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

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          Abstract

          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 β-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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          Mapping genes for complex traits in domestic animals and their use in breeding programmes.

          Genome-wide panels of SNPs have recently been used in domestic animal species to map and identify genes for many traits and to select genetically desirable livestock. This has led to the discovery of the causal genes and mutations for several single-gene traits but not for complex traits. However, the genetic merit of animals can still be estimated by genomic selection, which uses genome-wide SNP panels as markers and statistical methods that capture the effects of large numbers of SNPs simultaneously. This approach is expected to double the rate of genetic improvement per year in many livestock systems.
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            Strong control, conservative point estimation and simultaneous conservative consistency of false discovery rates: a unified approach

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              Primer3 on the WWW for General Users and for Biologist Programmers

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                Author and article information

                Journal
                Genetics
                Genetics
                Genetics Society of America
                0016-6731
                1943-2631
                May 05 2011
                May 2011
                May 2011
                March 08 2011
                : 188
                : 1
                : 197-214
                Article
                10.1534/genetics.110.125781
                3120141
                21385726
                0e272812-3ab3-4449-aafc-cb12ffc7ff2b
                © 2011
                History

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