Advances in sequencing and key character analysis of mango (Mangifera indica L.)

Miaoyu Song , Haomiao Wang , Zhiyi Fan , Hantang Huang , Huiqin Ma

Horticulture Research ›› 2023, Vol. 10 ›› Issue (2) : 259

PDF (715KB)
Horticulture Research ›› 2023, Vol. 10 ›› Issue (2) :259 DOI: 10.1093/hr/uhac259
Review Article
research-article
Advances in sequencing and key character analysis of mango (Mangifera indica L.)
Author information +
History +
PDF (715KB)

Abstract

Mango (Mangifera indica L.) is an important fruit crop in tropical and subtropical countries associated with many agronomic and horticultural problems, such as susceptibility to pathogens, including powdery mildew and anthracnose, poor yield and quality, and short shelf life. Conventional breeding techniques exhibit significant limitations in improving mango quality due to the characteristics of long ripening, self-incompatibility, and high genetic heterozygosity. In recent years, much emphasis has been placed on identification of key genes controlling a certain trait through genomic association analysis and directly breeding new varieties through transgene or genotype selection of offspring. This paper reviews the latest research progress on the genome and transcriptome sequencing of mango fruit. The rapid development of genome sequencing and bioinformatics provides effective strategies for identifying, labeling, cloning, and manipulating many genes related to economically important traits. Preliminary verification of the functions of mango genes has been conducted, including genes related to flowering regulation, fruit development, and polyphenol biosynthesis. Importantly, modern biotechnology can refine existing mango varieties to meet the market demand with high economic benefits.

Cite this article

Download citation ▾
Miaoyu Song, Haomiao Wang, Zhiyi Fan, Hantang Huang, Huiqin Ma. Advances in sequencing and key character analysis of mango (Mangifera indica L.). Horticulture Research, 2023, 10 (2) : 259 DOI:10.1093/hr/uhac259

登录浏览全文

4963

注册一个新账户 忘记密码

Author contribution

M.S. drafted the original manuscript. Critical inputs and corrections were successively provided by H.W., Z.F., and H.H. during the preparation process. H.M. is the project leader and helped in the conception and structure design of the manuscript and final proofing of the manuscript for submission.

Data availability

Authors confirm the availability of data and that any required links or identifiers for data are present in the manuscript as described.

Conflict of interest

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

References

[1]

Tharanathan RN, Yashoda HM, Prabha TN . Mango (Mangifera indica L.), “the king of fruits”-an overview. Food Rev Int. 2006; 22: 95-123.

[2]

Subramanyam H, Krishnamurthy S, Parpia HA . Physiology and biochemistry of mango fruit. Adv Food Res. 1975; 21: 223-305.

[3]

Ledesma N, Campbell RJ . The status of mango cultivars, market perspectives and mango cultivar improvement for the future. Acta Hortic. 2019; 1224: 23-8.

[4]

Sagar VR, Khurdiya DS, Balakrishnan KA . Quality of dehydrated ripe mango slices as affected by packaging material and mode of packaging. J Food Sci Tech Mys. 1999; 36: 67-70.

[5]

Iyer CPA, Subramanyam MD . Breeding Mango for Developing New Varieties. Acta hortic. 1991; 291: 151-3.

[6]

Mukherjee SK, Litz R. Introduction: Botany and Importance. In: Litz R E (ed) The mango: botany, production and uses, 2nd edn. CAB International, Wallingford, Oxfordshire, UK, 2009; pp 1-18.

[7]

CPA I, Dinesh M . Advances in classical breeding and genetics in mango. En V International Mango Symposium. 1997; 455: 252-67.

[8]

Viruel MA, Escribano P, Barbieri M et al. Fingerprinting, embryo type and geographic differentiation in mango (Mangifera indica L., Anacardiaceae) with microsatellites. Mol Breeding. 2005; 15: 383-93.

[9]

Yamanaka S, Hosaka F, Matsumura M et al. Genetic diversity and relatedness of mango cultivars assessed by SSR markers. Breed Sci. 2019; 69: 332-44.

