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Updated sesame genome assembly and fine mapping of plant height and seed coat color QTLs using a new high-density genetic map

Overview of attention for article published in BMC Genomics, January 2016
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Title
Updated sesame genome assembly and fine mapping of plant height and seed coat color QTLs using a new high-density genetic map
Published in
BMC Genomics, January 2016
DOI 10.1186/s12864-015-2316-4
Pubmed ID
Authors

Linhai Wang, Qiuju Xia, Yanxin Zhang, Xiaodong Zhu, Xiaofeng Zhu, Donghua Li, Xuemei Ni, Yuan Gao, Haitao Xiang, Xin Wei, Jingyin Yu, Zhiwu Quan, Xiurong Zhang

Abstract

Sesame is an important high-quality oil seed crop. The sesame genome was de novo sequenced and assembled in 2014 (version 1.0); however, the number of anchored pseudomolecules was higher than the chromosome number (2n = 2x = 26) due to the lack of a high-density genetic map with 13 linkage groups. We resequenced a permanent population consisting of 430 recombinant inbred lines and constructed a genetic map to improve the sesame genome assembly. We successfully anchored 327 scaffolds onto 13 pseudomolecules. The new genome assembly (version 2.0) included 97.5 % of the scaffolds greater than 150 kb in size present in assembly version 1.0 and increased the total pseudomolecule length from 233.7 to 258.4 Mb with 94.3 % of the genome assembled and 97.2 % of the predicted gene models anchored. Based on the new genome assembly, a bin map including 1,522 bins spanning 1090.99 cM was generated and used to identified 41 quantitative trait loci (QTLs) for sesame plant height and 9 for seed coat color. The plant height-related QTLs explained 3-24 % the phenotypic variation (mean value, 8 %), and 29 of them were detected in at least two field trials. Two major loci (qPH-8.2 and qPH-3.3) that contributed 23 and 18 % of the plant height were located in 350 and 928-kb spaces on Chr8 and Chr3, respectively. qPH-3.3, is predicted to be responsible for the semi-dwarf sesame plant phenotype and contains 102 candidate genes. This is the first report of a sesame semi-dwarf locus and provides an interesting opportunity for a plant architecture study of the sesame. For the sesame seed coat color, the QTLs of the color spaces L*, a*, and b* were detected with contribution rates of 3-46 %. qSCb-4.1 contributed approximately 39 % of the b* value and was located on Chr4 in a 199.9-kb space. A list of 32 candidate genes for the locus, including a predicted black seed coat-related gene, was determined by screening the newly anchored genome. This study offers a high-density genetic map and an improved assembly of the sesame genome. The number of linkage groups and pseudomolecules in this assembly equals the number of sesame chromosomes for the first time. The map and updated genome assembly are expected to serve as a platform for future comparative genomics and genetic studies.

Twitter Demographics

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Mendeley readers

The data shown below were compiled from readership statistics for 67 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 67 100%

Demographic breakdown

Readers by professional status Count As %
Student > Master 14 21%
Student > Ph. D. Student 11 16%
Researcher 10 15%
Student > Doctoral Student 4 6%
Professor > Associate Professor 4 6%
Other 9 13%
Unknown 15 22%
Readers by discipline Count As %
Agricultural and Biological Sciences 37 55%
Biochemistry, Genetics and Molecular Biology 8 12%
Pharmacology, Toxicology and Pharmaceutical Science 1 1%
Computer Science 1 1%
Medicine and Dentistry 1 1%
Other 0 0%
Unknown 19 28%

Attention Score in Context

This research output has an Altmetric Attention Score of 2. 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 12 January 2016.
All research outputs
#6,940,755
of 12,076,109 outputs
Outputs from BMC Genomics
#3,826
of 7,112 outputs
Outputs of similar age
#148,573
of 333,465 outputs
Outputs of similar age from BMC Genomics
#193
of 331 outputs
Altmetric has tracked 12,076,109 research outputs across all sources so far. This one is in the 40th percentile – i.e., 40% of other outputs scored the same or lower than it.
So far Altmetric has tracked 7,112 research outputs from this source. They receive a mean Attention Score of 4.3. This one is in the 41st percentile – i.e., 41% of its peers scored the same or lower than it.
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 333,465 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 52% of its contemporaries.
We're also able to compare this research output to 331 others from the same source and published within six weeks on either side of this one. This one is in the 34th percentile – i.e., 34% of its contemporaries scored the same or lower than it.