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Zhang R, Wang YH, Jin JJ, Stull GW, Bruneau A, Cardoso D, De Queiroz LP, Moore MJ, Zhang SD, Chen SY, Wang J, Li DZ, Yi TS. Exploration of Plastid Phylogenomic Conflict Yields New Insights into the Deep Relationships of Leguminosae. Syst Biol 2020; 69:613-622. [PMID: 32065640 PMCID: PMC7302050 DOI: 10.1093/sysbio/syaa013] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 02/02/2020] [Accepted: 02/07/2020] [Indexed: 01/02/2023] Open
Abstract
Phylogenomic analyses have helped resolve many recalcitrant relationships in the angiosperm tree of life, yet phylogenetic resolution of the backbone of the Leguminosae, one of the largest and most economically and ecologically important families, remains poor due to generally limited molecular data and incomplete taxon sampling of previous studies. Here, we resolve many of the Leguminosae's thorniest nodes through comprehensive analysis of plastome-scale data using multiple modified coding and noncoding data sets of 187 species representing almost all major clades of the family. Additionally, we thoroughly characterize conflicting phylogenomic signal across the plastome in light of the family's complex history of plastome evolution. Most analyses produced largely congruent topologies with strong statistical support and provided strong support for resolution of some long-controversial deep relationships among the early diverging lineages of the subfamilies Caesalpinioideae and Papilionoideae. The robust phylogenetic backbone reconstructed in this study establishes a framework for future studies on legume classification, evolution, and diversification. However, conflicting phylogenetic signal was detected and quantified at several key nodes that prevent the confident resolution of these nodes using plastome data alone. [Leguminosae; maximum likelihood; phylogenetic conflict; plastome; recalcitrant relationships; stochasticity; systematic error.].
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Affiliation(s)
- Rong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Yin-Huan Wang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- School of Primary Education, Chongqing Normal University, Chongqing 400700, China
| | - Jian-Jun Jin
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Gregory W Stull
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Department of Botany, Smithsonian Institution, Washington, DC 20013, USA
| | - Anne Bruneau
- Institut de recherche en biologie végétale & Département de Sciences biologiques, Université de Montréal, Montréal, QC H1X 2B2, Canada
| | - Domingos Cardoso
- Diversity, Biogeography and Systematics Laboratory, Instituto de Biologia, Universidade Federal da Bahia, Rua Barão de Jeremoabo, s.n., Ondina, 40170-115 Salvador, Bahia, Brazil
| | - Luciano Paganucci De Queiroz
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Av. Transnordestina, s/n, Novo Horizonte, 44036-900 Feira de Santana, Bahia, Brazil
| | - Michael J Moore
- Department of Biology, Oberlin College, Oberlin, OH 44074, USA
| | - Shu-Dong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Si-Yun Chen
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Jian Wang
- Queensland Herbarium, Department of Environment and Science, Brisbane Botanic Gardens, Mt Coot-tha Road, Brisbane 4066, Australia
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
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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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Romanov D, Divashuk M, Havey MJ, Khrustaleva L. Tyramide-FISH mapping of single genes for development of an integrated recombination and cytogenetic map of chromosome 5 of Allium cepa. Genome 2015; 58:111-9. [PMID: 26158384 DOI: 10.1139/gen-2015-0019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Chromosome 5 of onion carries major quantitative trait loci (QTL) that control dry-matter content, pungency and storability of bulbs, amounts and types of epicuticular waxes, and resistances to abiotic factors, all of which are of interest to breeders. SNPs, SSRs, and RFLPs in expressed regions of the onion genome have been genetically mapped, and we used these clones and sequences from the NCBI database to develop DNA probes for in situ hybridization to integrate the genetic and physical maps of onion chromosome 5. We produced genomic amplicons from expressed regions of the onion genome that carried both exons and introns in order to increase the hybridization specificity of the probes and to enlarge the target DNA sizes. Tyramide-FISH technique was used to increase the detection sensitivity of relatively short target DNA regions, which range from 950 to 2100 bp. Through the integration of genetic and chromosomal maps, we were able to estimate the distribution of recombination events along onion chromosome 5. We demonstrated the efficiency of chromosomal in situ mapping of exon-intron genomic clones for the extremely large genome of onion.
