Molecular Characterisation of a Supergene Conditioning Super-High Vitamin C in Kiwifruit Hybrids
John McCallum,
William Laing,
Sean Bulley,
Susan Thomson,
Andrew Catanach,
Martin Shaw,
Mareike Knaebel,
Jibran Tahir,
Simon Deroles,
Gail Timmerman-Vaughan,
Ross Crowhurst,
Elena Hilario,
Matthew Chisnall,
Robyn Lee,
Richard Macknight,
Alan Seal
Affiliations
John McCallum
New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited, Private Bag 4704, Christchurch 8140, New Zealand
William Laing
New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
Sean Bulley
New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
Susan Thomson
New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited, Private Bag 4704, Christchurch 8140, New Zealand
Andrew Catanach
New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited, Private Bag 4704, Christchurch 8140, New Zealand
Martin Shaw
New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited, Private Bag 4704, Christchurch 8140, New Zealand
Mareike Knaebel
New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
Jibran Tahir
New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
Simon Deroles
New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
Gail Timmerman-Vaughan
New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited, Private Bag 4704, Christchurch 8140, New Zealand
Ross Crowhurst
New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
Elena Hilario
New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
Matthew Chisnall
Biochemistry Department, University of Otago, Dunedin 9054, New Zealand
Robyn Lee
Biochemistry Department, University of Otago, Dunedin 9054, New Zealand
Richard Macknight
Biochemistry Department, University of Otago, Dunedin 9054, New Zealand
Alan Seal
New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited, 412 No 1 Road, RD 2 Te Puke 3182, New Zealand
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.