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International Journal of Horticulture 2024, Vol.14, No.5 http://hortherbpublisher.com/index.php/ijh © 2024 HortHerb Publisher, registered at the publishing platform that is operated by Sophia Publishing Group, founded in British Columbia of Canada. All Rights Reserved. Publisher HortHerb Publisher Edited by Editorial Team of International Journal of Horticulture Email: edit@ijh.hortherbpublisher.com Website: http://hortherbpublisher.com/index.php/ijh Address: 11388 Stevenston Hwy, PO Box 96016, Richmond, V7A 5J5, British Columbia Canada International Journal of Horticulture (ISSN 1927-5803) is an open access, peer reviewed journal published online by HortHerb Publisher. The journal publishes all the latest and outstanding research articles, letters and reviews in all aspects of horticultural and its relative science, containing horticultural products, protection; agronomic, entomology, plant pathology, plant nutrition, breeding, post harvest physiology, and biotechnology, are also welcomed; as well as including the tropical fruits, vegetables, ornamentals and industrial crops grown in the open and under protection. HortHerb Publisher is an international Open Access publisher specializing in horticulture, herbal sciences, and tea-related research registered at the publishing platform that is operated by Sophia Publishing Group (SPG), founded in British Columbia of Canada. All the articles published in International Journal of Horticulture are Open Access, and are distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. HortHerb Publisher uses CrossCheck service to identify academic plagiarism through the world’s leading plagiarism prevention tool, iParadigms, and to protect the original authors’ copyrights.
International Journal of Horticulture (online), 2024, Vol. 14, No.5 ISSN 1927-5803 http://hortherbpublisher.com/index.php/ijh © 2024 HortHerb Publisher, registered at the publishing platform that is operated by Sophia Publishing Group, founded in British Columbia of Canada. All Rights Reserved. Latest Content Assessment of Physical and Chemical Properties of Different Cultivars of Apple (Malus spp) in Mustang, Nepal Subash Saud, Padma Nath Atreya, Nitisha Bhattarai, Suman Dhakal, Amrit Kumar Bohara International Journal of Horticulture, 2024, Vol. 14, No. 5, 275-282 Decoding the Cucumber Genome: Functional Genomics and Its Applications in Genetic Improvement Xuewen Xu, Xiaodong Yang, Xuehao Chen International Journal of Horticulture, 2024, Vol. 14, No. 5, 283-296 Genetic Study of Pigment Synthesis and Related Genes in Dragon Fruit Jungui Xu, Zizhong Wang International Journal of Horticulture, 2024, Vol. 14, No. 5, 297-309 Effect of Drying Methods on Physicochemical Properties of Hot Pepper Milkesa Tujoo Feyera, Umer Asrat, Melkamu Hinsermu International Journal of Horticulture, 2024, Vol. 14, No. 5, 310-318 A Comprehensive Analysis of Genomic Advances and CRISPR/Cas9 Applications in Kiwifruit (Actinidia chinensis Planch.) Baofu Huang International Journal of Horticulture, 2024, Vol. 14, No. 5, 319-332
International Journal of Horticulture, 2024, Vol.14, No.5, 275-282 http://hortherbpublisher.com/index.php/ijh 275 Research Article Open Access Assessment of Physical and Chemical Properties of Different Cultivars of Apple (Malus spp) in Mustang, Nepal Subash Saud1 , Padma Nath Atreya2, Nitisha Bhattarai 1, Suman Dhakal 3, Amrit Kumar Bohara4 1 Faculty of Agriculture, Agriculture and Forestry University, Rampur, Chitwan, 44209, Nepal 2 Temperate Horticulture Development Center, Marpha, Mustang, 33100, Nepal 3 Department of Agronomy, Agriculture and Forestry University, Rampur, Chitwan, 44209, Nepal 4 Institute of Agriculture and Animal Sciences (IAAS), Prithu Technical College, Tribhuvan University, 22412, Nepal Corresponding author: subashsaud1111@gmail.com International Journal of Horticulture, 2024, Vol.14, No.5 doi: 10.5376/ijh.2024.14.0029 Received: 06 Jul., 2024 Accepted: 22 Aug., 2024 Published: 12 Sep., 2024 Copyright © 2024 Saud et al., This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Saud S., Atreya P.N., Bhattarai N., Dhakal S., and Bohara A.K., 2024, Assessment of physical and chemical properties of different cultivars of apple (Malus spp) in Mustang, Nepal, International Journal of Horticulture, 14(5): 275-282 (doi: 10.5376/ijh.2024.14.0029) Abstract This study was conducted at Temperate Horticulture Development Center, Marpha, Mustang to evaluate the physical and chemical properties of six different cultivars of apple (Tsukura, Saune, Red Delicious, Rich a Red Delicious, Royal Delicious and Golden Delicious) from January to September 2023. For the experiment, four trees of each cultivar were selected as replication and cultivar as treatment which was laid out in Randomized Complete Block Design (RCBD). Physical and chemical properties were studied by harvesting. Physical characteristics included individual fruit weight, fruit volume, fruit length, fruit width, individual seed weight, seed length and seed width and mesocarp thickness. Chemical characteristics included pH, TSS, TA and TSS/TA. Data analysis was done through R Studio. Physical and chemical characteristics varied considerably among cultivars. Physical characteristics revealed that the highest individual fruit weight (210.35 g) and size (Length 7.22 cm and Width 7.70 cm) was seen in Rich a Red Delicious and lowest in Tsukura whose weight was 22.25 g and size (Length 3.38 cm and Width 3.42 cm). Also, chemical analysis revealed that pH (4.57) was highest in Saune. TSS/TA was found maximum in Rich a Red Delicious (53.12) and minimum in Saune (17.30). From the study, it was found that Tsukura and Saune are suitable for juice purposes whereas the other four cultivars are suitable for fresh table consumption. Keywords Apple (Malus spp); Cultivar; Physical characteristics; Chemical characteristics 1 Introduction Apple is one of the edible fruits belonging to the genus Malus and family Rosaceae. Apple is a widely grown fruit tree especially grown in temperate regions of the world. Apple, with more than 7,500 (wild and commercial) cultivar types, a few are only famous (Kassebi and Korzenszky, 2022). Apples are bred for various tastes and uses, including cooking, and eating raw, dried apple, jam and cider production. The apple production, production area, and yield in Nepal are 52,753 Mt, 6,245 ha, and 8.45 Mt/ha, whereas in Mustang are 7,234 Mt, 565 ha, and 12.80 Mt/ha