Article
Agriculture, Multidisciplinary
Chao Kai-xiang, Wu Cai-juan, Li Juan, Wang Wen-li, Wang Bao-tong, Li Qiang
Summary: The study found that Wudubaijian, a wheat landrace in China, exhibits resistance to stripe rust, and two stable quantitative trait loci (QTLs) were identified through genetic mapping and molecular markers.
JOURNAL OF INTEGRATIVE AGRICULTURE
(2022)
Article
Agronomy
Marcos Malosetti, Laura B. Zwep, Kerrie Forrest, Fred A. van Eeuwijk, Mark Dieters
Summary: The study combined a fast breeding approach with intensive phenotypic selection to detect QTLs controlling Fusarium crown rot resistance in wheat. They identified 17 genomic regions associated with the response to selection, including both known QTLs and potentially novel regions contributing to resistance. The study demonstrated that QTL detection in breeding populations under selection can identify and increase the frequency of favorable alleles, providing valuable information for breeding applications.
THEORETICAL AND APPLIED GENETICS
(2021)
Article
Genetics & Heredity
Karansher S. Sandhu, Shruti Sunil Patil, Meriem Aoun, Arron H. Carter
Summary: This study explored the potential of using multi-trait genomic selection (GS) models to predict end-use quality traits in soft white wheat. The results showed that multi-trait models outperformed uni-trait models in within-environment and across-location predictions. Machine and deep learning models performed better than traditional GS models for across-location predictions, but their advantages diminished when considering genotype by environment interaction. The highest improvement in prediction accuracy was achieved for flour protein content using the multi-trait MLP model.
FRONTIERS IN GENETICS
(2022)
Article
Plant Sciences
Jiang Liu, David C. Cobertera, Robert S. Zemetra, Christopher C. Mundt
Summary: Wheat sharp eyespot (SES), caused by Rhizoctonia cerealis Van der Hoeven, is a common stem disease of wheat worldwide. In 2014, it caused a severe epidemic in the Willamette Valley of Oregon and has remained a significant wheat disease in the region. A study using a recombinant inbred line (RIL) population found four quantitative trait loci (QTL) associated with SES resistance, which may help in marker-assisted breeding. Genotyping by sequencing revealed low heritability across different environments.
Article
Agronomy
Kalpana Singh, Dinesh Kumar Saini, Gautam Saripalli, Ritu Batra, Tinku Gautam, Rakhi Singh, Sunita Pal, Manoj Kumar, Irfat Jan, Sahadev Singh, Anuj Kumar, Hemant Sharma, Jyoti Chaudhary, Kuldeep Kumar, Sourabh Kumar, Vikas Kumar Singh, Vivudh Pratap Singh, Deepak Kumar, Shiveta Sharma, Sachin Kumar, Rahul Kumar, Shailendra Sharma, Shailendra Singh Gaurav, Pradeep Kumar Sharma, Harindra Singh Balyan, Pushpendra Kumar Gupta
Summary: We have developed an updated and improved version of the wheat QTL database (WheatQTLdb V2.0) that includes information on hexaploid wheat and other related species. The database provides an improved list of QTL and additional options for searching and selecting QTL, making it valuable for research and breeding programs.
