts from genetic markers, thus assisting in precise line selection. This review highlighted several aspects of the molecular marker approach that opens up tremendous possibilities to reveal valuable information about genetic diversity and phylogeny to boost the efficacy of selection in temperate fruit crops through genome sequencing and thus cultivar improvement with respect to adaptability and biotic and abiotic stress resistance in temperate fruit and nut species.
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Affiliation(s)
- Ikra Manzoor
- Division of Fruit Science, Faculty of Horticulture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Kajal Samantara
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Siksha ‘O’ Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
| | - Momin Showkat Bhat
- Division of Floriculture and Landscape Architecture, Faculty of Horticulture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Iqra Farooq
- Field Station Bonera, Pulwama, Council of Industrial and Scientific Research (CSIR) Indian Institute of Integrative Medicine, J&K, Jammu, India
| | - Khalid Mushtaq Bhat
- Division of Fruit Science, Faculty of Horticulture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Mohammad Amin Mir
- Ambri Apple Research Centre, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shopian, India
| | - Shabir Hussain Wani
- Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Jammu and Kashmir, Anantnag, India
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9
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Kapazoglou A, Gerakari M, Lazaridi E, Kleftogianni K, Sarri E, Tani E, Bebeli PJ. Crop Wild Relatives: A Valuable Source of Tolerance to Various Abiotic Stresses. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12020328. [PMID: 36679041 PMCID: PMC9861506 DOI: 10.3390/plants12020328] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 05/27/2023]
Abstract
Global climate change is one of the major constraints limiting plant growth, production, and sustainability worldwide. Moreover, breeding efforts in the past years have focused on improving certain favorable crop traits, leading to genetic bottlenecks. The use of crop wild relatives (CWRs) to expand genetic diversity and improve crop adaptability seems to be a promising and sustainable approach for crop improvement in the context of the ongoing climate challenges. In this review, we present the progress that has been achieved towards CWRs exploitation for enhanced resilience against major abiotic stressors (e.g., water deficiency, increased salinity, and extreme temperatures) in crops of high nutritional and economic value, such as tomato, legumes, and several woody perennial crops. The advances in -omics technologies have facilitated the elucidation of the molecular mechanisms that may underlie abiotic stress tolerance. Comparative analyses of whole genome sequencing (WGS) and transcriptomic profiling (RNA-seq) data between crops and their wild relative counterparts have unraveled important information with respect to the molecular basis of tolerance to abiotic stressors. These studies have uncovered genomic regions, specific stress-responsive genes, gene networks, and biochemical pathways associated with resilience to adverse conditions, such as heat, cold, drought, and salinity, and provide useful tools for the development of molecular markers to be used in breeding programs. CWRs constitute a highly valuable resource of genetic diversity, and by exploiting the full potential of this extended allele pool, new traits conferring abiotic-stress tolerance may be introgressed into cultivated varieties leading to superior and resilient genotypes. Future breeding programs may greatly benefit from CWRs utilization for overcoming crop production challenges arising from extreme environmental conditions.
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Affiliation(s)
- Aliki Kapazoglou
- Institute of Olive Tree, Subtropical Crops and Viticulture (IOSV), Department of Vitis, Hellenic Agricultural Organization-Dimitra (ELGO-Dimitra), Sofokli Venizelou 1, Lykovrysi, 14123 Athens, Greece
| | - Maria Gerakari
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Efstathia Lazaridi
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Konstantina Kleftogianni
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Efi Sarri
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Eleni Tani
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Penelope J. Bebeli
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
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10
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Jahed KR, Hirst PM. Fruit growth and development in apple: a molecular, genomics and epigenetics perspective. FRONTIERS IN PLANT SCIENCE 2023; 14:1122397. [PMID: 37123845 PMCID: PMC10130390 DOI: 10.3389/fpls.2023.1122397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/13/2023] [Indexed: 05/03/2023]
Abstract
Fruit growth and development are physiological processes controlled by several internal and external factors. This complex regulatory mechanism comprises a series of events occurring in a chronological order over a growing season. Understanding the underlying mechanism of fruit development events, however, requires consideration of the events occurring prior to fruit development such as flowering, pollination, fertilization, and fruit set. Such events are interrelated and occur in a sequential order. Recent advances in high-throughput sequencing technology in conjunction with improved statistical and computational methods have empowered science to identify some of the major molecular components and mechanisms involved in the regulation of fruit growth and have supplied encouraging successes in associating genotypic differentiation with phenotypic observations. As a result, multiple approaches have been developed to dissect such complex regulatory machinery and understand the genetic basis controlling these processes. These methods include transcriptomic analysis, quantitative trait loci (QTLs) mapping, whole-genome approach, and epigenetics analyses. This review offers a comprehensive overview of the molecular, genomic and epigenetics perspective of apple fruit growth and development that defines the final fruit size and provides a detailed analysis of the mechanisms by which fruit growth and development are controlled. Though the main emphasis of this article is on the molecular, genomic and epigenetics aspects of fruit growth and development, we will also deliver a brief overview on events occurring prior to fruit growth.
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11
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Khan A, Korban SS. Breeding and genetics of disease resistance in temperate fruit trees: challenges and new opportunities. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3961-3985. [PMID: 35441862 DOI: 10.1007/s00122-022-04093-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 03/29/2022] [Indexed: 06/14/2023]
Abstract
Climate change, large monocultures of disease-susceptible cultivars, overuse of pesticides, and the emergence of new pathogens or pathogenic strains causing economic losses are all major threats to our environment, health, food, and nutritional supply. Temperate tree fruit crops belonging to the Rosaceae family are the most economically important and widely grown fruit crops. These long-lived crops are under attack from many different pathogens, incurring major economic losses. Multiple chemical sprays to control various diseases annually is a common practice, resulting in significant input costs, as well as environmental and health concerns. Breeding for disease resistance has been undertaken primarily in pome fruit crops (apples and pears) for a few fungal and bacterial diseases, and to a lesser extent in some stone fruit crops. These breeding efforts have taken multiple decades due to the biological constraints and complex genetics of these tree fruit crops. Over the past couple of decades, major advances have been made in genetic and physical mapping, genomics, biotechnology, genome sequencing, and phenomics, along with accumulation of large germplasm collections in repositories. These valuable resources offer opportunities to make significant advances in greatly reducing the time needed to either develop new cultivars or modify existing economic cultivars for enhanced resistance to multiple diseases. This review will cover current knowledge, challenges, and opportunities in breeding for disease resistance in temperate tree fruit crops.
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Affiliation(s)
- Awais Khan
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY, 14456, USA.
| | - Schuyler S Korban
- Department of Natural Sciences and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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12
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Prudencio AS, Devin SR, Mahdavi SME, Martínez-García PJ, Salazar JA, Martínez-Gómez P. Spontaneous, Artificial, and Genome Editing-Mediated Mutations in Prunus. Int J Mol Sci 2022; 23:ijms232113273. [PMID: 36362061 PMCID: PMC9653787 DOI: 10.3390/ijms232113273] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/27/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022] Open
Abstract
Mutation is a source of genetic diversity widely used in breeding programs for the acquisition of agronomically interesting characters in commercial varieties of the Prunus species, as well as in the rest of crop species. Mutation can occur in nature at a very low frequency or can be induced artificially. Spontaneous or bud sport mutations in somatic cells can be vegetatively propagated to get an individual with the mutant phenotype. Unlike animals, plants have unlimited growth and totipotent cells that let somatic mutations to be transmitted to the progeny. On the other hand, in vitro tissue culture makes it possible to induce mutation in plant material and perform large screenings for mutant’s selection and cleaning of chimeras. Finally, targeted mutagenesis has been boosted by the application of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas9 and Transcription activator-like effector nuclease (TALEN) editing technologies. Over the last few decades, environmental stressors such as global warming have been threatening the supply of global demand for food based on population growth in the near future. For this purpose, the release of new varieties adapted to such changes is a requisite, and selected or generated Prunus mutants by properly regulated mechanisms could be helpful to this task. In this work, we reviewed the most relevant mutations for breeding traits in Prunus species such as flowering time, self-compatibility, fruit quality, and disease tolerance, including new molecular perspectives in the present postgenomic era including CRISPR/Cas9 and TALEN editing technologies.
