High-density genetic map construction and identification of loci controlling flower-type traits in Chrysanthemum (Chrysanthemum × morifolium Ramat.)

Abstract

Flower type is an important and extremely complicated trait of chrysanthemum. The corolla tube merged degree (CTMD) and the relative number of ray florets (RNRF) are the two key factors affecting chrysanthemum flower type. However, few reports have clarified the inheritance of these two complex traits, which limits directed breeding for flower-type improvement. In this study, 305 F₁ hybrids were obtained from two parents with obvious differences in CTMD and RNRF performance. Using specific-locus amplified fragment sequencing (SLAF-seq) technology, we constructed a high-density genetic linkage map with an average map distance of 0.76 cM. Three major QTLs controlling CTMD and four major QTLs underlying RNRF were repeatedly detected in the 2 years. Moreover, the synteny between the genetic map and other Compositae species was investigated, and weak collinearity was observed. In QTL regions with a high degree of genomic collinearity, eight annotated genes were probed in the Helianthus annuus L. and Lactuca sativa L. var. ramosa Hort. genomes. Furthermore, 20 and 11 unigenes were identified via BLAST searches between the SNP markers of the QTL regions and the C. vestitum and C. lavandulifolium transcriptomes, respectively. These results lay a foundation for molecular marker-assisted breeding and candidate gene exploration in chrysanthemum without a reference assembly.

References

[1] Zhang, S. & Dai, S. Chinese Chrysanthemum Book (China Forestry Publishing, Beijing, 2013).

[2] Song, X. et al. Quantitative classification of the morphological traits of ray florets in large-flowered chrysanthemum. HortScience 53, 1258-1265 (2018).

[3] Anderson, N. O. Flower Breeding and Genetics: Issues, Challenges and Opportunities for the 21st Century (Springer Science & Business Media, 2006).

[4] Shi, H. & Jiang, L. Genetic variation of flower characteristics in a population derived from a cross between the chrysanthemum cultivars ‘Falcao’ and ‘Frill Green’. Horticulture Environ. Biotechnol. 55, 322-328 (2014).

[5] Song, X. et al. Genetic analysis of the corolla tube merged degree and the relative number of ray florets in chrysanthemum (Chrysanthemum × morifolium Ramat.). Sci. Hortic. 242, 214-224 (2018).

[6] Zhang, M., Huang, H., Wang, Q. & Dai, S. Cross breeding new cultivars of early-flowering multiflora chrysanthemum based on mathematical analysis. HortScience 53, 421-426 (2018).

[7] He, D. H. et al. QTL mapping for economic traits based on a dense genetic map of cotton with PCR-based markers using the interspecific cross of Gossypium hirsutum × Gossypium barbadense. Euphytica 153, 181-197 (2007).

[8] Fang, X. et al. A high density genetic map and QTL for agronomic and yield traits in Foxtail millet [Setaria italica (L.) P. Beauv.]. BMC Genomics 17, 336 (2016).

[9] Yagi, M. Recent progress in whole genome sequencing, high-density linkage maps, and genomic databases of ornamental plants. Breed. Sci. 68, 62-70 (2018).

[10] Baird, N. A. et al. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE 3, e3376 (2008).

[11] Elshire, R. J. et al. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6, e19379 (2012).

[12] Xiaowen, S. et al. SLAF-seq: an efficient method of large-scale de novo SNP discovery and genotyping using high-throughput sequencing. PLoS ONE 8, e58700 (2013).

[13] Henz, A., Debener, T. & Linde, M. Identification of major stable QTLs for flower color in roses. Mol. Breed. 35, 190 (2015).

[14] Zhang, J. et al. High-density genetic map construction and identification of a locus controlling weeping trait in an ornamental woody plant (Prunus mume Sieb. et Zucc). DNA Res. Int. J. Rapid Publ. Rep. Genes Genomes 22, 183 (2015).

[15] Liu, H., Cao, F., Yin, T. & Chen, Y. A highly dense genetic map for Ginkgo biloba constructed using sequence-based markers. Front. Plant Sci. 8, 1041 (2017).

[16] Fu, Y. et al. Genetic mapping and QTL analysis of Botrytis resistance in Gerbera hybrida. Mol. Breed. 37, 13 (2017).

[17] Tao, Y. Preliminary construction of ginkgo genetic map based on F1 population. Nanjing Forest. Univ. (PhD thesis, In Chinese) (2014).

[18] Cai, C., Cheng, F. Y., Wu, J., Zhong, Y. & Liu, G. The first high-density genetic map construction in tree peony (Paeonia Sect. Moutan) using genotyping by specific-locus amplified fragment sequencing. PLos ONE 10, e0128584 (2015).

[19] He, Y., Yuan, W., Dong, M., Han, Y. & Shang, F. The first genetic map in sweet osmanthus (Osmanthus fragrans Lour.) using specific locus amplified fragment sequencing. Front. Plant Sci. 8, 1621 (2017).

[20] Yang, X. Genetic diversity of sweet potato germplasm resources based on SSR, SNP and morphological markers. China Agric. Univ. (PhD thesis, In Chinese) (2016).

[21] Su, W. SNP locus development of sweet potato based on SLAF-seq technology. Chin. Agric. Sci. 49, 27-34 (2016).

[22] Su, W. et al. Genome-wide assessment of population structure and genetic diversity and development of a core germplasm set for sweet potato based on specific length amplified fragment (SLAF) sequencing. PLos ONE 12, e0172066 (2017).

