Proteomics enables the comprehensive analysis of proteins that drive cells and is thus the ultimate method for profiling biological systems. However, proteomics analyses are time‐consuming and expensive, which has limited their applications to basic science and advanced medical research. The recent development of technologies enabling the generalization of proteomics has led to its application in new fields. Artificial intelligence (AI) is particularly useful for mining of proteomics data to yield new knowledge, as it allows for the integration of a wide variety of metadata—information considered necessary to explain experimental data. Recent improvements in the capabilities of AI have facilitated the practical and social implementation of proteomics. In this review, we describe how AI proteomics has expanded the scope of biological testing and discuss its potential and prospects for applications in agriculture. The potential of AI proteomics to provide detailed information on the state of seed germination and dormancy is discussed. In addition, we will discuss results of an investigation into barley leaves using high‐throughput proteomics technology, which is the fundamental technology of AI proteomics. In the future, increasing the amount of data and analyzing it with AI is likely to yield insights that were not previously available. Furthermore, the introduction of this technology into the field is expected to enable more accurate and effective crop management.
{"title":"Toward the application of artificial intelligence (AI) proteomics in the agriculture","authors":"Nobuhiro Hayashi, Sing Ying Wong, Yudai Hiratsuka, Youko Oono, Shingo Nakamura","doi":"10.1002/csc2.70205","DOIUrl":"https://doi.org/10.1002/csc2.70205","url":null,"abstract":"Proteomics enables the comprehensive analysis of proteins that drive cells and is thus the ultimate method for profiling biological systems. However, proteomics analyses are time‐consuming and expensive, which has limited their applications to basic science and advanced medical research. The recent development of technologies enabling the generalization of proteomics has led to its application in new fields. Artificial intelligence (AI) is particularly useful for mining of proteomics data to yield new knowledge, as it allows for the integration of a wide variety of metadata—information considered necessary to explain experimental data. Recent improvements in the capabilities of AI have facilitated the practical and social implementation of proteomics. In this review, we describe how AI proteomics has expanded the scope of biological testing and discuss its potential and prospects for applications in agriculture. The potential of AI proteomics to provide detailed information on the state of seed germination and dormancy is discussed. In addition, we will discuss results of an investigation into barley leaves using high‐throughput proteomics technology, which is the fundamental technology of AI proteomics. In the future, increasing the amount of data and analyzing it with AI is likely to yield insights that were not previously available. Furthermore, the introduction of this technology into the field is expected to enable more accurate and effective crop management.","PeriodicalId":10849,"journal":{"name":"Crop Science","volume":"233 1","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145784826","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Sheila Scheffel, Bettina Lado, Fernando Pérez de Vida, Federico Molina, Juan D. Arbeláez, Juan E. Rosas
Increasing selection accuracy for parental lines in the early stages of a breeding program can significantly shorten the breeding cycle and accelerate genetic gain. Public breeding programs have limited resources, which in many cases implies not having enough funds for genomic selection. In this study, we propose a strategy that allows leveraging a data source that is often overlooked: the breeding program's historical data. We evaluated the impact of incorporating historical data through multi‐environment analysis for selection at early stages of evaluation in a public breeding program. Two distinct breeding goals were assessed: line advancement and parent selection. For the first objective we used available phenotypic data, and for the second objective we leveraged existing pedigree records in addition to the phenotypic data. The evaluation strategy employed replicated the breeding program's structure, accounting for the timing of data availability. We investigated five prediction strategies, starting from single trial analysis, incorporating one or 5 years of historical data, and including or not a genotype by environment interaction term. To compare the prediction strategies, we considered grain yield phenotypic variance partition and predictive ability. Joint analysis of multiple trials and environments led to more accurate estimations of variance components and higher predictive ability for early selection of parents and line advancement. Additionally, we found that modeling genotype by environment interaction did not consistently enhance predictive ability. This study highlights the benefits of joint analyses of multi‐environment trials for early selection of parents and lines in breeding programs.