[10]

Paranhos JG, Ishikawa FH, MAC d L et al. Estimation of genetic parameters and prediction of breeding values for fruit-quality traits in hybrid mangoes. Int J Fruit Sci. 2022; 22: 608-17.

[11]

Júnior J et al. Genetic diversity among mango hybrids in the Brazilian semi-arid region. Revista Caatinga. 2021; 34: 709-19.

[12]

Luo C, Shu B, Yao Q et al. Construction of a high-density genetic map based on large-scale marker development in mango using specific-locus amplified fragment sequencing (SLAF-seq). Front Plant Sci. 2016; 7: 1310.

[13]

Jena RC, Chand PK . DNA marker-based auditing of genetic diversity and population structuring of Indian mango (Mangifera indica L.) elites. Genet Resour Crop Ev. 2022; 69: 1595-626.

[14]

Ramachandra S, Srivastav M, Singh SK et al. New genomic markers for marker assisted breeding in mango (Mangifera indica L.). J Hortic Sci Biotechnol. 2021; 96: 624-33.

[15]

Kuhn DN, Dillon N, Bally I et al. Estimation of genetic diversity and relatedness in a mango germplasm collection using SNP markers and a simplified visual analysis method. Sci Hortic. 2019; 252: 156-68.

[16]

Mahato AK, Sharma N, Singh A et al. Leaf Transcriptome sequencing for identifying genic-SSR markers and SNP Heterozygosity in crossbred mango variety ’Amrapali’ (Mangifera indica L.). PLoS One 2016; 11: 0164325.

[17]

Tsai CC, YKH C, Chen CH et al. Cultivar identification and genetic relationship of mango (Mangifera indica) in Taiwan using 37 SSR markers. Sci Hortic. 2013; 164: 196-201.

[18]

Shudo A, Tarora K, Makishi Y et al. Development of CAPS markers and their application in breeding for mango, Mangifera indica L. Euphytica. 2013; 190: 345-55.

[19]

Nashima K, Terakami S, Kunihisa M et al. Retrotransposon-based insertion polymorphism markers in mango. Tree Genet Genomes. 2017; 13: 110.

[20]

Peng L, Gao W, Song M et al. Integrated Metabolome and Transcriptome analysis of fruit flavor and carotenoids biosynthesis differences between mature-green and tree-ripe of cv. "Golden Phoenix" mangoes (Mangifera indica L.). Front Plant Sci. 2022; 13: 816492.

[21]

Tafolla-Arellano JC, Zheng Y, Sun H et al. Transcriptome analysis of mango (Mangifera indica L.) fruit epidermal Peel to identify putative cuticle-associated genes. Sci Rep UK. 2017; 7: 46163.

[22]

Wang P, Luo Y, Huang J et al. The genome evolution and domestication of tropical fruit mango. Genome Biol. 2020; 21: 60.

[23]

Kuhn DN, ISE B, Dillon NL et al. Genetic map of mango: a tool for mango breeding. Front Plant Sci 2017; 8: 577.

[24]

Azim MK, Khan IA, Zhang Y . Characterization of mango (Mangifera indica L.) transcriptome and chloroplast genome. Plant Mol Biol. 2014; 85: 193-208.

[25]

Qamar-ul-Islam T, Khan M, Faizan R, Mahmood U . MGDb: an analyzed database and a genomic resource of mango (Mangifera Indica L.) cultivars for mango research. bioRxiv 2018; 301358. Preprint: not peer reviewed.

[26]

Mukherjee SK . The mango-its botany, cultivation, uses and future improvement, especially as observed in India. Econ Bot. 1953; 7: 130-62.

[27]

KEE A, Earle E . Nuclear DNA content of some important plant species. Plant Mol Biol Report. 1991; 9: 208-18.

[28]

Huang Jing WS, Weihong M, Weixing W et al. Mutagenesis of colchicine on stem tips of mango. J Southwest Agri Univ (Nat Sci). 2006; 28: 926-9.

[29]

Mo Rao LY, Shimin Z, Jinping L . Polyembryony in mango (Mangifera indica L.) and genetic analysis. J Trop Subtrop Bot. 2005; 13: 475-79.

[30]

Galán Saúco V et al. Occurrence of spontaneous Tetraploid Nucellar mango plants. HortScience. 2001; 36: 755-7.

