scholarly journals Gene Set Subtraction Reveals 633 Candidate Genes for Bamboo Culm Wall Thickening

Forests ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 1331
Author(s):  
Yaping Hu ◽  
Jie Zhou ◽  
Zhaoyan Yu ◽  
Jiajia Li ◽  
Jinfeng Cai ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Reference Genome ◽  
Wall Thickening ◽  
Phyllostachys Edulis ◽  
Genome Resequencing ◽  
Bamboo Culm ◽  
Gene Set ◽  
Physiological Processes ◽  
Culm Wall ◽  
Whole Genome Resequencing

Abundant research has been conducted on the physiological, biochemical, and anatomical aspects of bamboo culm wall thickening, but its molecular mechanism has not yet been investigated. In this study, we performed whole-genome resequencing of Phyllostachys edulis ‘Pachyloen’, Phyllostachys nidularia f. farcta, Phyllostachys heteroclada f. solida with significantly thicker culm walls, and Schizostachyum dumetorum var. xinwuense with extremely thin culm walls. Moreover, we pioneered the innovative use of gene set subtraction to explore candidate genes that regulate bamboo culm wall thickening. A candidate gene set, containing 633 genes, was obtained by eliminating shared genes that help maintain physiological processes after alignment with the P. edulis reference genome. Starch and sucrose, oxidative phosphorylation, and ribosome were the three most important pathways enriched by differentially expressed genes. Although it cannot be used for hyperfine localization of bamboo wall thickness-regulatory genes, gene set reduction narrows down the range of candidate genes at minimal cost and provides new clues for the application of bioinformatics in plant research.

scholarly journals The wild grape genome sequence provides insights into the transition from dioecy to hermaphroditism during grape domestication

2020 ◽  
Author(s):  
Hélène Badouin ◽  
Amandine Velt ◽  
François Gindraud ◽  
Timothée Flutre ◽  
Vincent Dumas ◽  
...  
Keyword(s):  
Vitis Vinifera ◽  
Sex Determination ◽  
Reference Genome ◽  
De Novo ◽  
Gene Content ◽  
Female Sterility ◽  
Genome Resequencing ◽  
Cultural Importance ◽  
Grape Genome ◽  
Whole Genome Resequencing

Grapevine has a major economical and cultural importance since antiquity. A key step in domestication was the transition from separate sexes (dioecy) in wild Vitis vinifera ssp. sylvestris (V. sylvestris) to hermaphroditism in cultivated Vitis vinifera ssp. vinifera. While the grapevine sex locus is known to be small, its precise boundaries, gene content and the sex-determining genes are unknown. Here we obtained a high-quality de novo reference genome for V. sylvestris and whole-genome resequencing data of a cross. Studying SNP segregation patterns, gene content and expression in wild and cultivated accessions allowed us to build a model for sex determination in grapevine. In this model, up- and down-regulation of a cytokinin regulator is sufficient to cause female sterility and reversal to hermaphroditism, respectively. This study highlights the importance of neo-functionalization of Y alleles in sex determination and provides a resource for studying genetic diversity in V. sylvestris and the genomic processes of grapevine domestication.

scholarly journals Whole‐genome resequencing to identify candidate genes for the QTL for oleic acid percentage in Japanese Black cattle

2019 ◽  
Vol 90 (4) ◽  
pp. 467-472 ◽  
Author(s):  
Fuki Kawaguchi ◽  
Hiroto Kigoshi ◽  
Moriyuki Fukushima ◽  
Eiji Iwamoto ◽  
Eiji Kobayashi ◽  
...  
Keyword(s):  
Oleic Acid ◽  
Candidate Genes ◽  
Whole Genome ◽  
Japanese Black Cattle ◽  
Genome Resequencing ◽  
Whole Genome Resequencing ◽  
Acid Percentage

scholarly journals Identification of candidate genes for leaf scorch in Populus deltoids by the whole genome resequencing analysis

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Weibing Zhuang ◽  
Tianyu Liu ◽  
Shenchun Qu ◽  
Binhua Cai ◽  
Yalong Qin ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Leaf Scorch ◽  
Whole Genome Resequencing ◽  
Populus Deltoids

Whole-genome resequencing identified candidate genes associated with the number of ribs in Hu sheep