respectively (MoALD, 2023). Jumla district is the largest producer (13,958 Mt) of apples, while Mustang district has the highest productivity (12.80 Mt/ha) of apples. The export trend of Nepal at present scenario is null but the export was about 46297051 kg in the FY 2022/23. In FY 2017/18, Nepal used to export 3,075 kg of apples in the form of dried apples (MOICS, 2023). Differentiating apple cultivars across regions is still lacking (Weihle et al., 2021). Some cultivars (local and novel) are not valued due to a lack of information regarding their features (Szot et al., 2022). Commercial use of different cultivars of apples is not properly known. Therefore, it is pivotal to determine the pomological and chemical characteristics of different apple cultivars to make their correct use. Physical characteristics refer to the fruit characteristics including fruit color, average fruit size, fruit firmness, number of fruits/kg, and average fruit weight. Chemical characteristics of apples include TSS, TA, pH, TSS/TA, etc. Physico-chemical properties (Fruit firmness, pH, TSS, and TA) of apples depend upon the cultivar, maturity stages, and temperature (Teferra et al., 2021).
International Journal of Horticulture, 2024, Vol.14, No.5, 275-282 http://hortherbpublisher.com/index.php/ijh 276 This study was carried out to determine the physical and chemical characteristics of six different cultivars of apples found at Temperate Horticulture Development Center. Physical characteristics included individual fruit weight, fruit volume, fruit length, fruit width, individual seed weight, seed length and seed width and mesocarp thickness. Chemical characteristics included pH, TSS, TA and TSS/TA. They are crucial to determining the commercial value and consumer preference for the sweetness of different apple cultivars. It is very common to use the TSS/TA ratio to obtain better predictions of sweetness (Harkar et al., 2002). Apple fruit with TSS/TA ratios over 20 is considered to be sweet, while values under 20 are considered to be sour (Monteiro et al., 2018). 2 Materials and Methods 2.1 Research site The research was carried out at Temperate Horticulture Development Center (THDC), located at Gharapjhong Rural Municipality-2, Marpha, Mustang district. The center is coordinated at 28o20’ to 29o05’ N and 83o30’ to 84o15’ E with an altitude of 2,650 masl. Among four blocks of THDC (A, B, C and D), the experiment was conducted in block A from January to September 2023. 2.2 Climatic observation The meteorological data (temperature, relative humidity and precipitation) were estimated from the automatic weather station (Meteorological Station, Thakmarpha (Index No. 0604), Mustang) present in ‘Block C’ of THDC, Marpha. It is under the supervision of the Government of Nepal (Ministry of Energy, Water Resources and Irrigation, Department of Hydrology and Meteorology). Climatic variables during the study period were observed (Figure 1). Figure 1 Mean daily minimum and maximum temperature, relative humidity and rainfall recorded at the experimental site 2.3 Plant materials and design The experiment was carried out in Randomized Complete Block Design (RCBD) with 6 treatments and 4 replications in a single flowering season. Six cultivars of apple (Tsukura, Saune, Red Delicious, Royal Delicious, Rich a Red Delicious and Golden Delicious) were selected as treatment which was replicated four times (four trees per treatment) (Table 1). Training of all the trees aged 12-13 years was done on the Open Centre System. The rootstock used was the crab apple. They were planted at 5 m × 5 m distance.
International Journal of Horticulture, 2024, Vol.14, No.5, 275-282 http://hortherbpublisher.com/index.php/ijh 277 Table 1 Plant materials used in research S.N. Cultivars Origin 1. Tsukura Japan 2. Saune (Local) Nepal 3. Red Delicious United States 4. Royal Delicious n.d. 5. Rich a Red Delicious United States 6. Golden Delicious United States 2.4 Harvesting Fruits were manually harvested on a random basis from each tree when they were fully ripened. They were harvested on different dates (Table 2) and then packaged in plastic bags and sent to the pomology lab of THDC for analysis. Poor quality and damaged fruits were eliminated and they were kept in a refrigerator chamber at 0 °C until use. Table 2 Harvesting time of different apple cultivars at THDC, Marpha, Mustang, 2023 S.N. Cultivars Harvesting date 1. Tsukura 2nd July, 2023 2. Saune 14 August, 2023 3. Red Delicious 27th September, 2023 4. Golden Delicious 27th September, 2023 5. Rich a Red Delicious 27th September, 2023 6. Royal Delicious 27th September, 2023 2.5 Determination of physical and chemical characteristics 2.5.1 Linear dimension Thirty samples of fully ripened fruits were taken randomly for the study. Fruit and seed linear dimension (Mesocarp thickness, Individual fruit length, Individual fruit width, Individual seed length, and Individual seed width) was measured by using a vernier caliper with a level of accuracy of 0.01 mm (Jakobek et al., 2020; Korkmaz and Okatan, 2021). 2.5.2 Weight and volume Thirty samples of fully ripened fruits were taken randomly for the study. The fruit and seed weight were measured using a digital weighing machine (Dolkar et al., 2021). The xylometric/water displacement method was applied to measure the fruit volume of the apple. Water cannot be compressed, thus as long as the fruit absorbs a tiny amount of water, the change in water height should provide a close approximation of the fruit volume (Moreda et al., 2009). To minimize the error, a measuring cylinder of a small volume (300 mL) was used. Distilled water was half-filled in the cylinder and a single fruit was dipped in the cylinder at a time. The fruit was allowed to dip fully in water with the help of a metal sponge sinker and the rise in height was recorded. The difference between the initial and final reading of water in the measuring cylinder gives the fruit volume. The volume thus obtained is expressed in terms of mL or cm3 as 1 mL of water is equal to 1 cm3. 2.5.3 pH The pH was measured using a digital pH meter containing electrodes for precision (Mehta et al., 2019). Before measurement, calibration of the pH meter was done. For calibration, the pH meter was put in the buffer solution of pH 4 and pH 7. Then, the pH meter was washed using distilled water and was made ready for measurement. After measurement, it was again washed with distilled water and calibrated for taking the next measurement.
