Genome Wide SNP Identification in Eucalyptus and its Application for Linkage Mapping and Adventitious Rooting Related QTL Analysis

Genome Wide SNP Identification in Eucalyptus and its Application for Linkage Mapping and Adventitious Rooting Related QTL Analysis

Authors

  •   Maheswari Patturaj   Institute of Forest Genetics and Tree Breeding, Coimbatore 641002
  •   A. Mayavel   Institute of Forest Genetics and Tree Breeding, Coimbatore 641002
  •   Modhumita Ghosh Dasgupta   Institute of Forest Genetics and Tree Breeding, Coimbatore 641002
  •   Binai Nagarajan   Institute of Forest Genetics and Tree Breeding, Coimbatore 641002
  •   D. Rajasugunasekar   Institute of Forest Genetics and Tree Breeding, Coimbatore 641002
  •   Veerasamy Sivakumar   Institute of Forest Genetics and Tree Breeding, Coimbatore 641002
  •   Ramasamy Yasodha   Institute of Forest Genetics and Tree Breeding, Coimbatore 641002

DOI:

https://doi.org/10.36808/if/2021/v147i11/166637

Keywords:

Eucalyptus tereticornis, E. camaldulensis, Genetic Map, Genotyping by Sequencing, Single Nucleotide Polymorphism, QTL, Adventitious Rooting Traits.

Abstract

Eucalyptus is a versatile genus with a particular significance for paper pulp, and it is extensively cultivated in India's marginal lands. Eucalyptus camaldulensis and E. tereticornis are highly preferred due to its optimal pulp yield, excellent fibre quality and good abiotic stress tolerance properties. Marker-assisted selections have played a major role in eucalyptus breeding programs. The use of genotyping-by-sequencing (GBS) approach for a largescale single nucleotide polymorphism (SNP) discovery and genotyping of an inter-specific mapping population, Eucalyptus tereticornis × E. camaldulensis are reported in this study. Reduced representation libraries of 81 F1 progeny were sequenced and number of SNPs considered for linkage analysis was 96,377 single nucleotide substitutions, most of which (54.03%) represented transition events. Totally, 1999 and 4206 SNP markers were mapped to female (Eucalyptus tereticornis) and male (Eucalyptus camaldulensis) map, respectively. Consensus map consisting of 4844 markers were placed on a linkage map, which spanned 1367.6 cM and had an average of one marker every 0.29 cM corresponding to a physical distance of about 0.66 Mb. The map was utilized to identify six quantitative trait loci (QTLs) associated with adventitious rooting traits of stem cuttings accounting for phenotypic variations ranging from 7.18% to 9.17%. Analysis of the genomic sequence corresponding to six QTLs led to the identification of 201 putative candidate genes and 4 key genes were related to adventitious rooting specific expression. The integrated strategy utilizing the identified QTLs along with the available genome could serve as a platform for candidate gene identification for molecular breeding of eucalypts.

References

Aregowda J., Prabhu S.T. and Patil R.S. (2010). Evaluation of botanicals and synthetic insecticides against Eucalyptus gall wasp, Leptocybeinvasa (Eulophidae: Hymenoptera). arnataka Journal of Agricultural Sciences, 23(1): 200-202.

Ballesta P., Maldonado C., Perez-Rodriguez P. and Mora F. (2019). SNP and Haplotype-based genomic selection of quantitative traits in Eucalyptus globulus. Plants 8: 331. DOI: 10.3390/plants8090331.

Bannoud F. and Bellini C. (2021). Adventitious rooting in Populus species: Update and perspectives. Front. Plant Sci., 12:668837. DOI: 10.3389/fpls.2021.668837.

Bartholomé J., Mandrou E., Mabiala A., Jenkins J., Nabihoudine I., Klopp C., Schmutz J., Plomion C. and Gion J.M. (2015). High-resolution genetic maps of Eucalyptus improve Eucalyptus grandis genome assembly. New Phytol., 206: 1283–1296. DOI: 10.1111/nph.13150.

Bhattacharjee R., Agre P., Bauchet G., de Koeyer D., LopezMontes A., Kumar P., Abberton M., Adebola P., Asfaw A. and Asiedu R. (2020). Genotyping-by-sequencing to unlock genetic diversity and population structure in white yam (Dioscorea rotundata Poir). Agron., 10(9): 1437. DOI: 10.3390/agronomy10091437.

