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Genetic dissection of thousand-seed weight and fine mapping of cqSW.A03-2 via linkage and association analysis in rapeseed (Brassica napus L.)

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Abstract

Key message

cqSW.A03-2, one of the six identified quantitative trait loci associated with thousand-seed weight in rapeseed, is mapped to a 61.6-kb region on chromosome A03 and corresponds to the candidate gene BnaA03G37960D.

Abstract

Seed weight is an important factor that determines the seed yield of oilseed rape (Brassica napus L.). To elucidate the genetic mechanism of thousand-seed weight (TSW), quantitative trait locus (QTL) mapping was conducted using a double haploid population derived from the cross between an elite line ZY50 and a pol cytoplasmic male sterility restorer line 7-5. The genetic basis of TSW was dissected into six major QTLs. One major QTL denoted as cqSW.A03-2, which explained 8.46–13.70% of the phenotypic variation, was detected across multiple environments. To uncover the genetic basis of cqSW.A03-2, a set of near-isogenic lines were developed. Based on the test of self-pollinated progenies, cqSW.A03-2 was identified as a single Mendelian factor and the ZY50 allele at cqSW.A03-2 showed a positive effect on TSW. Fine mapping delimited the cqSW.A03-2 locus into a 61.6-kb region, and 18 genes within this region were predicted. Candidate gene association analysis and expression analysis indicated that a histidine kinase gene (BnaA03G37960D) is likely to be the candidate gene for the cqSW.A03-2 locus. Our results may contribute to a better understanding of the molecular mechanism of seed weight regulation and promote the breeding program for yield improvement in rapeseed.

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Abbreviations

AHK:

Arabidopsis histidine kinase

BLAST:

Basic local alignment search tool

CDS:

Coding sequences

CIM:

Composite interval mapping

cM:

Centimorgan

DAP:

Days after pollination

DH:

Double haploid

GLM:

Generalized linear model

GWAS:

Genome-wide association study

InDel:

Insertion and deletion

LD:

Linkage disequilibrium

LOD:

Logarithm of the odds

MAS:

Marker-assisted selection

MBS:

Marker-assisted background selection

MLM:

Mixed linear model

NIL:

Near-isogenic line

PCA:

Principal component analysis

qRT-PCR:

Quantitative reverse transcription-PCR

QTL:

Quantitative trait locus

SEL:

Seed length

SES:

Seed size

SEW:

Seed width

SL:

Silique length

SN:

Seed number per silique

SNP:

Single nucleotide polymorphism

SSR:

Simple sequence repeat

TSW:

Thousand-seed weight

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Acknowledgements

We thank Dr. Liang Guo from Huazhong Agricultural University for providing phenotypic and genotypic data collected from natural population (data unpublished). This research was supported by Grants from the National 973 Project (2015CB150202).

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Authors and Affiliations

  1. National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China

    Hao Wang, Min Yan, Mei Xiong, Pengfei Wang, Ying Liu, Qiang Xin, Guangsheng Yang & Dengfeng Hong

  2. Institute of Crops, Wuhan Academy of Agricultural Sciences, Wuhan, 430065, Hubei, China

    Ying Liu & Lili Wan

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  1. Hao Wang
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Contributions

HW carried out most of the experiments, including QTL analysis, fine mapping, gene cloning and sequence analysis; MY participated phenotypic and genotypic analyses of DH population; MX participated in fine mapping; PW participated in data analysis; DH and GY designed and supervised the project. HW wrote the original draft. YL, QX, LW, DH and GY were involved in reviewing and editing of the manuscript. All authors read and contributed to the revision of manuscript.

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Correspondence to Guangsheng Yang or Dengfeng Hong.

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Fig. S1. Procedures for the development of NIL populations (TIFF 564 kb)

Fig. S2. High-density genetic linkage map of DH population harboring 2,302 loci (TIFF 2550 kb)

Fig. S3. Comparative mapping of the DH linkage map and physical map of B. napus (TIFF 2019 kb)

Fig. S4. Effects of cqSW.A03-2 on TSW in different generations and environments (TIFF 907 kb)

Fig. S5. Alignment of the translated amino acid sequences of BnaA03g37960D in ZY50 and 7-5 (TIFF 6546 kb)

Fig. S6. QTL analysis of TSW on A09 chromosome (TIFF 1374 kb)

Fig. S7. Correlation analysis for agronomic traits and seed size parameters in the 17B population. (TIFF 1545 kb)

Fig. S8. Comparisons of yield-related traits between NIL (ZY50) and NIL (7-5) in the 17B population (TIFF 831 kb)

122_2020_3553_MOESM9_ESM.pdf

Table S1. Primer sequences of markers used for various purposes in the study. Table S2. Descriptive statistics of TSW in parents and DH population. Table S3. Variance components for TSW in the DH population. Table S4. Summary statistics of the linkage groups. Table S5. List of all detected significant QTLs for TSW. Table S6. List of QTLs for TSW detected on A09 linkage group (PDF 163 kb)

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Wang, H., Yan, M., Xiong, M. et al. Genetic dissection of thousand-seed weight and fine mapping of cqSW.A03-2 via linkage and association analysis in rapeseed (Brassica napus L.). Theor Appl Genet 133, 1321–1335 (2020). https://doi.org/10.1007/s00122-020-03553-9

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