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Pilkington SM, Tahir J, Hilario E, Gardiner SE, Chagné D, Catanach A, McCallum J, Jesson L, Fraser LG, McNeilage MA, Deng C, Crowhurst RN, Datson PM, Zhang Q. Genetic and cytological analyses reveal the recombination landscape of a partially differentiated plant sex chromosome in kiwifruit. BMC Plant Biol 2019; 19:172. [PMID: 31039740 PMCID: PMC6492441 DOI: 10.1186/s12870-019-1766-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 04/08/2019] [Indexed: 05/10/2023]
Abstract
BACKGROUND Angiosperm sex chromosomes, where present, are generally recently evolved. The key step in initiating the development of sex chromosomes from autosomes is the establishment of a sex-determining locus within a region of non-recombination. To better understand early sex chromosome evolution, it is important to determine the process by which recombination is suppressed around the sex determining genes. We have used the dioecious angiosperm kiwifruit Actinidia chinensis var. chinensis, which has an active-Y sex chromosome system, to study recombination rates around the sex locus, to better understand key events in the development of sex chromosomes. RESULTS We have confirmed the sex-determining region (SDR) in A. chinensis var. chinensis, using a combination of high density genetic mapping and fluorescent in situ hybridisation (FISH) of Bacterial Artificial Chromosomes (BACs) linked to the sex markers onto pachytene chromosomes. The SDR is a subtelomeric non-recombining region adjacent to the nucleolar organiser region (NOR). A region of restricted recombination of around 6 Mbp in size in both male and female maps spans the SDR and covers around a third of chromosome 25. CONCLUSIONS As recombination is suppressed over a similar region between X chromosomes and between and X and Y chromosomes, we propose that recombination is suppressed in this region because of the proximity of the NOR and the centromere, with both the NOR and centromere suppressing recombination, and this predates suppressed recombination due to differences between X and Y chromosomes. Such regions of suppressed recombination in the genome provide an opportunity for the evolution of sex chromosomes, if a sex-determining locus develops there or translocates into this region.
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Affiliation(s)
- S. M. Pilkington
- The New Zealand Institute for Plant and Food Research Limited (PFR), Private Bag 92169, Auckland, 1142 New Zealand
| | - J. Tahir
- PFR, Private Bag 11600, Palmerston North, 4442 New Zealand
| | - E. Hilario
- The New Zealand Institute for Plant and Food Research Limited (PFR), Private Bag 92169, Auckland, 1142 New Zealand
| | - S. E. Gardiner
- PFR, Private Bag 11600, Palmerston North, 4442 New Zealand
| | - D. Chagné
- PFR, Private Bag 11600, Palmerston North, 4442 New Zealand
| | - A. Catanach
- PFR, Private Bag 4704, Christchurch, 8140 New Zealand
| | - J. McCallum
- PFR, Private Bag 4704, Christchurch, 8140 New Zealand
| | - L. Jesson
- PFR, Private Bag 1401, Havelock North, 4157 New Zealand
| | - L. G. Fraser
- The New Zealand Institute for Plant and Food Research Limited (PFR), Private Bag 92169, Auckland, 1142 New Zealand
| | - M. A. McNeilage
- The New Zealand Institute for Plant and Food Research Limited (PFR), Private Bag 92169, Auckland, 1142 New Zealand
| | - C. Deng
- The New Zealand Institute for Plant and Food Research Limited (PFR), Private Bag 92169, Auckland, 1142 New Zealand
| | - R. N. Crowhurst
- The New Zealand Institute for Plant and Food Research Limited (PFR), Private Bag 92169, Auckland, 1142 New Zealand
| | - P. M. Datson
- The New Zealand Institute for Plant and Food Research Limited (PFR), Private Bag 92169, Auckland, 1142 New Zealand
| | - Q. Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430074 China
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Guitton B, Kelner JJ, Celton JM, Sabau X, Renou JP, Chagné D, Costes E. Analysis of transcripts differentially expressed between fruited and deflowered 'Gala' adult trees: a contribution to biennial bearing understanding in apple. BMC Plant Biol 2016; 16:55. [PMID: 26924309 PMCID: PMC4770685 DOI: 10.1186/s12870-016-0739-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 02/17/2016] [Indexed: 05/20/2023]
Abstract
