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Gao M, Hua T, Niu G, Masabni J, Dewalt W. A locus-dependent mixed inheritance in the segmental allohexaploid sweetpotato ( Ipomoea batatas [L.] Lam). FRONTIERS IN PLANT SCIENCE 2024; 15:1398081. [PMID: 38863536 PMCID: PMC11165125 DOI: 10.3389/fpls.2024.1398081] [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: 03/08/2024] [Accepted: 05/06/2024] [Indexed: 06/13/2024]
Abstract
Two interrelated aspects of the sweetpotato genome, its polyploid origin and inheritance type, remain uncertain. We recently proposed a segmental allohexaploid sweetpotato and thus sought to clarify its inheritance type by direct analyses of homoeolog segregations at selected single-copy loci. For such analyses, we developed a digital quantitative PCR genotyping method using one nondiscriminatory and three discriminatory probes for each selected locus to discriminate and quantify three homoeolog-differentiating variation types (homoeolog-types) in genomic DNA samples for genotype fitting and constructed a F2 population for segregation analyses. We confirmed inter-subgenomic distinctions of three identified homoeolog-types at each of five selected loci by their interspecific differentiations among 14 species in Ipomoea section batatas and genotyped the loci in 549 F2 lines, selected F1 progenies, and their founding parents. Segregation and genotype analyses revealed a locus-dependent mixed inheritance (disomic, polysomic, and intermediate types) of the homoeolog-types at 4 loci in the F2 population, displaying estimated disomic-inheritance frequencies of 0, 2.72%, 14.52%, and 36.92%, and probably in the F1 population too. There were also low-frequency non-hexaploid F1 and F2 genotypes that were probably derived from double-reduction recombination or partially unreduced gametes, and F2 genotypes of apparent aneuploids/dysploids with neopolyploid-like frequencies. Additional analyses of homoeolog-type genotypes at the 5 loci in 46 lines from various regions revealed locus-dependent selection biases, favoring genotypes having more of one homoeolog-type, i.e. more of di- or homogenized homoeolog-type composition, and one-direction ploidy trending among apparent aneuploids/dysploids. These inheritance features pointed to an evolving segmental allohexaploid sweetpotato impacted by selection biases.
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Affiliation(s)
- Ming Gao
- Cooperative Agricultural Research Center, College of Agriculture, Food and Natural Resources, Prairie View A&M University, Prairie View, TX, United States
| | - Tien Hua
- Cooperative Agricultural Research Center, College of Agriculture, Food and Natural Resources, Prairie View A&M University, Prairie View, TX, United States
| | - Genhua Niu
- AgriLife Research and Extension Center at Dallas, Texas A&M University, Dallas, TX, United States
| | - Joe Masabni
- AgriLife Research and Extension Center at Dallas, Texas A&M University, Dallas, TX, United States
| | - Willie Dewalt
- Cooperative Agricultural Research Center, College of Agriculture, Food and Natural Resources, Prairie View A&M University, Prairie View, TX, United States
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2
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Nishio S, Shirasawa K, Nishimura R, Takeuchi Y, Imai A, Mase N, Takada N. A self-compatible pear mutant derived from γ-irradiated pollen carries an 11-Mb duplication in chromosome 17. FRONTIERS IN PLANT SCIENCE 2024; 15:1360185. [PMID: 38504898 PMCID: PMC10948449 DOI: 10.3389/fpls.2024.1360185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 02/13/2024] [Indexed: 03/21/2024]
Abstract
Self-compatibility is a highly desirable trait for pear breeding programs. Our breeding program previously developed a novel self-compatible pollen-part Japanese pear mutant (Pyrus pyrifolia Nakai), '415-1', by using γ-irradiated pollen. '415-1' carries the S-genotype S4dS5S5, with "d" indicating a duplication of S 5 responsible for breakdown of self-incompatibility. Until now, the size and inheritance of the duplicated segment was undetermined, and a reliable detection method was lacking. Here, we examined genome duplications and their inheritance in 140 F1 seedlings resulting from a cross between '515-20' (S1S3) and '415-1'. Amplicon sequencing of S-RNase and SFBB18 clearly detected S-haplotype duplications in the seedlings. Intriguingly, 30 partially triploid seedlings including genotypes S1S4dS5, S3S4dS5, S1S5dS5, S3S5dS5, and S3S4dS4 were detected among the 140 seedlings. Depth-of-coverage analysis using ddRAD-seq showed that the duplications in those individuals were limited to chromosome 17. Further analysis through resequencing confirmed an 11-Mb chromosome duplication spanning the middle to the end of chromosome 17. The duplicated segment remained consistent in size across generations. The presence of an S3S4dS4 seedling provided evidence for recombination between the duplicated S5 segment and the original S4haplotype, suggesting that the duplicated segment can pair with other parts of chromosome 17. This research provides valuable insights for improving pear breeding programs using partially triploid individuals.
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Affiliation(s)
- Sogo Nishio
- Deciduous Fruit Tree Breeding Group, Division of Fruit Tree Breeding Research, Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Kenta Shirasawa
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Ryotaro Nishimura
- Fruit Tree Smart Production Group, Division of Fruit Tree Production Research, Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization, Higashihiroshima, Japan
| | - Yukie Takeuchi
- Deciduous Fruit Tree Breeding Group, Division of Fruit Tree Breeding Research, Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Atsushi Imai
- Deciduous Fruit Tree Breeding Group, Division of Fruit Tree Breeding Research, Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Nobuko Mase
- Citrus Breeding and Production Group, Division of Citrus Research, Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization, Shizuoka, Japan
| | - Norio Takada
- Deciduous Fruit Tree Breeding Group, Division of Fruit Tree Breeding Research, Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization, Tsukuba, Japan
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Bilton TP, Sharma SK, Schofield MR, Black MA, Jacobs JME, Bryan GJ, Dodds KG. Construction of relatedness matrices in autopolyploid populations using low-depth high-throughput sequencing data. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:64. [PMID: 38430392 PMCID: PMC10908621 DOI: 10.1007/s00122-024-04568-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 01/30/2024] [Indexed: 03/03/2024]
Abstract
KEY MESSAGE An improved estimator of genomic relatedness using low-depth high-throughput sequencing data for autopolyploids is developed. Its outputs strongly correlate with SNP array-based estimates and are available in the package GUSrelate. High-throughput sequencing (HTS) methods have reduced sequencing costs and resources compared to array-based tools, facilitating the investigation of many non-model polyploid species. One important quantity that can be computed from HTS data is the genetic relatedness between all individuals in a population. However, HTS data are often messy, with multiple sources of errors (i.e. sequencing errors or missing parental alleles) which, if not accounted for, can lead to bias in genomic relatedness estimates. We derive a new estimator for constructing a genomic relationship matrix (GRM) from HTS data for autopolyploid species that accounts for errors associated with low sequencing depths, implemented in the R package GUSrelate. Simulations revealed that GUSrelate performed similarly to existing GRM methods at high depth but reduced bias in self-relatedness estimates when the sequencing depth was low. Using a panel consisting of 351 tetraploid potato genotypes, we found that GUSrelate produced GRMs from genotyping-by-sequencing (GBS) data that were highly correlated with a GRM computed from SNP array data, and less biased than existing methods when benchmarking against the array-based GRM estimates. GUSrelate provides researchers with a tool to reliably construct GRMs from low-depth HTS data.
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Affiliation(s)
- Timothy P Bilton
- AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand.
- Department of Mathematics and Statistics, University of Otago, Dunedin, New Zealand.
| | - Sanjeev Kumar Sharma
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, UK
| | - Matthew R Schofield
- Department of Mathematics and Statistics, University of Otago, Dunedin, New Zealand
| | - Michael A Black
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | | | - Glenn J Bryan
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, UK
| | - Ken G Dodds
- AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
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4
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Njuguna JN, Clark LV, Lipka AE, Anzoua KG, Bagmet L, Chebukin P, Dwiyanti MS, Dzyubenko E, Dzyubenko N, Ghimire BK, Jin X, Johnson DA, Kjeldsen JB, Nagano H, de Bem Oliveira I, Peng J, Petersen KK, Sabitov A, Seong ES, Yamada T, Yoo JH, Yu CY, Zhao H, Munoz P, Long SP, Sacks EJ. Impact of genotype-calling methodologies on genome-wide association and genomic prediction in polyploids. THE PLANT GENOME 2023; 16:e20401. [PMID: 37903749 DOI: 10.1002/tpg2.20401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 09/17/2023] [Accepted: 09/23/2023] [Indexed: 11/01/2023]
Abstract
Discovery and analysis of genetic variants underlying agriculturally important traits are key to molecular breeding of crops. Reduced representation approaches have provided cost-efficient genotyping using next-generation sequencing. However, accurate genotype calling from next-generation sequencing data is challenging, particularly in polyploid species due to their genome complexity. Recently developed Bayesian statistical methods implemented in available software packages, polyRAD, EBG, and updog, incorporate error rates and population parameters to accurately estimate allelic dosage across any ploidy. We used empirical and simulated data to evaluate the three Bayesian algorithms and demonstrated their impact on the power of genome-wide association study (GWAS) analysis and the accuracy of genomic prediction. We further incorporated uncertainty in allelic dosage estimation by testing continuous genotype calls and comparing their performance to discrete genotypes in GWAS and genomic prediction. We tested the genotype-calling methods using data from two autotetraploid species, Miscanthus sacchariflorus and Vaccinium corymbosum, and performed GWAS and genomic prediction. In the empirical study, the tested Bayesian genotype-calling algorithms differed in their downstream effects on GWAS and genomic prediction, with some showing advantages over others. Through subsequent simulation studies, we observed that at low read depth, polyRAD was advantageous in its effect on GWAS power and limit of false positives. Additionally, we found that continuous genotypes increased the accuracy of genomic prediction, by reducing genotyping error, particularly at low sequencing depth. Our results indicate that by using the Bayesian algorithm implemented in polyRAD and continuous genotypes, we can accurately and cost-efficiently implement GWAS and genomic prediction in polyploid crops.
