Targeted re-sequencing and genome-wide association analysis for wood property traits in breeding population of Eucalyptus tereticornis × E. grandis

Dasgupta, Modhumita Ghosh; Bari, Muneera Parveen Abdul; Senthilkumar, Shanmugavel; Dharanishanthi, Veeramuthu; Muthupandi, Muthusamy; Kumar, Naveen; Chauhan, Shakti; Kalaivanan, Jayabharathi; Mohan, Haritha; Krutovsky, Konstantin V.; Rajasugunasekar, D.

doi:10.1016/j.ygeno.2021.11.013

Cited by 9 publications

(4 citation statements)

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“…Research has revealed that XTH remolds the structure and ductility of the cell wall through bond breaking and glycoside rearrangement in xyloglucan chains ( Seale, 2020 ). At present, several XTH genes have been identified to participate in cell wall remodeling in woody plants ( Bourquin et al, 2002 ; Mellerowicz and Sundberg, 2008 ; Nishikubo et al, 2011 ; Sundell et al, 2017 ; Ghosh Dasgupta et al, 2021 ). For example, PttXET16A is involved in the formation of secondary vascular tissue in poplar ( Populus tremula × Populus tremuloides ; Bourquin et al, 2002 ).…”

Section: Introductionmentioning

confidence: 99%

“…Overexpression of PttXET16-34 increases xyloglucan levels in primary-walled xylem and promotes vascular growth and development but decreases in secondary-walled xylem ( Nishikubo et al, 2011 ). XTH activity is positively associated with the Runkel ratio (2 × fiber cell wall thickness/lumen diameter) in Eucalyptus grandis ( Ghosh Dasgupta et al, 2021 ). In addition, researchers have found that the higher the XTH activity during the cell elongation stage in cotton, the longer the fiber becomes ( Michailidis et al, 2009 ; Lee et al, 2010 ; Shao et al, 2011 ).…”

Section: Introductionmentioning

confidence: 99%

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The XTH Gene Family in Schima superba: Genome-Wide Identification, Expression Profiles, and Functional Interaction Network Analysis

Yang

Zhang²,

Zhou³

2022

Front. Plant Sci.

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Xyloglucan endotransglucosylase/hydrolase (XTH), belonging to glycoside hydrolase family 16, is one of the key enzymes in plant cell wall remodeling. Schima superba is an important timber and fireproof tree species in southern China. However, little is known about XTHs in S. superba. In the present study, a total of 34 SsuXTHs were obtained, which were classified into three subfamilies based on the phylogenetic relationship and unevenly distributed on 18 chromosomes. Furthermore, the intron–exon structure and conserved motif composition of them supported the classification and the members belonging to the same subfamily shared similar gene structures. Segmental and tandem duplication events did not lead to SsuXTH gene family expansion, and strong purifying selection pressures during evolution led to similar structure and function of SsuXTH gene family. The interaction network and cis-acting regulatory elements analysis revealed the SsuXTH expression might be regulated by multiple hormones, abiotic stresses and transcription factors. Finally, expression profiles and GO enrichment analysis showed most of the tandem repeat genes were mainly expressed in the phloem and xylem and they mainly participated in glycoside metabolic processes through the transfer and hydrolysis of xyloglucan in the cell wall and then regulated fiber elongation.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

The XTH Gene Family in Schima superba: Genome-Wide Identification, Expression Profiles, and Functional Interaction Network Analysis

Yang

Zhang²,

Zhou³

2022

Front. Plant Sci.

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“…In the Eucalyptus genus, despite its high cost, WGS was applied in some cases ( Kainer et al, 2019 ; Yong et al, 2021 ). RRS has been applied for association studies by using target re-sequencing of specific genes ( Ghosh Dasgupta et al, 2021 ; Candotti et al, 2023 ). Besides, sequence capture, where E. grandis reference genome ( Bartholomé et al, 2014 ; Myburg et al, 2014 ) was used to design probes and capture genomic regions to be sequenced, was evaluated ( de Moraes et al, 2018 ).…”

Section: Discussionmentioning

confidence: 99%

Comparison of ddRADseq and EUChip60K SNP genotyping systems for population genetics and genomic selection in Eucalyptus dunnii (Maiden)

Aguirre,

Villalba,

García

et al. 2024

Front. Genet.

