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Guo D, Wang R, Fang J, Zhong Y, Qi X. Development of sex-linked markers for gender identification of Actinidia arguta. Sci Rep 2023; 13:12780. [PMID: 37550389 PMCID: PMC10406875 DOI: 10.1038/s41598-023-39561-0] [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: 09/08/2021] [Accepted: 07/27/2023] [Indexed: 08/09/2023] Open
Abstract
The fruit of the dioecious plant Actinidia arguta has become a great attraction recently. It has long been difficult to distinguish the genders of hybrid seedlings before flowering, therefore increasing the expenditures of breeding. To produce reliable molecular marker for gender identification, this research utilized whole-genome re-sequencing of 15 males and 15 females from an 8-year-old cross population to develop gender specific markers. P51 and P11 were identified as sex-linked markers after verification. Both of these markers, according to the PCR results, only amplified a single band in male samples. These two markers were tested in 97 hybrids (52 females and 45 males) and 31 wild individuals (13 females and 18 males), with an accuracy of 96.88% and 96.09%, correspondingly. This research also verified the universalities of the two markers in Actinidia chinensis samples, and it could be inferred from the PCR results that neither marker was applicable to A. chinensis samples. The BLAST results of the two markers demonstrated that the two markers were closely aligned with different parts of the Y male-specific region of A. chinensis genome, thus they were likely to be useful for the research on the mechanism of sex determination of A. arguta. The two male-linked makers, P51 and P11, have already been used in sex-identification of A. arguta seedlings.
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Affiliation(s)
- Dandan Guo
- Key Laboratory for Fruit Tree Growth, Development and Quality Control, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Ran Wang
- Key Laboratory for Fruit Tree Growth, Development and Quality Control, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Jinbao Fang
- Key Laboratory for Fruit Tree Growth, Development and Quality Control, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Yunpeng Zhong
- Key Laboratory for Fruit Tree Growth, Development and Quality Control, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China.
| | - Xiujuan Qi
- Key Laboratory for Fruit Tree Growth, Development and Quality Control, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China.
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Wang R, Xing S, Bourke PM, Qi X, Lin M, Esselink D, Arens P, Voorrips RE, Visser RG, Sun L, Zhong Y, Gu H, Li Y, Li S, Maliepaard C, Fang J. Development of a 135K SNP genotyping array for Actinidia arguta and its applications for genetic mapping and QTL analysis in kiwifruit. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:369-380. [PMID: 36333116 PMCID: PMC9884011 DOI: 10.1111/pbi.13958] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/22/2022] [Accepted: 10/31/2022] [Indexed: 05/11/2023]
Abstract
Kiwifruit (Actinidia spp) is a woody, perennial and deciduous vine. In this genus, there are multiple ploidy levels but the main cultivated cultivars are polyploid. Despite the availability of many genomic resources in kiwifruit, SNP genotyping is still a challenge given these different levels of polyploidy. Recent advances in SNP array technologies have offered a high-throughput genotyping platform for genome-wide DNA polymorphisms. In this study, we developed a high-density SNP genotyping array to facilitate genetic studies and breeding applications in kiwifruit. SNP discovery was performed by genome-wide DNA sequencing of 40 kiwifruit genotypes. The identified SNPs were stringently filtered for sequence quality, predicted conversion performance and distribution over the available Actinidia chinensis genome. A total of 134 729 unique SNPs were put on the array. The array was evaluated by genotyping 400 kiwifruit individuals. We performed a multidimensional scaling analysis to assess the diversity of kiwifruit germplasm, showing that the array was effective to distinguish kiwifruit accessions. Using a tetraploid F1 population, we constructed an integrated linkage map covering 3060.9 cM across 29 linkage groups and performed QTL analysis for the sex locus that has been identified on Linkage Group 3 (LG3) in Actinidia arguta. Finally, our dataset presented evidence of tetrasomic inheritance with partial preferential pairing in A. arguta. In conclusion, we developed and evaluated a 135K SNP genotyping array for kiwifruit. It has the advantage of a comprehensive design that can be an effective tool in genetic studies and breeding applications in this high-value crop.
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Affiliation(s)
- Ran Wang
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
- Plant BreedingWageningen University & ResearchWageningenThe Netherlands
| | - Siyuan Xing
- Animal Breeding and GenomicsWageningen University & ResearchWageningenThe Netherlands
| | - Peter M. Bourke
- Plant BreedingWageningen University & ResearchWageningenThe Netherlands
| | - Xiuquan Qi
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Miaomiao Lin
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Danny Esselink
- Plant BreedingWageningen University & ResearchWageningenThe Netherlands
| | - Paul Arens
- Plant BreedingWageningen University & ResearchWageningenThe Netherlands
| | | | | | - Leiming Sun
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Yunpeng Zhong
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Hong Gu
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Yukuo Li
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Sikai Li
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Chris Maliepaard
- Plant BreedingWageningen University & ResearchWageningenThe Netherlands
| | - Jinbao Fang
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
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Transcriptome Analysis and Identification of a Female-Specific SSR Marker in Pistacia chinensis Based on Illumina Paired-End RNA Sequencing. Genes (Basel) 2022; 13:genes13061024. [PMID: 35741786 PMCID: PMC9222763 DOI: 10.3390/genes13061024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 05/27/2022] [Accepted: 05/31/2022] [Indexed: 02/08/2023] Open
Abstract
Pistacia chinensis Bunge (P. chinensis), a dioecious plant species, has been widely found in China. The female P. chinensis plants are more important than male plants in agricultural production, as their seeds can serve as an ideal feedstock for biodiesel. However, the sex of P. chinensis plants is hard to distinguish during the seedling stage due to the scarcity of available transcriptomic and genomic information. In this work, Illumina paired-end RNA sequencing assay was conducted to unravel the transcriptomic profiles of female and male P. chinensis flower buds. In total, 50,925,088 and 51,470,578 clean reads were obtained from the female and male cDNA libraries, respectively. After quality checks and de novo assembly, a total of 83,370 unigenes with a mean length of 1.3 kb were screened. Overall, 64,539 unigenes (77.48%) could be matched in at least one of the NR, NT, Swiss-Prot, COG, KEGG, and GO databases, 71 of which were putatively related to the floral development of P. chinensis. Additionally, 21,662 simple sequence repeat (SSR) motifs were identified in 17,028 unigenes of P. chinensis, and the mononucleotide motif was the most dominant type of repeats (52.59%) in P. chinensis, followed by dinucleotide (22.29%), trinucleotide (20.15%). The most abundant repeats were AG/CT (13.97%), followed by AAC/GTT (6.75%) and AT/TA (6.10%). Based on these SSR, 983 EST-SSR primers were designed, 151 of which were randomly chosen for validation. Of these validated EST-SSR markers, 25 SSR markers were found to be polymorphic between male and female plants. One SSR marker, namelyPCSSR55, displayed excellent specificity in female plants, which could clearly distinguish between male and female P. chinensis. Altogether, our findings not only reveal that the EST-SSR marker is extremely effective in distinguishing between male and female P. chinensis but also provide a solid framework for sex determination of plant seedlings.
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Transcriptomic Analysis of Sex-Associated DEGs in Female and Male Flowers of Kiwifruit (Actinidia deliciosa [A. Chev] C. F. Liang & A. R. Ferguson). HORTICULTURAE 2021. [DOI: 10.3390/horticulturae8010038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Kiwifruit (Actinidia deliciosa [A. Chev.], C.V. Liang & A. R. Ferguson, 1984) is a perennial plant, with morphologically hermaphroditic and functionally dioecious flowers. Fruits of this species are berries of great commercial and nutritional importance. Nevertheless, few studies have analyzed the molecular mechanisms involved in sexual differentiation in this species. To determine these mechanisms, we performed RNA-seq in floral tissue at stage 60 on the BBCH scale in cultivar ‘Hayward’ (H, female) and a seedling from ‘Green Light’ × ‘Tomuri’ (G × T, male). From these analyses, we obtained expression profiles of 24,888 (H) and 27,027 (G × T) genes, of which 6413 showed differential transcript abundance. Genetic ontology (GO) and KEGG analysis revealed activation of pathways associated with the translation of hormonal signals, plant-pathogen interaction, metabolism of hormones, sugars, and nucleotides. The analysis of the protein-protein interaction network showed that the genes ERL1, AG, AGL8, LFY, WUS, AP2, WRKY, and CO, are crucial elements in the regulation of the hormonal response for the formation and development of anatomical reproductive structures and gametophytes. On the other hand, genes encoding four Putative S-adenosyl-L-methionine-dependent methyltransferases (Achn201401, Achn281971, Achn047771 and Achn231981) were identified, which were up-regulated mainly in the male flowers. Moreover, the expression profiles of 15 selected genes through RT-qPCR were consistent with the results of RNA-seq. Finally, this work provides gene expression-based interactions between transcription factors and effector genes from hormonal signaling pathways, development of floral organs, biological and metabolic processes or even epigenetic mechanisms which could be involved in the kiwi sex-determination. Thus, in order to decode the nature of these interactions, it could be helpful to propose new models of flower development and sex determination in the Actinidia genus.
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Ruan R, Feng T, Li Y, Yue H, Ye H, Du H, Liu Q, Ruan J, Li C, Wei Q. Screening and identification of female-specific DNA sequences in octaploid sturgeon using comparative genomics with high-throughput sequencing. Genomics 2021; 113:4237-4244. [PMID: 34785350 DOI: 10.1016/j.ygeno.2021.11.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 01/15/2021] [Accepted: 11/10/2021] [Indexed: 10/19/2022]
Abstract
In this study, six candidate female-specific DNA sequences of octaploid Amur sturgeon (Acipenser schrenckii) were identified using comparative genomic approaches with high-throughput sequencing data. Their specificity was confirmed by traditional PCR. Two of these sex-specific sequences were also validated as female-specific in other eight sturgeon species and two hybrid sturgeons. The identified female-specific DNA fragments suggest that the family Acipenseridae has a ZZ/ZW sex-determining system. However, one of the two DNA sequences has been deleted in some sturgeons such as Sterlet sturgeon (Acipenser ruthenus), Beluga (Huso huso) and Kaluga (H. dauricus). The difference of sex-specific sequences among sturgeons indicates that there are different sex-specific regions among species of sturgeon. This study not only provided the sex-specific DNA sequences for management, conservation and studies of sex-determination mechanisms in sturgeons, but also confirmed the capability of the workflow to identify sex-specific DNA sequences in the polyploid species with complex genomes.
