Scientia Agricultura Sinica ›› 2015, Vol. 48 ›› Issue (18): 3727-3732.doi: 10.3864/j.issn.0578-1752.2015.18.016

• RESEARCH NOTES • Previous Articles     Next Articles

The Influence of Whole-Genome Triplication (WGT) on the Candidate Genes of Pollen Specific Expression in Brassica rapa

WANG Xiao-bo1, MA Yuan1,2, CHENG Feng1, WU Jian1, LIANG Jian-li1, WANG Xiao-wu1   

  1. 1Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences/Key Laboratory of Horticultural Crop Biology and Germplasm Creation of the Ministry of Agriculture, Beijing 100081
    2College of Life Sciences, Wuhan University/Key Laboratory  of the Ministry of Education for Plant Developmental Biology, Wuhan 430072
  • Received:2015-03-03 Online:2015-09-16 Published:2015-09-16

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Abstract: 【Objective】 The objective of this study is to research the evolution of the candidate genes of pollen specific expression in Brassica rapa after whole-genome triplication (WGT). This study will provide a theoretical basis for pollen specific expressed genes in B. rapa in the future research. 【Method】 The genes of pollen specific expression in B. rapa were acquired by SynOrths referred to Arabidopsis thaliana based on their syntenic relationship. InterproScan was used to get their Gene Ontology (GO), which were grouped into 13 categories related to pollen. To compare among three duplicated categories, the ratio of gene number of each GO to total number of genes in these categories was counted. Furthermore, these genes were grouped into three subgenomes based on their explicit dataset of B. rapa genes. Based on the syntenic relationship of tandem genes of pollen specific expression in B. rapa with genes in A. thaliana，whether these genes were generated before WGT or after the event was determined. 【Result】 Totally, 1962 candidate genes of pollen specific expression in B. rapa were verified via the syntenic relationship with 1651 genes in A. thaliana. There are 182 tandem genes in A. thaliana, while 137 tandem genes in B. rapa. The result showed that the number of pollen specific expressed genes between A. thaliana and B. rapa was almost equivalent, so it could be inferred that most of copy genes of B. rapa were lost after WGT event occurs. A total of 549 genes of pollen specific expression in A. thaliana were not found syntenic counterparts in B. rapa, so these genes might be also lost after WGT. There are 898 genes of pollen specific expression in A. thaliana corresponding to these genes with single-copy, double-copies or triple-copies in B. rapa. A total of 480 genes in A. thaliana with single-copy in B. rapa, accounting for 53.5%, which is the largest proportion. While 322 genes with double-copies account for about 35.8%, and only 96 genes with triple-copies account for 10.7%. The candidate genes of pollen specific expression with triple-copies in all three subgenomes of B. rapa were more than the other two copy classifies on seven functional categories, while the function of these genes with double-copies were dispersed into all functional categories. Most of tandem genes of pollen specific expression were turned into non-tandem genes, but some non-tandem genes of pollen specific expression developed into tandem genes in B. rapa after WGT. 【Conclusion】 These results indicated that the candidate genes of pollen specific expression had an ongoing evolution after WGT, and the WGT event may contribute to the functional difference existed in three classifies of copy genes in B. rapa.

Key words: Brassica rapa, pollen specific expression, whole-genome triplication, synteny, evolution

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