Association mapping identified novel candidate loci affecting wood formation in Norway spruce

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

doi:10.1101/292847

Cited by 10 publications

(9 citation statements)

References 26 publications

(30 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In order to independently evaluate the utility of the consensus map for downstream research, we used a subset of the data from Baison et al (2018) to estimate patterns of nucleotide diversity across the Norway spruce genome. The data from Baison et al originally contained 517 individuals sequenced with 40,018 probes designed for diploid spruce samples (Vidalis et al 2018).…”

Section: Methodsmentioning

confidence: 99%

An Ultra-Dense Haploid Genetic Map for Evaluating the Highly Fragmented Genome Assembly of Norway Spruce (Picea abies)

Bernhardsson

Vidalis

Wang

et al. 2019

G3 Genes|Genomes|Genetics

Self Cite

View full text Add to dashboard Cite

Norway spruce ( Picea abies (L.) Karst.) is a conifer species of substanital economic and ecological importance. In common with most conifers, the P. abies genome is very large (∼20 Gbp) and contains a high fraction of repetitive DNA. The current P. abies genome assembly (v1.0) covers approximately 60% of the total genome size but is highly fragmented, consisting of >10 million scaffolds. The genome annotation contains 66,632 gene models that are at least partially validated ( www.congenie.org ), however, the fragmented nature of the assembly means that there is currently little information available on how these genes are physically distributed over the 12 P. abies chromosomes. By creating an ultra-dense genetic linkage map, we anchored and ordered scaffolds into linkage groups, which complements the fine-scale information available in assembly contigs. Our ultra-dense haploid consensus genetic map consists of 21,056 markers derived from 14,336 scaffolds that contain 17,079 gene models (25.6% of the validated gene models) that we have anchored to the 12 linkage groups. We used data from three independent component maps, as well as comparisons with previously published Picea maps to evaluate the accuracy and marker ordering of the linkage groups. We demonstrate that approximately 3.8% of the anchored scaffolds and 1.6% of the gene models covered by the consensus map have likely assembly errors as they contain genetic markers that map to different regions within or between linkage groups. We further evaluate the utility of the genetic map for the conifer research community by using an independent data set of unrelated individuals to assess genome-wide variation in genetic diversity using the genomic regions anchored to linkage groups. The results show that our map is sufficiently dense to enable detailed evolutionary analyses across the P. abies genome.

show abstract

Section: Methodsmentioning

confidence: 99%

An Ultra-Dense Haploid Genetic Map for Evaluating the Highly Fragmented Genome Assembly of Norway Spruce (Picea abies)

Bernhardsson

Vidalis

Wang

et al. 2019

G3 Genes|Genomes|Genetics

Self Cite

View full text Add to dashboard Cite

show abstract

“…HaplotypeCaller was used for individual genotype identification and joint SNP calling was performed across all samples using GenotypeGVCFs. We then applied the same variant quality score recalibration protocols as Baison et al (2018), which were trained on a set of ~21,000 SNPs identified from a pedigree study ). This resulted in 2,406,289 SNPs after recalibration.…”

Section: Snp Identification and Estimation Of Genetic Diversitymentioning

confidence: 99%

“…Mapping to paralog sequences could also distort the distributions of quality scores. Instead of hard filtering based on arbitrary cutoffs, we applied a protocol of variant quality score recalibration, parameters of which were trained using set of SNPs discovered in a pedigree study (Baison et al 2018;Bernhardsson et al 2018). This should help reduce false positive discovery but may also bias towards shared SNPs and less private ones in P. obovata and P. omorika.…”

Section: Sources Of Sequencing Errorsmentioning

confidence: 99%

Genomic data provides new insights on the demographic history and the extent of recent material transfers in Norway spruce

