Identification of quantitative trait loci associated with flowering time in perilla using genotyping-by-sequencing
- 118 Downloads
Understanding the transition to the reproductive period is important for crop breeding. This information can facilitate the production of novel varieties that are better adapted to local environments or changing climatic conditions. Here, we report the development of a high-density linkage map based on genotyping-by-sequencing (GBS) for the genus perilla. Through GBS library construction and Illumina sequencing of an F2 population, a total of 9607 single-nucleotide polymorphism (SNP) markers were developed. The ten-group linkage map of 1309.39 cM contained 2518 markers, with an average marker density of 0.56 cM per linkage group (LG). Using this map, a total of six QTLs were identified. These quantitative trait loci (QTLs) are associated with three traits related to flowering time: days to visible flower bud, days to flowering, and days to maturity. Ortholog analysis conducted with known genes involved in the regulation of flowering time among different crop species identified GI, CO and ELF4 as putative perilla orthologs that are closely linked to the QTL regions associated with flowering time. These results provide a foundation that will be useful for future studies of flowering time in perilla using fine mapping, and marker-assisted selection for the development of new varieties of perilla.
KeywordsLinkage map Genotyping-by-sequencing Orthologs Crop breeding Flowering
This work was supported by a Grant from the National Agricultural Genome Project (Nos. PJ01040803, PJ01335503), Rural Development Administration, Republic of Korea.
YJ, BM, SH, and JH conceived and designed the experiments; YJ and BM conducted the SNP analysis, linkage map construction, and data analysis; MN constructed the GBS library; KW and MH developed the mapping population and evaluated the plant phenotypes; TH provided the draft genome and participated in discussions about the experiments; YJ, SH and JH wrote the manuscript; and SH and JH reviewed the manuscript.
Compliance with ethical standards
Conflict of interest
On behalf of all authors, the corresponding author states that there is no conflict of interest.
- 1.Park Y-J, Dixit A, Ma K-H, Lee J-K, Lee M-H, Chung C-S, Nitta M, Okuno K, Kim T-S, Cho E-G, Rao VR (2007) Evaluation of genetic diversity and relationships within an on-farm collection of Perilla frutescens (L.) Britt. using microsatellite markers. Genet Resour Crop Evol 55(4):523–535. https://doi.org/10.1007/s10722-007-9258-x CrossRefGoogle Scholar
- 6.Vigeolas H, van Dongen JT, Waldeck P, Huhn D, Geigenberger P (2003) Lipid storage metabolism is limited by the prevailing low oxygen concentrations within developing seeds of oilseed rape. Plant Physiol 133(4):2048–2060. https://doi.org/10.1104/pp.103.031963 CrossRefPubMedPubMedCentralGoogle Scholar
- 12.Notaguchi M, Abe M, Kimura T, Daimon Y, Kobayashi T, Yamaguchi A, Tomita Y, Dohi K, Mori M, Araki T (2008) Long-distance, graft-transmissible action of Arabidopsis FLOWERING LOCUS T protein to promote flowering. Plant Cell Physiol 49(11):1645–1658. https://doi.org/10.1093/pcp/pcn154 CrossRefPubMedGoogle Scholar
- 14.Yamanaka N, Watanabe S, Toda K, Hayashi M, Fuchigami H, Takahashi R, Harada K (2005) Fine mapping of the FT1 locus for soybean flowering time using a residual heterozygous line derived from a recombinant inbred line. Theor Appl Genet 110(4):634–639. https://doi.org/10.1007/s00122-004-1886-3 CrossRefPubMedGoogle Scholar
- 19.Lee MH, Yang KW, Ha TJ, Jung CS, Pae SB, Hwang CD, Park CH, Baek IY, Kim HK, Park SK (2011) Development of SCAR marker for identification of the Perilla species. Korean J Breed Sci 43(4):189–193Google Scholar
- 30.Bielenberg DG, Rauh B, Fan S, Gasic K, Abbott AG, Reighard GL, Okie WR, Wells CE (2015) Genotyping by sequencing for SNP-based linkage map construction and QTL analysis of chilling requirement and bloom date in Peach [Prunus persica (L.) Batsch]. PLoS ONE 10(10):e0139406. https://doi.org/10.1371/journal.pone.0139406 CrossRefPubMedPubMedCentralGoogle Scholar
- 31.Verma S, Gupta S, Bandhiwal N, Kumar T, Bharadwaj C, Bhatia S (2015) High-density linkage map construction and mapping of seed trait QTLs in chickpea (Cicer arietinum L.) using Genotyping-by-Sequencing (GBS). Sci Rep 5:17512. https://doi.org/10.1038/srep17512 CrossRefPubMedPubMedCentralGoogle Scholar
- 32.Hussain W, Baenziger PS, Belamkar V, Guttieri MJ, Venegas JP, Easterly A, Sallam A, Poland J (2017) Genotyping-by-Sequencing derived high-density linkage map and its application to QTL mapping of flag leaf traits in bread wheat. Sci Rep 7(1):16394. https://doi.org/10.1038/s41598-017-16006-z CrossRefPubMedPubMedCentralGoogle Scholar
- 33.Li L, Zhao S, Su J, Fan S, Pang C, Wei H, Wang H, Gu L, Zhang C, Liu G, Yu D, Liu Q, Zhang X, Yu S (2017) High-density genetic linkage map construction by F2 populations and QTL analysis of early-maturity traits in upland cotton (Gossypium hirsutum L.). PLoS One 12(8):e0182918. https://doi.org/10.1371/journal.pone.0182918 CrossRefPubMedPubMedCentralGoogle Scholar
- 34.Lee MH, Oh KW, Kim MS, Kim SU, Kim JI, Oh EY, Pae SB, Yeo US, Kim T-H, Lee JH, Jung CS, Kwak DY, Kim YC (2018) Detection of QTLs in an interspecific cross between Perilla citriodora × P hirtella mapping population. Korean J Breeding Sci 50(1):13–20. https://doi.org/10.9787/kjbs.2018.50.1.13 CrossRefGoogle Scholar
- 46.Wang S, Basten CJ, Zeng ZB (2012) Windows QTL Cartographer 2.5. Department of Statistics, North Carolina State University, Raleigh, NC. (http://statgen.ncsu.edu/qtlcart/WQTLCart.htm)
- 48.Stuber CW, Edwards MD, Wendel JF (1987) Molecular marker-facilitated investigations of quantitative trait loci in maize. II. Factors influencing yield and its component traits 1. Crop Sci 27(4):639–648. https://doi.org/10.2135/cropsci1987.0011183x002700040006x CrossRefGoogle Scholar
- 54.Fornara F, Panigrahi KC, Gissot L, Sauerbrunn N, Ruhl M, Jarillo JA, Coupland G (2009) Arabidopsis DOF transcription factors act redundantly to reduce CONSTANS expression and are essential for a photoperiodic flowering response. Dev Cell 17(1):75–86. https://doi.org/10.1016/j.devcel.2009.06.015 CrossRefPubMedGoogle Scholar
- 58.Yano M, Katayose Y, Ashikari M, Yamanouchi U, Monna L, Fuse T, Baba T, Yamamoto K, Umehara Y, Nagamura Y, Sasaki T (2000) Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gene CONSTANS. Plant Cell 12(12):2473–2484CrossRefGoogle Scholar