Assessing the allelotypic effect of two aminocyclopropane carboxylic acid synthase-encoding genes MdACS1 and MdACS3a on fruit ethylene production and softening in Malus.

Phytohormone ethylene largely determines apple fruit shelf life and storability. Previous studies demonstrated that MdACS1 and MdACS3a, which encode 1-aminocyclopropane-1-carboxylic acid synthases (ACS), are crucial in apple fruit ethylene production. MdACS1 is well-known to be intimately involved in the climacteric ethylene burst in fruit ripening, while MdACS3a has been regarded a main regulator for ethylene production transition from system 1 (during fruit development) to system 2 (during fruit ripening). However, MdACS3a was also shown to have limited roles in initiating the ripening process lately. To better assess their roles, fruit ethylene production and softening were evaluated at five time points during a 20-day post-harvest period in 97 Malus accessions and in 34 progeny from 2 controlled crosses. Allelotyping was accomplished using an existing marker (ACS1) for MdACS1 and two markers (CAPS866 and CAPS870) developed here to specifically detect the two null alleles (ACS3a-G289V and Mdacs3a) of MdACS3a. In total, 952 Malus accessions were allelotyped with the three markers. The major findings included: The effect of MdACS1 was significant on fruit ethylene production and softening while that of MdACS3a was less detectable; allele MdACS1-2 was significantly associated with low ethylene and slow softening; under the same background of the MdACS1 allelotypes, null allele Mdacs3a (not ACS3a-G289V) could confer a significant delay of ethylene peak; alleles MdACS1-2 and Mdacs3a (excluding ACS3a-G289V) were highly enriched in M. domestica and M. hybrid when compared with those in M. sieversii. These findings are of practical implications in developing apples of low and delayed ethylene profiles by utilizing the beneficial alleles MdACS1-2 and Mdacs3a.

Introduction

To make fresh apple fruit available year-round for consumers, the controlled atmosphere (CA) storage technology has been adapted widely in the apple industry. The technology primarily employs low temperature, low O2 and high CO2 in combination with an ethylene production inhibitor 1-methylcyclopropene and others. Apple fruit can be stored for >10 months under optimal CA conditions. However, physiological disorders associated with CA storage, such as injuries induced by cold and CO2 and flesh browning induced by 1-methylcyclopropene, can cause substantial loss for storage operators.[1-3] Such storage disorders have been reported for major apple varieties such as ‘Empire’ and ‘McIntosh’[2,4] and for rising cultivars such as ‘Honeycrisp’.[3] A strong need for new apples of long-shelf life and improved keeping quality with few or no storage disorders exists.

The gaseous phytohormone ethylene plays an important role in climacteric fruit ripening. The shelf life and storability of apple fruit are closely correlated with their ethylene production levels. Plant ethylene biosynthesis has been well-defined in Yang cycle that involves three enzymes: S-adenosylmethionine synthase, 1-aminocyclopropane-1-carboxylic acid (ACC) synthase (ACS) and ACC oxidase (ACO).[5] The enzymes ACS and ACO have been the subject of extensive studies to better understand plant ethylene production. Studies in many plant species including tomato and apple have shown that ACS and ACO are encoded by gene families of multiple members, that is, the ACS family and the ACO family, respectively.

There are two systems of ethylene production in plants: system 1 occurs during plant/fruit growth and development; and system 2 is defined exclusively for the floral senescence and fruit-ripening stages.[6] In tomato, system 1 ethylene biosynthesis involves LeACS6, 1A and LeACO1, 3, 4; whereas system 2 uses LeACS2, 4 and ACO1, 4.[7] In apple, at least five ACS (MdACS1–5) and four ACO (MdACO1–4) genes have been reported[8,9] and these genes appear to be operating similarly in the two systems for ethylene production. MdACS1 is considered a system 2 gene; and its expression is highly correlated with the ethylene production burst in ripening apples. There are two alleles for the MdACS1 gene, MdACS1-1 and MdACS1–2, and the former is often associated with high ethylene production while the latter with lower ethylene production during fruit ripening.[10-14] This observation has led to a marker-assisted selection strategy emphasizing on selection for allelotype (see Discussion for usage of term ‘allelotype’) MdACS1–2/2 for long-shelf life apples.[15] Indeed, some evidence suggests that modern apple-breeding practice has unintentionally favored selection for the MdACS1–2 allele in commercial apple cultivars,[16] presumably for fruit of low ethylene and long-shelf life.

However, early-ripening cultivars showed faster fruit softening, regardless of their MdACS1 allelotypes.[10] This is consistent with the observation that the polygalacturonase gene (MdPG1) involved in softening of fruit flesh is expressed irregularly among apple cultivars of identical MdACS1 allelotypes.[12] Therefore, there are other factors also affecting fruit shelf life in addition to MdACS1. Interestingly, findings in a recent report have suggested that allele variations of another ACS gene (U73816),[17] designated MdACS3a (AB243060), are an essential factor regulating apple fruit ripening and shelf life.[18] There are two natural mutant alleles of the wild-type allele MdACS3a: One is the functional null allele MdACS3a-G289V, arising from a point mutation that leads to an amino-acid substitution from G289 to V289 at an active region for the MdACS3A enzyme activity, resulting in a functionally inactive enzyme. In melon, a similar point mutation in a conserved active region of an ACS gene led to andromonoecy, a common sexual system in angiosperms characterized by carrying both male and bisexual flowers.[19] This is an excellent example demonstrating that point mutations in conserved active regions of an ACS enzyme could confer a major phenotypic variation in plants. The other, a transcriptionally null allele Mdacs3a, is characterized by non-detectable mRNA. Moreover, combinations of Mdacs3a and MdACS3a-G289V alleles, regardless of whether they are homozygous or heterozygous, are highly associated with lower ethylene production and long-shelf life. In the six apple varieties/selections of the two null alleles studied, all showed low ethylene production and long-shelf life, irrespective to their MdACS1 allelotypes and early, mid or late physiological maturation dates.[18] Furthermore, the expression of MdACS3a is fruit tissue specific and detectable only during the transition from system 1 to 2 ethylene biosynthesis.[8,9,18] These observations suggest that MdACS3a acts as a main regulator for the transition, and is thereby crucial in regulating the fruit-ripening process.[18]