Genomics ◽  
2021 ◽  
Vol 113 (4) ◽  
pp. 2077-2084
Author(s):  
Deyin Zhang ◽  
Xiaoxue Zhang ◽  
Fadi Li ◽  
Teng Liu ◽  
Zhihong Hu ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Whole Genome Resequencing ◽  
Hu Sheep

scholarly journals The Population Structure and Selection Signal Analysis of Shenxian Pigs based on Genome Resequencing Technology

2021 ◽  
Author(s):  
Liu Diao ◽  
Lu Chunlian ◽  
Li Shang ◽  
Jia Mengyu ◽  
Li Sai ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Signal Analysis ◽  
Genetic Resource ◽  
Genetic Relationships ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Large White ◽  
Bioinformatics Analyses ◽  
Whole Genome Resequencing ◽  
Selection Signal

ABSTRACTShenxian pigs are the only local black pig of Hebei Province, and were listed in the Genetics of Livestock and Poultry Resources of China in 2016. This breed of pig is considered to be a valuable local pig germplasm genetic resource in China. In the present study, in order to understand the genetic variations of Shenxian pigs, identify selected regions related to superior traits, and accelerate the breeding processes of Shenxian pigs, the whole genome of the Shenxian pigs was resequenced and compared with that of large white pigs. The goal was to explore the germplasm characteristics of Shenxian pigs.The results obtained in this research investigation revealed that the genetic relationships of the Shenxian pig breed were complex, and that sub-populations could be identified within the general population. A total of 23M SNP sites were obtained by whole genome resequencing, and 1,509 selected sites were obtained via bioinformatics analyses. It was determined after annotation that a total of 19 genes were enriched in three items of bioengineering, molecular function, and cell composition.During this research investigation, the aforementioned 19 genes were subjected to GO and KEGG analyses. Subsequently, the candidate genes related to cell proliferation were obtained (DMTF1 and WDR5), which were considered to possibly be related to the slow growth and development of Shenxian pigs. In addition, the candidate genes related to lactation were obtained (CSN2 and CSN3).

scholarly journals Identification of candidate genes for drought tolerance by whole-genome resequencing in maize

2014 ◽  
Vol 14 (1) ◽  
pp. 83 ◽  
Author(s):  
Jie Xu ◽  
Yibing Yuan ◽  
Yunbi Xu ◽  
Gengyun Zhang ◽  
Xiaosen Guo ◽  
...  
Keyword(s):  
Drought Tolerance ◽  
Candidate Genes ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Whole Genome Resequencing

scholarly journals WGVD: an integrated web-database for wheat genome variation and selective signatures

Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Jierong Wang ◽  
Weiwei Fu ◽  
Rui Wang ◽  
Dexiang Hu ◽  
Hong Cheng ◽  
...  
Keyword(s):  
Bread Wheat ◽  
Reference Genome ◽  
Wheat Genome ◽  
Exome Capture ◽  
Whole Genome ◽  
Web Database ◽  
Genome Resequencing ◽  
Genome Variation ◽  
Genomic Variations ◽  
Whole Genome Resequencing

Abstract Bread wheat is one of the most important crops worldwide. With the release of the complete wheat reference genome and the development of next-generation sequencing technology, a mass of genomic data from bread wheat and its progenitors has been yield and has provided genomic resources for wheat genetics research. To conveniently and effectively access and use these data, we established Wheat Genome Variation Database, an integrated web-database including genomic variations from whole-genome resequencing and exome-capture data for bread wheat and its progenitors, as well as selective signatures during the process of wheat domestication and improvement. In this version, WGVD contains 7 346 814 single nucleotide polymorphisms (SNPs) and 1 044 400 indels focusing on genic regions and upstream or downstream regions. We provide allele frequency distribution patterns of these variations for 5 ploidy wheat groups or 17 worldwide bread wheat groups, the annotation of the variant types and the genotypes of all individuals for 2 versions of bread wheat reference genome (IWGSC RefSeq v1.0 and IWGSC RefSeq v2.0). Selective footprints for Aegilops tauschii, wild emmer, domesticated emmer, bread wheat landrace and bread wheat variety are evaluated with two statistical tests (FST and Pi) based on SNPs from whole-genome resequencing data. In addition, we provide the Genome Browser to visualize the genomic variations, the selective footprints, the genotype patterns and the read coverage depth, and the alignment tool Blast to search the homologous regions between sequences. All of these features of WGVD will promote wheat functional studies and wheat breeding. Database URL http://animal.nwsuaf.edu.cn/code/index.php/Wheat

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