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Possible stochastic sex determination in Bursaphelenchus nematodes. Nat Commun 2022; 13:2574. [PMID: 35546147 PMCID: PMC9095866 DOI: 10.1038/s41467-022-30173-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 04/19/2022] [Indexed: 12/13/2022] Open
Abstract
Sex determination mechanisms evolve surprisingly rapidly, yet little is known in the large nematode phylum other than for Caenorhabditis elegans, which relies on chromosomal XX-XO sex determination and a dosage compensation mechanism. Here we analyze by sex-specific genome sequencing and genetic analysis sex determination in two fungal feeding/plant-parasitic Bursaphelenchus nematodes and find that their sex differentiation is more likely triggered by random, epigenetic regulation than by more well-known mechanisms of chromosomal or environmental sex determination. There is no detectable difference in male and female chromosomes, nor any linkage to sexual phenotype. Moreover, the protein sets of these nematodes lack genes involved in X chromosome dosage counting or compensation. By contrast, our genetic screen for sex differentiation mutants identifies a Bursaphelenchus ortholog of tra-1, the major output of the C. elegans sex determination cascade. Nematode sex determination pathways might have evolved by “bottom-up” accretion from the most downstream regulator, tra-1. In most species, sex is determined by genetic or environmental factors. Here, the authors present evidence that sex determination in Bursaphelenchus nematodes is instead likely to be regulated by a random, epigenetic mechanism.
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Lee YR, Kim CW, Han J, Choi HJ, Han K, Lee ES, Kim DS, Lee J, Siddique MI, Lee HE. Genotyping-by-Sequencing Derived Genetic Linkage Map and Quantitative Trait Loci for Sugar Content in Onion ( Allium cepa L.). PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112267. [PMID: 34834630 PMCID: PMC8625195 DOI: 10.3390/plants10112267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/19/2021] [Accepted: 10/19/2021] [Indexed: 05/02/2023]
Abstract
Onion (2n = 2x = 16) has been a nutritional, medicinal and economically valuable vegetable crop all over the world since ancient times. To accelerate the molecular breeding in onion, genetic linkage maps are prerequisite. However, construction of genetic linkage maps of onion remains relatively rudimentary due to a large genome (about 16.3 Gbp) as well as biennial life cycle, cross-pollinated nature, and high inbreeding depression. In this study, we constructed single nucleotide polymorphism (SNP)-based genetic linkage map of onion in an F2 segregating population derived from a cross between the doubled haploid line '16P118' and inbred line 'Sweet Green' through genotyping by sequencing (GBS). A total of 207.3 Gbp of raw sequences were generated using an Illumina HiSeq X system, and 24,341 SNPs were identified with the criteria based on three minimum depths, lower than 30% missing rate, and more than 5% minor allele frequency. As a result, an onion genetic linkage map consisting of 216 GBS-based SNPs were constructed comprising eight linkage groups spanning a genetic length of 827.0 cM. Furthermore, we identified the quantitative trait loci (QTLs) for the sucrose, glucose, fructose, and total sugar content across the onion genome. We identified a total of four QTLs associated with sucrose (qSC4.1), glucose (qGC5.1), fructose (qFC5.1), and total sugar content (qTSC5.1) explaining the phenotypic variation (R2%) ranging from 6.07-11.47%. This map and QTL information will contribute to develop the molecular markers to breed the cultivars with high sugar content in onion.
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Affiliation(s)
- Ye-Rin Lee
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Korea; (Y.-R.L.); (C.W.K.); (J.H.); (K.H.); (E.S.L.); (D.-S.K.); (M.I.S.)
| | - Cheol Woo Kim
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Korea; (Y.-R.L.); (C.W.K.); (J.H.); (K.H.); (E.S.L.); (D.-S.K.); (M.I.S.)
| | - JiWon Han
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Korea; (Y.-R.L.); (C.W.K.); (J.H.); (K.H.); (E.S.L.); (D.-S.K.); (M.I.S.)
| | - Hyun Jin Choi
- Postharvest Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Korea;
| | - Koeun Han
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Korea; (Y.-R.L.); (C.W.K.); (J.H.); (K.H.); (E.S.L.); (D.-S.K.); (M.I.S.)
| | - Eun Su Lee
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Korea; (Y.-R.L.); (C.W.K.); (J.H.); (K.H.); (E.S.L.); (D.-S.K.); (M.I.S.)
| | - Do-Sun Kim
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Korea; (Y.-R.L.); (C.W.K.); (J.H.); (K.H.); (E.S.L.); (D.-S.K.); (M.I.S.)
| | - Jundae Lee
- Department of Horticulture, Institute of Agricultural Science & Technology, Jeonbuk National University, Jeonju 54896, Korea;
| | - Muhammad Irfan Siddique
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Korea; (Y.-R.L.); (C.W.K.); (J.H.); (K.H.); (E.S.L.); (D.-S.K.); (M.I.S.)
| | - Hye-Eun Lee
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Korea; (Y.-R.L.); (C.W.K.); (J.H.); (K.H.); (E.S.L.); (D.-S.K.); (M.I.S.)