International Journal of Horticulture, 2024, Vol.14, No.5, 275-282 http://hortherbpublisher.com/index.php/ijh 278 2.5.4 Total soluble solids Total Soluble Solids (TSS) of the fruit was measured by using an ATC-1E automatic hand-held refractometer (Atago, Tokyo, Japan) with a 0-32 °Brix scale at 20 °C (Rydzak et al., 2021; Muharfiza et al., 2023). The refractometer was calibrated to zero using distilled water before using it. The fruit juice was drawn into a vessel and one to two drops of fruit juice was poured into the prismatic surface. After covering the prismatic surface with daylight diffusion cover, the TSS was observed from the eyepiece. 2.5.5 Titratable acidity 10 mL of juice was obtained by crushing apples. The titrable acidity (TA) of the fruit was determined as per the general procedures prescribed by (Paul et al., 2010; Teferra et al., 2021). Firstly, the juice from the fruit was extracted. 10 mL of extracted juice was taken in a conical container and an equal volume of distilled water was added. Further, two drops of phenolphthalein indicator were added to the container to determine the endpoint of the reaction. The burette was filled with 0.1N NaOH and the initial reading was taken. The diluted fruit juice was then titrated with 0.1 N NaOH until the color changed to pink. The color change represents the end point of the reaction and the final reading of the burette was taken. The difference between the initial and final reading of the burette gives the volume of NaOH consumed by fruit juice for neutralization. The TA thus obtained was expressed as the TA% or percentage of dominant organic acid or gram of dominant organic acid per 100 mL of fruit juice. The dominant organic acid found in the plum is malic acid and hence the TA% was expressed as % malic acid (gm malic acid/100 mL of juice). The TA of the fruit can be calculated as suggested by Paul et al. (2010): TA%= Vb ∗N∗Meq Va ∗100 Where, TA %: titrable acidity % or gm malic acid/100 mL of juice; Vb: total volume of NaOH consumed in the reaction, mL; N: normality of NaOH used (0.1N); Meq: milliequivalent of malic acid (0.067 for malic acid); Va: total volume of fruit juice used, ml (generally 10 mL is taken) 2.6 Statistical analysis Data entry was done with the help of MS Excel. All the data were subjected to one-way ANOVA (Analysis of Variance), with cultivars as the treatment. The differences between mean values were determined using Duncan’s multiple range test (DMRT) at a 5% significance level. DMRT is a simple and commonly used statistical tool for comparing the treatment means. All the statistical analyses were performed by using R packages. 3 Results and Analysis 3.1 Physical characteristics For individual fruit weight, the maximum was found in Rich a Red Delicious (210.35 g) and least was found in Tsukura (22.25 g). Golden Delicious (160.40 g) was statistically at par with Red Delicious (174.65 g) for fruit weight. Similarly, the highest and least value of fruit volume (200 cm3 and 20 cm3), fruit length (7.22 cm and 3.38 cm) and fruit width (7.70 cm and 3.42 cm) were observed in Rich a Red Delicious and Tsukura respectively. Royal Delicious (6.95 cm) showed statistically similar figure with Rich a Red Delicious and Saune (6.07 cm) was statistically at par with Golden Delicious (6.32 cm) for fruit length. For fruit width, Royal Delicious (7.17 cm), Golden Delicious (6.89 cm) and Red Delicious (7.70 cm) had similar figures. The highest value for individual seed weight was observed in Golden Delicious (0.40 g), seed length was observed in Rich a Red Delicious (0.80 cm), seed width was observed in Saune (0.40 cm), and the mesocarp thickness was seen in Royal Delicious and Rich a Red Delicious (2.72 cm). The lowest figures for individual seed weight (0.10 g), seed length (0.64 cm), seed width (0.27 cm) and mesocarp thickness (1.52 cm) was seen in Tsukura. For individual seed weight, Saune (0.32 g), Red Delicious (0.32 g), Rich a Red Delicious (0.39 g), Royal delicious (0.34 g) and Golden delicious were statistically similar. Red Delicious (0.75 cm), Golden Delicious (0.75 cm) and Royal Delicious (0.77 cm) were statistically at par with Rich a Red Delicious whereas Saune (0.70 cm) was statistically at par with Tsukura
International Journal of Horticulture, 2024, Vol.14, No.5, 275-282 http://hortherbpublisher.com/index.php/ijh 279 for seed length. Red Delicious (0.37 cm), Rich a Red Delicious (0.37 cm), and Golden Delicious (0.34 cm) were statistically at par with Saune whereas Royal Delicious (0.33 cm) was statistically par with Tsukura for seed width. Golden Delicious (2.45 cm) was statistically par with Rich a Red Delicious and Royal Delicious for mesocarp and Saune (1.72 cm) was statistically par with Tsukura for mesocarp thickness (Table 3; Table 4). Table 3 Physical characteristics of apple fruits from different cultivars at THDC, Marpha, Mustang, 2023 Cultivars Individual fruit weight (g) Fruit volume (cm3) Fruit length (cm) Fruit width (cm) Tsukura 22.25e 20.00e 3.38e 3.42d Saune 98.20d 93.75d 6.07d 6.38c Red Delicious 174.65c 173.75b 6.55bc 7.21b Golden Delicious 160.40c 157.5c 6.32cd 