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Development of gene-based markers from functional Arabidopsis thaliana genes involved in phosphorus homeostasis and mapping in Brassica napus

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Abstract

Brassica napus is an important oilseed and fodder crop grown throughout the world. Although it is widely grown, little is known about the molecular basis of phosphorus (P) homeostasis for this species. In this research, a population of 124 recombinant inbred lines (RILs) (designated as BE-RIL) derived from a cross between P-inefficient cv. ‘B104-2’ and P-efficient cv. ‘Eyou Changjia’ was used to construct a genetic map of P homeostasis genes. A set of gene-based markers (GBMs) was developed from functional genes involved in Arabidopsis thaliana P homeostasis. In total, 46 GBMs corresponding to 26 genes, assigned to eight functional categories, were integrated into the BE-RIL map. A total of 243 simple sequence repeat (SSR) markers were developed from 171 bacterial artificial chromosome (BAC) end sequences and/or B. rapa seed BAC sequences. Of these SSR markers, 74 were added to the BE-RIL map. Based on the newly constructed genetic map, comparative genetic analysis between A. thaliana and B. napus was performed. A total of 90 conserved genomic blocks were aligned between A. thaliana pseudochromosomes and the BE-RIL linkage groups. According to physical positions on the Arabidopsis genome, 1223 orthologs of 356 genes involved in Arabidopsis P homeostasis were mapped onto syntenic blocks and insertion segments. This high-density genetic map will be useful for identifying quantitative trait loci (QTL) that control P homeostasis and putative candidate genes for the efficient use of P in B. napus.

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Abbreviations

P:

Phosphorus

RIL:

Recombinant inbred line

GBM:

Gene-based marker

SSR:

Single sequence repeat

QTL:

Quantitative trait loci

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Acknowledgment

This work was supported by National Basic Research and Development Program [2011CB100301], China.

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Authors and Affiliations

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

    Guangda Ding, Yuan Liao, Mei Yang, Zunkang Zhao, Lei Shi & Fangsen Xu

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  1. Guangda Ding
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  2. Yuan Liao
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  3. Mei Yang
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  4. Zunkang Zhao
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  5. Lei Shi
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  6. Fangsen Xu
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Corresponding author

Correspondence to Fangsen Xu.

Electronic supplementary material

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Supplementary Table S1

List of 243 SSR loci indicating GenBank ID, BAC name, chromosomal location of B. rapa BAC, marker name, motif, primer sequences, Tm, expected product size, and primary homologous regions among the 5 chromosomes of the Arabidopsis genome (DOC 591 kb)

Supplementary Table S2

Linkage map of the 733 molecular markers constructed with the B. napus BE-RIL population (DOC 597 kb)

Supplementary Table S3

A total of 1223 orthologs of 356 genes involved in A. thaliana P homeostasis and their locations on B. napus BE-RIL linkage map by in silico mapping (DOC 1143 kb)

Supplementary Fig. S1

Functional classification of 46 mapped loci that represent different genes in the B. napus BE-RIL map (DOC 35 kb)

Supplementary Fig. S2

Comparative map analysis between the present study and results from Parkin et al. (2005) with the RFLP loci converted to their corresponding A. thaliana loci by Panjabi et al. (2008) (PPT 1415 kb)

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Ding, G., Liao, Y., Yang, M. et al. Development of gene-based markers from functional Arabidopsis thaliana genes involved in phosphorus homeostasis and mapping in Brassica napus . Euphytica 181, 305–322 (2011). https://doi.org/10.1007/s10681-011-0428-8

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