In a more recent report, however, the allelotypes of MdACS3a were demonstrated to affect the ripening initiation of late-maturing cultivars only, but not the early- or mid-maturing cultivars.[20] To better assess the roles of MdACS1 and MdACS3a, two approaches were taken in this study. The first approach was to estimate the allelotypic effect of the two genes by evaluating fruit ethylene production levels and softening rates in 97 diverse Malus accessions and 34 progeny from 2 controlled crosses. The second approach was to examine how variations in their allelotypic effect were associated with the frequency changes of the MdACS1 and MdACS3a alleles in M. domestica and M. hybrid as compared with those in M. sieversii, the major progenitor species of domestic apples, in 952 Malus accessions covering 53 Malus species. Allelotyping (see Discussion for usage of term ‘allelotyping’) of MdACS1 and MdACS3a was conducted using an existing marker for MdACS1 and two CAPS (cleaved amplified polymorphic sequence) markers specifically developed here to detect alleles ACS3a-G289V and Mdacs3a.

Materials and methods

Plant materials

Two sets of Malus accessions were used in this study, which have been planted and maintained in the Malus germplasm repository of the US Department of Agriculture (USDA) in Geneva, New York. The first set included a total of 952 accessions, covering 53 Malus species (Supplementary Table S1). Among them, Malus domestica of 508 accessions, M. hybrid (the breeding selections derived from crosses between M. domestica and other Malus species) of 146 and M. sieversii (the major progenitor species of M. domestica) of 78 were most commonly represented (Supplementary Table S1). The second set comprised 34 half-sib progeny selected from 2 interspecific crosses GMAL4592 (‘Royal Gala’×PI613978) and GMAL4593 (‘Royal Gala’×PI613981). ‘Royal Gala’, a widely grown apple cultivar (M. domestica), has an allelotype MdACS1–2/2 and MdACS3a/MdACS3a-G289V for genes MdACS1 and MdACS3a, respectively. PI613978 and PI613981 are among the elite selections of M. sieversii collected from Kazakhstan,[21] and they have the same allelotypes for the two ACS genes, that is, MdACS1-1/1 and MdACS3a/MdACS3a-G289V. Population GMAL4592 was used in one of our previous studies.[22] Both GMAL4592 and GMAL4593 were planted on their own seedling roots in 2004.

Measurements of fruit ethylene production and firmness

Fruit ethylene production and flesh firmness were measured for 97 of 952 Malus accessions in the first set and the 34 half-sib progeny in the second set as described previously.[23] Briefly, for each accession, at least 25 fruits were harvested at a target maturity level as determined by the starch index of 4–6 according to the Cornell Starch Chart.[24] The 25 fruits were evenly divided into 5 groups and were stored for 0, 5, 10, 15 and 20 days at room temperature (20–25 °C), respectively. Each fruit was weighed then enclosed in a gas-tight container (1.2 l) and kept for 1 h at room temperature. One milliliter of gas was sampled from the headspace in the container using a BD syringe (No. 309602, BD, Franklin Lakes, NJ, USA). The gas sample’s ethylene concentration was measured with a gas chromatograph HP 5890 series II (Hewlett-Packard, Palo Alto, CA, USA) equipped with a flame ionization detector. Before the gas samples were assayed, the gas chromatograph was calibrated with standard ethylene gas (NO. 34489, Restek, Bellefonte, PA, USA) at a series of concentrations—0.01, 0.1, 0.5, 1, 5, 10 and 100 p.p.m.—to obtain the linear relation between ethylene peak area and concentration. The fruit ethylene production was calculated with the following formula: Where E stands for fruit ethylene production rate in nanoliter per gram of fresh weight per hour (nL g−1 h−1), [C2H4] for ethylene concentration in p.p.m., V1 for the volume of container in mL, V2 for the volume of fruit in mL equivalent to fresh weight (W) in grams and T stands for the time in hours kept in the container.

Fruit flesh firmness was measured using a penetrometer (Fruit Tester, Wagner FTK100, Greenwich, CT, USA) with a probe of 11 mm in diameter. The probe tip was pressed vertically into the fruit pulp (after skin-disc removal) to a depth of 10 mm. For larger fruits, four skin discs were removed from opposite sides of each fruit along the equator, and for smaller fruits, three skin discs were removed at roughly equal distance. The firmness readings were expressed in kg cm−2, and firmness loss was measured by the percentage (%) of firmness reduced at days 5 to 20 as compared with the firmness at day 0. After the firmness was measured, fruits were sliced in half along the equator, dipped into a iodine-potassium iodide (I2-KI) solution, and then allowed the staining reaction for >1 min before reading Cornell Starch Index.[24]

