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Lu XM, Yu XF, Li GQ, Qu MH, Wang H, Liu C, Man YP, Jiang XH, Li MZ, Wang J, Chen QQ, Lei R, Zhao CC, Zhou YQ, Jiang ZW, Li ZZ, Zheng S, Dong C, Wang BL, Sun YX, Zhang HQ, Li JW, Mo QH, Zhang Y, Lou X, Peng HX, Yi YT, Wang HX, Zhang XJ, Wang YB, Wang D, Li L, Zhang Q, Wang WX, Liu Y, Gao L, Wu JH, Wang YC. Genome assembly of autotetraploid Actinidia arguta highlights adaptive evolution and enables dissection of important economic traits. PLANT COMMUNICATIONS 2024; 5:100856. [PMID: 38431772 PMCID: PMC11211551 DOI: 10.1016/j.xplc.2024.100856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 07/07/2023] [Accepted: 02/28/2024] [Indexed: 03/05/2024]
Abstract
Actinidia arguta, the most widely distributed Actinidia species and the second cultivated species in the genus, can be distinguished from the currently cultivated Actinidia chinensis on the basis of its small and smooth fruit, rapid softening, and excellent cold tolerance. Adaptive evolution of tetraploid Actinidia species and the genetic basis of their important agronomic traits are still unclear. Here, we generated a chromosome-scale genome assembly of an autotetraploid male A. arguta accession. The genome assembly was 2.77 Gb in length with a contig N50 of 9.97 Mb and was anchored onto 116 pseudo-chromosomes. Resequencing and clustering of 101 geographically representative accessions showed that they could be divided into two geographic groups, Southern and Northern, which first diverged 12.9 million years ago. A. arguta underwent two prominent expansions and one demographic bottleneck from the mid-Pleistocene climate transition to the late Pleistocene. Population genomics studies using paleoclimate data enabled us to discern the evolution of the species' adaptation to different historical environments. Three genes (AaCEL1, AaPME1, and AaDOF1) related to flesh softening were identified by multi-omics analysis, and their ability to accelerate flesh softening was verified through transient expression assays. A set of genes that characteristically regulate sexual dimorphism located on the sex chromosome (Chr3) or autosomal chromosomes showed biased expression during stamen or carpel development. This chromosome-level assembly of the autotetraploid A. arguta genome and the genes related to important agronomic traits will facilitate future functional genomics research and improvement of A. arguta.
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Affiliation(s)
- Xue-Mei Lu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Xiao-Fen Yu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Guo-Qiang Li
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Ming-Hao Qu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Huan Wang
- Wuhan Frasergen Bioinformatics Co., Ltd, Wuhan, Hubei, China
| | - Chuang Liu
- Institute of Soil and Fertilizer, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Yu-Ping Man
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Xiao-Han Jiang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Mu-Zi Li
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jian Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Qi-Qi Chen
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Rui Lei
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Cheng-Cheng Zhao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Yun-Qiu Zhou
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zheng-Wang Jiang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Zuo-Zhou Li
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Shang Zheng
- Wuhan Frasergen Bioinformatics Co., Ltd, Wuhan, Hubei, China
| | - Chang Dong
- College of Agricultural Sciences, Xichang University, Xichang, Sichuan, China
| | - Bai-Lin Wang
- Department of Horticulture, Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, China
| | - Yan-Xiang Sun
- College of Life Sciences, Langfang Normal University, Langfang, Hebei, China
| | - Hui-Qin Zhang
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Jie-Wei Li
- Guangxi Institute of Botany, Chinese Academy of Sciences, Guilin, Guangxi, China
| | - Quan-Hui Mo
- Guangxi Institute of Botany, Chinese Academy of Sciences, Guilin, Guangxi, China
| | - Ying Zhang
- Xi'an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, Xi'an, Shaanxi, China
| | - Xin Lou
- Institute of Modern Agricultural Research, Dalian University, Dalian, Liaoning, China
| | - Hai-Xu Peng
- Bioinformatics Center, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Ya-Ting Yi
- Bioinformatics Center, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - He-Xin Wang
- Institute of Modern Agricultural Research, Dalian University, Dalian, Liaoning, China
| | - Xiu-Jun Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Yi-Bo Wang
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Dan Wang
- College of Agriculture, Eastern Liaoning University, Dandong, Liaoning, China
| | - Li Li
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Qiong Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Wen-Xia Wang
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, China
| | - Yongbo Liu
- State Environmental Protection Key Laboratory of Regional Eco-process and Function Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China.
| | - Lei Gao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China; Hubei Hongshan Laboratory, Wuhan, Hubei, China.
| | - Jin-Hu Wu
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand.
| | - Yan-Chang Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China.
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Flay C, Tahir J, Hilario E, Fraser L, Stannard K, Symonds V, Datson P. Genomic architecture of resistance to latania scale (H. lataniae) in kiwifruit (A. chinensis var. chinensis). BMC PLANT BIOLOGY 2023; 23:530. [PMID: 37907872 PMCID: PMC10617205 DOI: 10.1186/s12870-023-04504-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 10/03/2023] [Indexed: 11/02/2023]
Abstract
BACKGROUND Latania scale (Hemiberlesia lataniae Signoret) is an armoured scale insect known to cause damage to kiwifruit plants and fruit, which ultimately reduces crop values and creates post-harvest export and quarantine issues. Resistance to H. lataniae does exist in some commercial cultivars of kiwifruit. However, some of the commercial cultivars bred in New Zealand have not inherited alleles for resistance to H. lataniae carried by their parents. To elucidate the architecture of resistance in the parents and develop molecular markers to assist breeding, these experiments analysed the inheritance of resistance to H. lataniae from families related to commercial cultivars. RESULTS The first experiment identified a 15.97 Mb genomic region of interest for resistance to H. lataniae in rtGBS data of 3.23 to 19.20 Mb on chromosome 10. A larger population was then QTL mapped, which confirmed the region of interest as the sole locus contributing to H. lataniae resistance. inDel markers mapping the region of low recombination under the QTL peak further narrowed the region associated with H. lataniae resistance to a 5.73 Mb region. CONCLUSIONS The kiwifruit populations and genomic methods used in this study identify the same non-recombinant region of chromosome 10 which confers resistance of A. chinensis var. chinensis to H. lataniae. The markers developed to target the H. lataniae resistance loci will reduce the amount of costly and time-consuming phenotyping required for breeding H. lataniae scale resistance into new kiwifruit cultivars.
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Affiliation(s)
- Casey Flay
- Massey University, Palmerston North, New Zealand.
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand.
| | - Jibran Tahir
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Elena Hilario
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Lena Fraser
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Kate Stannard
- 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
- Kiwifruit Breeding Centre, Te Puke, New Zealand
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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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4
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Non-amplification on-spot identifying the sex of dioecious kiwi plants by a portable Raman device. Talanta 2023; 258:124447. [PMID: 36921366 DOI: 10.1016/j.talanta.2023.124447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 03/01/2023] [Accepted: 03/09/2023] [Indexed: 03/14/2023]
Abstract
The kiwi plant is dioecious, and its sex is generally identified from flower morphology at blossoming, which takes several years. It is quite necessary but challenging to on-spot identify the plant sex in juvenile stage. Here the target DNA was obtained by screening the Friendly boy (FrBy) gene which is sex-related for different kiwi plant species. Its complementary sequence was divided into two parts as primer DNA and further attached to different gold nanoparticles (GNPs). The connection between target DNA and primer DNA will promote the formation of plasmonic dimers. Dark field microscopy (DFM) can distinguish particles in different aggregation states. Various conditions were optimized based on the standard of increasing the proportion of dimers while reducing that of large aggregates. Furthermore, two Raman reporters (RR) are separately labeled on the nanoprobes, and the plasmonic dimers lead to a tremendous Raman enhancement of two reporters located at the dimer nanogap. Double-blind tests proved the feasibility of this method on the actual samples of kiwi plant leaves. Our SERS method is sensitive, specific, and reliable for rapid sex identification analysis at the kiwi seeding stage, with great promise for decision-making in field management.
