Breeding more resilient soybeans may come down to test site selection
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MAPS FROM THE UNIVERSITY OF ILLINOIS URBANA-CHAMPAIGN STUDY SUGGEST OPTIMAL TESTING SITES BASED ON AGROECOLOGICAL ZONES (AEZS) AND SOYBEAN MATURITY GROUPS (00 TO IV+).
view moreCREDIT: UNIVERSITY OF ILLINOIS URBANA-CHAMPAIGN
URBANA, Ill. — In the quest to optimize crop productivity across environments, soybean breeders test new cultivars in multiple locations each year. The best-performing cultivars across these locations are selected for further breeding and eventual commercialization. However, a new study from the University of Illinois Urbana-Champaign suggests current soybean testing locations may not be delivering breeders the biggest bang for their buck.
“We met with most of the soybean breeders in public research universities across the Midwest and asked where they set up their trials over the last 30 to 40 years,” said Nicolas Martin, an associate professor in the Department of Crop Sciences, part of the College of Agricultural, Consumer and Environmental Sciences (ACES) at Illinois. “We found that they tend to select these sites a little bit by tradition.”
Convenience is a strong draw, as well.
“Certain types of sites are overrepresented because of tradition rather than their environmental utility; for example, sites near large research universities like Urbana, Illinois; Ames, Iowa; or Lafayette, Indiana. It’s not that we need a lot of data from those environments, but those test sites are convenient to access where cultivars are being developed,” said doctoral student Catherine Gilbert, the study’s first author.
The team analyzed long-term climate data and records of soybean trials to develop two new sets of maps that would help breeders strategize the placement and use of test sites. The first map represents common environments and favors generalist phenotypes that do well under most conditions. The second emphasizes environmental variation, optimizing specialized phenotypes that perform well in specific conditions.
“Breeding programs may have different philosophies,” Martin said. “One of them is to mimic where most farmers are growing. Others are looking to avoid redundancies in the locations where you train your cultivars. If you put them under diverse growing conditions, you see which ones are more resilient.”
In both cases, the analysis suggests breeders need to redistribute testing sites. Gilbert says there would need to be some fairly radical changes, including fully opening and closing test sites and dropping and adding hundreds of soybean varieties across the map.
“To optimize testing for general adaptation, we should expand in southern Minnesota, Iowa, and eastern South Dakota,” she said. “And for specialized adaptation, we need to put more testing sites in Nebraska and, again, in South Dakota.
When Martin and Gilbert presented their results to cooperating breeders, most said they would consider the information in decisions around moving, opening, or closing testing sites.
Basing testing networks on how well they represent the soybean growing environment, rather than on tradition or convenience, means the new maps can better account for a changing climate. The researchers hope their approach can help breeding programs select more resilient cultivars in the future.
“We think our results could guide future cultivar adaptation to growing conditions farmers are running into more frequently. Thus, our goal is to improve the environmental representation of the trials, which would let us more accurately evaluate cultivars based on their performance and select better-performing varieties,” Gilbert said.
Martin added, “The proposed site selection protocol not only enhances the accuracy of our cultivar testing but also opens doors to new regions exploring soybean cultivar adaptation. By allocating new resources in underrepresented areas that hold potential for soybean cultivar resilience, we can foster a proactive stance in cultivar development.”
The study, “Using agro-ecological zones to improve the representation of a multi-environment trial of soybean varieties,” is published in Frontiers in Plant Science [DOI:10.3389/fpls.2024.1310461].
JOURNAL
Frontiers in Plant Science
DOI
Unlocking the secrets of black raspberry resilience: genome-wide discovery and analysis of bZIP transcription factors
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MOLECULAR WEIGHT AND PROTEIN ISOELECTRIC POINT OF THE IDENTIFIED BZIPS IN EACH GROUP OF RUBUS SPECIES. ARABIDOPSIS PROTEINS ARE INCLUDED AS A REFERENCE.
view moreCREDIT: FRUIT RESEARCH
Transcription factors (TFs) like basic leucine zippers (bZIPs) play vital roles in various plant biological regulation, including stress responses. However, their presence in the Rubus species has received limited attention, especially regarding the function and interactions of bZIP groups S1 and C in the Rubus genus. The current challenge lies in deepening our knowledge of these bZIP networks in non-model plants, which could inform breeding strategies and improve crop resilience.