6.89b Rich a Red Delicious 210.35a 200.00a 7.22a 7.70a Royal Delicious 193.00b 190.15a 6.95ab 7.17b LSD(0.05) 16.77 15.34 0.43 0.49 SEm(±) 2.27 2.08 0.06 0.07 F probability <0.001 <0.001 <0.001 <0.001 CV(%) 7.77 7.32 4.68 5.00 Grandmean 143.14 139.19 6.08 6.46 Note: LSD= Least Significant Difference, SEm= Standard Error of Mean, CV: Coefficient of Variance; Means in the same column followed by the same letter(s) are not significantly different by DMRT at a 5% significance level Table 4 Physical characteristics of apple seeds from different cultivars at THDC, Marpha, Mustang, 2023 Cultivars Individual seed weight (g) Seed length (cm) Seed width (cm) Mesocarp thickness (cm) Tsukura 0.10b 0.64c 0.27c 1.52c Saune 0.32a 0.70bc 0.40a 1.72c Red Delicious 0.32a 0.75ab 0.37ab 2.30b Golden Delicious 0.40a 0.75ab 0.34ab 2.45ab Rich a Red Delicious 0.39a 0.80a 0.37ab 2.72a Royal Delicious 0.34a 0.77ab 0.33bc 2.72a LSD(0.05) 0.14 0.08 0.06 0.33 SEm(±) 0.02 0.01 0.01 0.04 F probability <0.01 <0.01 <0.01 <0.001 CV(%) 30.73 7.35 11.80 9.72 Grandmean 0.31 0.73 0.35 2.24 Note: LSD= Least Significant Difference, SEm= Standard Error of Mean, CV: Coefficient of Variance; Means in the same column followed by the same letter(s) are not significantly different by DMRT at a 5% significance level 3.2 Chemical characteristics The highest value of pH was found in Saune (4.30), TSS was found in Golden Delicious (11.87 °Brix), TA was found in Saune (0.60%) and TSS/TA was found in Rich a Red Delicious (53.12). The lowest value of pH was found in Golden Delicious (3.22), TSS was found in Tsukura (8.52 °Brix), TA was found in Rich a Red Delicious (0.20 %) and TSS/TA was found in Saune (17.30). Rich a Red Delicious (3.77) was statistically at par with Red Delicious and Royal Delicious having a pH of 3.87. Red Delicious (9.90 °Brix), Saune (10.27 °Brix) and Rich a Red Delicious (10.62 °Brix) were statistically at par with Royal Delicious (10.65 °Brix) for TSS. Red Delicious (0.23 %) and Golden Delicious (0.24 %) were statistically par with Rich a Red Delicious for TA. Tsukura (19.37) was statistically par with Saune for TSS/TA (Table 5).
International Journal of Horticulture, 2024, Vol.14, No.5, 275-282 http://hortherbpublisher.com/index.php/ijh 280 Table 5 Chemical characteristics of different apple cultivars at THDC, Marpha, Mustang, 2023 Cultivars pH TSS (°Brix) TA(%) TSS/TA Tsukura 4.30b 8.52c 0.44b 19.37e Saune 4.57a 10.27b 0.60a 17.30e Red Delicious 3.87c 9.90b 0.23d 43.04c Golden Delicious 3.22d 11.87a 0.24d 48.52b Rich a Red Delicious 3.77c 10.62b 0.20d 53.12a Royal Delicious 3.87c 10.65b 0.30c 34.95d LSD(0.05) 0.14 0.95 0.04 3.1 SEm(±) 0.02 0.13 0.01 0.42 F probability <0.001 <0.001 <0.001 <0.001 CV(%) 2.36 6.10 8.60 5.71 Grandmean 3.93 10.31 0.34 36.05 Note: LSD: Least Significance Difference, SEm: Standard Error of mean, CV: Coefficient of Variance; Means in the same column followed by the same letter(s) are not significantly different by DMRT at a 5% significance level 4 Discussion Poor yielding due to unfavorable climatic conditions (heavy rainfall during flowering season) could be the reason for significant variation in size among different cultivars (Yoon et al., 2020). Genetics study suggests that genes involved in cell division and cell expansion is potentially responsible for regulating fruit size (Devoghalaere et al., 2012). Furthermore, the differential genes related to auxin signaling, including the auxin synthetic genes MdTAR1 and MdYUCCA6 results in greater fruit weight in various cultivars (Bu et al., 2020). Thus, the higher fruit weight in Rich a Red Delicious cultivar may be primarily due to underlying genetic and environmental factors. Low fruit weight and firmness of native cultivars are due to adaptive mechanisms to environment and genetic factors (Teferra et al., 2021). The physicochemical properties of apples depend upon cultivars, maturity stages, and temperature. The difference in pomological characteristics may be a result of cultivar, rootstock, cultural practices as well as variations in fruit formation (Bogbuga and Pirlak, 2012). Dolkar et al. (2021) observed the fruit weight of Royal Delicious was significantly higher than all the native cultivars of the Ladakh region. Korkmaz and Okatan (2021) found that fruit widths were found to vary from 77.61 mm to 55.24 mm and fruit length values were found to be between 65.92 mm and 54.89 mm. The fruit weight of different genotypes was found between 81.3 and 125.4 g as observed by Gecer et al. (2020) similar to Saune. Individual fruit weight of Red Delicious was found higher than Golden Delicious as observed by Loncaric et al. (2019) and also observed highest fruit weight, height and width were measured in the conventional apple cultivar, ‘Red Delicious’, and the lowest in traditional apple cultivar which was similar to Tsukura and Saune. Loncaric et al. (2019) showed that the mass of average one healthy seed was higher for conventional cultivars (60±10 mg) than traditional cultivars (48±11 mg) and also Golden Delicious showed similar results as Red Delicious similar to my findings. Sedlackova et al. (2021) found