High-quality chromosome-scale assembly of the walnut (<i>Juglans regia</i>L) reference genome

Marrano, Annarita; Britton, Monica; Zaini, Paulo A.; Zimin, Aleksey V.; Workman, Rachael E.; Puiu, Daniela; Bianco, Luca; Pierro, Erica A. Di; Allen, Brian; Chakraborty, Sandeep; Troggio, Michela; Leslie, Charles A.; Timp, Winston; Dandekar, Abhaya M.; Salzberg, Steven L.; Neale, David B.

doi:10.1101/809798

Cited by 16 publications

(25 citation statements)

References 87 publications

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“…Candidate genes for bearing habit and phenology-related traits using the walnut genome By combining GWAS and QTL results and considering their consistency over phenotypic datasets, we decided to focus on a robust subset of eight loci to find candidate genes for bearing habit and phenology-related traits ( Table 5). Using HaploView v4.2 software and the new chromosome-scale reference walnut genome v2.0 [36], several interesting coding sequences were found within the defined Linkage Disequilibrium (LD) blocks for different traits. The SNP 'AX-171557178' on Chr2 and associated with budbreak date, falls within a candidate gene encoding for a putative BPI/LBP family protein At1g04970.…”

Section: Association and Linkage Mapping For Heterodichogamy And Malementioning

confidence: 99%

“…Maybe because our progeny is too small or because of segregation distorsion, we did not observe any terminal bearing individuals. Gene annotations may give clues to dissect genetic control of flowering process Availability of the new chromosome-scale reference genome Chandler v2.0 [36] allowed us to explore the gene space surrounding the most significant marker-trait associations identified for bearing habit and phenology. For instance, we found the chromosome transmission fidelity (ctf) protein 8 homolog gene as candidate gene for all female flowering dates.…”

Section: Genetic Bases For the Expression Of Lateral Bearingmentioning

confidence: 99%

“…The LD blocks were investigated using the method of confidence interval [75], and "solid spine of LD" method, in which the first and last SNPs in a block are in strong LD with all intermediate markers but the intermediate ones are not necessarily in LD with each other. The identified LD blocks were then searched for candidate genes using RefSeq walnut gene annotation (https://www.ncbi.nlm.nih.gov/genome/annotation_ euk/Juglans_regia/100/) and mapped onto the new chromosome-scale reference genome v2.0 [36] (https:// www.hardwoodgenomics.org/Genomeassembly/253906 9).…”

Section: Search Of Annotations Within Ld Blocks Of Associated Locimentioning

confidence: 99%

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Association and linkage mapping to unravel genetic architecture of phenological traits and lateral bearing in Persian walnut (Juglans regia L.)

et al. 2020

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Background: Unravelling the genetic architecture of agronomic traits in walnut such as budbreak date and bearing habit, is crucial for climate change adaptation and yield improvement. A Genome-Wide Association Study (GWAS) using multi-locus models was conducted in a panel of 170 walnut accessions genotyped using the Axiom™ J. regia 700 K SNP array, with phenological data from 2018, 2019 and legacy data. These accessions come from the INRAE walnut germplasm collection which is the result of important prospecting work performed in many countries around the world. In parallel, an F 1 progeny of 78 individuals segregating for phenology-related traits, was genotyped with the same array and phenotyped for the same traits, to construct linkage maps and perform Quantitative Trait Loci (QTLs) detection.Results: Using GWAS, we found strong associations of SNPs located at the beginning of chromosome 1 with both budbreak and female flowering dates. These findings were supported by QTLs detected in the same genomic region. Highly significant associated SNPs were also detected using GWAS for heterodichogamy and lateral bearing habit, both on chromosome 11. We developed a Kompetitive Allele Specific PCR (KASP) marker for budbreak date in walnut, and validated it using plant material from the Walnut Improvement Program of the University of California, Davis, demonstrating its effectiveness for marker-assisted selection in Persian walnut. We found several candidate genes involved in flowering events in walnut, including a gene related to heterodichogamy encoding a sugar catabolism enzyme and a cell division related gene linked to female flowering date. Conclusions: This study enhances knowledge of the genetic architecture of important agronomic traits related to male and female flowering processes and lateral bearing in walnut. The new marker available for budbreak date, one of the most important traits for good fruiting, will facilitate the selection and development of new walnut cultivars suitable for specific climates.

show abstract

Section: Association and Linkage Mapping For Heterodichogamy And Malementioning

confidence: 99%

Section: Genetic Bases For the Expression Of Lateral Bearingmentioning

confidence: 99%

Section: Search Of Annotations Within Ld Blocks Of Associated Locimentioning

confidence: 99%

See 1 more Smart Citation

Association and linkage mapping to unravel genetic architecture of phenological traits and lateral bearing in Persian walnut (Juglans regia L.)

et al. 2020

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show abstract

“…Availability of the new chromosome-scale reference genome Chandler v2.0 [36] allowed us to explore the gene space surrounding the most significant marker-trait associations identified for bearing habit and phenology. For instance, we found the chromosome transmission fidelity (ctf) protein 8 homolog gene as candidate gene for all female flowering dates.…”

Section: Gene Annotations May Give Clues To Dissect Genetic Control Omentioning

confidence: 99%

Association and Linkage Mapping to Unravel Genetic Architecture of Phenological Traits and Lateral Bearing in Persian Walnut (Juglans regia L.)