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Affiliation(s)
- Angel S. Prudencio
- Department of Plant Breeding, Centro de Edafología y Biología Apliacada del Segura-Consejo Superior de Investigaciones Científicas (CEBAS-CSIC), 30100 Espinardo, Spain
| | - Sama Rahimi Devin
- Department of Horticultural Science, College of Agriculture, Shiraz University, Shiraz 7144165186, Iran
| | | | - Pedro J. Martínez-García
- Department of Plant Breeding, Centro de Edafología y Biología Apliacada del Segura-Consejo Superior de Investigaciones Científicas (CEBAS-CSIC), 30100 Espinardo, Spain
| | - Juan A. Salazar
- Department of Plant Breeding, Centro de Edafología y Biología Apliacada del Segura-Consejo Superior de Investigaciones Científicas (CEBAS-CSIC), 30100 Espinardo, Spain
| | - Pedro Martínez-Gómez
- Department of Plant Breeding, Centro de Edafología y Biología Apliacada del Segura-Consejo Superior de Investigaciones Científicas (CEBAS-CSIC), 30100 Espinardo, Spain
- Correspondence: ; Tel.: +34-968-396-200
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13
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Volk GM, Peace CP, Henk AD, Howard NP. DNA profiling with the 20K apple SNP array reveals Malus domestica hybridization and admixture in M. sieversii, M. orientalis, and M. sylvestris genebank accessions. FRONTIERS IN PLANT SCIENCE 2022; 13:1015658. [PMID: 36311081 PMCID: PMC9606829 DOI: 10.3389/fpls.2022.1015658] [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: 08/09/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
The USDA-ARS National Plant Germplasm System (NPGS) apple collection in Geneva, NY, USA maintains accessions of the primary Malus domestica (Suckow) Borkh. progenitor species M. sieversii (Ledeb.) M. Roem., M. orientalis Uglitzk., and M. sylvestris (L.) Mill. Many of these accessions originated from seeds that were collected from wild populations in the species' centers of diversity. Some of these accessions have fruit phenotypes that suggest recent M. domestica hybridization, which if true would represent crop contamination of wild species populations and mislabeled species status of NPGS accessions. Pedigree connections and admixture between M. domestica and its progenitor species can be readily identified with apple SNP array data, despite such arrays not being designed for these purposes. To investigate species purity, most (463 accessions) of the NPGS accessions labeled as these three progenitor species were genotyped using the 20K apple SNP array. DNA profiles obtained were compared with a dataset of more than 5000 unique M. domestica apple cultivars. Only 212 accessions (151 M. sieversii, 26 M. orientalis, and 35 M. sylvestris) were identified as "pure" species representatives because their DNA profiles did not exhibit genotypic signatures of recent hybridization with M. domestica. Twenty-one accessions (17 M. sieversii, 1 M. orientalis, and 3 M. sylvestris) previously labeled as wild species were instead fully M. domestica. Previously unrealized hybridization and admixture between wild species and M. domestica was identified in 230 accessions (215 M. sieversii, 9 M. orientalis, and 6 M. sylvestris). Among these species-mislabeled accessions, 'Alexander', 'Gold Reinette', 'Charlamoff', 'Rosmarina Bianca', and 'King of the Pippins' were the most frequently detected M. domestica parents or grandparents. These results have implications for collection management, including germplasm distribution, and might affect conclusions of previous research focused on these three progenitor species in the NPGS apple collection. Specifically, accessions received from the NPGS for breeding and genomics, genetics, and evolutionary biology research might not be truly representative of their previously assigned species.
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Affiliation(s)
- Gayle M. Volk
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS) National Laboratory for Genetic Resources Preservation, Fort Collins, CO, United States
| | - Cameron P. Peace
- Department of Horticulture, Washington State University, Pullman, WA, United States
| | - Adam D. Henk
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS) National Laboratory for Genetic Resources Preservation, Fort Collins, CO, United States
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14
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Chasing Consistency: An Update of the TCP Gene Family of Malus × Domestica. Genes (Basel) 2022; 13:genes13101696. [PMID: 36292581 PMCID: PMC9601442 DOI: 10.3390/genes13101696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/09/2022] [Accepted: 09/17/2022] [Indexed: 11/17/2022] Open
Abstract
The 52 members of the Teosinte-Branched 1/Cycloidea/Proliferating Cell Factors (TCP) Transcription Factor gene family in Malus × domestica (M. × domestica) were identified in 2014 on the first genome assembly, which was released in 2010. In 2017, a higher quality genome assembly for apple was released and is now considered to be the reference genome. Moreover, as in several other species, the identified TCP genes were named based on the relative position of the genes on the chromosomes. The present work consists of an update of the TCP gene family based on the latest genome assembly of M. × domestica. Compared to the previous classification, the number of TCP genes decreased from 52 to 40 as a result of the addition of three sequences and the deduction of 15. An analysis of the intragenic identity led to the identification of 15 pairs of orthologs, shedding light on the forces that shaped the evolution of this gene family. Furthermore, a revised nomenclature system is proposed that is based both on the intragenic identity and the homology with Arabidopsis thaliana (A. thaliana) TCPs in an effort to set a common standard for the TCP classification that will facilitate any future interspecific analysis.
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15
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Asghar S, Xiong Y, Che M, Fan X, Li H, Wang Y, Xu X, Li W, Han Z. Transcriptome analysis reveals the effects of strigolactone on shoot regeneration of apple. PLANT CELL REPORTS 2022; 41:1613-1626. [PMID: 35680714 DOI: 10.1007/s00299-022-02882-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
We have demonstrated that strigolactone inhibitor, Tis108, could be used to improve shoot regeneration of apple, and provided insights into the molecular mechanism of strigolactone-mediated inhibition of adventitious shoot formation. Lack of an efficient transformation system largely stagnated the application of transgenic and CRISPR technology in apple rootstock. High shoot regeneration ability is an important basis for establishing an effective transformation system. In this study, we first demonstrated the inhibitory effects of strigolactones on the adventitious shoot formation of apple rootstock M26. Next, we successfully verified that strigolactone-biosynthesis inhibitor, Tis108, could be used to improve the shoot regeneration of woody plants. Our results also suggest strigolactone-biosynthesis gene, MdCCD7, can be a target gene for biotechnological improvements of shoot regeneration capacity. Furthermore, we have employed transcriptome analysis to reveal the molecular mechanism of strigolactone-mediated inhibition of adventitious shoot formation. Differentially expressed genes associated with photosynthesis, secondary growth, and organ development were identified. WGCNA suggests SLs might affect shoot regeneration through interaction with other hormones, especially, auxin, cytokinin, and ethylene. We were able to identify important candidate genes mediating the cross-talk between strigolactone and other hormones during the process of adventitious shoot formation. Overall, our findings not only propose a useful chemical for improving shoot regeneration in practice but also provide insights into the molecular mechanism of strigolactone-mediated inhibition of adventitious shoot formation.
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Affiliation(s)
- Sumeera Asghar
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yao Xiong
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Meng Che
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xingqiang Fan
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Hui Li
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yi Wang
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xuefeng Xu
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Wei Li
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China.
| | - Zhenhai Han
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China.
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16
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Tian Y, Thrimawithana A, Ding T, Guo J, Gleave A, Chagné D, Ampomah‐Dwamena C, Ireland HS, Schaffer RJ, Luo Z, Wang M, An X, Wang D, Gao Y, Wang K, Zhang H, Zhang R, Zhou Z, Yan Z, Zhang L, Zhang C, Cong P, Deng CH, Yao J. Transposon insertions regulate genome-wide allele-specific expression and underpin flower colour variations in apple (Malus spp.). PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1285-1297. [PMID: 35258172 PMCID: PMC9241373 DOI: 10.1111/pbi.13806] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 02/20/2022] [Accepted: 02/25/2022] [Indexed: 06/14/2023]
Abstract
Allele-specific expression (ASE) can lead to phenotypic diversity and evolution. However, the mechanisms regulating ASE are not well understood, particularly in woody perennial plants. In this study, we investigated ASE genes in the apple cultivar 'Royal Gala' (RG). A high quality chromosome-level genome was assembled using a homozygous tetra-haploid RG plant, derived from anther cultures. Using RNA-sequencing (RNA-seq) data from RG flower and fruit tissues, we identified 2091 ASE genes. Compared with the haploid genome of 'Golden Delicious' (GD), a parent of RG, we distinguished the genomic sequences between the two alleles of 817 ASE genes, and further identified allele-specific presence of a transposable element (TE) in the upstream region of 354 ASE genes. These included MYB110a that encodes a transcription factor regulating anthocyanin biosynthesis. Interestingly, another ASE gene, MYB10 also showed an allele-specific TE insertion and was identified using genome data of other apple cultivars. The presence of the TE insertion in both MYB genes was positively associated with ASE and anthocyanin accumulation in apple petals through analysis of 231 apple accessions, and thus underpins apple flower colour evolution. Our study demonstrated the importance of TEs in regulating ASE on a genome-wide scale and presents a novel method for rapid identification of ASE genes and their regulatory elements in plants.
