Article
Plant Sciences
Su-Kui Jin, Li-Na Xu, Qing-Qing Yang, Ming-Qiu Zhang, Shui-Lian Wang, Ruo-An Wang, Tao Tao, Lian-Min Hong, Qian-Qian Guo, Shu-Wen Jia, Tao Song, Yu-Jia Leng, Xiu-Ling Cai, Ji-Ping Gao
Summary: In this study, high-resolution QTL mapping was conducted to identify the genetic regions responsible for rice grain quality traits. A total of 15 QTLs were identified, including one overlapping with previously reported QTLs and the others being novel. These findings will facilitate the fine mapping and pyramiding of these QTLs, leading to genetic improvement of rice grain quality.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biotechnology & Applied Microbiology
Maya Hiltpold, Naveen Kumar Kadri, Fredi Janett, Ulrich Witschi, Fritz Schmitz-Hsu, Hubert Pausch
Summary: The study identified novel recessive QTL for male fertility in Brown Swiss cattle, with one QTL associated with sperm head shape anomalies. Fine-mapping approaches and whole-genome sequencing revealed candidate causal variants linked to these QTL, suggesting that non-coding variants may play a significant role in bull fertility variation.
Article
Agriculture, Dairy & Animal Science
Mamokoma Cathrine Modiba, Khathutshelo Agree Nephawe, Jun Wang, Nompilo Hlongwane, Khanyisile Hadebe, Wenfa Lu, Bohani Mtileni
Summary: This study identified the distribution of ROH in six beef cattle breeds and suggested nine candidate genes associated with semen QTL traits. The results showed moderate levels of inbreeding in some breeds and provided guidance for breeding programs.
Article
Plant Sciences
Erdem Kahveci, Zuebeyir Devran, Ercan oezkaynak, Yiguo Hong, David J. Studholme, Mahmut Toer
Summary: Cucumber vein yellowing virus (CVYV) causes economic losses in cucumber crops, with limited resistance sources and lack of tightly linked molecular markers hindering breeding progress. Genomic analysis and marker-assisted selection could aid in developing resistant lines against CVYV.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Agriculture, Dairy & Animal Science
Aluna R. Chawala, Enrique Sanchez-Molano, Richard J. Dewhurst, Andrew Peters, Mizeck G. G. Chagunda, Georgios Banos
Summary: Breeding strategies for smallholder dairy farming systems in Sub-Saharan Africa were evaluated, with a focus on traits identified as priorities by farmers. Strategies included importing genetically superior exotic dairy sire semen, using elite bulls on indigenous cows, and genetically selecting the best sires domestically. Positive genetic progress was observed for all traits, with the importation strategy showing the highest genetic response after 15 generations. Breeders have the opportunity to choose a suitable breeding strategy that fits the specific needs of smallholder dairy farmers.
JOURNAL OF ANIMAL BREEDING AND GENETICS
(2021)
Article
Agriculture, Dairy & Animal Science
B. Li, P. M. VanRaden, D. J. Null, J. R. O'Connell, J. B. Cole
Summary: This study aimed to identify potential quantitative trait loci (QTL) for 27 production, fitness, and conformation traits of Guernsey cattle through genome-wide association analyses, with a major QTL detected on BTA19 and the MYH10 gene within this region highly associated with milk production and body conformation traits. After fine mapping, only one significant SNP was found on BTA19 for most traits, with multiple independent significant SNPs identified for protein yield, dairy form, and stature. The haplotype hosting the major QTL on BTA19 was traced back to a US Guernsey born in 1954, indicating a long-term influence on the population.
JOURNAL OF DAIRY SCIENCE
(2021)
Article
Agriculture, Dairy & Animal Science
J. G. Burns, K. Glenk, V Eory, G. Simm, E. Wall
Summary: As resilience becomes more crucial, solely relying on short-term economic value of traits may lead decision makers to misrepresent the importance of certain traits, including those with significant contextual values in terms of resilience.
JOURNAL OF DAIRY SCIENCE
(2022)
Article
Genetics & Heredity
Bianca Maria Orlando Marchesano, Remo Chiozzotto, Irina Baccichet, Daniele Bassi, Marco Cirilli
Summary: This study demonstrated the feasibility of a novel High Resolution Melting Analysis (HRMA) approach for the massive screening of self-compatible and self-incompatible genotypes in apricot trees. The potential usefulness of this approach in optimizing and accelerating apricot breeding programs was shown.