{"title":"Use of historical data improves early selection in a public rice breeding program","authors":"Sheila Scheffel, Bettina Lado, Fernando Pérez de Vida, Federico Molina, Juan D. Arbeláez, Juan E. Rosas","doi":"10.1002/csc2.70211","DOIUrl":"https://doi.org/10.1002/csc2.70211","url":null,"abstract":"Increasing selection accuracy for parental lines in the early stages of a breeding program can significantly shorten the breeding cycle and accelerate genetic gain. Public breeding programs have limited resources, which in many cases implies not having enough funds for genomic selection. In this study, we propose a strategy that allows leveraging a data source that is often overlooked: the breeding program's historical data. We evaluated the impact of incorporating historical data through multi‐environment analysis for selection at early stages of evaluation in a public breeding program. Two distinct breeding goals were assessed: line advancement and parent selection. For the first objective we used available phenotypic data, and for the second objective we leveraged existing pedigree records in addition to the phenotypic data. The evaluation strategy employed replicated the breeding program's structure, accounting for the timing of data availability. We investigated five prediction strategies, starting from single trial analysis, incorporating one or 5 years of historical data, and including or not a genotype by environment interaction term. To compare the prediction strategies, we considered grain yield phenotypic variance partition and predictive ability. Joint analysis of multiple trials and environments led to more accurate estimations of variance components and higher predictive ability for early selection of parents and line advancement. Additionally, we found that modeling genotype by environment interaction did not consistently enhance predictive ability. This study highlights the benefits of joint analyses of multi‐environment trials for early selection of parents and lines in breeding programs.","PeriodicalId":10849,"journal":{"name":"Crop Science","volume":"46 1","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145784827","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Kairong Duan, Jiawei Song, Chengbin Qiao, Bi Zhang, Hao Xu, Donghua Ma, Jie Ran, Yue Dong, Ying Zhu, Shuaiguo Ma, Chengke Luo, Peifu Li, Lei Tian
The escalating issue of global soil salinization has significantly impacted the growth and productivity of rice ( Oryza sativa L). To investigate the mechanisms underlying rice seedlings’ response to salt stress, transcriptome analysis to examine gene expression changes in salt‐tolerant and salt‐sensitive rice varieties was conducted. Salt‐tolerant landrace rice, Faguodao, and salt‐sensitive cultivar rice, Nipponbare, were used in this study. Both were subjected to 125 mM NaCl treatment at the seedling stage, and transcriptome sequencing was employed to analyze stress‐responsive genes and regulatory networks. Differentially expressed genes in both rice varieties under salt stress were enriched in the abscisic acid (ABA) and jasmonic acid (JA) hormone signaling pathways. Key genes such as OsABIL1 (ABA signaling component) and OsJAZ11 (JA pathway repressor) were identified as pivotal regulators. OsABIL1 promoted ion homeostasis under salt stress, while OsJAZ11 suppression indicated JA signaling inhibition, highlighting ABA's dominance in salt tolerance. Exogenous ABA application significantly alleviated salt stress damage in both genotypes by modulating ion homeostasis, whereas exogenous JA suppressed ABA‐responsive gene expression (e.g., OsPYL4 and OsbZIP23), indicating an antagonistic interaction between the two hormones. Under salt stress, exogenous ABA effectively alleviates the damage in both salt‐tolerant and salt‐sensitive rice. In contrast, exogenous JA suppressed the expression of ABA‐related genes, diminishing ABA's alleviating effects and indicating an antagonistic interaction between ABA and JA in regulating rice salt tolerance. This study provides valuable insights into the intricate regulatory network of ABA and JA regulating salt tolerance in rice seedlings.
