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Minamikawa MF, Kunihisa M, Moriya S, Shimizu T, Inamori M, Iwata H. Genomic prediction and genome-wide association study using combined genotypic data from different genotyping systems: application to apple fruit quality traits. HORTICULTURE RESEARCH 2024; 11:uhae131. [PMID: 38979105 PMCID: PMC11228094 DOI: 10.1093/hr/uhae131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 04/25/2024] [Indexed: 07/10/2024]
Abstract
With advances in next-generation sequencing technologies, various marker genotyping systems have been developed for genomics-based approaches such as genomic selection (GS) and genome-wide association study (GWAS). As new genotyping platforms are developed, data from different genotyping platforms must be combined. However, the potential use of combined data for GS and GWAS has not yet been clarified. In this study, the accuracy of genomic prediction (GP) and the detection power of GWAS increased for most fruit quality traits of apples when using combined data from different genotyping systems, Illumina Infinium single-nucleotide polymorphism array and genotyping by random amplicon sequencing-direct (GRAS-Di) systems. In addition, the GP model, which considered the inbreeding effect, further improved the accuracy of the seven fruit traits. Runs of homozygosity (ROH) islands overlapped with the significantly associated regions detected by the GWAS for several fruit traits. Breeders may have exploited these regions to select promising apples by breeders, increasing homozygosity. These results suggest that combining genotypic data from different genotyping platforms benefits the GS and GWAS of fruit quality traits in apples. Information on inbreeding could be beneficial for improving the accuracy of GS for fruit traits of apples; however, further analysis is required to elucidate the relationship between the fruit traits and inbreeding depression (e.g. decreased vigor).
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Affiliation(s)
- Mai F Minamikawa
- Institute for Advanced Academic Research (IAAR), Chiba University, 1-33 Yayoi, Inage, Chiba, Chiba 263-8522, Japan
- Laboratory of Biometry and Bioinformatics, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Miyuki Kunihisa
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605, Japan
| | - Shigeki Moriya
- Institute of Fruit Tree and Tea Science, NARO, 92-24 Shimokuriyagawa Nabeyashiki, Morioka, Iwate 020-0123, Japan
| | - Tokurou Shimizu
- Institute of Fruit Tree and Tea Science, NARO, Okitsu Nakacho, Shimizu, Shizuoka 424-0292, Japan
| | - Minoru Inamori
- Laboratory of Biometry and Bioinformatics, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Hiroyoshi Iwata
- Laboratory of Biometry and Bioinformatics, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
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Keller B, Jung M, Bühlmann-Schütz S, Hodel M, Studer B, Broggini GAL, Patocchi A. The genetic basis of apple shape and size unraveled by digital phenotyping. G3 (BETHESDA, MD.) 2024; 14:jkae045. [PMID: 38441135 PMCID: PMC11075547 DOI: 10.1093/g3journal/jkae045] [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: 01/23/2024] [Accepted: 02/22/2024] [Indexed: 05/08/2024]
Abstract
Great diversity of shape, size, and skin color is observed among the fruits of different apple genotypes. These traits are critical for consumers and therefore interesting targets for breeding new apple varieties. However, they are difficult to phenotype and their genetic basis, especially for fruit shape and ground color, is largely unknown. We used the FruitPhenoBox to digitally phenotype 525 genotypes of the apple reference population (apple REFPOP) genotyped for 303,148 single nucleotide polymorphism (SNP) markers. From the apple images, 573 highly heritable features describing fruit shape and size as well as 17 highly heritable features for fruit skin color were extracted to explore genotype-phenotype relationships. Out of these features, seven principal components (PCs) and 16 features with the Pearson's correlation r < 0.75 (selected features) were chosen to carry out genome-wide association studies (GWAS) for fruit shape and size. Four PCs and eight selected features were used in GWAS for fruit skin color. In total, 69 SNPs scattered over all 17 apple chromosomes were significantly associated with round, conical, cylindrical, or symmetric fruit shapes and fruit size. Novel associations with major effect on round or conical fruit shapes and fruit size were identified on chromosomes 1 and 2. Additionally, 16 SNPs associated with PCs and selected features related to red overcolor as well as green and yellow ground color were found on eight chromosomes. The identified associations can be used to advance marker-assisted selection in apple fruit breeding to systematically select for desired fruit appearance.
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Affiliation(s)
- Beat Keller
- Division of Plant Breeding, Agroscope, Mueller-Thurgau-Strasse 29, Waedenswil 8820, Switzerland
| | - Michaela Jung
- Division of Plant Breeding, Agroscope, Mueller-Thurgau-Strasse 29, Waedenswil 8820, Switzerland
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, Zurich 8092, Switzerland
| | - Simone Bühlmann-Schütz
- Division of Plant Breeding, Agroscope, Mueller-Thurgau-Strasse 29, Waedenswil 8820, Switzerland
| | - Marius Hodel
- Division of Plant Breeding, Agroscope, Mueller-Thurgau-Strasse 29, Waedenswil 8820, Switzerland
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, Zurich 8092, Switzerland
| | - Giovanni A L Broggini
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, Zurich 8092, Switzerland
| | - Andrea Patocchi
- Division of Plant Breeding, Agroscope, Mueller-Thurgau-Strasse 29, Waedenswil 8820, Switzerland
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3
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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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4
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Yang C, Sun N, Qin X, Liu Y, Sui M, Zhang Y, Hu Y, Mao Z, Chen X, Mao Y, Shen X. Multi-omics analysis reveals the biosynthesis of flavonoids during the browning process of Malus sieversii explants. PHYSIOLOGIA PLANTARUM 2024; 176:e14238. [PMID: 38488414 DOI: 10.1111/ppl.14238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 01/23/2024] [Accepted: 02/04/2024] [Indexed: 03/19/2024]
Abstract
Malus sieversii is a precious apple germplasm resource. Browning of explants is one of the most important factors limiting the survival rate of plant tissue culture. In order to explore the molecular mechanism of the browning degree of different strains of Malus sieversii, we compared the dynamic changes of Malus sieversii and Malus robusta Rehd. during the whole browning process using a multi-group method. A total of 44 048 differentially expressed genes (DEGs) were identified by transcriptome analysis on the DNBSEQ-T7 sequencing platform. KEGG enrichment analysis showed that the DEGs were significantly enriched in the flavonoid biosynthesis pathway. In addition, metabonomic analysis showed that (-)-epicatechin, astragalin, chrysin, irigenin, isoquercitrin, naringenin, neobavaisoflavone and prunin exhibited different degrees of free radical scavenging ability in the tissue culture browning process, and their accumulation in different varieties led to differences in the browning degree among varieties. Comprehensive transcriptome and metabonomics analysis of the data related to flavonoid biosynthesis showed that PAL, 4CL, F3H, CYP73A, CHS, CHI, ANS, DFR and PGT1 were the key genes for flavonoid accumulation during browning. In addition, WGCNA analysis revealed a strong correlation between the known flavonoid structure genes and the selected transcriptional genes. Protein interaction predictions demonstrated that 19 transcription factors (7 MYBs and 12 bHLHs) and 8 flavonoid structural genes had targeted relationships. The results show that the interspecific differential expression of flavonoid genes is the key influencing factor of the difference in browning degree between Malus sieversii and Malus robusta Rehd., providing a theoretical basis for further study on the regulation of flavonoid biosynthesis.
