Two large-effect QTLs, Ma and Ma3, determine genetic potential for acidity in apple fruit: breeding insights from a multi-family study

Verma, Sujeet; Evans, Kate; Guan, Yingzhu; Luby, James J.; Rosyara, Umesh R.; Howard, Nicholas P.; Bassil, Nahla V.; Bink, M.C.A.M.; Weg, Eric van de; Peace, Cameron

doi:10.1007/s11295-019-1324-y

Cited by 60 publications

(102 citation statements)

References 70 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…5). These data confirm the relationship between Ma1 genotypes and fruit acidity and the incomplete dominance of Ma1 over ma1 reported earlier (Bai et al, 2012;Xu et al, 2012) and from subsequent investigations by other groups on different segregating populations (Khan et al, 2013;Jia et al, 2018;Verma et al, 2019) as well as over a wide range of Malus accessions (Ma et al, 2015). In addition, RNAi suppression of Ma1 expression in 'McIntosh' apple leaves, 'Empire' apple fruit, and 'Orin' calli significantly decreased the malate level ( Fig.…”

Section: Premature Stop Codon-led Mutation Is Genetically Responsiblesupporting

confidence: 89%

“…Third, a QTL originally identified in the cross 'Fiesta' 3 'Discovery' on linkage group 8 was recently confirmed in pedigree-connected germplasm of 16 full-sib families representing nine important breeding parents. This QTL was named Ma3 and also plays a significant role in determining malate accumulation in apple (Liebhard et al, 2003;Verma et al, 2019). Ma3 and Ma1 follow an additive allele dosage model and jointly explain about 66% of the variation in apple fruit acidity (Verma et al, 2019).…”

Section: Premature Stop Codon-led Mutation Is Genetically Responsiblementioning

confidence: 99%

“…Based on a strong association between a mutation-led truncation in the C-terminal end of Ma1 and low fruit acidity in apple (Bai et al, 2012) and subsequent genotyping and phenotyping of segregating populations and Malus spp. germplasm (Khan et al, 2013;Ma et al, 2015;Jia et al, 2018;Verma et al, 2019), we hypothesized that the truncated version of Ma1, ma1, has significantly lower malate transport activity than the full-length protein Ma1. In this work, we compare the functionality of Ma1 and ma1 expressed both in Xenopus laevis oocytes and Nicotiana benthamiana cells.…”

mentioning

confidence: 98%

See 2 more Smart Citations

Apple ALMT9 Requires a Conserved C-Terminal Domain for Malate Transport Underlying Fruit Acidity

Dougherty

Coluccio

et al. 2019

Plant Physiol.

View full text Add to dashboard Cite

Malate accumulation in the vacuole largely determines apple (Malus domestica) fruit acidity, and low fruit acidity is strongly associated with truncation of Ma1, an ortholog of ALUMINUM-ACTIVATED MALATE TRANSPORTER9 (ALMT9) in Arabidopsis (Arabidopsis thaliana). A mutation at base 1,455 in the open reading frame of Ma1 leads to a premature stop codon that truncates the protein by 84 amino acids at its C-terminal end. Here, we report that both the full-length protein, Ma1, and its naturally occurring truncated protein, ma1, localize to the tonoplast; when expressed in Xenopus laevis oocytes and Nicotiana benthamiana cells, Ma1 mediates a malate-dependent inward-rectifying current, whereas the ma1-mediated transmembrane current is much weaker, indicating that ma1 has significantly lower malate transport activity than Ma1. RNA interference suppression of Ma1 expression in 'McIntosh' apple leaves, 'Empire' apple fruit, and 'Orin' apple calli results in a significant decrease in malate level. Genotyping and phenotyping of 186 apple accessions from a diverse genetic background of 17 Malus species combined with the functional analyses described above indicate that Ma1 plays a key role in determining fruit acidity and that the truncation of Ma1 to ma1 is genetically responsible for low fruit acidity in apple. Furthermore, we identified a C-terminal domain conserved in all tonoplast-localized ALMTs essential for Ma1 function; protein truncations into this conserved domain significantly lower Ma1 transport activity. We conclude that the truncation of Ma1 to ma1 reduces its malate transport function by removing a conserved C-terminal domain, leading to low fruit acidity in apple.

show abstract

Section: Premature Stop Codon-led Mutation Is Genetically Responsiblesupporting

confidence: 89%

Section: Premature Stop Codon-led Mutation Is Genetically Responsiblementioning

confidence: 99%

mentioning

confidence: 98%

See 1 more Smart Citation

Apple ALMT9 Requires a Conserved C-Terminal Domain for Malate Transport Underlying Fruit Acidity

Dougherty

Coluccio

et al. 2019

Plant Physiol.

