scholarly journals QTL Analysis and Fine Mapping of a Major QTL Conferring Kernel Size in Maize (Zea mays)

2020 ◽  
Vol 11 ◽  
Author(s):  
Guiying Wang ◽  
Yanming Zhao ◽  
Wenbo Mao ◽  
Xiaojie Ma ◽  
Chengfu Su
Keyword(s):  
Fine Mapping ◽  
Interval Mapping ◽  
Chromosome 9 ◽  
Recurrent Parent ◽  
Kernel Size ◽  
Protein Coding ◽  
Kernel Length ◽  
Genetic Mechanisms ◽  
Donor Parent ◽  
Stable Qtls

Kernel size is an important agronomic trait for grain yield in maize. The purpose of this study is to map QTLs and predict candidate genes for kernel size in maize. A total of 199 F2 and its F2:3 lines from the cross between SG5/SG7 were developed. A composite interval mapping (CIM) method was used to detect QTLs in three environments of F2 and F2:3 populations. The result showed that a total of 10 QTLs for kernel size were detected, among which were five QTLs for kernel length (KL) and five QTLs for kernel width (KW). Two stable QTLs, qKW-1, and qKL-2, were mapped in all three environments. Three QTLs, qKL-1, qKW-1, and qKW-2, were overlapped with the QTLs identified from previous studies. In order to validate and fine map qKL-2, near-isogenic lines (NILs) were developed by continuous backcrossing between SG5 as the donor parent and SG7 as the recurrent parent. Marker-assisted selection was conducted from BC2F1 generation with molecular markers near qKL-2. A secondary linkage map with six markers around the qKL-2 region was developed and used for fine mapping of qKL-2. Finally, qKL-2 was confirmed in a 1.95 Mb physical interval with selected overlapping recombinant chromosomes on maize chromosome 9 by blasting with the Zea_Mays_B73 v4 genome. Transcriptome analysis showed that a total of 11 out of 40 protein-coding genes differently expressed between the two parents were detected in the identified qKL-2 interval. GRMZM2G006080 encoding a receptor-like protein kinase FERONIA, was predicted as a candidate gene to control kernel size. The work will not only help to understand the genetic mechanisms of kernel size of maize but also lay a foundation for further fine mapping and even cloning of the promising loci.

scholarly journals QTL analysis and fine mapping of a major QTL conferring kernel size in maize (Zea mays)

2020 ◽  
Author(s):  
Guiying Wang ◽  
Yanming Zhao ◽  
Zhen Zhu ◽  
Xinyuan Zhang ◽  
Minghua Jiang ◽  
...  
Keyword(s):  
Candidate Gene ◽  
Linkage Map ◽  
Fine Mapping ◽  
Marker Assisted Selection ◽  
Chromosome 9 ◽  
Recurrent Parent ◽  
Kernel Size ◽  
Kernel Length ◽  
Stable Qtls ◽  
Major Qtl

Abstract Background：Kernel size are important agronomic traits for grain yield in maize. The objective of this study is to map QTLs for kernel size, fine map a stable QTL qKL-2 and predict candidate genes for kernel length in maize. A total 199 F2:3 lines were obtained from selfing F2 individuals from the cross SG5/SG7. In this study, a high density genetic linkage map with 3305 bin-markers spanning a total length of 2236.66 cM on 10 chromosomes was applied for primary QTL mapping. Composite interval mapping (CIM) method was used for detecting QTLs in three environments of F2 and F2:3 populations. Results：The result showed that a total ten QTLs for kernel size were detected, among which five QTLs for kernel length (KL) and five QTLs for kernel width (KW). Two stable QTLs qKW-1 and qKL-2 were mapped in all three environments. In order to validate and fine map qKL-2 , near isogenic lines (NILs) were developed by continuous backcross between SG5 as the donor parent and SG7 as the recurrent parent. Marker assisted selection was conducted from BC2F1 generation with molecular markers near qKL-2. Secondary linkage map with six markers around the objective region was developed for fine mapping qKL-2. Finally, qKL-2 was mapped in a 1.95Mb physical interval on maize chromosome 9 by blasting with Zea_Mays_B73 v4 genome. The results were confirmed with selected overlapping recombinant chromosomes. A total 11 out of 40 protein coding genes in the identified interval differentially expressed after conducting transcriptomic analysis between the two parents. GRMZM2G006080, which encodes receptor-like protein kinase FERONIA was predicted as candidate gene to control kernel size. Conclusions：A total ten QTLs for kernel size were identified. Two stable QTLs qKL-2 and qKW-2 were mapped in three envionments. Major QTL qKL-2 for KL was validated and fine mapped in a 1.95Mb physical interval. GRMZM2G006080 was predicted as candidate gene for qKL-2 to control kernel length. The work will not only help to understand the mechanisms that control kernel size of maize, but also provide new gene for marker-assisted selection in further studies.