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Affiliation(s)
- Chen Yang
- College of Horticulture Science and Engineering, Shandong Agricultural University, China
| | - Nan Sun
- College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Xin Qin
- College of Horticulture Science and Engineering, Shandong Agricultural University, China
| | - Yangbo Liu
- College of Horticulture Science and Engineering, Shandong Agricultural University, China
| | - Mengyi Sui
- College of Horticulture Science and Engineering, Shandong Agricultural University, China
| | - Yawen Zhang
- College of Horticulture Science and Engineering, Shandong Agricultural University, China
| | - Yanli Hu
- College of Horticulture Science and Engineering, Shandong Agricultural University, China
| | - Zhiquan Mao
- College of Horticulture Science and Engineering, Shandong Agricultural University, China
| | - Xuesen Chen
- College of Horticulture Science and Engineering, Shandong Agricultural University, China
| | - Yunfei Mao
- College of Horticulture Science and Engineering, Shandong Agricultural University, China
| | - Xiang Shen
- College of Horticulture Science and Engineering, Shandong Agricultural University, China
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5
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Dujak C, Coleto-Alcudia V, Aranzana MJ. Genomic analysis of fruit size and shape traits in apple: unveiling candidate genes through GWAS analysis. HORTICULTURE RESEARCH 2024; 11:uhad270. [PMID: 38419968 PMCID: PMC10901474 DOI: 10.1093/hr/uhad270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 12/05/2023] [Indexed: 03/02/2024]
Abstract
Genomic tools facilitate the efficient selection of improved genetic materials within a breeding program. Here, we focus on two apple fruit quality traits: shape and size. We utilized data from 11 fruit morphology parameters gathered across three years of harvest from 355 genotypes of the apple REFPOP collection, which serves as a representative sample of the genetic variability present in European-cultivated apples. The data were then employed for genome-wide association studies (GWAS) using the FarmCPU and the BLINK models. The analysis identified 59 SNPs associated with fruit size and shape traits (35 with FarmCPU and 45 with BLINK) responsible for 71 QTNs. These QTNs were distributed across all chromosomes except for chromosomes 10 and 15. Thirty-four QTNs, identified by 27 SNPs, were related for size traits, and 37 QTNs, identified by 26 SNPs, were related to shape attributes. The definition of the haploblocks containing the most relevant SNPs served to propose candidate genes, among them the genes of the ovate family protein MdOFP17 and MdOFP4 that were in a 9.7kb haploblock on Chromosome 11. RNA-seq data revealed low or null expression of these genes in the oblong cultivar "Skovfoged" and higher expression in the flat "Grand'mere." The Gene Ontology enrichment analysis support a role of OFPs and hormones in shape regulation. In conclusion, this comprehensive GWAS analysis of the apple REFPOP collection has revealed promising genetic markers and candidate genes associated with apple fruit shape and size attributes, providing valuable insights that could enhance the efficiency of future breeding programs.
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Affiliation(s)
- Christian Dujak
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UABUB, Plant and Animal Genomics, Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Veredas Coleto-Alcudia
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UABUB, Plant and Animal Genomics, Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Maria José Aranzana
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UABUB, Plant and Animal Genomics, Campus UAB, 08193 Bellaterra, Barcelona, Spain
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Genomics and Biotechnology, 08140 Caldes de Montbui, Barcelona, Spain
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6
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Wen X, Yuan J, Bozorov TA, Waheed A, Kahar G, Haxim Y, Liu X, Huang L, Zhang D. An efficient screening system of disease-resistant genes from wild apple, Malus sieversii in response to Valsa mali pathogenic fungus. PLANT METHODS 2023; 19:138. [PMID: 38042829 PMCID: PMC10693133 DOI: 10.1186/s13007-023-01115-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/21/2023] [Indexed: 12/04/2023]
Abstract
For molecular breeding of future apples, wild apple (Malus sieversii), the primary progenitor of domesticated apples, provides abundant genetic diversity and disease-resistance traits. Valsa canker (caused by the fungal pathogen Valsa mali) poses a major threat to wild apple population as well as to cultivated apple production in China. In the present study, we developed an efficient system for screening disease-resistant genes of M. sieversii in response to V. mali. An optimal agrobacterium-mediated transient transformation of M. sieversii was first used to manipulate in situ the expression of candidate genes. After that, the pathogen V. mali was inoculated on transformed leaves and stems, and 3 additional methods for slower disease courses were developed for V. mali inoculation. To identify the resistant genes, a series of experiments were performed including morphological (incidence, lesion area/length, fungal biomass), physiological (H2O2 content, malondialdehyde content), and molecular (Real-time quantitative Polymerase Chain Reaction) approaches. Using the optimized system, we identified two transcription factors with high resistance to V. mali, MsbHLH41 and MsEIL3. Furthermore, 35 and 45 downstream genes of MsbHLH41 and MsEIL3 were identified by screening the V. mali response gene database in M. sieversii, respectively. Overall, these results indicate that the disease-resistant gene screening system has a wide range of applications for identifying resistant genes and exploring their immune regulatory networks.
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Affiliation(s)
- Xuejing Wen
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830000, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan, 838008, China
- National Positioning Observation and Research Station of Forest Ecosystem in Yili (XinJiang), Academy of Forestry in Yili, Yili, 835100, China
| | - Jiangxue Yuan
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830000, China
| | - Tohir A Bozorov
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830000, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan, 838008, China
| | - Abdul Waheed
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830000, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan, 838008, China
| | - Gulnaz Kahar
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830000, China
| | - Yakupjan Haxim
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830000, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan, 838008, China
| | - Xiaojie Liu
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830000, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan, 838008, China
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, China
| | - Daoyuan Zhang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China.
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830000, China.
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan, 838008, China.