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Affiliation(s)
- Joyce N Njuguna
- Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Lindsay V Clark
- Research Scientific Computing, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Alexander E Lipka
- Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Kossonou G Anzoua
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Japan
| | - Larisa Bagmet
- Vavilov All-Russian Institute of Plant Genetic Resources, St. Petersburg, Russian Federation
| | - Pavel Chebukin
- FSBSI "FSC of Agricultural Biotechnology of the Far East named after A.K. Chaiki", Ussuriysk, Russian Federation
| | - Maria S Dwiyanti
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Japan
| | - Elena Dzyubenko
- Vavilov All-Russian Institute of Plant Genetic Resources, St. Petersburg, Russian Federation
| | - Nicolay Dzyubenko
- Vavilov All-Russian Institute of Plant Genetic Resources, St. Petersburg, Russian Federation
| | - Bimal Kumar Ghimire
- Department of Crop Science, College of Sanghuh Life Science, Konkuk University, Seoul, South Korea
| | - Xiaoli Jin
- Agronomy Department, Key Laboratory of Crop Germplasm Research of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Douglas A Johnson
- USDA-ARS Forage and Range Research Lab, Utah State University, Logan, Utah, USA
| | | | - Hironori Nagano
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Japan
| | | | - Junhua Peng
- Spring Valley Agriscience Co. Ltd., Jinan, China
| | | | - Andrey Sabitov
- Vavilov All-Russian Institute of Plant Genetic Resources, St. Petersburg, Russian Federation
| | - Eun Soo Seong
- Division of Bioresource Sciences, Kangwon National University, Chuncheon, South Korea
| | - Toshihiko Yamada
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Japan
| | - Ji Hye Yoo
- Bioherb Research Institute, Kangwon National University, Chuncheon, South Korea
| | - Chang Yeon Yu
- Bioherb Research Institute, Kangwon National University, Chuncheon, South Korea
| | - Hua Zhao
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Patricio Munoz
- Horticultural Science Department, University of Florida, Gainesville, Florida, USA
| | - Stephen P Long
- Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Erik J Sacks
- Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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5
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Gerard D. Bayesian tests for random mating in polyploids. Mol Ecol Resour 2023; 23:1812-1822. [PMID: 37578636 DOI: 10.1111/1755-0998.13856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 07/24/2023] [Accepted: 08/03/2023] [Indexed: 08/15/2023]
Abstract
Hardy-Weinberg proportions (HWP) are often explored to evaluate the assumption of random mating. However, in autopolyploids, organisms with more than two sets of homologous chromosomes, HWP and random mating are different hypotheses that require different statistical testing approaches. Currently, the only available methods to test for random mating in autopolyploids (i) heavily rely on asymptotic approximations and (ii) assume genotypes are known, ignoring genotype uncertainty. Furthermore, these approaches are all frequentist, and so do not carry the benefits of Bayesian analysis, including ease of interpretability, incorporation of prior information, and consistency under the null. Here, we present Bayesian approaches to test for random mating, bringing the benefits of Bayesian analysis to this problem. Our Bayesian methods also (i) do not rely on asymptotic approximations, being appropriate for small sample sizes, and (ii) optionally account for genotype uncertainty via genotype likelihoods. We validate our methods in simulations and demonstrate on two real datasets how testing for random mating is more useful for detecting genotyping errors than testing for HWP (in a natural population) and testing for Mendelian segregation (in an experimental S1 population). Our methods are implemented in Version 2.0.2 of the hwep R package on the Comprehensive R Archive Network https://cran.r-project.org/package=hwep.
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Affiliation(s)
- David Gerard
- Department of Mathematics and Statistics, American University, Washington DC, USA
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6
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Gerard D. Double reduction estimation and equilibrium tests in natural autopolyploid populations. Biometrics 2023; 79:2143-2156. [PMID: 35848417 DOI: 10.1111/biom.13722] [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: 10/18/2021] [Accepted: 07/11/2022] [Indexed: 11/27/2022]
Abstract
Many bioinformatics pipelines include tests for equilibrium. Tests for diploids are well studied and widely available, but extending these approaches to autopolyploids is hampered by the presence of double reduction, the comigration of sister chromatid segments into the same gamete during meiosis. Though a hindrance for equilibrium tests, double reduction rates are quantities of interest in their own right, as they provide insights about the meiotic behavior of autopolyploid organisms. Here, we develop procedures to (i) test for equilibrium while accounting for double reduction, and (ii) estimate the double reduction rate given equilibrium. To do so, we take two approaches: a likelihood approach, and a novel U-statistic minimization approach that we show generalizes the classical equilibrium χ2 test in diploids. For small sample sizes and uncertain genotypes, we further develop a bootstrap procedure based on our U-statistic to test for equilibrium. We validate our methods on both simulated and real data.
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Affiliation(s)
- David Gerard
- Department of Mathematics and Statistics, American University, Washington, District of Columbia, USA
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7
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Haque E, Shirasawa K, Suematsu K, Tabuchi H, Isobe S, Tanaka M. Polyploid GWAS reveals the basis of molecular marker development for complex breeding traits including starch content in the storage roots of sweet potato. FRONTIERS IN PLANT SCIENCE 2023; 14:1181909. [PMID: 37342138 PMCID: PMC10277646 DOI: 10.3389/fpls.2023.1181909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/08/2023] [Indexed: 06/22/2023]
Abstract
Given the importance of prioritizing genome-based breeding of sweet potato to enable the promotion of food and nutritional security for future human societies, here, we aimed to dissect the genetic basis of storage root starch content (SC) when associated with a complex set of breeding traits including dry matter (DM) rate, storage root fresh weight (SRFW), and anthocyanin (AN) content in a mapping population containing purple-fleshed sweet potato. A polyploid genome-wide association study (GWAS) was extensively exploited using 90,222 single-nucleotide polymorphisms (SNPs) obtained from a bi-parental 204 F1 population between 'Konaishin' (having high SC but no AN) and 'Akemurasaki' (having high AN content but moderate SC). Through the comparison of polyploid GWAS on the whole set of the 204 F1, 93 high-AN-containing F1, and 111 low-AN-containing F1 populations, a total of two (consists of six SNPs), two (14 SNPs), four (eight SNPs), and nine (214 SNPs) significantly associated signals were identified for the variations of SC, DM, SRFW, and the relative AN content, respectively. Of them, a novel signal associated with SC, which was most consistent in 2019 and 2020 in both the 204 F1 and 111 low-AN-containing F1 populations, was identified in homologous group 15. The five SNP markers associated with homologous group 15 could affect SC improvement with a degree of positive effect (~4.33) and screen high-starch-containing lines with higher efficiency (~68%). In a database search of 62 genes involved in starch metabolism, five genes including enzyme genes granule-bound starch synthase I (IbGBSSI), α-amylase 1D, α-amylase 1E, and α-amylase 3, and one transporter gene ATP/ADP-transporter were located on homologous group 15. In an extensive qRT-PCR of these genes using the storage roots harvested at 2, 3, and 4 months after field transplantation in 2022, IbGBSSI, which encodes the starch synthase isozyme that catalyzes the biosynthesis of amylose molecule, was most consistently elevated during starch accumulation in sweet potato. These results would enhance our understanding of the underlying genetic basis of a complex set of breeding traits in the starchy roots of sweet potato, and the molecular information, particularly for SC, would be a potential platform for molecular marker development for this trait.
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Affiliation(s)
- Emdadul Haque
- Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Miyakonojo, Japan
| | - Kenta Shirasawa
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Keisuke Suematsu
- Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Miyakonojo, Japan
| | - Hiroaki Tabuchi
- Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Miyakonojo, Japan
| | - Sachiko Isobe
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Masaru Tanaka
- Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Miyakonojo, Japan
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8
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Sumitomo K, Shirasawa K, Isobe S, Hirakawa H, Harata A, Nakano M, Nakano Y, Yagi M, Hisamatsu T, Yamaguchi H, Taniguchi F. A genome-wide association and fine-mapping study of white rust resistance in hexaploid chrysanthemum cultivars with a wild diploid reference genome. HORTICULTURE RESEARCH 2022; 9:uhac170. [PMID: 36324641 PMCID: PMC9613985 DOI: 10.1093/hr/uhac170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 07/25/2022] [Indexed: 06/16/2023]
Abstract
White rust caused by Puccinia horiana is one of the most serious diseases of chrysanthemum (Chrysanthemum × morifolium). In this study, we report the DNA markers associated with resistance against P. horiana via a simple approach using the genome of a wild diploid relative, Chrysanthemum seticuspe. First, we identified the important region of the genome in the resistant cultivar "Ariesu" via a genome-wide association study. Simplex single nucleotide polymorphism (SNP) markers mined from ddRAD-Seq were used in a biparental population originating from crosses between resistant "Ariesu" and susceptible "Yellow Queen". The C. seticuspe genome was used as a reference. For the fine mapping of P. horiana resistance locus 2 (Phr2), a comparative whole genome sequencing study was conducted. Although the genome sequences of chrysanthemum cultivars assembled via the short-read approach were fragmented, reliable genome alignments were reconstructed by mapping onto the chromosome level of the C. seticuspe pseudomolecule. Base variants were then identified by comparing the assembled genome sequences of resistant "Ariesu" and susceptible "Yellow Queen". Consequently, SNP markers that were closer to Phr2 compared with ddRAD-Seq markers were obtained. These SNP markers co-segregated with resistance in F1 progenies originating from resistant "Ariesu" and showed robust transferability for detecting Phr2-conferring resistance among chrysanthemum genetic resources. The wild C. seticuspe pseudomolecule, a de facto monoploid genome used for ddRAD-Seq analysis and assembled genome sequence comparison, demonstrated this method's utility as a model for developing DNA markers in hexaploid chrysanthemum cultivars.
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Affiliation(s)
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818 Japan
| | - Sachiko Isobe
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818 Japan
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818 Japan
| | - Akiho Harata
- Kagoshima Prefectural Institute for Agricultural Development, Minamisatsuma, Kagoshima 899-3401, Japan
- CCS Inc., Kyoto, Kyoto 602-8019, Japan
| | - Michiharu Nakano
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
- Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi 783-8502, Japan
| | - Yoshihiro Nakano
- Institute of Vegetable and Floriculture Science, NARO, Tsukuba, Ibaraki 305-0852, Japan
| | - Masafumi Yagi
- Institute of Vegetable and Floriculture Science, NARO, Tsukuba, Ibaraki 305-0852, Japan
| | - Tamotsu Hisamatsu
- Institute of Vegetable and Floriculture Science, NARO, Tsukuba, Ibaraki 305-0852, Japan
| | - Hiroyasu Yamaguchi
- Institute of Vegetable and Floriculture Science, NARO, Tsukuba, Ibaraki 305-0852, Japan
| | - Fumiya Taniguchi
- Institute of Fruit Tree and Tea Science, NARO, Tsukuba, Ibaraki 305-8605, Japan
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9
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Gubaev R, Boldyrev S, Martynova E, Chernova A, Kovalenko T, Peretyagina T, Goryunova S, Goryunov D, Mukhina Z, Ben C, Gentzbittel L, Khaitovich P, Demurin Y. Genetic mapping of loci involved in oil tocopherol composition control in Russian sunflower ( Helianthus annuus L.) lines. G3 GENES|GENOMES|GENETICS 2022; 12:6527637. [PMID: 35150257 PMCID: PMC8982403 DOI: 10.1093/g3journal/jkac036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 01/25/2022] [Indexed: 11/14/2022]
Abstract
Abstract
Tocopherols are antioxidants that preserve oil lipids against oxidation and serve as a natural source of vitamin E in the human diet. Compared with other major oilseeds like rapeseed and soybean, sunflower (Helianthus annuus L.) exhibits low phenotypic diversity of tocopherol composition, both in wild and cultivated accessions from germplasm collections. Two major mutations that alter tocopherol composition were identified in genetic collections, and several studies suggested additional loci controlling tocopherol composition, with their expression possibly depending on the genetic background. In the present study, we performed QTL mapping of tocopherol composition in two independent F2 crosses between lines with contrasting tocopherol composition from the Pustovoit All-Russia Research Institute of Oil Crops (VNIIMK) collection. We used genotyping-bysequencing (GBS) to construct single nucleotide polymorphism-based genetic maps, and performed QTL mapping using quantitative and qualitative encoding for phenotypic traits. Our results support the notion that the tocopherol composition in the assessed crosses is controlled by two loci. We additionally selected and validated two single nucleotide polymorphism markers for each cross which could be used for marker-assisted selection.