Allelotyping of MdACS1 and MdACS3a

Allelotyping of MdACS1 was conducted with marker ACS1 using primers ACS1–5F/R (Supplementary Table S2) as reported previously.[10,15] However, allelotyping of MdACS3a was accomplished with two CAPS markers developed in this study using an online tool for identifying appropriate restriction enzymes[25] (see Results). These two markers, named CAPS866 and CAPS870, were capable of detecting the functional null allele MdACS3a-G289V and the transcriptional null allele Mdacs3a, respectively. In practice, the same primers ACS3a-289F/R (Supplementary Table S2) were used for PCR to amplify the targeted DNA fragment for both CAPS866 and CAPS870. PCRs were performed with 35 cycles of 94 °C for 30 s, 58 °C for 30 s, 72 °C for 1 min, with an initial 94 °C for 5 min and a final extension of 72 °C for 10 min. Each PCR reaction mix was set in 10 μL containing 20 ng genomic DNA, 0.2 mm each dNTP, 0.5 μm of each primer, 2.5 mm MgCl2, 2 μL 5× PCR Colorless GoTaq Reaction Buffer and 1 U of GoTaq DNA polymerase (Promega, Madison, WI, USA). To detect alleles MdACS3a-G289V and Mdacs3a, the PCR products were restricted with enzymes BstNI and TaqαI (New England Biolabs, Ipswich, MA, USA) following the manufacturer’s instruction, respectively. The restricted PCR products were assayed by electrophoresis on 1.5% agarose gel and then stained with ethidium bromide for visualization and documentation as described previously.[22]

Sanger DNA sequencing

The PCR products amplified by primers ACS3a-289F/R (Supplementary Table S2) were directly sequenced using a DNA Sequencer ABI3730XL (Applied Biosystems, Foster City, CA, USA) at the Cornell University Biotechnology Resource Center (Ithaca, NY, USA). The reverse PCR primer ACS3a-289R was used for DNA sequencing. DNA sequence analyses were performed using software Sequencher 5.2 (Gene Codes Corporation, Ann Arbor, MI, USA).

Statistical analysis

Pearson’s correlation analysis and one-way analysis of variance (ANOVA) of ethylene production and fruit firmness were conducted with software JMP Pro 10.0 (SAS institute, Cary, NC, USA). Significance levels in comparison of the means were determined by P<0.05 (Student’s t-test).

Results

Evaluation of fruit ethylene production and softening

Fruit ethylene production and softening were evaluated in 97 of 952 Malus accessions (Supplementary Tables S1 and S3). Their mature date was determined by Cornell starch index, which had a mean 5.5±1.4 at harvest. The 97 accessions varied widely not only in maturity date (from 16 August to 8 November 2011; Supplementary Figure S1a) and fruit weight (25.1–303.8 g, Supplementary Figure S1b), but also in ethylene production and firmness at harvest (day 0) and during the 20-day post-harvest period (Figures 1a and b). At day 0, for example, the ethylene levels ranged from 0.7 nL g−1 per h of PI588844 (‘Fuji’, M. domestica) to 679.3 nL g−1 per h of PI619168 (an accession of M. sylvestris), and fruit firmness varied from 3.8 kg cm−2 of PI589572 (E14–32, M. hybrid) to 12.7 kg cm−2 of PI589478 (‘Novosibirski Sweet’, M. domestica). Despite being highly variable, a trend line of bivariate function could be fit for fruit ethylene production (r2=0.120, P<0.0001, Figure 1a) and fruit firmness (r2=0.147, P<0.0001, Figure 1b).

Figure 1

Evaluation of fruit ethylene production (a) and firmness (b) in 97 Malus accessions during a 20-day post-harvest period under room temperature. The trend lines (curves in red) and the associated equations and coefficient of determination (R2) are presented.

The trend line of fruit ethylene showed a peak between days 10 and 15, which was largely a reflection of the mean fruit ethylene levels 75.5±100.5, 207.3±193.9, 272.8±249.6, 247.0±170.8 and 217.3±146.5 (nL g−1 h−1) at days 0, 5, 10, 15 and 20, respectively (Figure 1a). A majority (59/97, 60.8%) of the 97 Malus accessions reached their peak ethylene day at day 10 (25 accessions) or day 15 (34 accessions) while 2, 16 and 20 accessions topped their ethylene production at days 0, 5 and 20 (Supplementary Figure S1c). The peak ethylene reads were spread from 1.7 nL g−1 per h of PI589570 (E36-7, M. hybrid) at day 20 to 1022.2 nL g−1 per h of PI633801 (M. sieversii) at day 10 (Supplementary Table S3).

As expected, fruit firmness showed a continuous decreasing trend during the 20-day period (Figure 1b). This was also an approximation of the mean firmness 7.4±1.7 kg cm−2, 6.5±2.1 kg cm−2, 5.8±2.0 kg cm−2, 5.3±1.99 kg cm−2 and 5.3±1.92 kg cm−2 at days 0, 5, 10, 15 and 20, respectively. In other words, the mean fruit firmness was lost by 13.6% at day 5, 22.0% at day 10, 29.2% at day 15 and 29.0% at day 20.

Fruit ethylene production and firmness loss were significantly correlated (Table 1). The strongest correlation (r=0.564, P=0) was observed between ethylene at day 15 and fruit firmness loss at day 10, while the weakest (r=0.214, P=0.035) was between ethylene at day 10 and fruit firmness loss at day 5. Peak ethylene day (day of peak ethylene production during the 20-day post-harvest storage) was most significantly correlated with ethylene at day 5 (r=−0.479, P=6.9E−7), and it also significantly correlated with fruit firmness loss at day 10 (r=−0.258, P=0.011) and day 15 (r=−0.238, P=0.019) (Table 1).