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Eucalyptus dunnii is one of the most important Eucalyptus species for short-fiber pulp production in regions where other species of the genus are affected by poor soil and climatic conditions. In this context, E. dunnii holds promise as a resource to address and adapt to the challenges of climate change. Despite its rapid growth and favorable wood properties for solid wood products, the advancement of its improvement remains in its early stages. In this work, we evaluated the performance of two single nucleotide polymorphism, (SNP), genotyping methods for population genetics analysis and Genomic Selection in E. dunnii. Double digest restriction-site associated DNA sequencing (ddRADseq) was compared with the EUChip60K array in 308 individuals from a provenance-progeny trial. The compared SNP set included 8,011 and 19,008 informative SNPs distributed along the 11 chromosomes, respectively. Although the two datasets differed in the percentage of missing data, genome coverage, minor allele frequency and estimated genetic diversity parameters, they revealed a similar genetic structure, showing two subpopulations with little differentiation between them, and low linkage disequilibrium. GS analyses were performed for eleven traits using Genomic Best Linear Unbiased Prediction (GBLUP) and a conventional pedigree-based model (ABLUP). Regardless of the SNP dataset, the predictive ability (PA) of GBLUP was better than that of ABLUP for six traits (Cellulose content, Total and Ethanolic extractives, Total and Klason lignin content and Syringyl and Guaiacyl lignin monomer ratio). When contrasting the SNP datasets used to estimate PAs, the GBLUP-EUChip60K model gave higher and significant PA values for six traits, meanwhile, the values estimated using ddRADseq gave higher values for three other traits. The PAs correlated positively with narrow sense heritabilities, with the highest correlations shown by the ABLUP and GBLUP-EUChip60K. The two genotyping methods, ddRADseq and EUChip60K, are generally comparable for population genetics and genomic prediction, demonstrating the utility of the former when subjected to rigorous SNP filtering. The results of this study provide a basis for future whole-genome studies using ddRADseq in non-model forest species for which SNP arrays have not yet been developed.

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“…GWAS for complex traits has made significant progress not only in broad-leaved species such as poplar and eucalyptus [ 8 ], but also in coniferous species such as pine [ 2 , 9 ] and Picea abies [ 10 ]. Intriguingly, family-based GWAS designs, which could reduce bias in the estimates of direct genetic effects, have been developed and successfully applied to humans [ 11 ], chrysanthemum [ 12 ], and eucalyptus [ 13 ].…”

Section: Introductionmentioning

confidence: 99%

Association Mapping and Expression Analysis of the Genes Involved in the Wood Formation of Poplar

Wang

Zhang

Zhu

et al. 2023

IJMS

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Xylogenesis is a complex and sequential biosynthetic process controlled by polygenes. Deciphering the genetic architecture of this complex quantitative trait could provide valuable information for increasing wood biomass and improving its properties. Here, we performed genomic resequencing of 64 24-year-old trees (64 hybrids of section Aigeiros and their parents) grown in the same field and conducted full-sib family-based association analyses of two growth and six woody traits using GEMMA as a choice of association model selection. We identified 1342 significantly associated single nucleotide polymorphisms (SNPs), 673 located in the region upstream and downstream of 565 protein-encoding genes. The transcriptional regulation network of secondary cell wall (SCW) biosynthesis was further constructed based on the published data of poplar miRNA, transcriptome, and degradome. These provided a certain scientific basis for the in-depth understanding of the mechanism of poplar timber formation and the molecular-assisted breeding in the future.

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Targeted re-sequencing and genome-wide association analysis for wood property traits in breeding population of Eucalyptus tereticornis × E. grandis

Cited by 9 publications

References 147 publications

The XTH Gene Family in Schima superba: Genome-Wide Identification, Expression Profiles, and Functional Interaction Network Analysis

The XTH Gene Family in Schima superba: Genome-Wide Identification, Expression Profiles, and Functional Interaction Network Analysis

Comparison of ddRADseq and EUChip60K SNP genotyping systems for population genetics and genomic selection in Eucalyptus dunnii (Maiden)

Association Mapping and Expression Analysis of the Genes Involved in the Wood Formation of Poplar

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