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JOURNAL ARTICLE
Fauziatul Fitriyah, Hiroki Matsuo, Sachiko Isobe, Kenta Shirasawa, Ken Naito, Yosuke Yoshioka
Quantitative trait locus analysis identified independent novel loci in cucumbers responsible for resistance to races 0 and 1 of the anthracnose fungal pathogen Colletotrichum orbiculare. Cucumbers have been reported to be vulnerable to Colletotrichum orbiculare, causing anthracnose disease with significant yield loss under favorable conditions. The deployment of a single recessive Cssgr gene in cucumber breeding for anthracnose resistance was effective until a recent report on high-virulent strains infecting cucumbers in Japan conquering the resistance...
May 11, 2024: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
#2
JOURNAL ARTICLE
Zhiwen Zhai, Yuqing Che, Shuaifeng Geng, Shaoshuai Liu, Shuqin Zhang, Dada Cui, Zhongyin Deng, Mingxue Fu, Yang Li, Xinyu Zou, Jun Liu, Aili Li, Long Mao
JASMONATE-ZIM DOMAIN (JAZ) repressor proteins work as co-receptors in the jasmonic acid (JA) signalling pathway and are essential for plant development and environmental adaptation. Despite wheat being one of the main staple food crops, until recently, comprehensive analysis of its JAZ gene family has been limited due to the lack of complete and high-quality reference genomes. Here, using the latest reference genome, we identified 17 JAZ genes in the wheat D-genome donor Aegilops tauschii . Then, 54 TaJAZs were identified in common wheat...
April 30, 2024: Plants (Basel, Switzerland)
#3
JOURNAL ARTICLE
Pitsanupong Waengwan, Kularb Laosatit, Yun Lin, Tarika Yimram, Xingxing Yuan, Xin Chen, Prakit Somta
Powdery mildew (PM) caused by Erysiphe polygoni is an important foliar disease in mungbean ( Vigna radiata ). A previous study showed that QTL qPMRUM5-2 is a major locus for PM resistance in mungbean accession RUM5 (highly resistant). Bioinformatics analysis revealed that flanking markers of the qPMRUM5-2 covered a region of 1.93 Mb. In this study, we conducted fine mapping for the qPMRUM5-2 using the F2 population of 1156 plants of the cross between Chai Nat 60 (CN60; highly susceptible) and RUM5. PM resistance evaluation was performed under field conditions using F2:3 lines grown in three different environments...
April 29, 2024: Plants (Basel, Switzerland)
#4
REVIEW
John Christian Ontoy, Jong Hyun Ham
Rice ( Oryza sativa ), as a staple crop feeding a significant portion of the global population, particularly in Asian countries, faces constant threats from various diseases jeopardizing global food security. A precise understanding of disease resistance mechanisms is crucial for developing resilient rice varieties. Traditional genetic mapping methods, such as QTL mapping, provide valuable insights into the genetic basis of diseases. However, the complex nature of rice diseases demands a holistic approach to gain an accurate knowledge of it...
April 26, 2024: Plants (Basel, Switzerland)
#5
JOURNAL ARTICLE
Ashley R Henry, Nathan D Miller, Edgar P Spalding
Cell expansion in a discrete region called the elongation zone drives root elongation. Analyzing time lapse images can quantify the expansion in kinematic terms as if it were fluid flow. We used horizontal microscopes to collect images from which custom software extracted the length of the elongation zone, the peak relative elemental growth rate (REGR) within it, the axial position of the REGR peak, and the root elongation rate. Automation enabled these kinematic traits to be measured in 1575 Arabidopsis seedlings representing 162 recombinant inbred lines (RILs) derived from a cross of Cvi and Ler ecotypes...
April 25, 2024: Plants (Basel, Switzerland)
#6
JOURNAL ARTICLE
Mohammad Shafiqul Islam, Amit Ghimire, Liny Lay, Waleed Khan, Jeong-Dong Lee, Qijian Song, Hyun Jo, Yoonha Kim
Roots are the hidden and most important part of plants. They serve as stabilizers and channels for uptaking water and nutrients and play a crucial role in the growth and development of plants. Here, two-dimensional image data were used to identify quantitative trait loci (QTL) controlling root traits in an interspecific mapping population derived from a cross between wild soybean 'PI366121' and cultivar 'Williams 82'. A total of 2830 single-nucleotide polymorphisms were used for genotyping, constructing genetic linkage maps, and analyzing QTLs...