[31]

Yonemori K, Nishiyama K, Choi YA . Physical mapping of 5S and 45S rDNAs by fluorescent in situ hybridization in mango (Mangifera indica L.). Acta Hortic. 2010; 864: 133-9.

[32]

Li W, Zhu X, Zhang Q et al. SMRT sequencing generates the chromosome-scale reference genome of tropical fruit mango, Mangifera indica. bioRxiv 2020;25. Preprint: not peer reviewed.

[33]

Ma X, Luo X, Wei Y et al. Chromosome-scale genome and comparative Transcriptomic analysis reveal transcriptional regulators of beta-carotene biosynthesis in mango. Front Plant Sci. 2021; 12: 749108.

[34]

Bally ISE, Bombarely A, Chambers AH et al. The ’Tommy Atkins’ mango genome reveals candidate genes for fruit quality. BMC Plant Biol 2021; 21: 108.

[35]

Cortaga CQ, JAP L, Lantican DV et al. Genome-wide SNP and InDel analysis of three Philippine mango species inferred from whole-genome sequencing. J Genet Eng Biotechnol. 2022; 20: 46.

[36]

Wu HX, Jia HM, Ma XW et al. Transcriptome and proteomic analysis of mango (Mangifera indica Linn) fruits. J Proteome. 2014; 105: 19-30.

[37]

Luria N, Sela N, Yaari M et al. De-novo assembly of mango fruit peel transcriptome reveals mechanisms of mango response to hot water treatment. BMC Genomics. 2014; 15: 957.

[38]

Dautt-Castro M, Ochoa-Leyva A, Contreras-Vergara CA et al. Mango (Mangifera indica L.) cv. Kent fruit mesocarp de novo transcriptome assembly identifies gene families important for ripening. Front Plant Sci. 2015; 6: 62.

[39]

Hong KQ, Gong D, Zhang L et al. Transcriptome characterization and expression profiles of the related defense genes in postharvest mango fruit against Colletotrichum gloeosporioides. Gene 2016; 576: 275-83.

[40]

Sivankalyani V, Sela N, Feygenberg O et al. Transcriptome dynamics in mango fruit Peel reveals mechanisms of chilling stress. Front Plant Sci. 2016; 7: 1579.

[41]

Deshpande AB, Anamika K, Jha V et al. Transcriptional transitions in Alphonso mango (Mangifera indica L.) during fruit development and ripening explain its distinct aroma and shelf life characteristics. Sci Rep 2017; 7: 8711.

[42]

Dautt-Castro M, Ochoa-Leyva A, Contreras-Vergara CA et al. Mesocarp RNA-Seq analysis of mango (Mangifera indica L.) identify quarantine postharvest treatment effects on gene expression. Sci Hortic. 2018; 227: 146-53.

[43]

Bajpai A, Khan K, Muthukumar M et al. Molecular analysis of anthocyanin biosynthesis pathway genes and their differential expression in mango peel. Genome. 2018; 61: 157-66.

[44]

Chabikwa TG, Barbier FF, Tanurdzic M et al. Novo transcriptome assembly and annotation for gene discovery in avocado, macadamia and mango. Sci Data. 2020; 7: 9.

[45]

Khanum Z, Tiznado-Hernández ME, Ali A et al. Adaptation mechanism of mango fruit (Mangifera indica L. cv. Chaunsa white) to heat suggest modulation in several metabolic pathways. RSC Adv 2020; 10: 35531-44.

[46]

Sharma N, Singh AK, Singh SK et al. Comparative RNA sequencing based transcriptome profiling of regular bearing and alternate bearing mango (Mangifera indica L.) varieties reveals novel insights into the regulatory mechanisms underlying alternate bearing. Biotechnol Lett 2020; 42: 1035-50.

[47]

Xin M, Li C, Khoo HE et al. Dynamic analyses of Transcriptome and metabolic profiling: revealing molecular insight of aroma synthesis of mango (Mangifera indica L. Var. Tainong). Front Plant Sci. 2021; 12: 666805.