Table 1

Correlation coefficients between fruit ethylene production and firmness or firmness loss in 97 Malus accessionsa

	C2H4_d0	C2H4_d5	C2H4_d10	C2H4_d15	C2H4_d20	Firmness d0 (kg cm−2)	Firmness loss_d5 (%)	Firmness loss_d10 (%)	Firmness loss_d15 (%)	Firmness loss_d20 (%)	Peak C2H4 dayb
C2H4_d0	1.000**
C2H4_d5	0.434**	1.000**
C2H4_d10	0.410**	0.695**	1.000**
C2H4_d15	0.353**	0.734**	0.839**	1.000**
C2H4_d20	0.265**	0.733**	0.695**	0.871**	1.000**
Firmness d0 (kg cm−2)	−0.208*	−0.261**	−0.164	−0.239*	−0.220*	1.000**
Firmness loss_d5 (%)	0.324**	0.484**	0.214*	0.334**	0.431**	−0.198	1.000**
Firmness loss_d10 (%)	0.345**	0.538**	0.493**	0.564**	0.478**	−0.092	0.704**	1.000**
Firmness loss_d15 (%)	0.284**	0.446**	0.421**	0.481**	0.442**	−0.104	0.699**	0.863**	1.000**
Firmness loss_d20 (%)	0.306**	0.453**	0.388**	0.481**	0.438**	−0.041	0.596**	0.828**	0.853**	1.000**
Peak C2H4 dayb	−0.229*	−0.479**	−0.402**	−0.281**	−0.211*	0.219*	−0.112	−0.258*	−0.238*	−0.190	1.000**

Fruit firmness loss was measured in a 20-day post-harvest period under room temperature.

Peak C2H4 (ethylene) day: day of peak ethylene production during the 20-day post-harvest storage; signs '*' and '**' stand for significance levels exceeding P=0.05 (r=0.1996, n=97) and P=0.01 (r=0.2603, n=97), respectively.

Development of allelic specific markers for MdACS3a

The null allele MdACS3a-G289V is caused by a mutation from G866 to T866 at the 866th base in the coding sequence of MdACS3a.[18] Based on the web-based tool for single nucleotide polymorphism (SNP) analysis,[25] the mutation abolishes the recognition site CC866WGG of restriction enzyme BstNI (Figure 2). To develop a CAPS marker, two primers (ACS3a-289F/R, Supplementary Table S2) were designed to amplify a DNA fragment (480 bp) covering the SNP (G866/T866) specifically from MdACS3a although the three MdACS3 member genes MdACS3a (AB243060), MdACS3b (AB243061) and MdACS3c (AB243062) are of high identity in their DNA sequences.[18] The specificity of the primer pair to MdACS3a was confirmed by sequencing of the PCR products from 92 of the 97 Malus accessions (Figure 2, Supplementary Table S3). Digestion of the PCR products with BstNI yielded restriction bands as expected (Figure 3b), indicating the successful development of a CAPS marker detecting SNP G866/T866, designated CAPS866. Therefore, allele CAPSG represents the wild-type allele MdACS3a while CAPST stands for the functional null allele MdACS3a-G289V.

Figure 2

A chromatogram screenshot of the DNA sequence (partial) of MdACS3a encompassing SNPs G866/T866 and C870/T870 in six apple cultivars—‘Florina’, ’Fuji red sport’, ‘Gala’, ‘Golden Delicious’ and ‘Granny Smith’. The oval circles in brown and red indicate the homozygous or heterozygous status at the 866th and 870th nucleotides in the coding sequence of MdACS3a, respectively. The recognition sites of restriction enzymes BstNI and TaqαI are provided to show that the mutation from G866 to T866 abolishes the restriction site of BstNI while the mutation from C870 to T870 gives rise to a restriction site for TaqαI. The right panel shows allelotypes of MdACS3a as represented by the SNP alleles, where G866 stands for allele MdACS3a (wild type), T866 for MdACS3a-G289V (functional null allele), C870 also for allele MdACS3a and T870 for Mdacs3a (transcriptional null allele).

Figure 3

Agarose gel analyses of markers ACS1 (a), CAPS866 (b) and CAPS870 (c). For marker ACS1, the PCR products amplified by primers ACS1–5F/R were directly analyzed. Allelotypes MdACS1-1/1, MdACS1–2/2 and MdACS1-1/2 are denoted with ‘1/1’, ‘2/2’ and ‘1/2’, respectively. For marker CAPS866, the PCR products were first amplified by primers ACS3a-289F/R and then digested with enzyme BstNI, which restricts the MdACS3a (G866) allele into the two lower bands. Allelotypes MdACS3a/MdACS3a (G866/G866), MdACS3a/MdACS3a-G289V (G866/T866) and MdACS3a-G289V/G289V (T866/T866) are noted with ‘G/G’, ‘G/T’ and ‘T/T’, respectively. For marker CAPS870, enzyme TaqαI restricts the Mdacs3a (T870) allele into the two lower bands. Allelotypes MdACS3a/MdACS3a (C870/C870), MdACS3a/mdacs3a (C870/T870) and mdacs3a/mdacs3a (T870/T870) are noted with ‘C/C’, ‘C/T’ and ‘T/T’, respectively.