Bernard

Marrano

Donkpegan

et al. 2020

Preprint

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Background: Unravelling the genetic architecture of agronomic traits in walnut such as budbreak date and bearing habit, is crucial for climate change adaptation and yield improvement. A Genome-Wide Association Study (GWAS) using multi-locus models was conducted in a panel of 170 walnut accessions genotyped using the Axiom™ J. regia 700K SNP array, with phenological data from 2018, 2019 and legacy data. These accessions come from the INRAE walnut germplasm collection which is the result of important prospecting work performed in many countries around the world. In parallel, an F 1 progeny of 78 individuals segregating for phenology-related traits, was genotyped with the same array and phenotyped for the same traits, to construct linkage maps and perform Quantitative Trait Loci (QTLs) detection. Results: Using GWAS, we found strong associations of SNPs located at the beginning of chromosome 1 with both budbreak and female flowering dates. These findings were supported by QTLs detected in the same genomic region. Highly significant associated SNPs were also detected using GWAS for heterodichogamy and lateral bearing habit, both on chromosome 11. We developed a Kompetitive Allele Specific PCR (KASP) marker for budbreak date in walnut, and validated it using plant material from the Walnut Improvement Program of the University of California, Davis, demonstrating its effectiveness for marker-assisted selection in Persian walnut. We found several candidate genes involved in flowering events in walnut, including a gene related to heterodichogamy encoding a sugar catabolism enzyme and a cell division related gene linked to female flowering date. Conclusions: This study enhances knowledge of the genetic architecture of important agronomic traits related to male and female flowering processes and lateral bearing in walnut. The new marker available for budbreak date, one of the most important traits for good fruiting, will facilitate the selection and development of new walnut cultivars suitable for specific climates.

show abstract

“…Availability of the new chromosome-scale reference genome Chandler v2.0 [30] allowed us to explore the gene space surrounding the most significant marker-trait associations identified for bearing habit and phenology. For instance, we found the chromosome transmission fidelity (ctf) protein 8 homolog gene as candidate gene for all female flowering dates.…”

Section: Gene Annotations May Give Clues To Dissect Genetic Control Omentioning

confidence: 99%

Association and Linkage Mapping to Unravel Genetic Architecture of Phenology-Related Traits and Lateral Bearing in Persian Walnut (Juglans regia L.)

Bernard

Marrano

Donkpegan

et al. 2019

Preprint

Self Cite

View full text Add to dashboard Cite

Background: Unravelling the genetic architecture of agronomic traits in walnut such as budbreak date and bearing habit, is crucial for climate change adaptation and yield improvement. A Genome-Wide Association Study (GWAS) using multi-locus models was conducted in a panel of 170 walnut accessions genotyped using the Axiom™ J. regia 700K SNP array, with phenological data from several years. These accessions come from the INRAE walnut germplasm collection which is the result of important prospecting work performed in many countries around the world. In parallel, an F1 progeny of 78 individuals segregating for phenology-related traits, was genotyped with the same array and phenotyped for the same traits, to construct linkage maps and perform Quantitative Trait Loci (QTLs) detection. Results: Using GWAS, we found strong associations of SNPs located at the beginning of chromosome 1 with both budbreak and female flowering dates. These findings were supported by QTLs detected in the same genomic region. Highly significant associated SNPs were also detected using GWAS for heterodichogamy and lateral bearing habit, both on chromosome 11. We developed a Kompetitive Allele Specific PCR (KASP) marker for budbreak date in walnut, and validated it using plant material from the Walnut Improvement Program of the University of California, Davis, demonstrating its effectiveness for marker-assisted selection in Persian walnut. We found several candidate genes involved in flowering events in walnut, including a gene related to heterodichogamy encoding a sugar catabolism enzyme and a cell division related gene linked to female flowering date. Conclusions: This study enhances knowledge of the genetic architecture of important agronomic traits related to male and female flowering processes and lateral bearing in walnut. The new marker available for budbreak date, the first key trait for good fruiting, will facilitate the selection and development of new walnut cultivars suitable for specific climates.

show abstract

High-quality chromosome-scale assembly of the walnut (Juglans regiaL) reference genome

Cited by 16 publications

References 87 publications

Association and linkage mapping to unravel genetic architecture of phenological traits and lateral bearing in Persian walnut (Juglans regia L.)

Association and linkage mapping to unravel genetic architecture of phenological traits and lateral bearing in Persian walnut (Juglans regia L.)

Association and Linkage Mapping to Unravel Genetic Architecture of Phenological Traits and Lateral Bearing in Persian Walnut (Juglans regia L.)

Association and Linkage Mapping to Unravel Genetic Architecture of Phenology-Related Traits and Lateral Bearing in Persian Walnut (Juglans regia L.)

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