In February 2024, Fruit Research published a research entitled by “Heterodimeric interaction of the C/S1 basic leucine zipper transcription factors in black raspberry: a genome-wide identification and comparative analysis”.
In this study, researchers combined protein signature files from the Pfam database and a plant-specific Hidden Markov Model (HMM) to identify bZIP members. As a result, 49 candidate bZIP coding genes in both black and red raspberries were identified. These genes were confirmed to encode proteins with characteristic Basic Region (BR) and Leucine Zipper (LZ) domains, varying in length from 137 to 706 amino acids and molecular weights from 15.9 to 76.3 kDa. Phylogenetic analysis classified these into 13 phylogenetic clades, revealing interspecies clustering and suggesting an evolutionary conservation pre-dating species divergence. Additionally, genome-wide analyses revealed significant expansions or contractions in gene families, with gene duplication, especially dispersed and segmental duplications, playing a crucial role in the evolution of bZIP genes in Rubus. Comparative genomic analyses among ten Rosaceae species demonstrated a closer evolutionary relationship among roses, raspberries, and strawberries, and identified the Rubus genome as undergoing chromosomal rearrangements like those in wild strawberries.
Gene ontology annotation and expression analysis of RobZIP genes across different tissues highlighted their involvement in a wide array of cellular processes, including nitrogen metabolism and stress responses. The study also delved into the dimerization properties of the identified bZIPs, predicting potential protein interactions and validating them through yeast two-hybrid assays. Overall, this research not only provided insights into the functional redundancy and specific roles of bZIP TFs in Rubus but also underlined the evolutionary dynamics shaping their diversity across the Rosaceae family. Overall, likely due to stringent selection criteria, this research offers a foundational understanding of the bZIP gene family's contribution to the regulatory networks within and beyond the Rubus genus, paving the way for future studies on their functional mechanisms and interactions.
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References
DOI
Original Source URL
https://www.maxapress.com/article/doi/10.48130/frures-0024-0001
Authors
Ximeng Lin1,2, Mei Huang1, Jinwei He1, Ailing Min1, Ying Zhou1, Wendie Ma1, Xunju Liu3, Xiaorong Wang1,4, Haoru Tang1 & Qing Chen1,4,*
Affiliations
1College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
2College of Horticulture, Nanjing Agricultural University, Nanjing 210014, China
3University Bordeaux, INRAe, Biologie du Fruit et Pathologie, UMR 1332, av. Edouard Bourlaux, Villenave d’Ornon 33140, France
4Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Sichuan Agricultural University, Chengdu 611130, China
*Corresponding author
About Qing Chen
Professor, College of Horticulture, Sichuan Agricultural University. His main research interests are in horticultural plant genetic breeding, with raspberries and strawberries as the research targets, focusing on fruit flavonoid metabolism, sugar synthesis (concentrating on the relationship with pigment synthesis in flavonoids) as well as the biosynthesis of fruit cuticle and the relationship between structure and function of the cell wall.
JOURNAL
Fruit Research
METHOD OF RESEARCH
Experimental study
SUBJECT OF RESEARCH
Not applicable
ARTICLE TITLE
Heterodimeric interaction of the C/S1 basic leucine zipper transcription factors in black raspberry: a genome-wide identification and comparative analysis
Optimizing apple production: the interplay of crop load, rootstock, and chemical thinning on 'fuji' apples
MAXIMUM ACADEMIC PRESS
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EFFECT OF DIFFERENT CROP LOAD ON THE DEVELOPMENT OF TREE AND LEAVES.
view moreCREDIT: FRUIT RESEARCH
Apple (Malus × domestica) is globally valued for its taste and nutrition, yet achieving optimal quality is challenging due to the impact of factors like crop load and rootstock on fruit development. Current research focuses on the individual effects of these factors and the use of chemical thinning to manage crop load, improving fruit quality and tree health. However, the complexities of chemical thinning's effects on apple physiology and its interaction with rootstock and crop load dynamics are not fully understood. Identifying the optimal use of thinning agents and their impacts on apple development is essential for refining orchard management practices and enhancing apple production outcomes.