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Affiliation(s)
- Rui Ruan
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Tong Feng
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| | - Ying Li
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Huamei Yue
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Huan Ye
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Hao Du
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Qingyou Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| | - Jue Ruan
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
| | - Chuangju Li
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China.
| | - Qiwei Wei
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China.
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Liao G, Zhong M, Jiang Z, Tao J, Jia D, Qu X, Huang C, Liu Q, Xu X. Genome-Wide Association Studies Provide Insights into the Genetic Determination of Flower and Leaf Traits of Actinidia eriantha. FRONTIERS IN PLANT SCIENCE 2021; 12:730890. [PMID: 34490026 PMCID: PMC8417775 DOI: 10.3389/fpls.2021.730890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 07/23/2021] [Indexed: 06/13/2023]
Abstract
Kiwifruit (Actinidia eriantha) is a dioecious vine, and the pollen of its male cultivars has a direct effect on the quality of its fruits. In this study, to facilitate molecular breeding and gene identification, we performed genome-wide association studies (GWAS) on 11 traits of flower and leaf. A total of 946,337 highly consistent SNP markers were obtained in the whole genome. Phylogenetic tree analysis and population structure analysis showed that the 143 germplasms can be divided into two groups. The linkage disequilibrium analysis showed that A. eriantha have a relatively fast attenuation rate, and that the average attenuation distance of LD was 0.1-0.3 Kb. The MLM (QK) model was determined as best for correlation analysis, and eight and three SNPs associated with flower- and leaf-related traits were identified, respectively, at 0.01 significance level. However, SNP markers associated with stamen number per flower, pollen viability, total chlorophyll content, and total flavonoid content were not identified at the 0.01 significant level, although it is worth noting that one, one, five, and two SNPs were identified to be associated with these traits at the 0.05 significant level. This study provides insights into the complex flower- and leaf-related biology, and identifies genes controlling important traits in A. eriantha through GWAS, which extends the genetic resources and basis for facilitating molecular breeding in kiwifruits.
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Popowski E, Thomson SJ, Knäbel M, Tahir J, Crowhurst RN, Davy M, Foster TM, Schaffer RJ, Tustin DS, Allan AC, McCallum J, Chagné D. Construction of a high density genetic map for hexaploid kiwifruit (Actinidia chinensis var. deliciosa) using genotyping by sequencing. G3-GENES GENOMES GENETICS 2021; 11:6261761. [PMID: 34009255 PMCID: PMC8495948 DOI: 10.1093/g3journal/jkab142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 03/07/2021] [Indexed: 11/19/2022]
Abstract
Commercially grown kiwifruit (genus Actinidia) are generally of two sub-species which have a base haploid genome of 29 chromosomes. The yellow-fleshed Actinidia chinensis var. chinensis, is either diploid (2n = 2x = 58) or tetraploid (2n = 4x = 116) and the green-fleshed cultivar A. chinensis var. deliciosa “Hayward,” is hexaploid (2n = 6x = 174). Advances in breeding green kiwifruit could be greatly sped up by the use of molecular resources for more efficient and faster selection, for example using marker-assisted selection (MAS). The key genetic marker that has been implemented for MAS in hexaploid kiwifruit is for gender testing. The limited marker-trait association has been reported for other polyploid kiwifruit for fruit and production traits. We have constructed a high-density linkage map for hexaploid green kiwifruit using genotyping-by-sequence (GBS). The linkage map obtained consists of 3686 and 3940 markers organized in 183 and 176 linkage groups for the female and male parents, respectively. Both parental linkage maps are co-linear with the A. chinensis “Red5” reference genome of kiwifruit. The linkage map was then used for quantitative trait locus (QTL) mapping, and successfully identified QTLs for king flower number, fruit number and weight, dry matter accumulation, and storage firmness. These are the first QTLs to be reported and discovered for complex traits in hexaploid kiwifruit.
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Affiliation(s)
- Elizabeth Popowski
- The New Zealand Institute for Plant and Food Research Ltd (Plant & Food Research), Te Puke, New Zealand
| | | | | | | | | | - Marcus Davy
- The New Zealand Institute for Plant and Food Research Ltd (Plant & Food Research), Te Puke, New Zealand
| | | | - Robert J Schaffer
- Plant & Food Research, Motueka, New Zealand.,School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | | | - Andrew C Allan
- Plant & Food Research, Auckland, New Zealand.,School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | | | - David Chagné
- Plant & Food Research, Palmerston North, New Zealand
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Sex-Linked Molecular Markers Identify Female Lines in Endosperm-Derived Kiwifruit Callus and in Regenerants. PLANTS 2021; 10:plants10030526. [PMID: 33799868 PMCID: PMC7998832 DOI: 10.3390/plants10030526] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/05/2021] [Accepted: 03/09/2021] [Indexed: 11/17/2022]
Abstract
This is the first report of molecular markers application for the analysis of endosperm-derived callus and nonaploid kiwifruit (Actinidia chinensis var. deliciosa, formerly: Actinidia deliciosa) plants. As a source of explants, fruits of ‘Hayward’, the most popular cultivar, were used. Additionally, analyses of the nuclear DNA content and sex were conducted on the regenerated plants. Hexaploid seedlings were used as control for the flow cytometric analyses. Most of the plants (about 90%) regenerated via endosperm-derived callus possessed 2C = 9Cx DNA, which confirmed their endosperm origin and nonaploidy. Because Actinidia is a dioecious species, and female plants bearing fruits are desired by breeders, it is crucial to identify the sex of an individual at early stages of development. Analyses were conducted with ex vitro and in vitro samples. Results revealed that specific markers for a Y-chromosome applied at the callus stage allowed us to reliably predict the sex of plants regenerated from it. This is a novel application of sex-linked markers for early selection of female and male callus lines when the sex of the initial explants is still unknown, such as fresh isolated embryos and endosperm. It may have significant importance for breeding kiwifruit programs, which involve tissue culture techniques.
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Yu L, Ma X, Deng B, Yue J, Ming R. Construction of high-density genetic maps defined sex determination region of the Y chromosome in spinach. Mol Genet Genomics 2021; 296:41-53. [PMID: 32955620 DOI: 10.1007/s00438-020-01723-1724] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 09/04/2020] [Indexed: 05/18/2023]
Abstract
Spinach (Spinacia olracea L.) is a dioecious leafy vegetable with a highly repetitive genome of around 990 Mb, which is challenging for de-novo genome assembly. In our study, a segregating F1 (double pseudo-testcross) population from 'Viroflay' × 'Cornell-NO. 9' was used for genetic mapping by resequencing genotyping. In the paternal 'Cornell-NO. 9' map, 212,414 SNPs were mapped, and the total linkage distance was 476.83 cM; the maternal 'Viroflay' map included 29,282 SNPs with 401.28 cM total genetic distance. Both paternal and maternal maps have the expected number of six linkage groups (LGs). A non-recombining region with 5678 SNPs (39 bin markers) co-segregates with sex type which located at 45.2 cM of LG1 in the 'Cornell-NO. 9' map while indicates the sex determination region (SDR). Integration of two maps into a consensus map guided us to anchor additional 1242 contigs to six pseudomolecules from the published reference genome, which improved additional 233 Mb (23.4%) assembly based on spinach estimated genome size. Particularly, the X counterpart of SDR in our assembly is estimated around 18.4 Mb which locates at the largest chromosome, as consensus with sex-biased FISH signals from previous cytogenetics studies. The region is featured by reduced gene density, higher percentage of repetitive sequences, and no recombination. Our linkage maps provide the resource for improving spinach genome de-novo assembly and identification of sex-determining genes in spinach.
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Affiliation(s)
- Li'ang Yu
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Xiaokai Ma
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Ban Deng
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Jingjing Yue
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
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Construction of high-density genetic maps defined sex determination region of the Y chromosome in spinach. Mol Genet Genomics 2020; 296:41-53. [DOI: 10.1007/s00438-020-01723-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 09/04/2020] [Indexed: 12/18/2022]
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Molecular Sex Identification in the Hardy Rubber Tree ( Eucommia ulmoides Oliver) via ddRAD Markers. Int J Genomics 2020; 2020:2420976. [PMID: 32509842 PMCID: PMC7246395 DOI: 10.1155/2020/2420976] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/03/2020] [Indexed: 11/18/2022] Open
Abstract
Eucommia ulmoides, also known as the industrially and medicinally important hardy rubber tree, is the sole species of Eucommiaceae. Nevertheless, its dioecious property hinders sex recognition by traditional morphological observation at very early developmental stages, thus inhibiting breeding and economic cropping. In this study, double-digest restriction site-associated DNA sequencing (ddRAD-seq) was applied to screen sex-linked molecular markers for sex identification and investigation of the sex determination system in 20 male and female E. ulmoides individual plants, respectively. In consequence, five candidate male-specific loci but no female-specific loci were predicated among the 183,752 male and 147,122 female catalogue loci by bioinformatics analysis. Subsequent PCR (polymerase chain reaction) amplification and Sanger sequencing examinations were performed on another 24 individuals, 12 for each sex, from a separate population. One ideal sex-linked locus, MSL4, was identified among the five putative male-specific loci that were found using ddRAD data. MSL4 is 479 bp in length and highly conserved in all the male individuals, suggesting its feature of being stable and repeatable. Our results also indicated that the sex of E. ulmoides is likely determined genetically. In short, this study provides a consistent and reproducible ddRAD marker (MSL4) that is able to discriminate male from female seedlings in E. ulmoides, which will be valuable for rapid breeding practice and better commercial production of this economically important tree.
