Genome-wide identification of intron fragment insertion mutations and their potential use as SCAR molecular markers in the soybean

Background: Roots are essential for drought adaptation because of their involvement in water and nutrient uptake. As the study of the root system architecture (RSA) is costly and time-consuming, it is not generally considered in breeding programs. Thus, the identification of molecular markers linked to RSA traits is of special interest to the breeding community. The reported correlation between the RSA of seedlings and adult plants simplifies its assessment. Methods: In this study, a panel of 170 bread wheat landraces from 24 Mediterranean countries was used to identify molecular markers associated with the seminal RSA and related traits: seminal root angle, total root number, root dry weight, seed weight and shoot length, and grain yield (GY). Results: A genome-wide association study identified 135 marker-trait associations explaining 6% to 15% of the phenotypic variances for root related traits and 112 for GY. Fifteen QTL hotspots were identified as the most important for controlling root trait variation and were shown to include 31 candidate genes related to RSA traits, seed size, root development, and abiotic stress tolerance (mainly drought). Co-location for root related traits and GY was found in 17 genome regions. In addition, only four out of the fifteen QTL hotspots were reported previously. Conclusions: The variability found in the Mediterranean wheat landraces is a valuable source of root traits to introgress into adapted phenotypes through marker-assisted breeding. The study reveals new loci affecting root development in wheat.

Download Full-text

Resilience Effects of SGK1 and TAP1 DNA Markers during PRRSV Outbreaks in Reproductive Sows

Animals ◽

10.3390/ani10050902 ◽

2020 ◽

Vol 10 (5) ◽

pp. 902

Author(s):

Marina Laplana ◽

Joan Estany ◽

Lorenzo José Fraile ◽

Ramona Natacha Pena

Keyword(s):

Candidate Genes ◽

Reproductive Performance ◽

Dna Markers ◽

Health Problems ◽

Respiratory Syndrome Virus ◽

Large White ◽

Genome Wide ◽

Stable Performance ◽

Potential Use

The porcine reproductive and respiratory syndrome virus (PRRSV) is a major infectious stressor that causes serious health problems and productivity drops. Based on previous genome-wide analyses, we selected SGK1 and TAP1 as candidate genes for resilience, and genotyped three mutations, including a 3′UTR variant SGK1_rs338508371 and two synonymous variants TAP1_rs1109026889 and TAP1_rs80928141 in 305 Landrace × Large White sows. All polymorphisms affected the reproductive performance in the outbreak, but not during the endemic phase, thereby indicating a potential use of these markers for resilience. Moreover, some genotypes were associated with a stable performance across PRRSV phases. Thus, in the outbreak, the SGK1_rs338508371 AA sows had less piglets born alive (p < 0.0001) and more stillborns (p < 0.05) while other sows were able to keep their productivity. During the outbreak, TAP1_rs80928141 GG sows had less piglets born alive (p < 0.05) and both TAP1 polymorphisms influenced the number of mummies in an additive manner (p < 0.05). Remarkably, TAP1_rs80928141 AA sows had around one mummy more than GG sows (p < 0.01). Resilience to PRRSV could be improved by including the SGK1 and TAP1 markers in crossbreeding and/or selection schemes, as they contribute to maintaining a stable number of piglets born alive and lost, particularly mummies, despite the outbreak.

Download Full-text

Disclosure of Copy Number Alterations in AML with Normal Karyotype Using Matrix-Based Comparative Genomic Hybridization.

Blood ◽

10.1182/blood.v106.11.759.759 ◽

2005 ◽

Vol 106 (11) ◽

pp. 759-759

Author(s):

Frank G. Rucker ◽

Lars Bullinger ◽

Hans A. Kestler ◽

Peter Lichter ◽

Konstanze Dohner ◽

...