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7
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Minow MAA, Marand AP, Schmitz RJ. Leveraging Single-Cell Populations to Uncover the Genetic Basis of Complex Traits. Annu Rev Genet 2023; 57:297-319. [PMID: 37562412 PMCID: PMC10775913 DOI: 10.1146/annurev-genet-022123-110824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
The ease and throughput of single-cell genomics have steadily improved, and its current trajectory suggests that surveying single-cell populations will become routine. We discuss the merger of quantitative genetics with single-cell genomics and emphasize how this synergizes with advantages intrinsic to plants. Single-cell population genomics provides increased detection resolution when mapping variants that control molecular traits, including gene expression or chromatin accessibility. Additionally, single-cell population genomics reveals the cell types in which variants act and, when combined with organism-level phenotype measurements, unveils which cellular contexts impact higher-order traits. Emerging technologies, notably multiomics, can facilitate the measurement of both genetic changes and genomic traits in single cells, enabling single-cell genetic experiments. The implementation of single-cell genetics will advance the investigation of the genetic architecture of complex molecular traits and provide new experimental paradigms to study eukaryotic genetics.
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Affiliation(s)
- Mark A A Minow
- Department of Genetics, University of Georgia, Athens, Georgia, USA;
| | | | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, Georgia, USA;
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8
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Mansfeld BN, Yocca A, Ou S, Harkess A, Burchard E, Gutierrez B, van Nocker S, Gottschalk C. A haplotype resolved chromosome-scale assembly of North American wild apple Malus fusca and comparative genomics of the fire blight Mfu10 locus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:989-1002. [PMID: 37639371 DOI: 10.1111/tpj.16433] [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: 03/22/2023] [Revised: 07/08/2023] [Accepted: 08/12/2023] [Indexed: 08/31/2023]
Abstract
SUMMARYThe Pacific crabapple (Malus fusca) is a wild relative of the commercial apple (Malus × domestica). With a range extending from Alaska to Northern California, M. fusca is extremely hardy and disease resistant. The species represents an untapped genetic resource for the development of new apple cultivars with enhanced stress resistance. However, gene discovery and utilization of M. fusca have been hampered by the lack of genomic resources. Here, we present a high‐quality, haplotype‐resolved, chromosome‐scale genome assembly and annotation for M. fusca. The genome was assembled using high‐fidelity long‐reads and scaffolded using genetic maps and high‐throughput chromatin conformation capture sequencing, resulting in one of the most contiguous apple genomes to date. We annotated the genome using public transcriptomic data from the same species taken from diverse plant structures and developmental stages. Using this assembly, we explored haplotypic structural variation within the genome of M. fusca, identifying thousands of large variants. We further showed high sequence co‐linearity with other domesticated and wild Malus species. Finally, we resolve a known quantitative trait locus associated with resistance to fire blight (Erwinia amylovora). Insights gained from the assembly of a reference‐quality genome of this hardy wild apple relative will be invaluable as a tool to facilitate DNA‐informed introgression breeding.
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Affiliation(s)
- Ben N Mansfeld
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Alan Yocca
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Shujun Ou
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, USA
| | - Alex Harkess
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Erik Burchard
- USDA ARS, Appalachian Fruit Research Station, Kearneysville, West Virginia, USA
| | | | - Steve van Nocker
- Department of Horticulture, Michigan State University, East Lansing, Michigan, USA
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9
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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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10
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Hu Y, Yu Z, Gao X, Liu G, Zhang Y, Šmarda P, Guo Q. Genetic diversity, population structure, and genome-wide association analysis of ginkgo cultivars. HORTICULTURE RESEARCH 2023; 10:uhad136. [PMID: 37564270 PMCID: PMC10410194 DOI: 10.1093/hr/uhad136] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 07/02/2023] [Indexed: 08/12/2023]
Abstract
Ginkgo biloba is an economically valuable tree worldwide. The species has nearly become extinct during the Quaternary, which has likely resulted in reduction of its genetic variability. The genetic variability is now conserved in few natural populations in China and a number of cultivars that are, however, derived from a few ancient trees, helping the species survive in China through medieval times. Despite the recent interest in ginkgo, however, detailed knowledge of its genetic diversity, conserved in cultivated trees and cultivars, has remained poor. This limits efficient conservation of its diversity as well as efficient use of the existing germplasm resources. Here we performed genotyping-by-sequencing (GBS) on 102 cultivated germplasms of ginkgo collected to explore their genetic structure, kinship, and inbreeding prediction. For the first time in ginkgo, a genome-wide association analysis study (GWAS) was used to attempt gene mapping of seed traits. The results showed that most of the germplasms did not show any obvious genetic relationship. The size of the ginkgo germplasm population expanded significantly around 1500 years ago during the Sui and Tang dynasties. Classification of seed cultivars based on a phylogenetic perspective does not support the current classification criteria based on phenotype. Twenty-four candidate genes were localized after performing GWAS on the seed traits. Overall, this study reveals the genetic basis of ginkgo seed traits and provides insights into its cultivation history. These findings will facilitate the conservation and utilization of the domesticated germplasms of this living fossil plant.
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Affiliation(s)
- Yaping Hu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Zhaoyan Yu
- Coconut Research Institute of Chinese Academy of Tropical Agricultural Science, Wenchang, Hainan 571339, China
| | - Xiaoge Gao
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Ganping Liu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Yun Zhang
- Institute of Grassland, Flowers, and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Petr Šmarda
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Koltlářská 2, Brno 61137, Czech Republic
| | - Qirong Guo
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
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11
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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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12
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Awan SI, Thapa R, Svara A, Feulner H, Streb N, Khan A. Evaluation of Malus Germplasm Identifies Genetic Sources of Powdery Mildew and Frogeye Leaf Spot Resistance for Apple Breeding. PHYTOPATHOLOGY 2023; 113:1289-1300. [PMID: 36802874 DOI: 10.1094/phyto-11-22-0417-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Apple is an important fruit crop of temperate regions. The narrow genetic base of commercially cultivated apples has resulted in its vulnerability to a large number of fungal, bacterial, and viral pathogens. Apple breeders are always seeking new sources of resistance within the cross-compatible Malus species that can be deployed into elite genetic backgrounds. We have evaluated resistance to two major fungal diseases of apples: powdery mildew and frogeye leaf spot, using a germplasm collection of 174 Malus accessions to identify novel sources of genetic resistance. In 2020 and 2021, we evaluated these accessions for the incidence and severity of powdery mildew and frogeye leaf spot diseases at Cornell AgriTech, Geneva, New York, in a partially managed orchard. The severity and incidence of powdery mildew and frogeye leaf spot, as well as weather parameters were recorded in June, July, and August. Total incidence of powdery mildew and frogeye leaf spot infections increased from 33 to 38%, and 56 to 97% in 2020 and 2021, respectively. Our analysis showed that relative humidity and precipitation correlate with powdery mildew and frogeye leaf spot susceptibility. The predictor variables with highest impact to the variability of powdery mildew were accessions and relative humidity in May. A total of 65 Malus accessions were found to be resistant to powdery mildew, and only one accession showed moderate resistance to frogeye leaf spot. Several of these accessions belong to Malus hybrid species and domesticated apples and can therefore be potential sources of novel resistance alleles for apple breeding.
