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Molecular Genetics and Genomics

, Volume 293, Issue 6, pp 1421–1435 | Cite as

Combined QTL mapping, physiological and transcriptomic analyses to identify candidate genes involved in Brassica napus seed aging

  • Tengyue Wang
  • Lintao Hou
  • Hongju Jian
  • Feifei Di
  • Jiana Li
  • Liezhao Liu
Original Article

Abstract

Seed aging is an inevitable problem in the germplasm conservation of oil crops. Thus, clarifying the genetic mechanism of seed aging is important for rapeseed breeding. In this study, Brassica napus seeds were exposed to an artificial aging environment (40 °C and 90% relative humidity). Using a population of 172 recombinant inbred lines, 13 QTLs were detected on 8 chromosomes, which explained ~ 9.05% of the total phenotypic variation. The QTLs q2015AGIA-C08 and q2016AGI-C08-2 identified in the two environments were considered the same QTL. After artificial aging, lower germination index, increased relative electrical conductivity, malondialdehyde and proline content, and reduced soluble sugar, protein content and antioxidant enzyme activities were detected. Furthermore, seeds of extreme lines that were either left untreated (R0 and S0) or subjected to 15 days of artificial aging (R15 and S15) were used for transcriptome sequencing. In total, 2843, 1084, 429 and 1055 differentially expressed genes were identified in R15 vs. R0, S15 vs. S0, R0 vs. S0 and R15 vs. S15, respectively. Through integrated QTL mapping and RNA-sequencing analyses, seven genes, such as BnaA03g37460D, encoding heat shock transcription factor C1, and BnaA03g40360D, encoding phosphofructokinase 4, were screened as candidate genes involved in seed aging. Further researches on these candidate genes could broaden our understanding of the regulatory mechanisms of seed aging.

Keywords

Brassica napus Seed artificial aging Physiology QTL analysis Transcriptome 

Abbreviations

QTL

Quantitative trait locus

RIL

Recombinant inbred lines

MDA

Malondialdehyde

DEG

Differentially expressed genes

RH

Relative humidity

IF2

Immortalized F2

HSP

Heat shock proteins

PIMT

Protein l-isoaspartyl methyltransferase

LEA protein

Late embryogenesis abundant protein

SNP

Single-nucleotide polymorphism

CAT

Catalase

POD

Peroxidase

SOD

Superoxide dismutase

BSA

Bovine serum albumin

TCA

Trichloroacetic acid

ABA

Abscisic acid

GA

Gibberellin

HPLC–MS/MS

High-performance liquid chromatography–mass spectrometry

RIN

RNA integrity number

FPKM

Fragments per kilobase million

GO

Gene ontology

KEGG

Kyoto Encyclopedia of Genes and Genomes

LRR

Leucine-rich repeat

PFK4

Phosphofructokinase 4

EX1

Executer1

Notes

Funding

This work was supported by the National Natural Science Foundation of China (31371655, 31771830), the Fundamental Research Funds for Central Universities (XDJK2017A009 and XDJK2017D076), and the Chongqing Science and Technology Commission (cstc2016shmszx80083).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no competing interests.

Ethical standards

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

438_2018_1468_MOESM1_ESM.tif (516 kb)
Frequency distribution of the artificial aging seed germination index in the RIL population in 2015 and 2016 (TIF 515 KB)
438_2018_1468_MOESM2_ESM.tif (496 kb)
Statistics of the seed germination index in extreme plant materials under normal and artificial aging conditions. * denotes significant difference at the 0.05 level (TIF 496 KB)
438_2018_1468_MOESM3_ESM.tif (645 kb)
Relative conductivity and MDA content in seeds of extreme material under normal and artificial aging conditions. a. Relative conductivity of extreme material seeds after 15 d of aging treatment. b. Variation tendency of relative conductivity in seeds from five extreme materials at four time points (0 d, 5 d, 10 d, 15 d) during aging treatment. c. MDA content of extreme material seeds after 15 d of aging treatment. d. Variation tendency of MDA content in seeds of five extreme materials at four time points (0 d, 5 d, 10 d, 15 d) during aging treatment. Values represent the mean ± standard error (n=3); * and ** above the bars indicate P < 0.05 and P < 0.01, respectively (TIF 645 KB)
438_2018_1468_MOESM4_ESM.tif (652 kb)
Soluble sugar and protein content in seeds of extreme materials under normal and artificial aging conditions. a. Soluble sugar content of extreme material seeds after 15 d of aging treatment. b. Variation tendency of soluble sugar content in seeds of five extreme materials at four time points (0 d, 5 d, 10 d, 15 d) during aging treatment. c. Soluble protein content of extreme material seeds after 15 d of aging treatment. d. Variation tendency of soluble protein content in seeds of five extreme materials at four time points (0 d, 5 d, 10 d, 15 d) during aging treatment. Values represent the mean ± standard error (n=3); * and ** above the bars indicate P < 0.05 and P < 0.01, respectively (TIF 651 KB)
438_2018_1468_MOESM5_ESM.tif (363 kb)
Proline content in seeds of extreme materials under normal and artificial aging conditions. a. Proline content of extreme material seeds after 15 d of aging treatment. b. Variation tendency of proline content in seeds of five extreme materials at four time points (0 d, 5 d, 10 d, 15 d) during aging treatment. Values represent the mean ± standard error (n=3); ** above the bars indicates P < 0.01 (TIF 363 KB)
438_2018_1468_MOESM6_ESM.tif (789 kb)
CAT, POD and SOD activity in seeds of extreme material under normal and artificial aging conditions. a. CAT activity of extreme material seeds after 15 d of aging treatment. b. Variation tendency of CAT activity in seeds of five extreme materials at four time points (0 d, 5 d, 10 d, 15 d) during aging treatment. c. SOD activity of extreme material seeds after 15 d of aging treatment. d. Variation tendency of SOD activity in seeds of five extreme materials at four time points (0 d, 5 d, 10 d, 15 d) during aging treatment. e. POD activity of extreme material seeds after 15 d of aging treatment. f. Variation tendency of POD activity in seeds of five extreme materials at four time points (0 d, 5 d, 10 d, 15 d) during aging treatment. Values represent the mean ± standard error (n =3); * and ** above the bars indicate P < 0.05 and P < 0.01, respectively (TIF 789 KB)
438_2018_1468_MOESM7_ESM.tif (509 kb)
ABA and GA3 content in seeds of extreme material under normal and artificial aging conditions. Values represent the mean ± standard error (n =3) (TIF 508 KB)
438_2018_1468_MOESM8_ESM.tif (1.4 mb)
GO categories of the up-regulated DEGs in R15 Vs. R0 and S15 Vs. S0 (TIF 1430 KB)
438_2018_1468_MOESM9_ESM.xlsx (143 kb)
Supplementary material 9 (XLSX 142 KB)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Tengyue Wang
    • 1
  • Lintao Hou
    • 1
  • Hongju Jian
    • 1
  • Feifei Di
    • 1
  • Jiana Li
    • 1
  • Liezhao Liu
    • 1
  1. 1.College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Academy of Agricultural SciencesSouthwest UniversityChongqingChina

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