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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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Souleyre EJF, Nieuwenhuizen NJ, Wang MY, Winz RA, Matich AJ, Ileperuma NR, Tang H, Baldwin SJ, Wang T, List BW, Hoeata KA, Popowski EA, Atkinson RG. Alcohol acyl transferase genes at a high-flavor intensity locus contribute to ester biosynthesis in kiwifruit. PLANT PHYSIOLOGY 2022; 190:1100-1116. [PMID: 35916752 PMCID: PMC9516725 DOI: 10.1093/plphys/kiac316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
Volatile esters are key compounds contributing to flavor intensity in commonly consumed fruits including apple (Malus domestica), strawberry (Fragaria spp.), and banana (Musa sapientum). In kiwifruit (Actinidia spp.), ethyl butanoate and other esters have been proposed to contribute fruity, sweet notes to commercial cultivars. Here, we investigated the genetic basis for ester production in Actinidia in an A. chinensis mapping population (AcMPO). A major quantitative trait loci for the production of multiple esters was identified at the high-flavor intensity (HiFI) locus on chromosome 20. This locus co-located with eight tandemly arrayed alcohol acyl transferase genes in the Red5 genome that were expressed in a ripening-specific fashion that corresponded with ester production. Biochemical characterization suggested two genes at the HiFI locus, alcohol acyl transferase 16-b/c (AT16-MPb/c), probably contributed most to the production of ethyl butanoate. A third gene, AT16-MPa, probably contributed more to hexyl butanoate and butyl hexanoate production, two esters that segregated in AcMPO. Sensory analysis of AcMPO indicated that fruit from segregating lines with high ester concentrations were more commonly described as being "fruity" as opposed to "beany". The downregulation of AT16-MPa-c by RNAi reduced ester production in ripe "Hort16A" fruit by >90%. Gas chromatography-olfactometry indicated the loss of the major "fruity" notes contributed by ethyl butanoate. A comparison of unimproved Actinidia germplasm with those of commercial cultivars indicated that the selection of fruit with high concentrations of alkyl esters (but not green note aldehydes) was probably an important selection trait in kiwifruit cultivation. Understanding ester production at the HiFI locus is a critical step toward maintaining and improving flavor intensity in kiwifruit.
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Affiliation(s)
| | - Niels J Nieuwenhuizen
- The New Zealand Institute for Plant and Food Research Ltd (PFR), Auckland 1142, New Zealand
| | - Mindy Y Wang
- The New Zealand Institute for Plant and Food Research Ltd (PFR), Auckland 1142, New Zealand
| | - Robert A Winz
- The New Zealand Institute for Plant and Food Research Ltd (PFR), Auckland 1142, New Zealand
| | - Adam J Matich
- Plant and Food Research Ltd (PFR), Palmerston North 4442, New Zealand
| | - Nadeesha R Ileperuma
- The New Zealand Institute for Plant and Food Research Ltd (PFR), Auckland 1142, New Zealand
| | - Haidee Tang
- The New Zealand Institute for Plant and Food Research Ltd (PFR), Auckland 1142, New Zealand
| | | | - Tianchi Wang
- The New Zealand Institute for Plant and Food Research Ltd (PFR), Auckland 1142, New Zealand
| | - Blake W List
- Plant and Food Research Ltd (PFR), Lincoln, 7608, New Zealand
| | | | | | - Ross G Atkinson
- The New Zealand Institute for Plant and Food Research Ltd (PFR), Auckland 1142, New Zealand
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7
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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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8
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Dioecious hemp (Cannabis sativa L.) plants do not express significant sexually dimorphic morphology in the seedling stage. Sci Rep 2021; 11:16825. [PMID: 34413374 PMCID: PMC8376874 DOI: 10.1038/s41598-021-96311-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 07/30/2021] [Indexed: 11/19/2022] Open
Abstract
Some economically important crop species are dioecious, producing pollen and ovules on distinct, unisexual, individuals. On-the-spot diagnosis of sex is important to breeders and farmers for crop improvement and maximizing yield, yet diagnostic tools at the seedling stage are understudied and lack a scientific basis. Understanding sexual dimorphism in juvenile plants may provide key ecological, evolutionary and economic insights into dioecious plant species in addition to improving the process of crop cultivation. To address this gap in the literature, we asked: can we reliably differentiate males, females, and co-sexual individuals based on seedling morphology in Cannabis sativa, and do the traits used to distinguish sex at this stage vary between genotypes? To answer these questions, we collected data on phenotypic traits of 112 C. sativa plants (50 female, 52 male, 10 co-sexuals) from two hemp cultivars (CFX-1, CFX-2) during the second week of vegetative growth and used ANOVAs to compare morphology among sexes. We found males grew significantly longer hypocotyls than females by week 2, but this difference depended on the cultivar investigated. Preliminary evidence suggests that co-sexual plants may be distinguished from male and female plants using short hypocotyl length and seedling height, although this relationship requires more study since sample sizes of co-sexual plants were small. In one of the cultivars, two-week old male plants tend to produce longer hypocotyls than other plants, which may help to identify these plants prior to anthesis. We call for increased research effort on co-sexual plants, given their heavy economic cost in industrial contexts and rare mention in the literature. Our preliminary data suggests that short hypocotyl length may be an indicator of co-sexuality. These results are the first steps towards developing diagnostic tools for predicting sex using vegetative morphology in dioecious species and understanding how sexual dimorphism influences phenotype preceding sexual maturity.
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Neishabouri S, Rezaei M, Heidari P, Hokmabadi H. Variability of male and female pistachio genotypes with morphological and dominant DNA markers. THE NUCLEUS 2021. [DOI: 10.1007/s13237-021-00358-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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10
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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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11
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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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12
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De Mori G, Zaina G, Franco-Orozco B, Testolin R, De Paoli E, Cipriani G. Targeted Mutagenesis of the Female-Suppressor SyGI Gene in Tetraploid Kiwifruit by CRISPR/CAS9. PLANTS 2020; 10:plants10010062. [PMID: 33396671 PMCID: PMC7823651 DOI: 10.3390/plants10010062] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/18/2020] [Accepted: 12/27/2020] [Indexed: 11/16/2022]
Abstract
Kiwifruit belong to the genus Actinidia with 54 species apparently all functionally dioecious. The sex-determinants of the type XX/XY, with male heterogametic, operate independently of the ploidy level. Recently, the SyGI protein has been described as the suppressor of female development. In the present study, we exploited the CRISPR/Cas9 technology by targeting two different sites in the SyGI gene in order to induce a stable gene knock-out in two tetraploid male accessions of Actinidia chinensis var. chinensis. The two genotypes showed a regenerative efficiency of 58% and 73%, respectively. Despite not yet being able to verify the phenotypic effects on the flower structure, due to the long time required by tissue-cultured kiwifruit plants to flower, we obtained two regenerated lines showing near fixation of a unique modification in their genome, resulting in both cases in the onset of a premature stop codon, which induces the putative gene knock-out. Evaluation of gRNA1 locus for both regenerated plantlets resulted in co-amplification of a minor variant differing from the target region for a single nucleotide. A genomic duplication of the region in proximity of the Y genomic region could be postulated.
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Affiliation(s)
- Gloria De Mori
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via delle Scienze 206, 33100 Udine, Italy; (G.Z.); (B.F.-O.); (R.T.); (E.D.P.); (G.C.)
