Tags

Type your tag names separated by a space and hit enter

Identification of a stable major-effect QTL (Parth 2.1) controlling parthenocarpy in cucumber and associated candidate gene analysis via whole genome re-sequencing.
BMC Plant Biol. 2016 08 23; 16(1):182.BP

Abstract

BACKGROUND

Parthenocarpy is an important trait for yield and quality in many plants. But due to its complex interactions with genetic and physiological factors, it has not been adequately understood and applied to breeding and production. Finding novel and effective quantitative trait loci (QTLs) is a critical step towards understanding its genetic mechanism. Cucumber (Cucumis sativus L.) is a typical parthenocarpic plant but the QTLs controlling parthenocarpy in cucumber were not mapped on chromosomes, and the linked markers were neither user-friendly nor confirmed by previous studies. Hence, we conducted a two-season QTL study of parthenocarpy based on the cucumber genome with 145 F2:3 families derived from a cross between EC1 (a parthenocarpic inbred line) and 8419 s-1 (a non-parthenocarpic inbred line) in order to map novel QTLs. Whole genome re-sequencing was also performed both to develop effective linked markers and to predict candidate genes.

RESULTS

A genetic linkage map, employing 133 Simple Sequence Repeats (SSR) markers and nine Insertion/Deletion (InDel) markers spanning 808.1 cM on seven chromosomes, was constructed from an F2 population. Seven novel QTLs were identified on chromosomes 1, 2, 3, 5 and 7. Parthenocarpy 2.1 (Parth2.1), a QTL on chromosome 2, was a major-effect QTL with a logarithm of odds (LOD) score of 9.0 and phenotypic variance explained (PVE) of 17.0 % in the spring season and with a LOD score of 6.2 and PVE of 10.2 % in the fall season. We confirmed this QTL using a residual heterozygous line97-5 (RHL97-5). Effectiveness of linked markers of the Parth2.1 was validated in F3:4 population and in 21 inbred lines. Within this region, there were 57 genes with nonsynonymous SNPs/InDels in the coding sequence. Based on further combined analysis with transcriptome data between two parents, CsARF19, CsWD40, CsEIN1, CsPPR, CsHEXO3, CsMDL, CsDJC77 and CsSMAX1 were predicted as potential candidate genes controlling parthenocarpy.

CONCLUSIONS

A major-effect QTL Parth2.1 and six minor-effect QTLs mainly contribute to the genetic architecture of parthenocarpy in cucumber. SSR16226 and Indel-T-39 can be used in marker-assisted selection (MAS) of cucumber breeding. Whole genome re-sequencing enhances the efficiency of polymorphic marker development and prediction of candidate genes.

Authors+Show Affiliations

State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China. College of Horticulture, Shanxi Agricultural University, Shanxi, 030801, China.State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China. liji1981@njau.edu.cn.State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China. jfchen@njau.edu.cn.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