Development of a marker detecting the transcriptional null allele Mdacs3a was initially thought to be challenging as the null allele was reported not to show sequence variations from the wild-type allele.[18] However, sequencing analysis of the PCR products amplified by primers ACS3a-289F/R in the 92 accessions (Supplementary Table S3) not only identified the expected SNP G866/T866, but also a new SNP C870/T870 (Figure 2). Importantly, this new SNP can discriminate the two alleles of MdACS3a in ‘Fuji’ (Figure 2), which was known of allelotype MdACS3a/Mdacs3a.[18] Evidence from this and other studies (see Discussion) indicated that base T870 was associated with the Mdacs3a allele. Using a similar approach, another CAPS marker, named CAPS870, was developed to detect SNP C870/T870 using restriction enzyme TaqαI along with the same primers ACS3a-289F/R (Figure 3c). Therefore, allele CAPSC corresponds to the wild-type allele MdACS3a while CAPST corresponds to the transcriptional null allele Mdacs3a.

Effect of the allelotypes of MdACS1 and MdACS3a on ethylene production and firmness loss

To evaluate the effect of the allelotypes of MdACS1 and MdACS3a, the 97 Malus accessions were assayed with markers ACS1, CAPS866 and CAPS870 that can detect different alleles of MdACS1 and MdACS3a (Figures 3a–c). As a result, marker ACS1 identified 53, 36 and 8 accessions of allelotypes of MdACS1-1/MdACS1-1 (MdACS1-1/1), MdACS1-1/MdACS1–2 (MdACS1-1/2) and MdACS1–2/MdACS1–2 (MdACS1–2/2), respectively (Supplementary Table S3). Similarly, marker CAPS866 detected 75 accessions of allelotype CAPSG/CAPSG (CAPSG/G), 18 of CAPSG/CAPST (CAPSG/T) and 4 of CAPST/CAPST (CAPST/T); and marker CAPS870 uncovered 47 accessions of allelotype CAPSC/CAPSC (CAPSC/C), 40 of CAPSC/CAPST (CAPSC/T) and 10 of CAPSC/CAPST (CAPST/T) (Supplementary Table S3).

A series of one-way ANOVA of the fruit ethylene production and fruit firmness loss over the 20-day period within each of the three allelotype groups (Figure 4) indicated that the most differences were observed among the MdACS1 allelotypes. Allelotype MdACS1-1/1 showed significantly higher ethylene production (days 0–20) and firmness loss (days 5–20) than MdACS1-1/2 and MdACS1–2/2 allelotypes, but MdACS1-1/2 and MdACS1–2/2 did not differ in terms of ethylene production or firmness retention (Figures 4a and d). In contrast, there were no difference among the CAPS866 allelotypes in fruit ethylene production and firmness loss (Figures 4b and e). Among the CAPS870 allelotypes, significant difference was not detected for ethylene production, but there were differences in fruit firmness loss between allelotypes CAPSC/C and CAPSC/T at day 5 and between CAPSC/C and CAPST/T at day 10 (Figures 4c and f). This indicated that such differences in fruit firmness loss at day 5 and 10 in the CAPS870 allelotypes might be caused by other factors rather than their ethylene production levels.

Figure 4

Comparison of the means of fruit ethylene production and firmness or firmness loss among allelotypes of MdACS1 as defined by marker ACS1 (a and d), and among those of MdACS3a as defined by markers CAPS866 (b and e) and CAPS870 (c and f). The allelotypes are annotated similarly as those in the legend of Figure 3. Colors of column in blue, orange, green, purple and turquoise represent days 0, 5, 10, 15 and 20, respectively. The statistical tests were conducted independently within each of the five storage time points (days 0–20). Significance levels are indicated with letters (shown above the columns in the chart), where different letters indicate P<0.05. The numbers of accessions observed (n) for each allelotype are presented accordingly (shown above the letters for significance). Error bars indicate s.e.

To seek such factors, peak ethylene day, which measures ethylene peak timing, was examined (Figure 5) as this trait was negatively correlated with fruit firmness loss at day 10 (r=−0.258, P=0.011) although the correlation was insignificant at day 5 (r=−0.112, P=0.275) (Table 1). Encouragingly, the three CAPS870 allelotypes showed significant difference from each other, with CAPSC/T having peaked the earliest, CAPSC/C intermediate and CAPST/T the latest (Figure 5a). These data appeared to suggest that the earlier peak ethylene day of CAPSC/C might have contributed to its greater fruit firmness loss of CAPSC/C as compared with that of CAPST/T at day 10 (Figure 4f). However, the lowest fruit firmness loss of CAPSC/T at day 5 remained to be explained. Peak ethylene day was also analyzed in the other two groups of allelotypes. In the allelotypes of MdACS1, MdACS1-1/1 had an earlier peak ethylene than MdACS1–2/2, but showed no difference from MdACS1-1/2 (Figure 5a). In the three allelotypes of CAPS866, no significant difference was observed (Figure 5a).

Figure 5

Comparison of the means of peak ethylene day among the allelotypes of MdACS1 as defined by marker ACS1 (open column) and those of MdACS3a as defined by markers CAPS866 (dot-filled column) and CAPS870 (filled column) (a), and among the allelotypes of MdACS3a defined by markers CAPS866 (b) and CAPS870 (c) under the same background of MdACS1-1/1 or MdaCS1-1/2. The allelotypes, significance levels and observed numbers are represented similarly as those in Figures 3 and 4.

