Comparative genomic analysis of the compound Brassica napus Rf locus View Full Text


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Article Info

DATE

2016-10-26

AUTHORS

Lydiane Gaborieau, Gregory G. Brown

ABSTRACT

BackgroundThe plant trait of cytoplasmically-inherited male sterility (CMS) and its suppression by nuclear restorer-of-fertility (Rf) genes can be viewed as a genetic arms race between the mitochondrial and nuclear genomes. Most nuclear Rf genes have been shown to encode P-type pentatricopeptide repeat proteins (PPRs). Phylogenetic analysis of P-class PPRs from sequenced plants genomes has shown that Rf-proteins cluster in a distinct clade of P-class PPRs, RFL-PPRs, that display hallmarks of positive evolutionary selection. Genes encoding RFL-PPRs (RFLs) within a given plant genome tend to be closely related both in sequence and position, but a detailed understanding of how such species-specific expansion occurs is lacking. In the canola, (oilseed rape) species Brassica napus, previous work has indicated the nuclear restorer genes for the two native forms of CMS, Rfn (for nap CMS) and Rfp (pol CMS), represent alternate haplotypes, or alleles, of a single nuclear locus.ResultsFine genetic mapping indicates that Rfn does indeed localize to the same genomic region as Rfp. We find this region is enriched in RFL genes, three of which, based on their position and expression, represent potential candidates for Rfn; one of these genes, designated PPR4, is a preferred candidate in that it is not expressed in the nap CMS line. Comparison of the corresponding regions of the genomes of B. rapa, B. oleracea, Arabidopsis thaliana and A. lyrata provides insight into the expansion of this group of RFL genes in different lines of evolutionary descent.ConclusionsUnlike other nuclear restorer loci containing multiple RFL genes, the RFL genes in the Rf region of B. napus are not present in tandem arrays but rather are dispersed in genomic location. The genes do not share similar flanking non-coding regions and do not contain introns, indicating that they have duplicated primarily through a retrotransposition-mediated process. In contrast, segmental duplication has been responsible for the distribution of the 10 sequences we annotated as RFL genes in the corresponding region of the A. lyrata genome. Our observations define the Brassica Rf locus and indicate that different mechanisms may be responsible for the proliferation of RFL genes even among closely related genomes. More... »

PAGES

834

References to SciGraph publications

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  • 2009-11-18. High-resolution mapping of the Brassica napus Rfp restorer locus using Arabidopsis-derived molecular markers in THEORETICAL AND APPLIED GENETICS
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  • 1997-01. An open reading frame for a protein involved in cytochrome c biogenesis is split into two parts in Brassica mitochondria in CURRENT GENETICS
  • 1981-02. A further study of the problem of the maintenance of females in Gynodioecious species in HEREDITY
  • 2004-02-14. Positional cloning of the rice Rf-1 gene, a restorer of BT-type cytoplasmic male sterility that encodes a mitochondria-targeting PPR protein in THEORETICAL AND APPLIED GENETICS
  • 2005-08-03. Fertility restorer locus Rf1 of sorghum (Sorghum bicolor L.) encodes a pentatricopeptide repeat protein not present in the colinear region of rice chromosome 12 in THEORETICAL AND APPLIED GENETICS
  • 2011-08-28. The genome of the mesopolyploid crop species Brassica rapa in NATURE GENETICS
  • 2006-05. Towards Positional Cloning in Brassica napus: Generation and Analysis of Doubled Haploid B. rapa Possessing the B. napus pol CMS and Rfp Nuclear Restorer Gene in PLANT MOLECULAR BIOLOGY
  • 2012-05-22. Fine mapping and candidate gene analysis of the nuclear restorer gene Rfp for pol CMS in rapeseed (Brassica napus L.) in THEORETICAL AND APPLIED GENETICS
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    102 native form
    103 non-coding regions
    104 nuclear Rf genes
    105 nuclear genome
    106 nuclear loci
    107 nuclear restorer
    108 nuclear restorer genes
    109 nuclear restorer loci
    110 observations
    111 oleracea
    112 pentatricopeptide repeat protein
    113 phylogenetic analysis
    114 plant genomes
    115 plant traits
    116 position
    117 positive evolutionary selection
    118 potential candidate
    119 preferred candidate
    120 previous work
    121 process
    122 proliferation
    123 protein
    124 race
    125 rapa
    126 region
    127 repeat proteins
    128 restorer
    129 restorer gene
    130 restorer locus
    131 same genomic region
    132 segmental duplications
    133 selection
    134 sequence
    135 sequenced plant genomes
    136 single nuclear locus
    137 species-specific expansion
    138 sterility
    139 suppression
    140 tandem arrays
    141 thaliana
    142 traits
    143 understanding
    144 work
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