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Affiliation(s)
- Shahid Iqbal Awan
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY 14456
| | - Ranjita Thapa
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY 14456
| | - Anze Svara
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY 14456
| | - Hana Feulner
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY 14456
| | - Nicholas Streb
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY 14456
| | - Awais Khan
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY 14456
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13
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Ma C, Zhang C, Wang X, Zhu F, Wang X, Zhang M, Duan Y. Alternative Splicing Analysis Revealed the Role of Alpha-Linolenic Acid and Carotenoids in Fruit Development of Osmanthus fragrans. Int J Mol Sci 2023; 24:ijms24108666. [PMID: 37240011 DOI: 10.3390/ijms24108666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/26/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
Alternative splicing refers to the process of producing different splicing isoforms from the same pre-mRNA through different alternative splicing events, which almost participates in all stages of plant growth and development. In order to understand its role in the fruit development of Osmanthus fragrans, transcriptome sequencing and alternative splicing analysis was carried out on three stages of O. fragrans fruit (O. fragrans "Zi Yingui"). The results showed that the proportion of skipping exon events was the highest in all three periods, followed by a retained intron, and the proportion of mutually exclusive exon events was the lowest and most of the alternative splicing events occurred in the first two periods. The results of enrichment analysis of differentially expressed genes and differentially expressed isoforms showed that alpha-Linolenic acid metabolism, flavonoid biosynthesis, carotenoid biosynthesis, photosynthesis, and photosynthetic-antenna protein pathways were significantly enriched, which may play an important role in the fruit development of O. fragrans. The results of this study lay the foundation for further study of the development and maturation of O. fragrans fruit and further ideas for controlling fruit color and improving fruit quality and appearance.
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Affiliation(s)
- Cancan Ma
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing 210037, China
| | - Cheng Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing 210037, China
| | - Xiaoyan Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing 210037, China
| | - Fuyuan Zhu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing 210037, China
| | - Xianrong Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing 210037, China
| | - Min Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing 210037, China
| | - Yifan Duan
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing 210037, China
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14
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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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15
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Könyves K, Mian S, Johns J, Ruhsam M, Leitch IJ. The genome sequence of the apple, Malus domestica (Suckow) Borkh., 1803. Wellcome Open Res 2022. [DOI: 10.12688/wellcomeopenres.18646.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
We present genome assemblies from four Malus domestica cultivars (the apple; Streptophyta; Magnoliopsida; Rosales; Rosaceae). The genome sequences are 643–653 megabases in span. The greater part of each assembly length (99.24–99.74%) is scaffolded into 17 chromosomal pseudomolecules. The mitochondrial and plastid genomes were also assembled and are 400 kilobases and 167 kilobases in length respectively.
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16
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Yang X, Wu B, Liu J, Zhang Z, Wang X, Zhang H, Ren X, Zhang X, Wang Y, Wu T, Xu X, Han Z, Zhang X. A single QTL harboring multiple genetic variations leads to complicated phenotypic segregation in apple flesh firmness and crispness. PLANT CELL REPORTS 2022; 41:2379-2391. [PMID: 36208306 DOI: 10.1007/s00299-022-02929-z] [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: 06/14/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Within a QTL, the genetic recombination and interactions among five and two functional variations at MdbHLH25 and MdWDR5A caused much complicated phenotype segregation in apple FFR and FCR. The storability of climacteric fruit like apple is a quantitative trait. We previously identified 62 quantitative trait loci (QTLs) associating flesh firmness retainability (FFR) and flesh crispness retainability (FCR), but only a few functional genetic variations were identified and validated. The genetic variation network controlling fruit storability is far to be understood and diagnostic markers are needed for molecular breeding. We previously identified overlapped QTLs F16.1/H16.2 for FFR and FCR using an F1 population derived from 'Zisai Pearl' × 'Red Fuji'. In this study, five and two single-nucleotide polymorphisms (SNPs) were identified on the candidate genes MdbHLH25 and MdWDR5A within the QTL region. The SNP1 A allele at MdbHLH25 promoter reduced the expression and SNP2 T allele and/or SNP4/5 GT alleles at the exons attenuated the function of MdbHLH25 by downregulating the expression of the target genes MdACS1, which in turn led to a reduction in ethylene production and maintenance of higher flesh crispness. The SNPs did not alter the protein-protein interaction between MdbHLH25 and MdWDR5A. The joint effect of SNP genotype combinations by the SNPs on MdbHLH25 (SNP1, SNP2, and SNP4) and MdWDR5A (SNPi and SNPii) led to a much broad spectrum of phenotypic segregation in FFR and FCR. Together, the dissection of these genetic variations contributes to understanding the complicated effects of a QTL and provides good potential for marker development in molecular breeding.
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Affiliation(s)
- Xianglong Yang
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Bei Wu
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Jing Liu
- College of Horticultural Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066600, China
| | - Zhongyan Zhang
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xuan Wang
- College of Horticultural Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066600, China
| | - Haie Zhang
- College of Horticultural Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066600, China
| | - Xuejun Ren
- Testing and Analysis Center, Hebei Normal University of Science and Technology, Qinhuangdao, 066600, China
| | - Xi Zhang
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yi Wang
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Ting Wu
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xuefeng Xu
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Zhenhai Han
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, Beijing, 100193, China.
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17
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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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18
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Ha YH, Gil HY, Kim SC, Choi K, Kim JH. Genetic structure and geneflow of Malus across the Korean Peninsula using genotyping-by-sequencing. Sci Rep 2022; 12:16262. [PMID: 36171257 PMCID: PMC9519971 DOI: 10.1038/s41598-022-20513-z] [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: 05/17/2022] [Accepted: 09/14/2022] [Indexed: 11/09/2022] Open
Abstract
This study was to understand the genetic structure and diversity of the Korean Malus species. We used genotyping-by-sequencing (GBS) technology to analyze samples of 112 individuals belonging to 18 populations of wild Malus spp. Using GBS, we identified thousands of single nucleotide polymorphisms in the species analyzed. M. baccata and M. toringo, two dominant mainland species of the Korean Peninsula, were distinguishable based on their genetic structure. However, M. toringo collected from Jeju Island exhibited a different genetic profile than that from the mainland. We identified M. cf. micromalus as a hybrid resulting from the Jeju Island M. toringo (pollen donor) and the mainland M. baccata, (pollen recipient). Putative M. mandshurica distributed on the Korean Peninsula showed a high structural and genetic similarity with M. baccata, indicating that it might be an ecotype. Overall, this study contributes to the understanding of the population history and genetic structure of Malus in the Korean Peninsula.