Bolger A.M., Lohse M. and Usadel B. (2014). Trimmomatic: a flexible trimmer for illumina sequence data. Bioinformatics 30(15): 2114–2120. DOI: 10.1093/ bioinformatics/btu170.

Brondani G.E., Dutra L.F., Grossi F., Wendling I. And Hornig J. (2009). Establishment multiplication and elongation in vitro of Eucalyptus benthamii Maiden & Cambage × Eucalyptus dunnii Maiden. Rev. Arvore., 33: 11–19.

Combs E. and Bernardo R. (2013). Accuracy of genome wide selection for different traits with constant population size heritability and number of markers. Plant Genome 6(1): 1–7. DOI:10.3835/plantgenome2012.11.0030.

da Costa C.T., de Almeida M.R., Ruedell C.M., Schwambach J., Maraschin F.S. and Fett-Neto A.G. (2013). When stress and development go hand in hand: main hormonal controls of adventitious rooting in cuttings. Front. Plant Sci., 4:1-19. DOI:10.3389/fpls.2013.00133.

Druege U., Hilo A., Pérez-Pérez JM., Klopotek Y., Acosta M., Shahinnia F., Zerche S., Franken P. and Hajirezaei M.R. (2019). Molecular and physiological control of adventitious rooting in cuttings: phytohormone action meets resource allocation. Ann. Bot., 123(6): 929–950. DOI: 10.1093/aob/mcy234.

Eckert A.J., Bower A.D., Wegrzyn J.L., Pande B., Jermstad K.D., Krutovsky K.V., Clair J.B.S. and Neale D.B. (2009a). Association genetics of coastal douglas fir(Pseudotsugamenziesu var. menziesii, Pinaceae). I. Coldhardiness related traits. Genetics, 182(4): 1289-1302. DOI: 10.1534/genetics.109.102350.

Elshire R.J., Glaubitz J.C., Sun Q., Poland J.A., Kawamoto K., Buckler E.S. and Mitchell S.E. (2011). A Robust Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species. PLoS One. 6: e19379. DOI: 10.1371/journal.pone.0019379.

FSI. (2019). India State of Forest Report 2019. Forest Survey of India Ministry of Environment Forest and Climate Change Dehradun Uttarakhand India.

Fukuda Y., Hirao T., Mishima K., Ohira M., Hiraoka Y., Takahashi M. and Watanabe A. (2018). Transcriptome dynamics of rooting zone and aboveground parts of cuttings during adventitious root formation in Cryptomeria japonica D. Don. BMC Plant Biol., 18: 201.

Gonzalez-Martínez S.C, Wheeler N.C, Ersoz E., Nelson C.D. and Neale D.B. (2007). Association Genetics in Pinustaeda L. I. Wood Property Traits. Genetics, 175: 399-409. DOI: 10.1534/genetics.106.061127.

Kibe M., Nyaga C., Nair S.K., Beyene Y., Das B., M.S. L., Bright J.M., Makumbi D., Kinyua J., Olse M.S., Prasanna B.M. and Gowda M. (2020). Combination of Linkage Mapping, GWAS, and GP to Dissect the Genetic Basis of Common Rust Resistance in Tropical Maize Germplasm. Int. J. Mol. Sci., 21: 6518. DOI:10.3390/ijms21186518.

Lal P., Dogra A.S., Sharma S.C. and Chahal G.B.S. (2006). Evaluation of different clones of Eucalyptus in Punjab. Indian For., 132: 1383-1390. DOI:10.12944/CARJ.8.2.04.

Gion J.M., Hudson C.J., Lesur I., Vaillancourt R.E., Potts B.M. and Freeman J.S. (2016). Genome-wide variation in recombination rate in Eucalyptus. BMC Genomics 17: 590. DOI:10.1186/s12864-016-2884-y.

Glaubitz J.C., Casstevens T.M., Lu F., Harriman J., Elshire R.J., Sun Q. and Buckler E.S. (2014) TASSEL-GBS: A high capacity genotyping by sequencing analysis pipeline. PLoS One 9:9034.DOI: 10.1371/journal.pone.0090346.

