Quantitative Trait Locus Mapping and Identification of Candidate Genes Controlling Flowering Time in L

Overview

Journal Front Plant Sci

Date 2021 Feb 22

PMID 33613591

Citations 13

Authors

Yu Xu

Bingbing Zhang

Ning Ma

Xia Liu

Mengfan Qin

Yan Zhang

Kai Wang

Na Guo

Kaifeng Zuo

Xiang Liu

Miao Zhang

Zhen Huang

Aixia Xu

Affiliations

Soon will be listed here.

Abstract

Flowering time plays a vital role in determining the life-cycle period, yield, and seed quality of rapeseed ( L.) in certain environments. Quantitative trait locus (QTL) mapping to identify the genetic architecture of genes controlling flowering time helps accelerate the early maturity breeding process. In this study, simple sequence repeats (SSR) and specific-locus amplified fragment sequencing (SLAF-seq) technologies were adopted to map the QTLs for flowering time in four environments. As a result, three target intervals, , , and were identified. Among this, was considered as a novel interval, and as stable regions. Based on the parental re-sequencing data, 7,022 single nucleotide polymorphisms (SNPs) and 2,195 insertion-deletions (InDels) between the two parents were identified in these three target regions. A total of 186 genes possessed genetic variations in these intervals, 14 of which were related to flowering time involved in photoperiod, circadian clock, vernalization, and gibberellin pathways. Six InDel markers linked to flowering time were developed in the three target intervals, indicating that the results were credible in this study. These results laid a good foundation for further genetic studies on flowering-time regulation in L.

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References

Song J, Guan Z, Hu J, Guo C, Yang Z, Wang S . Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus. Nat Plants. 2020; 6(1):34-45. PMC: 6965005. DOI: 10.1038/s41477-019-0577-7. View

Shen Y, Xiang Y, Xu E, Ge X, Li Z . Major Co-localized QTL for Plant Height, Branch Initiation Height, Stem Diameter, and Flowering Time in an Alien Introgression Derived DH Population. Front Plant Sci. 2018; 9:390. PMC: 5883169. DOI: 10.3389/fpls.2018.00390. View

Cheung F, Trick M, Drou N, Lim Y, Park J, Kwon S . Comparative analysis between homoeologous genome segments of Brassica napus and its progenitor species reveals extensive sequence-level divergence. Plant Cell. 2009; 21(7):1912-28. PMC: 2729604. DOI: 10.1105/tpc.108.060376. View

Li H, Younas M, Wang X, Li X, Chen L, Zhao B . Development of a core set of single-locus SSR markers for allotetraploid rapeseed (Brassica napus L.). Theor Appl Genet. 2012; 126(4):937-47. DOI: 10.1007/s00122-012-2027-z. View

Fornara F, Montaigu A, Coupland G . SnapShot: Control of flowering in Arabidopsis. Cell. 2010; 141(3):550, 550.e1-2. DOI: 10.1016/j.cell.2010.04.024. View

van Os H, Stam P, Visser R, van Eck H . SMOOTH: a statistical method for successful removal of genotyping errors from high-density genetic linkage data. Theor Appl Genet. 2005; 112(1):187-94. DOI: 10.1007/s00122-005-0124-y. View

Liu D, Ma C, Hong W, Huang L, Liu M, Liu H . Construction and analysis of high-density linkage map using high-throughput sequencing data. PLoS One. 2014; 9(6):e98855. PMC: 4048240. DOI: 10.1371/journal.pone.0098855. View

Zhou Q, Zhou C, Zheng W, Mason A, Fan S, Wu C . Genome-Wide SNP Markers Based on SLAF-Seq Uncover Breeding Traces in Rapeseed ( L.). Front Plant Sci. 2017; 8:648. PMC: 5409215. DOI: 10.3389/fpls.2017.00648. View

Ali I, Teng Z, Bai Y, Yang Q, Hao Y, Hou J . A high density SLAF-SNP genetic map and QTL detection for fibre quality traits in Gossypium hirsutum. BMC Genomics. 2018; 19(1):879. PMC: 6282304. DOI: 10.1186/s12864-018-5294-5. View

10.

Raman H, Raman R, Qiu Y, Yadav A, Sureshkumar S, Borg L . GWAS hints at pleiotropic roles for FLOWERING LOCUS T in flowering time and yield-related traits in canola. BMC Genomics. 2019; 20(1):636. PMC: 6685183. DOI: 10.1186/s12864-019-5964-y. View

11.

Li H, Durbin R . Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25(14):1754-60. PMC: 2705234. DOI: 10.1093/bioinformatics/btp324. View

12.

Liu L, Qu C, Wittkop B, Yi B, Xiao Y, He Y . A high-density SNP map for accurate mapping of seed fibre QTL in Brassica napus L. PLoS One. 2014; 8(12):e83052. PMC: 3873396. DOI: 10.1371/journal.pone.0083052. View

13.

Wu D, Liang Z, Yan T, Xu Y, Xuan L, Tang J . Whole-Genome Resequencing of a Worldwide Collection of Rapeseed Accessions Reveals the Genetic Basis of Ecotype Divergence. Mol Plant. 2018; 12(1):30-43. DOI: 10.1016/j.molp.2018.11.007. View

14.

Robert L, Robson F, Sharpe A, Lydiate D, Coupland G . Conserved structure and function of the Arabidopsis flowering time gene CONSTANS in Brassica napus. Plant Mol Biol. 1998; 37(5):763-72. DOI: 10.1023/a:1006064514311. View

15.

McCouch S, Teytelman L, Xu Y, Lobos K, Clare K, Walton M . Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res. 2003; 9(6):199-207. DOI: 10.1093/dnares/9.6.199. View

16.

Yin S, Wan M, Guo C, Wang B, Li H, Li G . Transposon insertions within alleles of BnaFLC.A10 and BnaFLC.A2 are associated with seasonal crop type in rapeseed. J Exp Bot. 2020; 71(16):4729-4741. DOI: 10.1093/jxb/eraa237. View

17.

Jian H, Zhang A, Ma J, Wang T, Yang B, Shuang L . Joint QTL mapping and transcriptome sequencing analysis reveal candidate flowering time genes in Brassica napus L. BMC Genomics. 2019; 20(1):21. PMC: 6325782. DOI: 10.1186/s12864-018-5356-8. View

18.

Song Y, Song S, Schnell A . Model-Based Linkage Analysis of a Quantitative Trait. Methods Mol Biol. 2017; 1666:283-310. DOI: 10.1007/978-1-4939-7274-6_14. View

19.

Piquemal J, Cinquin E, Couton F, Rondeau C, Seignoret E, Doucet I . Construction of an oilseed rape (Brassica napus L.) genetic map with SSR markers. Theor Appl Genet. 2005; 111(8):1514-23. DOI: 10.1007/s00122-005-0080-6. View

20.

Michaels S, Bezerra I, Amasino R . FRIGIDA-related genes are required for the winter-annual habit in Arabidopsis. Proc Natl Acad Sci U S A. 2004; 101(9):3281-5. PMC: 365781. DOI: 10.1073/pnas.0306778101. View