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Affiliation(s)
- Rim Gubaev
- Skolkovo Institute of Science and Technology, Moscow 121205, Russia
- LLC “Oil Gene”, Moscow 121205, Russia
| | - Stepan Boldyrev
- Skolkovo Institute of Science and Technology, Moscow 121205, Russia
- LLC “Oil Gene”, Moscow 121205, Russia
| | - Elena Martynova
- Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Alina Chernova
- Skolkovo Institute of Science and Technology, Moscow 121205, Russia
- LLC “Oil Gene”, Moscow 121205, Russia
| | - Tatyana Kovalenko
- Pustovoit All-Russia Research Institute of Oil Crops, Krasnodar 350038, Russia
| | - Tatyana Peretyagina
- Pustovoit All-Russia Research Institute of Oil Crops, Krasnodar 350038, Russia
| | - Svetlana Goryunova
- Skolkovo Institute of Science and Technology, Moscow 121205, Russia
- Russian Potato Research Center, Kraskovo 140051, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119333, Russia
| | - Denis Goryunov
- Skolkovo Institute of Science and Technology, Moscow 121205, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Zhanna Mukhina
- All-Russia Rice Research Institute, Krasnodar 350921, Russia
| | - Cecile Ben
- Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | | | | | - Yakov Demurin
- Pustovoit All-Russia Research Institute of Oil Crops, Krasnodar 350038, Russia
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10
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Obata N, Tabuchi H, Kurihara M, Yamamoto E, Shirasawa K, Monden Y. Mapping of Nematode Resistance in Hexaploid Sweetpotato Using an Next-Generation Sequencing-Based Association Study. FRONTIERS IN PLANT SCIENCE 2022; 13:858747. [PMID: 35371138 PMCID: PMC8972059 DOI: 10.3389/fpls.2022.858747] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 02/11/2022] [Indexed: 06/14/2023]
Abstract
The southern root-knot nematode (SRKN; Meloidogyne incognita) is a typical parasitic nematode that affects sweetpotato [Ipomoea batatas (L.) Lam.], causing a significant decrease in crop yield and commercial value. In Japan, the SRKN is classified into 10 races: SP1-SP5, SP6-1, SP6-2, and SP7-SP9, with the dominant race differing according to the cultivation area. Soil insecticides have previously been used to reduce the soil density of SRKNs; however, this practice is both costly and labor intensive. Therefore, the development of SRKN-resistant sweetpotato lines and cultivars is necessary. However, due to the complexity of polyploid inheritance and the highly heterogeneous genomic composition of sweetpotato, genetic information and research for this species are significantly lacking compared to those for other major diploid crop species. In this study, we utilized the recently developed genome-wide association approach, which uses multiple-dose markers to assess autopolyploid species. We performed an association analysis to investigate resistance toward SRKN-SP2, which is the major race in areas with high sweetpotato production in Japan. The segregation ratio of resistant and susceptible lines in the F1 mapping population derived from the resistant "J-Red" and susceptible "Choshu" cultivars was fitted to 1: 3, suggesting that resistance to SP2 may be regulated by two loci present in the simplex. By aligning the double digest restriction-site associated DNA sequencing reads to the published Ipomoea trifida reference sequence, 46,982 single nucleotide polymorphisms (SNPs) were identified (sequencing depth > 200). The association study yielded its highest peak on chromosome 7 (Chr07) and second highest peak on chromosome 3 (Chr03), presenting as a single-dose in both loci. Selective DNA markers were developed to screen for resistant plants using the SNPs identified on Chr03 and Chr07. Our results showed that SRKN-SP2-resistant plants were selected with a probability of approximately 70% when combining the two selective DNA markers. This study serves as a model for the identification of genomic regions that control agricultural traits and the elucidation of their effects, and is expected to greatly advance marker-assisted breeding and association studies in polyploid crop species.
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Affiliation(s)
- Nozomi Obata
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Hiroaki Tabuchi
- Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Miyakonojo, Japan
| | - Miyu Kurihara
- Faculty of Agriculture, Okayama University, Okayama, Japan
| | - Eiji Yamamoto
- Graduate School of Agriculture, Meiji University, Kawasaki, Japan
| | - Kenta Shirasawa
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Yuki Monden
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
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11
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Yan H, Ma M, Ahmad MQ, Arisha MH, Tang W, Li C, Zhang Y, Kou M, Wang X, Gao R, Song W, Li Z, Li Q. High-Density Single Nucleotide Polymorphisms Genetic Map Construction and Quantitative Trait Locus Mapping of Color-Related Traits of Purple Sweet Potato [ Ipomoea batatas (L.) Lam.]. FRONTIERS IN PLANT SCIENCE 2022; 12:797041. [PMID: 35069654 PMCID: PMC8770336 DOI: 10.3389/fpls.2021.797041] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 11/15/2021] [Indexed: 06/14/2023]
Abstract
Flesh color (FC), skin color (SC), and anthocyanin content (AC) are three important traits being used for commodity evaluation in purple-fleshed sweet potato. However, to date, only a few reports are available on the inheritance of these traits. In this study, we used a biparental mapping population of 274 F1 progeny generated from a cross between a dark purple-fleshed (Xuzishu8) and white-fleshed (Meiguohong) sweet potato variety for genetic analyses. Correlation analysis showed a significant positive correlation among AC, SC, and FC. Medium-to-high heritability was observed for these traits. We detected single nucleotide polymorphisms (SNPs) by specific length amplified fragment sequencing (SLAF-seq) with the average sequencing depth of 51.72 and 25.76 for parents and progeny, respectively. Then we constructed an integrated genetic map consisting of 15 linkage groups (LGS) of sweet potato spanning on 2,233.66 cm with an average map distance of 0.71 cm between adjacent markers. Based on the linkage map, ten major quantitative trait loci (QTLs) associated to FC, SC, and AC were identified on LG12 between 0 and 64.97 cm distance, such as one QTL for SC and FC, respectively, which explained 36.3 and 45.9% of phenotypic variation; eight QTLs for AC, which explained 10.5-28.5% of the variation. These major QTLs were highly consistent and co-localized on LG12. Positive correlation, high heritability, and co-localization of QTLs on the same LG group confirm the significance of this study to establish a marker-assisted breeding program for sweet potato improvement.
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Affiliation(s)
- Hui Yan
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture, Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Xuzhou, China
| | - Meng Ma
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Muhammad Qadir Ahmad
- Department of Plant Breeding and Genetics, Bahauddin Zakariya University, Multan, Pakistan
| | - Mohamed Hamed Arisha
- Department of Horticulture, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Wei Tang
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture, Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Xuzhou, China
| | - Chen Li
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Yungang Zhang
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture, Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Xuzhou, China
| | - Meng Kou
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture, Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Xuzhou, China
| | - Xin Wang
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture, Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Xuzhou, China
| | - Runfei Gao
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture, Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Xuzhou, China
| | - Weihan Song
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture, Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Xuzhou, China
| | - Zongyun Li
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Qiang Li
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture, Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Xuzhou, China
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12
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Soares NR, Mollinari M, Oliveira GK, Pereira GS, Vieira MLC. Meiosis in Polyploids and Implications for Genetic Mapping: A Review. Genes (Basel) 2021; 12:genes12101517. [PMID: 34680912 PMCID: PMC8535482 DOI: 10.3390/genes12101517] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/24/2021] [Accepted: 09/24/2021] [Indexed: 02/06/2023] Open
Abstract
Plant cytogenetic studies have provided essential knowledge on chromosome behavior during meiosis, contributing to our understanding of this complex process. In this review, we describe in detail the meiotic process in auto- and allopolyploids from the onset of prophase I through pairing, recombination, and bivalent formation, highlighting recent findings on the genetic control and mode of action of specific proteins that lead to diploid-like meiosis behavior in polyploid species. During the meiosis of newly formed polyploids, related chromosomes (homologous in autopolyploids; homologous and homoeologous in allopolyploids) can combine in complex structures called multivalents. These structures occur when multiple chromosomes simultaneously pair, synapse, and recombine. We discuss the effectiveness of crossover frequency in preventing multivalent formation and favoring regular meiosis. Homoeologous recombination in particular can generate new gene (locus) combinations and phenotypes, but it may destabilize the karyotype and lead to aberrant meiotic behavior, reducing fertility. In crop species, understanding the factors that control pairing and recombination has the potential to provide plant breeders with resources to make fuller use of available chromosome variations in number and structure. We focused on wheat and oilseed rape, since there is an abundance of elucidating studies on this subject, including the molecular characterization of the Ph1 (wheat) and PrBn (oilseed rape) loci, which are known to play a crucial role in regulating meiosis. Finally, we exploited the consequences of chromosome pairing and recombination for genetic map construction in polyploids, highlighting two case studies of complex genomes: (i) modern sugarcane, which has a man-made genome harboring two subgenomes with some recombinant chromosomes; and (ii) hexaploid sweet potato, a naturally occurring polyploid. The recent inclusion of allelic dosage information has improved linkage estimation in polyploids, allowing multilocus genetic maps to be constructed.
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Affiliation(s)
- Nina Reis Soares
- Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba 13400-918, Brazil; (N.R.S.); (G.K.O.); (G.S.P.)
| | - Marcelo Mollinari
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695-7566, USA;
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695-7555, USA
| | - Gleicy K. Oliveira
- Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba 13400-918, Brazil; (N.R.S.); (G.K.O.); (G.S.P.)
| | - Guilherme S. Pereira
- Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba 13400-918, Brazil; (N.R.S.); (G.K.O.); (G.S.P.)
- Department of Agronomy, Federal University of Viçosa, Viçosa 36570-900, Brazil
| | - Maria Lucia Carneiro Vieira
- Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba 13400-918, Brazil; (N.R.S.); (G.K.O.); (G.S.P.)
- Correspondence:
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13
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Masuda K, Yamamoto E, Shirasawa K, Onoue N, Kono A, Ushijima K, Kubo Y, Tao R, Henry IM, Akagi T. Genome-wide study on the polysomic genetic factors conferring plasticity of flower sexuality in hexaploid persimmon. DNA Res 2021; 27:5858979. [PMID: 32761076 PMCID: PMC7406971 DOI: 10.1093/dnares/dsaa012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/10/2020] [Indexed: 11/17/2022] Open
Abstract
Sexuality is one of the fundamental mechanisms that work towards maintaining genetic diversity within a species. In diploid persimmons (Diospyros spp.), separated sexuality, the presence of separate male and female individuals (dioecy), is controlled by the Y chromosome-encoded small-RNA gene, OGI. On the other hand, sexuality in hexaploid Oriental persimmon (Diospyros kaki) is more plastic, with OGI-bearing genetically male individuals, able to produce both male and female flowers (monoecy). This is thought to be linked to the partial inactivation of OGI by a retrotransposon insertion, resulting in DNA methylation of the OGI promoter region. To identify the genetic factors regulating branch sexual conversion, genome-wide correlation/association analyses were conducted using ddRAD-Seq data from an F1 segregating population, and using both quantitative and diploidized genotypes, respectively. We found that allelic ratio at the Y-chromosomal region, including OGI, was correlated with male conversion based on quantitative genotypes, suggesting that OGI can be activated in cis in a dosage-dependent manner. Genome-wide association analysis based on diploidized genotypes, normalized for the effect of OGI allele dosage, detected three fundamental loci associated with male conversion. These loci underlie candidate genes, which could potentially act epigenetically for the activation of OGI expression.