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Affiliation(s)
- Young-Ho Ha
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Gyeonggi-do, 11186, Republic of Korea.,Department of Life Science, Gachon University, Seongnam, Gyeonggi-do, 13120, Republic of Korea
| | - Hee-Young Gil
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Gyeonggi-do, 11186, Republic of Korea
| | - Sang-Chul Kim
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Gyeonggi-do, 11186, Republic of Korea
| | - Kyung Choi
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Gyeonggi-do, 11186, Republic of Korea
| | - Joo-Hwan Kim
- Department of Life Science, Gachon University, Seongnam, Gyeonggi-do, 13120, Republic of Korea.
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19
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Khan A, Carey SB, Serrano A, Zhang H, Hargarten H, Hale H, Harkess A, Honaas L. A phased, chromosome-scale genome of 'Honeycrisp' apple ( Malus domestica). GIGABYTE 2022; 2022:gigabyte69. [PMID: 36824509 PMCID: PMC9693968 DOI: 10.46471/gigabyte.69] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 09/14/2022] [Indexed: 11/09/2022] Open
Abstract
The apple cultivar 'Honeycrisp' has superior fruit quality traits, cold hardiness, and disease resistance, making it a popular breeding parent. However, it suffers from several physiological disorders, production, and postharvest issues. Despite several available apple genome sequences, understanding of the genetic mechanisms underlying cultivar-specific traits remains lacking. Here, we present a highly contiguous, fully phased, chromosome-level genome of 'Honeycrisp' apples, using PacBio HiFi, Omni-C, and Illumina sequencing platforms, with two assembled haplomes of 674 Mbp and 660 Mbp, and contig N50 values of 32.8 Mbp and 31.6 Mbp, respectively. Overall, 47,563 and 48,655 protein-coding genes were annotated from each haplome, capturing 96.8-97.4% complete BUSCOs in the eudicot database. Gene family analysis reveals most 'Honeycrisp' genes are assigned into orthogroups shared with other genomes, with 121 'Honeycrisp'-specific orthogroups. This resource is valuable for understanding the genetic basis of important traits in apples and related Rosaceae species to enhance breeding efforts.
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Affiliation(s)
- Awais Khan
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY 14456, USA, Corresponding authors. E-mail: ;
| | - Sarah B. Carey
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL 36849, USA,HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Alicia Serrano
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY 14456, USA
| | - Huiting Zhang
- USDA ARS Tree Fruit Research Lab, Wenatchee, WA 98801, USA,Department of Horticulture, Washington State University, Pullman, WA, USA
| | | | - Haley Hale
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL 36849, USA,HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Alex Harkess
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL 36849, USA,HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Loren Honaas
- USDA ARS Tree Fruit Research Lab, Wenatchee, WA 98801, USA, Corresponding authors. E-mail: ;
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20
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Lempe J, Flachowsky H, Peil A. Exploring epigenetic variation for breeding climate resilient apple crops. PHYSIOLOGIA PLANTARUM 2022; 174:e13782. [PMID: 36151889 DOI: 10.1111/ppl.13782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/10/2022] [Accepted: 09/17/2022] [Indexed: 06/16/2023]
Abstract
Climate change with warmer winter and spring temperatures poses major challenges to apple fruit production. Long-term observations confirm the trend toward earlier flowering, which leads to an increased risk of frost damage. New breeding strategies are needed to generate cultivars that are able to stay largely unaffected by warmer temperatures. Recently, epigenetic variation has been proposed as a new resource for breeding purposes and seems suitable in principle for apple breeding. However, to serve as a new resource for apple breeding, it is necessary to clarify whether epigenetic variation can be induced by the environment, whether it can create phenotypic variation, and whether this variation is stable across generations. In this brief review, we summarize the impact of climate change on the timing of apple phenology, highlight how epigenetic variation can potentially support novel breeding strategies, and point out important features of epigenetic variation that are required for its application in breeding programs.
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Affiliation(s)
- Janne Lempe
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Dresden, Germany
| | - Henryk Flachowsky
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Dresden, Germany
| | - Andreas Peil
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Dresden, Germany
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21
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Liu Y, Gao XH, Tong L, Liu MZ, Zhou XK, Tahir MM, Xing LB, Ma JJ, An N, Zhao CP, Yao JL, Zhang D. Multi-omics analyses reveal MdMYB10 hypermethylation being responsible for a bud sport of apple fruit color. HORTICULTURE RESEARCH 2022; 9:uhac179. [PMID: 36338840 PMCID: PMC9627520 DOI: 10.1093/hr/uhac179] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 08/02/2022] [Indexed: 06/16/2023]
Abstract
Apple bud sports offer a rich resource for clonal selection of numerous elite cultivars. The accumulation of somatic mutations as plants develop may potentially impact the emergence of bud sports. Previous studies focused on somatic mutation in the essential genes associated with bud sports. However, the rate and function of genome-wide somatic mutations that accumulate when a bud sport arises remain unclear. In this study, we identified a branch from a 10-year-old tree of the apple cultivar 'Oregon Spur II' as a bud sport. The mutant branch showed reduced red coloration on fruit skin. Using this plant material, we assembled a high-quality haplotype reference genome consisting of 649.61 Mb sequences with a contig N50 value of 2.04 Mb. We then estimated the somatic mutation rate of the apple tree to be 4.56 × 10 -8 per base per year, and further identified 253 somatic single-nucleotide polymorphisms (SNPs), including five non-synonymous SNPs, between the original type and mutant samples. Transcriptome analyses showed that 69 differentially expressed genes between the original type and mutant fruit skin were highly correlated with anthocyanin content. DNA methylation in the promoter of five anthocyanin-associated genes was increased in the mutant compared with the original type as determined using DNA methylation profiling. Among the genetic and epigenetic factors that directly and indirectly influence anthocyanin content in the mutant apple fruit skin, the hypermethylated promoter of MdMYB10 is important. This study indicated that numerous somatic mutations accumulated at the emergence of a bud sport from a genome-wide perspective, some of which contribute to the low coloration of the bud sport.
