Insertion of a mMoshan transposable element in PpLMI1, is associated with the absence or globose phenotype of extrafloral nectaries in peach [Prunus persica (L.) Batsch]

Abstract

Most commercial peach [ Prunus persica (L.) Batsch] cultivars have leaves with extrafloral nectaries (EFNs). Breeders have selected this character over time, as they observed that the eglandular phenotype resulted in high susceptibility to peach powdery mildew, a major disease of peach trees. EFNs are controlled by a Mendelian locus (E), mapped on chromosome 7. However, the genetic factor underlying E was unknown. In order to address this point, we developed a mapping population of 833 individuals derived from the selfing of “Malo Konare”, a Bulgarian peach cultivar, heterozygous for the trait. This progeny was used to investigate the E-locus region, along with additional resources including peach genomic resequencing data, and 271 individuals from various origins used for validation. High-resolution mapping delimited a 40.6 kbp interval including the E-locus and four genes. Moreover, three double-recombinants allowed identifying Prupe.7G121100, a LMI1-like homeodomain leucine zipper (HD-Zip) transcription factor, as a likely candidate for the trait. By comparing peach genomic resequencing data from individuals with contrasted phenotypes, a MITE-like transposable element of the hAT superfamily (mMoshan) was identified in the third exon of Prupe.7G121100. It was associated with the absence or globose phenotype of EFNs. The insertion of the transposon was positively correlated with enhanced expression of Prupe.7G121100. Furthermore, a PCR marker designed from the sequence-variants, allowed to properly assign the phenotypes of all the individuals studied. These findings provide valuable information on the genetic control of a trait poorly known so far although selected for a long time in peach.

References

[1] Gregory CT . The taxonomic value and structure of the peach leaf glands. NY Cornell Agric Exp Sta Bull. 1915; 365: 183-222.

[2] Okie WR . Handbook of Peach and Nectarine Varieties . Byron, GA: USDA-ARS; 1998.

[3] Koptur S. Extrafloral nectary-mediated interactions between insects and plants. In: Bernays EA, ed. Insect-Plant Interactions Vol. IV. CRC Press: Boca Raton, FL, USA, 1992, 81-129.

[4] Marazzi B, Bronstein JL, Koptur S . The diversity, ecology and evolution of extrafloral nectaries: current perspectives and future challenges. Ann Bot. 2013; 111: 1243-50.

[5] Mathews CR, Bottrell DG, Brown MW . Extrafloral nectaries alter arthropod community structure and mediate peach (Prunus persica) plant defense. Ecol Appl. 2009; 19: 722-30.

[6] Jones IM, Koptur S, von Wettberg EJ . The use of extrafloral nectar in pest management: overcoming context dependence. The Journal of applied ecology. 2017; 54: 489-99.

[7] Weber MG, Porturas LD, Taylor SA . Foliar nectar enhances plant-mite mutualisms: the effect of leaf sugar on the control of powdery mildew by domatia-inhabiting mites. Ann Bot. 2016; 118: 459-66.

[8] Scorza R, Sherman WB . In: Janick J, Moore JN, eds. Peaches, Fruit Breeding, Volume 1: Tree and Tropical Fruits . John Wiley & Sons: NY, 1996, 325-440.

[9] Watiking W, Brown AG . Genetic response to selection in cultivated plants: gene frequencies in varieties of Prunus persica . Proc R Soc Lond B. 1956; 145: 337-47.

[10] Saunier R . Contribution to the study of relationships between certain characteristics of simple genetic determination in the peach tree and susceptibility of peach cultivars to oïdium, Sphaerotheca pannosa (Wallr.) . Lev Ann Amelior Plant. 1973; 441: 235-43.

[11] Weinhold AR . The orchard development of peach powdery mildew. Phytopathology. 1961; 51: 478-81.

[12] Pascal T, Pfeiffer F, Kervella J . Powdery mildew in the peach cultivar Pamirkij 5 is genetically linked to the gr gene for leaf color. Hort Sci. 2010; 45: 150-2.

[13] Connors CH . Inheritance of foliar glands of the peach. Proc Am Soc Hortic Sci. 1921; 18: 21-7.

[14] Dettori MT, Quarta R, Verde I . A peach linkage map integrating RFLPs, SSRs, RAPDs, and morphological markers. Genome. 2001; 44: 783-90.

[15] Dirlewanger E, Graziano E, Joobeur T et al. Comparative mapping and marker-assisted selection in Rosaceae fruit crops. Proc Natl Acad Sci U S A. 2004; 101: 9891-6.

[16] Verde I, Quarta R, Cedrola C et al. QTL analysis of agronomic traits in a BC1 peach population. Acta Hortic. 2002; 592: 291-7.

[17] Dabov S. Malo Konare - a new canning peach variety. Rastenievj Nauki. 1985; 22: 84-7.

[18] Desnoues E, Baldazzi V, Genard M et al. Dynamic QTLs for sugars and enzyme capacities provide an overview of genetic control of sugar metabolism during peach fruit development. J Exp Bot. 2016; 67: 3419-31.

[19] Micheletti D, Dettori MT, Micali S et al. Whole-genome analysis of diversity and SNP-major gene association in peach germplasm. PLoS One. 2015; 10: e0136803. 10.1371/journal.pone.0136803.

[20] Verde I, Bassil N, Scalabrin S et al. Development and evaluation of a 9K Array for peach by internationally coordinated SNP detection and validation in breeding germplasm. PLoS One. 2012; 7: e35668. 10.1371/journal.pone.0035668.