scholarly journals QTL Mapping and Validation for Kernel Area and Circumference in Common Wheat via High-Density SNP-Based Genotyping

2021 ◽  
Vol 12 ◽  
Author(s):  
Tianheng Ren ◽  
Tao Fan ◽  
Shulin Chen ◽  
Xia Ou ◽  
Yongyan Chen ◽  
...  
Keyword(s):  
Recombinant Inbred Lines ◽  
Snp Array ◽  
Interval Mapping ◽  
Mapping Method ◽  
Kernel Weight ◽  
Kernel Size ◽  
Specific Pcr ◽  
Wheat Kernel ◽  
Ril Population ◽  
Stable Qtls

As an important component, 1,000 kernel weight (TKW) plays a significant role in the formation of yield traits of wheat. Kernel size is significantly positively correlated to TKW. Although numerous loci for kernel size in wheat have been reported, our knowledge on loci for kernel area (KA) and kernel circumference (KC) remains limited. In the present study, a recombinant inbred lines (RIL) population containing 371 lines genotyped using the Wheat55K SNP array was used to map quantitative trait loci (QTLs) controlling the KA and KC in multiple environments. A total of 54 and 44 QTLs were mapped by using the biparental population or multienvironment trial module of the inclusive composite interval mapping method, respectively. Twenty-two QTLs were considered major QTLs. BLAST analysis showed that major and stable QTLs QKc.sau-6A.1 (23.12–31.64 cM on 6A) for KC and QKa.sau-6A.2 (66.00–66.57 cM on 6A) for KA were likely novel QTLs, which explained 22.25 and 20.34% of the phenotypic variation on average in the 3 year experiments, respectively. Two Kompetitive allele-specific PCR (KASP) markers, KASP-AX-109894590 and KASP-AX-109380327, were developed and tightly linked to QKc.sau-6A.1 and QKa.sau-6A.2, respectively, and the genetic effects of the different genotypes in the RIL population were successfully confirmed. Furthermore, in the interval where QKa.sau-6A.2 was located on Chinese Spring and T. Turgidum ssp. dicoccoides reference genomes, only 11 genes were found. In addition, digenic epistatic QTLs also showed a significant influence on KC and KA. Altogether, the results revealed the genetic basis of KA and KC and will be useful for the marker-assisted selection of lines with different kernel sizes, laying the foundation for the fine mapping and cloning of the gene(s) underlying the stable QTLs detected in this study.

Fine mapping of a kernel length-related gene with potential value for maize breeding

2021 ◽  
Author(s):  
Dianming Gong ◽  
Zengdong Tan ◽  
Hailiang Zhao ◽  
Zhenyuan Pan ◽  
Qin Sun ◽  
...  
Keyword(s):  
Fine Mapping ◽  
Related Gene ◽  
Maize Breeding ◽  
Potential Value ◽  
Kernel Length

scholarly journals Association Mapping and Transcriptome Analysis Reveal the Genetic Architecture of Maize Kernel Size

2021 ◽  
Vol 12 ◽  
Author(s):  
Juan Ma ◽  
Lifeng Wang ◽  
Yanyong Cao ◽  
Hao Wang ◽  
Huiyong Li
Keyword(s):  
Differential Expression ◽  
Genetic Architecture ◽  
Genome Wide Association Study ◽  
Differential Expression Analysis ◽  
Inbred Lines ◽  
Kernel Size ◽  
Maize Kernel ◽  
Association Panel ◽  
Kernel Length ◽  
A Genome

Kernel length, kernel width, and kernel thickness are important traits affecting grain yield and product quality. Here, the genetic architecture of the three kernel size traits was dissected in an association panel of 309 maize inbred lines using four statistical methods. Forty-two significant single nucleotide polymorphisms (SNPs; p < 1.72E-05) and 70 genes for the three traits were identified under five environments. One and eight SNPs were co-detected in two environments and by at least two methods, respectively, and they explained 5.87–9.59% of the phenotypic variation. Comparing the transcriptomes of two inbred lines with contrasting seed size, three and eight genes identified in the association panel showed significantly differential expression between the two genotypes at 15 and 39 days after pollination, respectively. Ten and 17 genes identified by a genome-wide association study were significantly differentially expressed between the two development stages in the two genotypes. Combining environment−/method-stable SNPs and differential expression analysis, ribosomal protein L7, jasmonate-regulated gene 21, serine/threonine-protein kinase RUNKEL, AP2-EREBP-transcription factor 16, and Zm00001d035222 (cell wall protein IFF6-like) were important candidate genes for maize kernel size and development.

