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Construction of high-density genetic maps defined sex determination region of the Y chromosome in spinach

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Abstract

Spinach (Spinacia olracea L.) is a dioecious leafy vegetable with a highly repetitive genome of around 990 Mb, which is challenging for de-novo genome assembly. In our study, a segregating F1 (double pseudo-testcross) population from ‘Viroflay’ × ‘Cornell-NO. 9′ was used for genetic mapping by resequencing genotyping. In the paternal ‘Cornell-NO. 9′ map, 212,414 SNPs were mapped, and the total linkage distance was 476.83 cM; the maternal ‘Viroflay’ map included 29,282 SNPs with 401.28 cM total genetic distance. Both paternal and maternal maps have the expected number of six linkage groups (LGs). A non-recombining region with 5678 SNPs (39 bin markers) co-segregates with sex type which located at 45.2 cM of LG1 in the ‘Cornell-NO. 9′ map while indicates the sex determination region (SDR). Integration of two maps into a consensus map guided us to anchor additional 1242 contigs to six pseudomolecules from the published reference genome, which improved additional 233 Mb (23.4%) assembly based on spinach estimated genome size. Particularly, the X counterpart of SDR in our assembly is estimated around 18.4 Mb which locates at the largest chromosome, as consensus with sex-biased FISH signals from previous cytogenetics studies. The region is featured by reduced gene density, higher percentage of repetitive sequences, and no recombination. Our linkage maps provide the resource for improving spinach genome de-novo assembly and identification of sex-determining genes in spinach.

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Data availability statements

The genomic sequences of spinach reference genome and gene annotation can be downloaded in the SpinachBase (https://www.spinachbase.org/). The improved genome assembly has been deposit in NCBI submission portal (ID: SUB7892681).

References

  • Akagi T, Henry IM, Tao R, Comai L (2014) A Y-chromosome—encoded small RNA acts as a sex determinant in persimmons. Science 346(6209):646–650

    Article  CAS  PubMed  Google Scholar 

  • Akagi T, Pilkington SM, Varkonyi-Gasic E, Henry IM, Sugano SS, Sonoda M, Tao R et al (2019) Two Y-chromosome-encoded genes determine sex in kiwifruit. Nat Plants 5(8):801–809

    Article  CAS  PubMed  Google Scholar 

  • Akamatsu T, Suzuki T (1999) Method for identifying the sex of spinach by DNA markers. Google Patents

  • Almeida P, Proux-Wera E, Churcher A, Soler L, Dainat J, Pucholt P, Nordlund J et al (2020) Genome assembly of the basket willow,Salix viminalis, reveals earliest stages of sex chromosome expansion. BMC Biol 18(1):1–18

    Article  CAS  Google Scholar 

  • Arumuganathan K, Earle E (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Report 9(3):208–218

    Article  CAS  Google Scholar 

  • Ashraf M, Foolad MR (2013) Crop breeding for salt tolerance in the era of molecular markers and marker-assisted selection. Plant Breed 132(1):10–20

    Article  Google Scholar 

  • Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30(15):2114–2120

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bowers JE, Bachlava E, Brunick RL, Rieseberg LH, Knapp SJ, Burke JM (2012) Development of a 10,000 locus genetic map of the sunflower genome based on multiple crosses. G3 Genes Genomes Genet 2(7):721–729

    CAS  Google Scholar 

  • Bowers JE, Pearl SA, Burke JM (2016) Genetic mapping of millions of SNPs in safflower (Carthamus tinctorius L.) via whole-genome resequencing. G3 Genes Genomes Genet 6(7):2203–2211

    Google Scholar 

  • Chapman JA, Mascher M, Buluç A, Barry K, Georganas E, Session A, Oliker L et al (2015) A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome. Genome Biol 16(1):26

    Article  PubMed  PubMed Central  Google Scholar 

  • Charlesworth B, Charlesworth D (1978) A model for the evolution of dioecy and gynodioecy. Am Nat 112(988):975–997

    Article  Google Scholar 

  • Consortium, I. B. G. S (2012) A physical, genetic and functional sequence assembly of the barley genome. Nature 491(7426):711