[48]

Deshpande AB, Chidley HG, Oak PS et al. Isolation and characterization of 9-lipoxygenase and epoxide hydrolase 2 genes: insight into lactone biosynthesis in mango fruit (Mangifera indica L.). Phytochem. 2017; 138: 65-75.

[49]

NMM M, Zhang P, Chen Y et al. Computational identification of miRNAs and temperature-responsive lncRNAs from mango (Mangifera indica L.). Front Genet. 2021; 12: 607248.

[50]

Mathiazhagan M, Chidambara B, Hunashikatti LR et al. Genomic approaches for improvement of tropical fruits: fruit quality, shelf life and nutrient content. Genes (Basel). 2021; 12: 1881.

[51]

Sela N, Luria N, Yaari M et al. Genome sequence of a potential new Benyvirus isolated from mango RNA-seq data. Genome Announc. 2016; 4: e01250-16.

[52]

Sherman A, Rubinstein M, Eshed R et al. Mango (Mangifera indica L.) germplasm diversity based on single nucleotide polymorphisms derived from the transcriptome. BMC Plant Biol. 2015; 15: 277.

[53]

Baird NA, Etter PD, Atwood TS et al. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One 2008; 3: e3376.

[54]

Miller MR, Dunham JP, Amores A et al. Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Res 2007; 17: 240-8.

[55]

Iquebal MA, Jaiswal S, Mahato AK et al. MiSNPDb: a web-based genomic resources of tropical ecology fruit mango (Mangifera indica L.) for phylogeography and varietal differentiation. Sci Rep 2017; 7: 14968.

[56]

Warschefsky EJ, von Wettberg EJB . Population genomic analysis of mango (Mangifera indica) suggests a complex history of domestication. New Phytol. 2019; 222: 2023-37.

[57]

VLT H, Innes DJ, Shaw PN et al. Sequence diversity and differential expression of major phenylpropanoid-flavonoid biosynthetic genes among three mango varieties. BMC Genomics. 2015; 16: 561.

[58]

Nakagawa M, Honsho C, Kanzaki S et al. Isolation and expression analysis of FLOWERING LOCUS T-like and gibberellin metabolism genes in biennial-bearing mango trees. Sci Hortic. 2012; 139: 108-17.

[59]

Das A, Geetha GA, Ravishankar KV et al. Interrelations of growth regulators, carbohydrates and expression of flowering genes (FT, LFY, AP1) in leaf and shoot apex of regular and alternate bearing mango (Mangifera indica L.) cultivars during flowering. Sci Hortic. 2019; 253: 263-9.

[60]

Wei JY, Liu DB, Liu GY et al. Molecular cloning, characterization, and expression of MiSOC1: a homolog of the flowering gene SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 from mango (Mangifera indica L). Front Plant Sci. 2016; 7: 1758.

[61]

Liu Y, Luo C, Zhang XJ et al. Overexpression of the mango MiCO gene delayed flowering time in transgenic Arabidopsis. Plant Cell Tiss Org. 2020; 143: 219-28.

[62]

Fan ZY, He XH, Fan Y et al. Isolation and functional characterization of three MiFTs genes from mango. Plant Physiol Bioch. 2020; 155: 169-76.

[63]

Guo YH, Luo C, Liu Y et al. Isolation and functional analysis of two CONSTANS-like 1 genes from mango. Plant Physiol Bioch. 2022; 172: 125-35.

[64]

Yadav A, Jayaswal PK, Venkat Raman K et al. Transcriptome analysis of flowering genes in mango (Mangifera indica L.) in relation to floral malformation. J Plant Biochem Biot. 2020; 29: 193-212.

[65]

Yu HX, Luo C, Fan Y et al. Isolation and characterization of two APETALA1-like genes from mango (Mangifera indica L.). Sci Hortic. 2020; 259: 108814.

[66]

Patil SI, Vyavahare SN, Krishna B et al. Studies on the expression patterns of the circadian rhythm regulated genes in mango. Physiol Mol Biol Pla. 2021; 27: 2009-25.

[67]

Wang YH, He XH, Yu HX et al. Overexpression of four MiTFL1 genes from mango delays the flowering time in transgenic Arabidopsis. BMC Plant Biol. 2021; 21: 407.