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Affiliation(s)
- Yi Tian
- Research Institute of PomologyChinese Academy of Agricultural SciencesXinchengChina
- Present address:
Hebei Agricultural UniversityBaodingChina
| | - Amali Thrimawithana
- The New Zealand Institute for Plant and Food Research Limited (PFR)Mount Albert Research CentreAucklandNew Zealand
| | - Tiyu Ding
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Jian Guo
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Andrew Gleave
- The New Zealand Institute for Plant and Food Research Limited (PFR)Mount Albert Research CentreAucklandNew Zealand
| | - David Chagné
- PFRPalmerston North Research CentrePalmerston NorthNew Zealand
| | - Charles Ampomah‐Dwamena
- The New Zealand Institute for Plant and Food Research Limited (PFR)Mount Albert Research CentreAucklandNew Zealand
| | - Hilary S. Ireland
- The New Zealand Institute for Plant and Food Research Limited (PFR)Mount Albert Research CentreAucklandNew Zealand
| | - Robert J. Schaffer
- The New Zealand Institute for Plant and Food Research Limited (PFR)Mount Albert Research CentreAucklandNew Zealand
- School of Biological SciencesAuckland Mail CentreThe University of AucklandAucklandNew Zealand
| | - Zhiwei Luo
- The New Zealand Institute for Plant and Food Research Limited (PFR)Mount Albert Research CentreAucklandNew Zealand
| | - Meili Wang
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Xiuhong An
- Research Institute of PomologyChinese Academy of Agricultural SciencesXinchengChina
- Present address:
Hebei Agricultural UniversityBaodingChina
| | - Dajiang Wang
- Research Institute of PomologyChinese Academy of Agricultural SciencesXinchengChina
| | - Yuan Gao
- Research Institute of PomologyChinese Academy of Agricultural SciencesXinchengChina
| | - Kun Wang
- Research Institute of PomologyChinese Academy of Agricultural SciencesXinchengChina
| | - Hengtao Zhang
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Ruiping Zhang
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Zhe Zhou
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Zhenli Yan
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Liyi Zhang
- Research Institute of PomologyChinese Academy of Agricultural SciencesXinchengChina
| | - Caixia Zhang
- Research Institute of PomologyChinese Academy of Agricultural SciencesXinchengChina
| | - Peihua Cong
- Research Institute of PomologyChinese Academy of Agricultural SciencesXinchengChina
| | - Cecilia H. Deng
- The New Zealand Institute for Plant and Food Research Limited (PFR)Mount Albert Research CentreAucklandNew Zealand
| | - Jia‐Long Yao
- The New Zealand Institute for Plant and Food Research Limited (PFR)Mount Albert Research CentreAucklandNew Zealand
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
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17
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Zhou Z, Zhang L, Shu J, Wang M, Li H, Shu H, Wang X, Sun Q, Zhang S. Root Breeding in the Post-Genomics Era: From Concept to Practice in Apple. PLANTS (BASEL, SWITZERLAND) 2022; 11:1408. [PMID: 35684181 PMCID: PMC9182997 DOI: 10.3390/plants11111408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/05/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
The development of rootstocks with a high-quality dwarf-type root system is a popular research topic in the apple industry. However, the precise breeding of rootstocks is still challenging, mainly because the root system is buried deep underground, roots have a complex life cycle, and research on root architecture has progressed slowly. This paper describes ideas for the precise breeding and domestication of wild apple resources and the application of key genes. The primary goal of this research is to combine the existing rootstock resources with molecular breeding and summarize the methods of precision breeding. Here, we reviewed the existing rootstock germplasm, high-quality genome, and genetic resources available to explain how wild resources might be used in modern breeding. In particular, we proposed the 'from genotype to phenotype' theory and summarized the difficulties in future breeding processes. Lastly, the genetics governing root diversity and associated regulatory mechanisms were elaborated on to optimize the precise breeding of rootstocks.
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Affiliation(s)
- Zhou Zhou
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (Z.Z.); (L.Z.); (M.W.); (H.L.); (H.S.); (X.W.)
| | - Lei Zhang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (Z.Z.); (L.Z.); (M.W.); (H.L.); (H.S.); (X.W.)
| | - Jing Shu
- College of Forestry Engineering, Shandong Agriculture and Engineering University, Jinan 250100, China;
| | - Mengyu Wang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (Z.Z.); (L.Z.); (M.W.); (H.L.); (H.S.); (X.W.)
| | - Han Li
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (Z.Z.); (L.Z.); (M.W.); (H.L.); (H.S.); (X.W.)
| | - Huairui Shu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (Z.Z.); (L.Z.); (M.W.); (H.L.); (H.S.); (X.W.)
| | - Xiaoyun Wang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (Z.Z.); (L.Z.); (M.W.); (H.L.); (H.S.); (X.W.)
| | - Qinghua Sun
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (Z.Z.); (L.Z.); (M.W.); (H.L.); (H.S.); (X.W.)
| | - Shizhong Zhang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (Z.Z.); (L.Z.); (M.W.); (H.L.); (H.S.); (X.W.)
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18
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Bilbrey EA, Williamson K, Hatzakis E, Miller DD, Fresnedo-Ramírez J, Cooperstone JL. Integrating genomics and multiplatform metabolomics enables metabolite quantitative trait loci detection in breeding-relevant apple germplasm. THE NEW PHYTOLOGIST 2021; 232:1944-1958. [PMID: 34472097 DOI: 10.1111/nph.17693] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 08/10/2021] [Indexed: 05/12/2023]
Abstract
Apple (Malus × domestica) has commercial and nutritional value, but breeding constraints of tree crops limit varietal improvement. Marker-assisted selection minimises these drawbacks, but breeders lack applications for targeting fruit phytochemicals. To understand genotype-phytochemical associations in apples, we have developed a high-throughput integration strategy for genomic and multiplatform metabolomics data. Here, 124 apple genotypes, including members of three pedigree-connected breeding families alongside diverse cultivars and wild selections, were genotyped and phenotyped. Metabolite genome-wide association studies (mGWAS) were conducted with c. 10 000 single nucleotide polymorphisms and phenotypic data acquired via LC-MS and 1 H NMR untargeted metabolomics. Putative metabolite quantitative trait loci (mQTL) were then validated via pedigree-based analyses (PBA). Using our developed method, 519, 726 and 177 putative mQTL were detected in LC-MS positive and negative ionisation modes, and NMR, respectively. mQTL were indicated on each chromosome, with hotspots on linkage groups 16 and 17. A chlorogenic acid mQTL was discovered on chromosome 17 via mGWAS and validated with a two-step PBA, enabling discovery of novel candidate gene-metabolite relationships. Complementary data from three metabolomics approaches and dual genomics analyses increased confidence in validity of compound annotation and mQTL detection. Our platform demonstrates the utility of multiomic integration to advance data-driven, phytochemical-based plant breeding.
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Affiliation(s)
- Emma A Bilbrey
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, 43210, USA
| | - Kathryn Williamson
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, 43210, USA
| | - Emmanuel Hatzakis
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, 43210, USA
| | - Diane Doud Miller
- Department of Horticulture and Crop Science, The Ohio State University, Wooster, OH, 44691, USA
| | | | - Jessica L Cooperstone
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, 43210, USA
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, 43210, USA
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19
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Liao L, Zhang W, Zhang B, Fang T, Wang XF, Cai Y, Ogutu C, Gao L, Chen G, Nie X, Xu J, Zhang Q, Ren Y, Yu J, Wang C, Deng CH, Ma B, Zheng B, You CX, Hu DG, Espley R, Lin-Wang K, Yao JL, Allan AC, Khan A, Korban SS, Fei Z, Ming R, Hao YJ, Li L, Han Y. Unraveling a genetic roadmap for improved taste in the domesticated apple. MOLECULAR PLANT 2021; 14:1454-1471. [PMID: 34022440 DOI: 10.1016/j.molp.2021.05.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 04/13/2021] [Accepted: 05/17/2021] [Indexed: 05/26/2023]
Abstract
Although taste is an important aspect of fruit quality, an understanding of its genetic control remains elusive in apple and other fruit crops. In this study, we conducted genomic sequence analysis of 497 Malus accessions and revealed erosion of genetic diversity caused by apple breeding and possible independent domestication events of dessert and cider apples. Signatures of selection for fruit acidity and size, but not for fruit sugar content, were detected during the processes of both domestication and improvement. Furthermore, we found that single mutations in major genes affecting fruit taste, including Ma1, MdTDT, and MdSOT2, dramatically decrease malate, citrate, and sorbitol accumulation, respectively, and correspond to important domestication events. Interestingly, Ma1 was identified to have pleiotropic effects on both organic acid content and sugar:acid ratio, suggesting that it plays a vital role in determining fruit taste. Fruit taste is unlikely to have been negatively affected by linkage drag associated with selection for larger fruit that resulted from the pyramiding of multiple genes with minor effects on fruit size. Collectively, our study provides new insights into the genetic basis of fruit quality and its evolutionary roadmap during apple domestication, pinpointing several candidate genes for genetic manipulation of fruit taste in apple.