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Wang Y, Jia HM, Shen YT, Zhao HB, Yang QS, Zhu CQ, Sun DL, Wang GY, Zhou CC, Jiao Y, Chai CY, Yan LJ, Li XW, Jia HJ, Gao ZS. Construction of an anchoring SSR marker genetic linkage map and detection of a sex-linked region in two dioecious populations of red bayberry. HORTICULTURE RESEARCH 2020; 7:53. [PMID: 32257239 PMCID: PMC7109115 DOI: 10.1038/s41438-020-0276-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 02/02/2020] [Accepted: 02/12/2020] [Indexed: 05/21/2023]
Abstract
Red bayberry (Morella rubra) is an evergreen fruit tree found in southern China whose whole-genome sequence has recently been published. We updated the linkage map of the species by adding 118 SSR markers and the female-specific marker MrFT2_BD-SEX. The integrated map included eight linkage groups and spanned 491 cM. Eleven sex-associated markers were identified, six of which were located in linkage group 8, in agreement with the previously reported location of the sex-determining region. The MrFT2_BD-SEX marker was genotyped in 203 cultivated accessions. Among the females of the accessions, we found two female-specific alleles, designated W-b (151 bp) and W-d (129 bp). We previously found that 'Dongkui', a female cultivar, could produce viable pollen (we refer to such plants 'Dongkui-male') and serve as the paternal parent in crosses. The genotypes of the MrFT2_BD-SEX marker were W-b/Z in 'Biqi' and W-d/Z in 'Dongkui-male'. The progeny of a cross between these parents produced a 3:1 female (W-) to male (ZZ) ratio and the expected 1:1:1:1 ratio of W-b/W-d: W-b/Z: W-d/Z: Z/Z. In addition, the flowering and fruiting phenotypes of all the F1 progeny fit their genotypes. Our results confirm the existence of ZW sex determination and show that the female phenotype is controlled by a single dominant locus (W) in a small genomic region (59 kb and less than 3.3 cM). Furthermore, we have produced a homozygous "super female" (WW) that should produce all-female offspring in the F2 generation, providing a foundation for commercial use and presenting great potential for use in modern breeding programs.
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Affiliation(s)
- Yan Wang
- Fruit Science Institute, College of Agriculture and Biotechnology, Zhejiang University, 310058 Hangzhou, China
| | - Hui-Min Jia
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 201602 Shanghai, China
| | - Yu-Tong Shen
- Fruit Science Institute, College of Agriculture and Biotechnology, Zhejiang University, 310058 Hangzhou, China
| | - Hai-Bo Zhao
- Fruit Science Institute, College of Agriculture and Biotechnology, Zhejiang University, 310058 Hangzhou, China
| | - Qin-Song Yang
- Fruit Science Institute, College of Agriculture and Biotechnology, Zhejiang University, 310058 Hangzhou, China
| | - Chang-Qing Zhu
- Fruit Science Institute, College of Agriculture and Biotechnology, Zhejiang University, 310058 Hangzhou, China
| | - De-Li Sun
- Fruit Science Institute, College of Agriculture and Biotechnology, Zhejiang University, 310058 Hangzhou, China
| | - Guo-Yun Wang
- Yuyao Forestry Technology Extension Center, 315400 Ningbo, China
| | - Chao-Chao Zhou
- Yuyao Forestry Technology Extension Center, 315400 Ningbo, China
| | - Yun Jiao
- Institute of Forestry, Ningbo Academy of Agricultural Science, Ningbo, China
| | - Chun-Yan Chai
- Cixi Forestry Technology Extension Center, 315300 Cixi, China
| | - Li-Ju Yan
- Linhai Forestry Technology Extension Center, 317000 Taizhou, China
| | - Xiong-Wei Li
- Forest & Fruit Tree Institute, Shanghai Academy of Agricultural Sciences, 201403 Shanghai, China
| | - Hui-Juan Jia
- Fruit Science Institute, College of Agriculture and Biotechnology, Zhejiang University, 310058 Hangzhou, China
| | - Zhong-Shan Gao
- Fruit Science Institute, College of Agriculture and Biotechnology, Zhejiang University, 310058 Hangzhou, China
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13
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Chalcone Synthase-Encoding AeCHS is Involved in Normal Petal Coloration in Actinidia eriantha. Genes (Basel) 2019; 10:genes10120949. [PMID: 31757002 PMCID: PMC6947247 DOI: 10.3390/genes10120949] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 11/13/2019] [Accepted: 11/18/2019] [Indexed: 11/17/2022] Open
Abstract
Studies on anthocyanin biosynthesis have been mainly concentrated on the fruit, whereas few have focused the mechanism of flower coloration in kiwifruit. Here, we report that the structural gene, AeCHS, is involved in anthocyanin accumulation and indispensable for normal petal coloration in Actinidia eriantha. Petals from three different species including Actinidia eriantha (red petals), Actinidia hemsleyana (light pink petals) and Actinidia arguta (white petals) were selected for anthocyanin determination and gene expression analysis. The anthocyanin components in A. eriantha were significantly higher than in A. hemsleyana or A. arguta. Consistently, gene expression profiles suggested that AeCHS expression in A. eriantha was higher than in A. hemsleyana or A. arguta. Cluster analysis showed that AeCHS was clustered into a single group and distinctly separated from other genes, indicating the expression pattern of AeCHS gene was different from any other. Additionally, correlation analysis revealed AeCHS expression significantly correlated with anthocyanin content. The complete coding sequence of AeCHS was cloned from petals of A. eriantha 'Zaoxu', showing the length of AeCHS was 1170 bp encoding a protein of 389 amino acids. AeCHS was located in the cytoplasm, indicating it is indeed a structural gene involved in anthocyanin biosynthesis. AeCHS silencing performed by infiltration grafting-mediated virus-induced gene silencing (VIGS) reduced petal anthocyanin content and bleached red petals in A. eriantha. Our results confirm a crucial role of AeCHS in anthocyanin biosynthesis and accumulation in A. eriantha petals; furthermore, they offer important basic information and constitute a reference point for further research.
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14
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Caporali E, Testolin R, Pierce S, Spada A. Sex change in kiwifruit (Actinidia chinensis Planch.): a developmental framework for the bisexual to unisexual floral transition. PLANT REPRODUCTION 2019; 32:323-330. [PMID: 31115664 DOI: 10.1007/s00497-019-00373-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 05/10/2019] [Indexed: 06/09/2023]
Abstract
The developmental morphology of male and female kiwifruit flowers is tracked to delimit a framework of events to aid the study of divergence in floral gene expression. The transition from hermaphrodite to unisexual development of kiwifruit (Actinidia chinensis Planch) flowers has been reported previously, but differences in gene expression controlling sexual development for this species have not been associated with the major developmental changes occurring within pistils. We investigated the key stages in male and female flower development to define the point at which meristematic activities diverge in the two sexes. A combination of scanning electron microscopy and light microscopy was used to investigate pistil development from the earliest stages. We identified seven distinct stages characterized by differences in ovary size and shape, macrosporogenesis, ovule primordium development, anther locule lengthening, microspore wall thickening, and pollen degeneration. Sex differences were evident from the initial stage of development, with a laterally compacted gynoecium in male flowers. However, the key developmental stage, at which tissue differentiation clearly deviated between the two sexes, was stage 3, when flowers were 3.5 to 4.5 mm in length at approximately 10 d from initiation of stamen development. At this stage, male flowers lacked evident carpel meristem development as denoted by a lack of ovule primordium formation. Pollen degeneration in female flowers, probably driven by programmed cell death, occurred at the late stage 6, while the final stage 7 was represented by pollen release. As the seven developmental stages are associated with specific morphological differences, including flower size, the scheme suggested here can provide the required framework for the future study of gene expression during the regulation of flower development in this crop species.
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Affiliation(s)
| | - Raffaele Testolin
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Simon Pierce
- Department of Agricultural and Environmental Sciences, University of Milan, Milan, Italy
| | - Alberto Spada
- Department of Agricultural and Environmental Sciences, University of Milan, Milan, Italy.
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15
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Akagi T, Pilkington SM, Varkonyi-Gasic E, Henry IM, Sugano SS, Sonoda M, Firl A, McNeilage MA, Douglas MJ, Wang T, Rebstock R, Voogd C, Datson P, Allan AC, Beppu K, Kataoka I, Tao R. Two Y-chromosome-encoded genes determine sex in kiwifruit. NATURE PLANTS 2019; 5:801-809. [PMID: 31383971 DOI: 10.1038/s41477-019-0489-6] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 07/02/2019] [Indexed: 05/20/2023]
Abstract
Dioecy, the presence of male and female individuals, has evolved independently in multiple flowering plant lineages1-3. Although theoretical models for the evolution of dioecy, such as the 'two-mutations' model, are well established4,5, little is known about the specific genes determining sex and their evolutionary history3. Kiwifruit, a major tree crop consumed worldwide, is a dioecious species. In kiwifruit we previously identified a Y-encoded sex-determinant candidate gene acting as the suppressor of feminization (SuF), named Shy Girl (SyGI)6. Here, we identify a second Y-encoded sex-determinant that we named Friendly Boy (FrBy), which exhibits strong expression in tapetal cells. Gene-editing and complementation analyses in Arabidopsis thaliana and Nicotiana tabacum indicated that FrBy acts for the maintenance of male (M) functions, independently of SyGI, and that these functions are conserved across angiosperm species. We further characterized the genomic architecture of the small (<1 megabase pairs (Mb)) male-specific region of the Y chromosome (MSY), which harbours only two genes expressed extensively in developing gynoecia and androecia, respectively: SyGI and FrBy. Re-sequencing of the genome of a natural hermaphrodite kiwifruit revealed that this individual is genetically male but carries deletion(s) of parts of the Y chromosome, including SyGI. Additionally, expression of FrBy in female kiwifruit resulted in hermaphrodite plants. These results clearly indicate that Y-encoded SyGI and FrBy act independently as the SuF and M factors in kiwifruit, respectively, and provide insight into not only the evolutionary path leading to a two-factor sex-determination system, but also a new breeding approach for dioecious species.
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Affiliation(s)
- Takashi Akagi
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
- JST, PRESTO, Kawaguchi-shi, Saitama, Japan.