It was clear that the effect of MdACS1 on ethylene production and fruit firmness loss was much stronger than that of MdACS3a (Figure 4). To see if the random presence of the MdACS1 alleles might have obscured the detection of the effect of MdACS3a allelotypes (Figures 4b, c, e and f), another series of ANOVA was conducted for the MdACS3a allelotypes of five or more accessions (Figure 6) under the same background of MdACS1 allelotypes MdACS1-1/1 and MdACS1-1/2, which occurred in 53 and 36 of the 97 accessions (Supplementary Table S3), respectively. The third allelotype MdACS1–2/2 was not included in the analysis (Figure 6) due to limited number of 8 accessions.

Figure 6

Comparison of the means of ethylene production and fruit firmness or firmness loss among the allelotypes of MdACS3a as defined by markers CAPS866 (a and c) and CAPS870 (b and d) under the same background of MdACS1-1/1 or MdaCS1-1/2. The allelotypes, column colors, statistical tests, significance levels and observed numbers are represented similarly as those in Figures 3 and 4.

For CAPS866, the ANOVA analyses were conducted for two allelotypes CAPSG/G and CAPSG/T under MdACS1-1/1, as well as under MdACS1-1/2 (Figures 5b and 6a,c). This allowed us to identify that allelotype CAPSG/T produced significantly higher levels of ethylene than CAPSG/G at day 10 under MdACS1-1/1 (Figure 6a). For CAPS870, three allelotypes CAPSC/C, CAPSC/T and CAPST/T under MdACS1-1/1 and two allelotypes CAPSC/C and CAPSC/T under MdACS1-1/2 were analyzed (Figures 5c and 6b,d). The results showed that allelotype CAPST/T had significant later peak ethylene day than CAPSC/C and CAPSC/T under MdACS1-1/1, and CAPSC/C had significant later peak ethylene than CAPSC/T under MdACS1-1/2 (Figure 5c). There were no significant differences detected between the other allelotypes of CAPS866 and CAPS870 at a given time point (Figures 5b and 6a–d). These observations suggested that the direct effect of MdACS3a on ethylene production and firmness loss was limited, but its effect on peak ethylene day was clearly detectable through allele Mdacs3a (CAPST/T).

The analyses also provided information regarding the effect of MdACS1 under the same background of CAPS866 (Figures 5b and 6a,c) or CAPS870 (Figures 5c and 6b,d) allelotypes. As expected, allelotype MdACS1-1/1 had higher ethylene production (Figures 6a and c) and more firmness loss (Figures 6b and d) than MdACS1–2/2, but had similar peak ethylene day as MdACS1-1/2 (Figures 5b and c) except under the CAPSC/C background (Figure 5c). These results suggested that the effect of MdACS1 on peak ethylene day was insignificant under the same background of MdACS3a, which was in disagreement with the observation that the effect of MdACS1 on peak ethylene day was significant when the background of MdACS3a was not considered (Figure 5a).

Since the MdACS3a allelotype CAPST/T (MdACS3a-G289V/G289V) was present only in 4 of 97 accessions, the 2 controlled crosses GMAL4592 and GMAL4593 segregating for CAPST/T under the same background of MdACS1-1/2 were used for better analysis. In total, 17 progeny of allelotype CAPSG/G (MdACS3a/MdACS3a) and another 17 of CAPST/T were similarly evaluated for ethylene production and fruit firmness loss. ANOVA analysis indicated that there were no significant differences between the two allelotypes CAPSG/G and CAPST/T in ethylene production and fruit firmness loss, nor in peak ethylene day from day 0 to day 20 (Supplementary Figures 2a–c), suggesting that no effect of allelotype CAPST/T (MdACS3a-G289V/G289V) was detectable in this study.

Allelotyping of MdACS1 and MdACS3a in a large set of Malus accessions

Additional 855 Malus accessions were surveyed with markers ACS1, CAPS866 and CAPS870, leading to a total of 952 Malus accessions allelotyped (Figure 7, Supplementary Table S1). The data showed that the three allelotypes MdACS1-1/1, MdACS1-1/2 and MdACS1–2/2 were of 665, 249 and 38 accessions, the allelotypes CAPSG/G, CAPSG/T and CAPST/T were of 770, 173 and 9 accessions, and the allelotypes CAPSC/C, CAPSC/T and CAPST/T were of 346, 400 and 206 accessions, respectively. Estimating the allele frequency in the 952 accessions revealed alleles MdACS1-1 and MdACS1–2 of 82.9% and 17.1%, CAPSG and CAPST of 90.0% and 10.0%, and CAPSC and CAPST of 57.4% and 42.6%, respectively (Figure 8a).

Figure 7

Allelotyping of MdACS1 and MdACS3a using markers ACS1, CAPS866 and CAPS870 in 952 Malus accessions. The numbers in parentheses stand for the total or subtotal number of Malus accessions in an allelotype proximately annotated. The allelotypes are represented similarly as those in Figure 3.

Figure 8

Frequency of the MdACS1 and MdACS3a alleles as defined by markers ACS1, CAPS866 and CAPS870 in all the 952 Malus accessions (a), M. domestica (b), M. hybrid (c) and M. sieversii (d).