Article
Genetics & Heredity
Maryam Esrafili Taze Kand Mohammaddiyeh, Seyed Abbas Rafat, Jalil Shodja, Arash Javanmard, Hadi Esfandyari
Summary: This study evaluates genotyping strategies in terms of prediction accuracy for the implementation of genomic selection in beef cattle. The results show improved accuracy with a limited number of genotyped animals. It is recommended to selectively genotype animals from both ancestral and younger generations, as well as animals from both sexes.
FRONTIERS IN GENETICS
(2023)
Review
Biochemistry & Molecular Biology
Gloria De Mori, Guido Cipriani
Summary: Breeding fruit trees is challenging due to their large trees, long juvenile periods, and environmental variability. The use of molecular markers to assist breeders in selecting genetically superior parents and progeny has been a difficult task. Important fruit traits such as size, weight, sugar and acid content, and ripening time are of interest to fruit breeders.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Agronomy
Chuang Gao, Gaili Song, Kefei Qu, Mengyu Li, Yumei Jiang, Guihong Yin, Jishan Niu, Jianwei Tang, Yan Gao, Qiaoyun Li
Summary: This study aimed to identify major quantitative trait loci (QTL) for resistance to black point disease in wheat and develop molecular markers for marker-assisted selection (MAS). A recombinant inbred line (RIL) population was evaluated for resistance to Bipolaris sorokiniana, and resistant and susceptible bulks were genotyped using a wheat 660 K SNP array. Several QTL for black point resistance were identified on three chromosomes, with potential markers for MAS-based breeding. These findings contribute to our understanding and potential improvement of black point disease management in wheat production.
MOLECULAR BREEDING
(2023)
Review
Biochemistry & Molecular Biology
Durre Shahwar, Zeba Khan, Younghoon Park
Summary: This review presents the genetic and molecular advances in qualitative and quantitative traits as well as biochemical compounds in melons, providing guidance for developing consumer-favored melon varieties with desirable characteristics and yield performance.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Genetics & Heredity
Dan Hao, Xiao Wang, Yu Yang, Hong Chen, Bo Thomsen, Lars-Erik Holm
Summary: In this study, SNPs in bovine miRNAs were detected using whole-genome re-sequencing data from 1632 cattle. A total of 1109 SNPs in the precursor region, 334 SNPs in the mature region, and 130 SNPs in the seed region were identified. Most SNPs were in Hardy-Weinberg equilibrium and SNPs in the seed region altered the repertoire of target genes, which were enriched in different pathways or functional annotations.
Article
Biochemical Research Methods
Chen Lyu, Manyan Huang, Nianjun Liu, Zhongxue Chen, Philip J. Lupo, Benjamin Tycko, John S. Witte, Charlotte A. Hobbs, Ming Li
Summary: The proposed Methylation Random Field (MRF) method offers advantages in detecting Methylation Quantitative Trait Loci (mQTLs) by utilizing a beta distribution and considering multiple common and rare genetic variants. Through simulations and application to a study on congenital heart defects, the MRF demonstrated improved power in detecting rare variants, especially with small sample sizes. This tool is useful for identifying novel mQTLs, particularly in studies with limited sample sizes.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Agriculture, Dairy & Animal Science
J. B. Clasen, C. Bengtsson, H. N. Kallstrom, E. Strandberg, W. F. Fikse, L. Rydhmer
Summary: Breeding technologies such as sexed semen, beef semen, genomic testing, and dairy crossbreeding are readily available to Swedish dairy farmers, but their use is limited in the country. A survey with a discrete choice experiment showed that farmers strongly prefer sexed semen and beef semen, while genomic testing is also widely favored. However, buying embryos was not preferred by any group of respondents.
Article
Biochemistry & Molecular Biology
H. Stocker, L. Perna, K. Weigl, T. Moellers, B. Schoettker, H. Thomsen, B. Holleczek, D. Rujescu, H. Brenner
Summary: The study found that the AD polygenic risk score (PRS) and APOE status could effectively predict the clinical diagnosis of AD, VD, MD, and all-cause dementia in a community-based cohort.
