scholarly journals Identification of potential candidate genes controlling pea aphid tolerance in a Pisum fulvum high‐density integrated DArTseq SNP‐based genetic map

2020 ◽  
Vol 76 (5) ◽  
pp. 1731-1742
Author(s):  
Eleonora Barilli ◽  
Estefanía Carrillo‐Perdomo ◽  
Maria José Cobos ◽  
Andrzej Kilian ◽  
Jason Carling ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Genetic Map ◽  
High Density ◽  
Pea Aphid ◽  
Potential Candidate ◽  
Pisum Fulvum ◽  
Aphid Tolerance

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 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 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 Identification of fruit size associated quantitative trait loci featuring SLAF based high-density linkage map of goji berry (Lycium spp.)

2020 ◽  
Author(s):  
Fazal Rehman ◽  
Haiguang Gong ◽  
Zhong Li ◽  
Shaohua Zeng ◽  
Tianshun Yang ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Linkage Map ◽  
Genetic Map ◽  
De Novo ◽  
Fruit Size ◽  
Leaf Size ◽  
High Density ◽  
Potential Candidate ◽  
Goji Berry ◽  
High Density Linkage Map

Abstract Background: Goji (Lycium spp., 2n = 24) is a perennial woody plant bearing functional properties. Fruit size associated attributes are important for evaluating small-fruited goji berry and plant architecture. The domestication traits are regulated quantitatively in crop plants but fewer studies have attempted on genomic regions corresponding to the fruit traits.Results: In this study, we established high-resolution map using SLAF-seq for de novo SNPs detection, based on 305 F1 offspring derived from L. chinense and L. barbarum. This genetic map contained 3,495 SNP markers on 12 LGs, spanning 1,649.03 cM with 0.47 cM average interval. Female and male parents had sequencing depth of 72.43-fold and 60.43-fold, respectively, while 15.23-fold detected for individuals. Phenotype data were obtained for 2 years and included 3rd year data as an average. QTL mapping analysis resulted in 117 QTLs corresponding to all traits, of which 23 QTLs in 2 years and 6 QTLs in 3rd years were detected. 6 promising QTLs, qFW10-3.1, qFL10-2.1, qLL10-2.1, qLD10-2.1, qLD12-4.1 and qLA10-2.1 were discovered influencing fruit weight, fruit length and leaf size related attributes covering an interval ranged 13.74-76.61 cM on LG10 with peak LOD up to 14.21 and PVE 19.3%. Additionally, 3 QTLs, qFS-1, qFS-2 and qFF-1, targeting fruit sweetness and fruit firmness were also identified in this study. Strikingly, among stable QTLs, qFL10-2.1, was co-localized to qLL10-2.1, qLD10-2.1, qLA10-2.1 and harbored significantly similar markers distribution, while qLL10-2.1 was the major and stable QTL with LOD ranged from 8.71-14.21 and PVE 12.3-19.3%. As LG10 harbored most of the fruit and leaf size related QTLs, we might speculate that it could be a hotspot region regulating fruit size and plant architectures.Conclusions: This report highlighted that the high-density linkage map construction using SLAF-seq is an important means for profound QTL mapping approach. Substantially, we utilized highly saturated genetic map to find out genetic locus targeting fruit and leaf size related attributes under QTL mapping. Our results will shed light on domestication traits and further strengthen molecular and genetic underpinnings of goji berry. Moreover, these findings would facilitate to assemble reference genome, determining potential candidate genes and marker-assisted breeding.

scholarly journals A High-Density Integrated DArTseq SNP-Based Genetic Map of Pisum fulvum and Identification of QTLs Controlling Rust Resistance

2018 ◽  
Vol 9 ◽  
Author(s):  
Eleonora Barilli ◽  
María J. Cobos ◽  
Estefanía Carrillo ◽  
Andrzej Kilian ◽  
Jason Carling ◽  
...  
Keyword(s):  
Genetic Map ◽  
Rust Resistance ◽  
High Density ◽  
Pisum Fulvum

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.

scholarly journals Genome-Wide Detection of Major and Epistatic Effect QTLs for Seed Protein and Oil Content in Soybean Under Multiple Environments Using High-Density Bin Map