To investigate whether and how human selection might have favored or repressed these alleles, their frequency in the most represented species M. domestica (508 accessions), M. hybrid (146) and M. sieversii (78), which collectively accounted for 76.9% of the 952 accessions (Supplementary Table S1), were independently estimated (Figures 8b–d). In comparison with M. sieversii, M. domestica and M. hybrid showed the largest allele frequency increases for alleles MdACS1–2 (from 0.6% to 18.8–24.5%) and CAPST (from 5.1% to 34.3–48.3%), or decreases for allele MdACS1-1 (from 99.4% to 81.2–75.5%) and CAPSC (from 94.9% to 65.7–51.7%), but minimal changes for the CAPSG (from 86.5% to 86.8–94.2%) and CAPST (from 13.5% to 13.2–5.8%) alleles (Figures 8b–d). These results suggested that apple-breeding practice may have selected for alleles MdACS1–2 and CAPST (Mdacs3a), against alleles MdACS1-1 and CAPSC, and is neutral for alleles CAPSG and CAPST (MdACS3a-G289V). Such human selection for alleles MdACS1–2 and Mdacs3a supported their observed significant effect on reduced or delayed ethylene production. Meanwhile, the minimal changes in the frequency of allele MdACS3a-G289V reinforced the unfound effect of this allele on ethylene.

Discussion

The effect of MdACS1 and MdACS3a and beneficial alleles

The allelic effect of MdACS1 on fruit ethylene production and softening was significant and detectable at nearly all time points tested during the 20-day post-harvest period in the 97 Malus accessions. This was consistent with the critical role of MdACS1 reported in many other studies.[10-16,26-29] Since the allele frequency of MdACS1–2 was 24.5% in M. domestica, 18.8% in M. hybrid and only 0.6% in M. sieversii (Figure 8), which is the major progenitor species of domestic apples, artificial selection has clearly favored MdACS1–2 over MdACS1-1. In fact, such allele preference of MdACS1–2 over MdACS1-1 was even reported within M. domestica when the frequencies of the two alleles in apple cultivars were plotted against their time of introduction.[16] These observations are in accordance with the finding that allele MdACS1–2 is a beneficial allele associated with low ethylene and slow softening (Figures 4 and 6).

MdACS3a was regarded a main regulator for ethylene production transition from system 1 to 2.[18] The gene was also similarly shown to be an accelerator[30] or an inducer[31] of apple fruit ripening based on its gene expression timing and patterns in apple cultivars of varying ethylene levels and softening rates. In this study, such roles of MdACS3a were also detected through examining the allelic effect of Mdacs3a (CAPST) on peak ethylene day, which reflects the timing of the climacteric ethylene burst. For example, under the same background of MdACS1-1/1, allelotype Mdacs3a/Mdacs3a (CAPST/T) showed a significant delay in peak ethylene day when compared with what was observed for allelotypes MdACS3a/MdACS3a (CAPSG/G) and MdACS3a/Mdacs3a (CAPSG/T) (Figure 5c). Moreover, the allele frequency of Mdacs3a (CAPST) was 34.3% in M. domestica and 48.3% in M. hybrid, a dramatic increase from the corresponding frequency of 5.1% in M. sieversii, indicating a strong human selection for allele Mdacs3a, presumably for the benefit of delayed ethylene production. Taken together, these data support the regulatory role of MdACS3a in ethylene production transition in apple fruit.

However, the allelic effect of MdACS3a-G289V on fruit ethylene production, softening and peak ethylene day was shown to be insignificant in the 97 Malus accessions, as well as in the 34 progeny from the 2 controlled crosses segregating for allelotype MdACS3a-G289V/G289V (CAPST/T) under the same background of MdACS1 allelotype. Furthermore, the allele frequency of MdACS3a-G289V (CAPST) was 13.5% in M. sieversii, 13.2% in M. domestica and 5.8% in M. hybrid, providing no evidence that MdACS3a-G289V (CAPST) has been enriched in response to selection. These results were surprising as MdACS3a-G289V was shown to be a functional null allele of MdACS3a.[18] In a previous study, the two null alleles MdACS3a-G289V (CAPST) and Mdacs3a (CAPST) were concluded to affect the ripening initiation only in late-season apple cultivars, but not in early- or mid-season ones.[20] Such discrepancy in different studies regarding the roles of the two null alleles of MdACS3a, particularly MdACS3a-G289V, calls for further investigations into the role of MdACS3a-G289V. Nevertheless, alleles MdACS1–2 and Mdacs3a (CAPST) are clearly demonstrated to be beneficial for breeding apples of low or delayed ethylene profiles in this study, a first effort that simultaneously assessed the roles of MdACS1 and MdACS3a in fruit ethylene production and softening in highly diverse Malus materials.

Markers ACS1, CAPS866 and CAPS870

The assessment of the roles of MdACS1 and MdACS3a in apple fruit ethylene production and softening largely relied on the previously developed marker ACS1[10,11] and the two markers CAPS866 and CAPS870 developed in this study. Since CAPS866 directly detects the mutation SNP G866/T866, CAPS866 is an unequivocal marker for identifying the functionally null allele MdACS3a-G289V.[18] Marker CAPS870 detects SNP C870/T870 that does not correspond to a change in the encoding amino acid, that is, CAPS870 detects a silent mutation in MdACS3a. Regardless of the nature of SNP C870/T870, T870 is a genetic signature for allele Mdacs3a as the mutation was identified in ‘Fuji’, the very source from which the transcriptional null allele Mdacs3a was originally defined.[18] Based on the genomic DNA sequences from ‘Fuji’, alleles MdACS3a (JF833309) and Mdacs3a (JF833309) differ by 14 nucleotides, and of these, only 4 were within the coding sequence.[20] Sequencing of the 92 Malus accessions in this study indicated that SNP C870/T870 is authentic and varying only between 2 nucleotides C870 and T870 (Figure 2, Supplementary Table S3). These data strongly support that CAPS870 is a reliable marker for detecting allele Mdacs3a. Since both CAPS866 and CAPS870 detect the characterized SNPs in the coding sequence of MdACS3a and can be simply performed by electrophoresis on agarose gels, the two markers are readily applicable for marker-assisted selection in apple breeding.

