Construction of a high-density genetic map and its application for leaf shape QTL mapping in poplar
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High-quality and dense genetic maps were constructed, and leaf shape variation was dissected by QTL mapping in poplar.
Species in the genus Populus, also known as poplars, are important woody species and considered model plants for perennial trees. High-density genetic maps are valuable genomic resources for population genetics. Here, we generated a high-quality and dense genetic map for an F1 poplar population using high-throughput NGS-based genotyping. A total of 92,097 high-quality SNP markers were developed by stringent filtering and identification. In total, 889 and 1650 SNPs formed the female and male genetic maps, respectively. To test the application of the genetic maps, QTL mapping of leaf shape was conducted for this F1 population. A total of nine parameters were scored for leaf shape variation in three different environments. Combining genetic maps and measurements of the nine leaf shape parameters, we mapped a total of 42 significant QTLs. The highest LOD score of all QTLs was 9.2, and that QTL explained the most (15.13%) trait variation. A total of nine QTLs could be detected in at least two environments, and they were located in two genomic regions. Within these two QTL regions, some candidate genes for regulating leaf shape were predicted through functional annotation. The successful mapping of leaf shape QTLs demonstrated the utility of our genetic maps. According to the performance of this study, we were able to provide high-quality and dense genetic maps and dissect the leaf shape variation in poplar.
KeywordsPoplars Genetic maps QTL mapping Leaf shape variation
Genotyping by sequencing
Leaf plastochron index
Logarithm of odds
Next generation sequencing
Quantity trait locus
Financial support for this work was provided by the National Natural Science Foundation of China (NSFC Accession No. 31670651 and No. 31570665) and Fundamental Research Funds for the Central Universities (No. 520902-0900202801). The authors are grateful to American Journal Experts (AJE) for improving the English in this paper.
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interest.
- Carletti G, Carra A, Allegro G, Vietto L, Desiderio F, Bagnaresi P, Gianinetti A, Cattivelli L, Vale G, Nervo G (2016) QTLs for woolly poplar aphid (Phloeomyzus passerinii L.) resistance detected in an inter-specific Populus deltoides × P. nigra mapping population. PLoS One 11(3):e0152569. https://doi.org/10.1371/journal.pone.0152569 CrossRefPubMedPubMedCentralGoogle Scholar
- Du Q, Gong C, Wang Q, Zhou D, Yang H, Pan W, Li B, Zhang D (2016) Genetic architecture of growth traits in Populus revealed by integrated quantitative trait locus (QTL) analysis and association studies. New Phytol 209(3):1067–1082. https://doi.org/10.1111/nph.13695 CrossRefPubMedPubMedCentralGoogle Scholar
- Eckenwalder J (1996) Systematics and evolution of Populus. In: Stettler RF, Bradshaw HD, Heilman JPE, Hinckley TM (eds) Biology of Populus and its implications for management and conservation. NRC Research Press, OttawaGoogle Scholar
- Ikezaki M, Kojima M, Sakakibara H, Kojima S, Ueno Y, Machida C, Machida Y (2010) Genetic networks regulated by ASYMMETRIC LEAVES1 (AS1) and AS2 in leaf development in Arabidopsis thaliana: KNOX genes control five morphological events. Plant J Cell Mol Biol 61(1):70–82. https://doi.org/10.1111/j.1365-313X.2009.04033.x CrossRefGoogle Scholar