    Article  CAS  Google Scholar 

  • Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Sherry ST et al (2011) The variant call format and VCFtools. Bioinformatics 27(15):2156–2158

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • de Sousa N, Carlier J, Santo T, Leitão J (2013) An integrated genetic map of pineapple (Ananas comosus (L.) Merr.). Sci Hortic 157:113–118

    Article  CAS  Google Scholar 

  • Delph LF, Arntz AM, Scotti-Saintagne C, Scotti I (2010) The genomic architecture of sexual dimorphism in the dioecious plant Silene latifolia. Evol Int J Org Evol 64(10):2873–2886

    Google Scholar 

  • Deng C, Qin R, Gao J, Cao Y, Li S, Gao W, Lu L (2012) Identification of sex chromosome of spinach by physical mapping of 45srDNAs by FISH. Caryologia 65(4):322–327

    Article  Google Scholar 

  • Deng C, Qin R, Cao Y, Gao J, Li S, Gao W, Lu L (2013) Microdissection and painting of the Y chromosome in spinach (Spinacia oleracea). J Plant Res 126(4):549–556

    Article  CAS  PubMed  Google Scholar 

  • Ellis J, Janick J (1960) The chromosomes of Splnacia oleracea. Am J Bot 47(3):210–214

    Article  Google Scholar 

  • Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6(5):e19379

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Grattapaglia D, Sederoff R (1994) Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-testcross: mapping strategy and RAPD markers. Genetics 137(4):1121–1137

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hahn MW, Zhang SV, Moyle LC (2014) Sequencing, assembling, and correcting draft genomes using recombinant populations. G3 Genes Genomes Genet 4(4):669–679

    Google Scholar 

  • Haigh J (1978) The accumulation of deleterious genes in a population—Muller's ratchet. TheorPopul Biol 14(2):251–267

    CAS  Google Scholar 

  • Harkess A, Zhou J, Xu C, Bowers JE, Van der Hulst R, Ayyampalayam S, Chen G et al (2017) The asparagus genome sheds light on the origin and evolution of a young Y chromosome. Nat Commun 8(1):1279

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Henry IM, Akagi T, Tao R, Comai L (2018) One hundred ways to invent the sexes: theoretical and observed paths to dioecy in plants. Annu Rev Plant Biol 69:553–575

    Article  CAS  PubMed  Google Scholar 

  • Janick J, Stevenson EC (1955) Genetics of the monoecious character in spinach. Genetics 40(4):429–437

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Janick J, Mahoney D, Pfahler P (1959) Thetrisomics of Spinacia oleracea. J Hered 50(2):47–50

    Article  Google Scholar 

  • Khattak JZ, Torp AM, Andersen SB (2006) A genetic linkage map of Spinacia oleracea and localization of a sex determination locus. Euphytica 148(3):311–318

    Article  CAS  Google Scholar 

  • Komai F (1999) Sex expression in plants regenerated from the root callus of female and male spinach (Spinaciaoleracea). Plant Sci 146(1):35–40

    Article  CAS  Google Scholar 

  • Kudoh T, Takahashi M, Osabe T, Toyoda A, Hirakawa H, Suzuki Y, Onodera Y et al (2018a) Molecular insights into the non-recombining nature of the spinach male-determining region. Mol Genet Genomics 293(2):557–568

    Article  CAS  PubMed  Google Scholar 

  • Lan T, Zhang S, Liu B, Li X, Chen R, Song W (2006) Differentiating sex chromosomes of the dioecious Spinacia oleracea L. (spinach) by FISH of 45SrDNA. Cytogenet Genome Res 114(2):175–177

    Article  CAS  PubMed  Google Scholar 

  • Li H, Durbin R (2010) Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics 26(5):589–595

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Li L, Deng CH, Knabel M, Chagne D, Kumar S, Sun J, Wu J et al (2017) Integrated high-density consensus genetic map of Pyrus and anchoring of the 'Bartlett' v1.0 (Pyrus communis) genome. DNA Res 24(3):289–301