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Affiliation(s)
- Liao Liao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Hubei Hongshan Laboratory, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430074, China; Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
| | - Weihan Zhang
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Bo Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Hubei Hongshan Laboratory, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Ting Fang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Hubei Hongshan Laboratory, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430074, China
| | - Xiao-Fei Wang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, China
| | - Yaming Cai
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Hubei Hongshan Laboratory, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Collins Ogutu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Hubei Hongshan Laboratory, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430074, China; Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Lei Gao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Hubei Hongshan Laboratory, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430074, China
| | - Gang Chen
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaoqing Nie
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinsheng Xu
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Quanyan Zhang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, China
| | - Yiran Ren
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, China
| | - Jianqiang Yu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, China
| | - Chukun Wang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, China
| | - Cecilia H Deng
- The New Zealand Institute for Plant & Food Research Limited, Auckland, New Zealand
| | - Baiquan Ma
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Hubei Hongshan Laboratory, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430074, China
| | - Beibei Zheng
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Hubei Hongshan Laboratory, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430074, China
| | - Chun-Xiang You
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, China
| | - Da-Gang Hu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, China
| | - Richard Espley
- The New Zealand Institute for Plant & Food Research Limited, Auckland, New Zealand
| | - Kui Lin-Wang
- The New Zealand Institute for Plant & Food Research Limited, Auckland, New Zealand
| | - Jia-Long Yao
- The New Zealand Institute for Plant & Food Research Limited, Auckland, New Zealand
| | - Andrew C Allan
- The New Zealand Institute for Plant & Food Research Limited, Auckland, New Zealand; School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Awais Khan
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY 14456, USA
| | - Schuyler S Korban
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yu-Jin Hao
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, China.
| | - Li Li
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
| | - Yuepeng Han
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Hubei Hongshan Laboratory, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430074, China; Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China; Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China.
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20
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Wu B, Shen F, Wang X, Zheng WY, Xiao C, Deng Y, Wang T, Yu Huang Z, Zhou Q, Wang Y, Wu T, Feng Xu X, Hai Han Z, Zhong Zhang X. Role of MdERF3 and MdERF118 natural variations in apple flesh firmness/crispness retainability and development of QTL-based genomics-assisted prediction. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1022-1037. [PMID: 33319456 PMCID: PMC8131039 DOI: 10.1111/pbi.13527] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 10/29/2020] [Accepted: 12/06/2020] [Indexed: 05/24/2023]
Abstract
Retention of flesh texture attributes during cold storage is critical for the long-term maintenance of fruit quality. The genetic variations determining flesh firmness and crispness retainability are not well understood. The objectives of this study are to identify gene markers based on quantitative trait loci (QTLs) and to develop genomics-assisted prediction (GAP) models for apple flesh firmness and crispness retainability. Phenotype data of 2664 hybrids derived from three Malus domestica cultivars and a M. asiatica cultivar were collected in 2016 and 2017. The phenotype segregated considerably with high broad-sense heritability of 83.85% and 83.64% for flesh firmness and crispness retainability, respectively. Fifty-six candidate genes were predicted from the 62 QTLs identified using bulked segregant analysis and RNA-seq. The genotype effects of the markers designed on each candidate gene were estimated. The genomics-predicted values were obtained using pyramiding marker genotype effects and overall mean phenotype values. Fivefold cross-validation revealed that the prediction accuracy was 0.5541 and 0.6018 for retainability of flesh firmness and crispness, respectively. An 8-bp deletion in the MdERF3 promoter disrupted MdDOF5.3 binding, reduced MdERF3 expression, relieved the inhibition on MdPGLR3, MdPME2, and MdACO4 expression, and ultimately decreased flesh firmness and crispness retainability. A 3-bp deletion in the MdERF118 promoter decreased its expression by disrupting the binding of MdRAVL1, which increased MdPGLR3 and MdACO4 expression and reduced flesh firmness and crispness retainability. These results provide insights regarding the genetic variation network regulating flesh firmness and crispness retainability, and the GAP models can assist in apple breeding.
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Affiliation(s)
- Bei Wu
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Fei Shen
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Xuan Wang
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Wen Yan Zheng
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Chen Xiao
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Yang Deng
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Ting Wang
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Zhen Yu Huang
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Qian Zhou
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Yi Wang
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Ting Wu
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Xue Feng Xu
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Zhen Hai Han
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Xin Zhong Zhang
- College of HorticultureChina Agricultural UniversityBeijingChina
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21
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Yamane H, Singh AK, Cooke JEK. Plant dormancy research: from environmental control to molecular regulatory networks. TREE PHYSIOLOGY 2021; 41:523-528. [PMID: 33834235 DOI: 10.1093/treephys/tpab035] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 02/22/2021] [Indexed: 05/26/2023]
Affiliation(s)
- Hisayo Yamane
- Graduate school of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Anil Kumar Singh
- School of Genetic Engineering, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi 834 003 India
| | - Janice E K Cooke
- Department of Biological Sciences, University of Alberta, Edmonton AB T6G 2E9, Alberta, Canada
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22
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Howard NP, Troggio M, Durel CE, Muranty H, Denancé C, Bianco L, Tillman J, van de Weg E. Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible calls. BMC Genomics 2021; 22:246. [PMID: 33827434 PMCID: PMC8028180 DOI: 10.1186/s12864-021-07565-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 03/30/2021] [Indexed: 11/23/2022] Open
Abstract
Background Single nucleotide polymorphism (SNP) array technology has been increasingly used to generate large quantities of SNP data for use in genetic studies. As new arrays are developed to take advantage of new technology and of improved probe design using new genome sequence and panel data, a need to integrate data from different arrays and array platforms has arisen. This study was undertaken in view of our need for an integrated high-quality dataset of Illumina Infinium® 20 K and Affymetrix Axiom® 480 K SNP array data in apple (Malus × domestica). In this study, we qualify and quantify the compatibility of SNP calling, defined as SNP calls that are both accurate and concordant, across both arrays by two approaches. First, the concordance of SNP calls was evaluated using a set of 417 duplicate individuals genotyped on both arrays starting from a set of 10,295 robust SNPs on the Infinium array. Next, the accuracy of the SNP calls was evaluated on additional germplasm (n = 3141) from both arrays using Mendelian inconsistent and consistent errors across thousands of pedigree links. While performing this work, we took the opportunity to evaluate reasons for probe failure and observed discordant SNP calls. Results Concordance among the duplicate individuals was on average of 97.1% across 10,295 SNPs. Of these SNPs, 35% had discordant call(s) that were further curated, leading to a final set of 8412 (81.7%) SNPs that were deemed compatible. Compatibility was highly influenced by the presence of alternate probe binding locations and secondary polymorphisms. The impact of the latter was highly influenced by their number and proximity to the 3′ end of the probe. Conclusions The Infinium and Axiom SNP array data were mostly compatible. However, data integration required intense data filtering and curation. This work resulted in a workflow and information that may be of use in other data integration efforts. Such an in-depth analysis of array concordance and accuracy as ours has not been previously described in the literature and will be useful in future work on SNP array data integration and interpretation, and in probe/platform development. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07565-7.
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Affiliation(s)
- Nicholas P Howard
- Institut für Biologie und Umweltwissenschaften, Carl von Ossietzky Univ., Oldenburg, Germany.,Department of Horticultural Science, Univ. of Minnesota, St Paul, USA
| | | | - Charles-Eric Durel
- Université d'Angers, Institut Agro, INRAE, IRHS, SFR 4207 QuaSaV, Beaucouzé, France
| | - Hélène Muranty
- Université d'Angers, Institut Agro, INRAE, IRHS, SFR 4207 QuaSaV, Beaucouzé, France
| | - Caroline Denancé
- Université d'Angers, Institut Agro, INRAE, IRHS, SFR 4207 QuaSaV, Beaucouzé, France
| | - Luca Bianco
- Fondazione Edmund Mach, San Michele all'Adige, TN, Italy
| | - John Tillman
- Department of Horticultural Science, Univ. of Minnesota, St Paul, USA
| | - Eric van de Weg
- Department of Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands.
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23
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Wedger MJ, Schumann AC, Gross BL. Candidate genes and signatures of directional selection on fruit quality traits during apple domestication. AMERICAN JOURNAL OF BOTANY 2021; 108:616-627. [PMID: 33837962 DOI: 10.1002/ajb2.1636] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 11/24/2020] [Indexed: 06/12/2023]
Abstract
PREMISE During plant domestication, traits can be subject to a variety of types of selection, ranging from strong directional selection for traits such as seed or fruit size to diversifying selection for traits like color or flavor. These types of selection interact with other evolutionary processes including genetic bottlenecks and interspecific gene flow to generate different levels of genetic diversity across the genome and at target genes in domesticated lineages, but little is known about the impacts of these processes in perennial fruit crops. METHODS We used sequence capture by hybridization to examine patterns of diversity at a suite of candidate domestication and anonymous background genes in domesticated apple (Malus ×domestica) in comparison to its wild relatives Malus sieversii and Malus orientalis. RESULTS We found no change in average diversity at these candidate domestication genes across the three species. However, a subset of the genes did exhibit patterns of very high or very low diversity in M. ×domestica compared to its progenitor, M. sieversii. Of the genes with characterized function, the low-diversity genes mainly contributed to fruit quality traits like color and flavor, predicted to be under conscious, directional selection relatively late in the domestication process, while the high-diversity genes included a variety of functions. CONCLUSIONS Overall, these results are consistent with predictions based on the likely timing and nature of selection during domestication and open new avenues for understanding genes with high diversity in a perennial crop compared to its wild relatives.