Gonzalez-Martinez S.C., Huber D., Ersoz E., Davis J.M. and Neale D.B. (2008). Association genetics in Pinus taeda L. II. Carbon isotope discrimination. Heredity 101: 19–26. DOI: 10.1038/hdy.2008.21.

Hendre P.S., Kamalakannan R. and Varghese M. (2012). Highthroughput and parallel SNP discovery in selected candidate genes in Eucalyptus camaldulensis using Illumina NGS platform. Plant Biotechnol. J., 10: 646-656. 10.1111/j.1467-7652.2012.00699.x.

Hudson C.J., Freeman J.S., Kullan A.R.K., Petroli C.D., Sansaloni C.P., Kilian A., Detering F., Grattapaglia D., Potts B.M., Myburg A.A. and Vaillancourt R.E. (2012). A reference linkage map for Eucalyptus. BMC Genomics, 13: 240. DOI:10.1186/1471-2164-13-240.

Ji L., Attaullah K., Wang J., Yu D., Yang Y., Yang L. and Lu Z. (2020). Root traits determine variation in nonstructural carbohydrates (NSCs) under different drought intensities and soil substrates in three temperate tree species. Forests 11(4): 415. DOI:10.3390/f11040415.

Karaman E., Lund M.S. and Su G. (2019). Multi-trait single-step genomic prediction accounting for heterogeneous (co) variances over the genome. Heredity, 124: 274–287. DOI: 10.1038/s41437-019-0273-4.

Kayondo S.I., Pino Del Carpio D., Lozano R., Ozimati A., Wolfe M., Baguma Y., Gracen V., Offei S., Ferguson M., Kawuki R. and Jannink J.L. (2018). Genome-wide association mapping and genomic prediction for CBSD resistance in Manihot esculenta. Sci. Rep., 8: 1549–1549. DOI:10.1038/s41598-018-19696-1.

Kosambi D.D. (1943). The estimation of map distances from recombination values. Ann. Eugen., 12: 172–175.

Kullan A.R., van Dyk M.M., Hefer C.A., Jones N., Kanzler A. and Myburg A.A. (2012). Genetic dissection of growth wood basic density and gene expression in interspecific backcrosses of Eucalyptus grandis and E. urophylla. BMC Genet., 13: 60. DOI: 10.1186/1471-2156-13-60.

Langmead B. and Salzberg S.L. (2012). Fast gapped-read alignment with Bowtie 2. Nat. Methods 9: 357-359. DOI:10.1038/nmeth.1923.

Lebedev V.G., Lebedeva T.N., Chernodubov A.I. andnShestibratov K.A. (2020). Genomic selection for Forest tree improvement: methods achievements and perspectives. Forests 11: 1190. DOI:10.3390/f11111190.

Li F., Zhou C., Weng Q., Li M., Yu X., Guo Y., Wang Y., Zhang and Gan S. (2015). Comparative genomics analyses reveal extensive chromosome colinearity and novel quantitative trait loci in Eucalyptus. PLoS One 10(12): e0145144. DOI: 10.1371/journal.pone.0145144.

Li K., Wei Y.H., Wang R.H., Mao J.P., Tian H.Y., Chen S.Y., Li S.H., Tahir M.M. and Zhang D. (2021). Mdm-MIR393b-mediated adventitious root formation by targeted regulation of MdTIR1A expression and weakened sensitivity to auxin in apple rootstock. Plant Sci., 308: 110909. DOI:10.1016/j.plantsci.2021.110909.

Liao P.Y. and Lee K.H. (2010). From SNPs to functional polymorphism: The insight into biotechnology applications. Biochem. Eng. J., 49: 149-158. DOI:10.1016/ j.bej.2009.12.021.

Lightfoot D.J., Jarvis D.E., Ramaraj T., Lee R., Jellen E.N. and Maughan P.J. (2017). Single-molecule sequencing and Hi-Cbased proximity-guided assembly of amaranth (Amaranthus hypochondriacus) chromosomes provide insights into genome evolution. BMC Biol., 15: 74.DOI:/10.1186/s12915-017-0412-4.

Minamikawa M.F., Nonaka K., Kaminuma E., Kajiya-Kanegae H., Onogi A., Goto S., Yoshioka T., Imai A., Hamada H., Hayashi T., Matsumoto S., Katayose Y., Toyoda A., Fujiyama A., Nakamura Y., Shimizu T. and Iwata H. (2017). Genome-wide association study and genomic prediction in citrus: potential genomics-assisted breeding for fruit quality traits. Sci. Rep., 4721. DOI:10.1038/s41598-017-05100-x.