- Correspondence: ; Tel.: +82-63-238-6674
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Construction of a high-density linkage map and graphical representation of the arrangement of transcriptome-based unigene markers on the chromosomes of onion, Allium cepa L. BMC Genomics 2021; 22:481. [PMID: 34174821 PMCID: PMC8236188 DOI: 10.1186/s12864-021-07803-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 06/13/2021] [Indexed: 11/10/2022] Open
Abstract
Background Genomic information for Allium cepa L. is limited as it is heterozygous and its genome is very large. To elucidate potential SNP markers obtained by NGS, we used a complete set of A. fistulosum L.-A. cepa monosomic addition lines (MALs) and doubled haploids (DHs). These were the parental lines of an A. cepa mapping population for transcriptome-based SNP genotyping. Results We mapped the transcriptome sequence reads from a series of A. fistulosum-A. cepa MALs onto the unigene sequence of the doubled haploid shallot A. cepa Aggregatum group (DHA) and compared the MAL genotype call for parental bunching onion and shallot transcriptome mapping data. We identified SNP sites with at least four reads on 25,462 unigenes. They were anchored on eight A. cepa chromosomes. A single SNP site was identified on 3,278 unigenes and multiple SNPs were identified on 22,184 unigenes. The chromosome marker information was made public via the web database Allium TDB (http://alliumtdb.kazusa.or.jp/). To apply transcriptome based genotyping approach for genetic mapping, we gathered RNA sequence data from 96 lines of a DHA × doubled haploid bulb onion A. cepa common onion group (DHC) mapping population. After selecting co-dominant SNP sites, 16,872 SNPs were identified in 5,339 unigenes. Of these, at least two SNPs with identical genotypes were found in 1,435 unigenes. We developed a linkage map using genotype information from these unigenes. All unigene markers mapped onto the eight chromosomes and graphical genotyping was conducted based on the unigene order information. Another 2,963 unigenes were allocated onto the eight chromosomes. To confirm the accuracy of this transcriptome-based genetic linkage map, conventional PCR-based markers were used for linkage analysis. All SNP - and PCR-based markers were mapped onto the expected linkage groups and no inconsistency was found among these chromosomal locations. Conclusions Effective transcriptome analysis with unique Allium resources successfully associated numerous chromosome markers with unigene information and a high-density A. cepa linkage map. The information on these unigene markers is valuable in genome sequencing and useful trait detection in Allium. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07803-y.
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Wesołowski W, Domnicz B, Augustynowicz J, Szklarczyk M. VCF2CAPS-A high-throughput CAPS marker design from VCF files and its test-use on a genotyping-by-sequencing (GBS) dataset. PLoS Comput Biol 2021; 17:e1008980. [PMID: 34014924 PMCID: PMC8186816 DOI: 10.1371/journal.pcbi.1008980] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 06/08/2021] [Accepted: 04/18/2021] [Indexed: 11/21/2022] Open
Abstract
Next-generation sequencing (NGS) is a powerful tool for massive detection of DNA sequence variants such as single nucleotide polymorphisms (SNPs), multi-nucleotide polymorphisms (MNPs) and insertions/deletions (indels). For routine screening of numerous samples, these variants are often converted into cleaved amplified polymorphic sequence (CAPS) markers which are based on the presence versus absence of restriction sites within PCR products. Current computational tools for SNP to CAPS conversion are limited and usually infeasible to use for large datasets as those generated with NGS. Moreover, there is no available tool for massive conversion of MNPs and indels into CAPS markers. Here, we present VCF2CAPS–a new software for identification of restriction endonucleases that recognize SNP/MNP/indel-containing sequences from NGS experiments. Additionally, the program contains filtration utilities not available in other SNP to CAPS converters–selection of markers with a single polymorphic cut site within a user-specified sequence length, and selection of markers that differentiate up to three user-defined groups of individuals from the analyzed population. Performance of VCF2CAPS was tested on a thoroughly analyzed dataset from a genotyping-by-sequencing (GBS) experiment. A selection of CAPS markers picked by the program was subjected to experimental verification. CAPS markers, also referred to as PCR-RFLPs, belong to basic tools exploited in plant, animal and human genetics. Our new software–VCF2CAPS–fills the gap in the current inventory of genetic software by high-throughput CAPS marker design from next-generation sequencing (NGS) data. The program should be of interest to geneticists involved in molecular diagnostics. In this paper we show a successful exemplary application of VCF2CAPS and we believe that its usefulness is guaranteed by the growing availability of NGS services.