April 25, 2024: International Journal of Molecular Sciences
#7
JOURNAL ARTICLE
Zhiyu Yu, Rudolph Fredua-Agyeman, Stephen E Strelkov, Sheau-Fang Hwang
In this study, a rutabaga ( Brassica napus ssp. napobrassica ) donor parent FGRA106, which exhibited broad-spectrum resistance to 17 isolates representing 16 pathotypes of Plasmodiophora brassicae , was used in genetic crosses with the susceptible spring-type canola ( B. napus ssp. napus ) accession FG769. The F2 plants derived from a clubroot-resistant F1 plant were screened against three P. brassicae isolates representing pathotypes 3A, 3D, and 3H. Chi-square (χ2 ) goodness-of-fit tests indicated that the F2 plants inherited two major clubroot resistance genes from the CR donor FGRA106...
April 23, 2024: International Journal of Molecular Sciences
#8
JOURNAL ARTICLE
Dingding Liu, Yuanyuan Ye, Rongjin Tang, Yang Gong, Si Chen, Chenyu Zhang, Piao Mei, Jiedan Chen, Liang Chen, Chunlei Ma
The highly unique zigzag-shaped stem phenotype in tea plants boasts significant ornamental value and is exceptionally rare. To investigate the genetic mechanism behind this trait, we developed BC1 artificial hybrid populations. Our genetic analysis revealed the zigzag-shaped trait as a qualitative trait. Utilizing whole-genome resequencing, we constructed a high-density genetic map from the BC1 population, incorporating 5,250 SNP markers across 15 linkage groups, covering 3,328.51 cM with an average marker interval distance of 0...
May 9, 2024: BMC Plant Biology
#9
JOURNAL ARTICLE
Sahana Basu, Monika, Surbhi Kumari, Gautam Kumar
Constant change in global climate has become the most important limiting factor to crop productivity. Asymmetrical precipitations are causing recurrent flood events around the world. Submergence is one of the most detrimental abiotic stresses for sustainable rice production in the rainfed ecosystems of Southeast Asia. Therefore, the development of submergence-tolerant rice is an essential requirement to encounter food security. Submergence tolerance in rice is governed by the major quantitative trait locus (QTL) designated as Submergence1 (Sub1) near the centromere of chromosome 9...
April 30, 2024: Plant Physiology and Biochemistry: PPB
#10
JOURNAL ARTICLE
C G Gokulan, Umakanth Bangale, Vishalakshi Balija, Suneel Ballichatla, Gopi Potupureddi, Deepti Rao, Prashanth Varma, Nakul Magar, Karteek Jallipalli, Sravan Manthri, A P Padmakumari, Gouri S Laha, L V Subba Rao, Kalyani M Barbadikar, Meenakshi Sundaram Raman, Hitendra K Patel, Sheshu Madhav Maganti, Ramesh V Sonti
By deploying a multi-omics approach, we unraveled the mechanisms that might help rice to combat Yellow Stem Borer infestation, thus providing insights and scope for developing YSB resistant rice varieties. Yellow Stem Borer (YSB), Scirpophaga incertulas (Walker) (Lepidoptera: Crambidae), is a major pest of rice, that can lead to 20-60% loss in rice production. Effective management of YSB infestation is challenged by the non-availability of adequate sources of resistance and poor understanding of resistance mechanisms, thus necessitating studies for generating resources to breed YSB resistant rice and to understand rice-YSB interaction...