Liu

Milesi

Jansson

et al. 2018

Preprint

Self Cite

View full text Add to dashboard Cite

Vendramin GG, and Lascoux M. (2018). Genomic data provides new insights on the demographic history and the extent of recent material transfers in Norway spruce. bioRxiv 402016, ver. 3 peer-reviewed and recommended by PCI Evol Biol. ABSTRACTPrimeval forests are today exceedingly rare in Europe and transfer of forest reproductive material for afforestation and improvement have been very common, especially over the last two centuries. This can be a serious impediment when inferring past population movements in response to past climate changes such as the last glacial maximum (LGM), some 18,000 years ago. In the present study, we genotyped 1,672 individuals from three Picea species (P. abies, P. obovata, and P. omorika) at 400K SNPs using exome capture to infer the past demographic history of Norway spruce and estimate the amount of recent introduction used to establish the Norway spruce breeding program in Southern Sweden. Most of these trees belong to P. abies and originate from the base population of the Swedish breeding program. Others originate from populations across the natural ranges of the three species. Of the 1,499 individuals stemming from the breeding program, a large proportion corresponds to recent introductions. The split of P. omorika occurred 23 million years ago (mya), while the divergence between P. obovata and P. abies began 17.6 mya. Demographic inferences retrieved the same main clusters within P. abies than previous studies, i.e. a vast northern domain ranging from Norway to central Russia, where the species is progressively replaced by Siberian spruce (P. obovata) and two smaller domains, an Alpine domain, and a Carpathian one, but also revealed further subdivision and gene flow among clusters. The three main domains divergence was ancient (15 mya) and all three went through a bottleneck corresponding to the LGM. Approximately 17% of P. abies Nordic domain migrated from P. obovata ~103K years ago, when both species had much larger effective population sizes. Our analysis of genome-wide polymorphism data thus revealed the complex demographic history of Picea genus in Western Europe and highlighted the importance of material transfer in Swedish breeding program.

show abstract

“…GS is a preferred method when studying complex traits that are affected by a large number of genes and are highly influenced by the environment. In the case of forest trees, several QTLs related to various traits of interest have been identified and mapped in association studies, such as growth [ 108 , 109 , 110 , 111 ], flowering components [ 112 , 113 , 114 ], pulpability [ 115 , 116 , 117 ] and wood properties [ 110 , 118 , 119 , 120 , 121 ]. However, effectively, the application of MAS in traits with polygenic inheritance has been limited.…”

Section: Genomic Selection/prediction An Extension Of Blup Methods To Maximize the Predictive Power Of Traits Of Interestmentioning

confidence: 99%

Achievements and Challenges of Genomics-Assisted Breeding in Forest Trees: From Marker-Assisted Selection to Genome Editing

Ahmar

Ballesta²,

Ali

et al. 2021

IJMS

View full text Add to dashboard Cite

Forest tree breeding efforts have focused mainly on improving traits of economic importance, selecting trees suited to new environments or generating trees that are more resilient to biotic and abiotic stressors. This review describes various methods of forest tree selection assisted by genomics and the main technological challenges and achievements in research at the genomic level. Due to the long rotation time of a forest plantation and the resulting long generation times necessary to complete a breeding cycle, the use of advanced techniques with traditional breeding have been necessary, allowing the use of more precise methods for determining the genetic architecture of traits of interest, such as genome-wide association studies (GWASs) and genomic selection (GS). In this sense, main factors that determine the accuracy of genomic prediction models are also addressed. In turn, the introduction of genome editing opens the door to new possibilities in forest trees and especially clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9 (CRISPR/Cas9). It is a highly efficient and effective genome editing technique that has been used to effectively implement targetable changes at specific places in the genome of a forest tree. In this sense, forest trees still lack a transformation method and an inefficient number of genotypes for CRISPR/Cas9. This challenge could be addressed with the use of the newly developing technique GRF-GIF with speed breeding.

show abstract

Association mapping identified novel candidate loci affecting wood formation in Norway spruce

Cited by 10 publications

References 26 publications

An Ultra-Dense Haploid Genetic Map for Evaluating the Highly Fragmented Genome Assembly of Norway Spruce (Picea abies)

An Ultra-Dense Haploid Genetic Map for Evaluating the Highly Fragmented Genome Assembly of Norway Spruce (Picea abies)

Genomic data provides new insights on the demographic history and the extent of recent material transfers in Norway spruce

Achievements and Challenges of Genomics-Assisted Breeding in Forest Trees: From Marker-Assisted Selection to Genome Editing

Contact Info

Product

Resources

About