Scientia Agricultura Sinica ›› 2026, Vol. 59 ›› Issue (6): 1286-1301.doi: 10.3864/j.issn.0578-1752.2026.06.011

• HORTICULTURE • Previous Articles     Next Articles

Identification of Short Hypocotyl Cucumber Germplasm Under Low Light Stress and QTL Mapping of the Trait

CAO HaiShun1(), ZHOU DongYuan1,2(), WANG Rui1, SHI ZhaoWan1, WU TingQuan1, ZHANG ChangYuan1,2()   

  1. 1 Institute of Facility Agriculture, Guangdong Academy of Agricultural Sciences, Guangzhou 510640
    2 College of Horticulture, South China Agricultural University, Guangzhou 510642
  • Received:2025-10-16 Accepted:2025-12-05 Online:2026-03-24 Published:2026-03-24
  • Contact: ZHANG ChangYuan

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Abstract:

【Objective】Cucumber is the most widely cultivated greenhouse vegetable in China. However, low light stress frequently occurs during protected cultivation, which often induces excessive stem elongation and spindly growth of cucumber plants. Screening for cucumber germplasm with reduced susceptibility to spindly growth under low light stress and identifying the underlying genes can provide a theoretical basis for genetic improvement of low light tolerance in cucumber. 【Method】Using a low light stress screening system, cucumber germplasm was evaluated. Subsequently, a segregating population was constructed. The Bulked Segregant Analysis sequencing (BSA-seq) method was employed to identify significant loci associated with the target trait. Functional annotation and gene family analysis were then performed to elucidate candidate genes involved in low light stress response. 【Result】Two distinct cucumber materials, designated as long hypocotyl (CS ) and short hypocotyl (CR), were initially identified. Light quality treatment assays indicated that the differential response of hypocotyl between CS and CR was primarily associated with far-red light perception. Using CS and CR as parental lines, F1 and F2 populations were developed. Genetic analysis of hypocotyl length under low light stress revealed that the trait was predominantly governed by two novel QTL loci—LSH1 (Chr.4) and LSH2 (Chr.5). Through bulked segregant analysis (BSA), these loci were predicted to encompass 373 and 163 candidate genes, respectively. Subsequently, key components of the far-red light signaling pathway were systematically identified in cucumber, including Phytochrome A (PHYA), FAR-RED ELONGATED HYPOCOTYL 1 (FHY1)/FHY1-LIKE (FHL), and FAR1 RELATED SEQUENCE (FRS) transcription factors. The analysis yielded two PHYA genes (CsPHYA1 and CsPHYA2) on chromosome 6, one CsFHY1 gene on chromosome 3, and 22 CsFRS transcription factor genes distributed across all chromosomes except chromosome 2. Notably, CsFRS12 was physically located within the LSH1 interval on chromosome 4. Phylogenetic and motif analyses indicated that CsFRS12 contained three conserved domains: a FAR1 DNA-binding domain, a MULE transposase domain, and a SWIM Zinc finger domain. CsFRS12 clustered within subfamily Ⅰ and showed closest homology to Arabidopsis AtFRS2 (AT2G32250), AtFAR1 (AT4G15090), and AtFHY3 (AT3G22170), all key regulators of far-red light signaling. Cloning and sequence comparison revealed multiple SNPs between CsFRS12CR and CsFRS12CS alleles, which were significantly correlated with hypocotyl length under low light stress. Yeast transcriptional activity assays demonstrated that CsFRS12CR possessed significantly lower transcriptional activity than CsFRS12CS. Expression profiling further indicated that CsFRS12 was highly expressed in the stem and hypocotyl tissues of cucumber. In summary, these findings highlight CsFRS12 as a promising candidate gene underlying low light-induced hypocotyl elongation in cucumber. 【Conclusion】Two cucumber materials with differential responses to low light stress were identified, and two significant loci (LSH1 and LSH2) associated with hypocotyl elongation under low light stress were mapped using BSA-seq. Furthermore, within the LSH1 interval, a key transcription factor CsFRS12, which participates in the far-red light signaling pathway, was found as a critical candidate gene for low light stress response in cucumber.

Key words: cucumber, far-red light, low light stress, BSA, FRS transcription factor, SNP

Fig. 1

Sensitivity analysis of cucumber hypocotyl to low light stress A: The hypocotyl length of different cucumber germplasms under control (CK) and low light stress; B: The ratio of hypocotyl length under low light stress to that under CK"

Fig. 2

Analysis and mapping of cucumber hypocotyl length phenotype and trait under low light stress A: Phenotypic of CS, CR, and F1 under low light stress conditions; B: Hypocotyl length CS, CR, and F1 under low light stress conditions; C: Distribution of the hypocotyl length among mapping individuals of F2 population; D: Manhattan plot showing the distribution of Δ(SNP-index) on cucumber chromosomes. The red line shows the association threshold value of 99%, the blue line shows the association threshold value of 95%"

Table 1

QTLs conferring hypocotyl length under low light stress by 3 methods for identification using BSA-seq"

