Fine mapping and identification of candidate genes for a QTL affecting Meloidogyne incognita reproduction in Upland cotton

Abstract Background: Gossypium hirsutum (upland cotton), the most widely cultivated cotton species in the world, is an important raw material for the textile industry. Using high-throughput sequencing to construct high-density genetic maps can be widely used in quantitative trait locus (QTL) mapping and molecular marker-assisted breeding.Results: In this study, an F2 population was used to construct a genetic map by parental resequencing and progeny SLAF-seq. The F2 population consisted of Gossypium hirsutum L. cultivars: CCRI 49 and 396289. The genetic map contained 4,607 single nucleotide polymorphisms markers, which overlapped a total length of 3,063.4 cM with an average genetic distance of 0.898 cM between adjacent markers. A high-density genetic map was used to map the QTLs of plant height in four environments. 16 QTLs were obtained, which could explain 2.07%–19.04% of the phenotypic variation. A total of 1,028 candidate genes were identified in the confidence interval and were categorized according to function through cluster of orthologous groups analysis, gene ntology analysis, and Kyoto Encyclopedia of Genes and Genomes analysis. Within the QTLs confidence interval, the D05 chromosome(ChrD05) was finely mapped using Mutmap-like strategy, and the reliability was validated by qRT-PCR of 18 candidate genes . Finally, we obtained 14 candidate genes that are most likely to be related to plant height.Conclusions: This study provides a successful application of parental sequencing and progeny SLAF-seq strategy in the genetic map of upland cotton in an F2 population. This study provides theoretical support for molecular marker-assisted breeding and plant height-heterosis in upland cotton and provides a fine mapping scheme for QTLs. In addition, the combination of multiple analytical methods also provided a solution for QTL fine mapping.

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Fine mapping and RNA-Seq unravels candidate genes for a major QTL controlling multiple fiber quality traits at the T1 region in upland cotton

BMC Genomics ◽

10.1186/s12864-016-2605-6 ◽

2016 ◽

Vol 17 (1) ◽

Cited By ~ 16

Author(s):

Dexin Liu ◽

Jian Zhang ◽

Xueying Liu ◽

Wenwen Wang ◽

Dajun Liu ◽

...

Keyword(s):

Candidate Genes ◽

Fine Mapping ◽

Upland Cotton ◽

Fiber Quality ◽

Quality Traits ◽

Rna Seq ◽

Fiber Quality Traits ◽

Major Qtl

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Retraction: “Screening of candidate genes and fine mapping of drought tolerance quantitative trait loci on chromosome 4 in rice (Oryza sativa L.) under drought stress” by Nie, Y. Y., L. Zhang, Y. H. Wu, H. J. Liu, W. W. Mao, J. Du, et al.

Ecology and Evolution ◽

10.1002/ece3.1855 ◽

2015 ◽

Vol 6 (1) ◽

pp. 375-375

Keyword(s):

Oryza Sativa ◽

Drought Stress ◽

Quantitative Trait Loci ◽

Drought Tolerance ◽

Candidate Genes ◽

Fine Mapping ◽

Quantitative Trait ◽

Oryza Sativa L ◽

Chromosome 4 ◽

Trait Loci

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Fine-mapping qFS07.1 controlling fiber strength in upland cotton (Gossypium hirsutum L.)

Theoretical and Applied Genetics ◽

10.1007/s00122-017-2852-1 ◽

2017 ◽

Vol 130 (4) ◽

pp. 795-806 ◽

Cited By ~ 17

Author(s):

Xiaomei Fang ◽

Xueying Liu ◽

Xiaoqin Wang ◽

Wenwen Wang ◽

Dexin Liu ◽

...

Keyword(s):

Gossypium Hirsutum ◽

Fine Mapping ◽

Upland Cotton ◽

Fiber Strength ◽

Gossypium Hirsutum L

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Abstract 1743: Identification of a Novel Susceptibility Locus at 9q21 for Familial Bicuspid Aortic Valve Disease

Circulation ◽

10.1161/circ.116.suppl_16.ii_368 ◽

2007 ◽

Vol 116 (suppl_16) ◽

Author(s):

Stephen H McKellar ◽

Marineh Yagubyan ◽

Ramanath Majumdar ◽

David J Tester ◽

Mariza de Andrade ◽

...