MOLECULAR BREEDING
(2022)
Article
Plant Sciences
Anne-Kathrin Pfrieme, Britta Ruckwied, Antje Habekuss, Torsten Will, Andreas Stahl, Klaus Pillen, Frank Ordon
Summary: This study aimed at screening WDV resistance and identifying QTL associated with resistance through GWAS. By phenotyping and genotyping a large number of wheat resources, potential WDV-resistant cultivars and relevant genetic loci were identified.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Dora Li, Esther Walker, Michael Francki
Summary: The study identified and mapped resistance genes associated with the fungal necrotrophic disease Septoria nodorum blotch on chromosomes 1BS and 5BL in bread wheat, highlighting the complexity of host response to the disease. The research also revealed significant genome rearrangements on 1BS between different wheat varieties, providing new insights into the genetic control of SNB response. Additionally, the study addressed limitations of using the reference sequence to identify all functional R-genes in modern wheat varieties.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Nannan Yang, Ben Ovenden, Brad Baxter, Megan V. C. McDonald, Peter S. S. Solomon, Andrew Milgate
Summary: Septoria tritici blotch (STB) is recognized as the third most important wheat disease worldwide, affecting a significant portion of wheat production. This study identified new quantitative trait loci (QTLs) responsible for seedling-stage resistance and adult-plant stage resistance (APR) against Zymoseptoria tritici. Additionally, a previously unidentified QTL providing multi-stage resistance (MSR) was characterized. Stacking multiple favorable MSR alleles was found to significantly improve resistance to Z. tritici.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Shuiyuan Hao, Hongyao Lou, Haiwei Wang, Jinghong Shi, Dan Liu, Baogerile, Jianguang Tao, Sanming Miao, Qunce Pei, Liangliang Yu, Min Wu, Ming Gao, Naihu Zhao, Jinchao Dong, Mingshan You, Mingming Xin
Summary: This study investigated the genetic loci associated with five quality traits in Chinese wheat grown in Inner Mongolia through genome wide association mapping. Multiple QTLs were found to be associated with various traits, and the distribution of favorable alleles of stable QTLs was validated. The study provides novel insights into the genetic basis of quality traits in wheat.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Sahbi Ferjaoui, Lamia Aouini, Rim B. Slimane, Karim Ammar, Suzanne Dreisigacker, Henk J. Schouten, Suraj Sapkota, Bochra A. Bahri, Sarrah Ben M'Barek, Richard G. F. Visser, Gert H. J. Kema, Sonia Hamza
Summary: This study identified broad resistance to Zymoseptoria tritici in the Tunisian durum wheat landrace accession 'Agili39' and mapped two major and two minor QTL associated with the resistance. The findings suggest that the natural pyramiding of these QTL in 'Agili 39' contributes to its broad efficacy against STB and can be utilized for effective breeding of Z. tritici resistance in durum wheat.
Article
Agronomy
Dehui Zhao, Jianqi Zeng, Dan Liu, Yubing Tian, Shawai Rabiu Sani, Xiaowan Xu, Yuanfeng Hao, Zhonghu He, Chunping Wang, Li Yang, Jingdong Liu, Yong Zhang
Summary: In this study, a total of 262 recombinant inbred lines derived from a cross between two wheat varieties were used to map powdery mildew resistance loci using a high-density SNP array. Three QTLs on chromosomes 2B, 5B, and 5D were identified, explaining 5.0%-37.0% of the phenotypic variances. The KASP markers linked to these QTLs were validated and can be used for marker-assisted breeding of powdery mildew resistance in wheat.
Article
Agronomy
Paul Telfer, James Edwards, Julian Taylor, Jason A. Able, Haydn Kuchel
Summary: Assessing adaptation to high temperature stress conditions through performance and responsiveness analysis offers breeders opportunities to select for grain yield stability across diverse environments and genotypes with higher relative yield in stress conditions. Genomic analysis identified 199 QTL, including 60 performance QTL and 139 responsiveness QTL, with potential applications in breeding for heat tolerance in wheat.
THEORETICAL AND APPLIED GENETICS
(2022)
Article
Plant Sciences
Carmen Santos, Davide Coelho Martins, Maria Jose Gonzalez-Bernal, Diego Rubiales, Maria Carlota Vaz Patto
Summary: In this study, a combination of phenotyping, gene expression, and linkage mapping was used to prioritize four candidate genes relevant for disease-resistance precision breeding in Lathyrus cicera. These genes are involved in adaptation to biotic stress, cellular and organelle homeostasis, and proteins directly involved in plant defense.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Qiong Yan, Guoyun Jia, Wenjing Tan, Ran Tian, Xiaochen Zheng, Junming Feng, Xiaoqin Luo, Binfan Si, Xin Li, Kebing Huang, Meinan Wang, Xianming Chen, Yong Ren, Suizhuang Yang, Xinli Zhou
Summary: This study identified nine quantitative trait loci (QTLs) for stripe rust resistance in a wheat population derived from the cross between PI 660122 and Zhengmai 9023. One major QTL on chromosome 4DS explained the highest percentage of phenotypic variation. These QTLs can be utilized for wheat breeding to improve resistance to stripe rust.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Harsimardeep S. Gill, Jyotirmoy Halder, Jinfeng Zhang, Navreet K. Brar, Teerath S. Rai, Cody Hall, Amy Bernardo, Paul St Amand, Guihua Bai, Eric Olson, Shaukat Ali, Brent Turnipseed, Sunish K. Sehgal
Summary: Genomic prediction is a promising tool for accelerating genetic gain in wheat breeding, but improving prediction accuracy remains a challenge. Multivariate models have shown potential in predicting multiple agronomic traits in advanced breeding lines, with the MT-CV2 and MTME models performing well in predicting traits and reducing phenotyping cost. The results demonstrate the great potential of multivariate genomic selection models in enhancing resource efficiency and implementing genomic selection in breeding programs.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Ecology
Xinyao He, Muhammad Rezaul Kabir, Krishna K. Roy, Felix Marza, Aakash Chawade, Etienne Duveiller, Carolina Saint Pierre, Pawan K. Singh
Summary: In this study, two recombinant inbred line populations were used to map QTL associated with head blast resistance in wheat. A major QTL was identified on the 2NS/2AS translocation region in both populations, along with several additional QTL on different chromosomes. The results confirmed the importance of the 2NS/2AS translocation in wheat blast resistance and identified some novel QTL for potential use in breeding programs, while also suggesting the need for further investigation into QTL with higher and more stable effects.
