Economic Importance, Breeding Objectives and Achievements

Plomion, Christophe; Bousquet, Jean; Kole, Chittaranjan

doi:10.1201/b11075-6

Cited by 29 publications

(41 citation statements)

References 115 publications

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“…These initiatives present significant challenges for assembling genomes in excess of 20,000 Mbp from heterozygous individuals without physical maps. The P. glauca gene SNP atlas represents a base resource for building high-density genetic maps (e.g., Pavy et al 2012a) to which genome sequence scaffolds could be robustly anchored through the annotated gene loci in order to create pseudo-chromosome sequences (Ritland et al 2011). It will also be useful to develop high-throughput genotyping assays (Pavy et al 2013) for a variety of investigations including ecological/population genomics analyses of adaptive mechanisms and the discovery of transcriptome-wide epistatic effects and gene networks, which is an emerging research issue in relation to monitoring and mitigating the effects of climatic change on biological diversity.…”

Section: Discussionmentioning

confidence: 99%

The Landscape of Nucleotide Polymorphism among 13,500 Genes of the Conifer Picea glauca, Relationships with Functions, and Comparison with Medicago truncatula

Pavy

Deschênes

Blais

et al. 2013

Genome Biology and Evolution

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Gene families differ in composition, expression, and chromosomal organization between conifers and angiosperms, but little is known regarding nucleotide polymorphism. Using various sequencing strategies, an atlas of 212k high-confidence single nucleotide polymorphisms (SNPs) with a validation rate of more than 92% was developed for the conifer white spruce (Picea glauca). Nonsynonymous and synonymous SNPs were annotated over the corresponding 13,498 white spruce genes representative of 2,457 known gene families. Patterns of nucleotide polymorphisms were analyzed by estimating the ratio of nonsynonymous to synonymous numbers of substitutions per site (A/S). A general excess of synonymous SNPs was expected and observed. However, the analysis from several perspectives enabled to identify groups of genes harboring an excess of nonsynonymous SNPs, thus potentially under positive selection. Four known gene families harbored such an excess: dehydrins, ankyrin-repeats, AP2/DREB, and leucine-rich repeat. Conifer-specific sequences were also generally associated with the highest A/S ratios. A/S values were also distributed asymmetrically across genes specifically expressed in megagametophytes, roots, or in both, harboring on average an excess of nonsynonymous SNPs. These patterns confirm that the breadth of gene expression is a contributing factor to the evolution of nucleotide polymorphism. The A/S ratios of Medicago truncatula genes were also analyzed: several gene families shared between P. glauca and M. truncatula data sets had similar excess of synonymous or nonsynonymous SNPs. However, a number of families with high A/S ratios were found specific to P. glauca, suggesting cases of divergent evolution at the functional level.

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Section: Discussionmentioning

confidence: 99%

The Landscape of Nucleotide Polymorphism among 13,500 Genes of the Conifer Picea glauca, Relationships with Functions, and Comparison with Medicago truncatula

Pavy

Deschênes

Blais

et al. 2013

Genome Biology and Evolution

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“…[6]). Genetic mapping activities, therefore, will continue to dominate research in conifer genetics [7] at least until a conifer genome sequence has been completely decoded.…”

Section: Introductionmentioning

confidence: 99%

Development and implementation of a highly-multiplexed SNP array for genetic mapping in maritime pine and comparative mapping with loblolly pine

et al. 2011

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BackgroundSingle nucleotide polymorphisms (SNPs) are the most abundant source of genetic variation among individuals of a species. New genotyping technologies allow examining hundreds to thousands of SNPs in a single reaction for a wide range of applications such as genetic diversity analysis, linkage mapping, fine QTL mapping, association studies, marker-assisted or genome-wide selection. In this paper, we evaluated the potential of highly-multiplexed SNP genotyping for genetic mapping in maritime pine (Pinus pinaster Ait.), the main conifer used for commercial plantation in southwestern Europe.ResultsWe designed a custom GoldenGate assay for 1,536 SNPs detected through the resequencing of gene fragments (707 in vitro SNPs/Indels) and from Sanger-derived Expressed Sequenced Tags assembled into a unigene set (829 in silico SNPs/Indels). Offspring from three-generation outbred (G2) and inbred (F2) pedigrees were genotyped. The success rate of the assay was 63.6% and 74.8% for in silico and in vitro SNPs, respectively. A genotyping error rate of 0.4% was further estimated from segregating data of SNPs belonging to the same gene. Overall, 394 SNPs were available for mapping. A total of 287 SNPs were integrated with previously mapped markers in the G2 parental maps, while 179 SNPs were localized on the map generated from the analysis of the F2 progeny. Based on 98 markers segregating in both pedigrees, we were able to generate a consensus map comprising 357 SNPs from 292 different loci. Finally, the analysis of sequence homology between mapped markers and their orthologs in a Pinus taeda linkage map, made it possible to align the 12 linkage groups of both species.ConclusionsOur results show that the GoldenGate assay can be used successfully for high-throughput SNP genotyping in maritime pine, a conifer species that has a genome seven times the size of the human genome. This SNP-array will be extended thanks to recent sequencing effort using new generation sequencing technologies and will include SNPs from comparative orthologous sequences that were identified in the present study, providing a wider collection of anchor points for comparative genomics among the conifers.

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“…One limitation with linkage mapping is its requirement for large families with known relatedness, i.e., full-sib families in plants or extended pedigrees in humans (Myles et al 2009). Furthermore, QTL do not replicate well across populations of different genetic background and across environments (Mackay 2001;Pelgas et al 2011;Ritland et al 2011).…”

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confidence: 99%

Association Genetics of Wood Physical Traits in the Conifer White Spruce and Relationships With Gene Expression

et al. 2011

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Marker-assisted selection holds promise for highly influencing tree breeding, especially for wood traits, by considerably reducing breeding cycles and increasing selection accuracy. In this study, we used a candidate gene approach to test for associations between 944 single-nucleotide polymorphism markers from 549 candidate genes and 25 wood quality traits in white spruce. A mixed-linear model approach, including a weak but nonsignificant population structure, was implemented for each marker-trait combination. Relatedness among individuals was controlled using a kinship matrix estimated either from the known half-sib structure or from the markers. Both additive and dominance effect models were tested. Between 8 and 21 single-nucleotide polymorphisms (SNPs) were found to be significantly associated (P # 0.01) with each of earlywood, latewood, or total wood traits. After controlling for multiple testing (Q # 0.10), 13 SNPs were still significant across as many genes belonging to different families, each accounting for between 3 and 5% of the phenotypic variance in 10 wood characters. Transcript accumulation was determined for genes containing SNPs associated with these traits. Significantly different transcript levels (P # 0.05) were found among the SNP genotypes of a 1-aminocyclopropane-1-carboxylate oxidase, a b-tonoplast intrinsic protein, and a long-chain acyl-CoA synthetase 9. These results should contribute toward the development of efficient marker-assisted selection in an economically important tree species.

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Economic Importance, Breeding Objectives and Achievements

Cited by 29 publications

References 115 publications

The Landscape of Nucleotide Polymorphism among 13,500 Genes of the Conifer Picea glauca, Relationships with Functions, and Comparison with Medicago truncatula

The Landscape of Nucleotide Polymorphism among 13,500 Genes of the Conifer Picea glauca, Relationships with Functions, and Comparison with Medicago truncatula

Development and implementation of a highly-multiplexed SNP array for genetic mapping in maritime pine and comparative mapping with loblolly pine

Association Genetics of Wood Physical Traits in the Conifer White Spruce and Relationships With Gene Expression

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