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Jia HM, Jiao Y, Wang GY, Li YH, Jia HJ, Wu HX, Chai CY, Dong X, Guo Y, Zhang L, Gao QK, Chen W, Song LJ, van de Weg E, Gao ZS. Genetic diversity of male and female Chinese bayberry (Myrica rubra) populations and identification of sex-associated markers. BMC Genomics 2015; 16:394. [PMID: 25986380 PMCID: PMC4436740 DOI: 10.1186/s12864-015-1602-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 05/01/2015] [Indexed: 11/25/2022] Open
Abstract
Background Chinese bayberry (Myrica rubra Sieb. & Zucc.) is an important subtropical evergreen fruit tree in southern China. Generally dioecious, the female plants are cultivated for fruit and have been studied extensively, but male plants have received very little attention. Knowledge of males may have a major impact on conservation and genetic improvement as well as on breeding. Using 84 polymorphic SSRs, we genotyped 213 M. rubra individuals (99 male individuals, 113 female varieties and 1 monoecious) and compared the difference in genetic diversity between the female and the male populations. Results Neighbour-joining cluster analysis separated M. rubra from three related species, and the male from female populations within M. rubra. By structure analysis, 178 M. rubra accessions were assigned to two subpopulations: Male dominated (98) and Female dominated (80). The well-known cultivars ‘Biqi’ and ‘Dongkui’, and the landraces ‘Fenhong’ are derived from three different gene pools. Female population had a slightly higher values of genetic diversity parameters (such as number of alleles and heterozygosity) than the male population, but not significantly different. The SSR loci ZJU062 and ZJU130 showed an empirical Fst value of 0.455 and 0.333, respectively, which are significantly above the 95 % confidence level, indicating that they are outlier loci related to sex separation. Conclusion The male and female populations of Chinese bayberry have similar genetic diversity in terms of average number of alleles and level of heterozygosity, but were clearly separated by genetic structure analysis due to two markers associated with sex type, ZJU062 and ZJU130. Zhejiang Province China could be the centre of diversity of M. rubra in China, with wide genetic diversity coverage; and the two representative cultivars ‘Biqi’ and ‘Dongkui’, and one landrace ‘Fenhong’ in three female subpopulations. This research provides genetic information on male and female Chinese bayberry and will act as a reference for breeding programs. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1602-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hui-min Jia
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, 310058, Hangzhou, Zhejiang, China.
| | - Yun Jiao
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, 310058, Hangzhou, Zhejiang, China.
| | - Guo-yun Wang
- Fruit Research Institute, 315400, Yuyao, Ningbo, PR China.
| | - Ying-hui Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA), Chinese Academy of Agricultural Sciences, Institute of Crop Science, 100081, Beijing, China.
| | - Hui-juan Jia
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, 310058, Hangzhou, Zhejiang, China.
| | - Hong-xia Wu
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, 310058, Hangzhou, Zhejiang, China.
| | - Chun-yan Chai
- Forestry Technology Extension Center, 315300, Cixi, Ningbo, China.
| | - Xiao Dong
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, 310058, Hangzhou, Zhejiang, China.
| | - Yanping Guo
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, 310058, Hangzhou, Zhejiang, China.
| | - Liping Zhang
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, 310058, Hangzhou, Zhejiang, China.
| | - Qi-kang Gao
- Bio-Macromolecules Analysis Lab, Analysis Center of Agrobiology, Environmental Sciences of Zhejiang University, 310058, Hangzhou, China.
| | - Wei Chen
- Zhejiang Institute of Subtropical Crops, Wenzhou, 325005, China.
| | - Li-Juan Song
- Wenzhou Vocational and Technical College, 325035, Wenzhou, China.
| | - Eric van de Weg
- Plant Breeding-Wageningen University and Research Centre, P.O. Box 16, 6700 AA, Wageningen, The Netherlands.
| | - Zhong-shan Gao
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, 310058, Hangzhou, Zhejiang, China.