[21] Wang L, Peng Q, Zhao J et al. Evolutionary origin of Rosaceae-specific active non-autonomous hAT elements and their contribution to gene regulation and genomic structural variation. Plant Mol Biol. 2016; 91: 179-91.

[22] Bennetzen JL, Wang H . The contributions of transposable elements to the structure, function, and evolution of plant genomes. Annu Rev Plant Biol. 2014; 65: 505-30.

[23] Chen J, Hu Q, Zhang Y et al. A database for plant miniature inverted-repeat transposable elements. Nucleic Acids Res. 2014; 42: Database issue.

[24] Lu C, Chen J, Zhang Y et al. Miniature inverted-repeat transposable elements (MITEs) have been accumulated through amplification bursts and play important roles in gene expression and species diversity in Oryza sativa . Mol Biol Evol. 2012; 29: 1005-17.

[25] Henriksson E, Olsson ASB, Johannesson H et al. Homeodomain leucine zipper class I genes in Arabidopsis. Expression patterns and phylogenetic relationships. Plant Physiol. 2005; 139: 509-18.

[26] Saddic LA, Huvermann B, Bezhani S et al. The LEAFY target LMI1 is a meristem identity regulator and acts together with LEAFY to regulate expression of CAULIFLOWER . Development. 2006; 133: 1673-82.

[27] Mangan S, Alon U . Structure and function of the feed-forward loop network motif. Proc Natl Acad Sci U S A. 2003; 100: 11980-5.

[28] Xu M, Hu T, Mckim SM et al. Arabidopsis BLADE-ON-PETIOLE1 and 2 promote floral meristem fate and determinacy in a previously undefined pathway targeting APETALA1 and AGAMOUS-LIKE. Plant J. 2010; 63: 974-89.

[29] Vlad D, Kierzkowski D, Rast MI et al. Leaf shape evolution through duplication, regulatory diversification, and loss of a homeobox gene. Science. 2014; 343: 780-3.

[30] Vuolo F, Kierzkowski D, Runions A et al. LMI1 homeodomain protein regulates organ proportions by spatial modulation of endoreduplication. Genes Dev. 2019; 33: 377.

[31] Andres RJ, Coneva V, Frank MH et al. Modifications to a LATE MERISTEM IDENTITY1 gene are responsible for the major leaf shapes of upland cotton (Gossypium hirsutum L.) . Proc Natl Acad Sci U S A. 2017; 114: E57-66.

[32] Maugarny-Calès A, Laufs P . Getting leaves into shape: a molecular, cellular, environmental and evolutionary view. Development. 2018; 145: dev161646.

[33] Chang LJ, Mei GF, Hu Y et al. LMI1-like and KNOX1 genes coordinately regulate plant leaf development in dicotyledons. Plant Mol Biol. 2019; 99: 449-60.

[34] Sicard A, Thamm A, Marona C et al. Repeated evolutionary changes of leaf morphology caused by mutations of a homeobox gene. Curr Biol. 2014; 24: 1880-6.

[35] Zhao JL, Pan JS, Guan Y et al. Transcriptome analysis in Cucumis sativus identifies genes involved in multicellular trichome development. Genomics. 2015; 105: 296-303.

[36] Hu W, Qin W, Jin Y et al. Genetic and evolution analysis of extrafloral nectary in cotton. Plant biotechnology journal. 2020; 18: 2081-95.

[37] Bowman JL, Smyth DR . CRABS CLAW, a gene that regulates carpel and nectary development in Arabidopsis, encodes a novel protein with zinc finger and helix-loop-helix domains . Development. 1999; 126: 2387-96.

[38] Gross T, Broholm S, Becker A . CRABS CLAW acts as a Bifunctional transcription factor in flower development. Front Plant Sci. 2018; 9: 835.

[39] Lee JY, Baum SF, Alvarez J et al. Activation of CRABS CLAW in the nectaries and carpels of Arabidopsis . Plant Cell. 2005a; 17: 25-36.

[40] Lee JY, Baum SF, Oh SH et al. Recruitment of CRABS CLAW to promote nectary development within the eudicot clade. Development. 2005b; 132: 5021-32.

[41] Bhosale R, Maere S, De Veylder L . Endoreplication as a potential driver of cell wall modifications. Current opinion in plant biology. 2019; 51: 58-65.

[42] Thorvaldsdóttir H, Robinson JT, Mesirov JP . Integrative genomics viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 2013; 14: 178-92.

[43] Untergasser A, Cutcutache I, Koressaar T et al. Primer3-new capabilities and interfaces. Nucleic Acids Res. 2012; 40: e115.

[44] Verde I, Jenkins J, Dondini L et al. The peach v2.0 release: high-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguity. BMC Genomics. 2017; 18: 225.

[45] Van Ooijen JW . JoinMap^® 4.1, Software for the calculation of genetic linkage maps in experimental populations of diploid species Kyazma B.V., Wageningen, Netherlands: Kyazma B.V., 2012.

[46] Kosambi DD . The estimation of map distance from recombination values. Ann Eugenics. 1943; 12: 172-5.

[47] Madeira F, Park YM, Lee J et al. The EMBL-EBI search and sequence analysis tools APIs in 2019. Nucleic Acids Res. 2019; 47: W636-41.

[48] Solovyev V, Kosarev P, Seledsov I et al. Automatic annotation of eukaryotic genes, pseudogenes and promoters. Genome Biol. 2006; 7: S10- 10.12.

[49] Bustin SA, Benes V, Garson J et al. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem. 2009; 55: 611-22.

[50] Hilliou F, Tran T . RqPCRAnalysis: analysis of quantitative real-time PCR data. Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms. 2013; 1: 202-11.

[51] R Core Team : A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/. (2020).