Keyword(s):

Aortic Valve ◽

Linkage Analysis ◽

Microsatellite Markers ◽

Candidate Gene ◽

Candidate Genes ◽

Bicuspid Aortic Valve ◽

Fine Mapping ◽

Aortic Valve Disease ◽

Biological Plausibility ◽

Genome Wide

Background: Bicuspid aortic valve disease (BAV), the most common congenital cardiovascular malformation, has an incidence of 0.5–1.0% of live births. While most cases of BAV appear to be sporadic, familial inheritance patterns have been observed consistent with autosomal dominant inheritance with variable penetrance. However, little is known about specific genetic loci responsible for familial BAV. Here, we performed linkage analysis on a large multi-generational pedigree affected with BAV. Methods: We identified a large, five-generation pedigree (136 family members) with 10 individuals having BAV. Two-dimensional echocardiography was used to assign aortic valve phenotype. Genome-wide linkage analysis using 430 microsatellite markers (Marshfield Clinic) and fine mapping using 100 single nucleotide polymorphisms (Affymetrix) on chromosome 9 was performed on genomic DNA from all available family members. Logarithm of odds (LOD) scores of >2.0 were considered suggestive of linkage. Comprehensive splice site/open reading frame mutational analysis of candidate genes residing in the putative locus is underway using PCR, DHPLC, and DNA sequencing. A candidate gene, KLF9, Krüppel-like factor 9 was analyzed for mutations because of its role in cardiogenesis. Results: Multi-point genome-wide linkage analysis demonstrated a 7 cM region on chromosome 9q21 that was suggestive of linkage for familial BAV with a maximum multipoint LOD score of 2.8 flanked by the microsatellite markers GATA7D12 and D9S1834. This region contains several candidate genes with biological plausibility for BAV phenotype. KLF9- encoded Krüppel-like factor 9, localized to chromosome 9q21, was targeted as a prime candidate gene for familial BAV. However, no mutations involving the translated exons of KLF9 were detected. Further fine mapping studies and candidate gene analysis are currently underway. Conclusions: We report a novel susceptibility locus on chromosome 9q21 for BAV in a large multi-generational family. Although coding region mutations in KLF9 are not responsible for BAV in this pedigree, several candidate genes with biological plausibility for the development of congenital BAV lie within this region and warrant further scrutiny.

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Fine mapping of the major QTL for seed coat color in Brassica rapa var. Yellow Sarson by use of NIL populations and transcriptome sequencing for identification of the candidate genes

PLoS ONE ◽

10.1371/journal.pone.0209982 ◽

2019 ◽

Vol 14 (2) ◽

pp. e0209982 ◽

Cited By ~ 6

Author(s):

Huiyan Zhao ◽

Urmila Basu ◽

Berisso Kebede ◽

Cunmin Qu ◽

Jiana Li ◽

...

Keyword(s):

Candidate Genes ◽

Brassica Rapa ◽

Fine Mapping ◽

Seed Coat ◽

Transcriptome Sequencing ◽

Coat Color ◽

Seed Coat Color ◽

Major Qtl

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

Plant and Soil ◽

10.1007/s11104-019-04261-0 ◽

2019 ◽

Vol 444 (1-2) ◽

pp. 119-137 ◽

Cited By ~ 1

Author(s):

Zhandong Cai ◽

Yanbo Cheng ◽

Peiqi Xian ◽

Rongbin Lin ◽

Qiuju Xia ◽

...

Keyword(s):

Candidate Genes ◽

Genetic Map ◽

Fine Mapping ◽

Aluminum Tolerance ◽

High Density

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Genome-Wide Association Study and Fine Mapping Reveals Candidate Genes for Birth Weight of Yorkshire and Landrace Pigs

Frontiers in Genetics ◽

10.3389/fgene.2020.00183 ◽

2020 ◽

Vol 11 ◽

Author(s):

Yong Li ◽

Bin Li ◽

Manman Yang ◽

Hu Han ◽

Tao Chen ◽

...

Keyword(s):

Birth Weight ◽

Association Study ◽

Candidate Genes ◽

Fine Mapping ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Genome Wide

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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

Czech Journal of Animal Science ◽

10.17221/50/2018-cjas ◽

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.

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