Moriya S., Iwanami H., Haji T., Okada K., Yamada M., Yamamoto T. and Abe K. (2015). Identification and genetic characterization of a quantitative trait locus for adventitious rooting from apple hardwood cuttings. Tree Genet. Genomes, 59: 1–11. DOI:10.1007/s11295-015-0883-9.

Muthulakshmi V., Vijayam C.V., Bachpai V.K.W., Sivakumar Muthulakshmi E., Shanmugavel S., Muneera Parveen A.B., Yasodha R., Rajasugunasekar D., Nagarajan B., Mayavel A. and Ghosh Dasgupta M. (2020). Genetic control of adventitious rooting traits in bi-parental pedigree of Eucalyptus tereticornis × camaldulensis. New For., 52(4): 585-603. DOI:10.1007/s11056020-09810-5.

Myburg A.A., Grattapaglia D., Tuskan G.A., Hellsten U., Hayes R.D., Grimwood J., Jenkins J., Lindquist E., Tice H., Bauer D al. (2014). The genome of Eucalyptus grandis. Nature, 510: 356–362. DOI: 10.1038/nature13308.

Mzena G.P., Kusolwa P., Rwegasira G.R. and Yao N. (2018). Discovery of novel single nucleotide polymorphic (SNP) markers for genetic mapping of cashew (Anacardium occidentale. L). Int. j. agric. environ. Bio-res., 3: 186-196.

Nambiar E.K.S., Harwood C.E. and Mendham D.S. (2018). Paths to sustainable wood supply to the pulp and paper industry in Indonesia after diseases have forced a change of species from acacia to eucalypts. Aust. For., 81(3): 148-161. DOI: 10.1080/00049158.2018.1482798.

Neale D.B. and Savolainen O. (2004). Association genetics of complex traits in conifers. Trends Plant Sci., 9(7): 325–330.DOI: 10.1016/j.tplants.2004.05.006

Neves L., Mamani E.M.C., Alfenas A., Kirst M. and Grattapaglia D. (2011). A high-density transcript linkage map with 1845 expressed genes positioned by microarray-based Single Feature Polymorphisms (SFP) in Eucalyptus. BMC Genomics, 12(1): 189. DOI: 10.1186/1471-2164-12-189.

Müller B.S.F., Filho J.E.A., Lima B.M., Garcia C.C., Missiaggia A., Aguiar A.M., Takahashi E., Kirst M., Gezan S.A., Silva-junior O.

Neves L.G. and Grattapaglia D. (2019). Independent and JointGWAS for growth traits in Eucalyptus by assembling genome-wide data for 3373 individuals across four breeding populations. New Phytol., 221: 818-833. DOI: 10.1111/nph.15449.

Otyama P.I., Wilkey A., Kulkarni R., Assefa T., Chu Y., Clevenger J., O'Connor D.J., Wright G.C., Dezern S.W., MacDonald G.E., Anglin N.L., Cannon E.K.S., Ozias-Akins P. and Cannon S.B. (2019). Evaluation of linkage disequilibrium, population structure, and genetic diversity in the U.S. peanut mini core collection. BMC Genomics, 20(1): 481. DOI:10.1186/s12864-019-5824-9.

Resende R.T., Resende M.D., Silva F.F., Azevedo C.F., Takahashi E.K., Silva-Junior O.B. and Grattapaglia D. (2017). Regional heritability mapping and genome-wide association identify loci for complex growth, wood and disease resistance traits in Eucalyptus. New Phytol., 213: 1287-1300. DOI: 10.1111/nph.14266.

Ribeiro C.L., Silva C.M., Drost D.R., Novaes E., Novaes C.R.D.B., Dervinis C. and Kirst M. (2016). Integration of genetic, genomic and transcriptomic information identifies putative regulators of adventitious root formation in Populus. BMC Plant Biol., 16: 66. DOI:10.1186/s12870-016-0753-0.

Shepherd M., Kasem S., Lee D. and Henry R. (2008b). Mapping species differences for adventitious rooting in a Corymbiatorelliana × Corymbiacitriodora subspecies variegata hybrid. Tree Genet.Genomes, 4(4): 715-725. DOI:10.1007/s11295-008-0145-1.