In March 2024, Fruit Research published a research entitled by “Evaluating the sustainable cultivation of 'Fuji' apples: suitable crop load and the impact of chemical thinning agents on fruit quality and transcription”.
To determine the optimal crop load for sustainable apple production across different rootstock types (vigorous, dwarfing, and dwarfing interstock), researchers adjusted crop loads to various levels and assessed the effects on tree growth and fruit quality. A crop load of 320 fruits per tree for vigorous rootstocks resulted in optimal tree height growth and branch diameter. Dwarfing rootstocks showed the best results with a crop load of 110 fruits, although the length of new branch growth was not significantly affected. Dwarfing interstock trees had optimal growth with a crop load of 210 fruits. Increased crop load in vigorous rootstocks also enhanced leaf area, chlorophyll content, and photosynthetic rates, suggesting a positive correlation between crop load and leaf functionality, unlike in dwarfing rootstocks where an optimal balance was needed to maintain leaf health and photosynthetic efficiency.
Fruit quality, assessed through weight, yield, and size, generally decreased with increasing crop load, but yield per acre increased. The study recommended specific crop loads for each rootstock type to balance tree health and fruit quality: 320 fruits for vigorous stock, 90 for dwarfing rootstock, and 100 for dwarfing interstock for quality fruits exceeding 80 mm in diameter. Chemical thinning, using carbaryl and 6-BA, was identified as effective in achieving optimal crop loads, with best practices involving specific concentrations and application timings.
Additionally, transcriptomic analysis of NAA-treated fruits revealed its inhibitory effect on fruit enlargement and identified potential regulatory genes involved in hormonal pathways affecting fruit development and ripening. Overall, this approach combining practical orchard management practices with molecular insights offers a pathway to enhancing apple production efficiency and fruit quality, recommending specific crop loads and thinning practices tailored to different rootstock types while elucidating the role of NAA in fruit development processes.
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References
DOI
Original Source URL
https://www.maxapress.com/article/doi/10.48130/frures-0024-0002
Authors
Shicong Wang1,#, Qianying Wang1,#, Weiyu Jiang1, Yixiong Wang1, Jinjiao Yan1, Xuewei Li1, Jiangbo Wang3,4, Qingmei Guan1, Fengwang Ma1, Jing Zhang1, Qianming Zheng2,*, Yangjun Zou1,*, & Jidi Xu1, *
# These authors contributed equally: Shicong Wang, Qianying Wang
Affiliations
1. State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
2. Institute of Pomology Science, Guizhou Academy of Agricultural Science, Guiyang 550006, China
3.The National and Local Joint Engineering Laboratory of High Efficiency and Superior-Quality Cultivation and Fruit Deep Processing Technology of Characteristic Fruit Trees in Southern Xinjiang, College of Horticulture and Forestry, Tarim University, Alar 843300, China
4. Xinjiang Production and Construction Corps Key Laboratory of Biological Resources Protection and Utilization in Tarim Basin, Alar 843300, China
# These authors contributed equally.
About Jidi Xu
Associate Professor, College of Horticulture, Northwest A&F University. His group aims to investigate the underlying mechanism of epigenetic regulation in apples under various abiotic stresses, including DNA/RNA modification, histone modification, and chromatin remodeling. Based on the mechanism exploring, epigenome editing engineering is applied to process the important traits improvement in apples.
JOURNAL
Fruit Research
METHOD OF RESEARCH
Experimental study
SUBJECT OF RESEARCH
Not applicable
ARTICLE TITLE
Evaluating the sustainable cultivation of 'Fuji' apples: suitable crop load and the impact of chemical thinning agents on fruit quality and transcription
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