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Affiliation(s)
- Kanae Masuda
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | - Eiji Yamamoto
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Noriyuki Onoue
- Institute of Fruit Tree and Tea Science, NARO, Hiroshima 739-2494, Japan
| | - Atsushi Kono
- Institute of Fruit Tree and Tea Science, NARO, Hiroshima 739-2494, Japan
| | - Koichiro Ushijima
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | - Yasutaka Kubo
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | - Ryutaro Tao
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Isabelle M Henry
- Department of Plant Biology and Genome Center, University of California, Davis, CA 95616, USA
| | - Takashi Akagi
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
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14
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Sumitomo K, Shirasawa K, Isobe SN, Hirakawa H, Harata A, Kawabe M, Yagi M, Osaka M, Kunihisa M, Taniguchi F. DNA marker for resistance to Puccinia horiana in chrysanthemum ( Chrysanthemum morifolium Ramat.) "Southern Pegasus". BREEDING SCIENCE 2021; 71:261-267. [PMID: 34377074 PMCID: PMC8329880 DOI: 10.1270/jsbbs.20063] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 01/04/2021] [Indexed: 06/13/2023]
Abstract
White rust caused by Puccinia horiana Henn. adversely affects chrysanthemum (Chrysanthemum morifolium Ramat.) production. The breeding of resistant varieties is effective in controlling the disease. Here we aimed to develop DNA markers for the strong resistance to P. horiana. We conducted a linkage analysis based on the genome-wide association study (GWAS) method. We employed a biparental population for the GWAS, wherein the single nucleotide polymorphism (SNP) allele frequency could be predicted. The population was derived from crosses between a strong resistant "Southern Pegasus" and a susceptible line. The GWAS used simplex and double-simplex SNP markers selected out of SNP candidates mined from ddRAD-Seq data of an F1 biparental population. These F1 individuals segregated in a 1:1 ratio of resistant to susceptible. Twenty-one simplex SNPs were significantly associated with P. horiana resistance in "Southern Pegasus" and generated one linkage group. These results show the presence of a single resistance gene in "Southern Pegasus". We identified the nearest SNP marker located 2.2 cM from P. horiana resistance locus and demonstrated this SNP marker-resistance link using an independent population. This is the first report of an effective DNA marker linked to a gene for P. horiana resistance in chrysanthemum.
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Affiliation(s)
- Katsuhiko Sumitomo
- Institute of Vegetable and Floriculture Science, NARO, Tsukuba, Ibaraki 305-0852, Japan
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | | | - Hideki Hirakawa
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Akiho Harata
- Kagoshima Prefectural Institute for Agricultural Development, Minamisatsuma, Kagoshima 899-3401, Japan
| | - Masato Kawabe
- Institute of Vegetable and Floriculture Science, NARO, Tsukuba, Ibaraki 305-0852, Japan
| | - Masafumi Yagi
- Institute of Vegetable and Floriculture Science, NARO, Tsukuba, Ibaraki 305-0852, Japan
| | - Masaaki Osaka
- Miyagi Prefectural Institute of Agriculture and Horticulture, Natori, Miyagi 981-1243, Japan
| | - Miyuki Kunihisa
- Institute of Fruit Tree and Tea Science, NARO, Tsukuba, Ibaraki 305-8605, Japan
| | - Fumiya Taniguchi
- Institute of Fruit Tree and Tea Science, NARO, Tsukuba, Ibaraki 305-8605, Japan
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15
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Kobayashi H, Shirasawa K, Fukino N, Hirakawa H, Akanuma T, Kitashiba H. Identification of genome-wide single-nucleotide polymorphisms among geographically diverse radish accessions. DNA Res 2021; 27:5739440. [PMID: 32065621 PMCID: PMC7315352 DOI: 10.1093/dnares/dsaa001] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 02/11/2020] [Indexed: 11/24/2022] Open
Abstract
Radish (Raphanus sativus L.) is cultivated around the world as a vegetable crop and exhibits diverse morphological and physiological features. DNA polymorphisms are responsible for differences in traits among cultivars. In this study, we determined genome-wide single-nucleotide polymorphisms (SNPs) among geographically diverse radish accessions using the double-digest restriction site-associated DNA sequencing (ddRAD-Seq) method. A total of 52,559 SNPs was identified in a collection of over 500 radish accessions (cultivated and wild) from East Asia, South and Southeast Asia, and the Occident and Near East. In addition, 2,624 SNP sites without missing data (referred to as common SNP sites) were identified among 510 accessions. Genetic diversity analyses, based on the common SNP sites, divided the cultivated radish accessions into four main groups, each derived from four geographical areas (Japan, East Asia, South and Southeast Asia, and the Occident and Near East). Furthermore, we discuss the origin of cultivated radish and its migration from the West to East Asia. SNP data generated in this work will facilitate further genetic studies on the radish breeding and production of DNA markers.
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Affiliation(s)
- Hiroto Kobayashi
- Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai 980-8572, Japan
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Nobuko Fukino
- Institute of Vegetable and Floriculture Science, NARO, Ano, Tsu 514-2392, Japan
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Takashi Akanuma
- Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai 980-8572, Japan
| | - Hiroyasu Kitashiba
- Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai 980-8572, Japan
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Genetic Mapping in Autohexaploid Sweet Potato with Low-Coverage NGS-Based Genotyping Data. G3-GENES GENOMES GENETICS 2020; 10:2661-2670. [PMID: 32482727 PMCID: PMC7407471 DOI: 10.1534/g3.120.401433] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Next-generation sequencing (NGS)-based genotyping methods can generate numerous genetic markers in a single experiment and have contributed to plant genetic mapping. However, for high precision genetic analysis, the complicated genetic segregation mode in polyploid organisms requires high-coverage NGS data and elaborate analytical algorithms. In the present study, we propose a simple strategy for the genetic mapping of polyploids using low-coverage NGS data. The validity of the strategy was investigated using simulated data. Previous studies indicated that accurate allele dosage estimation from low-coverage NGS data (read depth < 40) is difficult. Therefore, we used allele dosage probabilities calculated from read counts in association analyses to detect loci associated with phenotypic variations. The allele dosage probabilities showed significant detection power, although higher allele dosage estimation accuracy resulted in higher detection power. On the contrary, differences in the segregation patterns between the marker and causal genes resulted in a drastic decrease in detection power even if the marker and casual genes were in complete linkage and the allele dosage estimation was accurate. These results indicated that the use of a larger number of markers is advantageous, even if the accuracy of allele dosage estimation is low. Finally, we applied the strategy for the genetic mapping of autohexaploid sweet potato (Ipomoea batatas) populations to detect loci associated with agronomic traits. Our strategy could constitute a cost-effective approach for preliminary experiments done performed to large-scale studies.
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17
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ddRAD-seq derived genome-wide SNPs, high density linkage map and QTLs for fruit quality traits in strawberry ( Fragaria x ananassa). 3 Biotech 2020; 10:353. [PMID: 32760641 PMCID: PMC7385052 DOI: 10.1007/s13205-020-02291-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 06/07/2020] [Indexed: 12/31/2022] Open
Abstract
Understanding the genetic determinants are essential for improving the fruit quality traits of strawberry. In this study, we focused on mapping the loci for fruit-length (FL), -diameter (FD), -weight (FW) and -soluble solid content (SSC) using the genome-wide single nucleotide polymorphisms (SNPs) identified via ddRAD-sequencing of the F1 population raised from Maehyang (♀) X Festival (♂). A total of 12,698 high quality SNPs were identified of which 1554 SNPs that showed significant Mendelian segregation (p < 0.05) were mapped to 53 linkage groups (LG) spanning a total of 2937.93 cM with an average marker density of 2.14 cM/locus. Six QTLs for FL and four QTLs for each of FD, FW and SSC were identified that explained 24–35%, 21–42%, 24–54% and 23–50% of overall phenotypic variations, respectively. The genes that lie within these QTL regions were extracted and discussed thoroughly. In addition, a high resolution melting marker (MF154) were designed based on the SNP A1723G of the UDP-glucose 4-epimerase GEPI48-like gene FAN_iscf00021287. The marker detected the high vs low sugar containing F1 plants and commercial cultivars with 81.39% and 86.95% detection accuracy, respectively. These SNPs, linkage map, QTLs and candidate genes will be helpful in understanding and improving the fruit quality traits of strawberry.
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18
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Haque E, Tabuchi H, Monden Y, Suematsu K, Shirasawa K, Isobe S, Tanaka M. QTL analysis and GWAS of agronomic traits in sweetpotato ( Ipomoea batatas L.) using genome wide SNPs. BREEDING SCIENCE 2020; 70:283-291. [PMID: 32714050 PMCID: PMC7372034 DOI: 10.1270/jsbbs.19099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 12/08/2019] [Indexed: 05/16/2023]
Abstract
While sweetpotato (Ipomoea batatas L.) improvement has generally been done by field-based selection, molecular genetic studies on traits of interest, i.e., molecular markers are needed for enhancing the breeding program of this world's 7th most important crop, as such markers facilitate marker-assisted selection. Here, we performed a combined approach of QTLs analyses and GWAS of storage root β-carotene content (BC), dry-matter (DM) and starch content (SC) using the genetic linkage maps constructed with 5,952 and 5,640 SNPs obtained from F1 progenies between cultivars 'J-Red' and 'Choshu'. BC was negatively correlated with DM (r = -0.45) and SC (r = -0.51), while DM was positively correlated with SC (r = 0.94). In both parental maps, a total of five, two and five QTL regions on linkage groups 7 and 8 were associated with BC, DM and SC, respectively. In GWAS of BC, one strong signal (P = 1.04 × 10-9) was observed on linkage group 8, which co-located with one of the above QTL regions. The SNPs markers found here, particularly for β-carotene, would be useful base resources for future marker-assisted selection program with this trait.
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Affiliation(s)
- Emdadul Haque
- Kyushu Okinawa Agricultural Research Center, NARO, 6651-2 Yokoichi-cho, Miyakonojo, Miyazaki 885-0091, Japan
| | - Hiroaki Tabuchi
- Kyushu Okinawa Agricultural Research Center, NARO, 6651-2 Yokoichi-cho, Miyakonojo, Miyazaki 885-0091, Japan
| | - Yuki Monden
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushimanaka, Kita-ku, Okayama, Okayama 700-8530, Japan
| | - Keisuke Suematsu
- Kyushu Okinawa Agricultural Research Center, NARO, 6651-2 Yokoichi-cho, Miyakonojo, Miyazaki 885-0091, Japan
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Sachiko Isobe
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Masaru Tanaka
- Kyushu Okinawa Agricultural Research Center, NARO, 6651-2 Yokoichi-cho, Miyakonojo, Miyazaki 885-0091, Japan
- Corresponding author (e-mail: )
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19
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Ma Z, Gao W, Liu L, Liu M, Zhao N, Han M, Wang Z, Jiao W, Gao Z, Hu Y, Liu Q. Identification of QTL for resistance to root rot in sweetpotato (Ipomoea batatas (L.) Lam) with SSR linkage maps. BMC Genomics 2020; 21:366. [PMID: 32414325 PMCID: PMC7229581 DOI: 10.1186/s12864-020-06775-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 05/08/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sweetpotato root rot is a devastating disease caused by Fusarium solani that seriously endangers the yield of sweetpotato in China. Although there is currently no effective method to control the disease, breeding of resistant varieties is the most effective and economic option. Moreover, quantitative trait locus (QTL) associated with resistance to root rot have not yet been reported, and the biological mechanisms of resistance remain unclear in sweetpotato. Thus, increasing our knowledge about the mechanism of disease resistance and identifying resistance loci will assist in the development of disease resistance breeding. RESULTS In this study, we constructed genetic linkage maps of sweetpotato using a mapping population consisting of 300 individuals derived from a cross between Jizishu 1 and Longshu 9 by simple sequence repeat (SSR) markers, and mapped seven QTLs for resistance to root rot. In total, 484 and 573 polymorphic SSR markers were grouped into 90 linkage groups for Jizishu 1 and Longshu 9, respectively. The total map distance for Jizishu 1 was 3974.24 cM, with an average marker distance of 8.23 cM. The total map distance for Longshu 9 was 5163.35 cM, with an average marker distance of 9.01 cM. Five QTLs (qRRM_1, qRRM_2, qRRM_3, qRRM_4, and qRRM_5) were located in five linkage groups of Jizishu 1 map explaining 52.6-57.0% of the variation. Two QTLs (qRRF_1 and qRRF_2) were mapped on two linkage groups of Longshu 9 explaining 57.6 and 53.6% of the variation, respectively. Furthermore, 71.4% of the QTLs positively affected the variation. Three of the seven QTLs, qRRM_3, qRRF_1, and qRRF_2, were colocalized with markers IES43-5mt, IES68-6 fs**, and IES108-1 fs, respectively. CONCLUSIONS To our knowledge, this is the first report on the construction of a genetic linkage map for purple sweetpotato (Jizishu 1) and the identification of QTLs associated with resistance to root rot in sweetpotato using SSR markers. These QTLs will have practical significance for the fine mapping of root rot resistance genes and play an important role in sweetpotato marker-assisted breeding.