2019 ◽  
Vol 20 (4) ◽  
pp. 979 ◽  
Author(s):  
Benjamin Karikari ◽  
Shuguang Li ◽  
Javaid Bhat ◽  
Yongce Cao ◽  
Jiejie Kong ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Oil Content ◽  
Seed Protein ◽  
Average Distance ◽  
Epistatic Effect ◽  
High Density ◽  
Environment Interaction ◽  
Potential Candidate ◽  
Main Effect ◽  
Main Effect Qtls

Seed protein and oil content are the two important traits determining the quality and value of soybean. Development of improved cultivars requires detailed understanding of the genetic basis underlying the trait of interest. However, it is prerequisite to have a high-density linkage map for precisely mapping genomic regions, and therefore the present study used high-density genetic map containing 2267 recombination bin markers distributed on 20 chromosomes and spanned 2453.79 cM with an average distance of 1.08 cM between markers using restriction-site-associated DNA sequencing (RAD-seq) approach. A recombinant inbred line (RIL) population of 104 lines derived from a cross between Linhefenqingdou and Meng 8206 cultivars was evaluated in six different environments to identify main- and epistatic-effect quantitative trait loci (QTLs)as well as their interaction with environments. A total of 44 main-effect QTLs for protein and oil content were found to be distributed on 17 chromosomes, and 15 novel QTL were identified for the first time. Out of these QTLs, four were major and stable QTLs, viz., qPro-7-1, qOil-8-3, qOil-10-2 and qOil-10-4, detected in at least two environments plus combined environment with R2 values >10%. Within the physical intervals of these four QTLs, 111 candidate genes were screened for their direct or indirect involvement in seed protein and oil biosynthesis/metabolism processes based on gene ontology and annotation information. Based on RNA sequencing (RNA-seq) data analysis, 15 of the 111 genes were highly expressed during seed development stage and root nodules that might be considered as the potential candidate genes. Seven QTLs associated with protein and oil content exhibited significant additive and additive × environment interaction effects, and environment-independent QTLs revealed higher additive effects. Moreover, three digenic epistatic QTLs pairs were identified, and no main-effect QTLs showed epistasis. In conclusion, the use of a high-density map identified closely linked flanking markers, provided better understanding of genetic architecture and candidate gene information, and revealed the scope available for improvement of soybean quality through marker assisted selection (MAS).

scholarly journals Generation of a High-Density Genetic Map of Pepper (Capsicum annuum L.) by SLAF-seq and QTL Analysis of Phytophthora capsici Resistance

Horticulturae ◽  
2021 ◽  
Vol 7 (5) ◽  
pp. 92
Author(s):  
Yi-Fei Li ◽  
Shi-Cai Zhang ◽  
Xiao-Miao Yang ◽  
Chun-Ping Wang ◽  
Qi-Zhong Huang ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Capsicum Annuum ◽  
Genetic Map ◽  
Phytophthora Capsici ◽  
Female Parent ◽  
High Density ◽  
Phenotypic Variance ◽  
Capsicum Annuum L ◽  
Reverse Transcription Pcr ◽  
Mapping Panel

Pepper (Capsicum annuum L.) is an economically significant global crop and condiment. Its yield can be severely reduced by the oomycete plant pathogen, Phytophthora capsici (P. capsici). Here, a high-density genetic map was created with a mapping panel of F2 populations obtained from 150 individuals of parental lines PI201234 and 1287 and specific-locus amplified fragment sequencing (SLAF) that was then utilized to identify loci that are related to resistance to P. capsici. The sequencing depth of the genetic map was 108.74-fold for the male parent, 126.25-fold for the female parent, and 22.73-fold for the offspring. A high-resolution genetic map consisting of 5565 markers and 12 linkage groups was generated for pepper, covering 1535.69 cM and an average marker distance of 0.28 cM. One major quantitative trait locus (QTL) for the P. capsici resistance (CQPc5.1) was identified on Chr05 that explained the observed 11.758% phenotypic variance. A total of 23 candidate genes located within the QTL CQPc5.1 interval were identified, which included the candidate gene Capana05g000595 that encodes the RPP8-like protein as well as two candidate genes Capana05g000596 and Capana05g000597 that encodes a RPP13-like protein. Quantitative reverse-transcription PCR (qRT-PCR) revealed higher expression levels of Capana05g000595, Capana05g000596, and Capana05g000597 in P. capsici resistance accessions, suggesting their association with P. capsici resistance in pepper.

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