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Affiliation(s)
- Marshall J Wedger
- Department of Biology, Washington University, Campus Box 1137, St. Louis, MO, 63130, USA
| | - Abby C Schumann
- Minnesota Poultry Testing Laboratory, P.O. Box 126, 622 Bus. Hwy 71 NE, Wilmar, MN, 56201, USA
| | - Briana L Gross
- Department of Biology, University of Minnesota Duluth, 207 Swenson Science Building, 1035 Kirby Drive, Duluth, MN, 55812, USA
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24
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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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25
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Gottschalk C, Zhang S, Schwallier P, Rogers S, Bukovac MJ, van Nocker S. Genetic mechanisms associated with floral initiation and the repressive effect of fruit on flowering in apple (Malus x domestica Borkh). PLoS One 2021; 16:e0245487. [PMID: 33606701 PMCID: PMC7894833 DOI: 10.1371/journal.pone.0245487] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 01/02/2021] [Indexed: 11/19/2022] Open
Abstract
Many apple cultivars are subject to biennial fluctuations in flowering and fruiting. It is believed that this phenomenon is caused by a repressive effect of developing fruit on the initiation of flowers in the apex of proximal bourse shoots. However, the genetic pathways of floral initiation are incompletely described in apple, and the biological nature of floral repression by fruit is currently unknown. In this study, we characterized the transcriptional landscape of bourse shoot apices in the biennial cultivar, 'Honeycrisp', during the period of floral initiation, in trees bearing a high fruit load and in trees without fruit. Trees with high fruit load produced almost exclusively vegetative growth in the subsequent year, whereas the trees without fruit produced flowers on the majority of the potential flowering nodes. Using RNA-based sequence data, we documented gene expression at high resolution, identifying >11,000 transcripts that had not been previously annotated, and characterized expression profiles associated with vegetative growth and flowering. We also conducted a census of genes related to known flowering genes, organized the phylogenetic and syntenic relationships of these genes, and compared expression among homeologs. Several genes closely related to AP1, FT, FUL, LFY, and SPLs were more strongly expressed in apices from non-bearing, floral-determined trees, consistent with their presumed floral-promotive roles. In contrast, a homolog of TFL1 exhibited strong and persistent up-regulation only in apices from bearing, vegetative-determined trees, suggesting a role in floral repression. Additionally, we identified four GIBBERELLIC ACID (GA) 2 OXIDASE genes that were expressed to relatively high levels in apices from bearing trees. These results define the flowering-related transcriptional landscape in apple, and strongly support previous studies implicating both gibberellins and TFL1 as key components in repression of flowering by fruit.
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Affiliation(s)
- Chris Gottschalk
- Department of Horticulture, Plant and Soil Science Building, Michigan State University, East Lansing, Michigan, United States of America
| | - Songwen Zhang
- Department of Horticulture, Plant and Soil Science Building, Michigan State University, East Lansing, Michigan, United States of America
| | - Phil Schwallier
- Michigan State University Extension, East Lansing, Michigan, United States of America
| | - Sean Rogers
- Department of Horticulture, Plant and Soil Science Building, Michigan State University, East Lansing, Michigan, United States of America
| | - Martin J. Bukovac
- Department of Horticulture, Plant and Soil Science Building, Michigan State University, East Lansing, Michigan, United States of America
| | - Steve van Nocker
- Department of Horticulture, Plant and Soil Science Building, Michigan State University, East Lansing, Michigan, United States of America
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26
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Plant Proteomics and Systems Biology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1346:51-66. [DOI: 10.1007/978-3-030-80352-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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27
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Christodoulou MD, Culham A. Apples before the fall: Does shape stability coincide with maturity? QUANTITATIVE PLANT BIOLOGY 2021; 2:e5. [PMID: 37077215 PMCID: PMC10095885 DOI: 10.1017/qpb.2021.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 02/26/2021] [Accepted: 03/02/2021] [Indexed: 05/03/2023]
Abstract
Fruit shape is the result of the interaction between genetic, epigenetic, environmental factors and stochastic processes. As a core biological descriptor both for taxonomy and horticulture, the point at which shape stability is reached becomes paramount in apple cultivar identification, and authentication in commerce. Twelve apple cultivars were sampled at regular intervals from anthesis to harvest over two growing seasons. Linear and geometric morphometrics were analysed to establish if and when shape stabilised and whether fruit asymmetry influenced this. Shape stability was detected in seven cultivars, four asymmetric and three symmetric. The remaining five did not stabilise. Shape stability, as defined here, is cultivar-dependent, and when it occurs, it is late in the growing season. Geometric morphometrics detected stability more readily than linear, especially in symmetric cultivars. Key shape features are important in apple marketing, giving the distinctness and apparent uniformity between cultivars expected at point of sale.
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Affiliation(s)
- Maria D. Christodoulou
- Department of Statistics, University of Oxford, Oxford, United Kingdom
- University of Reading Herbarium, School of Biological Sciences, University of Reading, Reading, United Kingdom
- Authors for correspondence: M. D. Christodoulou, E-mail: ; and Alastair Culham, E-mail:
| | - Alastair Culham
- University of Reading Herbarium, School of Biological Sciences, University of Reading, Reading, United Kingdom
- Authors for correspondence: M. D. Christodoulou, E-mail: ; and Alastair Culham, E-mail:
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Wang X, Shen F, Gao Y, Wang K, Chen R, Luo J, Yang L, Zhang X, Qiu C, Li W, Wu T, Xu X, Wang Y, Cong P, Han Z, Zhang X. Application of genome-wide insertion/deletion markers on genetic structure analysis and identity signature of Malus accessions. BMC PLANT BIOLOGY 2020; 20:540. [PMID: 33256591 PMCID: PMC7708918 DOI: 10.1186/s12870-020-02744-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 11/17/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND Apple (Malus ssp.), one of the most important temperate fruit crops, has a long cultivation history and is economically important. To identify the genetic relationships among the apple germplasm accessions, whole-genome structural variants identified between M. domestica cultivars 'Jonathan' and 'Golden Delicious' were used. RESULTS A total of 25,924 insertions and deletions (InDels) were obtained, from which 102 InDel markers were developed. Using the InDel markers, we found that 942 (75.3%) of the 1251 Malus accessions from 35 species exhibited a unique identity signature due to their distinct genotype combinations. The 102 InDel markers could distinguish 16.7-71.4% of the 331 bud sports derived from 'Fuji', 'Red Delicious', 'Gala', 'Golden Delicious', and other cultivars. Five distinct genetic patterns were found in 1002 diploid accessions based on 78 bi-allele InDel markers. Genetic structure analysis indicated that M. domestica showed higher genetic diversity than the other species. Malus underwent a relatively high level of wild-to-crop or crop-to-wild gene flow. M. sieversii was closely related to both M. domestica and cultivated Chinese cultivars. CONCLUSIONS The identity signatures of Malus accessions can be used to determine distinctness, uniformity, and stability. The results of this study may also provide better insight into the genetic relationships among Malus species.
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Affiliation(s)
- Xuan Wang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Fei Shen
- College of Horticulture, China Agricultural University, Beijing, China
- Beijing Agro-biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yuan Gao
- Research Institute of Pomology, Chinese Academy of Agricultural Science, Xingcheng, Liaoning, China
| | - Kun Wang
- Research Institute of Pomology, Chinese Academy of Agricultural Science, Xingcheng, Liaoning, China
| | - Ruiting Chen
- College of Horticulture, China Agricultural University, Beijing, China
- Present Address: Shaanxi Haisheng Fruit Industry Development Co., Ltd., Shaanxi, Xian, China
| | - Jun Luo
- College of Information and Electrical Engineering, China Agricultural University, Beijing, China
| | - Lili Yang
- College of Information and Electrical Engineering, China Agricultural University, Beijing, China
| | - Xi Zhang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Changpeng Qiu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Wei Li
- College of Horticulture, China Agricultural University, Beijing, China
| | - Ting Wu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Xuefeng Xu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Yi Wang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Peihua Cong
- Research Institute of Pomology, Chinese Academy of Agricultural Science, Xingcheng, Liaoning, China
| | - Zhenhai Han
- College of Horticulture, China Agricultural University, Beijing, China
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, Beijing, China.