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Affiliation(s)
- Wojciech Wesołowski
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, Krakow, Poland
| | - Beata Domnicz
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, Krakow, Poland
| | - Joanna Augustynowicz
- Department of Botany, Physiology and Plant Protection, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, Krakow, Poland
| | - Marek Szklarczyk
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, Krakow, Poland
- * E-mail:
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Khandagale K, Krishna R, Roylawar P, Ade AB, Benke A, Shinde B, Singh M, Gawande SJ, Rai A. Omics approaches in Allium research: Progress and way ahead. PeerJ 2020; 8:e9824. [PMID: 32974094 PMCID: PMC7486827 DOI: 10.7717/peerj.9824] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 08/05/2020] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND The genus Allium (Family: Amaryllidaceae) is an economically important group of crops cultivated worldwide for their use as a vegetable and spices. Alliums are also well known for their nutraceutical properties. Among alliums, onion, garlic, leek, and chives cultivated worldwide. Despite their substantial economic and medicinal importance, the genome sequence of any of the Allium is not available, probably due to their large genome sizes. Recently evolved omics technologies are highly efficient and robust in elucidating molecular mechanisms of several complex life processes in plants. Omics technologies, such as genomics, transcriptomics, proteomics, metabolomics, metagenomics, etc. have the potential to open new avenues in research and improvement of allium crops where genome sequence information is limited. A significant amount of data has been generated using these technologies for various Allium species; it will help in understanding the key traits in Allium crops such as flowering, bulb development, flavonoid biosynthesis, male sterility and stress tolerance at molecular and metabolite level. This information will ultimately assist us in speeding up the breeding in Allium crops. METHOD In the present review, major omics approaches, and their progress, as well as potential applications in Allium crops, could be discussed in detail. RESULTS Here, we have discussed the recent progress made in Allium research using omics technologies such as genomics, transcriptomics, micro RNAs, proteomics, metabolomics, and metagenomics. These omics interventions have been used in alliums for marker discovery, the study of the biotic and abiotic stress response, male sterility, organ development, flavonoid and bulb color, micro RNA discovery, and microbiome associated with Allium crops. Further, we also emphasized the integrated use of these omics platforms for a better understanding of the complex molecular mechanisms to speed up the breeding programs for better cultivars. CONCLUSION All the information and literature provided in the present review throws light on the progress and potential of omics platforms in the research of Allium crops. We also mentioned a few research areas in Allium crops that need to be explored using omics technologies to get more insight. Overall, alliums are an under-studied group of plants, and thus, there is tremendous scope and need for research in Allium species.
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Affiliation(s)
- Kiran Khandagale
- Department of Botany, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Ram Krishna
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar, India
| | - Praveen Roylawar
- Department of Botany, S. N. Arts, D. J. M. Commerce and B. N. S. Science College, Sangamner, India
| | - Avinash B. Ade
- Department of Botany, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Ashwini Benke
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar, India
| | - Bharat Shinde
- Vidya Pratishthans’s Arts Science and commerce college, Baramati, India
| | - Major Singh
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar, India
| | | | - Ashutosh Rai
- Crop Improvement, ICAR-Indian Institute of Vegetable Research, Varanasi, India
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Construction of an Onion ( Allium cepa L.) Genetic Linkage Map using Genotyping-by-Sequencing Analysis with a Reference Gene Set and Identification of QTLs Controlling Anthocyanin Synthesis and Content. PLANTS 2020; 9:plants9050616. [PMID: 32408580 PMCID: PMC7285762 DOI: 10.3390/plants9050616] [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] [Received: 04/24/2020] [Revised: 05/07/2020] [Accepted: 05/11/2020] [Indexed: 02/01/2023]
Abstract
Anthocyanins, the pigmented flavonoids responsible for red and blue colors in horticultural products, promote human health by preventing cancers and lowering the risk of cardiovascular disease. Red onions contain several cyanidin- and peonidin-based anthocyanins. In this study, we constructed a single-nucleotide polymorphism (SNP)-based genetic linkage map in an F2 segregating population derived from a cross between the inbred line ‘SP3B’ (yellow bulb) and the doubled haploid line ‘H6′ (red bulb) to identify quantitative trait loci (QTLs) for total anthocyanin content of onion bulbs using a genotyping-by-sequencing (GBS) analysis based on a reference gene set. A total of 101.9 Gbp of raw sequences were generated using an Illumina HiSeq 2500 system and a total of 1625 SNP loci were identified with the criteria of three minimum depths, lower than 30% missing rate, and more than 5% minor allele frequency. As a result, an onion genetic linkage map consisting of 319 GBS-based SNP loci and 34 high-resolution melting (HRM) markers was constructed with eight linkage groups and a total genetic distance of 881.4 cM. In addition, the linkage groups were assigned to corresponding chromosomes by comparison with the reference genetic map OH1×5225 through marker development based on common transcripts. The analysis revealed one major QTL, qAS7.1, for anthocyanin synthesis and two significant QTLs, qAC4.1 and qAC4.2, for anthocyanin content. The QTL qAS7.1, located on chromosome 7 with a phenotypic variation of 87.61%, may be a dihydroflavonol 4-reductase (DFR) gene that determines whether the bulb color is red or yellow. The QTLs qAC4.1 and qAC4.2 are separately positioned on chromosome 4 with R2 values of 19.43% and 26.28%, respectively. This map and QTL information will contribute to marker development and breeding for high anthocyanin content in bulb onion.
