Please wait a minute...
Journal of Integrative Agriculture  2026, Vol. 25 Issue (2): 734-743    DOI: 10.1016/j.jia.2025.11.010
Horticulture Advanced Online Publication | Current Issue | Archive | Adv Search |
A new 10K liquid SNP genotyping array for wax gourd and its application in heterosis utilization and cultivars identification

Dan Liu1, 5*, Lingling Xie1, 5*, Yuting Lei3, 5, Bingchuan Tian3, 5, Daolong Liao4, Fangfang Wu2, 5#, Baobin Mi1, 5#

1 Hunan Vegetable Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China

2 Hunan Agricultural University, Changsha 410128, China

3 Higentec. Co., Ltd., Changsha 410125, China

4 Institute of Vegetables, Hainan Academy of Agricultural Sciences, Haikou 571100, China

5 Yuelushan Laboratory, Changsha 410128, China

 Highlights 

Developed the first high-density 10K SNP array for wax gourd using genotyping by target sequencing (GBTS) technology, comprising 10,722 genome-wide SNPs distributed across the genome, including 278 associated with functional trait loci.

Demonstrated its utility in heterosis prediction, population structure analysis, and cultivar fingerprinting, demonstrating its applicability in genetic research and breeding programs.

Download:  PDF in ScienceDirect  
Export:  BibTeX | EndNote (RIS)      
摘要  

高通量单核苷酸多态性(SNP)芯片已成为重要的基因分型工具,可显著加速育种进程并推动基础研究。本研究基于靶向测序基因分型(GBTS)技术,成功开发了用于冬瓜的高通量10 K SNP芯片,其包含的10,722SNP均匀分布在全部12条染色体上,其中278个是与重要经济性状相关的功能位点。为验证其应用,我们利用该芯片SNP数据计算了19个优良自交系之间的遗传距离,并分析了其与单果重杂种优势的相关性。结果表明,遗传距离越大,单果重的中亲杂种优势(MPH)越高。此外,我们对采集自八个地区的56个商业冬瓜品种进行了基因分型。群体结构、系统进化和主成分分析(PCA)结果一致表明,这些品种可分为两大类群。以黑皮或深绿皮冬瓜为代表的第一类群,其遗传多样性低于由绿皮或浅绿皮品种组成的第二类群,这反映出第一类群内部遗传距离较近。最终,我们筛选出60个多态性SNP位点,构建了可用于区分56个冬瓜品种的DNA指纹图谱。作为首个冬瓜高通量基因分型平台,该SNP芯片为遗传分析提供了高效强大的工具。



Abstract  

High-throughput single nucleotide polymorphism (SNP) arrays have emerged as essential genotyping tools, significantly accelerating breeding programs and advancing basic research.  In this study, a high-throughput 10K SNP genotyping array for wax gourd was developed using genotyping by target sequencing (GBTS), featuring 10,722 SNPs evenly distributed across all 12 chromosomes, including 278 functional loci associated with key economic traits.  To demonstrate its utility, genetic distances among 19 elite inbred lines were calculated from SNP data and correlated with heterosis for single fruit weight.  The results revealed that greater genetic distance was associated with higher middle parent heterosis (MPH) for single fruit weight.  Furthermore, 56 commercial wax gourd cultivars collected from eight regions were selected and genotyped.  Population structure analysis, phylogenetic analysis, and principal component analysis (PCA) collectively indicated that these cultivars fall into two major groups.  Group I, comprising black or dark green skinned wax gourds, exhibited lower genetic diversity than Group II, which includes green or light green skinned varieties, reflecting shorter genetic distances within Group I.  Finally, 60 polymorphic SNPs were used to construct DNA fingerprints for distinguishing the 56 cultivars.  As the first high-throughput genotyping platform for wax gourd, this SNP array provides an effective and powerful tool for genetic analysis.

