Genome‐wide association study identified novel candidate loci affecting wood formation in Norway spruce

Baison, John; Vidalis, Amaryllis; Zhou, Linghua; Chen, Zhiqiang; Li, Zitong; Sillanpää, Mikko; Bernhardsson, Carolina; Scofield, Douglas G.; Forsberg, Nils; Grahn, Thomas; Olsson, Lars E.; Karlsson, Bo; Wu, Harry X.; Ingvarsson, Pär K.; Lundqvist, Sven‐Olof; Niittylä, Totte; García‐Gil, Maria Rosario

doi:10.1111/tpj.14429

Cited by 50 publications

(56 citation statements)

References 103 publications

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“…A total of 1654 individuals (unrelated parents) originating from different latitudes across Sweden, were included in this study for analysis of the SNP variation following a latitudinal cline. Details regarding the DNA extraction, exome capture, genotyping and SNP annotation have been previously described in Baison et al (Baison et al , 2019). For the current analysis, trees were divided into six populations, S1-S6.…”

Section: Methodsmentioning

confidence: 99%

Molecular signatures of local adaptation to light in Norway Spruce: role of lignin mediated immunity

2020

Preprint

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Study of natural variation is an efficient method to elucidate how plants adapt to local climatic conditions, a key process for the evolution of a species. However, it is challenging to determine the genetic basis of adaptive variation especially in forest trees which have large and complex genomes. Norway spruce is a shade tolerant conifer in which the requirement of far-red light for growth increases latitudinally northwards. In the current work, hypocotyl-length followed a latitudinal cline in response to SHADE (low red:far-red ratio). RNA-sequencing revealed differential gene expression in response to SHADE, between a southern and a northern natural population in Sweden. Exome capture included analysis of uniquely large data set (1654 trees) that revealed missense variations in coding regions of nine differentially expressed candidate genes, which followed a latitudinal cline in allele and genotype frequencies. These genes included five transcription factors involved in vital processes like bud-set/bud-flush, lignin pathway and cold acclimation, and other genes that take part in cell-wall remodeling, secondary cell-wall thickening, response to starvation and immunity. Findings from this work primarily suggests that the northern populations of Norway spruce are better adapted towards disease resistance under shade by up-regulation of lignin pathway that is linked to immunity and it forms concrete basis for local adaptation to light quality in Norway spruce, one of the most economically important conifer tree species in Sweden.

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Section: Methodsmentioning

confidence: 99%

Molecular signatures of local adaptation to light in Norway Spruce: role of lignin mediated immunity

2020

Preprint

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“…Both trials were established in 1990 with a spacing 1.4m × 1.4 m. Originally, the experiments contained more than 12 progenies from 524 families at each of site, but after thinning activities in Höreda and Erikstorp in 2010 and 2008, respectively, fewer trees were left. In 2011 and 2012, six trees per site (524 * 12 ~ 6000 trees) were phenotyped 30 and the 524 mothers were genotyped using exome capture (single nucleotide polymorphism, SNP) 31 . Standing tree-based measurements with Pilodyn and Hitman were performed on the same trees in 2011 and 2013, respectively, after which further thinning was performed.…”

Section: Plant Materialsmentioning

confidence: 99%

“…Genotyping was conducted at Rapid Genomics, USA, using exom capture methodology. Sequence capture was performed using the 40 018 diploid probes previously designed and evaluated for P. abies 41 and samples were sequenced to an average depth of 15x using an Illumina HiSeq 2500 (San Diego, USA) 31 . Variant calling was performed using the Genome Analysis Toolkit (GATK) HaplotypeCaller 42 in Genome Variant Call Format (gVCF) output format.…”

Section: Genotypic Datamentioning

confidence: 99%

The effect of tree (and cambium) age on genomic prediction for solid wood properties in Norway spruce