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Affiliation(s)
- Zhimin Ma
- Key Laboratory of Sweetpotato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.,Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences/The Key Laboratory of Crop Genetics and Breeding of Hebei, Shijiazhuang, 050035, Hebei, China
| | - Wenchuan Gao
- Baoji Institute of Agriculture Science, Qishan, 722499, Shaanxi, China
| | - Lanfu Liu
- Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences/The Key Laboratory of Crop Genetics and Breeding of Hebei, Shijiazhuang, 050035, Hebei, China
| | - Minghui Liu
- Baoji Institute of Agriculture Science, Qishan, 722499, Shaanxi, China
| | - Ning Zhao
- Key Laboratory of Sweetpotato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Meikun Han
- Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences/The Key Laboratory of Crop Genetics and Breeding of Hebei, Shijiazhuang, 050035, Hebei, China
| | - Zhao Wang
- Baoji Institute of Agriculture Science, Qishan, 722499, Shaanxi, China
| | - Weijing Jiao
- Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences/The Key Laboratory of Crop Genetics and Breeding of Hebei, Shijiazhuang, 050035, Hebei, China
| | - Zhiyuan Gao
- Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences/The Key Laboratory of Crop Genetics and Breeding of Hebei, Shijiazhuang, 050035, Hebei, China
| | - Yaya Hu
- Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences/The Key Laboratory of Crop Genetics and Breeding of Hebei, Shijiazhuang, 050035, Hebei, China.
| | - Qingchang Liu
- Key Laboratory of Sweetpotato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
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20
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Multiple QTL Mapping in Autopolyploids: A Random-Effect Model Approach with Application in a Hexaploid Sweetpotato Full-Sib Population. Genetics 2020; 215:579-595. [PMID: 32371382 PMCID: PMC7337090 DOI: 10.1534/genetics.120.303080] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 04/26/2020] [Indexed: 11/18/2022] Open
Abstract
In developing countries, the sweetpotato, Ipomoea batatas (L.) Lam. [Formula: see text], is an important autopolyploid species, both socially and economically. However, quantitative trait loci (QTL) mapping has remained limited due to its genetic complexity. Current fixed-effect models can fit only a single QTL and are generally hard to interpret. Here, we report the use of a random-effect model approach to map multiple QTL based on score statistics in a sweetpotato biparental population ('Beauregard' × 'Tanzania') with 315 full-sibs. Phenotypic data were collected for eight yield component traits in six environments in Peru, and jointly adjusted means were obtained using mixed-effect models. An integrated linkage map consisting of 30,684 markers distributed along 15 linkage groups (LGs) was used to obtain the genotype conditional probabilities of putative QTL at every centiMorgan position. Multiple interval mapping was performed using our R package QTLpoly and detected a total of 13 QTL, ranging from none to four QTL per trait, which explained up to 55% of the total variance. Some regions, such as those on LGs 3 and 15, were consistently detected among root number and yield traits, and provided a basis for candidate gene search. In addition, some QTL were found to affect commercial and noncommercial root traits distinctly. Further best linear unbiased predictions were decomposed into additive allele effects and were used to compute multiple QTL-based breeding values for selection. Together with quantitative genotyping and its appropriate usage in linkage analyses, this QTL mapping methodology will facilitate the use of genomic tools in sweetpotato breeding as well as in other autopolyploids.
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21
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Sasai R, Tabuchi H, Shirasawa K, Kishimoto K, Sato S, Okada Y, Kuramoto A, Kobayashi A, Isobe S, Tahara M, Monden Y. Development of molecular markers associated with resistance to Meloidogyne incognita by performing quantitative trait locus analysis and genome-wide association study in sweetpotato. DNA Res 2020; 26:399-409. [PMID: 31377774 PMCID: PMC6796513 DOI: 10.1093/dnares/dsz018] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 07/16/2019] [Indexed: 12/21/2022] Open
Abstract
The southern root-knot nematode, Meloidogyne incognita, is a pest that decreases yield and the quality of sweetpotato [Ipomoea batatas (L.) Lam.]. There is a demand to produce resistant cultivars and develop DNA markers to select this trait. However, sweetpotato is hexaploid, highly heterozygous, and has an enormous genome (∼3 Gb), which makes genetic linkage analysis difficult. In this study, a high-density linkage map was constructed based on retrotransposon insertion polymorphism, simple sequence repeat, and single nucleotide polymorphism markers. The markers were developed using F1 progeny between J-Red, which exhibits resistance to multiple races of M. incognita, and Choshu, which is susceptible to multiple races of such pest. Quantitative trait locus (QTL) analysis and a genome-wide association study detected highly effective QTLs for resistance against three races, namely, SP1, SP4, and SP6-1, in the Ib01-6 J-Red linkage group. A polymerase chain reaction marker that can identify genotypes based on single nucleotide polymorphisms located in this QTL region can discriminate resistance from susceptibility in the F1 progeny at a rate of 70%. Thus, this marker could be helpful in selecting sweetpotato cultivars that are resistant to multiple races of M. incognita.
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Affiliation(s)
- Rumi Sasai
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Okayama, Japan
| | - Hiroaki Tabuchi
- Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Miyakonojo, Miyazaki, Japan
| | | | - Kazuki Kishimoto
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Okayama, Japan
| | - Shusei Sato
- Graduate School of Life Science, Tohoku University, Sendai, Miyagi, Japan
| | - Yoshihiro Okada
- Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Miyakonojo, Miyazaki, Japan
| | - Akihide Kuramoto
- Graduate School of Agriculture, Kyoto University, Kyoto, Kyoto, Japan
| | - Akira Kobayashi
- Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Miyakonojo, Miyazaki, Japan
| | - Sachiko Isobe
- Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
| | - Makoto Tahara
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Okayama, Japan
| | - Yuki Monden
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Okayama, Japan
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22
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Gerard D, Ferrão LFV. Priors for genotyping polyploids. BIOINFORMATICS (OXFORD, ENGLAND) 2020; 36:1795-1800. [PMID: 32176767 DOI: 10.1101/751784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/01/2019] [Accepted: 11/12/2019] [Indexed: 05/29/2023]
Abstract
MOTIVATION Empirical Bayes techniques to genotype polyploid organisms usually either (i) assume technical artifacts are known a priori or (ii) estimate technical artifacts simultaneously with the prior genotype distribution. Case (i) is unappealing as it places the onus on the researcher to estimate these artifacts, or to ensure that there are no systematic biases in the data. However, as we demonstrate with a few empirical examples, case (ii) makes choosing the class of prior genotype distributions extremely important. Choosing a class is either too flexible or too restrictive results in poor genotyping performance. RESULTS We propose two classes of prior genotype distributions that are of intermediate levels of flexibility: the class of proportional normal distributions and the class of unimodal distributions. We provide a complete characterization of and optimization details for the class of unimodal distributions. We demonstrate, using both simulated and real data that using these classes results in superior genotyping performance. AVAILABILITY AND IMPLEMENTATION Genotyping methods that use these priors are implemented in the updog R package available on the Comprehensive R Archive Network: https://cran.r-project.org/package=updog. All code needed to reproduce the results of this article is available on GitHub: https://github.com/dcgerard/reproduce_prior_sims. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- David Gerard
- Department of Mathematics and Statistics, American University, Washington, DC 20016, USA
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23
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Mollinari M, Olukolu BA, Pereira GDS, Khan A, Gemenet D, Yencho GC, Zeng ZB. Unraveling the Hexaploid Sweetpotato Inheritance Using Ultra-Dense Multilocus Mapping. G3 (BETHESDA, MD.) 2020; 10:281-292. [PMID: 31732504 PMCID: PMC6945028 DOI: 10.1534/g3.119.400620] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 11/12/2019] [Indexed: 12/18/2022]
Abstract
The hexaploid sweetpotato (Ipomoea batatas (L.) Lam., 2n = 6x = 90) is an important staple food crop worldwide and plays a vital role in alleviating famine in developing countries. Due to its high ploidy level, genetic studies in sweetpotato lag behind major diploid crops significantly. We built an ultra-dense multilocus integrated genetic map and characterized the inheritance system in a sweetpotato full-sib family using our newly developed software, MAPpoly. The resulting genetic map revealed 96.5% collinearity between I. batatas and its diploid relative I. trifida We computed the genotypic probabilities across the whole genome for all individuals in the mapping population and inferred their complete hexaploid haplotypes. We provide evidence that most of the meiotic configurations (73.3%) were resolved in bivalents, although a small portion of multivalent signatures (15.7%), among other inconclusive configurations (11.0%), were also observed. Except for low levels of preferential pairing in linkage group 2, we observed a hexasomic inheritance mechanism in all linkage groups. We propose that the hexasomic-bivalent inheritance promotes stability to the allelic transmission in sweetpotato.
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Affiliation(s)
- Marcelo Mollinari
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina,
- Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina
| | - Bode A Olukolu
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee
| | - Guilherme da S Pereira
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina
- Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina
| | - Awais Khan
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, New York, and
| | - Dorcus Gemenet
- International Potato Center, ILRI Campus, Nairobi, Kenya
| | - G Craig Yencho
- Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina
| | - Zhao-Bang Zeng
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina
- Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina
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24
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Mollinari M, Olukolu BA, Pereira GDS, Khan A, Gemenet D, Yencho GC, Zeng ZB. Unraveling the Hexaploid Sweetpotato Inheritance Using Ultra-Dense Multilocus Mapping. G3 (BETHESDA, MD.) 2020. [PMID: 31732504 DOI: 10.25387/g3.10255844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
The hexaploid sweetpotato (Ipomoea batatas (L.) Lam., 2n = 6x = 90) is an important staple food crop worldwide and plays a vital role in alleviating famine in developing countries. Due to its high ploidy level, genetic studies in sweetpotato lag behind major diploid crops significantly. We built an ultra-dense multilocus integrated genetic map and characterized the inheritance system in a sweetpotato full-sib family using our newly developed software, MAPpoly. The resulting genetic map revealed 96.5% collinearity between I. batatas and its diploid relative I. trifida We computed the genotypic probabilities across the whole genome for all individuals in the mapping population and inferred their complete hexaploid haplotypes. We provide evidence that most of the meiotic configurations (73.3%) were resolved in bivalents, although a small portion of multivalent signatures (15.7%), among other inconclusive configurations (11.0%), were also observed. Except for low levels of preferential pairing in linkage group 2, we observed a hexasomic inheritance mechanism in all linkage groups. We propose that the hexasomic-bivalent inheritance promotes stability to the allelic transmission in sweetpotato.