Article
Plant Sciences
Nerida Lozano-Ramirez, Susanne Dreisigacker, Carolina P. Sansaloni, Xinyao He, Sergio Sandoval Islas, Paulino Perez-Rodriguez, Aquiles Carballo Carballo, Cristian Nava-Diaz, Masahiro Kishii, Pawan K. Singh
Summary: Synthetic hexaploid wheat (SHW) has been found to have effective resistance to tan spot, a foliar disease caused by Pyrenophora tritici-repentis. Through evaluation and genotyping of 443 SHW plants, 30 significant marker-trait associations were identified, providing important candidate lines for wheat breeding with improved resistance to tan spot.
Article
Genetics & Heredity
Rahul M. Phuke, Xinyao He, Philomin Juliana, Muhammad R. Kabir, Krishna K. Roy, Felix Marza, Chandan Roy, Gyanendra P. Singh, Aakash Chawade, Arun K. Joshi, Pawan K. Singh
Summary: Wheat blast (WB) is a devastating fungal disease that poses a threat to wheat production in India. This study identified the 2NS translocation as the main source of resistance in Indian wheat genotypes. Wheat genotypes carrying the 2NS translocation showed better resistance, highlighting the need to find novel non-2NS resistance sources and genomic regions.
Article
Agriculture, Multidisciplinary
Rodomiro Ortiz, Fredrik Reslow, Jaime Cuevas, Jose Crossa
Summary: This research estimated the genetic gains of potato breeding in western Europe over the past 200 years under high yield potential and stress-prone environments. The results showed that the genetic gains of foreign cultivars were small or negative in the Nordic testing sites. Additionally, breeding contributed just over half of the productivity gains in potato grown in Sweden, and the genetic gains for flesh composition and disease resistance were also small.
JOURNAL OF AGRICULTURAL SCIENCE
(2022)
Article
Plant Sciences
Carlos Munoz-Zavala, Alexander Loladze, Mateo Vargas-Hernandez, Elizabeth Garcia-Leon, Amos Emitati Alakonya, Juan Manuel Tovar-Pedraza, Paul H. Goodwin, Santos Gerardo Leyva-Mir
Summary: Turcicum leaf blight (TLB) is a foliar disease of maize in Mexico caused by the fungal pathogen Exserohilum turcicum. The study found that among the 140 E. turcicum isolates, the most common physiological race was race 23. The disease was mainly found in tropical and temperate regions.
Article
Plant Sciences
Raysa Gevartosky, Humberto Fanelli Carvalho, Germano Costa-Neto, Osval A. Montesinos-Lopez, Jose Crossa, Roberto Fritsche-Neto
Summary: This study aimed to design optimized training sets for genomic prediction considering multi-trait multi-environment trials and how those methods may increase accuracy reducing phenotyping costs. The combined use of genomic and enviromic data efficiently designs optimized training sets for genomic prediction, improving the response to selection per dollar invested.
Article
Agronomy
J. Jesus Ceron-Rojas, Manje Gowda, Fernando Toledo, Yoseph Beyene, Alison R. Bentley, Leo Crespo-Herrera, Keith Gardner, Jose Crossa
Summary: The profit function is used to predict net genetic merit (H) in plant breeding by deriving trait economic weights using the linear phenotypic selection index (LPSI). Economic weight reflects the increase in profit achieved by improving a specific trait by one unit and should consider market situation rather than arbitrary values. To overcome the challenges in assigning economic weights in maize and wheat breeding programs, a profit function was constructed using the market price of grain yield and its conditional expectation, and validated using simulated and real datasets.