- Correspondence:
| | - Giusi Zaina
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via delle Scienze 206, 33100 Udine, Italy; (G.Z.); (B.F.-O.); (R.T.); (E.D.P.); (G.C.)
| | - Barbara Franco-Orozco
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via delle Scienze 206, 33100 Udine, Italy; (G.Z.); (B.F.-O.); (R.T.); (E.D.P.); (G.C.)
- Facultad de Ingeniería, Tecnológico de Antioquia–Institución Universitaria TdeA, Calle 78b No. 72A-220, Medellín-Antioquia 050001, Colombia
| | - Raffaele Testolin
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via delle Scienze 206, 33100 Udine, Italy; (G.Z.); (B.F.-O.); (R.T.); (E.D.P.); (G.C.)
| | - Emanuele De Paoli
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via delle Scienze 206, 33100 Udine, Italy; (G.Z.); (B.F.-O.); (R.T.); (E.D.P.); (G.C.)
| | - Guido Cipriani
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via delle Scienze 206, 33100 Udine, Italy; (G.Z.); (B.F.-O.); (R.T.); (E.D.P.); (G.C.)
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13
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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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14
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Wen G, Dang J, Xie Z, Wang J, Jiang P, Guo Q, Liang G. Molecular karyotypes of loquat ( Eriobotrya japonica) aneuploids can be detected by using SSR markers combined with quantitative PCR irrespective of heterozygosity. PLANT METHODS 2020; 16:22. [PMID: 32123538 PMCID: PMC7041098 DOI: 10.1186/s13007-020-00568-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 02/13/2020] [Indexed: 05/13/2023]
Abstract
BACKGROUND Aneuploidy, a condition caused by an imbalance between the relative dosages of chromosomes, generally produces a novel phenotype specific to the molecular karyotype. Few techniques are currently available for detecting the molecular karyotypes of aneuploids in plants. RESULTS Based on this imbalance in chromosome dosage, a new approach (referred to as 'SSR-qPCR') combining simple sequence repeat (SSR) markers and quantitative real-time PCR (qPCR) has been developed and utilized to detect some common aneuploids irrespective of heterozygosity. We screened 17 specific SSR markers covering all loquat linkage groups and redesigned 6 pairs of primers for SSR markers that can detect loquat chromosome aneuploidies. The SSR-qPCR detection results obtained for hybrid progeny and open-pollination progeny of triploid loquat showed diagnostic accuracies of 88.9% and 62.5%, respectively, compared with the chromosome preparation results. CONCLUSION SSR-qPCR can detect loquat aneuploids and be used to construct the entire molecular karyotypes of aneuploid individuals. Therefore, this method offers a novel alternative for the detection of chromosome aneuploidies.
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Affiliation(s)
- Guo Wen
- College of Horticulture and Landscape Architecture; Academy of Agricultural Sciences; Key Laboratory of Horticulture Science for Southern Mountain Regions of Ministry of Education; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Beibei, Chongqing, China
| | - Jiangbo Dang
- College of Horticulture and Landscape Architecture; Academy of Agricultural Sciences; Key Laboratory of Horticulture Science for Southern Mountain Regions of Ministry of Education; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Beibei, Chongqing, China
| | - Zhongyi Xie
- College of Horticulture and Landscape Architecture; Academy of Agricultural Sciences; Key Laboratory of Horticulture Science for Southern Mountain Regions of Ministry of Education; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Beibei, Chongqing, China
| | - Jinying Wang
- College of Horticulture and Landscape Architecture; Academy of Agricultural Sciences; Key Laboratory of Horticulture Science for Southern Mountain Regions of Ministry of Education; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Beibei, Chongqing, China
| | - Pengfei Jiang
- College of Horticulture and Landscape Architecture; Academy of Agricultural Sciences; Key Laboratory of Horticulture Science for Southern Mountain Regions of Ministry of Education; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Beibei, Chongqing, China
| | - Qigao Guo
- College of Horticulture and Landscape Architecture; Academy of Agricultural Sciences; Key Laboratory of Horticulture Science for Southern Mountain Regions of Ministry of Education; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Beibei, Chongqing, China
| | - Guolu Liang
- College of Horticulture and Landscape Architecture; Academy of Agricultural Sciences; Key Laboratory of Horticulture Science for Southern Mountain Regions of Ministry of Education; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Beibei, Chongqing, China
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15
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Akagi T, Shirasawa K, Nagasaki H, Hirakawa H, Tao R, Comai L, Henry IM. The persimmon genome reveals clues to the evolution of a lineage-specific sex determination system in plants. PLoS Genet 2020; 16:e1008566. [PMID: 32069274 PMCID: PMC7048303 DOI: 10.1371/journal.pgen.1008566] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 02/28/2020] [Accepted: 12/14/2019] [Indexed: 01/20/2023] Open
Abstract
Most angiosperms bear hermaphroditic flowers, but a few species have evolved outcrossing strategies, such as dioecy, the presence of separate male and female individuals. We previously investigated the mechanisms underlying dioecy in diploid persimmon (D. lotus) and found that male flowers are specified by repression of the autosomal gene MeGI by its paralog, the Y-encoded pseudo-gene OGI. This mechanism is thought to be lineage-specific, but its evolutionary path remains unknown. Here, we developed a full draft of the diploid persimmon genome (D. lotus), which revealed a lineage-specific whole-genome duplication event and provided information on the architecture of the Y chromosome. We also identified three paralogs, MeGI, OGI and newly identified Sister of MeGI (SiMeGI). Evolutionary analysis suggested that MeGI underwent adaptive evolution after the whole-genome duplication event. Transformation of tobacco plants with MeGI and SiMeGI revealed that MeGI specifically acquired a new function as a repressor of male organ development, while SiMeGI presumably maintained the original function. Later, a segmental duplication event spawned MeGI’s regulator OGI on the Y-chromosome, completing the path leading to dioecy, and probably initiating the formation of the Y-chromosome. These findings exemplify how duplication events can provide flexible genetic material available to help respond to varying environments and provide interesting parallels for our understanding of the mechanisms underlying the transition into dieocy in plants. Plant sexuality has fascinated scientists for decades. Most plants can self-reproduce but not all. For example, a small subset of species have evolved a system called dioecy, with separate male and female individuals. Dioecy has evolved multiple times independently and, while we do not understand the molecular mechanisms underlying dioecy in many of these species yet, a picture is starting to emerge with recent progress in several dioecious species. Here, we focused on the evolutionary events leading to dioecy in persimmon. Our previous work had identified a pair of genes regulating sex in this species, called OGI and MeGI. We drafted the whole genome sequence of diploid persimmon to investigate their evolutionary history. We discovered a lineage-specific whole-genome duplication event, and observed that MeGI underwent adaptive evolution after this event. Transgenic analyses validated that MeGI newly acquired a male-suppressor function, while the other copy of this gene, SiMeGI, did not. The regulator of MeGI, OGI, resulted from a second smaller-scale segmental duplication event, finalizing the system. This study sheds light on the role of duplication as a mechanism that promote flexible genes functions, and how it can affect important biological functions, such as the establishment of a new sexual system.