Keywords:  wax gourd       SNPs genotyping array       heterosis       cultivar identification       DNA fingerprint  
Received: 09 October 2024   Accepted: 01 September 2025 Online: 13 November 2025  
Fund: 

This work was supported by the Science and Technology Talent Support Project of Hunan Province, China (2022TJ-N15), the Hunan Agricultural Science and Technology Innovation Fund, China (2024CX90 and 2024CX65), the Science and Technology Innovation Program of Hunan Province, China (2021NK1006).

About author:  #Correspondence Fangfang Wu, E-mail: wufangfang@hunau.edu.cn; Baobin Mi, E-mail: mibaobin@hunaas.cn * These authors contributed equally to this study.

Cite this article: 

Dan Liu, Lingling Xie, Yuting Lei, Bingchuan Tian, Daolong Liao, Fangfang Wu, Baobin Mi. 2026. A new 10K liquid SNP genotyping array for wax gourd and its application in heterosis utilization and cultivars identification. Journal of Integrative Agriculture, 25(2): 734-743.

Van der Auwera G A, Carneiro M O, Hartl C, Poplin R, del Angel G, Levy-Moonshine A, Jordan T, Shakir K, Roazen D, Thibault J, Banks E, Garimella K V, Altshuler D, Gabriel S, DePristo M A. 2013. From FastQ data to high-confidence variant calls: The genome analysis toolkit best practices pipeline. Current Protocols in Bioinformatics43, 11.10.11–11.10.33.

Boeven P H G, Zhao Y S, Thorwarth P, Liu F, Maurer H P, Gils M, Schachschneider R, Schacht J, Ebmeyer E, Kazman E, Mirdita V, Dörnte J, Kontowski S, Horbach R, Cöster H, Holzapfel J, Jacobi A, Ramgraber L, Reinbrecht C, Starck N, et al. 2020. Negative dominance and dominance-by-dominance epistatic effects reduce grain-yield heterosis in wide crosses in wheat. Science Advances6, eaay4897.

Burridge A J, Winfield M, Przewieslik-Allen A, Edwards K J, Siddique I, Barral-Arca R, Griffiths S, Cheng S F, Huang Z J, Feng C, Dreisigacker S, Bentley A R, Brown-Guedira G, Barker G L. 2024. Development of a next generation SNP genotyping array for wheat. Plant Biotechnology Journal2, 2235–2247.

Chang J J, Liao D L, Li J L, Li J, Li Z, Chen X, Song Z, Zhang B. 2024. Calcium deficiency leads to fruit blackheart formation by disrupting glycometabolism and phenylpropanoid metabolism in wax gourd. Postharvest Biology and Technology211, 112851.

Chao J Q, Li Y, Yang S G, Chen X M, He Y L, Zhang J N, Yue Z L, Gao Q, Tian W M. 2024. Design and application of the HbGBTS80K liquid chip in rubber tree. Tropical Plants3, e014.

Cheng D H, Wang Z Y, Li S Y, Zhao J, Wei C H, Zhang Y. 2022. Genome-wide identification of CCD gene family in six cucurbitaceae species and its expression profiles in melon. Genes13, 262.

Cheng Z K, Liu Z G, Xu Y C, Ma L L, Chen J Y, Gou J Q, Su L W, Wu W T, Chen Y, Yu W J, Wang P. 2021. Fine mapping and identification of the candidate gene BFS for fruit shape in wax gourd (Benincasa hispida). Theoretical and Applied Genetics134, 3983–3995.

Dapp M, Reinders J, Bédiée A, Balsera C, Bucher E, Theiler G, Granier C, Paszkowski J. 2015. Heterosis and inbreeding depression of epigenetic Arabidopsis hybrids. Nature Plants1, 15092.

Daware A, Malik A, Srivastava R, Das D, Ellur R K, Singh A K, Tyagi A K, Parida S K. 2023. Rice Pangenome Genotyping Array: An efficient genotyping solution for pangenome-based accelerated genetic improvement in rice. The Plant Journal113, 26–46.

Ertiro B T, Ogugo V, Worku M, Das B, Olsen M, Labuschagne M, Semagn K. 2015. Comparison of Kompetitive Allele Specific PCR (KASP) and genotyping by sequencing (GBS) for quality control analysis in maize. BMC Genomics16, 908.