Pootakham W., Sonthirod C., Naktang C., Jomchai N., Sangsrakru D. And Tangphatsornruang S. (2016). Effects of methylation-sensitive enzymes on the enrichment of genic SNPs and the degree of genome complexity reduction in a twoenzyme genotyping-by-sequencing (GBS) approach: a case study in oil palm (Elaeis guineensis). Mol. Breed., 36(11): 154. DOI: 10.1007/s11032-016-0572-x.

Ren J., Li Z., Wu P., Zhang A., Liu Y., Hu G., Cao S., Qu J., Dhliwayo T., Zheng H., Olsen M., Prasanna B.M., San Vicente F. and Zhang X. (2021) Genetic Dissection of Quantitative Resistance to Common Rust (Puccinia sorghi) in Tropical Maize (Zea mays L.) by Combined Genome-Wide Association Study Linkage Mapping and Genomic Prediction. Front. Plant Sci., 12: 692205. DOI: 10.3389/fpls.2021.692205.

Rocha R.B., Barros E.G., Cruz C.D., Rosado A.M. and Araújo E.F. de (2007). Mapping of Qtls related with wood quality and developmental characteristics in hybrids (Eucalyptus grandis X Eucalyptus urophylla). Revista Arvore, 31: 13-24. DOI:10.1590/S0100-67622007000100003.

Rudolf-Pilih K., Petkovsek M., Jakse J., Stajner N., Murovec J. and Bohanec B. (2019). Proposal of a new hybrid breeding method based on genotyping inter-pollination phenotyping and paternity testing of selected elite F1 hybrids. Front. Plant Sci., 10: 1111. DOI: 10.3389/fpls.2019.01111.

Shepherd M., Huang S., Eggler P., Cross M., Dale G., Dieters M. and Henry R. (2006). Congruence in QTL for adventitious rooting in Pinus elliottii × Pinus caribaea hybrids resolves between and within-species effects. Mol. Breed., 18:11–28. DOI:10.1007/s11032-006-9006-5.

Shepherd M., Kasam S., Ablett G., Ochieng J.W. and Crawford A. (2008a). Genetic structuring of the spotted gum complex (genus Corymbia section Politaria). Aust. Syst. Bot., 21(1):1525. DOI:10.1071/SB07028.

Silva-Junior O.B and Grattapaglia D. (2015). Genome-wide patterns of recombination linkage disequilibrium and nucleotide diversity from pooled resequencing and single nucleotide polymorphism genotyping unlock the evolutionary history of Eucalyptus grandis. New Phytol., 208(3):830-845. DOI:10.1111/nph.13505.

Sumathi M., Bachpai V., Mayavel A., Dasgupta M.G., Nagarajan B., Rajasugunasekar D., Sivakumar V. and Yasodha R. (2018). Genetic linkage map and QTL identification for adventitious rooting traits in red gum eucalypts. 3 Biotech, 8(5): 242. DOI:10.1007/s13205-018-1276-1.

Sun P., Jia H., Zhang Y., Li J., Lu M. and Hu J. (2019). Deciphering genetic architecture of adventitious root and related shoot traits in Populus using QTL mapping and RNA-seq Data. Int. J. Mol. Sci., 20(24): 6114. DOI:10.3390/ijms20246114.

Thavamanikumar S., Southerton S.G., Bossinger G. and

Thumma B.R. (2013). Dissection of complex traits in forest trees - opportunities for marker-assisted selection. Tree Genet. Genomes 9: 627–639. DOI: 10.1007/s11295-013-0594-z.

Thavamanikumar S., McManus L.J., Ades P.K., Bossinger G., Stackpole D.J., Kerr R., Hadjigol S., Freeman J.S., Vaillancourt R.E., Zhu P. and Tibbits J.F.G. (2014). Association mapping for wood quality and growth traits in Eucalyptus globulus ssp. globulus Labill identifies nine stable marker-trait associations for seven traits. Tree Genet. Genomes, 10: 1661–1678. DOI: 10.1007/s11295-014-0787-0.