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Affiliation(s)
- Takashi Akagi
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
- Japan Science and Technology Agency (JST), PRESTO, Kawaguchi-shi, Saitama, Japan
- * E-mail: (TA); (IMH)
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, Kazusa-Kamatari, Kisarazu, Chiba, Japan
| | - Hideki Nagasaki
- Kazusa DNA Research Institute, Kazusa-Kamatari, Kisarazu, Chiba, Japan
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, Kazusa-Kamatari, Kisarazu, Chiba, Japan
| | - Ryutaro Tao
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Luca Comai
- Genome Center and Department of Plant Biology, University of California Davis, Davis, California, United States of America
| | - Isabelle M. Henry
- Genome Center and Department of Plant Biology, University of California Davis, Davis, California, United States of America
- * E-mail: (TA); (IMH)
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16
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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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17
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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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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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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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Pandian S, Satish L, Rameshkumar R, Muthuramalingam P, Rency AS, Rathinapriya P, Ramesh M. Analysis of population structure and genetic diversity in an exotic germplasm collection of Eleusine coracana (L.) Gaertn. using genic-SSR markers. Gene 2018; 653:80-90. [DOI: 10.1016/j.gene.2018.02.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 01/22/2018] [Accepted: 02/07/2018] [Indexed: 11/30/2022]
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Henry IM, Akagi T, Tao R, Comai L. One Hundred Ways to Invent the Sexes: Theoretical and Observed Paths to Dioecy in Plants. ANNUAL REVIEW OF PLANT BIOLOGY 2018; 69:553-575. [PMID: 29719167 DOI: 10.1146/annurev-arplant-042817-040615] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Dioecy, the presence of male and female flowers on separate individuals, is both widespread and uncommon within flowering plants, with only a few percent of dioecious species spread across most major phylogenetic taxa. It is therefore safe to assume that dioecy evolved independently in these different groups, which allows us to ask questions regarding the molecular and developmental mechanisms underlying these independent transitions to dioecy. We start this review by examining the problem from the standpoint of a genetic engineer trying to develop dioecy, discuss various potential solutions, and compare them to models proposed in the past and based on genetic and evolutionary considerations. Next, we present recent information regarding candidate sex determinants in three species, acquired using newly established genomic approaches. Although such specific information is still scarce, it is slowly becoming apparent that various genes or pathways can be altered to evolve dioecy.
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Affiliation(s)
- Isabelle M Henry
- Department of Plant Biology, University of California, Davis, California 95616, USA; ,
- Genome Center, University of California, Davis, California 95616, USA
| | - Takashi Akagi
- Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan; ,
| | - Ryutaro Tao
- Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan; ,
| | - Luca Comai
- Department of Plant Biology, University of California, Davis, California 95616, USA; ,
- Genome Center, University of California, Davis, California 95616, USA
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22
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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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23
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Kim MJ, Jeon CW, Cho G, Kim DR, Kwack YB, Kwak YS. Comparison of Microbial Community Structure in Kiwifruit Pollens. THE PLANT PATHOLOGY JOURNAL 2018; 34:143-149. [PMID: 29628821 PMCID: PMC5880359 DOI: 10.5423/ppj.nt.12.2017.0281] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 01/30/2018] [Accepted: 01/31/2018] [Indexed: 05/29/2023]
Abstract
Flowers of kiwifruit are morphologically hermaphroditic and survivable binucleate pollen is produced by the male flowers. In this study, we investigated microbial diversity in kiwifruit pollens by analyzing amplicon sequences of 16S rRNA. Four pollen samples were collected: 'NZ' was imported from New Zealand, 'CN' from China in year of 2014, respectively. 'KR13' and 'KR14' were collected in 2013' and 2014' in South Korea. Most of the identified bacterial phyla in the four different pollens were Proteobacteria, Actinobacteria and Firmicutes. However, the imported and the domestic pollen samples showed different aspects of microbial community structures. The domestic pollens had more diverse in diversity than the imported samples. Among top 20 OTUs, Pseudomonas spp. was the most dominant specie. Interestingly, a bacterial pathogen of kiwifruit canker, Pseudomonas syringae pv. actinidiae was detected in 'NZ' by the specific PCR. This study provides insights microbial distribution and community structure information in kiwifruit pollen.
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Affiliation(s)
- Min-Jung Kim
- Department of Plant Medicine, Institute of Agriculture & Life Science, Gyeongsang National University, Jinju 52828,
Korea
| | - Chang-Wook Jeon
- Dvision of Applied Life Science (BK21plus), Gyeongsang National University, Jinju 52828,
Korea
| | - Gyongjun Cho
- Dvision of Applied Life Science (BK21plus), Gyeongsang National University, Jinju 52828,
Korea
| | - Da-Ran Kim
- Department of Plant Medicine, Institute of Agriculture & Life Science, Gyeongsang National University, Jinju 52828,
Korea
| | | | - Youn-Sig Kwak
- Department of Plant Medicine, Institute of Agriculture & Life Science, Gyeongsang National University, Jinju 52828,
Korea
- Dvision of Applied Life Science (BK21plus), Gyeongsang National University, Jinju 52828,
Korea
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24
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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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25
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Wang W, Zhang X. Identification of the Sex-Biased Gene Expression and Putative Sex-Associated Genes in Eucommia ulmoides Oliver Using Comparative Transcriptome Analyses. Molecules 2017; 22:E2255. [PMID: 29258253 PMCID: PMC6149867 DOI: 10.3390/molecules22122255] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 11/29/2017] [Accepted: 12/14/2017] [Indexed: 12/04/2022] Open
Abstract
Eucommia ulmoides is a model representative of the dioecious plants with sex differentiation at initiation. Nevertheless, the genetic mechanisms of sexual dimorphism and sex determination in E. ulmoides remain poorly understood. In this study de novo transcriptome sequencing on Illumina platform generated >45 billion high-quality bases from fresh leaves of six male and female individuals of E. ulmoides. A total of 148,595 unigenes with an average length of 801 base-pairs (bp) were assembled. Through comparative transcriptome analyses, 116 differentially expressed genes (DEGs) between the males and the females were detected, including 73 male-biased genes and 43 female-biased genes. Of these DEGs, three female-biased genes were annotated to be related with the sexually dimorphic gutta content in E. ulmoides. One male-biased DEG was identified as putative MADS box gene APETALA3, a B class floral organ identity gene in the flowering plants. SNPs calling analyses further confirmed that the APETALA3-like gene was probably involved in the sex determination in E. ulmoides. Four other male-biased DEGs were potential sex-associated genes as well with segregated SNPs in accord with sex type. In addition, the SNPs density was 1.02 per kilobase (kb) in the expressed genes of E. ulmoides, implying a relatively high genetic diversity.
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Affiliation(s)
- Wencai Wang
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou 510000, China.
| | - Xianzhi Zhang
- Department of Forestry Protection, College of Forestry, Northwest A&F University, Yangling 712100, China.
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26
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Salzano AM, Sobolev A, Carbone V, Petriccione M, Renzone G, Capitani D, Vitale M, Minasi P, Pasquariello MS, Novi G, Zambrano N, Scortichini M, Mannina L, Scaloni A. A proteometabolomic study of Actinidia deliciosa fruit development. J Proteomics 2017; 172:11-24. [PMID: 29133123 DOI: 10.1016/j.jprot.2017.11.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 10/17/2017] [Accepted: 11/08/2017] [Indexed: 10/18/2022]
Affiliation(s)
- Anna Maria Salzano
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy
| | - Anatoly Sobolev
- Magnetic Resonance Laboratory "Annalaura Segre", Institute of Chemical Methodologies, National Research Council, 00015, Monterotondo, Rome, Italy
| | - Virginia Carbone
- Institute of Food Sciences, National Research Council, 83100 Avellino, Italy
| | - Milena Petriccione
- Centro di Ricerca per Olivicoltura, Frutticoltura e Agrumicoltura, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, 81100 Caserta, Italy
| | - Giovanni Renzone
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy
| | - Donatella Capitani
- Magnetic Resonance Laboratory "Annalaura Segre", Institute of Chemical Methodologies, National Research Council, 00015, Monterotondo, Rome, Italy
| | - Monica Vitale
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy; Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II", 80131 Naples, Italy
| | - Paola Minasi
- Institute of Food Sciences, National Research Council, 83100 Avellino, Italy
| | - Maria Silvia Pasquariello
- Centro di Ricerca per Olivicoltura, Frutticoltura e Agrumicoltura, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, 81100 Caserta, Italy
| | - Gianfranco Novi
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy
| | - Nicola Zambrano
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II", 80131 Naples, Italy; CEINGE Biotecnologie Avanzate, 80145 Naples, Italy
| | - Marco Scortichini
- Centro di Ricerca per Olivicoltura, Frutticoltura e Agrumicoltura, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, 81100 Caserta, Italy
| | - Luisa Mannina
- Magnetic Resonance Laboratory "Annalaura Segre", Institute of Chemical Methodologies, National Research Council, 00015, Monterotondo, Rome, Italy; Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, 00185 Rome, Italy.
| | - Andrea Scaloni
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy.