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Taylor A, Teakle GR, Walley PG, Finch-Savage WE, Jackson AC, Jones JE, Hand P, Thomas B, Havey MJ, Pink DAC, Clarkson JP. Assembly and characterisation of a unique onion diversity set identifies resistance to Fusarium basal rot and improved seedling vigour. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:3245-3264. [PMID: 31520085 PMCID: PMC6820603 DOI: 10.1007/s00122-019-03422-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 09/05/2019] [Indexed: 05/28/2023]
Abstract
KEY MESSAGE A unique, global onion diversity set was assembled, genotyped and phenotyped for beneficial traits. Accessions with strong basal rot resistance and increased seedling vigour were identified along with associated markers. Conserving biodiversity is critical for safeguarding future crop production. Onion (Allium cepa L.) is a globally important crop with a very large (16 Gb per 1C) genome which has not been sequenced. While onions are self-fertile, they suffer from severe inbreeding depression and as such are highly heterozygous as a result of out-crossing. Bulb formation is driven by daylength, and accessions are adapted to the local photoperiod. Onion seed is often directly sown in the field, and hence seedling establishment is a critical trait for production. Furthermore, onion yield losses regularly occur worldwide due to Fusarium basal rot caused by Fusarium oxysporum f. sp. cepae. A globally relevant onion diversity set, consisting of 10 half-sib families for each of 95 accessions, was assembled and genotyping carried out using 892 SNP markers. A moderate level of heterozygosity (30-35%) was observed, reflecting the outbreeding nature of the crop. Using inferred phylogenies, population structure and principal component analyses, most accessions grouped according to local daylength. A high level of intra-accession diversity was observed, but this was less than inter-accession diversity. Accessions with strong basal rot resistance and increased seedling vigour were identified along with associated markers, confirming the utility of the diversity set for discovering beneficial traits. The onion diversity set and associated trait data therefore provide a valuable resource for future germplasm selection and onion breeding.
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Affiliation(s)
- Andrew Taylor
- Warwick Crop Centre, School of Life Sciences, University of Warwick, Wellesbourne Campus, Wellesbourne, Warwick, CV35 9EF, UK.
| | - Graham R Teakle
- Warwick Crop Centre, School of Life Sciences, University of Warwick, Wellesbourne Campus, Wellesbourne, Warwick, CV35 9EF, UK
| | - Peter G Walley
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 3BX, UK
| | - William E Finch-Savage
- Warwick Crop Centre, School of Life Sciences, University of Warwick, Wellesbourne Campus, Wellesbourne, Warwick, CV35 9EF, UK
| | - Alison C Jackson
- Warwick Crop Centre, School of Life Sciences, University of Warwick, Wellesbourne Campus, Wellesbourne, Warwick, CV35 9EF, UK
| | - Julie E Jones
- Warwick Crop Centre, School of Life Sciences, University of Warwick, Wellesbourne Campus, Wellesbourne, Warwick, CV35 9EF, UK
| | - Paul Hand
- Crop and Environment Sciences, Harper Adams University, Newport, T10 8NB, UK
| | - Brian Thomas
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Michael J Havey
- USDA-ARS, Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, WI, 53706, USA
| | - David A C Pink
- Crop and Environment Sciences, Harper Adams University, Newport, T10 8NB, UK
| | - John P Clarkson
- Warwick Crop Centre, School of Life Sciences, University of Warwick, Wellesbourne Campus, Wellesbourne, Warwick, CV35 9EF, UK
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Comparative Tyramide-FISH mapping of the genes controlling flavor and bulb color in Allium species revealed an altered gene order. Sci Rep 2019; 9:12007. [PMID: 31427665 PMCID: PMC6700127 DOI: 10.1038/s41598-019-48564-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 08/07/2019] [Indexed: 01/29/2023] Open
Abstract
Evolutionarily related species often share a common order of genes along homeologous chromosomes. Here we report the collinearity disruption of genes located on homeologous chromosome 4 in Allium species. Ultra-sensitive fluorescence in situ hybridization with tyramide signal amplification (tyr-FISH) allowed the visualization of the alliinase multigene family, chalcon synthase gene and EST markers on Allium cepa and Allium fistulosum chromosomes. In A. cepa, bulb alliinase, root alliinase (ALL1) and chalcon synthase (CHS-B) genes were located in the long arm but EST markers (API18 and ACM082) were located in the short arm. In A. fistulosum, all the visualized genes and markers were located in the short arm. Moreover, root alliinase genes (ALL1 and AOB249) showed contrast patterns in number of loci. We suppose that the altered order of the genes/markers is the result of a large pericentric inversion. To get insight into the evolution of the chromosome rearrangement, we mapped the bulb alliinase gene in phylogenetically close and distant species. In the taxonomic clade including A. fistulosum, A. altaicum, A. oschaninii and A. pskemense and in phylogenetically distant species A. roylei and A. nutans, the bulb alliinase gene was located on the short arm of chromosome 4 while, in A. cepa and A. schoenoprasum, the bulb alliinase gene was located on the long arm of chromosome 4. These results have encouraging implications for the further tracing of inverted regions in meiosis of interspecific hybrids and studding chromosome evolution. Also, this finding may have a practical benefit as closely related species are actively used for improving onion crop stock.