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Jung M, Roth M, Aranzana MJ, Auwerkerken A, Bink M, Denancé C, Dujak C, Durel CE, Font I Forcada C, Cantin CM, Guerra W, Howard NP, Keller B, Lewandowski M, Ordidge M, Rymenants M, Sanin N, Studer B, Zurawicz E, Laurens F, Patocchi A, Muranty H. The apple REFPOP-a reference population for genomics-assisted breeding in apple. HORTICULTURE RESEARCH 2020; 7:189. [PMID: 33328447 PMCID: PMC7603508 DOI: 10.1038/s41438-020-00408-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 08/25/2020] [Accepted: 09/06/2020] [Indexed: 05/16/2023]
Abstract
Breeding of apple is a long-term and costly process due to the time and space requirements for screening selection candidates. Genomics-assisted breeding utilizes genomic and phenotypic information to increase the selection efficiency in breeding programs, and measurements of phenotypes in different environments can facilitate the application of the approach under various climatic conditions. Here we present an apple reference population: the apple REFPOP, a large collection formed of 534 genotypes planted in six European countries, as a unique tool to accelerate apple breeding. The population consisted of 269 accessions and 265 progeny from 27 parental combinations, representing the diversity in cultivated apple and current European breeding material, respectively. A high-density genome-wide dataset of 303,239 SNPs was produced as a combined output of two SNP arrays of different densities using marker imputation with an imputation accuracy of 0.95. Based on the genotypic data, linkage disequilibrium was low and population structure was weak. Two well-studied phenological traits of horticultural importance were measured. We found marker-trait associations in several previously identified genomic regions and maximum predictive abilities of 0.57 and 0.75 for floral emergence and harvest date, respectively. With decreasing SNP density, the detection of significant marker-trait associations varied depending on trait architecture. Regardless of the trait, 10,000 SNPs sufficed to maximize genomic prediction ability. We confirm the suitability of the apple REFPOP design for genomics-assisted breeding, especially for breeding programs using related germplasm, and emphasize the advantages of a coordinated and multinational effort for customizing apple breeding methods in the genomics era.
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Affiliation(s)
- Michaela Jung
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092, Zurich, Switzerland
- Breeding Research group, Agroscope, 8820, Wädenswil, Switzerland
| | - Morgane Roth
- Breeding Research group, Agroscope, 8820, Wädenswil, Switzerland
- GAFL, INRAE, 84140, Montfavet, France
| | - Maria José Aranzana
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), 08140, Caldes de Montbui, Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193, Bellaterra, Barcelona, Spain
| | | | - Marco Bink
- Biometris, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Hendrix Genetics Research, Technology and Services B.V., PO Box 114, 5830AC, Boxmeer, The Netherlands
| | - Caroline Denancé
- IRHS, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Christian Dujak
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193, Bellaterra, Barcelona, Spain
| | - Charles-Eric Durel
- IRHS, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Carolina Font I Forcada
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), 08140, Caldes de Montbui, Barcelona, Spain
| | - Celia M Cantin
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), 08140, Caldes de Montbui, Barcelona, Spain
- ARAID (Fundación Aragonesa para la Investigación y el Desarrollo), 50018, Zaragoza, Spain
| | | | - Nicholas P Howard
- Department of Horticultural Science, University of Minnesota, St. Paul, MN, 55108, USA
- Institute of Biology and Environmental Sciences, University of Oldenburg, 26129, Oldenburg, Germany
| | - Beat Keller
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092, Zurich, Switzerland
- Breeding Research group, Agroscope, 8820, Wädenswil, Switzerland
| | | | - Matthew Ordidge
- School of Agriculture, Policy and Development, University of Reading, Whiteknights, RG6 6AR, Reading, UK
| | - Marijn Rymenants
- Better3fruit N.V., 3202, Rillaar, Belgium
- Biometris, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Laboratory for Plant Genetics and Crop Improvement, KU Leuven, B-3001, Leuven, Belgium
| | - Nadia Sanin
- Research Centre Laimburg, 39040, Auer, Italy
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092, Zurich, Switzerland
| | - Edward Zurawicz
- Research Institute of Horticulture, 96-100, Skierniewice, Poland
| | - François Laurens
- IRHS, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Andrea Patocchi
- Breeding Research group, Agroscope, 8820, Wädenswil, Switzerland
| | - Hélène Muranty
- IRHS, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France.
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Iezzoni AF, McFerson J, Luby J, Gasic K, Whitaker V, Bassil N, Yue C, Gallardo K, McCracken V, Coe M, Hardner C, Zurn JD, Hokanson S, van de Weg E, Jung S, Main D, da Silva Linge C, Vanderzande S, Davis TM, Mahoney LL, Finn C, Peace C. RosBREED: bridging the chasm between discovery and application to enable DNA-informed breeding in rosaceous crops. HORTICULTURE RESEARCH 2020; 7:177. [PMID: 33328430 PMCID: PMC7603521 DOI: 10.1038/s41438-020-00398-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 07/16/2020] [Accepted: 08/30/2020] [Indexed: 05/05/2023]
Abstract
The Rosaceae crop family (including almond, apple, apricot, blackberry, peach, pear, plum, raspberry, rose, strawberry, sweet cherry, and sour cherry) provides vital contributions to human well-being and is economically significant across the U.S. In 2003, industry stakeholder initiatives prioritized the utilization of genomics, genetics, and breeding to develop new cultivars exhibiting both disease resistance and superior horticultural quality. However, rosaceous crop breeders lacked certain knowledge and tools to fully implement DNA-informed breeding-a "chasm" existed between existing genomics and genetic information and the application of this knowledge in breeding. The RosBREED project ("Ros" signifying a Rosaceae genomics, genetics, and breeding community initiative, and "BREED", indicating the core focus on breeding programs), addressed this challenge through a comprehensive and coordinated 10-year effort funded by the USDA-NIFA Specialty Crop Research Initiative. RosBREED was designed to enable the routine application of modern genomics and genetics technologies in U.S. rosaceous crop breeding programs, thereby enhancing their efficiency and effectiveness in delivering cultivars with producer-required disease resistances and market-essential horticultural quality. This review presents a synopsis of the approach, deliverables, and impacts of RosBREED, highlighting synergistic global collaborations and future needs. Enabling technologies and tools developed are described, including genome-wide scanning platforms and DNA diagnostic tests. Examples of DNA-informed breeding use by project participants are presented for all breeding stages, including pre-breeding for disease resistance, parental and seedling selection, and elite selection advancement. The chasm is now bridged, accelerating rosaceous crop genetic improvement.
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Affiliation(s)
- Amy F Iezzoni
- Michigan State University, East Lansing, MI, 48824, USA.
| | - Jim McFerson
- Washington State University, Wenatchee, WA, 98801, USA
| | - James Luby
- University of Minnesota, St. Paul, MN, 55108, USA
| | | | | | | | - Chengyan Yue
- University of Minnesota, St. Paul, MN, 55108, USA
| | | | | | - Michael Coe
- Cedar Lake Research Group, Portland, OR, 97215, USA
| | | | | | | | - Eric van de Weg
- Wageningen University and Research, 6700 AA, Wageningen, The Netherlands
| | - Sook Jung
- Washington State University, Pullman, WA, 99164, USA
| | - Dorrie Main
- Washington State University, Pullman, WA, 99164, USA
| | | | | | | | | | | | - Cameron Peace
- Washington State University, Pullman, WA, 99164, USA
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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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Liu J, Shen F, Xiao Y, Fang H, Qiu C, Li W, Wu T, Xu X, Wang Y, Zhang X, Han Z. Genomics-assisted prediction of salt and alkali tolerances and functional marker development in apple rootstocks. BMC Genomics 2020; 21:550. [PMID: 32778069 PMCID: PMC7430842 DOI: 10.1186/s12864-020-06961-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 07/29/2020] [Indexed: 12/18/2022] Open
Abstract
Background Saline, alkaline, and saline-alkaline stress severely affect plant growth and development. The tolerance of plants to these stressors has long been important breeding objectives, especially for woody perennials like apple. The aims of this study were to identify quantitative trait loci (QTLs) and to develop genomics-assisted prediction models for salt, alkali, and salt-alkali tolerance in apple rootstock. Results A total of 3258 hybrids derived from the apple rootstock cultivars ‘Baleng Crab’ (Malus robusta Rehd., tolerant) × ‘M9’ (M. pumila Mill., sensitive) were used to identify 17, 13, and two QTLs for injury indices of salt, alkali, and salt–alkali stress via bulked segregant analysis. The genotype effects of single nucleotide polymorphism (SNP) markers designed on candidate genes in each QTL interval were estimated. The genomic predicted value of an individual hybrid was calculated by adding the sum of all marker genotype effects to the mean phenotype value of the population. The prediction accuracy was 0.6569, 0.6695, and 0.5834 for injury indices of salt, alkali, and salt–alkali stress, respectively. SNP182G on MdRGLG3, which changes a leucine to an arginine at the vWFA-domain, conferred tolerance to salt, alkali, and salt-alkali stress. SNP761A on MdKCAB, affecting the Kv_beta domain that cooperated with the linked allelic variation SNP11, contributed to salt, alkali, and salt–alkali tolerance in apple rootstock. Conclusions The genomics-assisted prediction models can potentially be used in breeding saline, alkaline, and saline-alkaline tolerant apple rootstocks. The QTLs and the functional markers may provide insight for future studies into the genetic variation of plant abiotic stress tolerance.
