Whole genome homology-based identification of candidate genes for drought tolerance in sesame (Sesamum indicum L.)

Bamei mutton sheep is a Chinese domestic sheep breed developed by crossing German Mutton Merino sheep and indigenous Mongolian sheep for meat production. Here, we focused on detecting candidate genes associated with the increasing of the litter size in this breeds under recent artificial selection to improve the efficiency of mutton production. We selected five high- and five low-fecundity Bamei mutton sheep for whole-genome resequencing to identify candidate genes for sheep prolificacy. We used the FST and XP-EHH statistical approach to detect the selective sweeps between these two groups. Combining the two selective sweep methods, the reproduction-related genes JUN, ITPR3, PLCB2, HERC5, and KDM4B were detected. JUN, ITPR3, and PLCB2 play vital roles in GnRH (gonadotropin-releasing hormone), oxytocin, and estrogen signaling pathway. Moreover, KDM4B, which had the highest FST value, exhibits demethylase activity. It can affect reproduction by binding the promoters of estrogen-regulated genes, such as FOXA1 (forkhead box A1) and ESR1 (estrogen receptor 1). Notably, one nonsynonymous mutation (p.S936A) specific to the high-prolificacy group was identified at the TUDOR domain of KDM4B. These observations provide a new opportunity to research the genetic variation influencing fecundity traits within a population evolving under artificial selection. The identified genomic regions that are responsible for litter size can in turn be used for further selection.

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Transcriptomic analysis of sweet potato under dehydration stress identifies candidate genes for drought tolerance

Plant Direct ◽

10.1002/pld3.92 ◽

2018 ◽

Vol 2 (10) ◽

pp. e00092 ◽

Cited By ~ 6

Author(s):

Kin H. Lau ◽

María del Rosario Herrera ◽

Emily Crisovan ◽

Shan Wu ◽

Zhangjun Fei ◽

...

Keyword(s):

Drought Tolerance ◽

Candidate Genes ◽

Sweet Potato ◽

Transcriptomic Analysis ◽

Dehydration Stress

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The Population Structure and Selection Signal Analysis of Shenxian Pigs Based on Genome Resequencing Technology

10.21203/rs.3.rs-244687/v1 ◽

2021 ◽

Author(s):

Diao Liu ◽

Chunlian Lu ◽

Shang Li ◽

Mengyu Jia ◽

Yutao Miao ◽

...

Keyword(s):

Candidate Genes ◽

Meat Quality ◽

Genetic Relationships ◽

Animal Husbandry ◽

Hebei Province ◽

Whole Genome ◽

Genome Resequencing ◽

Large White ◽

Bioinformatics Analyses ◽

Pig Breeds

Abstract Shenxian 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. When compared with other introduced pig breeds, the Shenxian pig breed is characterized with early sexual maturity, short oestrus intervals, large litter sizes, and good meat quality, which are all of good research significance. However, the Shenxian pig variety was previously declared extinct in 2004 due to the introduction of a large number of foreign pig breeds. In order to preserve and study the Shenxian pig breed, the Hebei Zhengnong Animal Husbandry Co., Ltd. was established in Hebei Province for the purpose of preserving the purified Shenxian pig strain. 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). However, no genes related to meat quality traits were successfully screened.

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Misclassification of a whole genome sequence reference defined by the Human Microbiome Project: a detrimental carryover effect to microbiome studies

10.1101/19000489 ◽

2019 ◽

Author(s):

DJ Darwin R. Bandoy ◽

B Carol Huang ◽

Bart C. Weimer

Keyword(s):

Human Microbiome ◽

Human Microbiome Project ◽

Outbreak Detection ◽

Whole Genome Sequence ◽

Reference Database ◽

Whole Genome ◽

Reference Species ◽

Genome Sequences ◽

Genome Homology ◽

Microbiome Data

AbstractTaxonomic classification is an essential step in the analysis of microbiome data that depends on a reference database of whole genome sequences. Taxonomic classifiers are built on established reference species, such as the Human Microbiome Project database, that is growing rapidly. While constructing a population wide pangenome of the bacterium Hungatella, we discovered that the Human Microbiome Project reference species Hungatella hathewayi (WAL 18680) was significantly different to other members of this genus. Specifically, the reference lacked the core genome as compared to the other members. Further analysis, using average nucleotide identity (ANI) and 16s rRNA comparisons, indicated that WAL18680 was misclassified as Hungatella. The error in classification is being amplified in the taxonomic classifiers and will have a compounding effect as microbiome analyses are done, resulting in inaccurate assignment of community members and will lead to fallacious conclusions and possibly treatment. As automated genome homology assessment expands for microbiome analysis, outbreak detection, and public health reliance on whole genomes increases this issue will likely occur at an increasing rate. These observations highlight the need for developing reference free methods for epidemiological investigation using whole genome sequences and the criticality of accurate reference databases.

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