Multiple quantitative trait loci contribute tolerance to bacterial canker incited byPseudomonas syringaepv.actinidiaein kiwifruit (Actinidia chinensis)

Tahir, Jibran; Gardiner, Susan E.; Hoyte, S.M.; Bassett, H.; Brendolise, Cyril; Chatterjee, Abhishek; Templeton, Kerry; Deng, Cecilia; Crowhurst, Ross N.; Montefiori, Mirco; Morgan, E.R.; Wotton, Andrew; Funnell, Keith A.; Wiedow, Claudia; Knaebel, Mareike; Hedderley, Duncan I.; Vanneste, J. L.; McCallum, John; Hoeata, K.; Chagné, David; Gea, L. D.

doi:10.1101/526798

Cited by 2 publications

(6 citation statements)

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“…Inspection of chromosome 26 repeat density and recombination estimates from genetic mapping [15] shows that the location of qAsA26.1 coincides with the boundary of a region with high repeat density and lower recombination (Figure 7). Alignment of the chromosome 26 pseudomolecules from the assemblies of A. chinensis ‘Red5’ [4] and the A. eriantha ‘White’ [3] indicate that these are highly collinear apart from differences in the terminal repeat-rich region (Figure A1).…”

Section: Resultsmentioning

confidence: 99%

“…This data is from a single time point in an orchard environment and we expect it would be highly influenced by local variability in infection by the pandemic Pseudomonas syringae var. Actinidiae [15,23]. Targeted metabolomic analyses of fruit and vine tissues with standards, especially for antioxidant and key carbohydrates is desirable to better characterise the phenotype of qAsA26.1 alleles.…”

Section: Resultsmentioning

confidence: 99%

“…LTR retrotransposons were annotated using LTRHarvest [49]. Recombination distances for chromosome 26 were determined using Joinmap3 () from genotyping by sequencing data used to construct a genetic linkage map in the ‘Hort16A × P1’ family (N = 236) [15].…”

Section: Methodsmentioning

confidence: 99%

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Molecular Characterisation of a Supergene Conditioning Super-High Vitamin C in Kiwifruit Hybrids

McCallum

Laing

Bulley

et al. 2019

Plants

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During analysis of kiwifruit derived from hybrids between the high vitamin C (ascorbic acid; AsA) species Actinidia eriantha and A. chinensis, we observed bimodal segregation of fruit AsA concentration suggesting major gene segregation. To test this hypothesis, we performed whole-genome sequencing on pools of hybrid genotypes with either high or low AsA fruit. Pool-GWAS (genome-wide association study) revealed a single Quantitative Trait Locus (QTL) spanning more than 5 Mbp on chromosome 26, which we denote as qAsA26.1. A co-dominant PCR marker was used to validate this association in four diploid (A. chinensis × A. eriantha) × A. chinensis backcross families, showing that the A. eriantha allele at this locus increases fruit AsA levels by 250 mg/100 g fresh weight. Inspection of genome composition and recombination in other A. chinensis genetic maps confirmed that the qAsA26.1 region bears hallmarks of suppressed recombination. The molecular fingerprint of this locus was examined in leaves of backcross validation families by RNA sequencing (RNASEQ). This confirmed strong allelic expression bias across this region as well as differential expression of transcripts on other chromosomes. This evidence suggests that the region harbouring qAsA26.1 constitutes a supergene, which may condition multiple pleiotropic effects on metabolism.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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Molecular Characterisation of a Supergene Conditioning Super-High Vitamin C in Kiwifruit Hybrids

McCallum

Laing

Bulley

et al. 2019

Plants

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Section: Untargetted Metabolomicsmentioning

confidence: 99%

“…(https://www.kyazma.nl/index.php/JoinMap/) from GBS genotyping data used to construct a genetic linkage map in the 'Hort16A x P1' family (N=236) [16].…”

Section: Sequencing Data Processingmentioning

confidence: 99%

Molecular Characterization of a Supergene Conditioning Super-High Vitamin C in Kiwifruit Hybrids

McCallum¹,

Laing²,

Bulley³

et al. 2019

Preprint

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During analysis of kiwifruit derived from hybrids between the high AsA species Actinidia eriantha and A. chinensis var chinensis, we observed bimodal segregation of fruit AsA concentration suggesting major gene segregation. To test this hypothesis we performed whole-genome sequencing on pools of high and low AsA fruit from tetraploid A. chinensis var. deliciosa x A. eriantha backcross families. Pool-GWAS revealed a single QTL spanning more than 5 Mbp on chromosome 26, which we denote as qAsA26.1. A co-dominant PCR marker was used to validate this association in four diploid (A. chinensis x A. eriantha) x A. chinensis backcross families, showing that the eriantha allele at this locus increases fruit AsA levels by 250 mg/100 g fresh weight. Inspection of genome composition and recombination in other A. chinensis genetic maps confirmed that the qAsA26.1 region bears hallmarks of suppressed recombination. The molecular fingerprint of this locus was examined in leaves of backcross validation families by RNASEQ. This confirmed strong allelic expression bias across this region as well as differential expression of transcripts on other chromosomes. This evidence suggests that the region harboring qAsA26.1 constitutes a supergene, which may condition multiple pleiotropic effects on metabolism.

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Multiple quantitative trait loci contribute tolerance to bacterial canker incited byPseudomonas syringaepv.actinidiaein kiwifruit (Actinidia chinensis)

Abstract: 1 incited by Pseudomonas syringae pv. actinidiae in kiwifruit (Actinidia 2 chinensis) 3 4

Cited by 2 publications

References 86 publications

Molecular Characterisation of a Supergene Conditioning Super-High Vitamin C in Kiwifruit Hybrids

Molecular Characterisation of a Supergene Conditioning Super-High Vitamin C in Kiwifruit Hybrids

Molecular Characterization of a Supergene Conditioning Super-High Vitamin C in Kiwifruit Hybrids

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