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan.
| | - Sarah M Pilkington
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Erika Varkonyi-Gasic
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Isabelle M Henry
- Department of Plant Biology and Genome Center, University of California Davis, Davis, CA, USA
| | - Shigeo S Sugano
- JST, PRESTO, Kawaguchi-shi, Saitama, Japan
- R-GIRO, Ritsumeikan University, Shiga, Japan
| | - Minori Sonoda
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Alana Firl
- Department of Plant Biology and Genome Center, University of California Davis, Davis, CA, USA
| | - Mark A McNeilage
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Mikaela J Douglas
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Tianchi Wang
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Ria Rebstock
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Charlotte Voogd
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Paul Datson
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Andrew C Allan
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Kenji Beppu
- Faculty of Agriculture, Kagawa University, Miki, Kagawa, Japan
| | - Ikuo Kataoka
- Faculty of Agriculture, Kagawa University, Miki, Kagawa, Japan
| | - Ryutaro Tao
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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16
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Wilson CA, Titus T, Batzel P, Postlethwait JH, Raman R. A Search for Sex-Linked Loci in the Agamid Lizard, Calotes versicolor. Sex Dev 2019; 13:143-150. [PMID: 31247625 DOI: 10.1159/000500465] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2019] [Indexed: 11/19/2022] Open
Abstract
The Indian garden lizard, Calotes versicolor, lacks cytologically recognizable sex chromosomes, and its mechanism of sex determination is unclear. We evaluated genotype-to-sex-phenotype association using RAD-seq in wild-caught males and females, 30 of each sex. Of 210,736 unique, 96-nt long RAD-tags, 48% contained polymorphisms, 23% of which were present in at least 40 of 60 individuals. Twenty one RAD-tags neared, but none achieved, the inclusion criteria for sex enrichment, as expected if C. versicolor lacks highly differentiated sex chromosomes. Three RAD-tags with alleles most strongly associated with sex tended to be heterozygous in females and to lack male-specific alleles, suggesting a ZW female/ZZ male system. Putative female alleles, however, were present in some males and lacking from some females, suggesting either recombination between these markers and the sex locus or sex reversal due to environmental or genetic factors. Paired-end, 250-nt reads from 1 male provided a fragmented draft genome assembly. Four sex-associated RAD-tags were identical to portions of 4 unique C. versicolor genomic contigs rather than linked to a single putative sex-linked region. The lack of strongly sex-linked loci coupled with weak evidence for temperature-associated sex determination intensifies the need for further investigation of the puzzling sex determination mechanism in C. versicolor.
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17
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Li Y, Cui W, Wang R, Lin M, Zhong Y, Sun L, Qi X, Fang J. MicroRNA858-mediated regulation of anthocyanin biosynthesis in kiwifruit (Actinidia arguta) based on small RNA sequencing. PLoS One 2019; 14:e0217480. [PMID: 31120996 PMCID: PMC6532936 DOI: 10.1371/journal.pone.0217480] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 05/13/2019] [Indexed: 11/19/2022] Open
Abstract
As important regulators, miRNAs could play pivotal roles in regulation of fruit coloring. Actinidia arguta is a newly emerged fruit tree with extensively application prospects. However, miRNAs involved in A. arguta fruit coloring are unknown. In this study, A. arguta fruit were investigated at three developmental stages by small RNAs high-throughput sequencing. A total of 482 conserved miRNAs corresponding to 526 pre-miRNAs and 581 novel miRNAs corresponding to 619 pre-miRNAs were grouped into 46 miRNA families. Target gene prediction and analysis revealed that miR858, a strongly candidate miRNA, was involved in anthocyanin biosynthesis in which contributes to fruit coloring. The anthocyanin level was determined in three A. arguta cultivars by UPLC-MS/MS (ultra-performance liquid chromatography coupled with tandem mass spectrometry). In addition, qPCR (quantitative real-time PCR), cluster analysis were conducted as well as correlation analysis. All results were combined to propose a model in which describes an association of miRNA and anthocyanin biosynthesis in A. arguta. The data presented herein is the first report on miRNA profile analysis in A. arguta, which can provide valuable information for further research into the regulation of the miRNAs in anthocyanin biosynthesis and fruit coloring.
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Affiliation(s)
- Yukuo Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, P.R. China
| | - Wen Cui
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, P.R. China
| | - Ran Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, P.R. China
| | - Miaomiao Lin
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, P.R. China
| | - Yunpeng Zhong
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, P.R. China
| | - Leiming Sun
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, P.R. China
| | - Xiujuan Qi
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, P.R. China
- * E-mail: (JF); (XQ)
| | - Jinbao Fang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, P.R. China
- * E-mail: (JF); (XQ)
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18
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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 BIOLOGY 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] [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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19
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Tang W, Sun X, Yue J, Tang X, Jiao C, Yang Y, Niu X, Miao M, Zhang D, Huang S, Shi W, Li M, Fang C, Fei Z, Liu Y. Chromosome-scale genome assembly of kiwifruit Actinidia eriantha with single-molecule sequencing and chromatin interaction mapping. Gigascience 2019; 8:giz027. [PMID: 30942870 PMCID: PMC6446220 DOI: 10.1093/gigascience/giz027] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 11/12/2018] [Accepted: 03/01/2019] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Kiwifruit (Actinidia spp.) is a dioecious plant with fruits containing abundant vitamin C and minerals. A handful of kiwifruit species have been domesticated, among which Actinidiaeriantha is increasingly favored in breeding owing to its superior commercial traits. Recently, elite cultivars from A. eriantha have been successfully selected and further studies on their biology and breeding potential require genomic information, which is currently unavailable. FINDINGS We assembled a chromosome-scale genome sequence of A. eriantha cultivar White using single-molecular sequencing and chromatin interaction map-based scaffolding. The assembly has a total size of 690.6 megabases and an N50 of 21.7 megabases. Approximately 99% of the assembly were in 29 pseudomolecules corresponding to the 29 kiwifruit chromosomes. Forty-three percent of the A. eriantha genome are repetitive sequences, and the non-repetitive part encodes 42,988 protein-coding genes, of which 39,075 have homologues from other plant species or protein domains. The divergence time between A. eriantha and its close relative Actinidia chinensis is estimated to be 3.3 million years, and after diversification, 1,727 and 1,506 gene families are expanded and contracted in A. eriantha, respectively. CONCLUSIONS We provide a high-quality reference genome for kiwifruit A. eriantha. This chromosome-scale genome assembly is substantially better than 2 published kiwifruit assemblies from A. chinensis in terms of genome contiguity and completeness. The availability of the A. eriantha genome provides a valuable resource for facilitating kiwifruit breeding and studies of kiwifruit biology.
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Affiliation(s)
- Wei Tang
- School of Horticulture, Anhui Agricultural University, 130 Chang Jiang Xi Lu, Hefei, Anhui 230036, China
- Ministry of Education Key Laboratory for Bio-resource and Eco-environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, 29 Wang Jiang Lu, Sichuan University, Chengdu, Sichuan 610064, China
- School of Food Science and Engineering, Hefei University of Technology, 193 Tun Xi Lu, Hefei, Anhui 230009, China
| | - Xuepeng Sun
- Boyce Thompson Institute, Cornell University, 533 Tower Road, Ithaca, NY 14853, USA
| | - Junyang Yue
- School of Horticulture, Anhui Agricultural University, 130 Chang Jiang Xi Lu, Hefei, Anhui 230036, China
- School of Food Science and Engineering, Hefei University of Technology, 193 Tun Xi Lu, Hefei, Anhui 230009, China
| | - Xiaofeng Tang
- School of Horticulture, Anhui Agricultural University, 130 Chang Jiang Xi Lu, Hefei, Anhui 230036, China
- School of Food Science and Engineering, Hefei University of Technology, 193 Tun Xi Lu, Hefei, Anhui 230009, China
| | - Chen Jiao
- Boyce Thompson Institute, Cornell University, 533 Tower Road, Ithaca, NY 14853, USA
| | - Ying Yang
- School of Horticulture, Anhui Agricultural University, 130 Chang Jiang Xi Lu, Hefei, Anhui 230036, China
| | - Xiangli Niu
- School of Horticulture, Anhui Agricultural University, 130 Chang Jiang Xi Lu, Hefei, Anhui 230036, China
- School of Food Science and Engineering, Hefei University of Technology, 193 Tun Xi Lu, Hefei, Anhui 230009, China
| | - Min Miao
- School of Horticulture, Anhui Agricultural University, 130 Chang Jiang Xi Lu, Hefei, Anhui 230036, China
- School of Food Science and Engineering, Hefei University of Technology, 193 Tun Xi Lu, Hefei, Anhui 230009, China
| | - Danfeng Zhang
- School of Food Science and Engineering, Hefei University of Technology, 193 Tun Xi Lu, Hefei, Anhui 230009, China
| | - Shengxiong Huang
- School of Food Science and Engineering, Hefei University of Technology, 193 Tun Xi Lu, Hefei, Anhui 230009, China
| | - Wei Shi
- School of Food Science and Engineering, Hefei University of Technology, 193 Tun Xi Lu, Hefei, Anhui 230009, China
| | - Mingzhang Li
- Sichuan Academy of Natural Resource Sciences, 24 Yi Huan Lu Nan Er Duan, Chengdu, Sichuan 610015, China
| | - Congbing Fang
- School of Horticulture, Anhui Agricultural University, 130 Chang Jiang Xi Lu, Hefei, Anhui 230036, China
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, 533 Tower Road, Ithaca, NY 14853, USA
- U.S. Department of Agriculture–Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, 538 Tower Road, Ithaca, NY 14853, USA
| | - Yongsheng Liu
- School of Horticulture, Anhui Agricultural University, 130 Chang Jiang Xi Lu, Hefei, Anhui 230036, China
- Ministry of Education Key Laboratory for Bio-resource and Eco-environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, 29 Wang Jiang Lu, Sichuan University, Chengdu, Sichuan 610064, China
- School of Food Science and Engineering, Hefei University of Technology, 193 Tun Xi Lu, Hefei, Anhui 230009, China
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20
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Zhang S, Zhang X, Chen X, Xu T, Wang M, Qin Q, Zhong L, Jiang H, Zhu X, Liu H, Shao J, Zhu Z, Shi Q, Bian W, You X. Construction of a High-Density Linkage Map and QTL Fine Mapping for Growth- and Sex-Related Traits in Channel Catfish ( Ictalurus punctatus). Front Genet 2019; 10:251. [PMID: 30984241 PMCID: PMC6448050 DOI: 10.3389/fgene.2019.00251] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 03/06/2019] [Indexed: 12/11/2022] Open
Abstract
A high-density genetic linkage map is of particular importance in the fine mapping for important economic traits and whole genome assembly in aquaculture species. The channel catfish (Ictalurus punctatus), a species native to North America, is one of the most important commercial freshwater fish in the world. Outside of the United States, China has become the major producer and consumer of channel catfish after experiencing rapid development in the past three decades. In this study, based on restriction site associated DNA sequencing (RAD-seq), a high-density genetic linkage map of channel catfish was constructed by using single nucleotide polymorphisms (SNPs) in a F1 family composed of 156 offspring and their two parental individuals. A total of 4,768 SNPs were assigned to 29 linkage groups (LGs), and the length of the linkage map reached 2,480.25 centiMorgans (cM) with an average distance of 0.55 cM between loci. Based on this genetic linkage map, 223 genomic scaffolds were anchored to the 29 LGs of channel catfish, and a total length of 704.66 Mb was assembled. Quantitative trait locus (QTL) mapping and genome-wide association analysis identified 10 QTLs of sex-related and six QTLs of growth-related traits at LG17 and LG28, respectively. Candidate genes associated with sex dimorphism, including spata2, spata5, sf3, zbtb38, and fox, were identified within QTL intervals on the LG17. A sex-linked marker with simple sequence repeats (SSR) in zbtb38 gene of the LG17 was validated for practical verification of sex in the channel catfish. Thus, the LG17 was considered as a sex-related LG. Potential growth-related genes were also identified, including important regulators such as megf9, npffr1, and gas1. In a word, we constructed the high-density genetic linkage map and developed the sex-linked marker in channel catfish, which are important genetic resources for future marker-assisted selection (MAS) of this economically important teleost.
