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Identification of a stable major-effect QTL (Parth 2.1) controlling parthenocarpy in cucumber and associated candidate gene analysis via whole genome re-sequencing

Overview of attention for article published in BMC Plant Biology, August 2016
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About this Attention Score

  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (80th percentile)
  • High Attention Score compared to outputs of the same age and source (89th percentile)

Mentioned by

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1 blog
twitter
1 tweeter

Citations

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7 Dimensions

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19 Mendeley
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Title
Identification of a stable major-effect QTL (Parth 2.1) controlling parthenocarpy in cucumber and associated candidate gene analysis via whole genome re-sequencing
Published in
BMC Plant Biology, August 2016
DOI 10.1186/s12870-016-0873-6
Pubmed ID
Authors

Zhe Wu, Ting Zhang, Lei Li, Jian Xu, Xiaodong Qin, Tinglin Zhang, Li Cui, Qunfeng Lou, Ji Li, Jinfeng Chen

Abstract

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. 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. 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.

Twitter Demographics

The data shown below were collected from the profile of 1 tweeter who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 19 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Norway 1 5%
Unknown 18 95%

Demographic breakdown

Readers by professional status Count As %
Researcher 6 32%
Student > Ph. D. Student 4 21%
Student > Master 4 21%
Student > Doctoral Student 2 11%
Student > Bachelor 1 5%
Other 2 11%
Readers by discipline Count As %
Agricultural and Biological Sciences 12 63%
Unspecified 2 11%
Environmental Science 2 11%
Biochemistry, Genetics and Molecular Biology 2 11%
Earth and Planetary Sciences 1 5%
Other 0 0%

Attention Score in Context

This research output has an Altmetric Attention Score of 8. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 01 September 2016.
All research outputs
#1,153,289
of 8,314,034 outputs
Outputs from BMC Plant Biology
#109
of 1,139 outputs
Outputs of similar age
#50,179
of 254,001 outputs
Outputs of similar age from BMC Plant Biology
#5
of 47 outputs
Altmetric has tracked 8,314,034 research outputs across all sources so far. Compared to these this one has done well and is in the 86th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 1,139 research outputs from this source. They receive a mean Attention Score of 3.3. This one has done well, scoring higher than 89% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 254,001 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 80% of its contemporaries.
We're also able to compare this research output to 47 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 89% of its contemporaries.