全球土壤盐碱化问题日益严重，严重影响了水稻的生长和生产力。为了研究水稻幼苗对盐胁迫的响应机制，研究人员对耐盐和盐敏感水稻品种的基因表达变化进行了转录组分析。以耐盐的地方品种“法果稻”和盐敏感品种“日本裸”为研究对象。苗期均处理125 mM NaCl，利用转录组测序分析胁迫响应基因和调控网络。盐胁迫下两个水稻品种的差异表达基因均富集于脱落酸（ABA）和茉莉酸（JA）激素信号通路。关键基因OsABIL1 （ABA信号组分）和OsJAZ11 （JA通路抑制因子）被确定为关键调控因子。OsABIL1促进盐胁迫下离子稳态，而OsJAZ11的抑制表明JA信号被抑制，说明ABA在盐胁迫中的优势。外源ABA通过调节离子稳态，显著减轻了两种基因型的盐胁迫损伤，而外源JA抑制了ABA响应基因的表达（如OsPYL4和OsbZIP23），表明两种激素之间存在拮抗相互作用。在盐胁迫下，外源ABA能有效缓解耐盐水稻和盐敏感水稻的损伤。相比之下，外源JA抑制了ABA相关基因的表达，减弱了ABA的缓解作用，表明ABA和JA在调节水稻耐盐性方面存在拮抗作用。本研究对ABA和JA调控水稻幼苗耐盐性的复杂调控网络提供了有价值的见解。
{"title":"Abscisic acid and jasmonic acid crosstalk regulates seedling salt tolerance in rice varieties with different salinity tolerances","authors":"Kairong Duan, Jiawei Song, Chengbin Qiao, Bi Zhang, Hao Xu, Donghua Ma, Jie Ran, Yue Dong, Ying Zhu, Shuaiguo Ma, Chengke Luo, Peifu Li, Lei Tian","doi":"10.1002/csc2.70210","DOIUrl":"https://doi.org/10.1002/csc2.70210","url":null,"abstract":"The escalating issue of global soil salinization has significantly impacted the growth and productivity of rice ( <jats:italic>Oryza sativa</jats:italic> L). To investigate the mechanisms underlying rice seedlings’ response to salt stress, transcriptome analysis to examine gene expression changes in salt‐tolerant and salt‐sensitive rice varieties was conducted. Salt‐tolerant landrace rice, Faguodao, and salt‐sensitive cultivar rice, Nipponbare, were used in this study. Both were subjected to 125 mM NaCl treatment at the seedling stage, and transcriptome sequencing was employed to analyze stress‐responsive genes and regulatory networks. Differentially expressed genes in both rice varieties under salt stress were enriched in the abscisic acid (ABA) and jasmonic acid (JA) hormone signaling pathways. Key genes such as OsABIL1 (ABA signaling component) and OsJAZ11 (JA pathway repressor) were identified as pivotal regulators. OsABIL1 promoted ion homeostasis under salt stress, while OsJAZ11 suppression indicated JA signaling inhibition, highlighting ABA's dominance in salt tolerance. Exogenous ABA application significantly alleviated salt stress damage in both genotypes by modulating ion homeostasis, whereas exogenous JA suppressed ABA‐responsive gene expression (e.g., OsPYL4 and OsbZIP23), indicating an antagonistic interaction between the two hormones. Under salt stress, exogenous ABA effectively alleviates the damage in both salt‐tolerant and salt‐sensitive rice. In contrast, exogenous JA suppressed the expression of ABA‐related genes, diminishing ABA's alleviating effects and indicating an antagonistic interaction between ABA and JA in regulating rice salt tolerance. This study provides valuable insights into the intricate regulatory network of ABA and JA regulating salt tolerance in rice seedlings.","PeriodicalId":10849,"journal":{"name":"Crop Science","volume":"5 1","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145770716","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The re‐emergence of wheat stem rust disease, caused by Puccinia graminis Pers. f. sp. tritici (Eriks and E. Henn.) ( Pgt ), has recently been reported in Europe and North Africa. The prevalence of virulent Pgt genetic groups in Mediterranean basin countries, combined with the limited number of characterized resistance sources in durum wheat ( Triticum turgidum L., ssp. durum (Desf.) Husn.) germplasm, poses a serious threat to durum wheat production. In this study, we evaluated a collection of Mediterranean wheat accessions, mainly durum wheat, for seedling stage resistance to two Ug99 races (TTKTT and TTKSK) and the recently emerged and prevalent races TTRTF (aka Sicily race) and TKKTF. Although 24% of the genotypes exhibited resistant responses, phenotyping screening showed significant variation in seedling responses to the different races. Specifically, 27% and 30% of the genotypes were resistant to TTRTF and TTKSK, whereas only 17.5% and 18% exhibited resistance to TKKTF and TTKTT, respectively. Only 9.4% of genotypes ( n = 13) exhibited resistance or intermediate responses to all four tested races. Wheat accessions from Portugal, France, and Spain showed the highest resistance frequencies, ranging from 30% to 50%. Molecular analysis revealed the presence of the resistance gene Sr13 in 13 genotypes, eight of which originated from Tunisia (one landrace and seven varieties). The study demonstrates the importance of Mediterranean durum wheat accessions as sources of novel and diverse genetic resistance to the predominant races in the Mediterranean region, especially to the TTRTF, TKKTF, and Ug99 lineage races.
