Skip to main navigation menu Skip to main content Skip to site footer

Review Articles

Vol. 13 No. sp9 (2026): Recent Advances in Agriculture

Molecular tools complementing conventional breeding approaches in vegetable crops: A critical review

DOI
https://doi.org/10.14719/pst.15543
Submitted
14 May 2026
Published
04-11-2026

Abstract

Vegetable crops constitute an essential component of global food and nutritional security by providing vital vitamins, minerals, antioxidants and dietary fibre essential for maintaining human health and preventing nutritional deficiencies. With rapid demographic growth, accelerated urbanisation and climate-induced environmental fluctuations, the demand for high-yielding, resilient and nutritionally dense vegetable cultivars have increased substantially. However, vegetable production faces pervasive constraints, including devastating biotic pressures (fungi, bacteria, viruses, insect pests and nematodes) alongside abiotic stresses such as drought, extreme temperatures, salinity and water scarcity. Conventional breeding approaches have laid the cornerstone of vegetable improvement through recurrent selection, hybridisation and wide backcrossing. Nonetheless, empirical reliance on phenotypic evaluation renders conventional selection labour-intensive, time-consuming and prone to environmental noise, particularly for polygenic traits governed by complex genetic architectures and high genotype × environment interactions. The advent of molecular tools has revolutionised vegetable breeding by enabling accurate, genotype-based selection at the DNA level. This review provides a comprehensive critical synthesis of molecular technologies complementing conventional vegetable breeding, spanning diagnostic molecular markers, high-density quantitative trait locus mapping (QTL) mapping, marker-assisted backcrossing and multi-gene pyramiding across solanaceous, cucurbitaceous and cruciferous crops. Furthermore, this review addresses the cutting-edge innovations of the genomic era, including whole-genome resequencing, pangenomics, haplotype-led breeding, speed breeding protocols, doubled haploid technology, multi-omics integration, clustered regularly interspaced short palindromic repeats (CRISPR)-Cas genome editing and artificial intelligence-driven digital phenotyping. Current methodological bottlenecks, epigenetic nuances and synthetic biology avenues are critically evaluated to outline an agile roadmap for climate-resilient and biofortified vegetable development.