that the average weight of 10 seeds was 0.38-0.77/0.29-0.98 (g), the height of seeds was 6.68-9.90/6.16-9.83 (mm), and the diameter of seeds was 3.73-5.71/3.51-5.27 (mm), respectively for seeds of repository and self-grown seedling. Our measured value in chemical characteristics varied significantly probably due to inter annual climatic variability and accessions (Mignard et al., 2022). Sweetness and sourness are considered important drivers for consumer preference (Endrizzi et al., 2015). Increase in sorbitol content is positively correlated with increase in TSS. Thus, Highest TSS in Golden Delicious was due to highest level of sorbitol content. The increase in acidity in certain cultivars of apple is due to accumulation of malic acid and L-ascorbic acid (Yoon et al., 2020). Therefore, highest value of TA was detected in Saune due to presence of highest concentration of dominant organic acids. The TSS, TA and TSS/TA (ripening ratio) harvested in different dates varied from 8.52-13.2 °Brix, 0.21%-0.30% and 28.17-61.81 for Royal Delicious according to Chalise and Giri (2019). Bhusan and Thomas (1998) found that the pH of Red Delicious, Golden Delicious, Royal Delicious and Rich a Red Delicious to be 3.7, 3.5, 3.6 and 3.7 respectively and TA to be Golden Delicious, Royal Delicious, Red Delicious and Rich a Red Delicious were (0.24±0.02)%, (0.24±0.01)%, (0.23±0.02)% and (0.21±0.01)%, respectively, which showed
International Journal of Horticulture, 2024, Vol.14, No.5, 275-282 http://hortherbpublisher.com/index.php/ijh 281 correspondence with our research results. Dolkar et al. (2021) found that some native cultivars have the highest TA (0.71±0.02%) among other cultivars as Saune (0.60 %). Korkmaz and Okatan (2021) showed that the TA of all 6 apple genotypes was >0.64 %. Kalkisim et al. (2015) found the average pH value of the native cultivar to be 3.8 and TA to be 0.69 %. Molina-Corral et al. (2021) found TSS of Golden Delicious (12.7-13.1 °Brix) was higher than Red Delicious (11.3-11.7 °Brix) grown at both locations in Washington, USA, and Chihuahua, Mexico similar to our findings. 5 Conclusion From the study, it can be inferred that Rich a Red Delicious was found best cultivar in terms of sweetness, size and weight among six cultivars of apple. It is suggested that Tsukura and Saune (TSS/TA<20) can be cultivated targeting for juice purposes whereas the other four cultivars (TSS/TA>20) targeting for fresh table consumption in the Mustang region. Further investigation on physical and chemical properties of different cultivars of apple in Mustang is required before recommending different apple cultivars in Mustang, Nepal. Authors’ contributions SS and NB were involved in conceptualization, conducting the experiment, data curation, editing, data analysis, and writing the original draft. PNA and SD were involved in supervision, manuscript revision, and providing the final structure to the manuscript. AKB was involved in data curation, data analysis and reviewing the manuscript. All authors read and approved the final manuscript. Acknowledgment The authors would like to acknowledge the assistance of the Prime Minister Agriculture Modernization Project, Project Implementation Unit, Mustang for providing an opportunity to conduct field research. The author feels grateful especially to the office members of THDC, Marpha, Mustang, who provided technical support during the research period. Conflict of Interest Disclosure The authors affirm that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest. References Bhusan B., and Thomas P., 1998, Quality of apples following gamma irradiation and cold storage, International Journal of Food Sciences and Nutrition, 49: 485-492. https://doi.org/10.3109/09637489809086429 Bogbuga F., and Pirlak L., 2012, Determination of phenological and pomological characteristics of some apple cultivars in Nigde-Turkey ecological conditions, The Journal of Animal & Plant Sciences, 22(1): 183-187. Bu H., Yu W., Yuan H., Yue P., Wei Y., and Wang A., 2020, Endogenous auxin content contributes to larger size of apple fruit, Frontiers in Plant Science, 11: 1-11. https://doi.org/10.3389/fpls.2020.592540 Chalise B., and Giri R., 2019, Determination of optimum harvesting date for 'Royal Delicious' apple (Malus domestica Borkh.) at Jumla, Nepal, International Journal of Advanced Research in Biological Sciences, 6(12): 131-139. Devoghalaere F., Doucen T., Guitton B., Keeling J., Payne W., Ling T.J., Ross J.J., Hallett I.C., Kularajathevan G., Dayatilake G.A., Diak R., Breen K.C., Tustin D.S., Costes E., Chagne D., Schaffer R.J., and David K.M., 2012, A genomics approach to understanding the role of auxin in apple (Malus x domestica) fruit size control, BMC Plant Biology, 12: 1-15. https://doi.org/10.1186/1471-2229-12-7 Dolkar T., Kumar D., Chandel J., Angmo S., Chaurasiya O., and Stobdan T., 2021, Phenological and pomological characteristics of native apple (Malus domestica Borkh.) cultivars of trans-Himalayan Ladakh, India, Defence Life Science Journal, 6(1): 63-68. https://doi.org/10.14429/dlsj.6.15726 Endrizzi I., Torri L., Corollaro M.L., Demattè M.L., Aprea E., Charles M., Biasioli F., and Gasperi F., 2015, A conjoint study on apple acceptability: Sensory characteristics and nutritional information, Food Quality and Preference, 40: 39-48. https://doi.org/10.1016/j.foodqual.2014.08.007 Gecer M., Ozkan G., Sagbas H., Ilhan G., and Gundogdu M., 2020, Some important horticultural properties of summer apple genotypes from Coruh Valley in Turkey, International Journal of Fruit Science, 20(3): 1406-1414. https://doi.org/10.1080/15538362.2020.1796888 Harkar F., Marsh K., Young H., Murray S., Gunson F., and Walker S., 2002, Sensory interpretation of instrumental measurements: sweet and acid taste of apple fruit, Post Harvest Biology and Biotechnology, 24(3): 241-250. https://doi.org/10.1016/S0925-5214(01)00157-0
