Publications (23) View all
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Article: A genetic linkage map of Brassica carinata constructed with a doubled haploid population.
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ABSTRACT: Brassica carinata is an important oilseed crop with unique favourable traits that are desirable for other Brassica crops. However, given the limited research into genetic resources in B. carinata, knowledge of the genetic structure of this species is relatively poor. Nine homozygous, genetically distinct accessions of B. carinata were obtained via microspore culture, from which two divergent doubled haploid (DH) lines were used to develop a DH mapping population that consisted of 183 lines. The mapping population showed segregation of multiple traits of interest. A genetic map was constructed with PCR-based markers, and a total of 212 loci, which covered 1,703 cM, were assigned to eight linkage groups in the B genome and nine linkage groups in the C genome, which allowed comparison with genetic maps of other important Brassica species that contain the B/C genome(s). Loci for two Mendelian-inherited traits related to pigmentation (petal and anther tip colour) and one quantitative trait (seed coat colour) were identified using the linkage map. The significance of the mapping population in the context of genetic improvement of Brassica crops is discussed.Theoretical and Applied Genetics 06/2012; 125(6):1113-24. · 3.30 Impact Factor -
Article: Identification of quantitative trait loci associated with germination using chromosome segment substitution lines of rice (Oryza sativa L.).
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ABSTRACT: Rapid and uniform seed germination under diverse environmental conditions is a desirable characteristic for most crop plants, such as rice, wheat, and maize. However, the genetic base of the variations in the rate of germination is not well understood. In this study, quantitative trait loci (QTL) for germination rate were mapped with a set of 143 chromosome segment substitution lines (CSSL) each contains a small genomic fragment from a japonica variety Nipponbare in the uniform genetic background of an indica variety Zhenshan97. Nine CSSL showed significantly lower germination rate than that in Zhenshan97. Four germination-related QTL were identified located on chromosomes 2, 5, 6 and 10, at which all japonica alleles decreased germination rate. By using the CSSL-derived F2 population, a major QTL (qGR2) on chromosome 2 was confirmed, and delimited to a 10.4 kb interval containing three putative candidate genes, of which OsMADS29 was only expressed preferentially in the seed. These results would facilitate cloning of the major gene that affects germination rate, and provide an insight into the genetic basis of germination.Theoretical and Applied Genetics 04/2011; 123(3):411-20. · 3.30 Impact Factor -
Article: Diversity and selective sweep in the OsAMT1;1 genomic region of rice.
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ABSTRACT: Ammonium is one of the major forms in which nitrogen is available for plant growth. OsAMT1;1 is a high-affinity ammonium transporter in rice (Oryza sativa L.), responsible for ammonium uptake at low nitrogen concentration. The expression pattern of the gene has been reported. However, variations in its nucleotides and the evolutionary pathway of its descent from wild progenitors are yet to be elucidated. In this study, nucleotide diversity of the gene OsAMT1;1 and the diversity pattern of seven gene fragments spanning a genomic region approximately 150 kb long surrounding the gene were surveyed by sequencing a panel of 216 rice accessions including both cultivated rice and wild relatives. Nucleotide polymorphism (Pi) of OsAMT1;1 was as low as 0.00004 in cultivated rice (Oryza sativa), only 2.3% of that in the common wild rice (O. rufipogon). A single dominant haplotype was fixed at the locus in O. sativa. The test values for neutrality were significantly negative in the entire region stretching 5' upstream and 3' downstream of the gene in all accessions. The value of linkage disequilibrium remained high across a 100 kb genomic region around OsAMT1;1 in O. sativa, but fell rapidly in O. rufipogon on either side of the promoter of OsAMT1;1, demonstrating a strong natural selection within or nearby the ammonium transporter. The severe reduction in nucleotide variation at OsAMT1;1 in rice was caused by a selective sweep around OsAMT1;1, which may reflect the nitrogen uptake system under strong selection by the paddy soil during the domestication of rice. Purifying selection also occurred before the wild rice diverged into its two subspecies, namely indica and japonica. These findings would provide useful insights into the processes of evolution and domestication of nitrogen uptake genes in rice.BMC Evolutionary Biology 03/2011; 11:61. · 3.52 Impact Factor -
Article: Functional markers developed from multiple loci in GS3 for fine marker-assisted selection of grain length in rice.
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ABSTRACT: The gene GS3 has major effect on grain size and plays an important role in rice breeding. The C to A mutation in the second exon of GS3 was reported to be functionally associated with enhanced grain length in rice. In the present study, besides the C-A mutation at locus SF28, three novel polymorphic loci, SR17, RGS1, and RGS2, were discovered in the second intron, the last intron and the final exon of GS3, respectively. A number of alleles at these four polymorphic loci were observed in a total of 287 accessions including Chinese rice varieties (Oryza sativa), African cultivated rice (O. glaberrima) and AA-genome wild relatives. The haplotype analysis revealed that the simple sequence repeats (AT)(n) at RGS1 and (TCC)(n) at RGS2 had differentiated in the wild rice whilst the C-A mutation occurred in the cultivated rice recently during domestication. It also indicated that A allele at SF28 was highly associated with long rice grain whilst various motifs of (AT)(n) at RGS1 and (TCC)(n) at RGS2 were mainly associated with medium to short grain in Chinese rice. The C-A mutation at SF28 explained 33.4% of the grain length variation in the whole rice population tested in this study, whereas (AT)(n) at RGS1 and (TCC)(n) at RGS2 explained 26.4 and 26.2% of the variation, respectively. These results would be helpful for better understanding domestication of GS3 and its manipulation for grain size in rice. The genic marker RGS1 based on the motifs (AT)(n) was further validated as a functional marker using two sets of backcross recombinant inbred lines. These results suggested that the functional markers developed from four different loci within GS3 could be used for fine marker-assisted selection of grain length in rice breeding.Theoretical and Applied Genetics 03/2011; 122(5):905-13. · 3.30 Impact Factor -
Conference Proceeding: Distinct patterns of behaviour for specific and general combining ability in hybrid oilseed rape evaluated in Australia, China and India
The Abstract book of the 13th International Rapeseed Congress, Prague, Czech Republic; 01/2011