    PubMed  PubMed Central  Google Scholar 

  • Li S-F, Wang B-X, Guo Y-J, Deng C-L, Gao W-J (2018) Genome-wide characterization of microsatellites and genetic diversity assessment of spinach in the Chinese germplasm collection. Breed Sci 68(4):455–464

    Article  PubMed  PubMed Central  Google Scholar 

  • Mackay TF (2001) The genetic architecture of quantitative traits. Annu Rev Genet 35(1):303–339

    Article  CAS  PubMed  Google Scholar 

  • Massonnet M, Cochetel N, Minio A, Vondras AM, Lin J, Muyle A, Cantu D et al (2020) The genetic basis of sex determination in grapes. Nat Commun 11(1):2902

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Masuda FKK (2004) Plasticity in sex expression of spinach (Spinacia oleracea) regenerated fromroot tissues. Plant Cell Tissue Organ Culture 78:285–287

    Article  Google Scholar 

  • Ming R, Bendahmane A, Renner SS (2011) Sex chromosomes in land plants. Annu Rev Plant Biol 62:485–514

    Article  CAS  PubMed  Google Scholar 

  • Ming R, VanBuren R, Wai CM, Tang H, Schatz MC, Bowers JE, Biggers E et al (2015) The pineapple genome and the evolution of CAM photosynthesis. Nat Genet 47(12):1435

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Muller NA, Kersten B, LeiteMontalvao AP, Mahler N, Bernhardsson C, Brautigam K, Fladung M et al (2020) A single gene underlies the dynamic evolution of poplar sex determination. Nat Plants 6(6):630–637

    Article  PubMed  CAS  Google Scholar 

  • Mun J, Chung H, Chung W, Oh M, Jeong Y-M, Kim N, Lim K-B et al (2015) Construction of a reference genetic map of Raphanus sativus based on genotyping by whole-genome resequencing. TheorAppl Genet 128(2):259–272

    Article  CAS  Google Scholar 

  • Okazaki Y, Takahata S, Hirakawa H, Suzuki Y, Onodera Y (2019) Molecular evidence for recent divergence of X- and Y-linked gene pairs in Spinaciaoleracea L. PLoS ONE 14(4):e0214949

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Otto SP, Pannell JR, Peichel CL, Ashman T-L, Charlesworth D, Chippindale AK, McAllister BF et al (2011) About PAR: the distinct evolutionary dynamics of the pseudoautosomal region. Trends Genet 27(9):358–367

    Article  CAS  PubMed  Google Scholar 

  • Ouellette LA, Reid RW, Blanchard SG, Brouwer CR (2018) LinkageMapView—rendering high-resolution linkage and QTL maps. Bioinformatics 34(2):306–307

    Article  CAS  PubMed  Google Scholar 

  • Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE (2012) Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS ONE 7(5):e37135

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Qian W, Fan G, Liu D, Zhang H, Wang X, Wu J, Xu Z (2017) Construction of a high-density genetic map and the X/Y sex-determining gene mapping in spinach based on large-scale markers developed by specific-locus amplified fragment sequencing (SLAF-seq). BMC Genomics 18(1):276

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Rastas P (2017) Lep-MAP3: robust linkage mapping even for low-coverage whole genome sequencing data. Bioinformatics 33(23):3726–3732

    Article  CAS  PubMed  Google Scholar 

  • Renner SS (2014) The relative and absolute frequencies of angiosperm sexual systems: dioecy, monoecy, gynodioecy, and an updated online database. Am J Bot 101(10):1588–1596

    Article  PubMed  Google Scholar 

  • Segawa M, Kishi S, Tatuno S (1971) Sex chromosomes of Cycas revoluta. Jpn J Genet 46:33–39

    Article  Google Scholar 

  • Smit A, Hubley R, Green P (2014) RepeatModeler Open-1.0. 2008–2010. Access date Dec

  • Spigler RB, Lewers KS, Main DS, Ashman TL (2008) Genetic mapping of sex determination in a wild strawberry, Fragaria virginiana, reveals earliest form of sex chromosome. Heredity (Edinb) 101(6):507–517