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27
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Guo LN, Gao XF. Genetic diversity and population structure of Indigofera szechuensis complex (Fabaceae) based on EST-SSR markers. Gene 2017; 624:26-33. [DOI: 10.1016/j.gene.2017.04.047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 04/25/2017] [Accepted: 04/28/2017] [Indexed: 10/19/2022]
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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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Sarkar S, Banerjee J, Gantait S. Sex-oriented research on dioecious crops of Indian subcontinent: an updated review. 3 Biotech 2017; 7:93. [PMID: 28555429 PMCID: PMC5447520 DOI: 10.1007/s13205-017-0723-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 04/06/2017] [Indexed: 11/30/2022] Open
Abstract
A number of dioecious species are grown across India and some of those plants play a crucial role in the agro-based economy of the country. The diagnosis of sex is very difficult in the dioecious plant prior flowering wherein sex identification at the seedling stage is of great importance to breeders as well as farmers for crop improvement or production purpose. A comprehensive approach of sex determination comprising morphological, biochemical, cytological and molecular attributes is a must required for gender differentiation in dioecious plant species. In the present review, we highlighted the economical, medicinal as well as industrial importance of most of the dioecious species extensively grown in Indian subcontinent. In addition to that, the cytogenetic, genetic as well as molecular information in connection to their sex determination were critically discussed in this review.
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Affiliation(s)
- Sutanu Sarkar
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, Nadia, West Bengal 741252 India
- Crop Research Unit, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, Nadia, West Bengal 741252 India
| | - Joydeep Banerjee
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, Nadia, West Bengal 741252 India
- Survey, Selection and Mass Production, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, Nadia, West Bengal 741252 India
| | - Saikat Gantait
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, Nadia, West Bengal 741252 India
- All India Coordinated Research Project on Groundnut, Bidhan Chandra Krishi Viswavidyalaya, Kalyani, Nadia, West Bengal 741235 India
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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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Ainalidou A, Tanou G, Belghazi M, Samiotaki M, Diamantidis G, Molassiotis A, Karamanoli K. Integrated analysis of metabolites and proteins reveal aspects of the tissue-specific function of synthetic cytokinin in kiwifruit development and ripening. J Proteomics 2016; 143:318-333. [DOI: 10.1016/j.jprot.2016.02.013] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 02/12/2016] [Accepted: 02/17/2016] [Indexed: 12/30/2022]
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Abstract
Although individuals in most flowering plant species, and in many haploid plants, have both sex functions, dioecious species-in which individuals have either male or female functions only-are scattered across many taxonomic groups, and many species have genetic sex determination. Among these, some have visibly heteromorphic sex chromosomes, and molecular genetic studies are starting to uncover sex-linked markers in others, showing that they too have fully sex-linked regions that are either too small or are located in chromosomes that are too small to be cytologically detectable from lack of pairing, lack of visible crossovers, or accumulation of heterochromatin. Detailed study is revealing that, like animal sex chromosomes, plant sex-linked regions show evidence for accumulation of repetitive sequences and genetic degeneration. Estimating when recombination stopped confirms the view that many plants have young sex-linked regions, making plants of great interest for studying the timescale of these changes.
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Affiliation(s)
- Deborah Charlesworth
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom;
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Chen Y, Wang T, Fang L, Li X, Yin T. Confirmation of Single-Locus Sex Determination and Female Heterogamety in Willow Based on Linkage Analysis. PLoS One 2016; 11:e0147671. [PMID: 26828940 PMCID: PMC4734660 DOI: 10.1371/journal.pone.0147671] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Accepted: 01/06/2016] [Indexed: 01/02/2023] Open
Abstract
In this study, we constructed high-density genetic maps of Salix suchowensis and mapped the gender locus with an F1 pedigree. Genetic maps were separately constructed for the maternal and paternal parents by using amplified fragment length polymorphism (AFLP) markers and the pseudo-testcross strategy. The maternal map consisted of 20 linkage groups that spanned a genetic distance of 2333.3 cM; whereas the paternal map contained 21 linkage groups that covered 2260 cM. Based on the established genetic maps, it was found that the gender of willow was determined by a single locus on linkage group LG_03, and the female was the heterogametic gender. Aligned with mapped SSR markers, linkage group LG_03 was found to be associated with chromosome XV in willow. It is noteworthy that marker density in the vicinity of the gender locus was significantly higher than that expected by chance alone, which indicates severe recombination suppression around the gender locus. In conclusion, this study confirmed the findings on the single-locus sex determination and female heterogamety in willow. It also provided additional evidence that validated the previous studies, which found that different autosomes evolved into sex chromosomes between the sister genera of Salix (willow) and Populus (poplar).
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Affiliation(s)
- Yingnan Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Tiantian Wang
- Forestry Research Institute of Jingdezhen, Jiangxi, China
| | - Lecheng Fang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Xiaoping Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Tongming Yin
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu, China
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Breeding Systems, Mating Systems, and Genomics of Gender Determination in Angiosperm Trees. COMPARATIVE AND EVOLUTIONARY GENOMICS OF ANGIOSPERM TREES 2016. [DOI: 10.1007/7397_2016_21] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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36
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McAtee PA, Richardson AC, Nieuwenhuizen NJ, Gunaseelan K, Hoong L, Chen X, Atkinson RG, Burdon JN, David KM, Schaffer RJ. The hybrid non-ethylene and ethylene ripening response in kiwifruit (Actinidia chinensis) is associated with differential regulation of MADS-box transcription factors. BMC PLANT BIOLOGY 2015; 15:304. [PMID: 26714876 PMCID: PMC4696264 DOI: 10.1186/s12870-015-0697-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 12/21/2015] [Indexed: 05/04/2023]
Abstract
BACKGROUND Ripening in tomato is predominantly controlled by ethylene, whilst in fruit such as grape, it is predominantly controlled by other hormones. The ripening response of many kiwifruit (Actinidia) species is atypical. The majority of ripening-associated fruit starch hydrolysis, colour change and softening occurs in the apparent absence of ethylene production (Phase 1 ripening) whilst Phase 2 ripening requires autocatalytic ethylene production and is associated with further softening and an increase in aroma volatiles. RESULTS To dissect the ripening response in the yellow-fleshed kiwifruit A. chinensis ('Hort16A'), a two dimensional developmental stage X ethylene response time study was undertaken. As fruit progressed through maturation and Phase 1 ripening, fruit were treated with different concentrations of propylene and ethylene. At the start of Phase 1 ripening, treated fruit responded to ethylene, and were capable of producing endogenous ethylene. As the fruit progressed through Phase 1 ripening, the fruit became less responsive to ethylene and endogeneous ethylene production was partially repressed. Towards the end of Phase 1 ripening the fruit were again able to produce high levels of ethylene. Progression through Phase 1 ripening coincided with a developmental increase in the expression of the ethylene-unresponsive MADS-box FRUITFUL-like gene (FUL1). The ability to respond to ethylene however coincided with a change in expression of another MADS-box gene SEPALLATA4/RIPENING INHIBITOR-like (SEP4/RIN). The promoter of SEP4/RIN was shown to be transactivated by EIN3-like transcription factors, but unlike tomato, not by SEP4/RIN itself. Transient over-expression of SEP4/RIN in kiwifruit caused an increase in ethylene production. CONCLUSIONS These results suggest that the non-ethylene/ethylene ripening response observed in kiwifruit is a hybrid of both the tomato and grape ripening progression, with Phase 1 being akin to the RIN/ethylene inhibitory response observed in grape and Phase 2 akin to the RIN-associated autocatalytic ethylene response observed in tomato.