Since SNP C870/T870 is located only four bases downstream of SNP G866/T866, markers CAPS866 and CAPS870 were once considered to be used as a single marker in this study. However, such usage would lead to an ambiguous scenario for allelotype G866T866/C870T870 as it could be formed by a combination either between gametes G866T870 and T866C870 or between gametes G866C870 and T866T870. To avoid such possible uncertainty, the two markers were used independently.

Previously, an SSR marker targeting at the promoter region of MdACS3a was developed and used to allelotype MdACS3a in 103 apple varieties.[20] It was shown that three alleles (331, 353, and 359 bp) of the SSR marker corresponded to the wild-type allele MdACS3a (that is, MdACS3a-1 in ref. 20), two alleles (333 and 335 bp) to Mdacs3a (that is, MdACS3a-2) and one allele (361 bp) to MdACS3a-G289V (that is, MdACS3a-1V). This makes the corresponding relationship between the SSR marker alleles and the MdACS3a alleles somewhat indirect and inconvenient. Since the size of the SSR marker alleles frequently differ by 2 bp, an automatic DNA sequencer-based detection system is necessary, thereby requiring more sophisticated handling and analysis, compared with the agarose gel-based markers CAPS866 and CAPS870. However, identical allelotypes were observed for all 19 apple cultivars used by co-insistence in both studies (Supplementary Table S4), suggesting that the SSR marker and the 2 CAPS markers are useful for allelotyping of MdACS3a. As expected, identical allelotypes for MdACS1 were also obtained for the 19 common apple cultivars between these 2 studies (Supplementary Table S4).

It should be mentioned that two degenerated CAPS (dCAPS) markers were developed to confirm alleles Mdacs3a and MdACS3a-G289V in cDNA, but the two dCAPS markers were not used for allelotyping the MdACS3a alleles.[20] Therefore, the applicability of the dCAPS markers is unknown in diverse apples.

Utility of the data

Of the 952 Malus accessions, 97 were evaluated for their fruit ethylene production and softening at 5 time points over a 20-day post-harvest period (Supplementary Table S3). Although most accessions seemed to have predictable ethylene-regulated post-harvest behaviors, ‘Virginia Gold’ (PI588778, M. domestica) was unusual as it had minimal firmness loss (comparable to ‘Fuji’) during the 20-day storage while producing high levels of ethylene (comparable to ‘Golden Delicious’). This suggested that the slow softening (long-shelf life) character of ‘Virginia Gold’ is likely less dependent on ethylene production. More importantly, 'Virginia Gold' has also been shown with an excellent storability.[32] To understand the lack of ethylene-related softening in ‘Virginia Gold’, several preliminary experiments have been initiated by the authors. In melon, it was reported that flesh softening involved both ethylene-dependent and -independent components.[33] In tomato, the ethylene-independent aspects of fruit ripening were evidenced to be regulated by the FRUITFULL homologs.[34] It is possible that investigating fruit softening independent of or less dependent on ethylene production would lead to new knowledge for better understanding of the apple fruit-ripening process, promising an interesting research area in apple post-harvest biology.

In addition, the data set of allelotypes for genes MdACS1 and MdACS3a generated in the 952 Malus accessions would be useful for other future studies involving MdACS1 and MdACS3a, which are the only 2 apple ACS genes known to be expressed specifically in fruit and associated with apple fruit ethylene production and firmness.[8,9,13] The data set, together with three markers ACS1, CAPS866 and CAPS870, would be also useful for planning new crosses for developing improved apples with low ethylene and reduced loss of firmness.

Usage of terms allelotype and allelotyping

Term allelotype is defined as ‘the frequency of alleles in a breeding population.’ according to 'A Dictionary of Genetics'.[35] In this study, allelotype is referred to the allele composition at a specific gene locus, that is, MdACS1 or MdACS3a, in individual accessions, highly similar to term ‘genotype’ for a given DNA marker. Such usage of allelotype represents a drift from or an expansion for the original definition of allelotype defined in the dictionary. However, the usage offers convenience for describing allele composition at a specific gene locus. Indeed, such usage has been adapted already in literature.[14,18,20]

The definition for term allelotyping in ''Encyclopedia of Genetics, Genomics, Proteomics, and Informatics'[36] reads ‘Allelotyping is the determination of the spectrum and frequency of allelic variations in a population.’ The usage of allelotyping in this study is largely covered by the definition, but an extension to include activities for determining allelotype (allele composition at a specific gene locus) is also practiced.

Conclusions

A substantial effort to simultaneously assess the roles of MdACS1 and MdACS3a in fruit ethylene production and softening in diverse Malus materials is presented in this study. The most relevant findings include: (1) MdACS1 had much greater direct influence on fruit ethylene production and softening than MdACS3a. (2) Allele MdACS1–2 was associated with low ethylene and slow softening while MdACS1-1 with high ethylene and rapid softening. (3) Under the same background of MdACS1 allelotypes, the transcriptional null allele Mdacs3a, rather than the functional null allele ACS3a-G289V, significantly delayed the time required to reach the climacteric ethylene peak. (4) Alleles MdACS1–2 and Mdacs3a, but not ACS3a-G289V, were highly enriched in M. domestica and M. hybrid when compared with those in the M. sieversii. Overall, this study provides important information as to which alleles of MdACS1 and MdACS3a are beneficial for low and delayed ethylene production and how these beneficial alleles can be selected for apple improvement.