- Ma T, Wang J, Zhou G, Yue Z, Hu Q, Chen Y, Liu B, Qiu Q, Wang Z, Zhang J, Wang K, Jiang D, Gou C, Yu L, Zhan D, Zhou R, Luo W, Ma H, Yang Y, Pan S, Fang D, Luo Y, Wang X, Wang G, Wang J, Wang Q, Lu X, Chen Z, Liu J, Lu Y, Yin Y, Yang H, Abbott RJ, Wu Y, Wan D, Li J, Yin T, Lascoux M, Difazio SP, Tuskan GA, Wang J, Liu J (2013) Genomic insights into salt adaptation in a desert poplar. Nat Commun 4:2797. https://doi.org/10.1038/ncomms3797 CrossRefGoogle Scholar
- Monclus R, Leple JC, Bastien C, Bert PF, Villar M, Marron N, Brignolas F, Jorge V (2012) Integrating genome annotation and QTL position to identify candidate genes for productivity, architecture and water-use efficiency in Populus spp. BMC Plant Biol 12:173. https://doi.org/10.1186/1471-2229-12-173 CrossRefPubMedPubMedCentralGoogle Scholar
- Morreel K, Goeminne G, Storme V, Sterck L, Ralph J, Coppieters W, Breyne P, Steenackers M, Georges M, Messens E, Boerjan W (2006) Genetical metabolomics of flavonoid biosynthesis in Populus: a case study. Plant J Cell Mol Biol 47(2):224–237. https://doi.org/10.1111/j.1365-313X.2006.02786.x CrossRefGoogle Scholar
- Sun R, Chang Y, Yang F, Wang Y, Li H, Zhao Y, Chen D, Wu T, Zhang X, Han Z (2015) A dense SNP genetic map constructed using restriction site-associated DNA sequencing enables detection of QTLs controlling apple fruit quality. BMC Genom 16:747. https://doi.org/10.1186/s12864-015-1946-x CrossRefGoogle Scholar
- Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J, Chen GL, Cooper D, Coutinho PM, Couturier J, Covert S, Cronk Q, Cunningham R, Davis J, Degroeve S, Dejardin A, Depamphilis C, Detter J, Dirks B, Dubchak I, Duplessis S, Ehlting J, Ellis B, Gendler K, Goodstein D, Gribskov M, Grimwood J, Groover A, Gunter L, Hamberger B, Heinze B, Helariutta Y, Henrissat B, Holligan D, Holt R, Huang W, Islam-Faridi N, Jones S, Jones-Rhoades M, Jorgensen R, Joshi C, Kangasjarvi J, Karlsson J, Kelleher C, Kirkpatrick R, Kirst M, Kohler A, Kalluri U, Larimer F, Leebens-Mack J, Leple JC, Locascio P, Lou Y, Lucas S, Martin F, Montanini B, Napoli C, Nelson DR, Nelson C, Nieminen K, Nilsson O, Pereda V, Peter G, Philippe R, Pilate G, Poliakov A, Razumovskaya J, Richardson P, Rinaldi C, Ritland K, Rouze P, Ryaboy D, Schmutz J, Schrader J, Segerman B, Shin H, Siddiqui A, Sterky F, Terry A, Tsai CJ, Uberbacher E, Unneberg P, Vahala J, Wall K, Wessler S, Yang G, Yin T, Douglas C, Marra M, Sandberg G, Van de Peer Y, Rokhsar D (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313(5793):1596–1604. https://doi.org/10.1126/science.1128691 CrossRefPubMedGoogle Scholar
- Van OJ (2006) JoinMap 4, software for the calculation of genetic linkage maps in experimental populations. Kyazma BV, WageningenGoogle Scholar
- Wang N, Wang Y, Tian F, King GJ, Zhang C, Long Y, Shi L, Meng J (2008) A functional genomics resource for Brassica napus: development of an EMS mutagenized population and discovery of FAE1 point mutations by TILLING. New Phytol 180(4):751–765. https://doi.org/10.1111/j.1469-8137.2008.02619.x CrossRefPubMedPubMedCentralGoogle Scholar
- Wang N, Qian W, Suppanz I, Wei L, Mao B, Long Y, Meng J, Muller AE, Jung C (2011) Flowering time variation in oilseed rape (Brassica napus L.) is associated with allelic variation in the FRIGIDA homologue BnaA.FRI.a. J Exp Bot 62(15):5641–5658. https://doi.org/10.1093/jxb/err249 CrossRefPubMedPubMedCentralGoogle Scholar
- Wang NA, Cao P, Xia WX, Fang LC, Yu HY (2017) Identification and characterization of long non-coding RNAs in response to early infection by Melampsora larici-populina using genome-wide high-throughput RNA sequencing. Tree Genet Genomes. https://doi.org/10.1007/s11295-017-1116-1 CrossRefGoogle Scholar