References

  1. 1. Simko I, Jia M, Venkatesh J, Kang BC, Weng Y, Barcaccia G, et al. Genomics and marker-assisted improvement of vegetable crops. Crit Rev Plant Sci. 2021;40(4):303–65. https://doi.org/10.1080/07352689.2021.1941605
  2. 2. Collard BCY, Jahufer MZZ, Brouwer JB, Pang ECK. An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement. Euphytica.2005;142(1):169–96. https://doi.org/10.1007/s10681-005-1681-5
  3. 3. Devi R, Chauhan S, Dhillon TS. Genome editing for vegetable crop improvement: challenges and future prospects. Front Genet. 2022;13:1037091. https://doi.org/10.3389/fgene.2022.1037091
  4. 4. Pathirana R, Carimi F. Plant biotechnology-an indispensable tool for crop improvement. Plants. 2024;13(8):1133. https://doi.org/10.3390/plants13081133
  5. 5. Li G, An L, Yang W, Yang L, Wei T, Shi J, et al. Integrated biotechnological and AI innovations for crop improvement. Nature. 2025;643:925–37. https://doi.org/10.1038/s41586-025-09122-8
  6. 6. Winter P, Kahl G. Molecular marker technologies for plant improvement. World J Microbiol Biotechnol. 1995;11(4):438–48. https://doi.org/10.1007/BF00364619
  7. 7. Bernardo R. Molecular markers and selection for complex traits in plants: learning from the last 20 years. Crop Sci. 2008;48(5):1649–64. https://doi.org/10.2135/cropsci2008.03.0131
  8. 8. Natalia V, Levi A, Guner N, Wechter WP. Identification of microsatellite markers linked to powdery mildew resistance in watermelon on chromosome 2. HortScience. 2015;50(2):215–20.
  9. 9. Weng Y, Colle M, Wang Y, Yang L, Rubinstein M, Sherman A, et al. QTL mapping in multiple populations and development stages reveals dynamic quantitative trait loci for fruit size in cucumbers of different market classes. Theor Appl Genet. 2015;128(9):1747–63. https://doi.org/10.1007/s00122-015-2544-7
  10. 10. Nevame AYM, Eyun SI, Akoundze SM, Mao X, Chen J. Mapping and identification of six resistant genes (Ty-1 to Ty-6) for tomato leaf curl virus: a review. J Genet. 2018;97(5):1289–301.
  11. 11. Huang CC, Cui YY, Weng CR, Zabel P, Lindhout P. Development of PCR-based markers linked to powdery mildew resistance gene in tomato. Theor Appl Genet. 2000;100(6):918–24. https://doi.org/10.1007/s001220051562
  12. 12. Leastro MO, Pallás V, Resende RO, Sánchez-Navarro JA. The 21-amino acid viral effector epitope within the Sw-5b gene: a conserved resistance mechanism against Tospoviruses. Mol Plant Pathol. 2017;18(8):1022–35.
  13. 13. Oliveira LS, Boiteux LS, Kormelink R, Resende RO. The Sw-5 gene cluster: evolution of tospovirus resistance in Solanum species. Front Plant Sci. 2018;9:673.
  14. 14. Zhu M, van der Voort JR, Dijkhuis J. Characterization of the Sw-5b resistance gene in tomato against multiple tospovirus species. Phytopathology. 2017;107(1):123–32.
  15. 15. Shi L, Miao H, Gu X. Mapping of QTLs for resistance to cucumber mosaic virus (CMV) in cucumber using SSR markers on chromosome 6. Mol Breed. 2018;38(9):112.
  16. 16. Ansari AM, Singh YV. Molecular diversity of brinjal (Solanum melongena L.) genotypes revealed by RAPD marker. J Res (BAU). 2013;25(1):41–8.
  17. 17. Vosman B, Kashaninia A, van't Westende W, Meijer-Dekens F, van Eekelen H, Visser RGF, et al. QTL mapping of insect resistance components of Solanum galapagense. Theor Appl Genet. 2019;132(3):531–41. https://doi.org/10.1007/s00122-018-3239-7
  18. 18. Singh J, Kumar D, Chauhan S, Dhillon HK, Kumar S, Kumar V, et al. Role of omics approaches in vegetable breeding for insect pest resistance. Discov Appl Sci. 2023;5:384. https://doi.org/10.1007/s42452-023-05522-5
  19. 19. Singh S, Singh SP, Singh A, Yadav S. Molecular mapping and marker assisted selection for development edible colour, beta-carotene and anthocyanin bio-fortification in cole and root crops. Adv Crop Sci Tech. 2020;8(4):457.
  20. 20. Behera TK, Shrawan A. Advances in vegetable breeding for nutraceutical and quality traits. Indian J Genet. 2019;79(2):216–26.https://doi.org/10.31742/IJGPB.79S.1.12
  21. 21. Kalia P, Sood S, Muthukumar P. Marker-assisted introgression of the Or gene for enhancing beta-carotene in cauliflower. Acta Hortic. 2018;1203:121–8. https://doi.org/10.17660/ActaHortic.2018.1203.19
  22. 22. Zhong YJ, Zhou YY, Li JX, Yu T, Wu TQ, Luo JN, et al. A high-density linkage map and QTL mapping of fruit-related traits in pumpkin (Cucurbita moschata Duch.). Sci Rep. 2017;7:12785. https://doi.org/10.1038/s41598-017-13216-3
  23. 23. Yu H, Wang J, Sheng X, Zhao Z, Shen Y, Branca F, et al. High-density genetic map construction and identification of loci controlling anthocyanin traits in broccoli. BMC Plant Biol. 2019;19:228. https://doi.org/10.1186/s12870-019-1831-x
  24. 24. Staniaszek M, Szajko K, Kozik EU, Nowakowska M, Marczewski W. The novel ps and ps-2 specific markers for selection of functional male sterile tomato lines in breeding programs and hybrids seed production. J Agric Sci. 2012;4(10):61–67. https://doi.org/10.5539/jas.v4n10p61
  25. 25. Naresh P, Lin SW, Lin CY, Wang YW, Schafleitner R, Kilian A, et al. Molecular markers associated to two non-allelic genic male sterility genes in peppers (Capsicum annuum L.). Front Plant Sci. 2018;9:1343. https://doi.org/10.3389/fpls.2018.01343
  26. 26. Peng HF, Chen XH, Lu YP, et al. Fine mapping of a gene for non-pollen type thermosensitive genic male sterility in rice (Oryza sativa L.). Theor Appl Genet. 2010;120(5):1013–20. https://doi.org/10.1007/s00122-009-1229-5