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Affiliation(s)
- Dmitry Romanov
- a Center of Molecular Biotechnology, Russian State Agrarian University - MTAA, Moscow 127550, Russia
| | - Mikhail Divashuk
- a Center of Molecular Biotechnology, Russian State Agrarian University - MTAA, Moscow 127550, Russia
| | - Michael J Havey
- b USDA-ARS and Department of Horticulture, University of Wisconsin, Madison, WI 53706 USA
| | - Ludmila Khrustaleva
- a Center of Molecular Biotechnology, Russian State Agrarian University - MTAA, Moscow 127550, Russia
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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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Kumari M, Clarke HJ, des Francs-Small CC, Small I, Khan TN, Siddique KHM. Albinism does not correlate with biparental inheritance of plastid DNA in interspecific hybrids in Cicer species. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2011; 180:628-633. [PMID: 21421411 DOI: 10.1016/j.plantsci.2011.01.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2010] [Revised: 12/23/2010] [Accepted: 01/05/2011] [Indexed: 05/30/2023]
Abstract
Cultivated chickpea (Cicer arietinum) was crossed with its wild relatives from the genus Cicer to transfer favorable genes from the wider gene pool into the cultivar. Post-hybridization barriers led to yellowing and subsequent senescence from as early as 5 days after fertilization, however, the ovules of hybrid embryos could be rescued in vitro. Hybrids were classified as green, partially green or albino. The hybrid status of regenerated plantlets in vitro was confirmed by amplification of nuclear DNA markers. To check whether chloroplast development correlated with plastid DNA inheritance in these crosses, primers were designed using conserved plastid gene sequences from wild and cultivated species. All three possible plastid inheritance patterns were observed: paternal, maternal and biparental. This is the first report of biparental inheritance of plastid DNA in Cicer. No correlation was observed between parental origin of the plastid genome and degree of albinism, indicating that chloroplast development in hybrid genotypes was mostly influenced by nuclear factors.
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Affiliation(s)
- Maya Kumari
- Centre for Legumes in Mediterranean Agriculture, Faculty of Natural and Agricultural Sciences, The University of Western Australia, Crawley, WA 6009, Australia
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Korpelainen H. The evolutionary processes of mitochondrial and chloroplast genomes differ from those of nuclear genomes. Naturwissenschaften 2004; 91:505-18. [PMID: 15452701 DOI: 10.1007/s00114-004-0571-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
This paper first introduces our present knowledge of the origin of mitochondria and chloroplasts, and the organization and inheritance patterns of their genomes, and then carries on to review the evolutionary processes influencing mitochondrial and chloroplast genomes. The differences in evolutionary phenomena between the nuclear and cytoplasmic genomes are highlighted. It is emphasized that varying inheritance patterns and copy numbers among different types of genomes, and the potential advantage achieved through the transfer of many cytoplasmic genes to the nucleus, have important implications for the evolution of nuclear, mitochondrial and chloroplast genomes. Cytoplasmic genes transferred to the nucleus have joined the more strictly controlled genetic system of the nuclear genome, including also sexual recombination, while genes retained within the cytoplasmic organelles can be involved in selection and drift processes both within and among individuals. Within-individual processes can be either intra- or intercellular. In the case of heteroplasmy, which is attributed to mutations or biparental inheritance, within-individual selection on cytoplasmic DNA may provide a mechanism by which the organism can adapt rapidly. The inheritance of cytoplasmic genomes is not universally maternal. The presence of a range of inheritance patterns indicates that different strategies have been adopted by different organisms. On the other hand, the variability occasionally observed in the inheritance mechanisms of cytoplasmic genomes reduces heritability and increases environmental components in phenotypic features and, consequently, decreases the potential for adaptive evolution.
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Affiliation(s)
- Helena Korpelainen
- Department of Applied Biology, University of Helsinki, PO Box 27, 00014, Helsinki, Finland.
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Havey MJ, Galmarini CR, Gökçe AF, Henson C. QTL affecting soluble carbohydrate concentrations in stored onion bulbs and their association with flavor and health-enhancing attributes. Genome 2004; 47:463-8. [PMID: 15190363 DOI: 10.1139/g04-005] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Onion bulbs accumulate fructans, a type of soluble carbohydrate associated with lower rates of colorectal cancers. Higher fructan concentrations in bulbs are correlated with higher pungency, longer dormancy, and greater onion-induced antiplatelet activity (OIAA). We analyzed replicated field trials of a segregating family for types and concentrations of soluble carbohydrates in onion bulbs 90 days after harvest. Means were adjusted using dry weight as the covariant to reveal highly significant (P < 0.001) differences among parents and families for glucose, fructose, sucrose, and the fructans 1-kestose, neokestose, and (6G,1)-nystose. Fructan concentrations showed significant (P < 0.05) phenotypic correlations with each other and with sucrose, pungency, and OIAA. These observations are consistent with the hypothesis that onion bulbs accumulating fructans take up or retain less water, concentrating both soluble carbohydrates and thiosulfinates responsible for pungency and OIAA. Interval mapping of family means from the covariant analyses revealed regions on linkage groups A and D significantly (LOD > 2.68) affecting soluble carbohydrate concentrations. The enzyme catalyzing the first step of fructan polymerization, 1-sucrose-sucrose fructosyltransferase (1-SST), mapped independently of these genomic regions. One region on linkage group D near an acid-invertase gene was significantly (LOD = 3.45) associated with sucrose concentrations. This study reveals that the accumulation of sucrose in stored onion bulbs may allow for the combination of sweeter flavor with significant OIAA.Key words: quantitative trait locus, fructans, thiosulfinates, reducing sugars.
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Affiliation(s)
- Michael J Havey
- Agricultural Research Service, USDA, Department of Horticulture, University of Wisconsin, Madison 53706, USA.
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