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Affiliation(s)
- Marcelo Mollinari
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina,
- Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina
| | - Bode A Olukolu
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee
| | - Guilherme da S Pereira
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina
- Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina
| | - Awais Khan
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, New York, and
| | - Dorcus Gemenet
- International Potato Center, ILRI Campus, Nairobi, Kenya
| | - G Craig Yencho
- Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina
| | - Zhao-Bang Zeng
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina
- Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina
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25
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Feng J, Zhao S, Li M, Zhang C, Qu H, Li Q, Li J, Lin Y, Pu Z. Genome-wide genetic diversity detection and population structure analysis in sweetpotato (Ipomoea batatas) using RAD-seq. Genomics 2019; 112:1978-1987. [PMID: 31756427 DOI: 10.1016/j.ygeno.2019.11.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 11/15/2019] [Accepted: 11/17/2019] [Indexed: 11/29/2022]
Abstract
Sweetpotato (Ipomoea batatas L.) is one of the most important food and grain-forage crops globally. It has been planted in >100 countries. Due to the complexity of the sweetpotato genome, its research is far behind other major food crops. At present, limited information about the sweetpotato genome is available. Thus, it is central to find an efficient approach for the investigation of sweetpotato genome. In this study, RAD-seq (Restriction site-associated DNA sequencing) was used to evaluate sweetpotato genetic structure diversity and to develop relevant SSR markers. The study yielded >128 Gb reliable sequence data from 81 sweetpotato accessions. By analyzing polymorphic tags from each accession, a total of 55,622 restriction-site associated DNA sequencing tags (RAD-seq) were found, containing 907,010 SNP. Genetic analysis divided 81 accessions into five major clusters based on their SNP genotype, which matches the results of genetic analysis and the genetic family tree. In addition, 18,320 SSRs loci were detected and 9336 SSR primer pairs were developed. Eighty-three primer pairs were amplified in different sweetpotato genotypes, 76 of which successfully amplified polymorphism bands. These results provide significant information about sweetpotato genome, which can be used to identify novel gene and to further develop the gene chip. And more significant, clustering results based on the SNP genotype provide an essential reference for breeders to match parent plants in breeding program. Additionally, SSR markers developed in this study will supply a wealth of markers for marker-assisted selection in sweetpotato breeding.
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Affiliation(s)
- Junyan Feng
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610061, China.
| | - Shan Zhao
- Center of Analysis and Testing, Sichuan Academy of Agricultural Sciences, 610066, China
| | - Ming Li
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610061, China
| | - Cong Zhang
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610061, China
| | - Huijuan Qu
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610061, China
| | - Qing Li
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610061, China
| | - Jianwei Li
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610061, China
| | - Yang Lin
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610061, China
| | - Zhigang Pu
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610061, China.
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26
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Okada Y, Monden Y, Nokihara K, Shirasawa K, Isobe S, Tahara M. Genome-Wide Association Studies (GWAS) for Yield and Weevil Resistance in Sweet potato (Ipomoea batatas (L.) Lam). PLANT CELL REPORTS 2019; 38:1383-1392. [PMID: 31342081 DOI: 10.1007/s00299-019-02445-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 07/17/2019] [Indexed: 05/14/2023]
Abstract
We apply the GWAS to sweet potato genome, and identified the SNPs associated with yield and weevil resistance. The sweet potato (Ipomoea batatas (L.) Lam) is a highly heterozygous, outcrossing, polyploid species, which presents challenges for genetic analysis. Therefore, we considered that genome-wide association studies (GWAS) may be applied to the study of the sweet potato genome. The yield of two sweet potato varieties [Purple Sweet Lord (PSL) and 90IDN-47] was assessed at two locations (Kumamoto and Okinawa prefectures) in Japan in 2013 and the yield scores were used for GWAS. The results showed that there were several single nucleotide polymorphisms (SNP) above the significance thresholds in PSL; two peaks were detected in Kumamoto and Okinawa on the Ib03-3 and Ib01-4 linkage groups of PSL, respectively. As for 90IDN-47, one relatively high peak was detected in Kumamoto on the Ib13-8 linkage group. Interestingly, although high peaks above significance thresholds were detected in Kumamoto and Okinawa in PSL, the peaks were located in different linkage groups. This result suggests that the genetic regions controlling yield may change in response to environmental conditions. Additionally, we investigated the degree of weevil damage to the plants, which is the greatest problem in sweet potato cultivation in Okinawa. In this experiment, no SNPs were identified above the significance thresholds. However, one relatively high peak was found in the 90IDN-47 genotype, which showed resistance to weevils. On the other hand, one relatively high peak was also detected in the PSL genotype, which showed susceptibility to weevils. These results suggest that two regions could affect weevil resistance and may contain the gene(s) controlling weevil resistance.
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Affiliation(s)
- Yoshihiro Okada
- Kyushu Okinawa Agricultural Research Center, NARO, 820 Makabe, Itoman, Okinawa, 901-0336, Japan.
| | - Yuki Monden
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushimanaka Kitaku, Okayama, Okayama, 700-8530, Japan
| | - Kanoko Nokihara
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushimanaka Kitaku, Okayama, Okayama, 700-8530, Japan
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Sachiko Isobe
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Makoto Tahara
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushimanaka Kitaku, Okayama, Okayama, 700-8530, Japan
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27
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Isobe S, Shirasawa K, Hirakawa H. Current status in whole genome sequencing and analysis of Ipomoea spp. PLANT CELL REPORTS 2019; 38:1365-1371. [PMID: 31468128 PMCID: PMC6797701 DOI: 10.1007/s00299-019-02464-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 08/19/2019] [Indexed: 05/03/2023]
Abstract
The recent advances of next-generation sequencing have made it possible to construct reference genome sequences in divergent species. However, de novo assembly at the chromosome level remains challenging in polyploid species, due to the existence of more than two pairs of homoeologous chromosomes in one nucleus. Cultivated sweet potato (Ipomoea batatas (L.) Lam) is a hexaploid species with 90 chromosomes (2n = 6X = 90). Although the origin of sweet potato is also still under discussion, diploid relative species, I. trifida and I. triloba have been considered as one of the most possible progenitors. In this manuscript, we review the recent results and activities of whole-genome sequencing in the genus Ipomoea series Batatas, I. trifida, I. triloba and sweet potato (I. batatas). Most of the results of genome assembly suggest that the genomes of sweet potato consist of two pairs and four pairs of subgenomes, i.e., B1B1B2B2B2B2. The results also revealed the relation between sweet potato and other Ipomoea species. Together with the development of bioinformatics approaches, the large-scale publicly available genome and transcript sequence resources and international genome sequencing streams are expected to promote the genome sequence dissection in sweet potato.
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Affiliation(s)
- Sachiko Isobe
- Kazusa DNA Research Institute, Kazusa-Kamatari 2-6-7, Kisarazu, Chiba, Japan.
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, Kazusa-Kamatari 2-6-7, Kisarazu, Chiba, Japan
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, Kazusa-Kamatari 2-6-7, Kisarazu, Chiba, Japan
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28
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Linkage Analysis and Haplotype Phasing in Experimental Autopolyploid Populations with High Ploidy Level Using Hidden Markov Models. G3-GENES GENOMES GENETICS 2019; 9:3297-3314. [PMID: 31405891 PMCID: PMC6778803 DOI: 10.1534/g3.119.400378] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Modern SNP genotyping technologies allow measurement of the relative abundance of different alleles for a given locus and consequently estimation of their allele dosage, opening a new road for genetic studies in autopolyploids. Despite advances in genetic linkage analysis in autotetraploids, there is a lack of statistical models to perform linkage analysis in organisms with higher ploidy levels. In this paper, we present a statistical method to estimate recombination fractions and infer linkage phases in full-sib populations of autopolyploid species with even ploidy levels for a set of SNP markers using hidden Markov models. Our method uses efficient two-point procedures to reduce the search space for the best linkage phase configuration and reestimate the final parameters by maximizing the likelihood of the Markov chain. To evaluate the method, and demonstrate its properties, we rely on simulations of autotetraploid, autohexaploid and autooctaploid populations and on a real tetraploid potato data set. The results show the reliability of our approach, including situations with complex linkage phase scenarios in hexaploid and octaploid populations.
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29
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Mollinari M, Garcia AAF. Linkage Analysis and Haplotype Phasing in Experimental Autopolyploid Populations with High Ploidy Level Using Hidden Markov Models. G3 (BETHESDA, MD.) 2019. [PMID: 31405891 DOI: 10.1101/415232v2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Modern SNP genotyping technologies allow measurement of the relative abundance of different alleles for a given locus and consequently estimation of their allele dosage, opening a new road for genetic studies in autopolyploids. Despite advances in genetic linkage analysis in autotetraploids, there is a lack of statistical models to perform linkage analysis in organisms with higher ploidy levels. In this paper, we present a statistical method to estimate recombination fractions and infer linkage phases in full-sib populations of autopolyploid species with even ploidy levels for a set of SNP markers using hidden Markov models. Our method uses efficient two-point procedures to reduce the search space for the best linkage phase configuration and reestimate the final parameters by maximizing the likelihood of the Markov chain. To evaluate the method, and demonstrate its properties, we rely on simulations of autotetraploid, autohexaploid and autooctaploid populations and on a real tetraploid potato data set. The results show the reliability of our approach, including situations with complex linkage phase scenarios in hexaploid and octaploid populations.
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Affiliation(s)
- Marcelo Mollinari
- Department of Horticultural Science, Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, and
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30
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Sumitomo K, Shirasawa K, Isobe S, Hirakawa H, Hisamatsu T, Nakano Y, Yagi M, Ohmiya A. Genome-wide association study overcomes the genome complexity in autohexaploid chrysanthemum and tags SNP markers onto the flower color genes. Sci Rep 2019; 9:13947. [PMID: 31558738 PMCID: PMC6763435 DOI: 10.1038/s41598-019-50028-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 09/04/2019] [Indexed: 12/02/2022] Open
Abstract
The use of DNA markers has revolutionized selection in crop breeding by linkage mapping and QTL analysis, but major problems still remain for polyploid species where marker-assisted selection lags behind the situation in diploids because of its high genome complexity. To overcome the complex genetic mode in the polyploids, we investigated the development of a strategy of genome-wide association study (GWAS) using single-dose SNPs, which simplify the segregation patterns associated polyploids, with respect to the development of DNA markers. In addition, we employed biparental populations for the GWAS, wherein the SNP allele frequency could be predicted. The research investigated whether the method could be used to effectively develop DNA markers for petal color in autohexaploid chrysanthemum (Chrysanthemum morifolium; 2n = 6x = 54). The causal gene for this trait is already-known CmCCD4a encoding a dioxygenase which cleaves carotenoids in petals. We selected 9,219 single-dose SNPs, out of total 52,489 SNPs identified by dd-RAD-Seq, showing simplex (1 × 0) and double-simplex (1 × 1) inheritance pattern according to alternative allele frequency with respect to the SNP loci in the F1 population. GWAS, using these single-dose SNPs, discovered highly reproducible SNP markers tightly linked to the causal genes. This is the first report of a straightforward GWAS-based marker developing system for use in autohexaploid species.
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Affiliation(s)
- Katsuhiko Sumitomo
- Institute of Vegetable and Floriculture Sciences, NARO, Tsukuba, Ibaraki, 305-0852, Japan.