Fan X L, Liu X F, Feng B, Zhou Q, Deng G B, Long H, Cao J, Guo S D, Ji G S, Xu Z, Wang T. 2022. Construction of a novel wheat 55K SNP array-derived genetic map and its utilization in QTL mapping for grain yield and quality related traits. Frontiers in Genetics13, 978880.

Gao G, Waldbieser G C, Youngblood R C, Zhao D, Pietrak M R, Allen M S, Stannard J A, Buchanan J T, Long R L, Milligan M, Burr G, Mejía-Guerra K, Sheehan M J, Scheffler B E, Rexroad III C E, Peterson B C, Palti Y. 2023. The generation of the first chromosome-level de novo genome assembly and the development and validation of a 50K SNP array for the St. John River aquaculture strain of North American Atlantic salmon. G313, jkad138.

He J F, Zhao X Q, Laroche A, Lu Z X, Liu H K, Li Z Q. 2014. Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding. Frontiers in Plant Science5, 484.

Hu Q M, Wang H P, Jiang B, Zhu H Y, He X M, Song P Y, Song J P, Yang S, Shen J J, Li Z, Hu J B, Sun S R, Yang L M. 2022. Genome wide simple sequence repeats development and their application in genetic diversity analysis in wax gourd (Benincasa hispida). Plant Breeding141, 108–118.

Jamali S H, Cockram J, Hickey L T. 2019. Insights into deployment of DNA markers in plant variety protection and registration. Theoretical and Applied Genetics132, 1911–1929.

Jeon J Y, Shin Y, Mularo A J, Feng X, DeWoody J A. 2024. The integration of whole-genome resequencing and ecological niche modelling to conserve profiles of local adaptation. Diversity and Distributions30, e13847.

Kim K W, Nawade B, Nam J, Chu S H, Ha J, Park Y J. 2022. Development of an inclusive 580K SNP array and its application for genomic selection and genome-wide association studies in rice. Frontiers in Plant Science13, 1036177.

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup. 2009. The sequence alignment/map format and SAMtools. Bioinformatics25, 2078–2079.

Li X L, Singh J, Qin M F, Li S W, Zhang X, Zhang M Y, Khan A, Zhang S L, Wu J. 2019. Development of an integrated 200K SNP genotyping array and application for genetic mapping, genome assembly improvement and genome wide association studies in pear (Pyrus). Plant Biotechnology Journal17, 1582–1594.

Li X D, Liu X M, Fan Y H, Li S T, Yu M N, Qian M C, Chen Y L, Chen H Q, Li X C, Liu B, Xu X F, Qu C M, Li J N, Lu K. 2023. Development of a target capture sequencing SNP genotyping platform for genetic analysis and genomic breeding in rapeseed. The Crop Journal11, 499–510.

Li Y F, Li Y H, Su S S, Reif J C, Qi Z M, Wang X B, Wang X, Tian Y, Li D L, Sun R J, Liu Z X, Xu Z J, Fu G H, Ji Y L, Chen Q S, Liu J Q, Qiu L J. 2022. SoySNP618K array: A high-resolution single nucleotide polymorphism platform as a valuable genomic resource for soybean genetics and breeding. Journal of Integrative Plant Biology64, 632–648.

Lin W H, Xiao Q Z, Yu F, Han Z F, Liu J Y, Peng W Z, Huang Z K, Lei Y T, Li W G, You W W, Luo X, Ke C H. 2023. Development of a low-density SNP genotyping panel by a novel technology mGPS and its application in germplasm identification of abalone. Aquaculture565, 739089.

Lin Y, Yu W T, Zhou L, Fan X J, Wang F Q, Wang P J, Fang W P, Cai C P, Ye N X. 2019. Genetic diversity of oolong tea (Camellia sinensis) germplasms based on the nanofluidic array of single-nucleotide polymorphism (SNP) markers. Tree Genetics & Genomes16, 3.

Liu C, Liu X X, Wang X A, Han Y K, Meng H W, Cheng Z H. 2022. Heterosis prediction system based on non-additive genomic prediction models in cucumber (Cucumis sativus L.). Scientia Horticulturae293, 110677.