[68]

Mo X, Luo C, Yu H et al. Isolation and functional characterization of two SHORT VEGETATIVE PHASE homologous genes from mango. Int J Mol Sci. 2021; 22: 9802.

[69]

Liu Y, Luo C, Guo Y et al. Isolation and functional characterization of two CONSTANS-like 16 (MiCOL16) genes from mango. Int J Mol Sci. 2022; 23: 3075.

[70]

Wang YH, Yu H, He X et al. Isolation and functional characterization of a LEAFY gene in mango (Mangifera indica L.). Int J Mol Sci. 2022; 23: 3974.

[71]

Wei JY, Tang J, Liu DB et al. Cloning and expression analysis of SEPALAATA gene in mango (Mangifera indica L). Acta Botan Boreali-Occiden Sin. 2017; 71: 356-61.

[72]

Sane VA, Chourasia A, Nath P . Softening in mango (Mangifera indica cv. Dashehari) is correlated with the expression of an early ethylene responsive, ripening related expansin gene, MiExpA1. Postharvest Biol Tec. 2005; 38: 223-30.

[73]

Chourasia A, Sane VA, Singh RK et al. Isolation and characterization of the MiCel1 gene from mango: ripening related expression and enhanced endoglucanase activity during softening. Plant Growth Regul. 2008; 56: 117-27.

[74]

Ish-Shalom M, Dahan Y, Maayan I et al. Cloning and molecular characterization of an ethylene receptor gene, MiERS1, expressed during mango fruitlet abscission and fruit ripening. Plant Physiol Biochem 2011; 49: 931-6.

[75]

Zheng XL, Jing G, Liu Y et al. Expression of expansin gene, MiExpA1, and activity of galactosidase and polygalacturonase in mango fruit as affected by oxalic acid during storage at room temperature. Food Chem. 2012; 132: 849-54.

[76]

Rai AC, Halon E, Zemach H et al. Characterization of two Ethephon-induced IDA-like genes from mango, and elucidation of their involvement in regulating organ abscission. Genes-Basel. 2021; 12: 439.

[77]

Kanzaki S, Kamikawa S, Ichihi A et al. Isolation of UDP:flavonoid 3-O-glycosyltransferase (UFGT)-like genes and expression analysis of genes associated with anthocyanin accumulation in mango ’Irwin’ skin. Horticult J. 2019; 88: 435-43.

[78]

Zhao ZC, Gao AP, Luo RX et al. The different deletion mutation in the phenylalanine ammonia-lyase (PAL) gene affects the peel color of mango (Mangifera indica L.). Genet Resour Crop Ev. 2022; 69: 2301-6.

[79]

Shi B, Wu H, Zhu W et al. Genome-wide identification and expression analysis of WRKY genes during anthocyanin biosynthesis in the mango (Mangifera indica L.). Agriculture-Basel 2022; 12: 821.

[80]

Ma XW, Zheng B, Ma Y et al. Carotenoid accumulation and expression of carotenoid biosynthesis genes in mango flesh during fruit development and ripening. Sci Hortic. 2018; 237: 201-6.

[81]

Yungyuen W, Vo TT, Uthairatanakij A et al. Carotenoid accumulation and the expression of carotenoid metabolic genes in mango during fruit development and ripening. Appl Sci-Basel. 2021; 11: 4249.

[82]

Lawson T, Lycett GW, Mayes S et al. Transcriptome-wide identification and characterization of the Rab GTPase family in mango. Mol Biol Rep. 2020; 47: 4183-97.

[83]

Denisov Y, Glick S, Zviran T et al. Distinct organ-specific and temporal expression profiles of auxin-related genes during mango fruitlet drop. Plant Physiol Bioch. 2017; 115: 439-48.

[84]

Winterhagen P, Hagemann MH, Wunsche JN . Different regulatory modules of two mango ERS1 promoters modulate specific gene expression in response to phytohormones in transgenic model plants. Plant Sci. 2019; 289: 110269.

[85]

Hong K, Gong D, Xu H et al. Effects of salicylic acid and nitric oxide pretreatment on the expression of genes involved in the ethylene signalling pathway and the quality of postharvest mango fruit. New Zeal J Crop Hort. 2014; 42: 205-16.