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VanBuren R, Zeng F, Chen C, Zhang J, Wai CM, Han J, Aryal R, Gschwend AR, Wang J, Na JK, Huang L, Zhang L, Miao W, Gou J, Arro J, Guyot R, Moore RC, Wang ML, Zee F, Charlesworth D, Moore PH, Yu Q, Ming R. Origin and domestication of papaya Yh chromosome. Genome Res 2015; 25:524-33. [PMID: 25762551 PMCID: PMC4381524 DOI: 10.1101/gr.183905.114] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Accepted: 02/09/2015] [Indexed: 11/24/2022]
Abstract
Sex in papaya is controlled by a pair of nascent sex chromosomes. Females are XX, and two slightly different Y chromosomes distinguish males (XY) and hermaphrodites (XY(h)). The hermaphrodite-specific region of the Y(h) chromosome (HSY) and its X chromosome counterpart were sequenced and analyzed previously. We now report the sequence of the entire male-specific region of the Y (MSY). We used a BAC-by-BAC approach to sequence the MSY and resequence the Y regions of 24 wild males and the Y(h) regions of 12 cultivated hermaphrodites. The MSY and HSY regions have highly similar gene content and structure, and only 0.4% sequence divergence. The MSY sequences from wild males include three distinct haplotypes, associated with the populations' geographic locations, but gene flow is detected for other genomic regions. The Y(h) sequence is highly similar to one Y haplotype (MSY3) found only in wild dioecious populations from the north Pacific region of Costa Rica. The low MSY3-Y(h) divergence supports the hypothesis that hermaphrodite papaya is a product of human domestication. We estimate that Y(h) arose only ∼ 4000 yr ago, well after crop plant domestication in Mesoamerica >6200 yr ago but coinciding with the rise of the Maya civilization. The Y(h) chromosome has lower nucleotide diversity than the Y, or the genome regions that are not fully sex-linked, consistent with a domestication bottleneck. The identification of the ancestral MSY3 haplotype will expedite investigation of the mutation leading to the domestication of the hermaphrodite Y(h) chromosome. In turn, this mutation should identify the gene that was affected by the carpel-suppressing mutation that was involved in the evolution of males.
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Affiliation(s)
- Robert VanBuren
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China; Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Fanchang Zeng
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Cuixia Chen
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Jisen Zhang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Ching Man Wai
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Jennifer Han
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Rishi Aryal
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Andrea R Gschwend
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Jianping Wang
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Jong-Kuk Na
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Lixian Huang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Lingmao Zhang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Wenjing Miao
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Jiqing Gou
- Texas A&M AgriLife Research, Department of Plant Pathology and Microbiology, Texas A&M University System, Dallas, Texas 75252, USA
| | - Jie Arro
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Romain Guyot
- IRD, UMR DIADE, EVODYN, BP 64501, 34394 Montpellier Cedex 5, France
| | - Richard C Moore
- Department of Botany, Miami University, Oxford, Ohio 45056, USA
| | - Ming-Li Wang
- Hawaii Agriculture Research Center, Kunia, Hawaii 96759, USA
| | - Francis Zee
- USDA-ARS, Pacific Basin Agricultural Research Center, Hilo, Hawaii 96720, USA
| | - Deborah Charlesworth
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
| | - Paul H Moore
- Hawaii Agriculture Research Center, Kunia, Hawaii 96759, USA
| | - Qingyi Yu
- Texas A&M AgriLife Research, Department of Plant Pathology and Microbiology, Texas A&M University System, Dallas, Texas 75252, USA
| | - Ray Ming
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China; Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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Characterization of rubber tree microRNA in phytohormone response using large genomic DNA libraries, promoter sequence and gene expression analysis. Mol Genet Genomics 2014; 289:921-33. [PMID: 24859131 DOI: 10.1007/s00438-014-0862-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 05/05/2014] [Indexed: 10/25/2022]
Abstract
The para rubber tree is the most widely cultivated tree species for producing natural rubber (NR) latex. Unfortunately, rubber tree characteristics such as a long life cycle, heterozygous genetic backgrounds, and poorly understood genetic profiles are the obstacles to breeding new rubber tree varieties, such as those with improved NR yields. Recent evidence has revealed the potential importance of controlling microRNA (miRNA) decay in some aspects of NR regulation. To gain a better understanding of miRNAs and their relationship with rubber tree gene regulation networks, large genomic DNA insert-containing libraries were generated to complement the incomplete draft genome sequence and applied as a new powerful tool to predict a function of interested genes. Bacterial artificial chromosome and fosmid libraries, containing a total of 120,576 clones with an average insert size of 43.35 kb, provided approximately 2.42 haploid genome equivalents of coverage based on the estimated 2.15 gb rubber tree genome. Based on these library sequences, the precursors of 1 member of rubber tree-specific miRNAs and 12 members of conserved miRNAs were successfully identified. A panel of miRNAs was characterized for phytohormone response by precisely identifying phytohormone-responsive motifs in their promoter sequences. Furthermore, the quantitative real-time PCR on ethylene stimulation of rubber trees was performed to demonstrate that the miR2118, miR159, miR164 and miR166 are responsive to ethylene, thus confirmed the prediction by genomic DNA analysis. The cis-regulatory elements identified in the promoter regions of these miRNA genes help augment our understanding of miRNA gene regulation and provide a foundation for further investigation of the regulation of rubber tree miRNAs.