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Affiliation(s)
- Peter A McAtee
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand.
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
| | | | - Niels J Nieuwenhuizen
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand.
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
| | - Kularajathevan Gunaseelan
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand.
| | - Ling Hoong
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand.
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
| | - Xiuyin Chen
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand.
| | - Ross G Atkinson
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand.
| | - Jeremy N Burdon
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand.
| | - Karine M David
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
| | - Robert J Schaffer
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand.
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
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Yue J, Liu J, Ban R, Tang W, Deng L, Fei Z, Liu Y. Kiwifruit Information Resource (KIR): a comparative platform for kiwifruit genomics. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015; 2015:bav113. [PMID: 26656885 PMCID: PMC4674624 DOI: 10.1093/database/bav113] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 11/05/2015] [Indexed: 12/22/2022]
Abstract
The Kiwifruit Information Resource (KIR) is dedicated to maintain and integrate comprehensive datasets on genomics, functional genomics and transcriptomics of kiwifruit (Actinidiaceae). KIR serves as a central access point for existing/new genomic and genetic data. KIR also provides researchers with a variety of visualization and analysis tools. Current developments include the updated genome structure of Actinidia chinensis cv. Hongyang and its newest genome annotation, putative transcripts, gene expression, physical markers of genetic traits as well as relevant publications based on the latest genome assembly. Nine thousand five hundred and forty-seven new transcripts are detected and 21 132 old transcripts are changed. At the present release, the next-generation transcriptome sequencing data has been incorporated into gene models and splice variants. Protein–protein interactions are also identified based on experimentally determined orthologous interactions. Furthermore, the experimental results reported in peer-reviewed literature are manually extracted and integrated within a well-developed query page. In total, 122 identifications are currently associated, including commonly used gene names and symbols. All KIR datasets are helpful to facilitate a broad range of kiwifruit research topics and freely available to the research community. Database URL: http://bdg.hfut.edu.cn/kir/index.html.
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Affiliation(s)
- Junyang Yue
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei 230009, China
| | - Jian Liu
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei 230009, China
| | - Rongjun Ban
- School of Information Science and Technology, University of Science and Technology of China, Hefei 230009, China
| | - Wei Tang
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei 230009, China
| | - Lin Deng
- Information and Network Center, Hefei University of Technology, Hefei 230009, China
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research and USDA-ARS Robert W. Holley Center, Tower Road, Cornell University Campus, Ithaca, NY 14853, USA and
| | - Yongsheng Liu
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei 230009, China, Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Science and State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
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38
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Zhang Q, Liu C, Liu Y, VanBuren R, Yao X, Zhong C, Huang H. High-density interspecific genetic maps of kiwifruit and the identification of sex-specific markers. DNA Res 2015; 22:367-75. [PMID: 26370666 PMCID: PMC4596402 DOI: 10.1093/dnares/dsv019] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 08/19/2015] [Indexed: 01/25/2023] Open
Abstract
Kiwifruit (Actinidia chinensis Planchon) is an important specialty fruit crop that suffers from narrow genetic diversity stemming from recent global commercialization and limited cultivar improvement. Here, we present high-density RAD-seq-based genetic maps using an interspecific F1 cross between Actinidia rufa ‘MT570001’ and A. chinensis ‘Guihai No4’. The A. rufa (maternal) map consists of 2,426 single-nucleotide polymorphism (SNP) markers with a total length of 2,651 cM in 29 linkage groups (LGs) corresponding to the 29 chromosomes. The A. chinensis (paternal) map consists of 4,214 SNP markers over 3,142 cM in 29 LGs. Using these maps, we were able to anchor an additional 440 scaffolds from the kiwifruit draft genome assembly. Kiwifruit is functionally dioecious, which presents unique challenges for breeding and production. Three sex-specific simple sequence repeats (SSR) markers can be used to accurately sex type male and female kiwifruit in breeding programmes. The sex-determination region (SDR) in kiwifruit was narrowed to a 1-Mb subtelomeric region on chromosome 25. Localizing the SDR will expedite the discovery of genes controlling carpel abortion in males and pollen sterility in females.
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Affiliation(s)
- Qiong Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Chunyan Liu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yifei Liu
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | | | - Xiaohong Yao
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Caihong Zhong
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Hongwen Huang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
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Vyskot B, Hobza R. The genomics of plant sex chromosomes. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 236:126-35. [PMID: 26025526 DOI: 10.1016/j.plantsci.2015.03.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Revised: 02/27/2015] [Accepted: 03/26/2015] [Indexed: 05/18/2023]
Abstract
Around six percent of flowering species are dioecious, with separate female and male individuals. Sex determination is mostly based on genetics, but morphologically distinct sex chromosomes have only evolved in a few species. Of these, heteromorphic sex chromosomes have been most clearly described in the two model species - Silene latifolia and Rumex acetosa. In both species, the sex chromosomes are the largest chromosomes in the genome. They are hence easily distinguished, can be physically separated and analyzed. This review discusses some recent experimental data on selected model dioecious species, with a focus on S. latifolia. Phylogenetic analyses show that dioecy in plants originated independently and repeatedly even within individual genera. A cogent question is whether there is genetic degeneration of the non-recombining part of the plant Y chromosome, as in mammals, and, if so, whether reduced levels of gene expression in the heterogametic sex are equalized by dosage compensation. Current data provide no clear conclusion. We speculate that although some transcriptome analyses indicate the first signs of degeneration, especially in S. latifolia, the evolutionary processes forming plant sex chromosomes in plants may, to some extent, differ from those in animals.
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Affiliation(s)
- Boris Vyskot
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, 61265 Brno, Czech Republic.
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, 61265 Brno, Czech Republic
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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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Chawla A, Stobdan T, Srivastava RB, Jaiswal V, Chauhan RS, Kant A. Sex-Biased Temporal Gene Expression in Male and Female Floral Buds of Seabuckthorn (Hippophae rhamnoides). PLoS One 2015; 10:e0124890. [PMID: 25915052 PMCID: PMC4410991 DOI: 10.1371/journal.pone.0124890] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Accepted: 03/18/2015] [Indexed: 12/29/2022] Open
Abstract
Seabuckthorn is an economically important dioecious plant in which mechanism of sex determination is unknown. The study was conducted to identify seabuckthorn homologous genes involved in floral development which may have role in sex determination. Forty four putative Genes involved in sex determination (GISD) reported in model plants were shortlisted from literature survey, and twenty nine seabuckthorn homologous sequences were identified from available seabuckthorn genomic resources. Of these, 21 genes were found to differentially express in either male or female flower bud stages. HrCRY2 was significantly expressed in female flower buds only while HrCO had significant expression in male flowers only. Among the three male and female floral development stages (FDS), male stage II had significant expression of most of the GISD. Information on these sex-specific expressed genes will help in elucidating sex determination mechanism in seabuckthorn.