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McCallum J, Laing W, Bulley S, Thomson S, Catanach A, Shaw M, Knaebel M, Tahir J, Deroles S, Timmerman-Vaughan G, Crowhurst R, Hilario E, Chisnall M, Lee R, Macknight R, Seal A. Molecular Characterisation of a Supergene Conditioning Super-High Vitamin C in Kiwifruit Hybrids. PLANTS (BASEL, SWITZERLAND) 2019; 8:E237. [PMID: 31336644 PMCID: PMC6681377 DOI: 10.3390/plants8070237] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/15/2019] [Accepted: 07/16/2019] [Indexed: 12/20/2022]
Abstract
During analysis of kiwifruit derived from hybrids between the high vitamin C (ascorbic acid; AsA) species Actinidia eriantha and A. chinensis, we observed bimodal segregation of fruit AsA concentration suggesting major gene segregation. To test this hypothesis, we performed whole-genome sequencing on pools of hybrid genotypes with either high or low AsA fruit. Pool-GWAS (genome-wide association study) revealed a single Quantitative Trait Locus (QTL) spanning more than 5 Mbp on chromosome 26, which we denote as qAsA26.1. A co-dominant PCR marker was used to validate this association in four diploid (A. chinensis × A. eriantha) × A. chinensis backcross families, showing that the A. eriantha allele at this locus increases fruit AsA levels by 250 mg/100 g fresh weight. Inspection of genome composition and recombination in other A. chinensis genetic maps confirmed that the qAsA26.1 region bears hallmarks of suppressed recombination. The molecular fingerprint of this locus was examined in leaves of backcross validation families by RNA sequencing (RNASEQ). This confirmed strong allelic expression bias across this region as well as differential expression of transcripts on other chromosomes. This evidence suggests that the region harbouring qAsA26.1 constitutes a supergene, which may condition multiple pleiotropic effects on metabolism.
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Affiliation(s)
- John McCallum
- New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited, Private Bag 4704, Christchurch 8140, New Zealand.
- Biochemistry Department, University of Otago, Dunedin 9054, New Zealand.
| | - William Laing
- New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - Sean Bulley
- New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - Susan Thomson
- New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited, Private Bag 4704, Christchurch 8140, New Zealand
| | - Andrew Catanach
- New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited, Private Bag 4704, Christchurch 8140, New Zealand
| | - Martin Shaw
- New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited, Private Bag 4704, Christchurch 8140, New Zealand
| | - Mareike Knaebel
- New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - Jibran Tahir
- New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - Simon Deroles
- New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - Gail Timmerman-Vaughan
- New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited, Private Bag 4704, Christchurch 8140, New Zealand
| | - Ross Crowhurst
- New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
| | - Elena Hilario
- New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
| | - Matthew Chisnall
- Biochemistry Department, University of Otago, Dunedin 9054, New Zealand
| | - Robyn Lee
- Biochemistry Department, University of Otago, Dunedin 9054, New Zealand
| | - Richard Macknight
- Biochemistry Department, University of Otago, Dunedin 9054, New Zealand
| | - Alan Seal
- New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited, 412 No 1 Road, RD 2 Te Puke 3182, New Zealand
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Schwinn KE, Ngo H, Kenel F, Brummell DA, Albert NW, McCallum JA, Pither-Joyce M, Crowhurst RN, Eady C, Davies KM. The Onion ( Allium cepa L.) R2R3-MYB Gene MYB1 Regulates Anthocyanin Biosynthesis. FRONTIERS IN PLANT SCIENCE 2016; 7:1865. [PMID: 28018399 PMCID: PMC5146992 DOI: 10.3389/fpls.2016.01865] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 11/25/2016] [Indexed: 05/18/2023]
Abstract
Bulb color is an important consumer trait for onion (Allium cepa L., Allioideae, Asparagales). The bulbs accumulate a range of flavonoid compounds, including anthocyanins (red), flavonols (pale yellow), and chalcones (bright yellow). Flavonoid regulation is poorly characterized in onion and in other plants belonging to the Asparagales, despite being a major plant order containing many important crop and ornamental species. R2R3-MYB transcription factors associated with the regulation of distinct branches of the flavonoid pathway were isolated from onion. These belonged to sub-groups (SGs) that commonly activate anthocyanin (SG6, MYB1) or flavonol (SG7, MYB29) production, or repress phenylpropanoid/flavonoid synthesis (SG4, MYB4, MYB5). MYB1 was demonstrated to be a positive regulator of anthocyanin biosynthesis by the induction of anthocyanin production in onion tissue when transiently overexpressed and by reduction of pigmentation when transiently repressed via RNAi. Furthermore, ectopic red pigmentation was observed in garlic (Allium sativum L.) plants stably transformed with a construct for co-overexpression of MYB1 and a bHLH partner. MYB1 also was able to complement the acyanic petal phenotype of a defined R2R3-MYB anthocyanin mutant in Antirrhinum majus of the asterid clade of eudicots. The availability of sequence information for flavonoid-related MYBs from onion enabled phylogenetic groupings to be determined across monocotyledonous and dicotyledonous species, including the identification of characteristic amino acid motifs. This analysis suggests that divergent evolution of the R2R3-MYB family has occurred between Poaceae/Orchidaceae and Allioideae species. The DNA sequences identified will be valuable for future analysis of classical flavonoid genetic loci in Allium crops and will assist the breeding of these important crop species.