Keyword(s):

Molecular Markers ◽

High Resolution ◽

Comparative Genomic Hybridization ◽

Copy Number ◽

Normal Karyotype ◽

Comparative Genomic ◽

Copy Number Alterations ◽

Genomic Hybridization ◽

Genomic Imbalances ◽

Genome Wide

Abstract Clonal chromosome abnormalities represent one of the most important prognostic factors in adult acute myeloid leukemia (AML), and cytogenetic data are used for risk-adapted treatment strategies. By conventional cytogenetic analysis, approximately 50% of patients lack clonal chromosome aberrations, and normal cytogenetics are associated with an intermediate clinical outcome. This clinically heterogeneous group seems to be in part characterized by molecular markers, such as MLL, FLT3, CEBPA, and NPM1 mutations. In order to identify novel candidate regions of genomic imbalances, we applied comparative genomic hybridization to microarrays (matrix-CGH). Using this high-resolution genome-wide screening approach we analyzed 49 normal karyotype AML cases characterized for the most common clinically relevant molecular markers (MLL-PTD n=13, FLT3-ITD n=7, FLT3-ITD/NPM1+ n=4, MLL-PTD/FLT3-ITD n=3, CEBPA+ n=12, CEBPA+/FLT3-ITD n=1; CEBPA+/NPM1+ n=1; no molecular markers n=8) with a microarray platform consisting of 2799 different BAC or PAC clones. A set of 1500 of these clones covers the whole human genome with a physical distance of approximately 2 Mb. The remaining 1299 clones either contiguously span genomic regions known to be frequently involved in hematologic malignancies (e.g., 1p, 2p, 3q, 7q, 9p, 11q, 12q, 13q, 17p, 18q) (n=600) or contain oncogenes or tumor suppressor genes (n=699). In addition to known copy number polymorphisms in 5q11, 7q22, 7q35, 14q32, and 15q11, the CLuster Along Chromosomes method (CLAC; http://www-stat.stanford.edu/~wp57/CGH-Miner) disclosed copy number alterations (CNAs) in terms of gains in 1p, 11q, 12q, and 17p. CNAs in terms of losses were identified in 9p, 11q, 12p, 12q, and 13q. Two-class supervised analyses using the significance analysis of microarrays (SAM) method identified for the MLL-PTD cases a gain of a single clone harboring the MLL gene. While the significance of these findings, which are currently validated using fluorescence in-situ hybridization (FISH), still remains to be determined, our preliminary results already demonstrate the power and reliablity of this microarray-based technique allowing genome-wide screens of genomic imbalances as the MLL aberration was detected in all cases known to have a MLL-PTD. Furthermore, ongoing correlation of high-resolution genomic profiling with global gene expression studies will help to disclose pathways underlying normal karyotype AML, thereby leading to new insights of leukemogenesis.

Download Full-text

Genome-Wide Consistent Molecular Markers Associated with Phenology, Plant Production and Root Traits in Diverse Rice (Oryza sativa L.) Accessions under Drought in Rainfed Target Populations of the Environment

Current Science ◽

10.18520/cs/v114/i02/329-340 ◽

2018 ◽

Vol 114 (02) ◽

pp. 329 ◽

Cited By ~ 2

Author(s):

Vivek Deshmukh ◽

Sumeet Prabakar Mankar ◽

C. Muthukumar ◽

P. Divahar ◽

A. Bharathi ◽

...

Keyword(s):

Oryza Sativa ◽

Molecular Markers ◽

Root Traits ◽

Plant Production ◽

Target Populations ◽

Genome Wide

Download Full-text

Identification of molecular markers and signaling pathway in endometrial cancer in Hong Kong Chinese women by genome-wide gene expression profiling

Oncogene ◽

10.1038/sj.onc.1209986 ◽

2006 ◽

Vol 26 (13) ◽

pp. 1971-1982 ◽

Cited By ~ 79

Author(s):

Y F Wong ◽

T H Cheung ◽

K W K Lo ◽

S F Yim ◽

N S S Siu ◽

...