MOLECULAR PSYCHIATRY
(2021)
Article
Multidisciplinary Sciences
Hauke Thomsen, Xinjun Li, Kristina Sundquist, Jan Sundquist, Asta Foersti, Kari Hemminki
SCIENTIFIC REPORTS
(2020)
Article
Oncology
Therese Truong, Fabienne Lesueur, Pierre-Emmanuel Sugier, Julie Guibon, Constance Xhaard, Mojgan Karimi, Om Kulkarni, Elise A. Lucotte, Delphine Bacq-Daian, Anne Boland-Auge, Claire Mulot, Pierre Laurent-Puig, Claire Schvartz, Anne-Valerie Guizard, Yan Ren, Elisabeth Adjadj, Frederique Rachedi, Francoise Borson-Chazot, Rosa Maria Ortiz, Juan J. Lence-Anta, Celia Maria Pereda, Daniel F. Comiskey, Huiling He, Sandya Liyanarachchi, Albert de la Chapelle, Rossella Elisei, Federica Gemignani, Hauke Thomsen, Asta Forsti, Anthony F. Herzig, Anne-Louise Leutenegger, Carole Rubino, Evgenia Ostroumova, Ausrele Kesminiene, Marie-Christine Boutron-Ruault, Jean-Francois Deleuze, Pascal Guenel, Florent de Vathaire
Summary: The study investigated susceptibility loci for thyroid carcinoma in different ethnic groups, revealing shared and unique associations in individuals of European and Oceanian ancestry. Oceanians showed higher frequencies of risk alleles, suggesting a genetic predisposition. Further research is needed to fully comprehend the elevated incidence rates observed in these populations.
INTERNATIONAL JOURNAL OF CANCER
(2021)
Article
Genetics & Heredity
Yasmeen Niazi, Hauke Thomsen, Bozena Smolkova, Ludmila Vodickova, Sona Vodenkova, Michal Kroupa, Veronika Vymetalkova, Alena Kazimirova, Magdalena Barancokova, Katarina Volkovova, Marta Staruchova, Per Hoffmann, Markus M. Noethen, Maria Dusinska, Ludovit Musak, Pavel Vodicka, Asta Foersti, Kari Hemminki
Summary: The study found significant associations between single nucleotide polymorphisms tagging DNA repair genes and the frequency of CAs, with most associations seen in nucleotide excision repair pathway genes. Genes involved in mutation repair and maintaining genome stability were also related to CAs.
Article
Genetics & Heredity
Yasmeen Niazi, Hauke Thomsen, Bozena Smolkova, Ludmila Vodickova, Sona Vodenkova, Michal Kroupa, Veronika Vymetalkova, Alena Kazimirova, Magdalena Barancokova, Katarina Volkovova, Marta Staruchova, Per Hoffmann, Markus M. Noethen, Maria Dusinska, Ludovit Musak, Pavel Vodicka, Kari Hemminki, Asta Foersti
Summary: DNA damage, unrepaired DNA double-strand breaks, and telomere shortening contribute to chromosomal aberrations. DNA repair gene polymorphisms are associated with chromosomal abnormalities, highlighting the importance of studying individual sensitivity to genotoxic exposure.
FRONTIERS IN GENETICS
(2021)
Correction
Biochemistry & Molecular Biology
H. Stocker, L. Perna, K. Weigl, T. Moellers, B. Schoettker, H. Thomsen, B. Holleczek, D. Rujescu, H. Brenner
MOLECULAR PSYCHIATRY
(2021)
Letter
Oncology
Alyssa Clay-Gilmour, Subhayan Chattopadhyay, Michelle A. T. Hildebrandt, Hauke Thomsen, Niels Weinhold, Pavel Vodicka, Ludmila Vodickova, Per Hoffmann, Markus M. Nothen, Karl-Heinz Jockel, Borge Schmidt, Christian Langer, Roman Hajek, Goran Hallmans, Ulrika Pettersson-Kymmer, Claes Ohlsson, Florentin Spath, Richard Houlston, Hartmut Goldschmidt, Elisabet E. Manasanch, Aaron Norman, Shaji Kumar, S. Vincent Rajkumar, Susan Slager, Asta Forsti, Celine M. Vachon, Kari Hemminki
BLOOD CANCER JOURNAL
(2022)
Letter
Oncology