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Affiliation(s)
- Kathy E. Schwinn
- The New Zealand Institute for Plant & Food Research LimitedPalmerston North, New Zealand
| | - Hanh Ngo
- The New Zealand Institute for Plant & Food Research LimitedPalmerston North, New Zealand
| | - Fernand Kenel
- The New Zealand Institute for Plant & Food Research LimitedChristchurch, New Zealand
| | - David A. Brummell
- The New Zealand Institute for Plant & Food Research LimitedPalmerston North, New Zealand
| | - Nick W. Albert
- The New Zealand Institute for Plant & Food Research LimitedPalmerston North, New Zealand
| | - John A. McCallum
- The New Zealand Institute for Plant & Food Research LimitedChristchurch, New Zealand
| | - Meeghan Pither-Joyce
- The New Zealand Institute for Plant & Food Research LimitedChristchurch, New Zealand
| | - Ross N. Crowhurst
- The New Zealand Institute for Plant & Food Research LimitedAuckland, New Zealand
| | - Colin Eady
- The New Zealand Institute for Plant & Food Research LimitedChristchurch, New Zealand
| | - Kevin M. Davies
- The New Zealand Institute for Plant & Food Research LimitedPalmerston North, New Zealand
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11
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Khosa JS, Lee R, Bräuning S, Lord J, Pither-Joyce M, McCallum J, Macknight RC. Doubled Haploid 'CUDH2107' as a Reference for Bulb Onion (Allium cepa L.) Research: Development of a Transcriptome Catalogue and Identification of Transcripts Associated with Male Fertility. PLoS One 2016; 11:e0166568. [PMID: 27861615 PMCID: PMC5115759 DOI: 10.1371/journal.pone.0166568] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 10/31/2016] [Indexed: 11/21/2022] Open
Abstract
Researchers working on model plants have derived great benefit from developing genomic and genetic resources using ‘reference’ genotypes. Onion has a large and highly heterozygous genome making the sharing of germplasm and analysis of sequencing data complicated. To simplify the discovery and analysis of genes underlying important onion traits, we are promoting the use of the homozygous double haploid line ‘CUDH2107’ by the onion research community. In the present investigation, we performed transcriptome sequencing on vegetative and reproductive tissues of CUDH2107 to develop a multi-organ reference transcriptome catalogue. A total of 396 million 100 base pair paired reads was assembled using the Trinity pipeline, resulting in 271,665 transcript contigs. This dataset was analysed for gene ontology and transcripts were classified on the basis of putative biological processes, molecular function and cellular localization. Significant differences were observed in transcript expression profiles between different tissues. To demonstrate the utility of our CUDH2107 transcriptome catalogue for understanding the genetic and molecular basis of various traits, we identified orthologues of rice genes involved in male fertility and flower development. These genes provide an excellent starting point for studying the molecular regulation, and the engineering of reproductive traits.
