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

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.

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 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

Detection of Genomic Variation and Tepal Shape Related Genes Between Broad and Narrow Tepal Lotus (Nelumbo Adans.) by whole Genome Resequencing

2021 ◽  
Author(s):  
Feng-Luan Liu ◽  
Mi Qin ◽  
Shuo Li ◽  
Da-Sheng Zhang ◽  
Qing-Qing Liu ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Genomic Variation ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Wild Type ◽  
Genome Resequencing ◽  
Pollinator Attraction ◽  
Water Lily ◽  
Epidermal Growth ◽  
Whole Genome Resequencing

Abstract Background: The shape, color, and size of petals or tepals are vital attributes of flowering plants, as they affect the pollinator attraction ability, environmental stress adaptation, and ornamental value of plants. Compared with rose, chrysanthemum, and water lily, the tepal shapes of lotus (Nelumbo Adans.) exhibit low variation, and the absence of short-broad and long-narrow tepals limits the commercial value of lotus flowers. Therefore, this study aimed to uncover the genomic variation underlying the broad and narrow tepal phenotypes of lotus flowers, and to screen candidate genes associated with different tepal shapes.Results: Whole genome resequencing of two groups of lotus, NL (comprising three American lotus genotypes: broad tepal mutant, narrow tepal mutant, and wild type) and WSH (comprising two Asian lotus genotypes: narrow tepal mutant and wild type), generated 9.23–12.85 Gb clean data. A total of 716,656 single nucleotide polymorphisms (SNPs) and 221,688 insertion-deletion mutations (Indels) were obtained in the NL group, while 639,953 SNPs and 134,6118 Indels were obtained in the WSH group. Only a small proportion of these SNPs and Indels was mapped to exonic regions of genome: 1.92% and 0.47%, respectively, in the NL group, and 1.66% and 0.48%, respectively, in the WSH group. Gene Ontology (GO) analysis showed that out of 4,890 (NL group) and 1,272 (WSH group) annotated variant genes, 125 and 62 genes were enriched (Q < 0.05), respectively. Additionally, in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, 104 genes (NL group) and 35 genes (WSH group) were selected (P < 0.05). Finally, 41 genes were filtered and predicted to be associated with tepal shape in lotus.Conclusions: This is the first comprehensive report of genomic variation controlling tepal shape in lotus. Significant genetic variation was detected between the wild-type and mutant lotus genotypes, and varying levels of differentiation between groups NL and WSH. Candidate genes containing epidermal growth factor (EGF) and wall-associated receptor kinase (WAK) domains are considered important targets for further research on tepal development. Overall, the genomic data and candidate genes obtained in this study are essential references for future identification of tepal-shaped control genes in lotus combined with transcriptome analysis and quantitative trait loci (QTL) mapping.

scholarly journals Construction of a High-Density Genetic Map and Mapping of Firmness in Grapes (Vitis vinifera L.) Based on Whole-Genome Resequencing

2020 ◽  
Vol 21 (3) ◽  
pp. 797 ◽  
Author(s):  
Jianfu Jiang ◽  
Xiucai Fan ◽  
Ying Zhang ◽  
Xiaoping Tang ◽  
Xiaomei Li ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Genetic Map ◽  
High Density ◽  
Pcr Analysis ◽  
Vitis Vinifera L ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Phenotypic Data ◽  
Table Grapes ◽  
Whole Genome Resequencing

Berry firmness is one of the most important quality traits in table grapes. The underlying molecular and genetic mechanisms for berry firmness remain unclear. We constructed a high-density genetic map based on whole-genome resequencing to identify loci associated with berry firmness. The genetic map had 19 linkage groups, including 1662 bin markers (26,039 SNPs), covering 1463.38 cM, and the average inter-marker distance was 0.88 cM. An analysis of berry firmness in the F1 population and both parents for three consecutive years revealed continuous variability in F1, with a distribution close to the normal distribution. Based on the genetic map and phenotypic data, three potentially significant quantitative trait loci (QTLs) related to berry firmness were identified by composite interval mapping. The contribution rate of each QTL ranged from 21.5% to 28.6%. We identified four candidate genes associated with grape firmness, which are related to endoglucanase, abscisic acid (ABA), and transcription factors. A qRT-PCR analysis revealed that the expression of abscisic-aldehyde oxidase-like gene (VIT_18s0041g02410) and endoglucanase 3 gene (VIT_18s0089g00210) in Muscat Hamburg was higher than in Crimson Seedless at the veraison stage, which was consistent with that of parent berry firmness. These results confirmed that VIT_18s0041g02410 and VIT_18s0089g00210 are candidate genes associated with berry firmness.

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