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Affiliation(s)
- Shiyong Zhang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Xinhui Zhang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Beijing Genomics Institute, Shenzhen, China
| | - Xiaohui Chen
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Tengfei Xu
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Beijing Genomics Institute, Shenzhen, China
| | - Minghua Wang
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Qin Qin
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Liqiang Zhong
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Hucheng Jiang
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Xiaohua Zhu
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
| | - Hongyan Liu
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
| | - Junjie Shao
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
| | - Zhifei Zhu
- BGI-Zhenjiang Institute of Hydrobiology, Zhenjiang, China
| | - Qiong Shi
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Beijing Genomics Institute, Shenzhen, China
| | - Wenji Bian
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Xinxin You
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Beijing Genomics Institute, Shenzhen, China
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Fang S, Zhang Y, Shi X, Zheng H, Li S, Zhang Y, Fazhan H, Waiho K, Tan H, Ikhwanuddin M, Ma H. Identification of male-specific SNP markers and development of PCR-based genetic sex identification technique in crucifix crab (Charybdis feriatus) with implication of an XX/XY sex determination system. Genomics 2019; 112:404-411. [PMID: 30851358 DOI: 10.1016/j.ygeno.2019.03.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 02/24/2019] [Accepted: 03/05/2019] [Indexed: 12/21/2022]
Abstract
In this study, we first identified male-specific SNP markers using restriction site-associated DNA sequencing, and further developed a PCR-based sex identification technique for Charybdis feriatus. A total of 296.96 million clean reads were obtained, with 114.95 and 182.01 million from females and males. After assembly and alignment, 10 SNP markers were identified being heterozygous in males but homozygous in females. Five markers were further confirmed to be male-specific in a large number of individuals. Moreover, two male-specific sense primers and a common antisense primer were designed, using which, a PCR-based genetic sex identification method was successfully developed and used to identify the sex of 103 individuals, with a result of 49 females and 54 males. The presence of male-specific SNP markers suggests an XX/XY sex determination system for C. feriatus. These findings should be helpful for better understanding sex determination mechanism, and drafting artificial breeding program in crustaceans.
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Affiliation(s)
- Shaobin Fang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Yin Zhang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China
| | - Xi Shi
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China
| | - Huaiping Zheng
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China
| | - Shengkang Li
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China
| | - Yueling Zhang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China
| | - Hanafiah Fazhan
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China
| | - Khor Waiho
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China
| | - Huaqiang Tan
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China
| | - Mhd Ikhwanuddin
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China; Institute of Tropical Aquaculture, Universiti Malaysia Terengganu, Kuala Terengganu 21030, Malaysia
| | - Hongyu Ma
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
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22
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Jia H, Jia H, Cai Q, Wang Y, Zhao H, Yang W, Wang G, Li Y, Zhan D, Shen Y, Niu Q, Chang L, Qiu J, Zhao L, Xie H, Fu W, Jin J, Li X, Jiao Y, Zhou C, Tu T, Chai C, Gao J, Fan L, van de Weg E, Wang J, Gao Z. The red bayberry genome and genetic basis of sex determination. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:397-409. [PMID: 29992702 PMCID: PMC6335074 DOI: 10.1111/pbi.12985] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 07/01/2018] [Accepted: 07/04/2018] [Indexed: 05/12/2023]
Abstract
Morella rubra, red bayberry, is an economically important fruit tree in south China. Here, we assembled the first high-quality genome for both a female and a male individual of red bayberry. The genome size was 313-Mb, and 90% sequences were assembled into eight pseudo chromosome molecules, with 32 493 predicted genes. By whole-genome comparison between the female and male and association analysis with sequences of bulked and individual DNA samples from female and male, a 59-Kb region determining female was identified and located on distal end of pseudochromosome 8, which contains abundant transposable element and seven putative genes, four of them are related to sex floral development. This 59-Kb female-specific region was likely to be derived from duplication and rearrangement of paralogous genes and retained non-recombinant in the female-specific region. Sex-specific molecular markers developed from candidate genes co-segregated with sex in a genetically diverse female and male germplasm. We propose sex determination follow the ZW model of female heterogamety. The genome sequence of red bayberry provides a valuable resource for plant sex chromosome evolution and also provides important insights for molecular biology, genetics and modern breeding in Myricaceae family.
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Affiliation(s)
- Hui‐Min Jia
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Hui‐Juan Jia
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | | | - Yan Wang
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Hai‐Bo Zhao
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Wei‐Fei Yang
- Hangzhou 1 Gene LtdHangzhouChina
- Forestry Technology Extension CenterYuyaoNingboChina
- Present address:
Annoroad Gene Tech. Co., LtdBeijingChina
| | - Guo‐Yun Wang
- Forestry Technology Extension CenterYuyaoNingboChina
| | - Ying‐Hui Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | | | - Yu‐Tong Shen
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Qing‐Feng Niu
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
- Shanghai Center for Plant Stress Biology, and National Key Laboratory of Plant Molecular GeneticsCenter of Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghaiChina
| | - Le Chang
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Jie Qiu
- Institute of Crop Science & Institute of BioinformaticsCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Lan Zhao
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Han‐Bing Xie
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Wan‐Yi Fu
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Jing Jin
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Xiong‐Wei Li
- Forest & Fruit Tree InstituteShanghai Academy of Agricultural SciencesShanghaiChina
| | - Yun Jiao
- Institute of ForestryNingbo Academy of Agricultural ScienceNingboChina
| | | | - Ting Tu
- Shunmei Breeding and Propagation Centre for Chinese BayberryYuyaoChina
| | | | | | - Long‐Jiang Fan
- Institute of Crop Science & Institute of BioinformaticsCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Eric van de Weg
- Plant Breeding‐Wageningen University and ResearchWageningenThe Netherlands
| | | | - Zhong‐Shan Gao
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
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23
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Shi X, Waiho K, Li X, Ikhwanuddin M, Miao G, Lin F, Zhang Y, Li S, Zheng H, Liu W, Aweya JJ, Azmie G, Baylon JC, Quinitio ET, Ma H. Female-specific SNP markers provide insights into a WZ/ZZ sex determination system for mud crabs Scylla paramamosain, S. tranquebarica and S. serrata with a rapid method for genetic sex identification. BMC Genomics 2018; 19:981. [PMID: 30594128 PMCID: PMC6311006 DOI: 10.1186/s12864-018-5380-8] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 12/16/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Mud crabs, Scylla spp., are commercially important large-size marine crustaceans in the Indo-West Pacific region. As females have the higher growth rate and economic value, the production of all female stocks is extremely essential in aquaculture. However, the sex determination mechanism is still unclear. Development of sex-specific genetic markers based on next-generation sequencing proved to be an effective tool for discovering sex determination system in various animals. RESULTS Restriction-site associated DNA sequencing (RAD-seq) was employed to isolate sex-specific SNP markers for S. paramamosain. A total of 335.6 million raw reads were obtained from 20 individuals, of which 204.7 million were from 10 females and 130.9 million from 10 males. After sequence assembly and female-male comparison, 20 SNP markers were identified to be sex-specific. Furthermore, ten SNPs in a short sequence (285 bp) were confirmed heterozygous in females and homozygous in males in a large population by PCR amplification and sequencing. Subsequently, a female-specific primer was successfully designed according to the female-specific nucleotide which could amplify an expected band from females but not from males. Thus, a rapid and effective method for molecular sexing in S. paramamosain was developed, meanwhile, this method could successfully identify the sex of S. tranquebarica and S. serrata. Finally, nine and four female-specific SNP markers were detected in S. tranquebarica and S. serrata, respectively. CONCLUSIONS Sex-specific SNP markers were firstly identified in crab species and showed female heterogamety and male homogamety, which provided strong genetic evidence for a WZ/ZZ sex determination system in mud crabs S. paramamosain, S. tranquebarica and S. serrata. These findings will lay a solid foundation for the study of sex determination mechanism, sex chromosome evolution, and the development of mono-sex population in crustaceans.