Liu D, Xie L, Xiao W, Xie T, Wu F F, Mi B B. 2024. Production of haploid plants in wax gourd through parthenogenesis induced by gamma-irradiated pollen. Scientia Horticulturae336, 113450.

Liu X F, Chen J C, Zhang X L. 2021. Genetic regulation of shoot architecture in cucumber. Horticulture Research8, 143.

Luo C, Yan J Q, Liu W R, Xu Y C, Sun P Y, Wang M, Xie D S, Jiang B. 2022. Genetic mapping and genome-wide association study identify BhYAB4 as the candidate gene regulating seed shape in wax gourd (Benincasa hispida). Frontiers in Plant Science13, 961864.

Luo W L, Yan J Q, Luo S W, Liu W R, Xie D S, Jiang B. 2023. A chromosome-level reference genome of the wax gourd (Benincasa hispida). Scientific Data10, 78.

Marrano A, Martínez-García P J, Bianco L, Sideli G M, Di Pierro E A, Leslie C A, Stevens K A, Crepeau M W, Troggio M, Langley C H, Neale D B. 2019. A new genomic tool for walnut (Juglans regia L.): Development and validation of the high-density Axiom™ Jregia 700K SNP genotyping array. Plant Biotechnology Journal17, 1027–1036.

Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira M A R, Bender D, Maller J, Sklar P, de Bakker P I W, Daly M J, Sham P C. 2007. PLINK: A tool set for whole-genome association and population-based linkage analyses. The American Journal of Human Genetics81, 559–575.

Rahman M M, Sarker U, Swapan M A, Raihan M S, Oba S, Alamri S, Siddiqui M H. 2022. Combining ability analysis and marker-based prediction of heterosis in yield reveal prominent heterotic combinations from diallel population of rice. Agronomy12, 1797.

Rasheed A, Hao Y F, Xia X C, Khan A, Xu Y B, Varshney R K, He Z H. 2017. Crop breeding chips and genotyping platforms: Progress, challenges, and perspectives. Molecular Plant10, 1047–1064.

Sun C W, Dong Z D, Zhao L, Ren Y, Zhang N, Chen F. 2020. The Wheat 660K SNP array demonstrates great potential for marker-assisted selection in polyploid wheat. Plant Biotechnology Journal18, 1354–1360.

Thomson M J, Singh N, Dwiyanti M S, Wang D R, Wright M H, Perez F A, DeClerck G, Chin J H, Malitic-Layaoen G A, Juanillas V M, Dilla-Ermita C J, Mauleon R, Kretzschmar T, McCouch S R. 2017. Large-scale deployment of a rice 6 K SNP array for genetics and breeding applications. Rice10, 40.

Tian H L, Yang Y, Yi H M, Xu L W, He H, Fan Y M, Wang L, Ge J R, Liu Y W, Wang F G, Zhao J R. 2021. New resources for genetic studies in maize (Zea mays L.): A genome-wide Maize6H-60K single nucleotide polymorphism array and its application. The Plant Journal105, 1113–1122.

Ting N C, Ordway J M, van de Weg E, Mohamed Serdari N, Low E T L, Mustaffa S, Wischmeyer C, Smulders M J M, Sambanthamurthi R, Singh R. 2023. Development and applications of the Oil Palm 78K Infinium® HD SNP Array for linkage analysis and chromosome scanning. Scientia Horticulturae318, 112104.

Wang Y P, Wang J F, Guo S G, Tian S W, Zhang J Z, Ren Y, Li M Y, Gong G Y, Zhang H Y, Xu Y. 2021. CRISPR/Cas9-mediated mutagenesis of ClBG1 decreased seed size and promoted seed germination in watermelon. Horticulture Research8, 70.

Xie D S, Xu Y C, Wang J P, Liu W R, Zhou Q, Luo S B, Huang W, He X M, Li Q, Peng Q W, Yang X Y, Yuan J Q, Yu J G, Wang X Y, Lucas W J, Huang S W, Jiang B, Zhang Z H. 2019. The wax gourd genomes offer insights into the genetic diversity and ancestral cucurbit karyotype. Nature Communications10, 5158.