Article
Biodiversity Conservation
Nick S. Fradgley, James Bacon, Alison R. Bentley, Germano Costa-Neto, Andrew Cottrell, Jose Crossa, Jaime Cuevas, Matthew Kerton, Edward Pope, Stephanie M. Swarbreck, Keith A. Gardner
Summary: Wheat, a major global crop, is highly valued for its grain quality. This study used quantitative genetics and climate model outputs to investigate genotypic adaptation for wheat quality traits in the UK. The research found that the impact of climate change on wheat quality varies geographically and current wheat germplasm in the UK has low adaptability to future climates.
GLOBAL CHANGE BIOLOGY
(2022)
Article
Genetics & Heredity
Germano Costa-Neto, Leonardo Crespo-Herrera, Nick Fradgley, Keith Gardner, Alison R. Bentley, Susanne Dreisigacker, Roberto Fritsche-Neto, Osval A. Montesinos-Lopez, Jose Crossa
Summary: This study developed a data-driven approach based on Environment-Phenotype Association (EPA) to recycle important G x E information from historical breeding data. The results showed that introducing EPA as an intermediary learning step significantly improved G x E prediction accuracy.
G3-GENES GENOMES GENETICS
(2023)
Article
Genetics & Heredity
Susanne Dreisigacker, Paulino Perez-Rodriguez, Leonardo Crespo-Herrera, Alison R. Bentley, Jose Crossa
Summary: This study demonstrates the potential of rapid-cycle recurrent genomic selection (RCRGS) to increase grain yield in wheat, achieving a consistent genetic gain of 12.3% over 3 cycles of recombination.
G3-GENES GENOMES GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Guillermo Garcia-Barrios, Jose Crossa, Serafin Cruz-Izquierdo, Victor Heber Aguilar-Rincon, J. Sergio Sandoval-Islas, Tarsicio Corona-Torres, Nerida Lozano-Ramirez, Susanne Dreisigacker, Xinyao He, Pawan Kumar Singh, Rosa Angela Pacheco-Gil
Summary: Genomic prediction is used to predict breeding values based on molecular and phenotypic data. This study evaluated the performance of different models in predicting disease resistance in synthetic hexaploid wheat. The results showed that the combination of genomic and pedigree information (A+G BLUP) had the highest prediction accuracy, while the single trait and multi-trait models had similar accuracies. This suggests that the use of genomic information can improve breeding programs.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Genetics & Heredity
Abelardo Montesinos-Lopez, Carolina Rivera, Francisco Pinto, Francisco Pinera, David Gonzalez, Mathew Reynolds, Paulino Perez-Rodriguez, H. Li, Osval A. Montesinos-Lopez, Jose Crossa
Summary: By comparing a novel DL method with conventional GP models, this study found that DL method has higher accuracy in predicting genomic phenotypes in plant breeding research and can account for the complexity of genotype-environment interaction. However, traditional GP models can also achieve high accuracy in certain situations.
G3-GENES GENOMES GENETICS
(2023)
Article
Plant Sciences
Osval A. Montesinos-Lopez, Brandon A. Mosqueda-Gonzalez, Josafat Salinas-Ruiz, Abelardo Montesinos-Lopez, Jose Crossa
Summary: Sparse testing is crucial for improving the efficiency of genomic selection by reducing the number of genotypes evaluated. We evaluated four methods for allocating lines to environments and found that M4 was the best method, while M1 was the worst. There were no significant differences between M3 and M4. We concluded that both M4 and M3 are efficient in the context of sparse testing for multi-trait prediction.
Article
Plant Sciences
Osval A. Montesinos-Lopez, Alison R. Bentley, Carolina Saint Pierre, Leonardo Crespo-Herrera, Leonardo Rebollar-Ruellas, Patricia Edwigis Valladares-Celis, Morten Lillemo, Abelardo Montesinos-Lopez, Jose Crossa
Summary: Genomic selection (GS), proposed by Meuwissen et al. more than 20 years ago, is revolutionizing plant and animal breeding. In our study of 14 real datasets, we found that the average gain in prediction accuracy when genomic information is considered was 26.31%. The quality of the markers and relatedness of the individuals can greatly impact the increase in prediction accuracy.
Article
Genetics & Heredity
Osval A. Montesinos Lopez, Brandon Alejandro Mosqueda Gonzalez, Abelardo Montesinos Lopez, Jose Crossa
Summary: Genomic selection (GS) is revolutionizing plant breeding, but a basic understanding of statistical machine-learning methods is necessary. We introduce the Sparse Kernel Methods (SKM) R library, which provides complete guidelines for implementing seven statistical machine-learning methods for genomic prediction, making it easier for breeders and scientists to use these methods.