May 7, 2024: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
#11
Michael E Belloy, Yann Le Guen, Ilaria Stewart, Joachim Herz, Richard Sherva, Rui Zhang, Victoria Merritt, Matthew S Panizzon, Richard L Hauger, J Michael Gaziano, Mark Logue, Valerio Napolioni, Michael D Greicius
IMPORTANCE: The X chromosome has remained enigmatic in Alzheimer's disease (AD), yet it makes up 5% of the genome and carries a high proportion of genes expressed in the brain, making it particularly appealing as a potential source of unexplored genetic variation in AD. OBJECTIVES: Perform the first large-scale X chromosome-wide association study (XWAS) of AD. Primary analyses are non-stratified, while secondary analyses evaluate sex-stratified effects. DESIGN: Meta-analysis of genetic association studies in case-control, family-based, population-based, and longitudinal AD-related cohorts from the US Alzheimer's Disease Genetics Consortium (ADGC) and Alzheimer's Disease Sequencing Project (ADSP), the UK Biobank (UKB), the Finnish health registry (FinnGen), and the US Million Veterans Program (MVP)...
April 23, 2024: medRxiv
#12
Nora I Strom, Zachary F Gerring, Marco Galimberti, Dongmei Yu, Matthew W Halvorsen, Abdel Abdellaoui, Cristina Rodriguez-Fontenla, Julia M Sealock, Tim Bigdeli, Jonathan R Coleman, Behrang Mahjani, Jackson G Thorp, Katharina Bey, Christie L Burton, Jurjen J Luykx, Gwyneth Zai, Silvia Alemany, Christine Andre, Kathleen D Askland, Nerisa Banaj, Cristina Barlassina, Judith Becker Nissen, O Joseph Bienvenu, Donald Black, Michael H Bloch, Julia Boberg, Sigrid Børte, Rosa Bosch, Michael Breen, Brian P Brennan, Helena Brentani, Joseph D Buxbaum, Jonas Bybjerg-Grauholm, Enda M Byrne, Judit Cabana-Dominguez, Beatriz Camarena, Adrian Camarena, Carolina Cappi, Angel Carracedo, Miguel Casas, Maria Cristina Cavallini, Valentina Ciullo, Edwin H Cook, Jesse Crosby, Bernadette A Cullen, Elles J De Schipper, Richard Delorme, Srdjan Djurovic, Jason A Elias, Xavier Estivill, Martha J Falkenstein, Bengt T Fundin, Lauryn Garner, Chris German, Christina Gironda, Fernando S Goes, Marco A Grados, Jakob Grove, Wei Guo, Jan Haavik, Kristen Hagen, Kelly Harrington, Alexandra Havdahl, Kira D Höffler, Ana G Hounie, Donald Hucks, Christina Hultman, Magdalena Janecka, Eric Jenike, Elinor K Karlsson, Kara Kelley, Julia Klawohn, Janice E Krasnow, Kristi Krebs, Christoph Lange, Nuria Lanzagorta, Daniel Levey, Kerstin Lindblad-Toh, Fabio Macciardi, Brion Maher, Brittany Mathes, Evonne McArthur, Nathaniel McGregor, Nicole C McLaughlin, Sandra Meier, Euripedes C Miguel, Maureen Mulhern, Paul S Nestadt, Erika L Nurmi, Kevin S O'Connell, Lisa Osiecki, Olga Therese Ousdal, Teemu Palviainen, Nancy L Pedersen, Fabrizio Piras, Federica Piras, Sriramya Potluri, Raquel Rabionet, Alfredo Ramirez, Scott Rauch, Abraham Reichenberg, Mark A Riddle, Stephan Ripke, Maria C Rosário, Aline S Sampaio, Miriam A Schiele, Anne Heidi Skogholt, Laura G Sloofman G Sloofman, Jan Smit, María Soler Artigas, Laurent F Thomas, Eric Tifft, Homero Vallada, Nathanial van Kirk, Jeremy Veenstra-VanderWeele, Nienke N Vulink, Christopher P Walker, Ying Wang, Jens R Wendland, Bendik S Winsvold, Yin Yao, Hang Zhou, Arpana Agrawal, Pino Alonso, Götz Berberich, Kathleen K Bucholz, Cynthia M Bulik, Danielle Cath, Damiaan Denys, Valsamma Eapen, Howard Edenberg, Peter Falkai, Thomas V Fernandez, Abby J Fyer, J M Gaziano, Dan