Paloma Garcia-Martin, Ana Moniz Diez, Jose Manuel Sanchez Maldonado, Antonio Jose Cabrera Serrano, Rob ter Horst, Yolanda Benavente, Stefano Landi, Angelica Macauda, Alyssa Clay-Gilmour, Francisca Hernandez-Mohedo, Yasmeen Niazi, Pedro Gonzalez-Sierra, Blanca Espinet, Juan Jose Rodriguez-Sevilla, Rossana Maffei, Gonzalo Blanco, Matteo Giaccherini, Anna Puiggros, James Cerhan, Roberto Marasca, Marisa Canadas-Garre, Miguel Angel Lopez-Nevot, Tzu Chen-Liang, Hauke Thomsen, Irene Gamez, Victor Moreno, Rafael Marcos-Gragera, Maria Garcia-Alvarez, Javier Llorca, Andres Jerez, Sonja Berndt, Aleksandra Butrym, Aaron D. Norman, Delphine Casabonne, Mario Luppi, Susan L. Slager, Kari Hemminki, Yang Li, Miguel Alcoceba, Daniele Campa, Federico Canzian, Silvia de Sanjose, Asta Foersti, Mihai G. Netea, Manuel Jurado, Juan Sainz
BLOOD CANCER JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Antonio Jose Cabrera-Serrano, Jose Manuel Sanchez-Maldonado, Rob ter Horst, Angelica Macauda, Paloma Garcia-Martin, Yolanda Benavente, Stefano Landi, Alyssa Clay-Gilmour, Yasmeen Niazi, Blanca Espinet, Juan Jose Rodriguez-Sevilla, Eva Maria Perez, Rossana Maffei, Gonzalo Blanco, Matteo Giaccherini, James R. Cerhan, Roberto Marasca, Miguel Angel Lopez-Nevot, Tzu Chen-Liang, Hauke Thomsen, Irene Gamez, Daniele Campa, Victor Moreno, Silvia de Sanjose, Rafael Marcos-Gragera, Maria Garcia-Alvarez, Trinidad Dierssen-Sotos, Andres Jerez, Aleksandra Butrym, Aaron D. Norman, Mario Luppi, Susan L. Slager, Kari Hemminki, Yang Li, Sonja I. Berndt, Delphine Casabonne, Miguel Alcoceba, Anna Puiggros, Mihai G. Netea, Asta Foersti, Federico Canzian, Juan Sainz
Summary: Chronic lymphocytic leukemia (CLL) is the most common leukemia among adults worldwide. However, a study found that the GWAS-identified risk variants for CLL do not significantly impact overall survival and disease progression in CLL patients. The polygenic risk scores (PRSs) built with these risk variants also have limited accuracy in predicting patient survival and disease progression.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Letter
Hematology
Manfred Schmidt, Graham R. Foster, Michiel Coppens, Hauke Thomsen, Ricardo Dolmetsch, Liesbeth Heijink, Paul E. Monahan, Steven W. Pipe
Article
Agriculture, Dairy & Animal Science
Hamed Asadollahi, Saeid Ansari Mahyari, Rasoul Vaez Torshizi, Hossein Emrani, Alireza Ehsani
Summary: This study evaluated the population structure of an F2 population derived from Arian and Urmia chickens using genome-wide analysis, clustering the chickens into eight sub-populations with relatively high genetic variability.
ANIMAL SCIENCE PAPERS AND REPORTS
(2021)
Article
Immunology
Xinjun Li, Hauke Thomsen, Kristina Sundquist, Jan Sundquist, Asta Forsti, Kari Hemminki
Summary: The study found high familial risks for pernicious anemia, suggesting a multifactorial genetic etiology. The results call for further population-level studies to unravel mechanisms of familial pernicious anemia which may help to understand the etiology of this disease.
AUTOIMMUNE DISEASES
(2021)
Article
Agronomy
Thamer R. S. Aljubouri, Amad F. Hassan, Mohammed Baqur S. Al-Shuhaib, Saeid Ansari Mahyari
Summary: The study identified a strong association between the polymorphisms of the GnRH1 gene and growth traits in sheep, with significant correlations found between breed, sex, and dam-age. Individuals with the AA genotype tended to show better performance in growth traits.
AGRICULTURAL RESEARCH
(2021)
Article
Immunology
Hauke Thomsen, Xinjun Li, Kristina Sundquist, Jan Sundquist, Asta Foersti, Kari Hemminki
JOURNAL OF TRANSLATIONAL AUTOIMMUNITY
(2020)
Article
Rheumatology
Hauke Thomsen, Xinjun Li, Kristina Sundquist, Jan Sundquist, Asta Foersti, Kari Hemminki
RHEUMATOLOGY ADVANCES IN PRACTICE
(2020)