{"title":"Mediterranean durum wheat: Seedling resistance to Ug99 and recent emergent stem rust races","authors":"Wided Abdedayem, Mehran Patpour, Marwa Laribi, Amor Yahyaoui, Sonia Hamza, Mahbubjon Rahmatov, Sarrah Ben M'Barek","doi":"10.1002/csc2.70207","DOIUrl":"https://doi.org/10.1002/csc2.70207","url":null,"abstract":"The re‐emergence of wheat stem rust disease, caused by <jats:italic>Puccinia graminis</jats:italic> Pers. f. sp. <jats:italic>tritici</jats:italic> (Eriks and E. Henn.) ( <jats:italic>Pgt</jats:italic> ), has recently been reported in Europe and North Africa. The prevalence of virulent <jats:italic>Pgt</jats:italic> genetic groups in Mediterranean basin countries, combined with the limited number of characterized resistance sources in durum wheat ( <jats:italic>Triticum turgidum</jats:italic> L., ssp. <jats:italic>durum</jats:italic> (Desf.) Husn.) germplasm, poses a serious threat to durum wheat production. In this study, we evaluated a collection of Mediterranean wheat accessions, mainly durum wheat, for seedling stage resistance to two Ug99 races (TTKTT and TTKSK) and the recently emerged and prevalent races TTRTF (aka Sicily race) and TKKTF. Although 24% of the genotypes exhibited resistant responses, phenotyping screening showed significant variation in seedling responses to the different races. Specifically, 27% and 30% of the genotypes were resistant to TTRTF and TTKSK, whereas only 17.5% and 18% exhibited resistance to TKKTF and TTKTT, respectively. Only 9.4% of genotypes ( <jats:italic>n</jats:italic> = 13) exhibited resistance or intermediate responses to all four tested races. Wheat accessions from Portugal, France, and Spain showed the highest resistance frequencies, ranging from 30% to 50%. Molecular analysis revealed the presence of the resistance gene <jats:italic>Sr13</jats:italic> in 13 genotypes, eight of which originated from Tunisia (one landrace and seven varieties). The study demonstrates the importance of Mediterranean durum wheat accessions as sources of novel and diverse genetic resistance to the predominant races in the Mediterranean region, especially to the TTRTF, TKKTF, and Ug99 lineage races.","PeriodicalId":10849,"journal":{"name":"Crop Science","volume":"1 1","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145770715","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jeffrey D. Boehm, Nathan Palmer, Xiwen Cai, Fernando Miguez
Genetic gain is an annualized measure of trait improvement used to estimate plant breeding progress, wherein the performances of old versus new variety releases are compared over time. Herein, we present data from the United States Department of Agriculture‐coordinated hard winter wheat ( Triticum aestivum L.) Southern regional performance nursery (SRPN) collected from 1959 to 2024 for grain yield, grain volume weight, days‐to‐heading, and plant height and use it to estimate absolute and relative rates of genetic gain (loss) of the control cultivar Kharkof for winter wheats adapted to the Southern Great Plains of North America. Regression analyses revealed significant relative grain yield increases of 0.90% Kharkof year −1 and 24.4 kg ha −1 year −1 for the SRPN over the 66‐year period. Notwithstanding, nonlinear statistical modeling of SRPN relative and absolute grain yield datasets provided the most parsimonious fit of the data, revealing highly significant linear breakpoints (i.e., plateaus) beginning in 1998 for relative %Kharkof yield, with quadratic models best explaining absolute (kg ha −1 year −1 ) yield data for the region, suggesting a more gradual leveling off of grain yield over time instead of an abrupt breakpoint. Trends for both relative and absolute grain yield of 0.57% Kharkof year −1 and 15.4 kg ha −1 year −1 , respectively, since 1984 further demonstrate reduced annualized gains in comparison to the 66‐year trendlines. These broad‐sense, proxy estimates of genetic gain reported herein reconfirm that wheat breeding progress remains difficult in many marginal production environments constituting the US Southern Plains, but the parabolic best‐fit curve for absolute kg ha −1 year −1 grain yield of 5MP and all SRPN entries indicates that yield gains are still moderately increasing.
遗传增益是用于估计植物育种进展的性状改进的年度度量，其中新旧品种发布的性能随时间进行比较。在此，我们提供了来自美国农业部协调的硬冬小麦（Triticum aestivum L.）的数据。南方区域性能苗圃（SRPN）收集了1959年至2024年的粮食产量、籽粒体积重、日数比抽穗和株高，并利用它来估计适应北美南部大平原冬小麦的对照品种Kharkof的遗传增益（损失率）的绝对和相对比率。回归分析显示，在66年的时间里，SRPN的相对产量增加了0.90% （Kharkof - 1年）和24.4 kg （ha - 1年）。尽管如此，对SRPN相对和绝对粮食产量数据集的非线性统计建模提供了最简洁的数据拟合，揭示了1998年开始的相对%Kharkof产量的高度显著的线性断点（即高原），二次模型最好地解释了该地区的绝对（kg ha - 1年- 1）产量数据，表明粮食产量随着时间的推移逐渐趋于平稳，而不是突然的断点。1984年以来的相对和绝对粮食产量趋势分别为0.57%和15.4公斤公顷，进一步表明与66年的趋势线相比，年化收益有所减少。本文报道的这些广义的遗传增益的代理估计再次证实，在构成美国南部平原的许多边际生产环境中，小麦育种进展仍然困难，但5MP的绝对公斤公顷- 1年- 1谷物产量的抛物线最佳拟合曲线和所有SRPN项表明，产量增益仍在适度增加。