A Geller, Hans J Grabe, Benjamin D Greenberg, Gregory L Hanna, Ian B Hickie, David M Hougaard, Norbert Kathmann, James Kennedy, Dongbing Lai, Mikael Landén, Stéphanie Le Hellard, Marion Leboyer, Christine Lochner, James T McCracken, Sarah E Medland, Preben B Mortensen, Benjamin M Neale, Humberto Nicolini, Merete Nordentoft, Michele Pato, Carlos Pato, David L Pauls, John Piacentini, Christopher Pittenger, Danielle Posthuma, Josep Antoni Ramos-Quiroga, Steven A Rasmussen, Margaret A Richter, David R Rosenberg, Stephan Ruhrmann, Jack F Samuels, Sven Sandin, Paul Sandor, Gianfranco Spalletta, Dan J Stein, S Evelyn Stewart, Eric A Storch, Barbara E Stranger, Maurizio Turiel, Thomas Werge, Ole A Andreassen, Anders D Børglum, Susanne Walitza, Kristian Hveem, Bjarne K Hansen, Christian P Rück, Nicholas G Martin, Lili Milani, Ole Mors, Ted Reichborn-Kjennerud, Marta Ribasés, Gerd Kvale, David Mataix-Cols, Katharina Domschke, Edna Grünblatt, Michael Wagner, John-Anker Zwart, Gerome Breen, Gerald Nestadt, Jaakko Kaprio, Paul D Arnold, Dorothy E Grice, James A Knowles, Helga Ask, Karin J Verweij, Lea K Davis, Dirk J Smit, James J Crowley, Jeremiah M Scharf, Murray B Stein, Joel Gelernter, Carol A Mathews, Eske M Derks, Manuel Mattheisen
Obsessive-compulsive disorder (OCD) affects ∼1% of the population and exhibits a high SNP-heritability, yet previous genome-wide association studies (GWAS) have provided limited information on the genetic etiology and underlying biological mechanisms of the disorder. We conducted a GWAS meta-analysis combining 53,660 OCD cases and 2,044,417 controls from 28 European-ancestry cohorts revealing 30 independent genome-wide significant SNPs and a SNP-based heritability of 6.7%. Separate GWAS for clinical, biobank, comorbid, and self-report sub-groups found no evidence of sample ascertainment impacting our results...
March 13, 2024: medRxiv
#13
JOURNAL ARTICLE
Yongjie Tang, Jinning Zhang, Wenlong Li, Xueqin Liu, Siqian Chen, Siyuan Mi, Jinyan Yang, Jinyan Teng, Lingzhao Fang, Ying Yu
BACKGROUND: Characterization of regulatory variants (e.g., gene expression quantitative trait loci, eQTL; gene splicing QTL, sQTL) is crucial for biologically interpreting molecular mechanisms underlying loci associated with complex traits. However, regulatory variants in dairy cattle, particularly in specific biological contexts (e.g., distinct lactation stages), remain largely unknown. In this study, we explored regulatory variants in whole blood samples collected during early to mid-lactation (22-150 days after calving) of 101 Holstein cows and analyzed them to decipher the regulatory mechanisms underlying complex traits in dairy cattle...
May 6, 2024: BMC Genomics
#14
JOURNAL ARTICLE
Anneke Brümmer, Sven Bergmann
Expression quantitative trait loci (eQTL) studies typically consider exon expression of genes and discard intronic RNA sequencing reads despite their information on RNA metabolism. Here, we quantify genetic effects on exon and intron levels of genes and their ratio in lymphoblastoid cell lines, revealing thousands of cis-QTLs of each type. While genetic effects are often shared between cis-QTL types, 7814 (47%) are not detected as top cis-QTLs at exon levels. We show that exon levels preferentially capture genetic effects on transcriptional regulation, while exon-intron-ratios better detect those on co- and post-transcriptional processes...