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - Sachiko Isobe
- Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - Tamotsu Hisamatsu
- Institute of Vegetable and Floriculture Sciences, NARO, Tsukuba, Ibaraki, 305-0852, Japan
| | - Yoshihiro Nakano
- Institute of Vegetable and Floriculture Sciences, NARO, Tsukuba, Ibaraki, 305-0852, Japan
| | - Masafumi Yagi
- Institute of Vegetable and Floriculture Sciences, NARO, Tsukuba, Ibaraki, 305-0852, Japan
| | - Akemi Ohmiya
- Institute of Vegetable and Floriculture Sciences, NARO, Tsukuba, Ibaraki, 305-0852, Japan
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Yamashita H, Katai H, Kawaguchi L, Nagano AJ, Nakamura Y, Morita A, Ikka T. Analyses of single nucleotide polymorphisms identified by ddRAD-seq reveal genetic structure of tea germplasm and Japanese landraces for tea breeding. PLoS One 2019; 14:e0220981. [PMID: 31393947 PMCID: PMC6687169 DOI: 10.1371/journal.pone.0220981] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 07/28/2019] [Indexed: 11/19/2022] Open
Abstract
To obtain genetic information about the germplasm of tea (Camellia sinensis L.) in Japan, 167 accessions including 138 var. sinensis (96 Japanese var. sinensis and 42 exotic var. sinensis) and 29 Assam hybrids were analyzed using single nucleotide polymorphisms (SNPs) markers identified by double-digest restriction-site-associated DNA sequencing (ddRAD-seq) analysis. Approximately 10,000 SNPs were identified by ddRAD-seq and were mapped across the whole genome. The 167 tea accessions were classified into three genetic subgroups: (1) Japanese var. sinensis; (2) Japanese and exotic var. sinensis; (3) Assam hybrids and exotic var. sinensis. Leaf morphology varied widely within each genetic subgroups. The 96 Japanese var. sinensis were classified into four genetic subgroups as follows; two subgroups of Shizuoka (the largest tea production region) landraces, Uji (most ancient tea production region) landraces, and the pedigree of 'Yabukita', the leading green tea cultivar in Japan. These results indicated that the SNP markers obtained from ddRAD-seq are a useful tool to investigate the geographical background and breeding history of Japanese tea. This genetic information revealed the ancestral admixture situation of the 'Yabukita' pedigree, and showed that the genome structure of 'Yabukita' is clearly different from those of other Japanese accessions.
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Affiliation(s)
- Hiroto Yamashita
- Faculty of Agriculture, Shizuoka University, Ohya, Shizuoka, Japan
- United Graduate School of Agricultural Science, Gifu University, Yanagito, Gifu, Japan
| | - Hideyuki Katai
- Shizuoka Prefectural Research Institute of Agriculture and Forestry, Tea Research Center, Kurasawa, Kikugawa, Shizuoka, Japan
| | - Lina Kawaguchi
- Faculty of Agriculture, Ryukoku University, Yokotani, Seta Oe-cho, Otsu, Shiga, Japan
| | - Atsushi J. Nagano
- Faculty of Agriculture, Ryukoku University, Yokotani, Seta Oe-cho, Otsu, Shiga, Japan
| | - Yoriyuki Nakamura
- School of Food and Nutritional Sciences, University of Shizuoka, Yada, Shizuoka, Japan
| | - Akio Morita
- Faculty of Agriculture, Shizuoka University, Ohya, Shizuoka, Japan
| | - Takashi Ikka
- Faculty of Agriculture, Shizuoka University, Ohya, Shizuoka, Japan
- * E-mail:
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Hirakawa H, Sumitomo K, Hisamatsu T, Nagano S, Shirasawa K, Higuchi Y, Kusaba M, Koshioka M, Nakano Y, Yagi M, Yamaguchi H, Taniguchi K, Nakano M, Isobe SN. De novo whole-genome assembly in Chrysanthemum seticuspe, a model species of Chrysanthemums, and its application to genetic and gene discovery analysis. DNA Res 2019; 26:195-203. [PMID: 30689773 PMCID: PMC6589549 DOI: 10.1093/dnares/dsy048] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 01/02/2019] [Indexed: 11/13/2022] Open
Abstract
Cultivated chrysanthemum (Chrysanthemum morifolium Ramat.) is one of the most economically important ornamental crops grown worldwide. It has a complex hexaploid genome (2n = 6x = 54) and large genome size. The diploid Chrysanthemum seticuspe is often used as a model of cultivated chrysanthemum, since the two species are closely related. To expand our knowledge of the cultivated chrysanthemum, we here performed de novo whole-genome assembly in C. seticuspe using the Illumina sequencing platform. XMRS10, a C. seticuspe accession developed by five generations of self-crossing from a self-compatible strain, AEV2, was used for genome sequencing. The 2.72 Gb of assembled sequences (CSE_r1.0), consisting of 354,212 scaffolds, covered 89.0% of the 3.06 Gb C. seticuspe genome estimated by k-mer analysis. The N50 length of scaffolds was 44,741 bp. For protein-encoding genes, 71,057 annotated genes were deduced (CSE_r1.1_cds). Next, based on the assembled genome sequences, we performed linkage map construction, gene discovery and comparative analyses for C. seticuspe and cultivated chrysanthemum. The generated C. seticuspe linkage map revealed skewed regions in segregation on the AEV2 genome. In gene discovery analysis, candidate flowering-related genes were newly found in CSE_r1.1_cds. Moreover, single nucleotide polymorphism identification and annotation on the C. × morifolium genome showed that the C. seticuspe genome was applicable to genetic analysis in cultivated chrysanthemums. The genome sequences assembled herein are expected to contribute to future chrysanthemum studies. In addition, our approach demonstrated the usefulness of short-read genome assembly and the importance of choosing an appropriate next genome sequencing technology based on the purpose of the post-genome analysis.
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Affiliation(s)
| | - Katsuhiko Sumitomo
- Institute of Vegetable and Floriculture Sciences, NARO, Tsukuba, Ibaraki, Japan
| | - Tamotsu Hisamatsu
- Institute of Vegetable and Floriculture Sciences, NARO, Tsukuba, Ibaraki, Japan
| | - Soichiro Nagano
- Kazusa DNA Research Institute, Kisarazu, Chiba, Japan.,Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Juo, Hitachi, Ibaraki, Japan
| | | | - Yohei Higuchi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Makoto Kusaba
- Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Masaji Koshioka
- College of Bioresource Sciences, Nihon University, Kameino, Fujisawa, Kanagawa, Japan
| | - Yoshihiro Nakano
- Institute of Vegetable and Floriculture Sciences, NARO, Tsukuba, Ibaraki, Japan
| | - Masafumi Yagi
- Institute of Vegetable and Floriculture Sciences, NARO, Tsukuba, Ibaraki, Japan
| | - Hiroyasu Yamaguchi
- Institute of Vegetable and Floriculture Sciences, NARO, Tsukuba, Ibaraki, Japan
| | - Kenji Taniguchi
- Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Michiharu Nakano
- Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
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High density linkage map construction and QTL mapping for runner production in allo-octoploid strawberry Fragaria × ananassa based on ddRAD-seq derived SNPs. Sci Rep 2019; 9:3275. [PMID: 30824841 PMCID: PMC6397268 DOI: 10.1038/s41598-019-39808-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 01/29/2019] [Indexed: 11/08/2022] Open
Abstract
Recent advances in high-throughput genome sequencing technologies are now making the genetic dissection of the complex genome of cultivated strawberry easier. We sequenced Maehyang (short-day cultivar) × Albion (day-neutral cultivar) crossing populations using double digest restriction-associated DNA (ddRAD) sequencing technique that yielded 978,968 reads, 80.2% of which were aligned to strawberry genome allowing the identification of 13,181 high quality single nucleotide polymorphisms (SNPs). Total 3051 SNPs showed Mendelian segregation in F1, of which 1268 were successfully mapped to 46 linkage groups (LG) spanning a total of 2581.57 cM with an average interval genetic distance of 2.22 cM. The LGs were assigned to the 28 chromosomes of Fragaria × ananassa as determined by positioning the sequence tags on F. vesca genome. In addition, seven QTLs namely, qRU-5D, qRU-3D1, qRU-1D2, qRU-4D, qRU-4C, qRU-5C and qRU-2D2 were identified for runner production with LOD value ranging from 3.5–7.24 that explained 22–38% of phenotypic variation. The key candidate genes having putative roles in meristem differentiation for runnering and flowering within these QTL regions were identified. These will enhance our understanding of the vegetative vs sexual reproductive behavior in strawberry and will aid in setting breeding targets for developing perpetual flowering and profuse runnering cultivar.
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Ferreira RCU, Lara LADC, Chiari L, Barrios SCL, do Valle CB, Valério JR, Torres FZV, Garcia AAF, de Souza AP. Genetic Mapping With Allele Dosage Information in Tetraploid Urochloa decumbens (Stapf) R. D. Webster Reveals Insights Into Spittlebug ( Notozulia entreriana Berg) Resistance. FRONTIERS IN PLANT SCIENCE 2019; 10:92. [PMID: 30873183 PMCID: PMC6401981 DOI: 10.3389/fpls.2019.00092] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 01/21/2019] [Indexed: 05/08/2023]
Abstract
Urochloa decumbens (Stapf) R. D. Webster is one of the most important African forage grasses in Brazilian beef production. Currently available genetic-genomic resources for this species are restricted mainly due to polyploidy and apomixis. Therefore, crucial genomic-molecular studies such as the construction of genetic maps and the mapping of quantitative trait loci (QTLs) are very challenging and consequently affect the advancement of molecular breeding. The objectives of this work were to (i) construct an integrated U. decumbens genetic map for a full-sibling progeny using GBS-based markers with allele dosage information, (ii) detect QTLs for spittlebug (Notozulia entreriana) resistance, and (iii) seek putative candidate genes involved in defense against biotic stresses. We used the Setaria viridis genome a reference to align GBS reads and selected 4,240 high-quality SNP markers with allele dosage information. Of these markers, 1,000 were distributed throughout nine homologous groups with a cumulative map length of 1,335.09 cM and an average marker density of 1.33 cM. We detected QTLs for resistance to spittlebug, an important pasture insect pest, that explained between 4.66 and 6.24% of the phenotypic variation. These QTLs are in regions containing putative candidate genes related to defense against biotic stresses. Because this is the first genetic map with SNP autotetraploid dosage data and QTL detection in U. decumbens, it will be useful for future evolutionary studies, genome assembly, and other QTL analyses in Urochloa spp. Moreover, the results might facilitate the isolation of spittlebug-related candidate genes and help clarify the mechanism of spittlebug resistance. These approaches will improve selection efficiency and accuracy in U. decumbens molecular breeding and shorten the breeding cycle.
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Affiliation(s)
| | | | - Lucimara Chiari
- Embrapa Beef Cattle, Brazilian Agricultural Research Corporation, Campo Grande, Brazil
| | | | | | - José Raul Valério
- Embrapa Beef Cattle, Brazilian Agricultural Research Corporation, Campo Grande, Brazil
| | | | | | - Anete Pereira de Souza
- Center for Molecular Biology and Genetic Engineering, University of Campinas, Campinas, Brazil
- Plant Biology Department, Biology Institute, University of Campinas, Campinas, Brazil
- *Correspondence: Anete Pereira de Souza,
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Beilsmith K, Thoen MPM, Brachi B, Gloss AD, Khan MH, Bergelson J. Genome-wide association studies on the phyllosphere microbiome: Embracing complexity in host-microbe interactions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:164-181. [PMID: 30466152 DOI: 10.1111/tpj.14170] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 11/08/2018] [Accepted: 11/16/2018] [Indexed: 05/18/2023]
Abstract
Environmental sequencing shows that plants harbor complex communities of microbes that vary across environments. However, many approaches for mapping plant genetic variation to microbe-related traits were developed in the relatively simple context of binary host-microbe interactions under controlled conditions. Recent advances in sequencing and statistics make genome-wide association studies (GWAS) an increasingly promising approach for identifying the plant genetic variation associated with microbes in a community context. This review discusses early efforts on GWAS of the plant phyllosphere microbiome and the outlook for future studies based on human microbiome GWAS. A workflow for GWAS of the phyllosphere microbiome is then presented, with particular attention to how perspectives on the mechanisms, evolution and environmental dependence of plant-microbe interactions will influence the choice of traits to be mapped.