BACKGROUND The transition from vegetative to floral state in shoot apical meristems (SAM) is a key event in plant development and is of crucial importance for reproductive success. In perennial plants, this event is recurrent during tree life and subject to both within-tree and between-years heterogeneity. In the present study, our goal was to identify candidate processes involved in the repression or induction of flowering in apical buds of adult apple trees. RESULTS Genes differentially expressed (GDE) were examined between trees artificially set in either 'ON' or 'OFF' situation, and in which floral induction (FI) was shown to be inhibited or induced in most buds, respectively, using qRT-PCR and microarray analysis. From the period of FI through to flower differentiation, GDE belonged to four main biological processes (i) response to stimuli, including response to oxidative stress; (ii) cellular processes, (iii) cell wall biogenesis, and (iv) metabolic processes including carbohydrate biosynthesis and lipid metabolic process. Several key regulator genes, especially TEMPRANILLO (TEM), FLORAL TRANSITION AT MERISTEM (FTM1) and SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) were found differentially expressed. Moreover, homologs of SPL and Leucine-Rich Repeat proteins were present under QTL zones previously detected for biennial bearing. CONCLUSIONS This data set suggests that apical buds of 'ON' and 'OFF' trees were in different physiological states, resulting from different metabolic, hormonal and redox status which are likely to contribute to FI control in adult apple trees. Investigations on carbohydrate and hormonal fluxes from sources to SAM and on cell detoxification process are expected to further contribute to the identification of the underlying physiological mechanisms of FI in adult apple trees.
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Affiliation(s)
- B Guitton
- INRA, UMR AGAP, CIRAD-INRA-SupAgro, AFEF team (Architecture et Fonctionnement des Espèces Fruitières) TA 108/03, Avenue Agropolis, 34398, Montpellier, CEDEX 5, France.
- ICRISAT, Samanko station, BP320, Bamako, Mali.
- CIRAD, UMR AGAP, CIRAD-INRA-SupAgro, TA 108/03, Avenue Agropolis, 34398, Montpellier, CEDEX 5, France.
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Palmerston North, 4442, New Zealand.
| | - J J Kelner
- SupAgro, UMR AGAP, CIRAD-INRA-SupAgro, AFEF team (Architecture et Fonctionnement des Espèces Fruitières) TA 108/03, Avenue Agropolis, 34398, Montpellier, CEDEX 5, France.
| | - J M Celton
- INRA, UMR1345 IRHS, Institut de Recherche en Horticulture et Semences, AgroCampus-Ouest-INRA- QUASAV, Bretagne-Loire University, 49071, Beaucouzé, France.
| | - X Sabau
- CIRAD, UMR AGAP, CIRAD-INRA-SupAgro, TA 108/03, Avenue Agropolis, 34398, Montpellier, CEDEX 5, France.
| | - J P Renou
- INRA, UMR1345 IRHS, Institut de Recherche en Horticulture et Semences, AgroCampus-Ouest-INRA- QUASAV, Bretagne-Loire University, 49071, Beaucouzé, France.
| | - D Chagné
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Palmerston North, 4442, New Zealand.
| | - E Costes
- INRA, UMR AGAP, CIRAD-INRA-SupAgro, AFEF team (Architecture et Fonctionnement des Espèces Fruitières) TA 108/03, Avenue Agropolis, 34398, Montpellier, CEDEX 5, France.
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Bushakra JM, Krieger C, Deng D, Stephens MJ, Allan AC, Storey R, Symonds VV, Stevenson D, McGhie T, Chagné D, Buck EJ, Gardiner SE. QTL involved in the modification of cyanidin compounds in black and red raspberry fruit. Theor Appl Genet 2013; 126:847-65. [PMID: 23224381 DOI: 10.1007/s00122-012-2022-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 11/15/2012] [Indexed: 05/24/2023]
Abstract
Fruit from Rubus species are highly valued for their flavor and nutritive qualities. Anthocyanin content contributes to these qualities, and although many studies have been conducted to identify and quantify the major anthocyanin compounds from various Rubus species, the genetic control of the accumulation of these complex traits in Rubus is not yet well understood. The identification of the regions of the genome involved in the production of anthocyanins is an important first step in identifying the genes underlying their expression. In this study, ultra and high-performance liquid chromatography (UHPLC and HPLC) and two newly developed Rubus linkage maps were used to conduct QTL analyses to explore the presence of associations between concentrations of five anthocyanins in fruit and genotype. In total, 27 QTL were identified on the Rubus linkage maps, four of which are associated with molecular markers designed from transcription factors and three of which are associated with molecular markers designed from anthocyanin biosynthetic pathway candidate genes. The results of this study suggest that, while QTL for anthocyanin accumulation have been identified on six of seven Rubus linkage groups (RLG), the QTL on RLG2 and RLG7 may be very important for genetic control of cyanidin modification in Rubus.