    Article  CAS  Google Scholar 

  • Sun X, Liu D, Zhang X, Li W, Liu H, Hong W, Zeng H et al (2013) SLAF-seq: an efficient method of large-scale de novo SNP discovery and genotyping using high-throughput sequencing. PLoS ONE 8(3):e58700

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Takahata S, Yago T, Iwabuchi K, Hirakawa H, Suzuki Y, Onodera Y (2016) Comparison of spinach sex chromosomes with sugar beet autosomes reveals extensive synteny and low recombination at the male-determining locus. J Hered 107(7):679–685

    Article  CAS  PubMed  Google Scholar 

  • Tang H, Zhang X, Miao C, Zhang J, Ming R, Schnable JC, Lu J et al (2015) ALLMAPS: robust scaffold ordering based on multiple maps. Genome Biol 16(1):3

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tarailo-Graovac M, Chen N (2009) Using RepeatMasker to identify repetitive elements in genomic sequences. Curr Protoc Bioinform 25(1):4–10

    Article  Google Scholar 

  • Torres MF, Mathew LS, Ahmed I, Al-Azwani IK, Krueger R, Rivera-Nunez D, Malek JA et al (2018) Genus-wide sequencing supports a two-locus model for sex-determination in Phoenix. Nat Commun 9(1):3969

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Wadlington WH, Ming R (2018) Development of an X-specific marker and identification of YY individuals in spinach. TheorAppl Genet 131(9):1987–1994

    Article  CAS  Google Scholar 

  • Walker MA, Pedamallu CS, Ojesina AI, Bullman S, Sharpe T, Whelan CW, Meyerson M (2018) GATKPathSeq: a customizable computational tool for the discovery and identification of microbial sequences in libraries from eukaryotic hosts. Bioinformatics 34(24):4287–4289

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wang J, Na J-K, Yu Q, Gschwend AR, Han J, Zeng F, Zhang W et al (2012) Sequencing papaya X and Yh chromosomes reveals molecular basis of incipient sex chromosome evolution. Proc Natl Acad Sci 109(34):13710–13715

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wu J, Li L-T, Li M, Khan MA, Li X-G, Chen H, Zhang S-L et al (2014) High-density genetic linkage map construction and identification of fruit-related QTLs in pear using SNP and SSR markers. J Exp Bot 65(20):5771–5781

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xie W, Feng Q, Yu H, Huang X, Zhao Q, Xing Y, Zhang Q et al (2010) Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing. Proc Natl Acad Sci 107(23):10578–10583

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xu C, Jiao C, Sun H, Cai X, Wang X, Ge C, Xu Y et al (2017) Draft genome of spinach and transcriptome diversity of 120 Spinacia accessions. Nat Commun 8:15275

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yamamoto K, Oda Y, Haseda A, Fujito S, Mikami T, Onodera Y (2014) Molecular evidence that the genes for dioecism and monoecism in Spinacia oleracea L. are located at different loci in a chromosomal region. Heredity (Edinb) 112(3):317–324

    Article  CAS  Google Scholar 

  • Yang HW, Akagi T, Kawakatsu T, Tao R (2019) Gene networks orchestrated by MeGI: a single-factor mechanism underlying sex determination in persimmon. Plant J 98(1):97–111

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang Q, Liu C, Liu Y, VanBuren R, Yao X, Zhong C, Huang H (2015) High-density interspecific genetic maps of kiwifruit and the identification of sex-specific markers. DNA Res 22(5):367–375

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhou Q, Miao H, Li S, Zhang S, Wang Y, Weng Y, Gu X et al (2015) A sequencing-based linkage map of cucumber. Mol Plant 8(6):961–963

    Article  PubMed  CAS  Google Scholar 

  • Zhou R, Macaya-Sanz D, Carlson CH, Schmutz J, Jenkins JW, Kudrna D, DiFazio SP et al (2020) A willow sex chromosome reveals convergent evolution of complex palindromic repeats. Genome Biol 21(1):38

    Article  PubMed  PubMed Central  CAS  Google Scholar 

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Acknowledgements

This work was supported by the National Science Foundation (NSF) Plant Genome Research Program Award BI-1546890, Natural Science Foundation of Fujian Province, China 2018J01606, and startup fund from Fujian Agriculture and Forestry University. We appreciate the suggestions from Dr. Jun Wu and Wei Wei for projects and manuscript.