{"title":"Yield trends for genetic improvement of winter wheat ( Triticum aestivum L.) grain yield in the southern Great Plains of North America, 1959–2024","authors":"Jeffrey D. Boehm, Nathan Palmer, Xiwen Cai, Fernando Miguez","doi":"10.1002/csc2.70135","DOIUrl":"https://doi.org/10.1002/csc2.70135","url":null,"abstract":"Genetic gain is an annualized measure of trait improvement used to estimate plant breeding progress, wherein the performances of old versus new variety releases are compared over time. Herein, we present data from the United States Department of Agriculture‐coordinated hard winter wheat ( <jats:italic>Triticum aestivum</jats:italic> L.) Southern regional performance nursery (SRPN) collected from 1959 to 2024 for grain yield, grain volume weight, days‐to‐heading, and plant height and use it to estimate absolute and relative rates of genetic gain (loss) of the control cultivar Kharkof for winter wheats adapted to the Southern Great Plains of North America. Regression analyses revealed significant relative grain yield increases of 0.90% Kharkof year <jats:sup>−1</jats:sup> and 24.4 kg ha <jats:sup>−1</jats:sup> year <jats:sup>−1</jats:sup> for the SRPN over the 66‐year period. Notwithstanding, nonlinear statistical modeling of SRPN relative and absolute grain yield datasets provided the most parsimonious fit of the data, revealing highly significant linear breakpoints (i.e., plateaus) beginning in 1998 for relative %Kharkof yield, with quadratic models best explaining absolute (kg ha <jats:sup>−1</jats:sup> year <jats:sup>−1</jats:sup> ) yield data for the region, suggesting a more gradual leveling off of grain yield over time instead of an abrupt breakpoint. Trends for both relative and absolute grain yield of 0.57% Kharkof year <jats:sup>−1</jats:sup> and 15.4 kg ha <jats:sup>−1</jats:sup> year <jats:sup>−1</jats:sup> , respectively, since 1984 further demonstrate reduced annualized gains in comparison to the 66‐year trendlines. These broad‐sense, proxy estimates of genetic gain reported herein reconfirm that wheat breeding progress remains difficult in many marginal production environments constituting the US Southern Plains, but the parabolic best‐fit curve for absolute kg ha <jats:sup>−1</jats:sup> year <jats:sup>−1</jats:sup> grain yield of 5MP and all SRPN entries indicates that yield gains are still moderately increasing.","PeriodicalId":10849,"journal":{"name":"Crop Science","volume":"30 1","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145770714","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
In snap bean ( Phaseolus vulgaris L.) production, herbicides are essential for weed control, requiring crop tolerance to avoid injury. The study aimed to link genomic loci to agronomic traits, explore the extent of herbicide cross‐tolerance, and identify loci influencing seed vigor and herbicide tolerance traits. A panel was evaluated for seven agronomic traits and two measures of tolerance to eight herbicides. Genome‐wide association studies (GWASs) identified marker‐trait associations (MTA) and candidate genes. Heritability confirmed genetic control over agronomic traits. Seed weight and traits measuring seed and at‐flowering vigor showed positive correlations. Multilocus GWAS identified 179 MTA for seven agronomic traits, with 28 regions linked to multiple traits. Candidate genes included those involved in cell wall synthesis, DNA repair and methylation, radical oxygen species scavenging, and signal transduction. Identified candidate genes related to flowering provide insights into flowering control beyond TFL 1. Positive correlation between herbicide cross‐tolerance and seed vigor traits suggests shared mechanisms. Multi‐trait GWAS identified genomic regions linked to herbicide cross‐tolerance and seed vigor traits. Across all trait groupings, 69 multi‐trait MTAs were identified. Chromosomes 1, 2, 4, and 8 regions were associated with seed vigor measures under herbicide and control conditions in multiple analyses. Favorable alleles for stress tolerance operate independently of growth habit and ancestry and were present in higher frequencies in lines with Middle American ancestry. This research highlights genetic links between herbicide tolerance and plant fitness, identifying loci associated with agronomic traits, and provides resources for breeding of snap beans with enhanced resilience and agronomic performance.