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Affiliation(s)
| | - Robyn Lee
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Sophia Bräuning
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
- Department of Botany, University of Otago, Dunedin, New Zealand
| | - Janice Lord
- Department of Botany, University of Otago, Dunedin, New Zealand
| | | | - John McCallum
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
- New Zealand Institute for Plant & Food Research, Lincoln, New Zealand
| | - Richard C. Macknight
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
- New Zealand Institute for Plant & Food Research, Lincoln, New Zealand
- * E-mail:
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12
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Scholten OE, van Kaauwen MP, Shahin A, Hendrickx PM, Keizer LP, Burger K, van Heusden AW, van der Linden CG, Vosman B. SNP-markers in Allium species to facilitate introgression breeding in onion. BMC PLANT BIOLOGY 2016; 16:187. [PMID: 27576474 PMCID: PMC5006257 DOI: 10.1186/s12870-016-0879-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 08/18/2016] [Indexed: 05/05/2023]
Abstract
BACKGROUND Within onion, Allium cepa L., the availability of disease resistance is limited. The identification of sources of resistance in related species, such as Allium roylei and Allium fistulosum, was a first step towards the improvement of onion cultivars by breeding. SNP markers linked to resistance and polymorphic between these related species and onion cultivars are a valuable tool to efficiently introgress disease resistance genes. In this paper we describe the identification and validation of SNP markers valuable for onion breeding. RESULTS Transcriptome sequencing resulted in 192 million RNA seq reads from the interspecific F1 hybrid between A. roylei and A. fistulosum (RF) and nine onion cultivars. After assembly, reliable SNPs were discovered in about 36 % of the contigs. For genotyping of the interspecific three-way cross population, derived from a cross between an onion cultivar and the RF (CCxRF), 1100 SNPs that are polymorphic in RF and monomorphic in the onion cultivars (RF SNPs) were selected for the development of KASP assays. A molecular linkage map based on 667 RF-SNP markers was constructed for CCxRF. In addition, KASP assays were developed for 1600 onion-SNPs (SNPs polymorphic among onion cultivars). A second linkage map was constructed for an F2 of onion x A. roylei (F2(CxR)) that consisted of 182 onion-SNPs and 119 RF-SNPs, and 76 previously mapped markers. Markers co-segregating in both the F2(CxR) and the CCxRF population were used to assign the linkage groups of RF to onion chromosomes. To validate usefulness of these SNP markers, QTL mapping was applied in the CCxRF population that segregates for resistance to Botrytis squamosa and resulted in a QTL for resistance on chromosome 6 of A. roylei. CONCLUSIONS Our research has more than doubled the publicly available marker sequences of expressed onion genes and two onion-related species. It resulted in a detailed genetic map for the interspecific CCxRF population. This is the first paper that reports the detection of a QTL for resistance to B. squamosa in A. roylei.
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Affiliation(s)
- Olga E. Scholten
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, PO Box 386, Wageningen, 6700 AJ The Netherlands
| | - Martijn P.W. van Kaauwen
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, PO Box 386, Wageningen, 6700 AJ The Netherlands
| | - Arwa Shahin
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, PO Box 386, Wageningen, 6700 AJ The Netherlands
| | - Patrick M. Hendrickx
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, PO Box 386, Wageningen, 6700 AJ The Netherlands
| | - L.C. Paul Keizer
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, PO Box 386, Wageningen, 6700 AJ The Netherlands
| | - Karin Burger
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, PO Box 386, Wageningen, 6700 AJ The Netherlands
| | - Adriaan W. van Heusden
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, PO Box 386, Wageningen, 6700 AJ The Netherlands
| | - C. Gerard van der Linden
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, PO Box 386, Wageningen, 6700 AJ The Netherlands
| | - Ben Vosman
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, PO Box 386, Wageningen, 6700 AJ The Netherlands
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13
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Schlick-Steiner BC, Arthofer W, Moder K, Steiner FM. Recent insertion/deletion (reINDEL) mutations: increasing awareness to boost molecular-based research in ecology and evolution. Ecol Evol 2014; 5:24-35. [PMID: 25628861 PMCID: PMC4298431 DOI: 10.1002/ece3.1330] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 10/27/2014] [Accepted: 10/30/2014] [Indexed: 01/18/2023] Open
Abstract
Today, the comparative analysis of DNA molecules mainly uses information inferred from nucleotide substitutions. Insertion/deletion (INDEL) mutations, in contrast, are largely considered uninformative and discarded, due to our lacking knowledge on their evolution. However, including rather than discarding INDELs would be relevant to any research area in ecology and evolution that uses molecular data. As a practical approach to better understanding INDEL evolution in general, we propose the study of recent INDEL (reINDEL) mutations – mutations where both ancestral and derived state are seen in the sample. The precondition for reINDEL identification is knowledge about the pedigree of the individuals sampled. Sound reINDEL knowledge will allow the improved modeling needed for including INDELs in the downstream analysis of molecular data. Both microsatellites, currently still the predominant marker system in the analysis of populations, and sequences generated by next-generation sequencing, a promising and rapidly developing range of technologies, offer the opportunity for reINDEL identification. However, a 2013 sample of animal microsatellite studies contained unexpectedly few reINDELs identified. As most likely explanation, we hypothesize that reINDELs are underreported rather than absent and that this underreporting stems from common reINDEL unawareness. If our hypothesis applies, increased reINDEL awareness should allow gathering data rapidly. We recommend the routine reporting of either the absence or presence of reINDELs together with standardized key information on the nature of mutations when they are detected and the use of the keyword “reINDEL” to increase visibility in both instances of successful and unsuccessful search.