方法
Method		 数量性状基因座名称
QTL name		 起始位点
Start position (bp)		 终止位点
End position (bp)		 染色体
Chromosome		 峰值
Peak		 基因数目
Gene numbers
单核苷酸多态性指数 Δ(SNP-index) LSH1 20300001 24200000 Chr.4 0.505331835 371
LSH2 6700001 10200000 Chr.5 0.532489898 163
G统计值
G-statistic		 LSH1 21100001 23300000 Chr.4 11.26343258 196
LSH2 7100001 9200000 Chr.5 13.22583847 74
欧氏距离
Euclidean distance		 LSH1 21000001 23500000 Chr.4 0.489802113 229
LSH2 8000001 9200000 Chr.5 0.463019996 37

Fig. 3

The hypocotyl phenotype (A) and length (B) of cucumber seedlings (CR and CS) grown under red, far-red, blue light and dark, respectively"

Table 2

The information of FRS transcription factor in cucumber"

基因序号
Gene ID		 基因名称
Name		 染色体
Chromosome		 起始位点
Start position (bp)		 终止位点
Stop position (bp)		 正反链
Strand		 编码框长度
CDS length (bp)		 蛋白长度
Protein length (aa)
CsaV3_1G010190.1 CsFRS1 Chr.1 6322731 6327319 - 2565 855
CsaV3_1G042070.1 CsFRS2 Chr.1 26879471 26883820 + 2628 876
CsaV3_3G013860.1 CsFRS3 Chr.3 10392246 10397538 - 2364 788
CsaV3_3G034800.1 CsFHY1 Chr.3 29369257 29371197 + 1041 347
CsaV3_3G039150.1 CsFRS4 Chr.3 32174695 32179211 + 1170 390
CsaV3_3G046280.1 CsFRS5 Chr.3 37806932 37811364 + 1818 606
CsaV3_4G001920.1 CsFRS6 Chr.4 1130443 1133692 + 2232 744
CsaV3_4G001930.1 CsFRS7 Chr.4 1135597 1138623 + 2007 669
CsaV3_4G003380.1 CsFRS8 Chr.4 2056681 2059569 + 765 255
CsaV3_4G003760.1 CsFRS9 Chr.4 2290171 2295355 + 750 250
CsaV3_4G007310.1 CsFRS10 Chr.4 4973487 4978240 - 2424 808
CsaV3_4G007320.1 CsFRS11 Chr.4 4978958 4986126 - 2538 846
CsaV3_4G032340.1 CsFRS12 Chr4 22862562 22866893 + 2325 775
CsaV3_5G014020.1 CsFRS13 Chr.5 10880232 10889015 - 2040 680
CsaV3_6G009980.1 CsFRS14 Chr.6 8087498 8091321 + 1488 496
CsaV3_6G036060.1 CsPHYA1 Chr.6 20015890 20021182 - 3450 1150
CsaV3_6G036100.1 CsPHYA2 Chr.6 20046075 20053349 + 3375 1125
CsaV3_6G048310.1 CsFRS15 Chr.6 28368052 28370312 + 2076 692
CsaV3_6G053050.1 CsFRS16 Chr.6 30971693 30975462 - 2241 747
CsaV3_7G002210.1 CsFRS17 Chr.7 1754310 1760052 + 2370 790
CsaV3_7G002550.1 CsFRS18 Chr.7 1993692 2004852 + 2316 772
CsaV3_7G026930.1 CsFRS19 Chr.7 16558935 16562421 - 666 222
CsaV3_7G027310.1 CsFRS20 Chr.7 16862778 16871926 + 1491 497
CsaV3_7G032290.1 CsFRS21 Chr.7 20436138 20438129 + 1989 663
CsaV3_UNG168310.1 CsFRS22 Scaffold.77 105440 114205 + 2028 676

Fig. 4

Conservative motif and gene structure analysis of CsFRS transcription factor in cucumber"

Fig. 5

Gene expression analysis of CsFRS transcription factor in cucumber A: Tissue expression analysis; B: Expression patterns under biotic and abiotic stress. HP: Hypocotyl; RD: Radicle; CT: Cotyledon; FstLB: First leaf blade; SLB: Second leaf blade; FthLB: Forth leaf blade; JSM: Juvenile stem; JRT: Juvenile root; SAM: Shoot apical meristem; ART: Adult root; ALF: Adult leaf blade; ASM: Adult stem; TN: Tendril; OA_2DBF: Ovary of 2 days before flower; OA_0DAF: Ovary of 0 day after flower; PT_MF: Petal of male flower; SA_MF: Stamen of male flower; PT_FF: Petal of female flower; GN_FF: Gynoecium of female flower; EN: Endocarp; MS: Mesocarp; EX: Exocarp; NC: Fruit neck; SD: Seed"

Fig. 6

Chromosomal localization, synteny, and phylogenetic analysis of CsFRS transcription factor in cucumber A: Chromosomal localization and synteny analysis of CsFRS transcription factor; B: Phylogenetic analysis of CsFRS transcription factor. AT: Arabidopsis thaliana; Cla: Citrullus lanatus; Csa: Cucumis sativus; Cmo: Cucurbita moschata; MELO: Cucumis melo; Solyc: Solanum lycopersicum; Moc: Momordica charantia"

Fig. 7

The nucleotide and amino acid sequences difference of CsFRS12 between CR and CS"

Fig. 8

The transcription activity and gene expression pattern of CsFRS12 A: The transcription activity analysis; B: Gene expression analysis of CsFRS12"

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