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Affiliation(s)
- Xi Shi
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, 243 Daxue Road, Shantou, 515063 China
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063 China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071 China
| | - Khor Waiho
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, 243 Daxue Road, Shantou, 515063 China
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063 China
| | - Xincang Li
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, 200090 China
| | - Mhd Ikhwanuddin
- Institute of Tropical Aquaculture, Universiti Malaysia Terengganu, 21030 Kuala Terengganu, Malaysia
| | - Guidong Miao
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, 243 Daxue Road, Shantou, 515063 China
| | - Fan Lin
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, 243 Daxue Road, Shantou, 515063 China
| | - Yueling Zhang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, 243 Daxue Road, Shantou, 515063 China
| | - Shengkang Li
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, 243 Daxue Road, Shantou, 515063 China
| | - Huaiping Zheng
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, 243 Daxue Road, Shantou, 515063 China
| | - Wenhua Liu
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, 243 Daxue Road, Shantou, 515063 China
| | - Jude Juventus Aweya
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, 243 Daxue Road, Shantou, 515063 China
| | - Ghazali Azmie
- Institute of Tropical Aquaculture, Universiti Malaysia Terengganu, 21030 Kuala Terengganu, Malaysia
| | - Juliana C. Baylon
- Division of Biological Sciences, College of Arts and Sciences, University of the Philippines, Visayas, 5023 Miagao, Philippines
| | - Emilia T. Quinitio
- Aquaculture Department, Southeast Asian Fisheries Development Center, 5021 Tigbauan, Philippines
| | - Hongyu Ma
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, 243 Daxue Road, Shantou, 515063 China
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063 China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071 China
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24
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Li B, Lu X, Dou J, Aslam A, Gao L, Zhao S, He N, Liu W. Construction of A High-Density Genetic Map and Mapping of Fruit Traits in Watermelon ( Citrullus Lanatus L.) Based on Whole-Genome Resequencing. Int J Mol Sci 2018; 19:ijms19103268. [PMID: 30347873 PMCID: PMC6214002 DOI: 10.3390/ijms19103268] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 10/15/2018] [Accepted: 10/18/2018] [Indexed: 12/26/2022] Open
Abstract
Watermelon (Citrullus lanatus L.) is an important horticultural crop that is grown worldwide and has a high economic value. To dissect the loci associated with important horticultural traits and to analyze the genetic and genomic information of this species, a high-density genetic map was constructed based on whole-genome resequencing (WGR), a powerful high-resolution method for single-nucleotide polymorphism (SNP) marker development, genetic map construction, and gene mapping. Resequencing of both parental lines and 126 recombinant inbred lines (RIL) resulted in the detection of 178,762 single-nucleotide polymorphism (SNP) markers in the parental lines at a sequencing depth greater than four-fold. Additionally, 2132 recombination bin markers comprising 103,029 SNP markers were mapped onto 11 linkage groups (LGs). Substantially more SNP markers were mapped to the genetic map compared with other recent studies. The total length of the linkage map was 1508.94 cM, with an average distance of 0.74 cM between adjacent bin markers. Based on this genetic map, one locus for fruit bitterness, one locus for rind color, and one locus for seed coat color with high LOD scores (58.361, 18.353, 26.852) were identified on chromosome 1, chromosome 8, and chromosome 3, respectively. These prominent loci were identified in a region of 6.16 Mb, 2.07 Mb, and 0.37 Mb, respectively. On the basis of current research, the high-density map and mapping results will provide a valuable tool for identifying candidate genes, map-based gene cloning, comparative mapping, and marker-assisted selection (MAS) in watermelon breeding.
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Affiliation(s)
- Bingbing Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Xuqiang Lu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Junling Dou
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Ali Aslam
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Lei Gao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Shengjie Zhao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Nan He
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Wenge Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
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25
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Abstract
Levels and patterns of genetic diversity can provide insights into a population’s history. In species with sex chromosomes, differences between genomic regions with unique inheritance patterns can be used to distinguish between different sets of possible demographic and selective events. This review introduces the differences in population history for sex chromosomes and autosomes, provides the expectations for genetic diversity across the genome under different evolutionary scenarios, and gives an introductory description for how deviations in these expectations are calculated and can be interpreted. Predominantly, diversity on the sex chromosomes has been used to explore and address three research areas: 1) Mating patterns and sex-biased variance in reproductive success, 2) signatures of selection, and 3) evidence for modes of speciation and introgression. After introducing the theory, this review catalogs recent studies of genetic diversity on the sex chromosomes across species within the major research areas that sex chromosomes are typically applied to, arguing that there are broad similarities not only between male-heterogametic (XX/XY) and female-heterogametic (ZZ/ZW) sex determination systems but also any mating system with reduced recombination in a sex-determining region. Further, general patterns of reduced diversity in nonrecombining regions are shared across plants and animals. There are unique patterns across populations with vastly different patterns of mating and speciation, but these do not tend to cluster by taxa or sex determination system.
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Affiliation(s)
- Melissa A Wilson Sayres
- School of Life Sciences, Center for Evolution and Medicine, The Biodesign Institute, Arizona State University
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26
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Veltsos P, Cossard G, Beaudoing E, Beydon G, Savova Bianchi D, Roux C, C González-Martínez S, R Pannell J. Size and Content of the Sex-Determining Region of the Y Chromosome in Dioecious Mercurialis annua, a Plant with Homomorphic Sex Chromosomes. Genes (Basel) 2018; 9:E277. [PMID: 29844299 PMCID: PMC6027223 DOI: 10.3390/genes9060277] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 05/16/2018] [Accepted: 05/23/2018] [Indexed: 01/01/2023] Open
Abstract
Dioecious plants vary in whether their sex chromosomes are heteromorphic or homomorphic, but even homomorphic sex chromosomes may show divergence between homologues in the non-recombining, sex-determining region (SDR). Very little is known about the SDR of these species, which might represent particularly early stages of sex-chromosome evolution. Here, we assess the size and content of the SDR of the diploid dioecious herb Mercurialis annua, a species with homomorphic sex chromosomes and mild Y-chromosome degeneration. We used RNA sequencing (RNAseq) to identify new Y-linked markers for M. annua. Twelve of 24 transcripts showing male-specific expression in a previous experiment could be amplified by polymerase chain reaction (PCR) only from males, and are thus likely to be Y-linked. Analysis of genome-capture data from multiple populations of M. annua pointed to an additional six male-limited (and thus Y-linked) sequences. We used these markers to identify and sequence 17 sex-linked bacterial artificial chromosomes (BACs), which form 11 groups of non-overlapping sequences, covering a total sequence length of about 1.5 Mb. Content analysis of this region suggests that it is enriched for repeats, has low gene density, and contains few candidate sex-determining genes. The BACs map to a subset of the sex-linked region of the genetic map, which we estimate to be at least 14.5 Mb. This is substantially larger than estimates for other dioecious plants with homomorphic sex chromosomes, both in absolute terms and relative to their genome sizes. Our data provide a rare, high-resolution view of the homomorphic Y chromosome of a dioecious plant.
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Affiliation(s)
- Paris Veltsos
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
- Department of Biology, Jordan Hall, 1001 East Third Street, Indiana University, Bloomington, IN 47405, USA.
| | - Guillaume Cossard
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
| | - Emmanuel Beaudoing
- Faculty of Biology and Medicine, University of Lausanne, Bâtiment Génopode, 1014 Lausanne, Switzerland.
| | - Genséric Beydon
- National Centre for Genomic Resources (CNRGV), 24 Chemin de Borde Rouge-Auzeville-CS52627, 31326 Castanet Tolosan Cedex, France.
| | | | - Camille Roux
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
- CNRS, University of Lille, UMR 8198-Evo-Eco-Paleo, F-59000 Lille, France.
| | - Santiago C González-Martínez
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
- BIOGECO, INRA, University of Bordeaux, 33610 Cestas, France.
| | - John R Pannell
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
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27
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Li Y, Fang J, Qi X, Lin M, Zhong Y, Sun L, Cui W. Combined Analysis of the Fruit Metabolome and Transcriptome Reveals Candidate Genes Involved in Flavonoid Biosynthesis in Actinidia arguta. Int J Mol Sci 2018; 19:ijms19051471. [PMID: 29762529 PMCID: PMC5983832 DOI: 10.3390/ijms19051471] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 05/09/2018] [Accepted: 05/09/2018] [Indexed: 12/12/2022] Open
Abstract
To assess the interrelation between the change of metabolites and the change of fruit color, we performed a combined metabolome and transcriptome analysis of the flesh in two different Actinidia arguta cultivars: "HB" ("Hongbaoshixing") and "YF" ("Yongfengyihao") at two different fruit developmental stages: 70d (days after full bloom) and 100d (days after full bloom). Metabolite and transcript profiling was obtained by ultra-performance liquid chromatography quadrupole time-of-flight tandem mass spectrometer and high-throughput RNA sequencing, respectively. The identification and quantification results of metabolites showed that a total of 28,837 metabolites had been obtained, of which 13,715 were annotated. In comparison of HB100 vs. HB70, 41 metabolites were identified as being flavonoids, 7 of which, with significant difference, were identified as bracteatin, luteolin, dihydromyricetin, cyanidin, pelargonidin, delphinidin and (-)-epigallocatechin. Association analysis between metabolome and transcriptome revealed that there were two metabolic pathways presenting significant differences during fruit development, one of which was flavonoid biosynthesis, in which 14 structural genes were selected to conduct expression analysis, as well as 5 transcription factor genes obtained by transcriptome analysis. RT-qPCR results and cluster analysis revealed that AaF3H, AaLDOX, AaUFGT, AaMYB, AabHLH, and AaHB2 showed the best possibility of being candidate genes. A regulatory network of flavonoid biosynthesis was established to illustrate differentially expressed candidate genes involved in accumulation of metabolites with significant differences, inducing red coloring during fruit development. Such a regulatory network linking genes and flavonoids revealed a system involved in the pigmentation of all-red-fleshed and all-green-fleshed A. arguta, suggesting this conjunct analysis approach is not only useful in understanding the relationship between genotype and phenotype, but is also a powerful tool for providing more valuable information for breeding.
