First simple sequence repeat-based genetic linkage map reveals a major QTL for leafing time in walnut (Juglans regia L.)

Kefayati, Sina; Ikhsan, Adi Surya; Sütyemez, Mehmet; Paizila, Aibibula; Topçu, Hayat; Bükücü, Şakir Burak; Kafkas, Salih

doi:10.1007/s11295-019-1318-9

Cited by 21 publications

(23 citation statements)

References 55 publications

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“…For the first time, it was possible to explore the gene space of Persian walnut with the prediction of 32,498 gene models, providing the basis to untangle complex phenotypic pathways, such as those responsible for the synthesis of phenolic compounds. The availability of a reference genome marked the beginning of a genomics phase in Persian walnut, allowing whole-genome resequencing (Stevens et al 2018; Zhang et al 2019), the development of high-density genotyping tools (Marrano et al 2018; Kefayati et al 2018) and the genetic dissection of important agronomical traits in walnut (Arab et al 2019; Famula et al 2019; Marrano et al 2019). However, the Chandler v1.0 assembly is highly fragmented, compromising the accuracy of gene prediction and the fulfillment of advanced genomics studies necessary to resolve many, still unanswered questions in walnut research.…”

Section: Introductionmentioning

confidence: 99%

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

Marrano

Britton

Zaini

et al. 2019

Preprint

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27The release of the first reference genome of walnut (Juglans regia L.) enabled many achievements 28 in the characterization of walnut genetic and functional variation. However, it is highly 29 fragmented, preventing the integration of genetic, transcriptomic, and proteomic information to 30 fully elucidate walnut biological processes. Here we report the new chromosome-scale assembly 31 of the walnut reference genome (Chandler v2.0) obtained by combining Oxford Nanopore long-32 read sequencing with chromosome conformation capture (Hi-C) technology. Relative to the 33 previous reference genome, the new assembly features an 84.4-fold increase in N50 size, and the 34 full sequence of all 16 chromosomal pseudomolecules, nine of which present telomere sequences 35 at both ends. Using full-length transcripts from single-molecule real-time sequencing, we predicted 36 40,491 gene models, with a mean gene length higher than the previous gene annotations. Most of 37 the new protein-coding genes (90%) are full-length, which represents a significant improvement 38 compared to Chandler v1.0 (only 48%). We then tested the potential impact of the new 39 chromosome-level genome on different areas of walnut research. By studying the proteome 40 changes occurring during catkin development, we observed that the virtual proteome obtained 41 from Chandler v2.0 presents fewer artifacts than the previous reference genome, enabling the 42 identification of a new potential pollen allergen in walnut. Also, the new chromosome-scale 43 genome facilitates in-depth studies of intraspecies genetic diversity by revealing previously 44 undetected autozygous regions in Chandler, likely resulting from inbreeding, and 195 genomic 45 regions highly differentiated between Western and Eastern walnut cultivars. Overall, Chandler 46 v2.0 is a valuable resource to understand and explore walnut biology better.47 48Persian walnut (Juglans regia L.) is among the top three most-consumed nuts in the world, and 50 over the last ten years, its global production increased by 37% (International Nut and Dried Fruit 51

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Section: Introductionmentioning

confidence: 99%

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

Marrano

Britton

Zaini

et al. 2019

Preprint

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“…In addition, we obtained some small linkage groups, the same as in Juglans regia [31]. These phenomena have been found in many species [16,18,31,33,40,41] and indicate that some gaps prevent connection between linkage groups belonging to the same chromosome, which needs to be optimised in the future by expanding mapping population, increasing parental combinations and adopting new markers. By contrast with the variety of mapping populations in crops [42,43], the growth cycle of trees was long, and the genetic offspring was difficult to be obtained.…”

Section: Genetic Linkage Mapmentioning

confidence: 52%

“…Hence, the F1 progenies showed a rapid increase in tree height, ground diameter and crown diameter after adapting to the new environment. However, the slow growth of 9a (2018) and 10a (2019), especially the stagnant growth of crown diameter, may have been caused by the limited growth space, indicating that the phenotype was decided by the interaction of genotype and environment [31]. The research objects in this experiment were decennial high trees with a massive root system.…”

Section: Growth Traitsmentioning

confidence: 99%

“…The markers used in this study were also obtained from the transcriptome database, and 4.87% segregation distortion (SD) were detected, which was lower than for Castanea sativa (sweet chesnut) [18], Populus spp. (poplar) [30], Juglans regia (walnut) [31], Ziziphus jujuba (jujube) [32] and Citrus clementina (clement pomelo) [33]. Segregation distortion is a common problem in population mapping, and a number of variables could have led to SD [34][35][36][37][38].…”

Section: Ssr Marker and Segregation Distortionmentioning

confidence: 99%

“…The number of linkage groups (the mapped marker number was over 15) in the E. ulmoides linkage map was updated from 13 to 19 [21], which was larger than the chromosome haploid number (17). In addition, we obtained some small linkage groups, the same as in Juglans regia [31]. These phenomena have been found in many species [16,18,31,33,40,41] and indicate that some gaps prevent connection between linkage groups belonging to the same chromosome, which needs to be optimised in the future by expanding mapping population, increasing parental combinations and adopting new markers.…”

Section: Genetic Linkage Mapmentioning

confidence: 99%

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Update of Genetic Linkage Map and QTL Analysis for Growth Traits in Eucommia ulmoides Oliver

Jin

et al. 2020

Forests

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Eucommia ulmoides (Tu-chung) is an economically and ecologically important tree species which has attracted worldwide attention due to its application in pharmacology, landscaping, wind sheltering and sand fixation. Molecular marker technologies can elucidate the genetic mechanism and substantially improve the breeding efficiency of E. ulmoides. The current research updated the original linkage map, and quantitative trait loci (QTL) analysis was performed on tree growth traits measured over 10 consecutive years in an E. ulmoides F1 population (“Xiaoye” × “Qinzhong No.1”). In total, 452 polymorphic markers were scored from 365 simple sequence repeat (SSR) primers, with an average of 1.24 polymorphic markers per primer combination. The integrated map was 1913.29 cM (centimorgan) long, covering 94.10% of the estimated genome and with an average marker density of 2.20 cM. A total of 869 markers were mapped into 19 major independent linkage groups. Growth-related traits measured over 10 consecutive years showed a significant correlation, and 89 hypothetical QTLs were forecasted and divided into 27 distinct loci. Three traits for tree height, ground diameter and crown diameter detected 25 QTLs (13 loci), 32 QTLs (17 loci) and 15 QTLs (10 loci), respectively. Based on BLASTX search results in the NCBI database, six candidate genes were obtained. It is important to explore the growth-related genetic mechanism and lay the foundation for the genetic improvement of E. ulmoides at the molecular level.

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The Pomological Diversity of F1 Walnut (Juglans regia L.) Progenies and Differences Between Their Parents

Bükücü

2022

Erwerbs-Obstbau

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First simple sequence repeat-based genetic linkage map reveals a major QTL for leafing time in walnut (Juglans regia L.)

Cited by 21 publications

References 55 publications

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

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

Update of Genetic Linkage Map and QTL Analysis for Growth Traits in Eucommia ulmoides Oliver

The Pomological Diversity of F1 Walnut (Juglans regia L.) Progenies and Differences Between Their Parents

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