  27. 27. Hazra P, Roy T, Choudhury J, Atanassova B. Male sterility in tomato (Lycopersicon esculentum Mill.) and brinjal (Solanum melongena). Int J Plant Breed. 2007;1(1):41–5.
  28. 28. Isshiki S, Kawajiri N. Effect of cytoplasm of Solanum violaceum Ort. on fertility of eggplant (S. melongena L.). Sci Hortic. 2002;93(1):9–18. https://doi.org/10.1016/S0304-4238(01)00314-4
  29. 29. Isshiki S, Yoshida S. Characteristics of the cytoplasmic male sterility in the eggplant (Solanum melongena L.) carrying cytoplasm of S. violaceum Ort. Bull Fac Agric Saga Univ. 2002;87:67–93. https://doi.org/10.1016/S0304-4238(01)00314-4
  30. 30. Hasnunnahar M, Khan MMR, Isshiki S. Inheritance analysis of fertility restoration genes (Rf) in a male sterile system of eggplant using cytoplasm of Solanum grandifolium. Sci Hortic. 2012;150:425–29.
  31. 31. Gorguet B, Eggink PM, Ocaña J, Tiwari A, Schipper D, Finkers R, et al. Mapping and characterization of novel parthenocarpy QTLs in tomato. Theor Appl Genet. 2008;116(6):755–67. https://doi.org/10.1007/s00122-007-0708-9
  32. 32. Zaelani A. Genetic analysis of parthenocarpic ability in melon (Cucumis melo L. var. makuwa) [dissertation]. Tsukuba: University of Tsukuba; 2015.
  33. 33. Miyatake K, Saito T, Nunome T, Yamaguchi H, Negoro S, Ohyama A, et al. Fine mapping of a major locus representing the lack of prickles in eggplant revealed the availability of a 0.5-kb insertion/deletion for marker-assisted selection. Breed Sci. 2020;70(4):438–48. https://doi.org/10.1270/jsbbs.20004
  34. 34. Matsuo S, Miyatake K, Endo M, Urashimo S, Kawanishi T, Negoro S, et al. Loss of function of the Pad-1 aminotransferase gene, which is involved in auxin homeostasis, induces parthenocarpy in Solanaceae plants. Proc Natl Acad Sci USA. 2020;117(23):12784–90. https://doi.org/10.1073/pnas.2001211117
  35. 35. Saini DK, Kaushik P. Visiting eggplant from a biotechnological perspective: a review. Sci Hortic. 2019;253:327–40. https://doi.org/10.1016/j.scienta.2019.04.042
  36. 36. Branham SE, Levi A, Farnham MW, Wechter WP. A GBS-SNP-based linkage map and quantitative trait loci (QTL) associated with resistance to Fusarium oxysporum f. sp. niveum race 2 identified in Citrullus lanatus var. citroides. Theor Appl Genet. 2017;130(2):319–30. https://doi.org/10.1007/s00122-016-2813-0
  37. 37. Gao ZH, Zhang HY, Cao CX, Han J, Li H, Ren Z. QTL mapping for cucumber fruit size and shape with populations from long and round fruited inbred lines. Hortic Plant J. 2020;6(3):132–44. https://doi.org/10.1016/j.hpj.2020.04.004
  38. 38. Ashrafi H, Kinkade MP, Merk HL, Foolad MR. Identification of novel quantitative trait loci for increased lycopene content and other fruit quality traits in tomato. Mol Breed. 2012;30(1):549–67. https://doi.org/10.1007/s11032-011-9643-1
  39. 39. Badri A, Bae I, Lee S. Marker-assisted evaluation of powdery mildew resistance candidate genes in cucumber. Agronomy. 2021;11(11):2191. https://doi.org/10.3390/agronomy11112191
  40. 40. Dormatey R, Sun C, Ali K, Coulter JA, Bi Z, Bai J. Gene pyramiding for sustainable crop improvement against biotic and abiotic stresses. Agronomy. 2020;10(9):1255. https://doi.org/10.3390/agronomy10091255
  41. 41. Saha P, Ghoshal C, Saha ND, Verma A, Srivastava M, Kalia P, et al. Marker-assisted pyramiding of downy mildew and black rot resistance genes in cauliflower. Front Plant Sci. 2021;12:603600. https://doi.org/10.3389/fpls.2021.603600
  42. 42. Demir K, Bakir M, Sarikamis G, Acunal S. Genetic diversity of eggplant germplasm assessed by SSR and RAPD markers. Genet Mol Res. 2010;9(3):1568–76. https://doi.org/10.4238/vol9-3gmr878
  43. 43. Jaganathan D, Dutta B, Basu S, Bag S, Srinivasan R, Eybishitz A, et al. Breeding vegetables for whitefly resistance: past, present and future in the AI era. Front Plant Sci. 2026;16:1724403. https://doi.org/10.3389/fpls.2025.1724403
  44. 44. Echevarria Angel RDV, Campbell A, Theodore JKR, Silvasy T, Moore S, Kantar MB. Quantitative trait loci (QTL) analysis of fruit and agronomic traits of tropical pumpkin (Cucurbita moschata) in an organic production system. Horticulturae. 2020;6(1):14. https://doi.org/10.3390/horticulturae6010014
  45. 45. Bennewitz S, Liu J, Bergau N, Tissier A, Kaster AK. Identification of QTLs for glandular trichomes and their metabolites in Solanum species. Theor Appl Genet. 2018;131(7):1541–54.
  46. 46. Chang CW, Wang YH, Tung CW. Genome-wide single nucleotide polymorphism discovery and the construction of a high-density genetic map for melon (Cucumis melo L.) using genotyping-by-sequencing. Front Plant Sci. 2017;8:125. https://doi.org/10.3389/fpls.2017.00125
  47. 47. Kumar P, Siddiqui MW, Irfan M. From classical breeding to modern biotechnological advancement in horticultural crops. Front Plant Sci. 2025;16:1542012. https://doi.org/10.3389/fpls.2025.1598544
  48. 48. Emmadishetty CS, Gurjar D. Biotechnology in agriculture: a modern tool for crop improvement. Pharma Innov J. 2022;11(3):1606–11.
  49. 49. Gill SS, Macovei A, Jimenez-Bremont JF, Khan NA, Tuteja N. Biotechnology and crop improvement under changing environment: current interventions. Plant Gene. 2022;32:100376. https://doi.org/10.1016/j.plgene.2022.100376

Downloads

Download data is not yet available.