Xie L L, Wang J, Liu F, Zhou H Q, Chen Y, Pan L Z, Xiao W, Luo Y, Mi B B, Sun X W, Xiong C. 2022. Integrated analysis of multi-omics and fine-mapping reveals a candidate gene regulating pericarp color and flavonoids accumulation in wax gourd (Benincasa hispida). Frontiers in Plant Science13, 1019787.

Xuereb A, Nahuelpi R M, Normandeau E, Babin C, Laporte M, Mallet A, Yáñez J M, Mallet M, Bernatchez L. 2023. Design and validation of a high-density single nucleotide polymorphism array for the Eastern oyster (Crassostrea virginica). G313, jkad071.

Yan J Q, Chen F, Sun P Y, Liu W R, Xie D S, Qian Y L, Jiang B. 2022. Genome-wide association study and genetic mapping of BhWAX conferring mature fruit cuticular wax in wax gourd. BMC Plant Biology22, 539.

Yang J J, Zhang J, Du H S, Zhao H, Mao A J, Zhang X F, Jiang L, Zhang H Y, Wen C L, Xu Y. 2022. Genetic relationship and pedigree of Chinese watermelon varieties based on diversity of perfect SNPs. Horticultural Plant Journal8, 489–498.

Yu D L, Gu X F, Zhang S P, Dong S Y, Miao H, Gebretsadik K, Bo K. 2021. Molecular basis of heterosis and related breeding strategies reveal its importance in vegetable breeding. Horticulture Research8, 120.

Yu G N, Cui Y R, Jiao Y X, Zhou K, Wang X, Yang W Y, Xu Y Y, Yang K, Zhang X C, Li P C, Yang Z F, Xu Y, Xu C W. 2023. Comparison of sequencing-based and array-based genotyping platforms for genomic prediction of maize hybrid performance. The Crop Journal11, 490–498.

Yu Q, Li S, Su X F, Chen X X, Dong Y H, Yao Z W, Jiang N Y, Chai S, Zhang Z H, Xu K P. 2024. Melon2K array: A versatile 2K liquid SNP chip for melon genetics and breeding. Horticultural Plant Journal11, 314–322.

Zhang J, Yang J J, Fu S Z, Ren J, Zhang X F, Xia C X, Zhao H, Yang K, Wen C L. 2022. Comparison of DUS testing and SNP fingerprinting for variety identification in cucumber. Horticultural Plant Journal8, 575–582.

Zhang J, Yang J J, Zhang L, Luo J, Zhao H, Zhang J N, Wen C L. 2020. A new SNP genotyping technology target SNP-seq and its application in genetic analysis of cucumber varieties. Scientific Reports10, 5623.

Zhou S H, Zhang J P, Che Y H, Liu W H, Lu Y Q, Yang X M, Li X Q, Jia J Z, Liu X, Li L H. 2018. Construction of Agropyron Gaertn. genetic linkage maps using a wheat 660K SNP array reveals a homoeologous relationship with the wheat genome. Plant Biotechnology Journal16, 818–827.

