Identification of Genetic Loci and Molecular Marker Development of Salt Tolerance in Tomato Seedlings

doi:10.16420/j.issn.0513-353x.2023-0739

Acta Horticulturae Sinica ›› 2024, Vol. 51 ›› Issue (2): 239-252.doi: 10.16420/j.issn.0513-353x.2023-0739

• Genetic&Breeding?Germplasm Resources?Molecular Biology • Previous Articles Next Articles

Identification of Genetic Loci and Molecular Marker Development of Salt Tolerance in Tomato Seedlings

XU Qin¹, WANG Jiaying¹, ZHANG Mannan¹, XIAO Zhihao¹, ZHENG Hankai¹, LU Yong'en¹, WANG Taotao¹, ZHANG Yuyang¹^,², ZHANG Junhong¹^,², YE Zhibiao¹^,², YE Jie¹^,²^,^*()

¹ National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops，College of Horticulture & Forestry Sciences，Huazhong Agricultural University，Wuhan 430070，China
² Hubei Hongshan Laboratory，Wuhan 430070，China

Received:2023-09-25 Revised:2023-11-23 Online:2024-02-25 Published:2024-02-26
Contact: YE Jie

Abstract

Abstract:

To identify the genetic components of salt tolerance at the seedling stage of tomato，the contents of sodium（Na⁺）and potassium（K⁺）were determined，and genome-wide association analysis was further performed for shoot Na⁺/K⁺ ratio in a population consisting of 501 tomato accessions. The decrease in salt tolerance from wild tomatoes to large-fruited tomatoes is due to the decrease in Na⁺ content and Na⁺/K⁺ ratio during tomato domestication and improvement. The most significant loci associated with shoot Na⁺ content and Na⁺/K⁺ ratio were identified on chromosome 7，which contained two genes with known function，HKT1;1and HKT1;2. Sequence analysis，and haplotype analysis identified a 6 bp InDel（InDel_6）on the promoter of HKT1;2 showed highly correlated with Na⁺ content and Na⁺/K⁺ ratio，and salt treatment of different genotype accessions based on the InDel_6 confirmed that this mutation was the causative variant associated with Na⁺/K⁺ ratio and confer salt tolerance in tomato. Based on this causative variant，a codominant molecular marker that can quickly and accurately verify the salt tolerance of tomatoes at the seedling stage were developed.

Key words: tomato, salt tolerance, sodium, potassium, genome-wide association analysis, molecular marker

XU Qin, WANG Jiaying, ZHANG Mannan, XIAO Zhihao, ZHENG Hankai, LU Yong'en, WANG Taotao, ZHANG Yuyang, ZHANG Junhong, YE Zhibiao, YE Jie. Identification of Genetic Loci and Molecular Marker Development of Salt Tolerance in Tomato Seedlings[J]. Acta Horticulturae Sinica, 2024, 51(2): 239-252.

Figures/Tables 6

Fig. 1 The Na+ and K+ content and Na+/K+ ratio in roots and shoots of three subgroups of tomato accessions PIM：Solanum pimpinellifolium（46）；CER：S. lycopersicum var. cerasiforme（180）；BIG：S. lycopersicum（275）. * P < 0.05；** P < 0.01；*** P < 0.001.

Fig. 2 Results of genome-wide association analysis of Na+ and K+ content in shoot of tomato germplasm resources

Fig. 3 Screening of highly associated loci of Na+ content and analysis of Na+ content and Na+/K+ ratio of different haplotypes A：Member of potassium ion transport family SlHKT1;1 and SlHKT1;2 analysis of nearby significant sites；B：Haplotype analysis of Na+ contentof 18 bp indel and 6 bp indel；C：Haplotype analysis of Na+/K+ ratio of four genotypes，Hap_1：Del_18/Del_6，Hap_2：Ins_18/Del_6，Hap_3：Del_18/Ins_6，Hap_4：Ins_18/Ins_6；D，E：Genotype sequencing results of 18 bp and 6 bp indel（TS-9，TS-16，TS-50，TS-680，TS-17，TS-18，TS-123，TS-156）.

Fig. 4 Relative changes in plant height，root length，and fresh mass and examples of phenotypes in tomato with different salt treated

Fig. 5 Examples of electrophoretic detection results of molecular markers

Fig. 6 Detection results of molecular markers in tomato materials with different haplotypes

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Identification of Genetic Loci and Molecular Marker Development of Salt Tolerance in Tomato Seedlings

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