Fine-mapping QTLs and the validation of candidate genes for Aluminum tolerance using a high-density genetic map

2019 ◽  
Vol 444 (1-2) ◽  
pp. 119-137 ◽  
Author(s):  
Zhandong Cai ◽  
Yanbo Cheng ◽  
Peiqi Xian ◽  
Rongbin Lin ◽  
Qiuju Xia ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Genetic Map ◽  
Fine Mapping ◽  
Aluminum Tolerance ◽  
High Density

scholarly journals QTL fine mapping for intramuscular fat and fatty acid composition using high-density SNP chip array on SSC12 in Korean native pig × Yorkshire F2 population  

2019 ◽  
Vol 64 (No. 4) ◽  
pp. 180-188
Author(s):  
Sangwook Kim ◽  
Byeonghwi Lim ◽  
Kwansuk Kim ◽  
Kyoungtag Do
Keyword(s):  
Fatty Acid Composition ◽  
Fatty Acid ◽  
Candidate Genes ◽  
Acid Composition ◽  
Fine Mapping ◽  
Intramuscular Fat ◽  
Economic Benefits ◽  
High Density ◽  
Chromosome 12 ◽  
Qtl Fine Mapping

Intramuscular fat (IMF) and fatty acid composition are characteristics that are used as important indicators of evaluating high quality pork and contribute to the economic benefits of the pig farming industry. In this study, quantitative trait loci (QTL) fine mapping of chromosome 12 was performed in a population of F2 intercross between Yorkshire (YS) and Korean native pigs (KNPs) by adopting combined linkage and linkage disequilibrium method using high-density SNP chips. QTLs for IMF (H3GA0034813 to H3GA0034965) and oleic acid (C18:1) (ASGA0054380 to ALGA0066299) were located at 120 cM (54.112–57.610 kb) and 85 cM (36.097–38.601 kb), respectively, within chromosome 12 (Sscrofa11.1 genomic reference). In addition, 31 candidate genes present within the IMF QTL region and 28 candidate genes existing within C18:1 QTL region were chosen. In order to understand the function of these candidate genes at the molecular level, these candidate genes were functionally categorized by studying gene ontology and analyzing network and pathway. Among the 59 candidate genes within the region of IMF QTL and C18:1 QTL, five (MYH1, MYH2, MYH4, ACACA, and RPS6KB1) directly interacting candidate genes were found. Furthermore, the RPS6KB1 gene was assumed to be an important candidate gene that is involved in leptin and insulin signaling pathway and participates in controlling adipogenic differentiation, fat deposition, and fatty acid composition, which is related to obesity of pigs.  

scholarly journals A high-density SNP-based genetic map and several economic traits-related loci in Pelteobagrus vachelli

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Guosong Zhang ◽  
Jie Li ◽  
Jiajia Zhang ◽  
Xia Liang ◽  
Tao Wang ◽  
...  
Keyword(s):  
Sex Determination ◽  
Linkage Map ◽  
Candidate Genes ◽  
Genetic Map ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
High Density ◽  
Hypoxia Tolerance ◽  
Genome Wide ◽  
Pelteobagrus Vachelli

Abstract Background A high-density genetic linkage map is essential for QTL fine mapping, comparative genome analysis, identification of candidate genes and marker-assisted selection in aquaculture species. Pelteobagrus vachelli is a very popular commercial species in Asia. However, some specific characters hindered achievement of the traditional selective breeding based on phenotypes, such as lack of large-scale genomic resource and short of markers tightly associated with growth, sex determination and hypoxia tolerance related traits. Results By making use of 5059 ddRAD markers in P. vachelli, a high-resolution genetic linkage map was successfully constructed. The map’ length was 4047.01 cM by using an interval of 0.11 cm, which is an average marker standard. Comparative genome mapping revealed that a high proportion (83.2%) of markers with a one-to-one correspondence were observed between P. vachelli and P. fulvidraco. Based on the genetic map, 8 significant genome-wide QTLs for 4 weight, 1 body proportion, 2 sex determination, and 1 hypoxia tolerance related traits were detected on 4 LGs. Some SNPs from these significant genome-wide QTLs were observably associated with these phenotypic traits in other individuals by Kompetitive Allele Specific PCR. In addition, two candidate genes for weight, Sipa1 and HSD11B2, were differentially expressed between fast-, medium- and slow-growing P. vachelli. Sema7a, associated with hypoxia tolerance, was induced after hypoxia exposure and reoxygenation. Conclusions We mapped a set of suggestive and significant QTLs as well as candidate genes for 12 growth, 1 sex determination and 1 hypoxia tolerance related traits based on a high-density genetic linkage map by making use of SNP markers for P. fulvidraco. Our results have offered a valuable method about the much more efficient production of all-male, fast growth and hypoxia tolerance P. vachelli for the aquaculture industry.

scholarly journals High-density genetic map using whole-genome resequencing for fine mapping and candidate gene discovery for disease resistance in peanut

2018 ◽  
Vol 16 (11) ◽  
pp. 1954-1967 ◽  
Author(s):  
Gaurav Agarwal ◽  
Josh Clevenger ◽  
Manish K. Pandey ◽  
Hui Wang ◽  
Yaduru Shasidhar ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Candidate Gene ◽  
Genetic Map ◽  
Fine Mapping ◽  
Gene Discovery ◽  
High Density ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Whole Genome Resequencing

scholarly journals Construction of a High-density Genetic Map and Identification of Candidate Genes for Resistance to Fusarium Wilt based on the Resequencing of Recombinant Inbred Line Population in Gossypium Barbadense