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Affiliation(s)
- J M Bushakra
- The New Zealand Institute for Plant & Food Research Limited (PFR), Batchelar Road, Private Bag 11600, Palmerston North, 4442, New Zealand.
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Bushakra JM, Stephens MJ, Atmadjaja AN, Lewers KS, Symonds VV, Udall JA, Chagné D, Buck EJ, Gardiner SE. Construction of black (Rubus occidentalis) and red (R. idaeus) raspberry linkage maps and their comparison to the genomes of strawberry, apple, and peach. Theor Appl Genet 2012; 125:311-27. [PMID: 22398438 DOI: 10.1007/s00122-012-1835-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Accepted: 02/17/2012] [Indexed: 05/23/2023]
Abstract
The genus Rubus belongs to the Rosaceae and is comprised of 600-800 species distributed world-wide. To date, genetic maps of the genus consist largely of non-transferable markers such as amplified fragment length polymorphisms. An F(1) population developed from a cross between an advanced breeding selection of Rubus occidentalis (96395S1) and R. idaeus 'Latham' was used to construct a new genetic map consisting of DNA sequence-based markers. The genetic linkage maps presented here are constructed of 131 markers on at least one of the two parental maps. The majority of the markers are orthologous, including 14 Rosaceae conserved orthologous set markers, and 60 new gene-based markers developed for raspberry. Thirty-four published raspberry simple sequence repeat markers were used to align the new maps to published raspberry maps. The 96395S1 genetic map consists of six linkage groups (LG) and covers 309 cM with an average of 10 cM between markers; the 'Latham' genetic map consists of seven LG and covers 561 cM with an average of 5 cM between markers. We used BLAST analysis to align the orthologous sequences used to design primer pairs for Rubus genetic mapping with the genome sequences of Fragaria vesca 'Hawaii 4', Malus × domestica 'Golden Delicious', and Prunus 'Lovell'. The alignment of the orthologous markers designed here suggests that the genomes of Rubus and Fragaria have a high degree of synteny and that synteny decreases with phylogenetic distance. Our results give unprecedented insights into the genome evolution of raspberry from the putative ancestral genome of the single ancestor common to Rosaceae.
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Affiliation(s)
- J M Bushakra
- The New Zealand Institute for Plant & Food Research Limited, Batchelar Road, Private Bag 11600, Palmerston North 4442, New Zealand.
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Simpson RM, Newcomb RD, Gatehouse HS, Crowhurst RN, Chagné D, Gatehouse LN, Markwick NP, Beuning LL, Murray C, Marshall SD, Yauk YK, Nain B, Wang YY, Gleave AP, Christeller JT. Expressed sequence tags from the midgut of Epiphyas postvittana (Walker) (Lepidoptera: Tortricidae). Insect Mol Biol 2007; 16:675-690. [PMID: 18092997 DOI: 10.1111/j.1365-2583.2007.00763.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The midgut is a key tissue in insect science. Physiological roles include digestion and peritrophic membrane function, as well as being an important target for insecticides. We used an expressed sequence tag (EST) approach to identify candidate genes and gene families involved in these processes in the light brown apple moth, Epiphyas postvittana (Walker) (Lepidoptera: Tortricidae). Two cDNA libraries were constructed from dissected midgut of third to fifth instar larvae. Clustering analysis of 6416 expressed sequence tags produced 1178 tentative unique genes comprising 725 tentative contigs and 453 singletons. The sequences show similar codon usage to sequences from other lepidopterans, a Kozak consensus sequence similar to Drosophila and single nucleotide polymorphisms (SNPs) were detected at a frequency of 1.35/kb. The identity of the most common Interpro families correlates well with major known functions of the midgut. Phylogenetic analysis was conducted on representative sequences from selected multigene families. Gene families include a broad range of digestive proteases, lipases and carbohydrases that appear to have degradative capacity against the major food components found in leaves, the diet of these larvae; and carboxylesterases, glutathione-S-transferases and cytochrome P450 monooxygenases, potentially involved in xenobiotic degradation. Two of the larger multigene families, serine proteases and lipases, expressed a high proportion of genes that are likely to be catalytically inactive.