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Affiliation(s)
- Yu Liu
- College of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiu-hua Gao
- College of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, Northwest A&F University, Yangling, Shaanxi, China
| | - Lu Tong
- College of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, Northwest A&F University, Yangling, Shaanxi, China
| | - Mei-zi Liu
- College of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, Northwest A&F University, Yangling, Shaanxi, China
| | | | - Muhammad Mobeen Tahir
- College of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, Northwest A&F University, Yangling, Shaanxi, China
| | - Li-bo Xing
- College of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, Northwest A&F University, Yangling, Shaanxi, China
| | - Juan-juan Ma
- College of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, Northwest A&F University, Yangling, Shaanxi, China
| | - Na An
- College of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, Northwest A&F University, Yangling, Shaanxi, China
| | - Cai-ping Zhao
- College of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, Northwest A&F University, Yangling, Shaanxi, China
| | - Jia-Long Yao
- The New Zealand Institute for Plant and Food Research Ltd, Private Bag 92169, Auckland 1142, New Zealand
| | - 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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22
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Migicovsky Z, Douglas GM, Myles S. Genotyping-by-sequencing of Canada’s apple biodiversity collection. Front Genet 2022; 13:934712. [PMID: 36092877 PMCID: PMC9452695 DOI: 10.3389/fgene.2022.934712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/21/2022] [Indexed: 11/22/2022] Open
Affiliation(s)
- Zoë Migicovsky
- Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
| | | | - Sean Myles
- Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
- *Correspondence: Sean Myles,
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23
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Nishiyama S, Sato K, Tao R. Integer programming for selecting set of informative markers in paternity inference. BMC Bioinformatics 2022; 23:265. [PMID: 35804290 PMCID: PMC9264695 DOI: 10.1186/s12859-022-04801-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 06/09/2022] [Indexed: 11/24/2022] Open
Abstract
Background Parentage information is fundamental to various life sciences. Recent advances in sequencing technologies have made it possible to accurately infer parentage even in non-model species. The optimization of sets of genome-wide markers is valuable for cost-effective applications but requires extremely large amounts of computation, which presses for the development of new efficient algorithms. Results Here, for a closed half-sib population, we generalized the process of marker loci selection as a binary integer programming problem. The proposed systematic formulation considered marker localization and the family structure of the potential parental population, resulting in an accurate assignment with a small set of markers. We also proposed an efficient heuristic approach, which effectively improved the number of markers, localization, and tolerance to missing data of the set. Applying this method to the actual genotypes of apple (Malus × domestica) germplasm, we identified a set of 34 SNP markers that distinguished 300 potential parents crossed to a particular cultivar with a greater than 99% accuracy. Conclusions We present a novel approach for selecting informative markers based on binary integer programming. Since the data generated by high-throughput sequencing technology far exceeds the requirement for parentage assignment, a combination of the systematic marker selection with targeted SNP genotyping, such as KASP, allows flexibly enlarging the analysis up to a scale that has been unrealistic in various species. The method developed in this study can be directly applied to unsolved large-scale problems in breeding, reproduction, and ecological research, and is expected to lead to novel knowledge in various biological fields. The implementation is available at https://github.com/SoNishiyama/IP-SIMPAT. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04801-z.
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Affiliation(s)
| | - Kengo Sato
- School of System Design and Technology, Tokyo Denki University, Tokyo, Japan
| | - Ryutaro Tao
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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24
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Tao W, Bian J, Tang M, Zeng Y, Luo R, Ke Q, Li T, Li Y, Cui L. Genomic insights into positive selection during barley domestication. BMC PLANT BIOLOGY 2022; 22:267. [PMID: 35641942 PMCID: PMC9158214 DOI: 10.1186/s12870-022-03655-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Cultivated barley (Hordeum vulgare) is widely used in animal feed, beverages, and foods and has become a model crop for molecular evolutionary studies. Few studies have examined the evolutionary fates of different types of genes in barley during the domestication process. RESULTS The rates of nonsynonymous substitution (Ka) to synonymous substitution (Ks) were calculated by comparing orthologous genes in different barley groups (wild vs. landrace and landrace vs. improved cultivar). The rates of evolution, properties, expression patterns, and diversity of positively selected genes (PSGs) and negatively selected genes (NSGs) were compared. PSGs evolved more rapidly, possessed fewer exons, and had lower GC content than NSGs; they were also shorter and had shorter intron, exon, and first exon lengths. Expression levels were lower, the tissue specificity of expression was higher, and codon usage bias was weaker for PSGs than for NSGs. Nucleotide diversity analysis revealed that PSGs have undergone a more severe genetic bottleneck than NSGs. Several candidate PSGs were involved in plant growth and development, which might make them as excellent targets for the molecular breeding of barley. CONCLUSIONS Our comprehensive analysis of the evolutionary, structural, and functional divergence between PSGs and NSGs in barley provides new insight into the evolutionary trajectory of barley during domestication. Our findings also aid future functional studies of PSGs in barley.
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Affiliation(s)
- Wenjing Tao
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045 China
| | - Jianxin Bian
- Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, 261325 China
| | - Minqiang Tang
- College of Forestry, Hainan University, Haikou, Hainan, 570228 China
| | - Yan Zeng
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045 China
| | - Ruihan Luo
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045 China
| | - Qinglin Ke
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045 China
| | - Tingting Li
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045 China
| | - Yihan Li
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045 China
| | - Licao Cui
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045 China
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25
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Davies T, Watts S, McClure K, Migicovsky Z, Myles S. Phenotypic divergence between the cultivated apple (Malus domestica) and its primary wild progenitor (Malus sieversii). PLoS One 2022; 17:e0250751. [PMID: 35320270 PMCID: PMC8942233 DOI: 10.1371/journal.pone.0250751] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 02/22/2022] [Indexed: 11/18/2022] Open
Abstract
An understanding of the relationship between the cultivated apple (Malus domestica) and its primary wild progenitor species (M. sieversii) not only provides an understanding of how apples have been improved in the past, but may be useful for apple improvement in the future. We measured 10 phenotypes in over 1000 unique apple accessions belonging to M. domestica and M. sieversii from Canada's Apple Biodiversity Collection. Using principal components analysis (PCA), we determined that M. domestica and M. sieversii differ significantly in phenotypic space and are nearly completely distinguishable as two separate groups. We found that M. domestica had a shorter juvenile phase than M. sieversii and that cultivated trees produced flowers and ripe fruit later than their wild progenitors. Cultivated apples were also 3.6 times heavier, 43% less acidic, and had 68% less phenolic content than wild apples. Using historical records, we found that apple breeding over the past 200 years has resulted in a trend towards apples that have higher soluble solids, are less bitter, and soften less during storage. Our results quantify the significant changes in phenotype that have taken place since apple domestication, and provide evidence that apple breeding has led to continued phenotypic divergence of the cultivated apple from its wild progenitor species.