2021 ◽  
Author(s):  
Wanli Han ◽  
Jieyin Zhao ◽  
Xiaojuan Deng ◽  
Aixing Gu ◽  
Duolu Li ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Genetic Map ◽  
Fusarium Wilt ◽  
Recombinant Inbred ◽  
Gene Annotation ◽  
Recombinant Inbred Lines ◽  
Fiber Quality ◽  
Gossypium Barbadense ◽  
High Density ◽  
Pcr Analysis

Abstract Background: Resistance to Fusarium wilt (FW) is of great significance for increasing the yield of Gossypium barbadense. Most published genetic studies on G. barbadense focus on yield and fiber quality traits, while there are few reports on resistance to FW. Results: To understand the genetic basis of cotton resistance to FW, this study used 110 recombinant inbred lines (RILs) of G. barbadense obtained from the parental materials Xinhai 14 and 06-146, and Nannong was used to construct a high-density genetic linkage map. The high-density genetic map was based on the resequencing of 933,845 single-nucleotide polymorphism (SNP) markers, and 3627 bins covering 2483.17 cM were finally obtained. The collinearity matched the physical map. A total of 9 QTLs for FW resistance were identified, each QTL explained 4.27-14.92% of the observed phenotypic variation, and qFW-Dt3-1 was identified in at least two environments. According to gene annotation information from multiple databases, promoter homeopathic elements and transcriptome data, 10 candidate genes were screened in a stable QTL interval. qRT-PCR analysis showed that the GOBAR_DD06292 gene was differentially expressed in the roots of the two parents under FW stress and exhibited the same expression trend in the G. barbadense resource materials.Conclusions: These results indicate the importance of the GOBAR_DD06292 gene in FW resistance in G. barbadense and lay a molecular foundation for the analysis of the molecular mechanism of FW in G. barbadense.

scholarly journals High-density SNP map facilitates fine mapping of QTLs and candidate genes discovery for Aspergillus flavus resistance in peanut (Arachis hypogaea)

2020 ◽  
Vol 133 (7) ◽  
pp. 2239-2257 ◽  
Author(s):  
Shahid Ali Khan ◽  
Hua Chen ◽  
Ye Deng ◽  
Yuhua Chen ◽  
Chong Zhang ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Arachis Hypogaea ◽  
Aspergillus Flavus ◽  
Fine Mapping ◽  
High Density ◽  
Snp Map

scholarly journals QTL analysis for cooking traits of super rice with a high‐density SNP genetic map and fine mapping of a novel boiled grain length locus

2015 ◽  
Vol 134 (5) ◽  
pp. 535-541 ◽  
Author(s):  
Yuanyuan Li ◽  
Hongjian Tao ◽  
Jie Xu ◽  
Zhenyuan Shi ◽  
Weijun Ye ◽  
...  
Keyword(s):  
Genetic Map ◽  
Fine Mapping ◽  
Qtl Analysis ◽  
High Density ◽  
Grain Length

scholarly journals A Novel Stable QTL in Chromosome A04 for Salt Tolerance at the Seed Germination Stage of Upland Cotton via a Resequencing-Based High-Density Genetic Map

2021 ◽  
Author(s):  
Qishen Gu ◽  
Huifeng Ke ◽  
Chenchen Liu ◽  
Xing Lv ◽  
Zhengwen Sun ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Candidate Genes ◽  
Genetic Map ◽  
Germination Rate ◽  
High Density ◽  
Virus Induced Gene Silencing ◽  
Stable Quantitative Trait Locus ◽  
Trait Locus ◽  
Functional Analyses

Abstract Key message Two candidate genes GhGASA1 and GhADC2 playing negative roles by modulating the GA and PA signaling pathway, respectively, were identified in a major QTL for germination under salt stress.The successful transition of a seed into a seedling is the prerequisite for plant propagation and crop yield. Germination is a vulnerable stage in a plant’s life cycle which is strongly affected by environmental conditions, such as salinity. In this study, we identified a novel stable quantitative trait locus (QTL) qRGR-A04-1 associated with relative germination rate (RGR) after treatment with salt stress based on a high-density genetic map under phytotron and filed conditions, with LOD values of 6.65-16.83 and 6.11-12.63% of phenotypic variations in all five environment tests. Two candidate genes with significantly differential expression between two parents were finally identified through RNA-seq and qRT-PCR analyses. Further functional analyses showed that GhGASA1- and GhADC2-overexpression lines were more sensitive to salt stress than wild-type in Arabidopsis through regulating the transcript levels of gibberellic acid (GA) and polyamine (PA) -related genes implicating in GA and PA biosynthesis with reducing the accumulation of GA and PA under salt stress, respectively. Virus-induced gene silencing analysis showed that TRV:GASA1 and TRV:ADC2 displayed more tolerant to salt stress by increasing the expression of GA-synthesis genes and decreasing the H2O2 content, respectively. Taken together, our results suggested that QTL qRGR-A04-1 and its harbored two genes, GhGASA1 and GhADC2, were promising candidates for salt tolerance improvement in cotton.

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