[1] Yuanmei Wang, Jingwei Yuan, Yanyan Sun, Aixin Ni, Jinmeng Zhao, Yunlei Li, Panlin Wang, Lei Shi, Yunhe Zong, Pingzhuang Ge, Shixiong Bian, Hui Ma, Jilan Chen. Genome-wide circular RNAs signatures involved in sexual maturation and its heterosis in chicken[J]. >Journal of Integrative Agriculture, 2025, 24(2): 697-711.
[2] SANG Zhi-qin, ZHANG Zhan-qin, YANG Yu-xin, LI Zhi-wei, LIU Xiao-gang, XU Yunbi, LI Wei-hua. Heterosis and heterotic patterns of maize germplasm revealed by a multiple-hybrid population under well-watered and drought-stressed conditions[J]. >Journal of Integrative Agriculture, 2022, 21(9): 2477-2491.
[3] YANG Wei-bing, QIN Zhi-lie, SUN Hui, HOU Qi-ling, GAO Jian-gang, CHEN Xian-chao, ZHANG Li-ping, WANG Yong-bo, ZHAO Chang-ping, ZHANG Feng-ting. Analysis of combining ability for stem-related traits and its correlations with lodging resistance heterosis in hybrid wheat[J]. >Journal of Integrative Agriculture, 2022, 21(1): 26-35.
[4] WANG Xiu-juan, KANG Meng-zhen, FAN Xing-rong, YANG Li-li, ZHANG Bao-gui, HUANG San-wen, Philippe DE REFFYE, WANG Fei-yue. What are the differences in yield formation among two cucumber (Cucumis sativus L.) cultivars and their F1 hybrid?[J]. >Journal of Integrative Agriculture, 2020, 19(7): 1789-1801.
[5] YANG Wei-bing, QIN Zhi-lie, SUN Hui, LIAO Xiang-zheng, GAO Jian-gang, WANG Yong-bo, HOU Qi-ling, CHEN Xian-chao, TIAN Li-ping, ZHANG li-ping, MA Jin-xiu, CHEN Zhao-bo, ZHANG Feng-ting, ZHAO Chang-ping. Yield-related agronomic traits evaluation for hybrid wheat and relations of ethylene and polyamines biosynthesis to filling at the mid-grain filling stage[J]. >Journal of Integrative Agriculture, 2020, 19(10): 2407-2418.
[6] ZHANG Gui-quan . Prospects of utilization of inter-subspecific heterosis between indica and japonica rice[J]. >Journal of Integrative Agriculture, 2020, 19(1): 1-10.
[7] TANG Liang, XU Zheng-jin, CHEN Wen-fu. Advances and prospects of super rice breeding in China[J]. >Journal of Integrative Agriculture, 2017, 16(05): 984-991.
[8] Saeed Rauf, Maria Zaharieva, Marilyn L Warburton, ZHANG Ping-zhi, Abdullah M AL-Sadi, Farghama Khalil, Marcin Kozak, Sultan A Tariq. Breaking wheat yield barriers requires integrated efforts in developing countries[J]. >Journal of Integrative Agriculture, 2015, 14(8): 1447-1474.
[9] FENG Guo-yi1, 2 , GAN Xiu-xia1, YAO Yan-di1, LUO Hong-hai1, ZHANG Ya-li1 and ZHANG Wangfeng1. Comparisons of Photosynthetic Characteristics in Relation to Lint Yield Among F1 Hybrids, Their F2 Descendants and Parental Lines of Cotton[J]. >Journal of Integrative Agriculture, 2014, 13(9): 1909-1920.
[10] LI Jing, SONG Su-sheng, ZHAO Yu-sheng, GUO Wei-wei, GUO Guang-hui, PENG Hui-ru, NI Zhong-fu. Wheat 14-3-3 Protein Conferring Growth Retardation in Arabidopsis[J]. >Journal of Integrative Agriculture, 2013, 12(2): 209-217.
[11] ZHANG Ti-fu, LI Bo, ZHANG Deng-feng, JIA Guan-qing, LI Zhi-yong, WANG Shou-cai. Genome-Wide Transcriptional Analysis of Yield and Heterosis-Associated Genes in Maize (Zea mays L.)[J]. >Journal of Integrative Agriculture, 2012, 12(8): 1245-1256.
[12] LI Zhi-yong, ZHANG Ti-fu, WANG Shou-cai. Transcriptomic Analysis of the Highly Heterotic Maize Hybrid Zhengdan 958 and Its Parents During Spikelet and Floscule Differentiation[J]. >Journal of Integrative Agriculture, 2012, 12(11): 1783-1793.
[13] ZHANG Hai-zhen, SHI Chun-hai , WU Jian-guo. Analysis of Genetic Effects for Heterosis of Erucic Acid and Glucosinolate Contents in Rapeseed (Brassica napus L.)[J]. >Journal of Integrative Agriculture, 2011, 10(10): 1525-1531.
No Suggested Reading articles found!