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Affiliation(s)
- Yukuo Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Jinbao Fang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Xiujuan Qi
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Miaomiao Lin
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Yunpeng Zhong
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Leiming Sun
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Wen Cui
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
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28
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Pilkington SM, Crowhurst R, Hilario E, Nardozza S, Fraser L, Peng Y, Gunaseelan K, Simpson R, Tahir J, Deroles SC, Templeton K, Luo Z, Davy M, Cheng C, McNeilage M, Scaglione D, Liu Y, Zhang Q, Datson P, De Silva N, Gardiner SE, Bassett H, Chagné D, McCallum J, Dzierzon H, Deng C, Wang YY, Barron L, Manako K, Bowen J, Foster TM, Erridge ZA, Tiffin H, Waite CN, Davies KM, Grierson EP, Laing WA, Kirk R, Chen X, Wood M, Montefiori M, Brummell DA, Schwinn KE, Catanach A, Fullerton C, Li D, Meiyalaghan S, Nieuwenhuizen N, Read N, Prakash R, Hunter D, Zhang H, McKenzie M, Knäbel M, Harris A, Allan AC, Gleave A, Chen A, Janssen BJ, Plunkett B, Ampomah-Dwamena C, Voogd C, Leif D, Lafferty D, Souleyre EJF, Varkonyi-Gasic E, Gambi F, Hanley J, Yao JL, Cheung J, David KM, Warren B, Marsh K, Snowden KC, Lin-Wang K, Brian L, Martinez-Sanchez M, Wang M, Ileperuma N, Macnee N, Campin R, McAtee P, Drummond RSM, Espley RV, Ireland HS, Wu R, Atkinson RG, Karunairetnam S, Bulley S, Chunkath S, Hanley Z, Storey R, Thrimawithana AH, Thomson S, David C, Testolin R, Huang H, Hellens RP, Schaffer RJ. A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants. BMC Genomics 2018; 19:257. [PMID: 29661190 PMCID: PMC5902842 DOI: 10.1186/s12864-018-4656-3] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Accepted: 04/10/2018] [Indexed: 11/29/2022] Open
Abstract
Background Most published genome sequences are drafts, and most are dominated by computational gene prediction. Draft genomes typically incorporate considerable sequence data that are not assigned to chromosomes, and predicted genes without quality confidence measures. The current Actinidia chinensis (kiwifruit) ‘Hongyang’ draft genome has 164 Mb of sequences unassigned to pseudo-chromosomes, and omissions have been identified in the gene models. Results A second genome of an A. chinensis (genotype Red5) was fully sequenced. This new sequence resulted in a 554.0 Mb assembly with all but 6 Mb assigned to pseudo-chromosomes. Pseudo-chromosomal comparisons showed a considerable number of translocation events have occurred following a whole genome duplication (WGD) event some consistent with centromeric Robertsonian-like translocations. RNA sequencing data from 12 tissues and ab initio analysis informed a genome-wide manual annotation, using the WebApollo tool. In total, 33,044 gene loci represented by 33,123 isoforms were identified, named and tagged for quality of evidential support. Of these 3114 (9.4%) were identical to a protein within ‘Hongyang’ The Kiwifruit Information Resource (KIR v2). Some proportion of the differences will be varietal polymorphisms. However, as most computationally predicted Red5 models required manual re-annotation this proportion is expected to be small. The quality of the new gene models was tested by fully sequencing 550 cloned ‘Hort16A’ cDNAs and comparing with the predicted protein models for Red5 and both the original ‘Hongyang’ assembly and the revised annotation from KIR v2. Only 48.9% and 63.5% of the cDNAs had a match with 90% identity or better to the original and revised ‘Hongyang’ annotation, respectively, compared with 90.9% to the Red5 models. Conclusions Our study highlights the need to take a cautious approach to draft genomes and computationally predicted genes. Our use of the manual annotation tool WebApollo facilitated manual checking and correction of gene models enabling improvement of computational prediction. This utility was especially relevant for certain types of gene families such as the EXPANSIN like genes. Finally, this high quality gene set will supply the kiwifruit and general plant community with a new tool for genomics and other comparative analysis. Electronic supplementary material The online version of this article (10.1186/s12864-018-4656-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sarah M Pilkington
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Ross Crowhurst
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Elena Hilario
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Simona Nardozza
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Lena Fraser
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Yongyan Peng
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand.,School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Kularajathevan Gunaseelan
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Robert Simpson
- PFR, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Jibran Tahir
- PFR, Private Bag 11600, Palmerston North, 4442, New Zealand
| | | | - Kerry Templeton
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Zhiwei Luo
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Marcus Davy
- PFR, 412 No 1 Road, Te Puke, Bay of Plenty, 3182, New Zealand
| | - Canhong Cheng
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Mark McNeilage
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Davide Scaglione
- IGA Technology Services, Parco Scientifico e Tecnologico, Udine, Italy
| | - Yifei Liu
- South China Botanic Gardens, Chinese Academy of Sciences, Guangzhou, 510650, Guangdong, China
| | - Qiong Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Wuhan, China
| | - Paul Datson
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Nihal De Silva
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | | | | | - David Chagné
- PFR, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - John McCallum
- PFR, Private Bag 4704, Christchurch, 8140, New Zealand
| | - Helge Dzierzon
- PFR, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Cecilia Deng
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Yen-Yi Wang
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Lorna Barron
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Kelvina Manako
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Judith Bowen
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Toshi M Foster
- PFR, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Zoe A Erridge
- PFR, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Heather Tiffin
- PFR, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Chethi N Waite
- PFR, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Kevin M Davies
- PFR, Private Bag 11600, Palmerston North, 4442, New Zealand
| | | | | | - Rebecca Kirk
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Xiuyin Chen
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Marion Wood
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Mirco Montefiori
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | | | | | | | - Christina Fullerton
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Dawei Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Wuhan, China
| | | | - Niels Nieuwenhuizen
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Nicola Read
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Roneel Prakash
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Don Hunter
- PFR, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Huaibi Zhang
- PFR, Private Bag 11600, Palmerston North, 4442, New Zealand
| | | | - Mareike Knäbel
- PFR, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Alastair Harris
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Andrew C Allan
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand.,School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Andrew Gleave
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Angela Chen
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Bart J Janssen
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Blue Plunkett
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Charles Ampomah-Dwamena
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Charlotte Voogd
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Davin Leif
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand.,School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Declan Lafferty
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Edwige J F Souleyre
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Erika Varkonyi-Gasic
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Francesco Gambi
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Jenny Hanley
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Jia-Long Yao
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Joey Cheung
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Karine M David
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Ben Warren
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Ken Marsh
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Kimberley C Snowden
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Kui Lin-Wang
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Lara Brian
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Marcela Martinez-Sanchez
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Mindy Wang
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Nadeesha Ileperuma
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Nikolai Macnee
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Robert Campin
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Peter McAtee
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Revel S M Drummond
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Richard V Espley
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Hilary S Ireland
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Rongmei Wu
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Ross G Atkinson
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Sakuntala Karunairetnam
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Sean Bulley
- PFR, 412 No 1 Road, Te Puke, Bay of Plenty, 3182, New Zealand
| | - Shayhan Chunkath
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Zac Hanley
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Roy Storey
- PFR, 412 No 1 Road, Te Puke, Bay of Plenty, 3182, New Zealand
| | - Amali H Thrimawithana
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Susan Thomson
- PFR, Private Bag 4704, Christchurch, 8140, New Zealand
| | - Charles David
- PFR, Private Bag 4704, Christchurch, 8140, New Zealand
| | - Raffaele Testolin
- IGA Technology Services, Parco Scientifico e Tecnologico, Udine, Italy.,Department of Agricultural and Environmental Sciences, University of Udine, Via delle Scienze 208, 33100, Udine, Italy
| | - Hongwen Huang
- South China Botanic Gardens, Chinese Academy of Sciences, Guangzhou, 510650, Guangdong, China.,Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Wuhan, China
| | - Roger P Hellens
- Institute for Future Environments, Queensland University of Technology (QUT), Brisbane, 4001, Australia
| | - Robert J Schaffer
- The New Zealand Institute for Plant & Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand. .,School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.
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29
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Akagi T, Henry IM, Ohtani H, Morimoto T, Beppu K, Kataoka I, Tao R. A Y-Encoded Suppressor of Feminization Arose via Lineage-Specific Duplication of a Cytokinin Response Regulator in Kiwifruit. THE PLANT CELL 2018; 30:780-795. [PMID: 29626069 PMCID: PMC5969274 DOI: 10.1105/tpc.17.00787] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 03/13/2018] [Accepted: 04/05/2018] [Indexed: 05/19/2023]
Abstract
Dioecy, the presence of male and female flowers on distinct individuals, has evolved independently in multiple plant lineages, and the genes involved in this differential development are just starting to be uncovered in a few species. Here, we used genomic approaches to investigate this pathway in kiwifruits (genus Actinidia). Genome-wide cataloging of male-specific subsequences, combined with transcriptome analysis, led to the identification of a type-C cytokinin response regulator as a potential sex determinant gene in this genus. Functional transgenic analyses in two model systems, Arabidopsis thaliana and Nicotiana tabacum, indicated that this gene acts as a dominant suppressor of carpel development, prompting us to name it Shy Girl (SyGI). Evolutionary analyses in a panel of Actinidia species revealed that SyGI is located in the Y-specific region of the genome and probably arose from a lineage-specific gene duplication. Comparisons with the duplicated autosomal counterpart, and with orthologs from other angiosperms, suggest that the SyGI-specific duplication and subsequent evolution of cis-elements may have played a key role in the acquisition of separate sexes in this species.