Thumma B.R., Southerton S.G., Bell J.C., Owen J.V., Henery M.L. and Moran G.F. (2010). Quantitative trait locus (QTL) analysis of wood quality traits in Eucalyptus nitens. Tree Genet. Genomes, 6: 305–317. DOI:10.1007/s11295-009-0250-9.

Valenzuela C.E., Ballesta P., Maldonado C., Baettig R., Arriagada O., Sousa Mafra G. and Mora F. (2019). Bayesian mapping reveals large–effect pleiotropic QTLs for wood density and slenderness index in 17–year–old trees of Eucalyptus cladocalyx. Forests, 10: 241. DOI: 10.3390/f10030241.

Van Ooijen J.W. (2006). JoinMap 4 Software for the calculation of genetic linkage maps in experimental populations. Kyazma BV Wageningen Netherlands.

Van Ooijen J.W. (2018). JoinMap® 5: Software for the calculation of genetic linkage maps in experimental populations of diploid species. Kyazma BV Wageningen.

Varghese M., Harwood C.E., Bush D.J., Baltunis B., Kamalakannan R., Suraj P.G., Hegde D. and Meder R. (2017). Growth and wood properties of natural provenances local seed sources and clones of Eucalyptus camaldulensis in southern India: implications for breeding and deployment. New For., 48: 67–82. DOI:10.1007/s11056-016-9556-2.

Venkatesh C.S. and Sharma V.K. (1977). Rapid growth and higher yield potential of heterotic eucalyptus hybrids FRI-4 and FRI-5. Indian Forester, 103: 795–801.

Vielba J.M., Vidal N., San José M.C., Rico S. and Sánchez C. (2020). Recent advances in adventitious root formation in Chestnut. Plants, 9(11): 1543. DOI:10.3390/plants9111543.

Voorrips R.E. (2002). MapChart: software for the graphical presentation of linkage maps and QTLs. J. Hered., 93: 77–78. DOI:10.1093/jhered/93.1.77.

Wang S., Basten C.J., and Zeng Z.B. (2012). Windows QTL Cartographer 2.5. Department of Statistics North Carolina State University Raleigh NC. (http://statgen.ncsu.edu/qtlcart/ WQTLCart.htm).

Zheng C., Shen F., Wang Y., Wu T., Xu X., Zhang X. and Han Z. (2020). Intricate genetic variation networks control the adventitious root growth angle in apple. BMC Genomics, 21: 852. DOI: 10.1186/s12864-020-07257-8.

Zhang Z., Wei T., Zhong Y., Li X. and Huang J. (2016). Construction of a high-density genetic map of Ziziphus jujuba Mill. using genotyping by sequencing technology. Tree Genetics & Genomes 12 76 (). https://doi.org/ 10.1007/s11295-016-1032-9.

Varghese M., Kamalakannan R., Harwood C.E., Lindgren D. and Mcdonald M.W. (2009). Changes in growth performance and fecundity of Eucalyptus camaldulensis and E. tereticornis during domestication in southern India. Tree Genet. Genomes, 5: 629-640. DOI: 10.1007/s11295-009-0215-z.

Yang H., Xu F., Liao H., Zhang W., Yang X., Xu B. and Pan W. (2020). Correction to: genome-wide assessment of population structure and genetic diversity of Eucalyptus urophylla based on a multispecies single-nucleotide polymorphism chip analysis. Tree Genet. Genomes., 16(3): 1-11. DOI: 10.1007/s11295-020-01441-3.

Zhao J., Jian J., Liu G., Wang J., Lin M. and Ming Y. et al. (2014). Rapid SNP discovery and a RAD-based high-density linkage map in jujube (Ziziphus Mill.). PLoS One, 9:e109850.DOI: 10.1371/journal.pone.0109850.

Downloads

Download data is not yet available.

Author Biography

Maheswari Patturaj, Institute of Forest Genetics and Tree Breeding, Coimbatore 641002

uttarakhand

Published

2021-12-03

How to Cite

Patturaj, M., Mayavel, A., Dasgupta, M. G., Nagarajan, B., Rajasugunasekar, D., Sivakumar, V., & Yasodha, R. (2021). Genome Wide SNP Identification in <i>Eucalyptus</i> and its Application for Linkage Mapping and Adventitious Rooting Related QTL Analysis. Indian Forester, 147(11), 1088–1102. https://doi.org/10.36808/if/2021/v147i11/166637
Loading...