View full text Add to dashboard Cite

show abstract

“…The approach can potentially increase the QTL detection power and the accuracy of QTL positioning (Liu, Reif, Ranc, Porta, & Wurschum, 2012) and provide knowledge that is more applicable to marker-assisted selection on critical loci and alleles over a range of genetic backgrounds (Bink et al, 2014). Verma et al (2019) and van de Weg et al (2018) identified large-effect QTLs determining the acidity and resistance to fire blight in apple fruit (Malus spp. ), respectively.…”

Section: Introductionmentioning

confidence: 99%

Efficiency of Bayesian quantitative trait loci mapping with full‐sib progeny

et al. 2020

View full text Add to dashboard Cite

Quantitative trait loci (QTL) mapping with perennial crops is based on one or more full‐sib progeny because homozygous genotypes are difficult to obtain. The objective of this study was to assess the efficiency of Bayesian QTL mapping with full‐sib progeny. The analyses used two simulated data sets, one assuming genotyping for 292 simple sequence repeats (SSR) loci (density of 10 cM) and the other assuming genotyping for 2969 single nucleotide polymorphisms (SNPs) (density of 1 cM). Each data set consisted of 50 replications of 40 full‐sib progeny of size 400. We assumed a broad sense heritability of 60%, genetic control by 10 QTLs and 90 minor genes, and positive dominance. The QTL heritability values ranged from 1 to 12%. The scenarios included one and multiple progeny. In the best scenarios for the low (four progeny of size 400) and high marker density (one progeny of size 400), the average power of detection was 52 and 67% for the low heritability QTLs, 83 and 95% for the average heritability QTLs, and 95 and 94% for the high heritability QTLs, respectively. The observed false discovery rate (FDR) was 15 and 9% with low and high density, respectively. The Bayesian QTL mapping provides a precise localization of candidate genes with a bias in the QTL position of approximately 4–6 cM. The polygenic effect is important to control the false discovery rate (FDR) and to provide a higher power of QTL detection with multiple progeny.

show abstract

“…Q2 had a less strong effect and was present in each of our parents, underlining its general occurrence in our breeding program. The use of multiparent populations for finding multiple functional alleles of different effect was also reported for two acidity QTLs/genes in apple by [30].…”

Section: Blushmentioning

confidence: 82%

Identification and characterization of QTLs for blush, soluble solids concentration (SSC), and titratable acidity (TA) in peach through a multi-family approach

Rawandoozi¹,

Hartmann²,

Carpenedo³

et al. 2020

Preprint

View full text Add to dashboard Cite

25Background: Fruit quality traits have a significant effect on consumer acceptance and 26 subsequently on peach (Prunus persica (L.) Batsch) consumption. Determining the genetic 27 bases of key fruit quality traits is essential for industry to improve fruit quality and increase 28 consumption. A Bayesian approach embedded in the FlexQTL software increases the 29 accuracy of QTL mapping and the probability of identifying new and validating known QTLs 30 across a wide range of genetic backgrounds. 31Results: Phenotypic data of seven F1 low to medium chill full-sib families were collected over 32 two years at two locations and genotyped using the 9K SNP Illumina array. One major QTL 33 for fruit blush was found on linkage group 4 (LG4) at 40-46 cM that explained from 20 to 32% 34 of the total phenotypic variance and showed three QTL alleles of different effects. For SSC, 35 one QTL was mapped on LG5 at 60-72cM and explained from 17 to 39% of the phenotypic 36 variance. A major QTL for TA that co-localized with the major locus for low-acid fruit (D-locus) 37 was mapped at the proximal end of LG5 and explained 35 to 80% of the phenotypic variance. 38The new QTL for TA on the distal end of LG5 explained 14 to 22% of the phenotypic variance. 39This QTL co-localized with the QTL for SSC and affected TA only when the first QTL is 40 homozygous for high acidity (epistasis). Haplotype analyses revealed SNP haplotypes and 41 predictive SNP marker(s) associated with desired QTL alleles. 42 Conclusions:A multi-family-based QTL discovery approach enhanced the ability to discover 43 a new TA QTL and validated other QTLs which were reported in previous studies. Identified 44 predictive SNPs and their original sources will facilitate the selection of parents and/or 45 seedlings that have desired haplotype alleles. Our findings will help peach breeders develop 46 new predictive, DNA-based molecular marker tests for routine use in marker-assisted 3 Background 51Peach [Prunus persica (L.) Batsch] is the third most important temperate fruit crop globally in terms of 52 production [1]. Peach fruit quality traits such as flesh texture, color, sweetness, acidity, and other 53 organoleptic attributes affect consumer preference and consumption [2]. Most of these traits are 54 quantitatively inherited and their genetic control is still unclear [3]. 55In the last decade, the rate of fresh consumption has decreased from 2.3 to 1.3 kg per capita per 56year in the U.S. [4]. The lack of consistent quality (poor firmness, lack of flavor, low level of 57 sweetness, and non-ripening fruit) is a main reason consumers do not purchase peaches [5]. The 58 primary reason for poor quality is harvesting at immature stages, a lack of good postharvest handling 59 practices, the need for high yields but not necessarily high quality to make production profitable and 60 the relative ease for selecting for external versus internal fruit traits. Consumers are willing to pay more 61 for fruits of better quality [6] which is the reason for developing branded fru...

show abstract

Two large-effect QTLs, Ma and Ma3, determine genetic potential for acidity in apple fruit: breeding insights from a multi-family study

Cited by 60 publications

References 70 publications

Apple ALMT9 Requires a Conserved C-Terminal Domain for Malate Transport Underlying Fruit Acidity

Apple ALMT9 Requires a Conserved C-Terminal Domain for Malate Transport Underlying Fruit Acidity

Efficiency of Bayesian quantitative trait loci mapping with full‐sib progeny

Identification and characterization of QTLs for blush, soluble solids concentration (SSC), and titratable acidity (TA) in peach through a multi-family approach

Contact Info

Product

Resources

About