{"title":"Linking herbicide cross‐tolerance to agronomic and seed vigor traits: A multi‐trait genome‐wide association study in snap bean ( Phaseolus vulgaris L.)","authors":"Ana Saballos, Martin M. Williams","doi":"10.1002/csc2.70201","DOIUrl":"https://doi.org/10.1002/csc2.70201","url":null,"abstract":"In snap bean ( <jats:italic>Phaseolus vulgaris</jats:italic> L.) production, herbicides are essential for weed control, requiring crop tolerance to avoid injury. The study aimed to link genomic loci to agronomic traits, explore the extent of herbicide cross‐tolerance, and identify loci influencing seed vigor and herbicide tolerance traits. A panel was evaluated for seven agronomic traits and two measures of tolerance to eight herbicides. Genome‐wide association studies (GWASs) identified marker‐trait associations (MTA) and candidate genes. Heritability confirmed genetic control over agronomic traits. Seed weight and traits measuring seed and at‐flowering vigor showed positive correlations. Multilocus GWAS identified 179 MTA for seven agronomic traits, with 28 regions linked to multiple traits. Candidate genes included those involved in cell wall synthesis, DNA repair and methylation, radical oxygen species scavenging, and signal transduction. Identified candidate genes related to flowering provide insights into flowering control beyond <jats:italic>TFL</jats:italic> 1. Positive correlation between herbicide cross‐tolerance and seed vigor traits suggests shared mechanisms. Multi‐trait GWAS identified genomic regions linked to herbicide cross‐tolerance and seed vigor traits. Across all trait groupings, 69 multi‐trait MTAs were identified. Chromosomes 1, 2, 4, and 8 regions were associated with seed vigor measures under herbicide and control conditions in multiple analyses. Favorable alleles for stress tolerance operate independently of growth habit and ancestry and were present in higher frequencies in lines with Middle American ancestry. This research highlights genetic links between herbicide tolerance and plant fitness, identifying loci associated with agronomic traits, and provides resources for breeding of snap beans with enhanced resilience and agronomic performance.","PeriodicalId":10849,"journal":{"name":"Crop Science","volume":"40 1","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145770717","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Emmanuel U. Nwachukwu, Jack D. Fry, Jacob C. Domenghini, Ross C. Braun
Tall fescue (TF) [ Schedonorus arundinaceus (Schreb.) Dumort.] continues to increase in popularity in the northern and transitional climatic zone of the United States because of its superior heat and drought tolerance compared to Kentucky bluegrass (KB) ( Poa pratensis L.). However, most turf‐type TF cultivars have a bunch‐type growth habit that hinders their potential to produce high sod strength for sod producers. New TF cultivars have been marketed as “spreading” or “rhizomatous” tall fescue (RTF); however, research is needed on establishment, rhizome, and sod strength characteristics. Repeated field experiments at Kansas State University were conducted to measure establishment speed and sod strength and handling at three harvests: 9, 10, and 12 months after planting. Additionally, controlled‐environment experiments were conducted to measure germination speed and rhizome characteristics. While TF cultivars had faster establishment speed and germination speed compared to KB, both bunch‐type TF and RTF cultivars did not produce similar high‐quality sod strength when compared to a 100% KB sod, which produced the highest sod strength across all three sod harvests. Controlled environment experiments revealed that KB cultivars produced ≥ 96% greater rhizome lengths compared to RTF after 4.3 months. Rhizome lengths averaged ≤3.1 mm in RTF compared to >80 mm in KB. However, there was no relationship present between rhizome characteristics and earliest sod strength data. Rhizome production and sod strength is considerably less in both bunch‐type TF and RTF compared to KB, and results will assist sod producers and turfgrass breeders in future selections to meet increasing challenges and market demands.
{"title":"Sod strength and rhizome characteristics of rhizomatous tall fescue","authors":"Emmanuel U. Nwachukwu, Jack D. Fry, Jacob C. Domenghini, Ross C. Braun","doi":"10.1002/csc2.70214","DOIUrl":"https://doi.org/10.1002/csc2.70214","url":null,"abstract":"Tall fescue (TF) [ <jats:italic>Schedonorus arundinaceus</jats:italic> (Schreb.) Dumort.] continues to increase in popularity in the northern and transitional climatic zone of the United States because of its superior heat and drought tolerance compared to Kentucky bluegrass (KB) ( <jats:italic>Poa pratensis</jats:italic> L.). However, most turf‐type TF cultivars have a bunch‐type growth habit that hinders their potential to produce high sod strength for sod producers. New TF cultivars have been marketed as “spreading” or “rhizomatous” tall fescue (RTF); however, research is needed on establishment, rhizome, and sod strength characteristics. Repeated field experiments at Kansas State University were conducted to measure establishment speed