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International Journal of Horticulture, 2024, Vol.14, No.5, 283-296 http://hortherbpublisher.com/index.php/ijh 283 Feature Review Open Access Decoding the Cucumber Genome: Functional Genomics and Its Applications in Genetic Improvement Xuewen Xu, Xiaodong Yang, Xuehao Chen School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, Jiangsu, China Corresponding author: xhchen@yzu.edu.cn International Journal of Horticulture, 2024, Vol.14, No.5 doi: 10.5376/ijh.2024.14.0030 Received: 18 Jul., 2024 Accepted: 25 Aug., 2024 Published: 20 Sep., 2024 Copyright © 2024 Xu et al., This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Xu X.W., Yang X.D., and Chen X.H., 2024, Decoding the cucumber genome: functional genomics and its applications in genetic improvement, International Journal of Horticulture, 14(5): 283-296 (doi: 10.5376/ijh.2024.14.0030) Abstract Cucumber (Cucumis sativus L.), as an important global economic crop, has significant implications for enhancing yield and quality through the decoding of its genome. The development of functional genomics provides powerful tools for cucumber genome research. Utilizing high-throughput sequencing and gene editing technologies, researchers can gain insights into the structure and function of the cucumber genome. This review uses functional genomics to analyze key genes in the cucumber genome, exploring their roles in disease resistance, fruit quality, and stress tolerance. The results showed that through a comprehensive analysis of the cucumber genome, a series of disease resistance-related genes were identified, and the disease resistance of cucumbers was successfully enhanced through gene editing technology. Additionally, by regulating genes related to fruit development, the quality of cucumber fruits was significantly improved, and the yield under stress conditions was increased. These findings highlight the potential of functional genomics in cucumber improvement, providing new ideas and approaches for crop breeding. This review not only supports theoretical research on gene function in cucumbers but also offers valuable references for functional genomics in other crops. Keywords Cucumber genome; Functional genomics; Crop improvement; High-throughput sequencing; Disease resistance 1 Introduction Cucumber (Cucumis sativus L.) is a significant vegetable crop cultivated worldwide, valued for its nutritional content and economic importance. It is a rich source of vitamins and minerals, making it a staple in many diets (Han et al., 2022). Additionally, cucumber serves as a model system for studying sex determination and plant vascular biology, further highlighting its scientific relevance (Huang et al., 2009; Li et al., 2019). The crop's relatively small, diploid genome, short life cycle, and self-compatible mating system offer advantages for genetic studies and breeding programs (Wang et al., 2020). Research on the cucumber genome has advanced significantly over the years. The initial draft genome sequence of Cucumis sativus var. sativus L. was assembled using a combination of traditional Sanger and next-generation Illumina GA sequencing technologies, achieving 72.2-fold genome coverage (Huang et al., 2009). This foundational work revealed key insights into the cucumber's genetic structure, including the absence of recent whole-genome duplication and the presence of few tandem duplications, which explain the small number of genes in the cucumber (Huang et al., 2009). Subsequent efforts have improved the quality and completeness of the cucumber genome assembly. For instance, a high-quality reference genome was generated using single-molecule real-time (SMRT) long reads, yielding more sequence data and identified novel genes and retrotransposons (Li et al., 2019). These advancements have facilitated the identification of genes and quantitative trait loci (QTL) responsible for key phenotypic traits, aiding in marker-assisted selection and breeding (Wang et al., 2018; Wang et al., 2020). In this review, we summarized advancements in cucumber genome decoding and its applications for crop improvement. And extensively discussed the identification of genes associated with key horticultural traits such as disease resistance, fruit quality, and stress tolerance through genomic technologies and genetic analysis.