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Affiliation(s)
- Thomas Davies
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
| | - Sophie Watts
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
| | - Kendra McClure
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
| | - Zoë Migicovsky
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
| | - Sean Myles
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
- * E-mail:
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26
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Jung M, Keller B, Roth M, Aranzana MJ, Auwerkerken A, Guerra W, Al-Rifaï M, Lewandowski M, Sanin N, Rymenants M, Didelot F, Dujak C, Font i Forcada C, Knauf A, Laurens F, Studer B, Muranty H, Patocchi A. Genetic architecture and genomic predictive ability of apple quantitative traits across environments. HORTICULTURE RESEARCH 2022; 9:uhac028. [PMID: 35184165 PMCID: PMC8976694 DOI: 10.1093/hr/uhac028] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 12/09/2021] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Implementation of genomic tools is desirable to increase the efficiency of apple breeding. Recently, the multi-environment apple reference population (apple REFPOP) proved useful for rediscovering loci, estimating genomic predictive ability, and studying genotype by environment interactions (G × E). So far, only two phenological traits were investigated using the apple REFPOP, although the population may be valuable when dissecting genetic architecture and reporting predictive abilities for additional key traits in apple breeding. Here we show contrasting genetic architecture and genomic predictive abilities for 30 quantitative traits across up to six European locations using the apple REFPOP. A total of 59 stable and 277 location-specific associations were found using GWAS, 69.2% of which are novel when compared with 41 reviewed publications. Average genomic predictive abilities of 0.18-0.88 were estimated using main-effect univariate, main-effect multivariate, multi-environment univariate, and multi-environment multivariate models. The G × E accounted for up to 24% of the phenotypic variability. This most comprehensive genomic study in apple in terms of trait-environment combinations provided knowledge of trait biology and prediction models that can be readily applied for marker-assisted or genomic selection, thus facilitating increased breeding efficiency.
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Affiliation(s)
- Michaela Jung
- Agroscope, Breeding Research Group, 8820 Wädenswil, Switzerland
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092 Zurich, Switzerland
| | - Beat Keller
- Agroscope, Breeding Research Group, 8820 Wädenswil, Switzerland
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092 Zurich, Switzerland
| | - Morgane Roth
- Agroscope, Breeding Research Group, 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
| | | | | | - Mehdi Al-Rifaï
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QuaSaV, F-49000 Angers, France
| | - Mariusz Lewandowski
- The National Institute of Horticultural Research, Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland
| | | | - Marijn Rymenants
- Better3fruit N.V., 3202 Rillaar, Belgium
- Laboratory for Plant Genetics and Crop Improvement, KU Leuven, B-3001 Leuven, Belgium
| | | | - Christian Dujak
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Carolina Font i Forcada
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), 08140 Caldes de Montbui, Barcelona, Spain
| | - Andrea Knauf
- Agroscope, Breeding Research Group, 8820 Wädenswil, Switzerland
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092 Zurich, Switzerland
| | - François Laurens
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QuaSaV, F-49000 Angers, France
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092 Zurich, Switzerland
| | - Hélène Muranty
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QuaSaV, F-49000 Angers, France
| | - Andrea Patocchi
- Agroscope, Breeding Research Group, 8820 Wädenswil, Switzerland
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27
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An Apple a Day Keeps the Doctor Away: Potential Role of miRNA 146 on Macrophages Treated with Exosomes Derived from Apples. Biomedicines 2022; 10:biomedicines10020415. [PMID: 35203624 PMCID: PMC8962404 DOI: 10.3390/biomedicines10020415] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/02/2022] [Accepted: 02/06/2022] [Indexed: 12/12/2022] Open
Abstract
The constant dialogue between the plant world and the animal world (including man among them) has been known since the time of Adam and Eve, where an apple was the origin of the evils of the world. Apart from Snow White—who might have something to object to when it comes to the use of apples—fruits, plants, and natural extracts have been known for millennia as remedies for human health-related ailments. In the light of such evidence, the aim of the present work was to investigate from a biological point of view the potential role of apple exosomes in inflammatory processes on human cells. To this end we isolated and characterized apple exosomes and treated human cells such as macrophages and NCTC L929 as cancer cells in order to evaluate the tumorigenic and anti-inflammatory effect of apple exomes. Microscopic and molecular biology analyses were conducted to characterize exosomes and to assess cell proliferation, death, and miRNA line, as well as gene expression and the uptake of exosomes by cells. The results confirm the absolute biological safety of exosomes and their anti-inflammatory effect, mediated mainly by miRNA146 production by M2 macrophages.
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28
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Howard NP, van de Weg E, Luby JJ. A new method to reconstruct the direction of parent-offspring duo relationships using SNP array data and its demonstration on ancient and modern cultivars in the outcrossing species malus × domestica. HORTICULTURE RESEARCH 2022; 9:uhab069. [PMID: 35043196 PMCID: PMC8881379 DOI: 10.1093/hr/uhab069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 10/17/2021] [Accepted: 10/28/2021] [Indexed: 06/14/2023]
Abstract
Unordered parent-offspring (PO) relationships are an outstanding issue in pedigree reconstruction studies. Resolution of the order of these relationships would expand the results, conclusions, and usefulness of such studies; however, no such PO order resolution (POR) tests currently exist. This study describes two such tests, demonstrated using SNP array data in the outcrossing species apple (Malus × domestica) on a PO relationship of known order ("Keepsake" as a parent of "Honeycrisp") and two PO relationships previously ordered only via provenance information. The first test, POR-1, tests whether some of the extended haplotypes deduced from homozygous SNP calls from one individual in an unordered PO duo are composed of recombinant haplotypes from accurately phased SNP genotypes from the second individual. If so, the first individual would be the offspring of the second individual, otherwise the opposite relationship would be present. The second test, POR-2, does not require phased SNP genotypes and uses similar logic as the POR-1 test, albeit in a different approach. The POR-1 and POR-2 tests determined the correct relationship between "Keepsake" and "Honeycrisp". The POR-2 test confirmed "Reinette Franche" as a parent of "Nonpareil" and "Brabant Bellefleur" as a parent of "Court Pendu Plat". The latter finding conflicted with the recorded provenance information, demonstrating the need for these tests. The successful demonstration of these tests suggests they can add insights to future pedigree reconstruction studies, though caveats, like extreme inbreeding or selfing, would need to be considered where relevant.