scholarly journals Mutational analysis of driver genes with tumor suppressive and oncogenic roles in gastric cancer

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3585 ◽  
Author(s):  
Tianfang Wang ◽  
Yining Liu ◽  
Min Zhao
Keyword(s):  
Gastric Cancer ◽  
Cancer Progression ◽  
Complex Disease ◽  
Mutational Analysis ◽  
Driver Mutations ◽  
Driver Genes ◽  
Protein Coding ◽  
Mirna Genes ◽  
Genetic Mechanisms ◽  
New Treatment

Gastric cancer (GC) is a complex disease with heterogeneous genetic mechanisms. Genomic mutational profiling of gastric cancer not only expands our knowledge about cancer progression at a fundamental genetic level, but also could provide guidance on new treatment decisions, currently based on tumor histology. The fact that precise medicine-based treatment is successful in a subset of tumors indicates the need for better identification of clinically related molecular tumor phenotypes, especially with regard to those driver mutations on tumor suppressor genes (TSGs) and oncogenes (ONGs). We surveyed 313 TSGs and 160 ONGs associated with 48 protein coding and 19 miRNA genes with both TSG and ONG roles. Using public cancer mutational profiles, we confirmed the dual roles of CDKN1A and CDKN1B. In addition to the widely recognized alterations, we identified another 82 frequently mutated genes in public gastric cancer cohort. In summary, these driver mutation profiles of individual GC will form the basis of personalized treatment of gastric cancer, leading to substantial therapeutic improvements.

scholarly journals Identification of Quantitative Trait Loci That Determine Plasma Total-Cholesterol and Triglyceride Concentrations in DDD/Sgn and C57BL/6J Inbred Mice

Cholesterol ◽  
2017 ◽  
Vol 2017 ◽  
pp. 1-10 ◽  
Author(s):  
Jun-ichi Suto ◽  
Misaki Kojima
Keyword(s):  
Quantitative Trait Loci ◽  
Total Cholesterol ◽  
Quantitative Trait ◽  
Inbred Mice ◽  
Plasma Lipid ◽  
Interval Mapping ◽  
Plasma Total Cholesterol ◽  
Phenotypic Effect ◽  
Trait Loci ◽  
Genetic Mechanisms

DDD/Sgn mice have significantly higher plasma lipid concentrations than C57BL/6J mice. In the present study, we performed quantitative trait loci (QTL) mapping for plasma total-cholesterol (CHO) and triglyceride (TG) concentrations in reciprocal F2 male intercross populations between the two strains. By single-QTL scans, we identified four significant QTL on chromosomes (Chrs) 1, 5, 17, and 19 for CHO and two significant QTL on Chrs 1 and 12 for TG. By including cross direction as an interactive covariate, we identified separate significant QTL on Chr 17 for CHO but none for TG. When the large phenotypic effect of QTL on Chr 1 was controlled by composite interval mapping, we identified three additional significant QTL on Chrs 3, 4, and 9 for CHO but none for TG. QTL on Chr 19 was a novel QTL for CHO and the allelic effect of this QTL significantly differed between males and females. Whole-exome sequence analysis in DDD/Sgn mice suggested that Apoa2 and Acads were the plausible candidate genes underlying CHO QTL on Chrs 1 and 5, respectively. Thus, we identified a multifactorial basis for plasma lipid concentrations in male mice. These findings will provide insight into the genetic mechanisms of plasma lipid metabolism.

Mouse chromosome 9 quantitative trait loci for soft tissue regeneration: Congenic analysis and fine mapping

2007 ◽  
Vol 15 (6) ◽  
pp. 922-927 ◽  
Author(s):  
Hongrun Yu ◽  
David J. Baylink ◽  
Godfred L. Masinde ◽  
Runzhi Li ◽  
Bay Nguyen ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Soft Tissue ◽  
Mouse Chromosome ◽  
Tissue Regeneration ◽  
Fine Mapping ◽  
Quantitative Trait ◽  
Chromosome 9 ◽  
Soft Tissue Regeneration ◽  
Trait Loci

scholarly journals Fine Mapping of Cla015407 Controlling Plant Height in Watermelon

