A fine‐scale genetic linkage map reveals genomic regions associated with economic traits in walnut (<i>Juglans regia</i>)

Aradhya, Mallikarjuna K.; Velasco, Dianne; Wang, Ji‐Rui; Ramasamy, Ramesh; You, Frank M.; Leslie, Chuck; Dandekar, Abhaya M.; Luo, Ming‐Cheng; Dvořák, Jan

doi:10.1111/pbr.12703

Cited by 11 publications

(9 citation statements)

References 28 publications

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“…Using a large F 2 progeny from 'Chandler', a lateral bearing cultivar heterozygous for this locus, the genetic basis of lateral fruitfulness was found to be located in the centromeric region of Chr11 [29]. The same location was obtained using F 1 progeny from 'Chandler' by 'Idaho' cross [43]. Additional associations for lateral bearing were found using GWAS in a region covering 25 Mb on Chr11, and a major QTL was detected in 'Chandler' in proximity to the centromeric region (peak at 17,341,634 bp) of Chr11 [35].…”

Section: Genetic Bases For the Expression Of Lateral Bearingmentioning

confidence: 90%

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.

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Section: Genetic Bases For the Expression Of Lateral Bearingmentioning

confidence: 90%

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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“…Serr maps, in addition to being longer than the J. microcarpa maps, also exceeded the lengths of the maps of J. regia cv. Chandler published earlier 5 , 20 , 24 . Chandler, like the J. microcarpa mother trees 31.01 and 31.09, was used as the female parent.…”

Section: Discussionmentioning

confidence: 98%

Co-located quantitative trait loci mediate resistance to Agrobacterium tumefaciens, Phytophthora cinnamomi, and P. pini in Juglans microcarpa × J. regia hybrids

et al. 2021

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Soil-borne plant pathogens represent a serious threat that undermines commercial walnut (Juglans regia) production worldwide. Crown gall, caused by Agrobacterium tumefaciens, and Phytophthora root and crown rots, caused by various Phytophthora spp., are among the most devastating walnut soil-borne diseases. A recognized strategy to combat soil-borne diseases is adoption of resistant rootstocks. Here, resistance to A. tumefaciens, P. cinnamomi, and P. pini is mapped in the genome of Juglans microcarpa, a North American wild relative of cultivated walnut. Half-sib J. microcarpa mother trees DJUG 31.01 and DJUG 31.09 were crossed with J. regia cv. Serr, producing 353 and 400 hybrids, respectively. Clonally propagated hybrids were genotyped by sequencing to construct genetic maps for the two populations and challenged with the three pathogens. Resistance to each of the three pathogens was mapped as a major QTL on the long arm of J. microcarpa chromosome 4D and was associated with the same haplotype, designated as haplotype b, raising the possibility that the two mother trees were heterozygous for a single Mendelian gene conferring resistance to all three pathogens. The deployment of this haplotype in rootstock breeding will facilitate breeding of a walnut rootstock resistant to both crown gall and Phytophthora root and crown rots.

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“…Using a large F 2 progeny from 'Chandler', a lateral bearing cultivar heterozygous for this locus, the genetic basis of lateral fruitfulness was found to be located in the centromeric region of Chr11 [23]. The same location was obtained using F 1 progeny from 'Chandler' by 'Idaho' cross [37]. Additional associations for lateral bearing were found using GWAS in a region covering 25 Mb on Chr11, and a major QTL was detected in 'Chandler' in proximity to the centromeric region (peak at 17,341,634 bp) of Chr11 [29].…”

Section: Genetic Bases For the Expression Of Lateral Bearingmentioning

confidence: 90%

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

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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 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

A fine‐scale genetic linkage map reveals genomic regions associated with economic traits in walnut (Juglans regia)

Cited by 11 publications

References 28 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.)

Co-located quantitative trait loci mediate resistance to Agrobacterium tumefaciens, Phytophthora cinnamomi, and P. pini in Juglans microcarpa × J. regia hybrids

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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