Keyword(s):

Gene Expression ◽

Endometrial Cancer ◽

Hong Kong ◽

Molecular Markers ◽

Gene Expression Profiling ◽

Expression Profiling ◽

Chinese Women ◽

Hong Kong Chinese ◽

Genome Wide ◽

Genome Wide Gene Expression

Download Full-text

Genome-Wide Profiling of Methylation in Endometriosis Reveals New Molecular Markers for the Disease and Clues for Its Pathophysiology

Journal of Minimally Invasive Gynecology ◽

10.1016/j.jmig.2010.08.261 ◽

2010 ◽

Vol 17 (6) ◽

pp. S52-S53

Author(s):

B. Borghese ◽

S. Barbaux ◽

F. Mondon ◽

P. Santulli ◽

G. Pierre ◽

...

Keyword(s):

Molecular Markers ◽

Genome Wide

Download Full-text

Plant genetic resources and molecular markers: variety registration in a new era

Plant Genetic Resources ◽

10.1079/pgr200312 ◽

2003 ◽

Vol 1 (2-3) ◽

pp. 81-87 ◽

Cited By ~ 10

Author(s):

Robert J. Cooke ◽

James C. Reeves

Keyword(s):

Molecular Markers ◽

Genetic Resource ◽

Plant Genetic Resources ◽

Nucleotide Polymorphisms ◽

The European Union ◽

Single Nucleotide ◽

New Era ◽

Dus Testing ◽

The Common ◽

Potential Use

AbstractVariety registration is an important area of plant genetic resource characterization and utilization. Within the European Union, varieties must be included on a National List (NL) of a member state or on the Common Catalogue (a compilation of the NLs of the member states) before seed can be sold. This requires a series of tests and trials which assess if the variety is distinct, uniform and stable (DUS) and if it has sufficient value for cultivation and use (VCU). The same DUS criteria are also used world-wide for the granting of Plant Breeders' Rights (PBR), an intellectual property protection system. Both DUS and VCU are currently assessed primarily using field-based trials. However, the potential use of biochemical and molecular markers for DUS purposes is being actively investigated and such markers could have an important role to play in maintaining the quality and scope of PBR in an environment where the increasing number of countries involved in DUS testing and the number of variety comparisons to be made are causing logistical difficulties. More recently, given firstly the increase in the availability of markers from expressed regions of the genome, and secondly the possibilities raised by detailed DNA sequencing programmes and the association of markers (particularly single nucleotide polymorphisms, SNPs) with specific genes, the prospects for a more molecular approach to VCU are also being discussed. This paper reviews the current situation with regard to the use of molecular markers for DUS and VCU testing and considers future prospects for variety registration in the 21st century, ‘-omics’, era.

Download Full-text

Breeding potential and genetic diversity of "Híbrido do Timor" coffee evaluated by molecular markers

Cropp Breeding and Applied Biotechnology ◽

10.1590/s1984-70332010000400003 ◽

2010 ◽

Vol 10 (4) ◽

pp. 298-304 ◽

Cited By ~ 12

Author(s):

Tesfahun Alemu Setotaw ◽

Eveline Teixeira Caixeta ◽

Guilherme Ferreira Pena ◽

Eunize Maciel Zambolim ◽

Antonio Alves Pereira ◽

...

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Molecular Markers ◽

Genetic Structure ◽

Gene Diversity ◽

High Genetic Diversity ◽

Breeding Programs ◽

Information Index ◽

Upgma Cluster Analysis ◽

Potential Use

AFLP, RAPD and SSR molecular markers were used to study the genetic diversity and genetic structure of the Híbrido de Timor germplasm. The principal coordinate analysis, UPGMA cluster analysis based on genetic dissimilarity of Jaccard, Bayesian model-based cluster analysis, percentage of polymorphic loci, Shannon's information index and Nei gene diversity were employed to assess the genetic diversity. The analyses demonstrated a high genetic diversity among Híbrido de Timor accessions. UPGMA and Bayesian cluster analyses grouped the accessions into three clusters. The genetic structure of Híbrido de Timor is reported. The management of Híbrido de Timor germplasm variability and its potential use in breeding programs are discussed.

Download Full-text