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Affiliation(s)
- R M Simpson
- Horticulture and Food Research Institute, Palmerston North, New Zealand
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Chagné D, Chaumeil P, Ramboer A, Collada C, Guevara A, Cervera MT, Vendramin GG, Garcia V, Frigerio JM, Echt C, Richardson T, Plomion C. Cross-species transferability and mapping of genomic and cDNA SSRs in pines. Theor Appl Genet 2004; 109:1204-14. [PMID: 15448894 DOI: 10.1007/s00122-004-1683-z] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2004] [Accepted: 03/30/2004] [Indexed: 05/24/2023]
Abstract
Two unigene datasets of Pinus taeda and Pinus pinaster were screened to detect di-, tri- and tetranucleotide repeated motifs using the SSRIT script. A total of 419 simple sequence repeats (SSRs) were identified, from which only 12.8% overlapped between the two sets. The position of the SSRs within their coding sequences were predicted using FrameD. Trinucleotides appeared to be the most abundant repeated motif (63 and 51% in P. taeda and P. pinaster, respectively) and tended to be found within translated regions (76% in both species), whereas dinucleotide repeats were preferentially found within the 5'- and 3'-untranslated regions (75 and 65%, respectively). Fifty-three primer pairs amplifying a single PCR fragment in the source species (mainly P. taeda), were tested for amplification in six other pine species. The amplification rate with other pine species was high and corresponded with the phylogenetic distance between species, varying from 64.6% in P. canariensis to 94.2% in P. radiata. Genomic SSRs were found to be less transferable; 58 of the 107 primer pairs (i.e. 54%) derived from P. radiata amplified a single fragment in P. pinaster. Nine cDNA-SSRs were located to their chromosomes in two P. pinaster linkage maps. The level of polymorphism of these cDNA-SSRs was compared to that of previously and newly developed genomic-SSRs. Overall, genomic SSRs tend to perform better in terms of heterozygosity and number of alleles. This study suggests that useful SSR markers can be developed from pine ESTs.
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Affiliation(s)
- D Chagné
- UMR 1202 BIOGECO-INRA, Equipe de génétique, 69 route d'Arcachon, 33610, Cestas Cédex, France
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Mariette S, Chagné D, Lézier C, Pastuszka P, Raffin A, Plomion C, Kremer A. Genetic diversity within and among Pinus pinaster populations: comparison between AFLP and microsatellite markers. Heredity (Edinb) 2001; 86:469-79. [PMID: 11520347 DOI: 10.1046/j.1365-2540.2001.00852.x] [Citation(s) in RCA: 105] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Twenty-three populations of Pinus pinaster (13 Aquitaine populations and 10 Corsican populations) were analysed at three microsatellite loci and 122 AFLP loci. The aims of the study were: (i) to compare levels of within-population and among-population diversity assessed with both kinds of markers; (ii) to compare Aquitaine and Corsican provenances of P. pinaster; and (iii) to know if both markers gave the same information for conservation purposes. Classical population genetics statistics were estimated and the ranking of populations obtained using different markers and/or parameters were compared by computing Spearman's rank correlations. Even though microsatellites showed a higher within-population diversity, they showed the same level of differentiation as AFLP markers. Moreover, both markers also showed a higher genetic diversity in the Aquitaine provenance and a higher differentiation among Corsican populations. AFLPs and microsatellites gave different population diversity rankings. Consequently, the results do not support the potential population identification within each provenance for conservation purposes.
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Affiliation(s)
- S Mariette
- INRA, Equipe de Génétique et Amélioration des Arbres Forestiers, BP45, F-33610 Cestas, France.
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