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Affiliation(s)
- Birgit C Schlick-Steiner
- Molecular Ecology Group, Institute of Ecology, University of Innsbruck Technikerstr. 25, 6020, Innsbruck, Austria
| | - Wolfgang Arthofer
- Molecular Ecology Group, Institute of Ecology, University of Innsbruck Technikerstr. 25, 6020, Innsbruck, Austria
| | - Karl Moder
- Institute of Applied Statistics and Computing, University of Natural Resources and Life Sciences Peter Jordan-Str. 82, 1180, Vienna, Austria
| | - Florian M Steiner
- Molecular Ecology Group, Institute of Ecology, University of Innsbruck Technikerstr. 25, 6020, Innsbruck, Austria
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14
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FLOWERING LOCUS T genes control onion bulb formation and flowering. Nat Commun 2014; 4:2884. [PMID: 24300952 DOI: 10.1038/ncomms3884] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 11/06/2013] [Indexed: 12/20/2022] Open
Abstract
Onion (Allium cepa L.) is a biennial crop that in temperate regions is planted in the spring and, after a juvenile stage, forms a bulb in response to the lengthening photoperiod of late spring/summer. The bulb then overwinters and in the next season it flowers and sets seed. FLOWERING LOCUS T (FT) encodes a mobile signaling protein involved in regulating flowering, as well as other aspects of plant development. Here we show that in onions, different FT genes regulate flowering and bulb formation. Flowering is promoted by vernalization and correlates with the upregulation of AcFT2, whereas bulb formation is regulated by two antagonistic FT-like genes. AcFT1 promotes bulb formation, while AcFT4 prevents AcFT1 upregulation and inhibits bulbing in transgenic onions. Long-day photoperiods lead to the downregulation of AcFT4 and the upregulation of AcFT1, and this promotes bulbing. The observation that FT proteins can repress and promote different developmental transitions highlights the evolutionary versatility of FT.
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15
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Baldwin S, Revanna R, Pither-Joyce M, Shaw M, Wright K, Thomson S, Moya L, Lee R, Macknight R, McCallum J. Genetic analyses of bolting in bulb onion (Allium cepa L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:535-547. [PMID: 24247236 DOI: 10.1007/s00122-013-2232-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 10/31/2013] [Indexed: 06/02/2023]
Abstract
We present the first evidence for a QTL conditioning an adaptive trait in bulb onion, and the first linkage and population genetics analyses of candidate genes involved in photoperiod and vernalization physiology. Economic production of bulb onion (Allium cepa L.) requires adaptation to photoperiod and temperature such that a bulb is formed in the first year and a flowering umbel in the second. 'Bolting', or premature flowering before bulb maturation, is an undesirable trait strongly selected against by breeders during adaptation of germplasm. To identify genome regions associated with adaptive traits we conducted linkage mapping and population genetic analyses of candidate genes, and QTL analysis of bolting using a low-density linkage map. We performed tagged amplicon sequencing of ten candidate genes, including the FT-like gene family, in eight diverse populations to identify polymorphisms and seek evidence of differentiation. Low nucleotide diversity and negative estimates of Tajima's D were observed for most genes, consistent with purifying selection. Significant population differentiation was observed only in AcFT2 and AcSOC1. Selective genotyping in a large 'Nasik Red × CUDH2150' F2 family revealed genome regions on chromosomes 1, 3 and 6 associated (LOD > 3) with bolting. Validation genotyping of two F2 families grown in two environments confirmed that a QTL on chromosome 1, which we designate AcBlt1, consistently conditions bolting susceptibility in this cross. The chromosome 3 region, which coincides with a functionally characterised acid invertase, was not associated with bolting in other environments, but showed significant association with bulb sucrose content in this and other mapping pedigrees. These putative QTL and candidate genes were placed on the onion map, enabling future comparative studies of adaptive traits.
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Affiliation(s)
- Samantha Baldwin
- New Zealand Institute for Plant and Food Research, Private Bag, 4704, Christchurch, New Zealand
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16
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Duangjit J, Bohanec B, Chan AP, Town CD, Havey MJ. Transcriptome sequencing to produce SNP-based genetic maps of onion. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:2093-101. [PMID: 23689743 DOI: 10.1007/s00122-013-2121-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 05/08/2013] [Indexed: 05/10/2023]
Abstract
We used the Roche-454 platform to sequence from normalized cDNA libraries from each of two inbred lines of onion (OH1 and 5225). From approximately 1.6 million reads from each inbred, 27,065 and 33,254 cDNA contigs were assembled from OH1 and 5225, respectively. In total, 3,364 well supported single nucleotide polymorphisms (SNPs) on 1,716 cDNA contigs were identified between these two inbreds. One SNP on each of 1,256 contigs was randomly selected for genotyping. OH1 and 5225 were crossed and 182 gynogenic haploids extracted from hybrid plants were used for SNP mapping. A total of 597 SNPs segregated in the OH1 × 5225 haploid family and a genetic map of ten linkage groups (LOD ≥8) was constructed. Three hundred and thirty-nine of the newly identified SNPs were also mapped using a previously developed segregating family from BYG15-23 × AC43, and 223 common SNPs were used to join the two maps. Because these new SNPs are in expressed regions of the genome and commonly occur among onion germplasms, they will be useful for genetic mapping, gene tagging, marker-aided selection, quality control of seed lots, and fingerprinting of cultivars.
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Affiliation(s)
- J Duangjit
- Department of Horticulture, University of Wisconsin, Madison, WI 53706, USA
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