27553196

Citation

Wu, Zhe, et al. "Identification of a Stable Major-effect QTL (Parth 2.1) Controlling Parthenocarpy in Cucumber and Associated Candidate Gene Analysis Via Whole Genome Re-sequencing." BMC Plant Biology, vol. 16, no. 1, 2016, p. 182.
Wu Z, Zhang T, Li L, et al. Identification of a stable major-effect QTL (Parth 2.1) controlling parthenocarpy in cucumber and associated candidate gene analysis via whole genome re-sequencing. BMC Plant Biol. 2016;16(1):182.
Wu, Z., Zhang, T., Li, L., Xu, J., Qin, X., Zhang, T., Cui, L., Lou, Q., Li, J., & Chen, J. (2016). Identification of a stable major-effect QTL (Parth 2.1) controlling parthenocarpy in cucumber and associated candidate gene analysis via whole genome re-sequencing. BMC Plant Biology, 16(1), 182. https://doi.org/10.1186/s12870-016-0873-6
Wu Z, et al. Identification of a Stable Major-effect QTL (Parth 2.1) Controlling Parthenocarpy in Cucumber and Associated Candidate Gene Analysis Via Whole Genome Re-sequencing. BMC Plant Biol. 2016 08 23;16(1):182. PubMed PMID: 27553196.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Identification of a stable major-effect QTL (Parth 2.1) controlling parthenocarpy in cucumber and associated candidate gene analysis via whole genome re-sequencing. AU - Wu,Zhe, AU - Zhang,Ting, AU - Li,Lei, AU - Xu,Jian, AU - Qin,Xiaodong, AU - Zhang,Tinglin, AU - Cui,Li, AU - Lou,Qunfeng, AU - Li,Ji, AU - Chen,Jinfeng, Y1 - 2016/08/23/ PY - 2016/01/14/received PY - 2016/08/15/accepted PY - 2016/8/25/entrez PY - 2016/8/25/pubmed PY - 2017/8/19/medline KW - Candidate genes KW - Cucumber KW - Parthenocarpy KW - QTL KW - Re-sequencing SP - 182 EP - 182 JF - BMC plant biology JO - BMC Plant Biol VL - 16 IS - 1 N2 - BACKGROUND: Parthenocarpy is an important trait for yield and quality in many plants. But due to its complex interactions with genetic and physiological factors, it has not been adequately understood and applied to breeding and production. Finding novel and effective quantitative trait loci (QTLs) is a critical step towards understanding its genetic mechanism. Cucumber (Cucumis sativus L.) is a typical parthenocarpic plant but the QTLs controlling parthenocarpy in cucumber were not mapped on chromosomes, and the linked markers were neither user-friendly nor confirmed by previous studies. Hence, we conducted a two-season QTL study of parthenocarpy based on the cucumber genome with 145 F2:3 families derived from a cross between EC1 (a parthenocarpic inbred line) and 8419 s-1 (a non-parthenocarpic inbred line) in order to map novel QTLs. Whole genome re-sequencing was also performed both to develop effective linked markers and to predict candidate genes. RESULTS: A genetic linkage map, employing 133 Simple Sequence Repeats (SSR) markers and nine Insertion/Deletion (InDel) markers spanning 808.1 cM on seven chromosomes, was constructed from an F2 population. Seven novel QTLs were identified on chromosomes 1, 2, 3, 5 and 7. Parthenocarpy 2.1 (Parth2.1), a QTL on chromosome 2, was a major-effect QTL with a logarithm of odds (LOD) score of 9.0 and phenotypic variance explained (PVE) of 17.0 % in the spring season and with a LOD score of 6.2 and PVE of 10.2 % in the fall season. We confirmed this QTL using a residual heterozygous line97-5 (RHL97-5). Effectiveness of linked markers of the Parth2.1 was validated in F3:4 population and in 21 inbred lines. Within this region, there were 57 genes with nonsynonymous SNPs/InDels in the coding sequence. Based on further combined analysis with transcriptome data between two parents, CsARF19, CsWD40, CsEIN1, CsPPR, CsHEXO3, CsMDL, CsDJC77 and CsSMAX1 were predicted as potential candidate genes controlling parthenocarpy. CONCLUSIONS: A major-effect QTL Parth2.1 and six minor-effect QTLs mainly contribute to the genetic architecture of parthenocarpy in cucumber. SSR16226 and Indel-T-39 can be used in marker-assisted selection (MAS) of cucumber breeding. Whole genome re-sequencing enhances the efficiency of polymorphic marker development and prediction of candidate genes. SN - 1471-2229 UR - https://www.unboundmedicine.com/medline/citation/27553196/Identification_of_a_stable_major_effect_QTL__Parth_2_1__controlling_parthenocarpy_in_cucumber_and_associated_candidate_gene_analysis_via_whole_genome_re_sequencing_ L2 - https://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-016-0873-6 DB - PRIME DP - Unbound Medicine ER -