May 6, 2024: Nature Communications
#15
JOURNAL ARTICLE
Wenjia Zhang, Xinyi Chen, Kai Yang, Siyuan Chang, Xue Zhang, Mingde Liu, Longfei Wu, Mingming Xin, Zhaorong Hu, Jie Liu, Huiru Peng, Zhongfu Ni, Qixin Sun, Yingyin Yao, Jinkun Du
This study precisely mapped and validated a quantitative trait locus (QTL) located on chromosome 4B for flag leaf angle in wheat. Flag leaf angle (FLANG) is closely related to crop architecture and yield. We previously identified the quantitative trait locus (QTL) QFLANG-4B for FLANG on chromosome 4B, located within a 14-cM interval flanked by the markers Xbarc20 and Xzyh357, using a mapping population of recombinant inbred lines (RILs) derived from a cross between Nongda3331 (ND3331) and Zang1817. In this study, we fine-mapped QFLANG-4B and validated its associated genetic effect...
May 6, 2024: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
#16
JOURNAL ARTICLE
Anne Webb, Tom R Reynolds, Tally I C Wright, Rosa Caiazzo, David C Lloyd, Jane E Thomas, Thomas A Wood
INTRODUCTION: Chocolate spot, caused by the ascomycete fungus Botrytis fabae , is a devastating foliar disease and a major constraint on the quality and yield of faba beans ( Vicia faba ). The use of fungicides is the primary strategy for controlling the disease. However, high levels of partial genetic resistance have been identified and can be exploited to mitigate the disease. METHODS: The partially resistant V. faba cultivar Maris Bead and susceptible Egyptian accession ig70726 were crossed, and a genetic mapping population of 184 individuals was genotyped in the F2 generation and screened for resistance to B...
2024: Frontiers in Plant Science
#17
REVIEW
Amruta Swaminathan, Fanning Xia, Nicolas Rohner
How genotype determines phenotype is a well-explored question, but genotype-environment interactions and their heritable impact on phenotype over the course of evolution are not as thoroughly investigated. The fish Astyanax mexicanus , consisting of surface and cave ecotypes, is an ideal emerging model to study the genetic basis of adaptation to new environments. This model has permitted quantitative trait locus mapping and whole-genome comparisons to identify the genetic bases of traits such as albinism and insulin resistance and has helped to better understand fundamental evolutionary mechanisms...
January 2024: Trends in Genetics: TIG
#18
JOURNAL ARTICLE
Abdulqader Jighly
The date palm is economically vital in the Middle East and North Africa, providing essential fibres, vitamins, and carbohydrates. Understanding the genetic architecture of its traits remains complex due to the tree's perennial nature and long generation times. This study aims to address these complexities by employing advanced genome-wide association (GWAS) and genomic prediction models using previously published data involving fruit acid content, sugar content, dimension, and colour traits. The multivariate GWAS model identified seven QTL, including five novel associations, that shed light on the genetic control of these traits...
May 2, 2024: Plant Science: An International Journal of Experimental Plant Biology
#19
JOURNAL ARTICLE
Donglan Zhao, Shizhuo Xiao, An Zhang, Lingxiao Zhao, Xibin Dai, Rui Yuan, Jie Wang, Yao Wang, Qinglian Li, Zhilin Zhou
Sweetpotato, Ipomoea batatas (L.) Lam., is an important worldwide crop used as feed, food, and fuel. However, its polyploidy, high heterozygosity and self-incompatibility makes it difficult to study its genetics and genomics. Longest vine length (LVL), yield per plant (YPP), dry matter content (DMC), starch content (SC), soluble sugar content (SSC), and carotenoid content (CC) are some of the major agronomic traits being used to evaluate sweetpotato. However limited research has actually examined how these traits are inherited...
April 18, 2024: Plant Physiology and Biochemistry: PPB
#20
JOURNAL ARTICLE
Nitish Ranjan Prakash, Kuldeep Kumar, Vignesh Muthusamy, Rajkumar Uttamrao Zunjare, Firoz Hossain
'Sikkim Primitive' maize landrace, unique for prolificacy (7-9 ears per plant) possesses unique genomic architecture in branching and inflorescence-related gene(s), and locus Zm00001eb365210 encoding glycosyltransferases was identified as the putative candidate gene underlying QTL (qProl-SP-8.05) for prolificacy. The genotype possesses immense usage in breeding high-yielding baby-corn genotypes. 'Sikkim Primitive' is a native landrace of North Eastern Himalayas, and is characterized by having 7-9 ears per plant compared to 1-2 ears in normal maize...
May 3, 2024: Plant Cell Reports
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