International Journal of Horticulture, 2024, Vol.14, No.5, 283-296 http://hortherbpublisher.com/index.php/ijh 284 Additionally, we highlighted recent progress in developing molecular markers and genetic maps for breeding programs aimed at enhancing desirable traits. This review provides valuable insights for genetic research, gene discovery, and the development of superior cucumber varieties, thereby supporting the sustainable advancement of cucumber breeding. 2 Cucumber Genome Structure 2.1 Genome size and organization The cucumber genome is relatively small, with an estimated size of approximately 367 Mbp. Recent advancements in sequencing technologies have enabled the assembly of high-quality reference genomes. For instance, the research team generated a high-quality cucumber reference genome using advanced technologies such as PacBio, 10X Genomics, and Hi-C, resulting in a total length of 226.2 Mb and an N50 of 8.9 Mb (Li et al., 2019). This assembly revealed new features, including 1,374 full-length long terminal retrotransposons and 1,078 novel genes, showcasing many new characteristics of the cucumber genome (Li et al., 2019). Additionally, the genome of Cucumis hystrix, a wild species closely related to cucumber, was assembled to a size of 289 Mb, providing insights into the genetic diversity and potential for introgression in cucumber breeding (Qin et al., 2021). The study indicates that Cucumis hystrix is cross-compatible with cultivated cucumber, which offers the potential for enriching the cucumber gene pool and improving traits such as disease resistance and stress tolerance. 2.2 Chromosome mapping Chromosome mapping in cucumber has been significantly advanced through various genomic and cytogenetic techniques. Li et al. (2019) assembled a high-quality cucumber genome reference, which includes 174 contigs with a total length of 226.2 Mb and an N50 of 8.9 Mb, providing 29.0 Mb more sequence data than previous versions. Through the use of 10X Genomics and Hi-C data, 89 contigs (approximately 211.0 Mb) were directly connected into 7 pseudomolecule sequences. This high-quality genome reveals new features of the cucumber genome and serves as a valuable resource for cucumber and plant comparative genomics studies (Li et al., 2019). Turek et al. (2023) conducted a structural analysis of the B10v3 cucumber genome by integrating biological and bioinformatics data. The study demonstrated that by aligning sequences with the reference genome, the RagTag program was used to reorder the sequenced contigs, confirming the chromosomal positions of approximately 98% of protein-coding genes. Additionally, BLAST analysis revealed similarities and differences between the B10v3 genome and other cucumber cultivar genomes (Turek et al., 2023). These studies indicate that by integrating advanced genomic sequencing technologies such as SMRT long-read sequencing, 10X Genomics, and Hi-C data, cucumber chromosomal mapping and genome assembly have reached a new level, providing a solid foundation for cucumber genomics research and breeding. 2.3 Gene content and distribution The cucumber genome contains a diverse array of genes, and significant progress has been made in the functional annotation of protein-coding genes. A recent study identified 94,486 pairs of homologous protein-coding genes between cucumber and 14 other angiosperm species (Song et al., 2018). These homologous genes were used as proxies for functional annotation, significantly improving the accuracy of gene function prediction in cucumber. The study ultimately assigned Gene Ontology (GO) terms to 10,885 cucumber protein-coding genes, demonstrating improved annotation accuracy compared to existing methods (Song et al., 2018). Genome-wide association studies (GWAS) have identified regions associated with important horticultural traits, providing valuable resources for crop improvement (Wang et al., 2018). Additionally, the identification of QTL and molecular marker genes has further deepened the understanding of the genetic basis of key phenotypic traits in cucumber (Wang et al., 2020).
International Journal of Horticulture, 2024, Vol.14, No.5, 283-296 http://hortherbpublisher.com/index.php/ijh 285 3 Functional Genomics of Cucumber Functional genomics is a field of molecular biology that attempts to describe gene functions and interactions. In cucumbers, functional genomics encompasses various omics technologies, including transcriptomics, proteomics, and metabolomics, to understand the complex biological processes and improve crop traits. 3.1 Transcriptomics Transcriptomics involves the study of the entire set of RNA transcripts produced by the genome under specific conditions or within specific cells. In cucumber, transcriptome analysis has played a significant role in identifying gene expression patterns related to various traits such as fruit development, stress response, and disease resistance. For example, the 'Chinese Long' cucumber variety has undergone whole-genome sequencing, and transcriptomic, proteomic, and metabolomic data have been obtained. These research data provide scientists with a comprehensive understanding of the physiological characteristics and molecular developmental mechanisms of 'Chinese Long' cucumber, particularly in the improvement of fruit quality (Han et al., 2022). Moreover, the WRKY gene family plays an essential role in stress response. Extensive research using transcriptomics has revealed specific genes that respond to biotic and abiotic stresses (Chen et al., 2020). The study identified 61 WRKY genes in cucumber and explored their roles in responding to various biotic and abiotic stresses (Figure 1). Through gene expression analysis, it was found that CsWRKY27, CsWRKY50, and CsWRKY52 were significantly expressed under all stress treatments, indicating that these genes might play a crucial role in stress tolerance in cucumber (Chen et al., 2020). Additionally, CsWRKY46 was expressed only under biotic stress, while CsWRKY57 showed a significant response to salt and heat stress. These findings provide new insights into the functional roles of WRKYgenes in cucumber stress responses. 3.2 Proteomics Proteomics is the large-scale study of proteins, particularly their structures and functions. In cucumber, proteomic studies have been employed to understand the protein expression profiles and their modifications under different conditions. One study by Hao et al. (2020) analyzed the differentially expressed proteins in cucumber fruits under nitrogen deficiency using proteomics methods, finding that these proteins were mainly associated with carbon metabolism, amino acid synthesis, ascorbate metabolism, and the proteasome. Nitrogen deficiency enhanced the glucose phosphorylation process while inhibiting the pentose phosphate pathway, significantly affecting carbon metabolism and the synthesis of most amino acids, and possibly leading to the accumulation of ascorbate in cucumber fruits. Another study provided updated functional annotations for protein-coding genes in the cucumber genome. By comparing the genomes of 15 species, the study identified 94,486 orthologous protein-coding gene pairs (OPPs) between cucumber and 14 other angiosperms and assigned GO terms to 10,885 cucumber protein-coding genes. This study proposed an effective strategy for transferring functional information from protein-coding genes in model plants to newly sequenced or "non-model" plant species (Song et al., 2018). Additionally, the development of an EMS mutant library facilitated the identification of proteins associated with various phenotypic traits, thereby deepening the understanding of the genetic basis of these traits (Chen et al., 2018). 3.3 Metabolomics Metabolomics is the study of chemical processes involving metabolites, the small molecule substrates, intermediates, and products of metabolism. In cucumbers, metabolomic analyses have been used to profile the metabolites associated with fruit quality and stress responses. The integration of metabolomic data with transcriptomic and proteomic data has provided a comprehensive understanding of the metabolic pathways and their regulation. For example, the complete sequencing of the "Chinese Long" cucumber genome has enabled the identification of key metabolites involved in fruit quality and stress tolerance, which are crucial for molecular breeding programs aimed at improving cucumber varieties (Kumar et al., 2020; Han et al., 2022).