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Cação SMB, Silva NV, Domingues DS, Vieira LGE, Diniz LEC, Vinecky F, Alves GSC, Andrade AC, Carpentieri-Pipolo V, Pereira LFP. Construction and characterization of a BAC library from the Coffea arabica genotype Timor Hybrid CIFC 832/2. Genetica 2013; 141:217-26. [PMID: 23677718 DOI: 10.1007/s10709-013-9720-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 05/02/2013] [Indexed: 10/26/2022]
Abstract
Most of the world's coffee production originates from Coffea arabica, an allotetraploid species with low genetic diversity and for which few genomic resources are available. Genomic libraries with large DNA fragment inserts are useful tools for the study of plant genomes, including the production of physical maps, integration studies of physical and genetic maps, genome structure analysis and gene isolation by positional cloning. Here, we report the construction and characterization of a Bacterial Artificial Chromosome (BAC) library from C. arabica Timor Hybrid CIFC 832/2, a parental genotype for several modern coffee cultivars. The BAC library consists of 56,832 clones with an average insert size of 118 kb, which represents a dihaploid genome coverage of five to sixfold. The content of organellar DNA was estimated at 1.04 and 0.5 % for chloroplast and mitochondrial DNA, respectively. The BAC library was screened for the NADPH-dependent mannose-6-phosphate reductase gene (CaM6PR) with markers positioned on four linkage groups of a partial C. arabica genetic map. A mixed approach using PCR and membrane hybridization of BAC pools allowed for the discovery of nine BAC clones with the CaM6PR gene and 53 BAC clones that were anchored to the genetic map with simple sequence repeat markers. This library will be a useful tool for future studies on comparative genomics and the identification of genes and regulatory elements controlling major traits in this economically important crop species.
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Affiliation(s)
- S M B Cação
- Laboratory of Plant Biotechnology, Instituto Agronomico do Paraná, CP 481 Londrina, Paraná 86001-970, Brazil
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Na JK, Wang J, Murray JE, Gschwend AR, Zhang W, Yu Q, Navajas-Pérez R, Feltus FA, Chen C, Kubat Z, Moore PH, Jiang J, Paterson AH, Ming R. Construction of physical maps for the sex-specific regions of papaya sex chromosomes. BMC Genomics 2012; 13:176. [PMID: 22568889 PMCID: PMC3430574 DOI: 10.1186/1471-2164-13-176] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Accepted: 03/12/2012] [Indexed: 12/26/2022] Open
Abstract
Background Papaya is a major fruit crop in tropical and subtropical regions worldwide. It is trioecious with three sex forms: male, female, and hermaphrodite. Sex determination is controlled by a pair of nascent sex chromosomes with two slightly different Y chromosomes, Y for male and Yh for hermaphrodite. The sex chromosome genotypes are XY (male), XYh (hermaphrodite), and XX (female). The papaya hermaphrodite-specific Yh chromosome region (HSY) is pericentromeric and heterochromatic. Physical mapping of HSY and its X counterpart is essential for sequencing these regions and uncovering the early events of sex chromosome evolution and to identify the sex determination genes for crop improvement. Results A reiterate chromosome walking strategy was applied to construct the two physical maps with three bacterial artificial chromosome (BAC) libraries. The HSY physical map consists of 68 overlapped BACs on the minimum tiling path, and covers all four HSY-specific Knobs. One gap remained in the region of Knob 1, the only knob structure shared between HSY and X, due to the lack of HSY-specific sequences. This gap was filled on the physical map of the HSY corresponding region in the X chromosome. The X physical map consists of 44 BACs on the minimum tiling path with one gap remaining in the middle, due to the nature of highly repetitive sequences. This gap was filled on the HSY physical map. The borders of the non-recombining HSY were defined genetically by fine mapping using 1460 F2 individuals. The genetically defined HSY spanned approximately 8.5 Mb, whereas its X counterpart extended about 5.4 Mb including a 900 Kb region containing the Knob 1 shared by the HSY and X. The 8.5 Mb HSY corresponds to 4.5 Mb of its X counterpart, showing 4 Mb (89%) DNA sequence expansion. Conclusion The 89% increase of DNA sequence in HSY indicates rapid expansion of the Yh chromosome after genetic recombination was suppressed 2–3 million years ago. The genetically defined borders coincide with the common BACs on the minimum tiling paths of HSY and X. The minimum tiling paths of HSY and its X counterpart are being used for sequencing these X and Yh-specific regions.
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Affiliation(s)
- Jong-Kuk Na
- Department of Plant Biology, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
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