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Affiliation(s)
- Aseem Chawla
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, India
| | - Tsering Stobdan
- Defence Institute of High Altitude Research, Defence R & D Organisation, Leh, Jammu, and Kashmir, India
| | - Ravi B. Srivastava
- Defence Institute of High Altitude Research, Defence R & D Organisation, Leh, Jammu, and Kashmir, India
| | - Varun Jaiswal
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, India
| | - Rajinder S. Chauhan
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, India
| | - Anil Kant
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, India
- * E-mail:
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42
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Abstract
Dioecy (separate male and female individuals) ensures outcrossing and is more prevalent in animals than in plants. Although it is common in bryophytes and gymnosperms, only 5% of angiosperms are dioecious. In dioecious higher plants, flowers borne on male and female individuals are, respectively deficient in functional gynoecium and androecium. Dioecy is inherited via three sex chromosome systems: XX/XY, XX/X0 and WZ/ZZ, such that XX or WZ is female and XY, X0 or ZZ are males. The XX/XY system generates the rarer XX/X0 and WZ/ZZ systems. An autosome pair begets XY chromosomes. A recessive loss-of-androecium mutation (ana) creates X chromosome and a dominant gynoecium-suppressing (GYS) mutation creates Y chromosome. The ana/ANA and gys/GYS loci are in the sex-determining region (SDR) of the XY pair. Accumulation of inversions, deleterious mutations and repeat elements, especially transposons, in the SDR of Y suppresses recombination between X and Y in SDR, making Y labile and increasingly degenerate and heteromorphic from X. Continued recombination between X and Y in their pseudoautosomal region located at the ends of chromosomal arms allows survival of the degenerated Y and of the species. Dioecy is presumably a component of the evolutionary cycle for the origin of new species. Inbred hermaphrodite species assume dioecy. Later they suffer degenerate-Y-led population regression. Cross-hybridization between such extinguishing species and heterologous species, followed by genome duplication of segregants from hybrids, give rise to new species.
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43
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Kafkas S, Khodaeiaminjan M, Güney M, Kafkas E. Identification of sex-linked SNP markers using RAD sequencing suggests ZW/ZZ sex determination in Pistacia vera L. BMC Genomics 2015; 16:98. [PMID: 25765114 PMCID: PMC4336685 DOI: 10.1186/s12864-015-1326-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 02/06/2015] [Indexed: 01/09/2023] Open
Abstract
Background Pistachio (Pistacia vera L.) is a dioecious species that has a long juvenility period. Therefore, development of marker-assisted selection (MAS) techniques would greatly facilitate pistachio cultivar-breeding programs. The sex determination mechanism is presently unknown in pistachio. The generation of sex-linked markers is likely to reduce time, labor, and costs associated with breeding programs, and will help to clarify the sex determination system in pistachio. Results Restriction site-associated DNA (RAD) markers were used to identify sex-linked markers and to elucidate the sex determination system in pistachio. Eight male and eight female F1 progenies from a Pistacia vera L. Siirt × Bağyolu cross, along with the parents, were subjected to RAD sequencing in two lanes of a Hi-Seq 2000 sequencing platform. This generated 449 million reads, comprising approximately 37.7 Gb of sequences. There were 33,757 polymorphic single nucleotide polymorphism (SNP) loci between the parents. Thirty-eight of these, from 28 RAD reads, were detected as putative sex-associated loci in pistachio. Validation was performed by SNaPshot analysis in 42 mature F1 progenies and in 124 cultivars and genotypes in a germplasm collection. Eight loci could distinguish sex with 100% accuracy in pistachio. To ascertain cost-effective application of markers in a breeding program, high-resolution melting (HRM) analysis was performed; four markers were found to perfectly separate sexes in pistachio. Because of the female heterogamety in all candidate SNP loci, we report for the first time that pistachio has a ZZ/ZW sex determination system. As the reported female-to-male segregation ratio is 1:1 in all known segregating populations and there is no previous report of super-female genotypes or female heteromorphic chromosomes in pistachio, it appears that the WW genotype is not viable. Conclusion Sex-linked SNP markers were identified and validated in a large germplasm and proved their suitability for MAS in pistachio. HRM analysis successfully validated the sex-linked markers for MAS. For the first time in dioecious pistachio, a female heterogamety ZW/ZZ sex determination system is suggested.
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Affiliation(s)
- Salih Kafkas
- Department of Horticulture, Faculty of Agriculture, University of Çukurova, Adana, Turkey.
| | - Mortaza Khodaeiaminjan
- Department of Horticulture, Faculty of Agriculture, University of Çukurova, Adana, Turkey.
| | - Murat Güney
- Department of Horticulture, Faculty of Agriculture, University of Çukurova, Adana, Turkey.
| | - Ebru Kafkas
- Department of Horticulture, Faculty of Agriculture, University of Çukurova, Adana, Turkey.
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44
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Abstract
The kiwifruit (Actinidia chinensis) is an economically and nutritionally important fruit crop with remarkably high vitamin C content. Here we report the draft genome sequence of a heterozygous kiwifruit, assembled from ~140-fold next-generation sequencing data. The assembled genome has a total length of 616.1 Mb and contains 39,040 genes. Comparative genomic analysis reveals that the kiwifruit has undergone an ancient hexaploidization event (γ) shared by core eudicots and two more recent whole-genome duplication events. Both recent duplication events occurred after the divergence of kiwifruit from tomato and potato and have contributed to the neofunctionalization of genes involved in regulating important kiwifruit characteristics, such as fruit vitamin C, flavonoid and carotenoid metabolism. As the first sequenced species in the Ericales, the kiwifruit genome sequence provides a valuable resource not only for biological discovery and crop improvement but also for evolutionary and comparative genomics analysis, particularly in the asterid lineage. The kiwifruit is an economically and nutritionally important fruit crop with high vitamin C content. Here, the authors report the draft genome sequence of a heterozygous kiwifruit and through comparative genomic analysis provide valuable insight into kiwifruit evolution.
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45
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Akagi T, Kajita K, Kibe T, Morimura H, Tsujimoto T, Nishiyama S, Kawai T, Yamane H, Tao R. Development of Molecular Markers Associated with Sexuality in Diospyros lotus L. and Their Application in D. kaki Thunb. ACTA ACUST UNITED AC 2014. [DOI: 10.2503/jjshs1.ch-109] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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46
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Falasca G, D'Angeli S, Biasi R, Fattorini L, Matteucci M, Canini A, Altamura MM. Tapetum and middle layer control male fertility in Actinidia deliciosa. ANNALS OF BOTANY 2013; 112:1045-55. [PMID: 23965617 PMCID: PMC3783237 DOI: 10.1093/aob/mct173] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
BACKGROUND AND AIMS Dioecism characterizes many crop species of economic value, including kiwifruit (Actinidia deliciosa). Kiwifruit male sterility occurs at the microspore stage. The cell walls of the microspores and the pollen of the male-sterile and male-fertile flowers, respectively, differ in glucose and galactose levels. In numerous plants, pollen formation involves normal functioning and degeneration timing of the tapetum, with calcium and carbohydrates provided by the tapetum essential for male fertility. The aim of this study was to determine whether the anther wall controls male fertility in kiwifruit, providing calcium and carbohydrates to the microspores. METHODS The events occurring in the anther wall and microspores of male-fertile and male-sterile anthers were investigated by analyses of light microscopy, epifluorescence, terminal deoxynucleotidyl transferase-mediated dUTP nick-end labelling (TUNEL assay) and transmission electron microscopy coupled with electron spectroscopy. The possibility that male sterility was related to anther tissue malfunctioning with regard to calcium/glucose/galactose provision to the microspores was also investigated by in vitro anther culture. KEY RESULTS Both tapetum and the middle layer showed secretory activity and both degenerated by programmed cell death (PCD), but PCD was later in male-sterile than in male-fertile anthers. Calcium accumulated in cell walls of the middle layer and tapetum and in the exine of microspores and pollen, reaching higher levels in anther wall tissues and dead microspores of male-sterile anthers. A specific supply of glucose and calcium induced normal pollen formation in in vitro-cultured anthers of the male-sterile genotype. CONCLUSIONS The results show that male sterility in kiwifruit is induced by anther wall tissues through prolonged secretory activity caused by a delay in PCD, in the middle layer in particular. In vitro culture results support the sporophytic control of male fertility in kiwifruit and open the way to applications to overcome dioecism and optimize kiwifruit production.