[86]

Li LS, Luo C, Huang F et al. Identification and characterization of the mango eIF gene family reveals MieIF1A-a, which confers tolerance to salt stress in transgenic Arabidopsis. Sci Hortic. 2019; 248: 274-81.

[87]

Tan L, Salih H, NNW H et al. Genomic analysis of WD40 protein family in the mango reveals a TTG1 protein enhances root growth and abiotic tolerance in Arabidopsis. Sci Rep. 2021; 11: 2266.

[88]

Zhu J, Yan X, Liu S et al. Alternative splicing of CsJAZ1 negatively regulates flavan-3-ol biosynthesis in tea plants. Plant J. 2022; 110: 243-61.

[89]

Xia L, He X, Huang X et al. Genome-wide identification and expression analysis of the 14-3-3 gene family in mango (Mangifera indica L.). Int J Mol Sci. 2022; 23: 1593.

[90]

Lei XT, Yao QS, Xu XR et al. Isolation and characterization of NBS-LRR resistance gene analogues from mango. Biotechnol Biotec Eq. 2014; 28: 417-24.

[91]

Luo C, He XH, Chen H et al. Molecular cloning and expression analysis of four actin genes (MiACT) from mango. Biol Plant. 2013; 57: 238-44.

[92]

Valverde F, Mouradov A, Soppe W et al. Photoreceptor regulation of CONSTANS protein in photoperiodic flowering. Science. 2004; 303: 1003-6.

[93]

Luo C, Yu HX, Fan Y et al. Research advance on the flowering mechanism of mango. Acta Horticulturae. 2019; 1244: 17-22.

[94]

Lee JH, Yoo SJ, Park SH et al. Role of SVP in the control of flowering time by ambient temperature in Arabidopsis. Genes Dev. 2007; 21: 397-402.

[95]

Wang W, Feng J, Wei L et al. Transcriptomics integrated with free and bound Terpenoid aroma profiling during "Shine Muscat" (Vitis labrusca x V. vinifera) grape berry development reveals coordinate regulation of MEP pathway and Terpene synthase gene expression. J Agric Food Chem. 2021; 69: 1413-29.

[96]

Keeling CI, Weisshaar S, Ralph SG et al. Transcriptome mining, functional characterization, and phylogeny of a large terpene synthase gene family in spruce (Picea spp.). BMC Plant Biol. 2011; 11: 43.

[97]

Wei Y, Pu J, Zhang H et al. The laccase gene (LAC1) is essential for Colletotrichum gloeosporioides development and virulence on mango leaves and fruits. Physiol Mol Plant P. 2017; 99: 55-64.

[98]

Zhu J, He XH, Li YZ et al. Genome-wide analysis of the mango SPL family and overexpression of MiSPL13 confers early flowering and stress tolerance in transgenic Arabidopsis. Sci Hortic. 2022; 305: 111363.

[99]

Gao LZ . SMRT sequencing generates the chromosome-scale reference genome of tropical fruit mango. Mangifera indica. bioRxiv 2020; 25. Preprint: not peer reviewed.

[100]

Singh T, Yadav SK, Vainstein A et al. Genome recoding strategies to improve cellular properties: mechanisms and advances. Abiotech. 2021; 2: 79-95.

[101]

Dautt-Castro M, López-Virgen AG, Ochoa-Leyva A et al. Genome-wide identification of mango (Mangifera indica L.) Polygalacturonases: expression analysis of family members and Total enzyme activity during fruit ripening. Front Plant Sci. 2019; 10: 969.

[102]

Salih H, Tan L, NNW H . Genome-wide identification, characterization of bHLH transcription factors in mango. Trop Plant Biol. 2021; 14: 72-81.

[103]

Li YH, Zou MH, Feng BH et al. Molecular cloning and characterization of the genes encoding an auxin efflux carrier and the auxin influx carriers associated with the adventitious root formation in mango (Mangifera indica L.) cotyledon segments. Plant Physiol Bioch. 2012; 55: 33-42.

PDF (715KB)

79

Accesses

0

Citation

Detail

Sections
Recommended

/