and sod strength and handling at three harvests: 9, 10, and 12 months after planting. Additionally, controlled‐environment experiments were conducted to measure germination speed and rhizome characteristics. While TF cultivars had faster establishment speed and germination speed compared to KB, both bunch‐type TF and RTF cultivars did not produce similar high‐quality sod strength when compared to a 100% KB sod, which produced the highest sod strength across all three sod harvests. Controlled environment experiments revealed that KB cultivars produced ≥ 96% greater rhizome lengths compared to RTF after 4.3 months. Rhizome lengths averaged ≤3.1 mm in RTF compared to >80 mm in KB. However, there was no relationship present between rhizome characteristics and earliest sod strength data. Rhizome production and sod strength is considerably less in both bunch‐type TF and RTF compared to KB, and results will assist sod producers and turfgrass breeders in future selections to meet increasing challenges and market demands.","PeriodicalId":10849,"journal":{"name":"Crop Science","volume":"3 1","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145765088","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Shelby Hammond, Malarvizhi Sathasivam, Benjamin Fallen, James Smith, William C. Bridges, Sachin Rustgi, Sruthi Narayanan
Breeding for heat tolerance in soybean [ Glycine max (L.) Merr.] is constrained by limited genetic diversity for heat tolerance, lack of efficient selection criteria, and incomplete knowledge of heat tolerance mechanisms. The objectives of this study were to characterize the heat tolerance of a soybean recombinant inbred line (RIL) population based on physiological traits defining leaf function, pollen viability, and yield, and identify genotypes and traits that can be included in breeding programs for heat tolerance selection. Field trials were conducted in South Carolina in 2022 and 2023 to test 192 RILs (derived from DS 25‐1 [heat‐tolerant] × DT97‐4290 [heat‐susceptible]), parental lines, and 12 check genotypes. Plants were initially grown at ambient temperatures, and the heat stress treatment (38°C–42°C for at least 4 h during the daytime) was established using heat tents for 14 days during the R2–R4 growth stages. RILs 22, 26, 38, 54, 78, and 115 were identified as the most heat‐tolerant, and the RILs 174, 182, and 192 as the most heat‐sensitive based on leaf physiological traits (chlorophyll index, chlorophyll fluorescence, lipid peroxidation, and photosynthesis), pollen viability, aboveground biomass, seed number, seed yield, and 100‐seed weight. Seed yield was positively correlated with chlorophyll index, photosynthesis, aboveground biomass, and seed number under heat stress. Aboveground biomass had the highest heritability ( H2 = 0.48), reinforcing its significance as a key selection criterion for heat tolerance in soybean. New heat‐tolerant germplasms identified in this research and the three physiological traits for improving selection efficiency provide valuable resources for soybean varietal development programs.
{"title":"Identification of new germplasm sources and physiological traits for breeding heat‐tolerant soybean varieties","authors":"Shelby Hammond, Malarvizhi Sathasivam, Benjamin Fallen, James Smith, William C. Bridges, Sachin Rustgi, Sruthi Narayanan","doi":"10.1002/csc2.70209","DOIUrl":"https://doi.org/10.1002/csc2.70209","url":null,"abstract":"Breeding for heat tolerance in soybean [ <jats:italic>Glycine max</jats:italic> (L.) Merr.] is constrained by limited genetic diversity for heat tolerance, lack of efficient selection criteria, and incomplete knowledge of heat tolerance mechanisms. The objectives of this study were to characterize the heat tolerance of a soybean recombinant inbred line (RIL) population based on physiological traits defining leaf function, pollen viability, and yield, and identify genotypes and traits that can be included in breeding programs for heat tolerance selection. Field trials were conducted in South Carolina in 2022 and 2023 to test 192 RILs (derived from DS 25‐1 [heat‐tolerant] × DT97‐4290 [heat‐susceptible]), parental lines, and 12 check genotypes. Plants were initially grown at ambient temperatures, and the heat stress treatment (38°C–42°C for at least 4 h during the daytime) was established using heat tents for 14 days during the R2–R4 growth stages. RILs 22, 26, 38, 54, 78, and 115 were identified as the most heat‐tolerant, and the RILs 174, 182, and 192 as the most heat‐sensitive based on leaf physiological traits (chlorophyll index, chlorophyll fluorescence, lipid peroxidation, and photosynthesis), pollen viability, aboveground biomass, seed number, seed yield, and 100‐seed weight. Seed yield was positively correlated with chlorophyll index, photosynthesis, aboveground biomass, and seed number under heat stress. Aboveground biomass had the highest heritability ( <jats:italic>H</jats:italic> <jats:sup>2</jats:sup> = 0.48), reinforcing its significance as a key selection criterion for heat tolerance in soybean. New heat‐tolerant germplasms identified in this research and the three physiological traits for improving selection efficiency provide valuable resources for soybean varietal development programs.","PeriodicalId":10849,"journal":{"name":"Crop Science","volume":"36 1","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145765085","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Valdenise Simone Melo Moulin Breda, Rogério Figueiredo Daher, Maxwel Rodrigues Nascimento, Josefa Grasiela Silva Santana, Moisés Ambrósio, Ana Kesia Faria Vidal, Rafael Souza Freitas, Alexandre Gomes de Souza, Paulo Ricardo dos Santos, Josilene Vargas Xavier, Geraldo de Amaral Gravina, Benedito Fernandes de Souza Filho, Ester da Silva Costa