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Affiliation(s)
- Kathleen Beilsmith
- Department of Ecology and Evolution, University of Chicago, 1101 E 57th St, Chicago, IL, 60637, USA
| | - Manus P M Thoen
- Department of Ecology and Evolution, University of Chicago, 1101 E 57th St, Chicago, IL, 60637, USA
| | - Benjamin Brachi
- BIOGECO, INRA, University of Bordeaux, 33610, Cestas, France
| | - Andrew D Gloss
- Department of Ecology and Evolution, University of Chicago, 1101 E 57th St, Chicago, IL, 60637, USA
| | - Mohammad H Khan
- Department of Ecology and Evolution, University of Chicago, 1101 E 57th St, Chicago, IL, 60637, USA
| | - Joy Bergelson
- Department of Ecology and Evolution, University of Chicago, 1101 E 57th St, Chicago, IL, 60637, USA
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Gerard D, Ferrão LFV, Garcia AAF, Stephens M. Genotyping Polyploids from Messy Sequencing Data. Genetics 2018; 210:789-807. [PMID: 30185430 PMCID: PMC6218231 DOI: 10.1534/genetics.118.301468] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 08/21/2018] [Indexed: 12/30/2022] Open
Abstract
Detecting and quantifying the differences in individual genomes (i.e., genotyping), plays a fundamental role in most modern bioinformatics pipelines. Many scientists now use reduced representation next-generation sequencing (NGS) approaches for genotyping. Genotyping diploid individuals using NGS is a well-studied field, and similar methods for polyploid individuals are just emerging. However, there are many aspects of NGS data, particularly in polyploids, that remain unexplored by most methods. Our contributions in this paper are fourfold: (i) We draw attention to, and then model, common aspects of NGS data: sequencing error, allelic bias, overdispersion, and outlying observations. (ii) Many datasets feature related individuals, and so we use the structure of Mendelian segregation to build an empirical Bayes approach for genotyping polyploid individuals. (iii) We develop novel models to account for preferential pairing of chromosomes, and harness these for genotyping. (iv) We derive oracle genotyping error rates that may be used for read depth suggestions. We assess the accuracy of our method in simulations, and apply it to a dataset of hexaploid sweet potato (Ipomoea batatas). An R package implementing our method is available at https://cran.r-project.org/package=updog.
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Affiliation(s)
- David Gerard
- Department of Mathematics and Statistics, American University, Washington, DC 20016
| | | | - Antonio Augusto Franco Garcia
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, 13418-900, Brazil
| | - Matthew Stephens
- Department of Human Genetics, University of Chicago, Illinois 60637
- Department of Statistics, University of Chicago, Illinois 60637
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Kim HS, Yoon UH, Lee CJ, Kim SE, Ji CY, Kwak SS. Status of research on the sweetpotato biotechnology and prospects of the molecular breeding on marginal lands. ACTA ACUST UNITED AC 2018. [DOI: 10.5010/jpb.2018.45.3.196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Ho Soo Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Ung-Han Yoon
- Genomics Division, National Academy of Agricultural Science, Jeonju 54875, Korea
| | - Chan-Ju Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - So-Eun Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Chang Yoon Ji
- Research & Development Center, Korea Scientific Technique Industry Co., Ltd., 67, Saneop-ro 92, Gwonseon-gu, Suwon-si 16643, Korea
| | - Sang-Soo Kwak
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
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Bourke PM, Voorrips RE, Visser RGF, Maliepaard C. Tools for Genetic Studies in Experimental Populations of Polyploids. FRONTIERS IN PLANT SCIENCE 2018; 9:513. [PMID: 29720992 PMCID: PMC5915555 DOI: 10.3389/fpls.2018.00513] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 04/04/2018] [Indexed: 05/19/2023]
Abstract
Polyploid organisms carry more than two copies of each chromosome, a condition rarely tolerated in animals but which occurs relatively frequently in the plant kingdom. One of the principal challenges faced by polyploid organisms is to evolve stable meiotic mechanisms to faithfully transmit genetic information to the next generation upon which the study of inheritance is based. In this review we look at the tools available to the research community to better understand polyploid inheritance, many of which have only recently been developed. Most of these tools are intended for experimental populations (rather than natural populations), facilitating genomics-assisted crop improvement and plant breeding. This is hardly surprising given that a large proportion of domesticated plant species are polyploid. We focus on three main areas: (1) polyploid genotyping; (2) genetic and physical mapping; and (3) quantitative trait analysis and genomic selection. We also briefly review some miscellaneous topics such as the mode of inheritance and the availability of polyploid simulation software. The current polyploid analytic toolbox includes software for assigning marker genotypes (and in particular, estimating the dosage of marker alleles in the heterozygous condition), establishing chromosome-scale linkage phase among marker alleles, constructing (short-range) haplotypes, generating linkage maps, performing genome-wide association studies (GWAS) and quantitative trait locus (QTL) analyses, and simulating polyploid populations. These tools can also help elucidate the mode of inheritance (disomic, polysomic or a mixture of both as in segmental allopolyploids) or reveal whether double reduction and multivalent chromosomal pairing occur. An increasing number of polyploids (or associated diploids) are being sequenced, leading to publicly available reference genome assemblies. Much work remains in order to keep pace with developments in genomic technologies. However, such technologies also offer the promise of understanding polyploid genomes at a level which hitherto has remained elusive.
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Affiliation(s)
| | | | | | - Chris Maliepaard
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
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Arafa RA, Rakha MT, Soliman NEK, Moussa OM, Kamel SM, Shirasawa K. Rapid identification of candidate genes for resistance to tomato late blight disease using next-generation sequencing technologies. PLoS One 2017; 12:e0189951. [PMID: 29253902 PMCID: PMC5734779 DOI: 10.1371/journal.pone.0189951] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 12/05/2017] [Indexed: 11/19/2022] Open
Abstract
Tomato late blight caused by Phytophthora infestans (Mont.) de Bary, also known as the Irish famine pathogen, is one of the most destructive plant diseases. Wild relatives of tomato possess useful resistance genes against this disease, and could therefore be used in breeding to improve cultivated varieties. In the genome of a wild relative of tomato, Solanum habrochaites accession LA1777, we identified a new quantitative trait locus for resistance against blight caused by an aggressive Egyptian isolate of P. infestans. Using double-digest restriction site-associated DNA sequencing (ddRAD-Seq) technology, we determined 6,514 genome-wide SNP genotypes of an F2 population derived from an interspecific cross. Subsequent association analysis of genotypes and phenotypes of the mapping population revealed that a 6.8 Mb genome region on chromosome 6 was a candidate locus for disease resistance. Whole-genome resequencing analysis revealed that 298 genes in this region potentially had functional differences between the parental lines. Among of them, two genes with missense mutations, Solyc06g071810.1 and Solyc06g083640.3, were considered to be potential candidates for disease resistance. SNP and SSR markers linking to this region can be used in marker-assisted selection in future breeding programs for late blight disease, including introgression of new genetic loci from wild species. In addition, the approach developed in this study provides a model for identification of other genes for attractive agronomical traits.
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Affiliation(s)
- Ramadan A. Arafa
- Plant Pathology Research Institute, Agricultural Research Center, Giza, Egypt
| | - Mohamed T. Rakha
- Department of Horticulture, Faculty of Agriculture, University of Kafrelsheikh, Kafr El-Sheikh, Egypt
| | - Nour Elden K. Soliman
- Department of Plant Pathology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Olfat M. Moussa
- Department of Plant Pathology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Said M. Kamel
- Plant Pathology Research Institute, Agricultural Research Center, Giza, Egypt
| | - Kenta Shirasawa
- Department of Frontier Science, Kazusa DNA Research Institute, Chiba, Japan
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van Geest G, Bourke PM, Voorrips RE, Marasek-Ciolakowska A, Liao Y, Post A, van Meeteren U, Visser RGF, Maliepaard C, Arens P. An ultra-dense integrated linkage map for hexaploid chrysanthemum enables multi-allelic QTL analysis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:2527-2541. [PMID: 28852802 PMCID: PMC5668331 DOI: 10.1007/s00122-017-2974-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/18/2017] [Indexed: 05/21/2023]
Abstract
KEY MESSAGE We constructed the first integrated genetic linkage map in a polysomic hexaploid. This enabled us to estimate inheritance of parental haplotypes in the offspring and detect multi-allelic QTL. Construction and use of linkage maps are challenging in hexaploids with polysomic inheritance. Full map integration requires calculations of recombination frequency between markers with complex segregation types. In addition, detection of QTL in hexaploids requires information on all six alleles at one locus for each individual. We describe a method that we used to construct a fully integrated linkage map for chrysanthemum (Chrysanthemum × morifolium, 2n = 6x = 54). A bi-parental F1 population of 406 individuals was genotyped with an 183,000 SNP genotyping array. The resulting linkage map consisted of 30,312 segregating SNP markers of all possible marker dosage types, representing nine chromosomal linkage groups and 107 out of 108 expected homologues. Synteny with lettuce (Lactuca sativa) showed local colinearity. Overall, it was high enough to number the chrysanthemum chromosomal linkage groups according to those in lettuce. We used the integrated and phased linkage map to reconstruct inheritance of parental haplotypes in the F1 population. Estimated probabilities for the parental haplotypes were used for multi-allelic QTL analyses on four traits with different underlying genetic architectures. This resulted in the identification of major QTL that were affected by multiple alleles having a differential effect on the phenotype. The presented linkage map sets a standard for future genetic mapping analyses in chrysanthemum and closely related species. Moreover, the described methods are a major step forward for linkage mapping and QTL analysis in hexaploids.
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Affiliation(s)
- Geert van Geest
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6708 PB, Wageningen, The Netherlands.
- Deliflor Chrysanten B.V., Korte Kruisweg 163, 2676 BS, Maasdijk, The Netherlands.
- Horticulture and Product Physiology, Department of Plant Sciences, Wageningen University, P.O. Box 16, 6700 AA, Wageningen, The Netherlands.
| | - Peter M Bourke
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6708 PB, Wageningen, The Netherlands
| | - Roeland E Voorrips
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6708 PB, Wageningen, The Netherlands
| | | | - Yanlin Liao
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6708 PB, Wageningen, The Netherlands
| | - Aike Post
- Deliflor Chrysanten B.V., Korte Kruisweg 163, 2676 BS, Maasdijk, The Netherlands
| | - Uulke van Meeteren
- Horticulture and Product Physiology, Department of Plant Sciences, Wageningen University, P.O. Box 16, 6700 AA, Wageningen, The Netherlands
| | - Richard G F Visser
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6708 PB, Wageningen, The Netherlands
| | - Chris Maliepaard
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6708 PB, Wageningen, The Netherlands
| | - Paul Arens
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6708 PB, Wageningen, The Netherlands
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