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Affiliation(s)
- Nicholas P Howard
- Institut für Biologie und Umweltwissenschaften, Carl von Ossietzky University, Oldenburg, 26129 Germany
- Department of Horticultural Science, University of Minnesota, St. Paul, 55108 United States of America
| | - Eric van de Weg
- Plant Breeding, Wageningen University and Research, Wageningen, 6708 PB The Netherlands
| | - James J Luby
- Department of Horticultural Science, University of Minnesota, St. Paul, 55108 United States of America
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29
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Oztolan-Erol N, Helmstetter AJ, İnan A, Buggs RJA, Lucas SJ. Unraveling Genetic Diversity Amongst European Hazelnut ( Corylus avellana L.) Varieties in Turkey. FRONTIERS IN PLANT SCIENCE 2021; 12:661274. [PMID: 34276724 PMCID: PMC8282208 DOI: 10.3389/fpls.2021.661274] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 05/31/2021] [Indexed: 06/13/2023]
Abstract
European hazelnut (Corylus avellana) is a diploid (2n = 22), monecious and wind-pollinated species, extensively cultivated for its nuts. Turkey is the world-leading producer of hazelnut, supplying 70-80% of the world's export capacity. Hazelnut is mostly grown in the Black Sea Region, and maintained largely through clonal propagation. Understanding the genetic variation between hazelnut varieties, and defining variety-specific and disease resistance-associated alleles, would facilitate hazelnut breeding in Turkey. Widely grown varieties 'Karafındık' (2), 'Sarıfındık' (5), and 'Yomra' (2) were collected from Akçakoca in the west, while 'Tombul' (8), 'Çakıldak' (3), 'Mincane' (2), 'Allahverdi' (2), 'Sivri' (4), and 'Palaz' (5) were collected from Ordu and Giresun provinces in the east (numbers in parentheses indicate sample sizes for each variety). Powdery mildew resistant and susceptible hazelnut genotypes were collected from the field gene bank and heavily infected orchards in Giresun. Every individual was subjected to double digest restriction enzyme-associated DNA sequencing (ddRAD-seq) and a RADtag library was created. RADtags were aligned to the 'Tombul' reference genome, and Stacks software used to identify polymorphisms. 101 private and six common alleles from nine hazelnut varieties, four private from resistants and only one from susceptible were identified for diagnosis of either a certain hazelnut variety or powdery mildew resistance. Phylogenetic analysis and population structure calculations indicated that 'Mincane', 'Sarıfındık', 'Tombul', 'Çakıldak', and 'Palaz' were genetically close to each other; however, individuals within every varietal group were found in different sub-populations. Our findings indicated that years of clonal propagation of some preferred varieties across the Black Sea Region has resulted in admixed sub-populations and great genetic diversity within each variety. This impedes the development of a true breeding variety. For example, 'Tombul' is the most favored Turkish variety because of its high quality nuts, but an elite 'Tombul' line does not yet exist. This situation continues due to the lack of a breed protection program for commercially valuable hazelnut varieties. This study provides molecular markers suitable for establishing such a program.
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Affiliation(s)
- Nihal Oztolan-Erol
- Sabancı University Nanotechnology Research and Application Center, İstanbul, Turkey
| | | | - Asuman İnan
- Sabancı University Nanotechnology Research and Application Center, İstanbul, Turkey
| | - Richard J. A. Buggs
- Jodrell Laboratory, Royal Botanic Gardens, Kew, United Kingdom
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Stuart J. Lucas
- Sabancı University Nanotechnology Research and Application Center, İstanbul, Turkey
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30
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Migicovsky Z, Yeats TH, Watts S, Song J, Forney CF, Burgher-MacLellan K, Somers DJ, Gong Y, Zhang Z, Vrebalov J, van Velzen R, Giovannoni JG, Rose JKC, Myles S. Apple Ripening Is Controlled by a NAC Transcription Factor. Front Genet 2021; 12:671300. [PMID: 34239539 PMCID: PMC8258254 DOI: 10.3389/fgene.2021.671300] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/10/2021] [Indexed: 12/12/2022] Open
Abstract
Softening is a hallmark of ripening in fleshy fruits, and has both desirable and undesirable implications for texture and postharvest stability. Accordingly, the timing and extent of pre-harvest ripening and associated textural changes following harvest are key targets for improving fruit quality through breeding. Previously, we identified a large effect locus associated with harvest date and firmness in apple (Malus domestica) using genome-wide association studies (GWAS). Here, we present additional evidence that polymorphisms in or around a transcription factor gene, NAC18.1, may cause variation in these traits. First, we confirmed our previous findings with new phenotype and genotype data from ∼800 apple accessions. In this population, we compared a genetic marker within NAC18.1 to markers targeting three other firmness-related genes currently used by breeders (ACS1, ACO1, and PG1), and found that the NAC18.1 marker was the strongest predictor of both firmness at harvest and firmness after 3 months of cold storage. By sequencing NAC18.1 across 18 accessions, we revealed two predominant haplotypes containing the single nucleotide polymorphism (SNP) previously identified using GWAS, as well as dozens of additional SNPs and indels in both the coding and promoter sequences. NAC18.1 encodes a protein that is orthogolous to the NON-RIPENING (NOR) transcription factor, a regulator of ripening in tomato (Solanum lycopersicum). We introduced both NAC18.1 transgene haplotypes into the tomato nor mutant and showed that both haplotypes complement the nor ripening deficiency. Taken together, these results indicate that polymorphisms in NAC18.1 may underlie substantial variation in apple firmness through modulation of a conserved ripening program.
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Affiliation(s)
- Zoë Migicovsky
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
| | - Trevor H Yeats
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States.,Boyce Thompson Institute, Cornell University, Ithaca, NY, United States
| | - Sophie Watts
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
| | - Jun Song
- Agriculture and Agri-Food Canada, Kentville, NS, Canada
| | | | | | - Daryl J Somers
- Vineland Research and Innovation Centre, Vineland Station, ON, Canada
| | - Yihui Gong
- College of Horticulture, South China Agriculture University, Guangzhou, China
| | - Zhaoqi Zhang
- College of Horticulture, South China Agriculture University, Guangzhou, China
| | - Julia Vrebalov
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States.,Boyce Thompson Institute, Cornell University, Ithaca, NY, United States
| | - Robin van Velzen
- Biosystematics Group, Wageningen University, Wageningen, Netherlands
| | - James G Giovannoni
- Boyce Thompson Institute, Cornell University, Ithaca, NY, United States.,United States Department of Agriculture, Robert W. Holley Center, Cornell University, Ithaca, NY, United States
| | - Jocelyn K C Rose
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Sean Myles
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
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Recent Large-Scale Genotyping and Phenotyping of Plant Genetic Resources of Vegetatively Propagated Crops. PLANTS 2021; 10:plants10020415. [PMID: 33672381 PMCID: PMC7926561 DOI: 10.3390/plants10020415] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/19/2021] [Accepted: 02/19/2021] [Indexed: 12/12/2022]
Abstract
Several recent national and international projects have focused on large-scale genotyping of plant genetic resources in vegetatively propagated crops like fruit and berries, potatoes and woody ornamentals. The primary goal is usually to identify true-to-type plant material, detect possible synonyms, and investigate genetic diversity and relatedness among accessions. A secondary goal may be to create sustainable databases that can be utilized in research and breeding for several years ahead. Commonly applied DNA markers (like microsatellite DNA and SNPs) and next-generation sequencing each have their pros and cons for these purposes. Methods for large-scale phenotyping have lagged behind, which is unfortunate since many commercially important traits (yield, growth habit, storability, and disease resistance) are difficult to score. Nevertheless, the analysis of gene action and development of robust DNA markers depends on environmentally controlled screening of very large sets of plant material. Although more time-consuming, co-operative projects with broad-scale data collection are likely to produce more reliable results. In this review, we will describe some of the approaches taken in genotyping and/or phenotyping projects concerning a wide variety of vegetatively propagated crops.
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