Zhou¹,

Chen²,

Olsson

et al. 2020

Preprint

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Genomic selection (GS) or genomic prediction is considered as a promising approach to accelerate tree breeding and increase genetic gain by shortening breeding cycle. We investigated the predictive ability (PA) of GS based on 484 progeny trees from 62 half-sib families in Norway spruce ( Picea abies (L.) Karst.) for wood density, modulus of elasticity (MOE) and microfibril angle (MFA) measured with SilviScan, as well as for measurements on standing trees by Pilodyn and Hitman instruments. GS predictive abilities (PA) were comparable with those based on pedigree-based selection. The highest PAs were reached with at least 80-90% of the dataset used as training set. Use of different statistical methods had no significant impact on the estimated PAs. We also compared the abilities to predict density, MFA and MOE of 19 year old trees with use of models trained on data from coring at different ages and to different depths into the stem. The comparison indicated that close to the maximal PAs can be reached at age 10-12 by drilling only half way (ringwise) towards the pith, thereby reducing the impact on the tree.

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“…Genotyping was conducted at Rapid Genomics, USA, using exom capture methodology same as the method used in Baison et. al 2019 40 . Sequence capture was performed using the 40 018 diploid probes previously designed and evaluated for P. abies 41 and samples were sequenced to an average depth of 15x using an Illumina HiSeq 2500 (San Diego, USA) 40 .…”

Section: Genotypic Datamentioning

confidence: 99%

“…al 2019 40 . Sequence capture was performed using the 40 018 diploid probes previously designed and evaluated for P. abies 41 and samples were sequenced to an average depth of 15x using an Illumina HiSeq 2500 (San Diego, USA) 40 . Variant calling was performed using the Genome Analysis Toolkit (GATK) HaplotypeCaller v3.6 42 in Genome Variant Call Format (gVCF) output format.…”

Section: Genotypic Datamentioning

confidence: 99%

Effect of number of annual rings and tree ages on genomic predictive ability for solid wood properties of Norway spruce

Zhou¹,

Chen²,

Olsson

et al. 2020

Preprint

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BACKGROUND: Genomic selection (GS) or genomic prediction is considered as a promising approach to accelerate tree breeding and increase genetic gain by shortening breeding cycle, but the efforts to develop routines for operational breeding are so far limited. We investigated the predictive ability (PA) of GS based on 484 progeny trees from 62 half-sib families in Norway spruce (Picea abies (L.) Karst.) for wood density, modulus of elasticity (MOE) and microfibril angle (MFA) measured with SilviScan, as well as for measurements on standing trees by Pilodyn and Hitman instruments. RESULTS: GS predictive abilities were comparable with those based on pedigree-based prediction. Marker-based PAs were generally 25-30% higher for traits density, MFA and MOE measured with SilviScan than for their respective standing tree-based method which measured with Pilodyn and Hitman. Prediction accuracy (PC) of the standing tree-based methods were similar or even higher than increment core-based method. 78-95% of the maximal PAs of density, MFA and MOE obtained from coring to the pith at high age were reached by using data possible to obtain by drilling 3-5 rings towards the pith at tree age 10-12. CONCLUSIONS: This study indicates standing tree-based measurements is a cost-effective alternative method for GS. PA of GS methods were comparable with those pedigree-based prediction. The highest PAs were reached with at least 80-90% of the dataset used as training set. Density could be conducted at an earlier age than for MFA and MOE. Operational breeding can also be optimized by training the model at an earlier age or using 3 to 5 outermost rings at tree age 10 to 12 years, thereby shortening the cycle and reducing the impact on the tree.

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Genome‐wide association study identified novel candidate loci affecting wood formation in Norway spruce

Cited by 50 publications

References 103 publications

Molecular signatures of local adaptation to light in Norway Spruce: role of lignin mediated immunity

Molecular signatures of local adaptation to light in Norway Spruce: role of lignin mediated immunity

The effect of tree (and cambium) age on genomic prediction for solid wood properties in Norway spruce

Effect of number of annual rings and tree ages on genomic predictive ability for solid wood properties of Norway spruce

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