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Affiliation(s)
- Jing Liu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Fei Shen
- College of Horticulture, China Agricultural University, Beijing, China
| | - Yao Xiao
- College of Horticulture, China Agricultural University, Beijing, China
| | - Hongcheng Fang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Changpeng Qiu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Wei Li
- College of Horticulture, China Agricultural University, Beijing, China
| | - Ting Wu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Xuefeng Xu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Yi Wang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, Beijing, China.
| | - Zhenhai Han
- College of Horticulture, China Agricultural University, Beijing, China
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Wang W, Celton JM, Buck-Sorlin G, Balzergue S, Bucher E, Laurens F. Skin Color in Apple Fruit ( Malus × domestica): Genetic and Epigenetic Insights. EPIGENOMES 2020; 4:epigenomes4030013. [PMID: 34968286 PMCID: PMC8594686 DOI: 10.3390/epigenomes4030013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/09/2020] [Accepted: 07/09/2020] [Indexed: 11/16/2022] Open
Abstract
Apple skin color is an important trait for organoleptic quality. In fact, it has a major influence on consumer choice. Skin color is, thus, one of the most important criteria taken into account by breeders. For apples, most novel varieties are so-called "mutants" or "sports" that have been identified in clonal populations. Indeed, many "sports" exist that show distinct phenotypic differences compared to the varieties from which they originated. These differences affect a limited number of traits of economic importance, including skin color. Until recently, the detailed genetic or epigenetic changes resulting in heritable phenotypic changes in sports was largely unknown. Recent technological advances and the availability of several high-quality apple genomes now provide the bases to understand the exact nature of the underlying molecular changes that are responsible for the observed phenotypic changes observed in sports. The present review investigates the molecular nature of sports affected in apple skin color giving arguments in favor of the genetic or epigenetic explanatory models.
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Affiliation(s)
- Wuqian Wang
- IRHS (Institut de Recherche en Horticulture et Semences), UMR 1345, INRAE, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, F-49071 Beaucouzé, France; (W.W.); (J.-M.C.); (G.B.-S.); (S.B.)
| | - Jean-Marc Celton
- IRHS (Institut de Recherche en Horticulture et Semences), UMR 1345, INRAE, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, F-49071 Beaucouzé, France; (W.W.); (J.-M.C.); (G.B.-S.); (S.B.)
| | - Gerhard Buck-Sorlin
- IRHS (Institut de Recherche en Horticulture et Semences), UMR 1345, INRAE, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, F-49071 Beaucouzé, France; (W.W.); (J.-M.C.); (G.B.-S.); (S.B.)
| | - Sandrine Balzergue
- IRHS (Institut de Recherche en Horticulture et Semences), UMR 1345, INRAE, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, F-49071 Beaucouzé, France; (W.W.); (J.-M.C.); (G.B.-S.); (S.B.)
| | - Etienne Bucher
- Plant Breeding and Genetic Resources, Agroscope, 1260 Nyon, Switzerland;
| | - François Laurens
- IRHS (Institut de Recherche en Horticulture et Semences), UMR 1345, INRAE, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, F-49071 Beaucouzé, France; (W.W.); (J.-M.C.); (G.B.-S.); (S.B.)
- Correspondence:
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Ambrosino L, Colantuono C, Diretto G, Fiore A, Chiusano ML. Bioinformatics Resources for Plant Abiotic Stress Responses: State of the Art and Opportunities in the Fast Evolving -Omics Era. PLANTS 2020; 9:plants9050591. [PMID: 32384671 PMCID: PMC7285221 DOI: 10.3390/plants9050591] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/24/2020] [Accepted: 04/29/2020] [Indexed: 12/13/2022]
Abstract
Abiotic stresses are among the principal limiting factors for productivity in agriculture. In the current era of continuous climate changes, the understanding of the molecular aspects involved in abiotic stress response in plants is a priority. The rise of -omics approaches provides key strategies to promote effective research in the field, facilitating the investigations from reference models to an increasing number of species, tolerant and sensitive genotypes. Integrated multilevel approaches, based on molecular investigations at genomics, transcriptomics, proteomics and metabolomics levels, are now feasible, expanding the opportunities to clarify key molecular aspects involved in responses to abiotic stresses. To this aim, bioinformatics has become fundamental for data production, mining and integration, and necessary for extracting valuable information and for comparative efforts, paving the way to the modeling of the involved processes. We provide here an overview of bioinformatics resources for research on plant abiotic stresses, describing collections from -omics efforts in the field, ranging from raw data to complete databases or platforms, highlighting opportunities and still open challenges in abiotic stress research based on -omics technologies.
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Affiliation(s)
- Luca Ambrosino
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici (Na), Italy; (L.A.); (C.C.)
- Department of Research Infrastructures for Marine Biological Resources (RIMAR), 80121 Naples, Italy
| | - Chiara Colantuono
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici (Na), Italy; (L.A.); (C.C.)
- Department of Research Infrastructures for Marine Biological Resources (RIMAR), 80121 Naples, Italy
| | - Gianfranco Diretto
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), 00123 Rome, Italy; (G.D.); (A.F.)
| | - Alessia Fiore
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), 00123 Rome, Italy; (G.D.); (A.F.)
| | - Maria Luisa Chiusano
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici (Na), Italy; (L.A.); (C.C.)
- Department of Research Infrastructures for Marine Biological Resources (RIMAR), 80121 Naples, Italy
- Correspondence: ; Tel.: +39-081-253-9492
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Kviklys D, Samuolienė G. Relationships Among the Rootstock, Crop Load, and Sugar Hormone Signaling of Apple Tree, and Their Effects on Biennial Bearing. FRONTIERS IN PLANT SCIENCE 2020; 11:1213. [PMID: 32849752 PMCID: PMC7427310 DOI: 10.3389/fpls.2020.01213] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 07/24/2020] [Indexed: 05/09/2023]
Abstract
Adjustable crop load primarily involves bud manipulation, and usually switches from vegetative to reproductive buds. While this switch is not fully understood, it is still controlled by the ratio of hormones, which promote or inhibit bud formation. To determine the reasons for biennial bearing, the effect of apple rootstock, scion cultivar, crop load, as well as metabolic changes of endogenous phytohormones [zeatin, jasmonic acid, indole-3 acetic acid (IAA), abscisic acid (ABA), and gibberellins 1, 3, and 7 (GAs)], and soluble sugars (glucose, fructose, and sorbitol) were evaluated, and their connections with return bloom and yield of apple tree buds were analyzed. Cultivars "Ligol" and "Auksis" were tested on five rootstocks contrasting in induced vigor: semi-dwarfing M.26; dwarfing M.9, B.396, and P 67; and super-dwarfing P 22. Crop load levels were adjusted before flowering, leaving 75, 113, and 150 fruits per tree. Principal component analysis (PCA) scatter plot of the metabolic response of phytohormones and sugars indicated that the effect of the semi-dwarfing M.26 rootstock was significantly different from that of the dwarfing M.9 and P 67, as well as the super-dwarfing P 22 rootstocks in both varieties. The most intensive crop load (150 fruits per tree) produced a significantly different response compared to less intensive crop loads (113 and 75) in both varieties. In contrast to soluble sugar accumulation, increased crop load resulted in an increased accumulation of phytohormones, except for ABA. Dwarfing rootstocks M.9, B.396, and P 67, as well as super-dwarf P 22 produced an altered accumulation of promoter phytohormones, while the more vigorous semi-dwarfing M.26 rootstock induced a higher content of glucose and inhibitory phytohormones, by increasing content of IAA, ABA, and GAs. The most significant decrease in return bloom resulted from the highest crop load in "Auksis" grafted on M.9 and P 22 rootstocks. Average difference in flower number between crop loads of 75 and 150 fruits per tree in "Ligol" was 68%, while this difference reached ~ 90% for P 22, and ~ 75% for M.9 and M.26 rootstocks. Return bloom was dependent on the previous year's crop load, cultivar, and rootstock.
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Affiliation(s)
- Darius Kviklys
- Lithuanian Research Centre for Agriculture and Forestry, Institute of Horticulture, Babtai, Lithuania
- Department of Horticulture, Norwegian Institute of Bioeconomy Research—NIBIO Ullensvang, Lofthus, Norway
- *Correspondence: Darius Kviklys,
| | - Giedrė Samuolienė
- Lithuanian Research Centre for Agriculture and Forestry, Institute of Horticulture, Babtai, Lithuania
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Linsmith G, Rombauts S, Montanari S, Deng CH, Celton JM, Guérif P, Liu C, Lohaus R, Zurn JD, Cestaro A, Bassil NV, Bakker LV, Schijlen E, Gardiner SE, Lespinasse Y, Durel CE, Velasco R, Neale DB, Chagné D, Van de Peer Y, Troggio M, Bianco L. Pseudo-chromosome-length genome assembly of a double haploid "Bartlett" pear (Pyrus communis L.). Gigascience 2019; 8:giz138. [PMID: 31816089 PMCID: PMC6901071 DOI: 10.1093/gigascience/giz138] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/18/2019] [Accepted: 10/30/2019] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND We report an improved assembly and scaffolding of the European pear (Pyrus communis L.) genome (referred to as BartlettDHv2.0), obtained using a combination of Pacific Biosciences RSII long-read sequencing, Bionano optical mapping, chromatin interaction capture (Hi-C), and genetic mapping. The sample selected for sequencing is a double haploid derived from the same "Bartlett" reference pear that was previously sequenced. Sequencing of di-haploid plants makes assembly more tractable in highly heterozygous species such as P. communis. FINDINGS A total of 496.9 Mb corresponding to 97% of the estimated genome size were assembled into 494 scaffolds. Hi-C data and a high-density genetic map allowed us to anchor and orient 87% of the sequence on the 17 pear chromosomes. Approximately 50% (247 Mb) of the genome consists of repetitive sequences. Gene annotation confirmed the presence of 37,445 protein-coding genes, which is 13% fewer than previously predicted. CONCLUSIONS We showed that the use of a doubled-haploid plant is an effective solution to the problems presented by high levels of heterozygosity and duplication for the generation of high-quality genome assemblies. We present a high-quality chromosome-scale assembly of the European pear Pyrus communis and demostrate its high degree of synteny with the genomes of Malus x Domestica and Pyrus x bretschneideri.