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Affiliation(s)
- Giuseppina Falasca
- Department of Environmental Biology, ‘Sapienza’ University of Rome, Rome, Italy
| | - Simone D'Angeli
- Department of Environmental Biology, ‘Sapienza’ University of Rome, Rome, Italy
| | - Rita Biasi
- Department of Science and Technologies for Agriculture, Forests, Nature and Energy, Viterbo, Tuscia University, Italy
| | - Laura Fattorini
- Department of Environmental Biology, ‘Sapienza’ University of Rome, Rome, Italy
| | - Maja Matteucci
- Department of Environmental Biology, ‘Sapienza’ University of Rome, Rome, Italy
| | | | - Maria Maddalena Altamura
- Department of Environmental Biology, ‘Sapienza’ University of Rome, Rome, Italy
- For correspondence. E-mail
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47
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Fraser LG, Seal AG, Montefiori M, McGhie TK, Tsang GK, Datson PM, Hilario E, Marsh HE, Dunn JK, Hellens RP, Davies KM, McNeilage MA, De Silva HN, Allan AC. An R2R3 MYB transcription factor determines red petal colour in an Actinidia (kiwifruit) hybrid population. BMC Genomics 2013; 14:28. [PMID: 23324587 PMCID: PMC3618344 DOI: 10.1186/1471-2164-14-28] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Accepted: 01/07/2013] [Indexed: 11/21/2022] Open
Abstract
Background Red colour in kiwifruit results from the presence of anthocyanin pigments. Their expression, however, is complex, and varies among genotypes, species, tissues and environments. An understanding of the biosynthesis, physiology and genetics of the anthocyanins involved, and the control of their expression in different tissues, is required. A complex, the MBW complex, consisting of R2R3-MYB and bHLH transcription factors together with a WD-repeat protein, activates anthocyanin 3-O-galactosyltransferase (F3GT1) to produce anthocyanins. We examined the expression and genetic control of anthocyanins in flowers of Actinidia hybrid families segregating for red and white petal colour. Results Four inter-related backcross families between Actinidia chinensis Planch. var. chinensis and Actinidia eriantha Benth. were identified that segregated 1:1 for red or white petal colour. Flower pigments consisted of five known anthocyanins (two delphinidin-based and three cyanidin-based) and three unknowns. Intensity and hue differed in red petals from pale pink to deep magenta, and while intensity of colour increased with total concentration of anthocyanin, no association was found between any particular anthocyanin data and hue. Real time qPCR demonstrated that an R2R3 MYB, MYB110a, was expressed at significant levels in red-petalled progeny, but not in individuals with white petals. A microsatellite marker was developed that identified alleles that segregated with red petal colour, but not with ovary, stamen filament, or fruit flesh colour in these families. The marker mapped to chromosome 10 in Actinidia. The white petal phenotype was complemented by syringing Agrobacterium tumefaciens carrying Actinidia 35S::MYB110a into the petal tissue. Red pigments developed in white petals both with, and without, co-transformation with Actinidia bHLH partners. MYB110a was shown to directly activate Actinidia F3GT1 in transient assays. Conclusions The transcription factor, MYB110a, regulates anthocyanin production in petals in this hybrid population, but not in other flower tissues or mature fruit. The identification of delphinidin-based anthocyanins in these flowers provides candidates for colour enhancement in novel fruits.
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Affiliation(s)
- Lena G Fraser
- The New Zealand Institute for Plant & Food Research Limited, 120 Mt. Albert Road, Auckland 1142, New Zealand.
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48
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Abstract
It is now well established that plants have an important place in studies of sex chromosome evolution because of the repeated independent evolution of separate sexes and sex chromosomes. There has been considerable recent progress in studying plant sex chromosomes. In this review, I focus on how these recent studies have helped clarify or answer several important questions about sex chromosome evolution, and I shall also try to clarify some common misconceptions. I also outline future work that will be needed to make further progress, including testing some important ideas by genetic, molecular, and developmental approaches. Systems with different ages can clearly help show the time course of events during changes from an ancestral co-sexual state (hermaphroditism or monoecy), and I will also explain how different questions can be studied in lineages whose dioecy or sex chromosomes evolved at different times in the past.
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Affiliation(s)
- Deborah Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, The University of Edinburgh, The King's Buildings, West Mains Road, Edinburgh EH9 3JT, UK.
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49
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Abstract
Polyploids are defined as either autopolyploids or allopolyploids, depending on their mode of origin and/or chromosome pairing behaviour. Autopolyploids have chromosome sets that are the result of the duplication or combination of related genomes (e.g., AAAA), while allopolyploids result from the combination of sets of chromosomes from two or more different taxa (e.g., AABB, AABBCC). Allopolyploids are expected to show preferential pairing of homologous chromosomes from within each parental sub-genome, leading to disomic inheritance. In contrast, autopolyploids are expected to show random pairing of chromosomes (non-preferential pairing), potentially leading to polysomic inheritance. The two main cultivated taxa of Actinidia (kiwifruit) are A. chinensis (2x and 4x) and A. chinensis var. deliciosa (6x). There is debate whether A. chinensis var. deliciosa is an autopolyploid derived solely from A. chinensis or whether it is an allopolyploid derived from A. chinensis and one or two other Actinidia taxa. To investigate whether preferential or non-preferential chromosome pairing occurs in A. chinensis var. deliciosa, the inheritance of microsatellite alleles was analysed in the tetraploid progeny of a cross between A. chinensis var. deliciosa and the distantly related Actinidia eriantha Benth. (2x). The frequencies of inherited microsatellite allelic combinations in the hybrids suggested that non-preferential chromosome pairing had occurred in the A. chinensis var. deliciosa parent. Meiotic chromosome analysis showed predominantly bivalent formation in A. chinensis var. deliciosa, but a low frequency of quadrivalent chromosome formations was observed (1 observed in 20 pollen mother cells).
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50
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Seal AG, Ferguson AR, de Silva HN, Zhang JL. The effect of 2n gametes on sex ratios in Actinidia. ACTA ACUST UNITED AC 2012; 25:197-203. [PMID: 22739644 DOI: 10.1007/s00497-012-0191-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Accepted: 06/11/2012] [Indexed: 10/28/2022]
Abstract
Sex can sometimes lead to complications. In some crops, 2n gametes have been exploited by plant breeders to transfer genetic variation between taxa of different ploidy levels. However, their role and use in dioecious genera have received relatively little attention. In the dioecious genus Actinidia (kiwifruit), seedling populations usually segregate equally for females and males as sex is determined by an XX female/XY male system. While fertilization involving 2n egg cells is not expected to affect the sex ratios of progenies, fertilization involving 2n pollen is likely to produce progenies with excess males. The extent of sex ratio distortion will depend on the relative contributions of first and second division restitution, and the frequency and location of cross-overs in meiosis. In this study, seedlings recovered from crosses between females of hexaploid Actinidia deliciosa and males of two diploid species, Actinidia chinensis and Actinidia eriantha, included a proportion of pentaploid hybrids presumably derived from fertilization involving 2n pollen. Most of these pentaploids were male, and a proportion of them were likely to be carrying two Y chromosomes. If used as parents in further crosses, males with multiple Y chromosomes are likely to cause distorted sex ratios in their immediate progenies. In dioecious genera such as Actinidia, the effects on sex ratios of different mechanisms of ploidy change need to be taken into account when considering the evolution of polyploidy and the design of breeding strategies involving ploidy manipulation.
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Affiliation(s)
- Alan G Seal
- The New Zealand Institute for Plant & Food Research Ltd, Te Puke Research Centre, RD 2, Te Puke 3182, New Zealand.
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