2021 ◽  
pp. 1-26
Author(s):  
Taifeng Zhang ◽  
Jiajun Liu ◽  
Sikandar Amanullah ◽  
Zhuo Ding ◽  
Haonan Cui ◽  
...  
Keyword(s):  
Gibberellic Acid ◽  
Fine Mapping ◽  
Growth Habit ◽  
Gene Annotation ◽  
Bulked Segregant Analysis ◽  
Citrullus Lanatus ◽  
Chromosome 9 ◽  
Land Utilization ◽  
Site Mutation ◽  
Significant Difference

The plant compact and dwarf growth habit is an important agronomic trait when breeding watermelon (Citrullus lanatus) cultivars because of their reduced vine length, high-density planting, and better land utilization; however, the genetic basis of the dwarf growth habit is not well-known. In this study, the plant population of six generations, P1, P2, F1, F2, BC1P1, and BC1P2, were studied. A genetic segregation analysis demonstrated that dwarfism is mainly controlled by a single recessive Cldw gene. Furthermore, whole-genome sequencing of two distinct watermelon cultivars, W1-1 (P1) and 812 (P2), was performed and preliminarily mapped through a bulked segregant analysis of F2 individuals that revealed the Cldw gene locus on chromosome 9. Two candidate genes, Cla015407 and Cla015408, were discovered at the delimited region of 43.2 kb by fine mapping, and gene annotation exposed that the Cla015407 gene encodes gibberellic acid 3β-hydroxylase protein. In addition, a comparative analysis of gene sequence and cultivars sequences across the reference genome of watermelon revealed the splice site mutation in the intron region of the Cldw gene in dwarf-type cultivar 812. The quantitative real-time polymerase chain reaction exhibited a significantly higher expression of the Cla015407 gene in cultivar W1-1 compared with 812. There was no significant difference in the vine length of both cultivars after gibberellic acid treatment. In brief, our fine mapping demonstrated that Cla015407 is a candidate gene controlling dwarfism of watermelon plants.

Abstract 055: Locating Genetic Determinants Of Translational Significance Using The Rat Genome

Hypertension ◽  
2014 ◽  
Vol 64 (suppl_1) ◽  
Author(s):  
Ying Nie ◽  
Sivarajan Kumaraswamy ◽  
Xi Cheng ◽  
Harshal Waghulde ◽  
Blair Mel ◽  
...  
Keyword(s):  
Blood Pressure ◽  
Human Chromosome ◽  
Chromosome 9 ◽  
Genome Wide Association Studies ◽  
Chromosome 2 ◽  
Protein Coding ◽  
Positional Candidate ◽  
Genetic Elements ◽  
Protein Coding Genes ◽  
Rat Genome

Genome-wide association studies (GWAS) have detected associations of genetic elements on human chromosome 2 with hypertension but lack the ability to discern whether these associations are/are not causal factors for hypertension. Using rat genetic models of hypertension, we have identified that factors linked to the inheritance of hypertension map to rat chromosome 9, which is homologous to human chromosome 2. Here we report that by applying high resolution mapping approaches, we have prioritized two regions on rat chromosome 9, one spanning < 788kb and a second region spanning < 81.8kb, as genomic segments containing novel inherited genetic elements controlling blood pressure. The <788kb region contains 3 protein coding genes, Trmp8 , Spp2 and Arl4c , which are also associated with human hypertension. Of these, there was only one nonsynonymous polymorphism within the gene Spp2 between the Dahl S and S.SHR strains used to map this locus. The expression of Spp2 was significantly higher in the S.SHR rat compared with S. We therefore prioritize Spp2 as a positional candidate for the <788kb region. The <81.8kb region contains no known/predicted protein-coding genes. We hypothesized that polymorphisms within gene regulatory elements underlie the <81.8kb locus. By combining the locations of the relevant polymorphisms with promoters predicted by the Proscan promoter prediction software, 5 regions were prioritized for further analysis. Alleles from the normotensive R rat from 1 out of these 5 regions had a 5.14 fold higher luciferase activity compared with that of the hypertensive S rat alleles (p<0.05). This region maps from chr9:80880396 to chr9:80882643 (Rnor5.0) on the rat genome. The downstream target for this promoter activity is unknown. Interestingly, within 110,419bp downstream of this region, there is a predicted long non-coding RNA in the mouse (AK079660) and in humans ( DIRC4) . By RT-PCR using rat kidney, we detected a novel rat transcript that is potentially a rat homologue of the mouse and human predictions. Collectively, these data point to conserved syntenic regions in rats and humans that contain novel promoter sequence variants and variants within the conserved gene, Spp2 , as potential quantitative trait nucleotides for blood pressure regulation.

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