International Journal of Horticulture, 2024, Vol.14, No.5, 283-296 http://hortherbpublisher.com/index.php/ijh 286 Additionally, Miao et al. (2019) demonstrated that grafting has a significant impact on the flavor of cucumber fruits. After grafting with different rootstocks, there were notable changes in the metabolites, such as sugars and amino acids, within cucumber fruits. Through an integrated analysis of metabolomics and transcriptomics, candidate genes related to sugar metabolism and volatile compound synthesis were identified, providing scientific evidence for improving the fruit flavor of grafted cucumbers (Miao et al., 2019). The integration of transcriptomics, proteomics, and metabolomics in cucumber research has significantly advanced our understanding of the functional genomics of this important crop. These omics technologies provide valuable insights into the genetic and molecular mechanisms underlying key traits, thereby facilitating the development of improved cucumber varieties through molecular breeding techniques. Figure 1 Expression profiles of CsWRKYgenes in response to various abiotic stress treatments (Adopted from Chen et al., 2020) Image caption: The figure shows the expression patterns of cucumber WRKY genes under different abiotic stresses (salt stress and heat stress), with changes in gene expression before and after stress treatments displayed in the form of a heatmap. The color gradient from green to red represents a decrease or increase in gene expression levels. The results indicate that several WRKY genes exhibit significant expression changes under salt and heat stress, particularly WRKY27, WRKY50, and WRKY52, which respond significantly to both types of stress. This suggests that these genes may play a key role in cucumber's response to abiotic stress, revealing the potential function of WRKY genes in enhancing cucumber's stress tolerance and providing important insights for further exploration of their specific mechanisms in stress responses (Adapted from Chen et al., 2020)
International Journal of Horticulture, 2024, Vol.14, No.5, 283-296 http://hortherbpublisher.com/index.php/ijh 287 4 Key Genes and Pathways in Cucumber 4.1 Disease resistance genes Cucumber plants have developed various genetic mechanisms to resist diseases, particularly those caused by pathogens such as the root-knot nematode (Meloidogyne incognita). Research has identified several key genes and pathways involved in this resistance. For instance, the comparative transcriptomic analysis between susceptible cucumber inbred line Q24 and resistant Cucumis metuliferus (CM) revealed that genes associated with Ca2+ signaling, salicylic acid (SA)/jasmonate (JA) signaling, and auxin (IAA) signaling pathways play crucial roles in mediating resistance. Genes for calmodulin and calcium-binding proteins were upregulated in CM, while SA/JA synthesis and signal transduction genes were markedly activated, and IAA signaling pathway genes were inhibited upon infection (Li et al., 2021). Cheng et al. (2019) conducted a genome-wide analysis and identified several candidate genes within QTL regions associated with resistance to root-knot nematodes in cucumber. These genes are primarily involved in the expression of disease resistance proteins and the regulation of plant hormone signaling pathways, such as the SA and JA signaling pathways. Additionally, WRKY transcription factors have been shown to respond to biotic stresses, including infections from downy mildew and powdery mildew, indicating their role in disease resistance (Chen et al., 2020). 4.2 Growth and development pathways The growth and development of cucumber plants are regulated by various transcription factors and gene families. The GRAS transcription factors, for example, are involved in regulating plant growth and development. CsGRAS2 (DELLA) and CsGRAS26(LISCL) have been identified as key regulators in cucumber, influencing growth through their response to phytohormones such as gibberellin (GA) and abscisic acid (ABA) (Li et al., 2020a). Similarly, the WRKY gene family has been implicated in plant growth and organ development, with certain WRKY genes showing organ-specific expression patterns (Chen et al., 2020). The DUF966 genes also play a significant role in fruit development, with CsDUF966_4.cand CsDUF966_7.cbeing strongly selected during cucumber breeding programs for their regulation of fruit growth (Tian et al., 2022). 4.3 Stress response mechanisms Cucumber plants encounter various abiotic stresses, such as salinity, heat, and drought, which necessitate robust stress response mechanisms. The GRAS transcription factors, particularly CsGRAS2 and CsGRAS26, are involved in the response to multiple abiotic stresses, including low and high temperatures and salinity (Li et al., 2020b). The WRKY gene family also plays a critical role in abiotic stress responses, with several WRKYgenes responding to salt and heat stresses (Chen et al., 2020). Additionally, the basic/helix-loop-helix (bHLH) transcription factor family, specifically CsbHLH041, has been shown to enhance tolerance to salt and ABA in transgenic Arabidopsis and cucumber seedlings, indicating its importance in abiotic stress response (Li et al., 2020b). The PYL gene family, which is central to ABA signal transduction, also contributes to stress responses, with most PYL genes being upregulated under ABA, PEG, and salt stress treatments (Zhang et al., 2022). Furthermore, the HSP20 gene family is involved in heat stress response, withmany CsHSP20 genes being upregulated under high-temperature conditions (Huang et al., 2022). 5 Genetic Variation and Breeding 5.1 Sources of genetic variation Genetic variation is the cornerstone of breeding programs aimed at crop improvement. In cucumber, significant genetic diversity has been identified through various genomic studies. The USDA cucumber collection, for instance, has been characterized using high-throughput genotyping-by-sequencing (GBS) technology, revealing over 23,000 high-quality single-nucleotide polymorphisms (SNPs) that highlight the genetic diversity and population structure within the collection (Wang et al., 2018). Additionally, whole-genome re-sequencing has identified numerous insertion and deletion (InDel) markers, which are associated with genetic variation and can be
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