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Affiliation(s)
- Takashi Akagi
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
- Japan Science and Technology Agency, PRESTO, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Isabelle M Henry
- Genome Center and Department of Plant Biology, University of California, Davis, California 95616
| | - Haruka Ohtani
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Takuya Morimoto
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Kenji Beppu
- Faculty of Agriculture, Kagawa University, Miki, Kagawa 761-0795, Japan
| | - Ikuo Kataoka
- Faculty of Agriculture, Kagawa University, Miki, Kagawa 761-0795, Japan
| | - Ryutaro Tao
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
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30
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Li Y, Fang J, Qi X, Lin M, Zhong Y, Sun L. A key structural gene, AaLDOX, is involved in anthocyanin biosynthesis in all red-fleshed kiwifruit (Actinidia arguta) based on transcriptome analysis. Gene 2018; 648:31-41. [PMID: 29309888 DOI: 10.1016/j.gene.2018.01.022] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 12/31/2017] [Accepted: 01/05/2018] [Indexed: 12/22/2022]
Abstract
Study on kiwifruit (Actinidia chinensis and A. deliciosa) color mainly concentrated in green and yellow-fleshed cultivars, less about molecular mechanism of red-fleshed trait formation, rarely in all red-fleshed fruit. Using 'Tianyuanhong' and 'Yongfengyihao' ('TY', a kind of all red-fleshed cultivar, from Actinidia arguta; 'YF', a kind of all green-fleshed cultivar, also from Actinidia arguta) as experimental material, we performed RNA-seq to obtain 202,742 unigenes with an average length of 603bp and N50 of 873bp via transcriptome data analysis. Of these unigenes, 72,508 (35.76%) were annotated and 997 were assigned to secondary metabolic pathways, of which 104 unigenes were involved in flavonoid and anthocyanin biosynthesis. According to the parameter log2fold-change and p-adjusted, 12 differentially expressed structural genes were selected for performing expression profiles and cluster analysis. Physiological traits including color ration, hue angle, and anthocyanin content were also investigated. From the results, we concluded AaLDOX (genes encoding leucoanthocyanidin dioxygenase) maybe the key gene controlling anthocyanin biosynthesis in flesh of 'TY' kiwifruit, which promoted accumulation of anthocyanin, finally leading to the red flesh coloration.
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Affiliation(s)
- Yukuo Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, PR China
| | - Jinbao Fang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, PR China.
| | - Xiujuan Qi
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, PR China.
| | - Miaomiao Lin
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, PR China.
| | - Yunpeng Zhong
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, PR China
| | - Leiming Sun
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, PR China
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31
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Mei L, Dong N, Li F, Li N, Yao M, Chen F, Tang L. Transcriptome analysis of female and male flower buds of Idesia polycarpa Maxim. var. vestita Diels. ELECTRON J BIOTECHN 2017. [DOI: 10.1016/j.ejbt.2017.07.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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32
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Wang J, Su K, Guo Y, Xing H, Zhao Y, Liu Z, Li K, Guo X. Construction of a high-density genetic map for grape using specific length amplified fragment (SLAF) sequencing. PLoS One 2017; 12:e0181728. [PMID: 28746364 PMCID: PMC5528875 DOI: 10.1371/journal.pone.0181728] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 07/06/2017] [Indexed: 12/30/2022] Open
Abstract
Genetic maps are important tools in plant genomics and breeding. We report a large-scale discovery of single nucleotide polymorphisms (SNPs) using the specific length amplified fragment sequencing (SLAF-seq) technique for the construction of high-density genetic maps for two elite wine grape cultivars, ‘Chardonnay’ and ‘Beibinghong’, and their 130 F1 plants. A total of 372.53 M paired-end reads were obtained after preprocessing. The average sequencing depth was 33.81 for ‘Chardonnay’ (the female parent), 48.20 for ‘Beibinghong’ (the male parent), and 12.66 for the F1 offspring. We detected 202,349 high-quality SLAFs of which 144,972 were polymorphic; 10,042 SNPs were used to construct a genetic map that spanned 1,969.95 cM, with an average genetic distance of 0.23 cM between adjacent markers. This genetic map contains the largest molecular marker number of the grape maps so far reported. We thus demonstrate that SLAF-seq is a promising strategy for the construction of high-density genetic maps; the map that we report here is a good potential resource for QTL mapping of genes linked to major economic and agronomic traits, map-based cloning, and marker-assisted selection of grape.
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Affiliation(s)
- Jiahui Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, P.R. China
| | - Kai Su
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, P.R. China
| | - Yinshan Guo
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, P.R. China
- * E-mail: (YSG); (XWG)
| | - Huiyang Xing
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, P.R. China
| | - Yuhui Zhao
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, P.R. China
| | - Zhendong Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, P.R. China
| | - Kun Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, P.R. China
| | - Xiuwu Guo
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, P.R. China
- * E-mail: (YSG); (XWG)
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33
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Tang P, Zhang Q, Yao X. Comparative transcript profiling explores differentially expressed genes associated with sexual phenotype in kiwifruit. PLoS One 2017; 12:e0180542. [PMID: 28672040 PMCID: PMC5495465 DOI: 10.1371/journal.pone.0180542] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 06/16/2017] [Indexed: 12/02/2022] Open
Abstract
Background Kiwifruit is a perennial, deciduous and functionally dioecious plant. However, very little is known about the whole-genome molecular mechanisms contributing to distinct sexual phenotypes. To gain a global view of genes differentially expressed between male and female flowers, we analyzed genome-wide gene expression profiles in the flowers of male and female plants using high-throughput RNA sequencing. Results A total of 53.5 million reads were generated. Based on the alignments of unigenes to kiwifruit genome predicted genes, a total of 39,040 unique genes with a mean length of 970 bp were identified. There were 2,503 UniGenes differentially expressed between female and male flowers, with 1,793 up-regulated and 710 down-regulated in the female flowers. Moreover, the gene expression pattern of 17 out of 19 unigenes differentially expressed between male and female flowers revealed by RNA-Seq was confirmed by real-time quantitative PCR (qRT-PCR). Conclusions Here, we obtained a large number of EST sequences from female and male flowers of kiwifruit. This comparative transcriptome analysis provides an invaluable resource for gene expression, genomics, and functional genomic studies in A. chinensis and its related species. This study also represents a first step toward the investigation of genes involved in kiwifruit sex determination.
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Affiliation(s)
- Ping Tang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Qiong Zhang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Xiaohong Yao
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan, Hubei, China
- * E-mail:
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34
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Sousa A, Fuchs J, Renner SS. Cytogenetic comparison of heteromorphic and homomorphic sex chromosomes in Coccinia (Cucurbitaceae) points to sex chromosome turnover. Chromosome Res 2017; 25:191-200. [PMID: 28343268 DOI: 10.1007/s10577-017-9555-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 02/17/2017] [Accepted: 02/27/2017] [Indexed: 11/26/2022]
Abstract
Our understanding of the evolution of plant sex chromosomes is increasing rapidly due to high-throughput sequencing data and phylogenetic and molecular-cytogenetic approaches that make it possible to infer the evolutionary direction and steps leading from homomorphic to heteromorphic sex chromosomes. Here, we focus on four species of Coccinia, a genus of 25 dioecious species, including Coccinia grandis, the species with the largest known plant Y chromosome. Based on a phylogeny for the genus, we selected three species close to C. grandis to test the distribution of eight repetitive elements including two satellites, and several plastid and mitochondrial probes, that we had previously found to have distinct accumulation patterns in the C. grandis genome. Additionally, we determined C-values and performed immunostaining experiments with (peri-)centromere-specific antibodies on two species (for comparison with C. grandis). In spite of no microscopic chromosomal heteromorphism, single pairs of chromosomes in male cells of all three species accumulate some of the very same repeats that are enriched on the C. grandis Y chromosome, pointing to either old (previous) sex chromosomes or incipient (newly arising) ones, that is, to sex chromosome turnover. A 144-bp centromeric satellite repeat (CgCent) that characterizes all C. grandis chromosomes except the Y is highly abundant in all centromeric regions of the other species, indicating that the centromeric sequence of the Y chromosome diverged very recently.
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Affiliation(s)
- Aretuza Sousa
- Department of Biology, University of Munich (LMU), 80638, Munich, Germany.
| | - Jörg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany
| | - Susanne S Renner
- Department of Biology, University of Munich (LMU), 80638, Munich, Germany.
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35
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Tennessen JA, Govindarajulu R, Liston A, Ashman T. Homomorphic ZW chromosomes in a wild strawberry show distinctive recombination heterogeneity but a small sex-determining region. THE NEW PHYTOLOGIST 2016; 211:1412-23. [PMID: 27102236 PMCID: PMC5074332 DOI: 10.1111/nph.13983] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 03/21/2016] [Indexed: 05/10/2023]
Abstract
Recombination in ancient, heteromorphic sex chromosomes is typically suppressed at the sex-determining region (SDR) and proportionally elevated in the pseudoautosomal region (PAR). However, little is known about recombination dynamics of young, homomorphic plant sex chromosomes. We examine male and female function in crosses and unrelated samples of the dioecious octoploid strawberry Fragaria chiloensis in order to map the small and recently evolved SDR controlling both traits and to examine recombination patterns on the incipient ZW chromosome. The SDR of this ZW system is located within a 280 kb window, in which the maternal recombination rate is lower than the paternal one. In contrast to the SDR, the maternal PAR recombination rate is much higher than the rates of the paternal PAR or autosomes, culminating in an elevated chromosome-wide rate. W-specific divergence is elevated within the SDR and a single polymorphism is observed in high species-wide linkage disequilibrium with sex. Selection for recombination suppression within the small SDR may be weak, but fluctuating sex ratios could favor elevated recombination in the PAR to remove deleterious mutations on the W. The recombination dynamics of this nascent sex chromosome with a modestly diverged SDR may be typical of other dioecious plants.
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Affiliation(s)
- Jacob A. Tennessen
- Department of Integrative BiologyOregon State UniversityCorvallisOR97331USA
| | | | - Aaron Liston
- Department of Botany and Plant PathologyOregon State UniversityCorvallisOR97331USA
| | - Tia‐Lynn Ashman
- Department of Biological SciencesUniversity of PittsburghPittsburghPA15260‐3929USA
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