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

Abstract

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.

Kiwifruit MYBS1‐like and GBF3 transcription factors influence l‐ascorbic acid biosynthesis by activating transcription of GDP‐L‐galactose phosphorylase 3

“…There is very similar MYBS1 on chr26 which lies within the recently identified high AsA quantitative trait loci (QTL) interval (McCallum et al, 2019) but it has much lower expression than the chr16 AeMYBS1 gene described here. The high similarity suggests that it might also activate GGP transcription and the A. eriantha allele has some interesting polymorphisms which could alter its TF properties (data not presented here).…”

“…Examples of these AsA superfruits include some species of the Actinidia genus (kiwifruit), Rosa roxburghii (chestnut rose), Myrciaria dubia (camu–camu) (Castro et al ., 2015), Terminalia ferdinandiana (Kakadu plum) and Malpighia glabra (acerola) (Badejo et al ., 2007). Indeed the high AsA trait carried by A. eriantha recently has been mapped to chromosome 26 and segregates as a large nonrecombinant portion of chromosome in A. eriantha × A. deliciosa × A. chinensis hybrids (McCallum et al ., 2019).…”

Regulation of Plant Vitamin Metabolism: Backbone of Biofortification for the Alleviation of Hidden Hunger

“…In recent years, scientists have made some progress in mapping vitamin accumulation QTLs, including one metabolic QTL (mQTL) for vitB6 in the model grass Brachypodium distachyon (Onda et al, 2019); two QTLs for vitB9 in maize (Guo et al, 2019); and single-nucleotide polymorphism markers for vitB9 in potato (Bali et al, 2018) and pea (Jha et al, 2020). Moreover, some new candidate genes/QTLs that participate in vitC biosynthesis have been identified, e.g., the b subunit of pyrophosphatefructose 6-phosphate 1-phosphotransferase (Calafiore et al, 2019), the transcription factor SlbHLH59 (Ye et al, 2019), and a single QTL in kiwifruit (McCallum et al, 2019). It is conceivable that new information about vitamin metabolism will accompany the identification of new genes discovered by QTL mapping.…”

First Chromosome-Scale Assembly and Deep Floral-Bud Transcriptome of a Male Kiwifruit

“…With its center of origin and distribution in south-central and southeast China ( Huang, 2016 ), kiwifruit was originally referred to as “Monkey Peach” or Mihoutao. High vitamin C content ( McCallum et al, 2019 ) combined with exquisitely diverse flavors and pigment contents ( Zhang et al, 2017 ) are among the top breeding targets ( Webby et al, 1994 ; Laing et al, 2007 ; Ampomah-Dwamena et al, 2009 ; Montefiori et al, 2011 ) for today’s billion-dollar kiwifruit industry.…”