[23] Tang, F., Chen, F., Chen, S., Teng, N. & Fang, W. Intergeneric hybridization and relationship of genera within the tribe Anthemideae Cass. (I. Dendranthema crassum (kitam.) kitam. × Crossostephium chinense (L.) Makino. Euphytica 169, 133-140 (2009).

[24] Li, C., Chen, S., Chen, F., Li, J. & Fang, W. Cytogenetic study of three edible chrysanthemum cultivars. Russ. J. Genet. 47, 176-181 (2011).

[25] Fei, Z., Chen, S., Chen, F., Fang, W. & Li, F. A preliminary genetic linkage map of chrysanthemum (Chrysanthemum morifolium) cultivars using RAPD, ISSR and AFLP markers. Sci. Hortic. 125, 422-428 (2010).

[26] Zhang, F. et al. SRAP-based mapping and QTL detection for inflorescence-related traits in chrysanthemum (Dendranthema morifolium). Mol. Breed. 27, 11-23 (2011).

[27] Geest, G. V. et al. An ultra-dense integrated linkage map for hexaploid chrysanthemum enables multi-allelic QTL analysis. Theor. Appl. Genet. 130, 2527-2541 (2017).

[28] Badouin, H. et al. The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution. Nature 546, 148 (2017).

[29] Reyeschinwo, S. et al. Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce. Nat. Commun. 8, 14953 (2017).

[30] Hirakawa, H. et al. De novo whole-genome assembly in Chrysanthemum seticuspe, a model species of Chrysanthemums, and its application to genetic and gene discovery analysis. DNA Res. 26, 195-203 (2019).

[31] Liu, Y. A method for SNP detection of polyploid crops based on transcriptome sequencing and no reference sequence. Zhejiang Univ. (Thesis, In Chinese) (2012).

[32] Zhang, Y., Zhu, M. L. & Dai, S. L. Analysis of karyotype diversity of 40 Chinese chrysanthemum cultivars. J. Syst. Evol. 51, 335-352 (2013).

[33] Cui, N., Chen, F., Zhao, H., Fang, W. & Wang, Z. Observation on meiosis behavior of several species of chrysanthemum and their interspecies hybrids. Acta Hortic. Sin. 33, 1033-1038 (2006).

[34] Chen, F. D., Li, F. T., Chen, S. M., Guan, Z. Y. & Fang, W. M. Meiosis and pollen germinability in small-flowered anemone type chrysanthemum cultivars. Plant Syst. Evolution 280, 143-151 (2009).

[35] Kumar, S., Kumar, M., Yadav, H. & Sharma, S. Genetic diversity and population structure analysis of chrysanthemum (Dendranthema grandiflora Tzvelev) germplasm based on RAPD markers. J. Environ. Biol. 38, 457 (2017).

[36] Sang, K. P., Arens, P., Esselink, D., Jin, H. L. & Shin, H. K. Analysis of inheritance mode in chrysanthemum using EST-derived SSR markers. Sci. Horticulturae 192, 80-88 (2015).

[37] Geest, G. V. et al. Conclusive evidence for hexasomic inheritance in chrysanthemum based on analysis of a 183 k SNP array. BMC Genomics 18, 585 (2017).

[38] Klie, M., Schie, S., Linde, M. & Debener, T. The type of ploidy of chrysanthemum is not black or white: a comparison of a molecular approach to published cytological methods. Front. Plant Sci. 5, 479 (2014).

[39] Langton, F. A. Chimerical structure and carotenoid inheritance in Chrysanthemum morifolium (Ramat.). Euphytica 29, 807-812 (1980).

[40] Su, J. et al. Dynamic and epistatic QTL mapping reveals the complex genetic architecture of waterlogging tolerance in chrysanthemum. Planta 247, 899-924 (2018).

[41] Juntheikki-Palovaara, I. et al. Functional diversification of duplicated CYC2 clade genes in regulation of inflorescence development in Gerbera hybrida (Asteraceae). Plant J. 79, 783-796 (2014).

[42] Mizzotti, C. et al. A CYCLOIDEA-like gene mutation in sunflower determines an unusual floret type able to produce filled achenes at the periphery of the pseudanthium. Botany 93, 171-181 (2015).

[43] Tan, C. T. et al. Development and validation of KASP markers for the greenbug resistance gene Gb7 and the Hessian fly resistance gene H32 in wheat. Theor. Appl. Genet. 130, 1-18. (2017).

[44] Steele, K. A. et al. Accelerating public sector rice breeding with high-density KASP markers derived from whole genome sequencing of indica rice. Mol. Breed. 38, 38 (2018).

[45] Liu, G. et al. Molecular mapping of the Cf-10 gene by combining SNP/InDel-index and linkage analysis in tomato (Solanum lycopersicum). BMC Plant Biol. 19, 15 (2019).

[46] Luo, C. 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. 7, 1310(2016).

[47] Kent, W. J. BLAT-the BLAST-like alignment tool. Genome Res. 12, 656-664 (2002).

[48] Dongyuan, L. et al. Construction and analysis of high-density linkage map using high-throughput sequencing data. PLos ONE 9, e98855 (2014).

[49] Van Ooijen, J. W. Multipoint maximum likelihood mapping in a full-sib family of an outbreeding species. Genet. Res. 93, 343-349 (2011).

[50] Krzywinski, M. & Schein, J. I. Circos: an information aesthetic for comparative genomics. Genome Res. 19, 1639-1645 (2009).