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Authors and Affiliations

  1. Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA

    Li’ang Yu & Ray Ming

  2. Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China

    Xiaokai Ma, Ban Deng, Jingjing Yue & Ray Ming

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  1. Li’ang Yu
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  2. Xiaokai Ma
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  3. Ban Deng
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  4. Jingjing Yue
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  5. Ray Ming
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Contributions

RM conceived the spinach sex chromosomes project, and LY constructed the spinach population, extracted the DNA, conducted the data analysis, and wrote the manuscript. XM and BD prepared the sequencing libraries. JY and XM proofread the manuscript. RM revised the manuscript.

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Correspondence to Ray Ming.

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438_2020_1723_MOESM1_ESM.xlsx

Supplementary file1Supplementary S1 Summary of re-sequencing data. The numbers of clean reads, average depth, GC content, Q20, and Q30 information were summarized (XLSX 10 kb)

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Supplementary file2Supplementary S2 Segregation patterns of F1 plants. Types of segregation patterns of F1 plants were summarized (XLSX 10 kb)

438_2020_1723_MOESM3_ESM.txt

Supplementary file3Supplementary S3 Selected SNPs for ‘Viroflay’ map construction. The file includes all selected SNP with ‘nnxnp’ genotype code from transformed variant calling files (VCFs) (TXT 6969 kb)

438_2020_1723_MOESM4_ESM.txt

Supplementary file4Supplementary S4 Selected SNPs for ‘Cornell-NO. 9’ map construction. The file includes all selected loci with ‘lmxll’ genotype code from transformed variant calling files (VCFs) (TXT 44937 kb)

438_2020_1723_MOESM5_ESM.xlsx

Supplementary file5Supplementary S5 Linkage map of ‘Viroflay’ × ‘Cornell-NO. 9’. The table includes genotypes for each F1 individual across all bins from ‘Virofaly’ map and ‘Cornell-NO. 9’ map. The first column represents the genetic distance, second column represents name for each bin, third column represents genomic size for each bin and the fourth column represent numbers of SNPs within each bin (XLSX 1009 kb)

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Supplementary file6Supplementary S6 AGP table of map-based spinach genome assembly. The table includes corresponded genomic region coordinates between map-based genome assembly and published reference genome (XLSX 2330 kb)

438_2020_1723_MOESM7_ESM.xlsx

Supplementary file7Supplementary S7 Genotype for SNPs identified from sex-linked region derived from ‘Cornell-NO. 9’ map. The worksheet includes genotypes identified from sex-linked region based on coordinates from each contig or scaffold (XLSX 1624 kb)

438_2020_1723_MOESM8_ESM.xlsx

Supplementary file8Supplementary S8 Statistics of segregation distorted bins from two maps. The Chi-square test value, ratio between numbers of homozygous and heterozygous genotypes for 80 individuals were summarized (XLSX 135 kb)

438_2020_1723_MOESM9_ESM.xlsx

Supplementary file9Supplementary S9 Summary of sex-linked genomic regions. The corresponded genomic region between map-based assembly and published reference genome was summarized, includes numbers of genes, numbers of SNPs, SNP coverage (XLSX 12 kb)

438_2020_1723_MOESM10_ESM.xlsx

Supplementary file10Supplementary S10 Summary of sex-linked uni-genes from previous studies. Uni-genes identified from previous studies were summarized based on coordinate from corresponded genomic position and occurrence in X counterpart of SDR defined from map-based genome assembly (XLSX 16 kb)

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Yu, L., Ma, X., Deng, B. et al. Construction of high-density genetic maps defined sex determination region of the Y chromosome in spinach. Mol Genet Genomics 296, 41–53 (2021). https://doi.org/10.1007/s00438-020-01723-4

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