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Affiliation(s)
- Gareth Linsmith
- Center for Plant Systems Biology, VIB, Technologiepark 71, 9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Gent, Belgium
- Fondazione Edmund Mach, via E. Mach 1, 38010, San Michele all'Adige (TN), Italy
| | - Stephane Rombauts
- Center for Plant Systems Biology, VIB, Technologiepark 71, 9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Gent, Belgium
| | - Sara Montanari
- University of California Davis, Department of Plant Sciences, One Shields Ave, Davis, CA 95616, USA
| | - Cecilia H Deng
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre,120 Mt Albert Road, Sandringham, Auckland, 1025, New Zealand
| | - Jean-Marc Celton
- IRHS, INRA, Agrocampus-Ouest, Université d'Angers, SFR 4207 Quasav, 42 rue Georges Morel, F-49071 Beaucouzé, France
| | - Philippe Guérif
- IRHS, INRA, Agrocampus-Ouest, Université d'Angers, SFR 4207 Quasav, 42 rue Georges Morel, F-49071 Beaucouzé, France
| | - Chang Liu
- ZMBP, Allgemeine Genetik, Universität Tübingen, Auf der Morgenstelle 32, D-72076 Tübingen, Germany
| | - Rolf Lohaus
- Center for Plant Systems Biology, VIB, Technologiepark 71, 9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Gent, Belgium
| | - Jason D Zurn
- USDA-ARS National Clonal Germplasm Repository, 33447 Peoria Road, Corvallis, OR 97333, USA
| | - Alessandro Cestaro
- Fondazione Edmund Mach, via E. Mach 1, 38010, San Michele all'Adige (TN), Italy
| | - Nahla V Bassil
- USDA-ARS National Clonal Germplasm Repository, 33447 Peoria Road, Corvallis, OR 97333, USA
| | - Linda V Bakker
- Wageningen UR – Bioscience P.O. Box 16, 6700AA, Wageningen, The Netherlands
| | - Elio Schijlen
- Wageningen UR – Bioscience P.O. Box 16, 6700AA, Wageningen, The Netherlands
| | - Susan E Gardiner
- The New Zealand Institute for Plant & Food Research Limited (PFR), Palmerston North Research Centre, Palmerston North, New Zealand
| | - Yves Lespinasse
- IRHS, INRA, Agrocampus-Ouest, Université d'Angers, SFR 4207 Quasav, 42 rue Georges Morel, F-49071 Beaucouzé, France
| | - Charles-Eric Durel
- IRHS, INRA, Agrocampus-Ouest, Université d'Angers, SFR 4207 Quasav, 42 rue Georges Morel, F-49071 Beaucouzé, France
| | - Riccardo Velasco
- CREA Research Centre for Viticulture and Enology, Via XXVIII Aprile 26, 31015 Conegliano (TV), Italy
| | - David B Neale
- University of California Davis, Department of Plant Sciences, One Shields Ave, Davis, CA 95616, USA
| | - David Chagné
- The New Zealand Institute for Plant & Food Research Limited (PFR), Palmerston North Research Centre, Palmerston North, New Zealand
| | - Yves Van de Peer
- Center for Plant Systems Biology, VIB, Technologiepark 71, 9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Gent, Belgium
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Roper street, Pretoria 0028, South Africa
| | - Michela Troggio
- Fondazione Edmund Mach, via E. Mach 1, 38010, San Michele all'Adige (TN), Italy
| | - Luca Bianco
- Fondazione Edmund Mach, via E. Mach 1, 38010, San Michele all'Adige (TN), Italy
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37
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Cornille A, Antolín F, Garcia E, Vernesi C, Fietta A, Brinkkemper O, Kirleis W, Schlumbaum A, Roldán-Ruiz I. A Multifaceted Overview of Apple Tree Domestication. TRENDS IN PLANT SCIENCE 2019; 24:770-782. [PMID: 31296442 DOI: 10.1016/j.tplants.2019.05.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 05/15/2019] [Accepted: 05/20/2019] [Indexed: 05/19/2023]
Abstract
The apple is an iconic tree and a major fruit crop worldwide. It is also a model species for the study of the evolutionary processes and genomic basis underlying the domestication of clonally propagated perennial crops. Multidisciplinary approaches from across Eurasia have documented the pace and process of cultivation of this remarkable crop. While population genetics and genomics have revealed the overall domestication history of apple across Eurasia, untangling the evolutionary processes involved, archeobotany has helped to document the transition from gathering and using apples to the practice of cultivation. Further studies integrating archeogenetic and archeogenomic approaches will bring new insights about key traits involved in apple domestication. Such knowledge has potential to boost innovation in present-day apple breeding.
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Affiliation(s)
- Amandine Cornille
- Génétique Quantitative et Evolution- Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France.
| | - Ferran Antolín
- Integrative Prehistory and Archeological Science (IPNA/IPAS), Department of Environmental Sciences, University of Basel, Spalenring 145, 4055 Basel, Switzerland
| | - Elena Garcia
- Department of Horticulture, University of Arkansas, Fayetteville, AR, USA
| | - Cristiano Vernesi
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre - Fondazione Edmund Mach, via Edmund Mach 1, 38010 San Michele all'Adige, TN, Italy
| | - Alice Fietta
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre - Fondazione Edmund Mach, via Edmund Mach 1, 38010 San Michele all'Adige, TN, Italy
| | - Otto Brinkkemper
- Cultural Heritage Agency, PO Box 1600, 3800 BP Amersfoort, The Netherlands
| | - Wiebke Kirleis
- Institute for Prehistoric and Protohistoric Archeology/Graduate School Human Development in Landscapes, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Angela Schlumbaum
- Integrative Prehistory and Archeological Science (IPNA/IPAS), Department of Environmental Sciences, University of Basel, Spalenring 145, 4055 Basel, Switzerland
| | - Isabel Roldán-Ruiz
- Flanders Research Institute for Agriculture, Fisheries, and Food (ILVO), Plant Sciences Unit, Caritasstraat 39, 9090 Melle, Belgium; Ghent University, Faculty of Sciences, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium
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38
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High-quality, genome-wide SNP genotypic data for pedigreed germplasm of the diploid outbreeding species apple, peach, and sweet cherry through a common workflow. PLoS One 2019; 14:e0210928. [PMID: 31246947 PMCID: PMC6597046 DOI: 10.1371/journal.pone.0210928] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 04/19/2019] [Indexed: 12/14/2022] Open
Abstract
High-quality genotypic data is a requirement for many genetic analyses. For any crop, errors in genotype calls, phasing of markers, linkage maps, pedigree records, and unnoticed variation in ploidy levels can lead to spurious marker-locus-trait associations and incorrect origin assignment of alleles to individuals. High-throughput genotyping requires automated scoring, as manual inspection of thousands of scored loci is too time-consuming. However, automated SNP scoring can result in errors that should be corrected to ensure recorded genotypic data are accurate and thereby ensure confidence in downstream genetic analyses. To enable quick identification of errors in a large genotypic data set, we have developed a comprehensive workflow. This multiple-step workflow is based on inheritance principles and on removal of markers and individuals that do not follow these principles, as demonstrated here for apple, peach, and sweet cherry. Genotypic data was obtained on pedigreed germplasm using 6-9K SNP arrays for each crop and a subset of well-performing SNPs was created using ASSIsT. Use of correct (and corrected) pedigree records readily identified violations of simple inheritance principles in the genotypic data, streamlined with FlexQTL software. Retained SNPs were grouped into haploblocks to increase the information content of single alleles and reduce computational power needed in downstream genetic analyses. Haploblock borders were defined by recombination locations detected in ancestral generations of cultivars and selections. Another round of inheritance-checking was conducted, for haploblock alleles (i.e., haplotypes). High-quality genotypic data sets were created using this workflow for pedigreed collections representing the U.S. breeding germplasm of apple, peach, and sweet cherry evaluated within the RosBREED project. These data sets contain 3855, 4005, and 1617 SNPs spread over 932, 103, and 196 haploblocks in apple, peach, and sweet cherry, respectively. The highly curated phased SNP and haplotype data sets, as well as the raw iScan data, of germplasm in the apple, peach, and sweet cherry Crop Reference Sets is available through the Genome Database for Rosaceae.
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