Common bean ( Phaseolus vulgaris L.) is considered a staple of the Brazilian diet and one of the most important grains in the diets of populations in several countries across Latin America, Africa, and Asia, as it is an excellent source of proteins, vitamins, carbohydrates, minerals, and fiber. This study aimed to evaluate the adaptability and stability parameters of grain yield in black common bean using methods based on analysis of variance, as well as simple and two‐segment linear regression. The trials were conducted using a randomized block design with three replicates, in three municipalities, in 2016 and 2017, totaling six environments. Each experimental unit consisted of four 4‐m‐long rows, spaced 0.5 m apart, totaling a population of 240,000 plants ha −1 . The usable area comprised the two central rows, excluding 0.5 m from each end, totaling 3 m 2 . Six genotypes, including four elite lines, had yields above the overall mean and were considered the best adapted. The methodologies proposed by Eberhart and Russel, Wricke, Lin and Binns, and Cruz et al. showed agreement in identifying the Centro Nacional de Pesquisa em Feijão Preto (CNFP) 15684 inbred line as having broad phenotypic stability. The Eberhart and Russel method was effective in identifying genotypes with broad adaptability and high phenotypic stability, indicating the CNFP 15685 genotype for cultivation in the north and northwest regions of Rio de Janeiro. No ideal genotype—that is, one that is productive, adapted to unfavorable environments, responsive to environmental improvement, and highly stable—was identified by the method of Cruz et al.
{"title":"Genotype × environment interaction and estimates of grain yield adaptability and stability in black common bean genotypes in Brazil","authors":"Valdenise Simone Melo Moulin Breda, Rogério Figueiredo Daher, Maxwel Rodrigues Nascimento, Josefa Grasiela Silva Santana, Moisés Ambrósio, Ana Kesia Faria Vidal, Rafael Souza Freitas, Alexandre Gomes de Souza, Paulo Ricardo dos Santos, Josilene Vargas Xavier, Geraldo de Amaral Gravina, Benedito Fernandes de Souza Filho, Ester da Silva Costa","doi":"10.1002/csc2.70213","DOIUrl":"https://doi.org/10.1002/csc2.70213","url":null,"abstract":"Common bean ( <jats:italic>Phaseolus vulgaris</jats:italic> L.) is considered a staple of the Brazilian diet and one of the most important grains in the diets of populations in several countries across Latin America, Africa, and Asia, as it is an excellent source of proteins, vitamins, carbohydrates, minerals, and fiber. This study aimed to evaluate the adaptability and stability parameters of grain yield in black common bean using methods based on analysis of variance, as well as simple and two‐segment linear regression. The trials were conducted using a randomized block design with three replicates, in three municipalities, in 2016 and 2017, totaling six environments. Each experimental unit consisted of four 4‐m‐long rows, spaced 0.5 m apart, totaling a population of 240,000 plants ha <jats:sup>−1</jats:sup> . The usable area comprised the two central rows, excluding 0.5 m from each end, totaling 3 m <jats:sup>2</jats:sup> . Six genotypes, including four elite lines, had yields above the overall mean and were considered the best adapted. The methodologies proposed by Eberhart and Russel, Wricke, Lin and Binns, and Cruz et al. showed agreement in identifying the Centro Nacional de Pesquisa em Feijão Preto (CNFP) 15684 inbred line as having broad phenotypic stability. The Eberhart and Russel method was effective in identifying genotypes with broad adaptability and high phenotypic stability, indicating the CNFP 15685 genotype for cultivation in the north and northwest regions of Rio de Janeiro. No ideal genotype—that is, one that is productive, adapted to unfavorable environments, responsive to environmental improvement, and highly stable—was identified by the method of Cruz et al.","PeriodicalId":10849,"journal":{"name":"Crop Science","volume":"157 1","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145765083","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Namita Sinha, Dan Jeffers, Ramandeep Sharma, Raju Bheemanahalli, Vaughn Reed, W. Brien Henry, Ebrahiem Babiker, Dylan Williams, Jagman Dhillon
Fumonisins are mycotoxins produced by the fungal pathogen, Fusarium verticillioides, and they are widespread in corn (Zea mays L.), especially in the Southeastern United States. While there are several post-harvest mitigation strategies to reduce fumonisin, there are limited studies testing pre-harvest strategies. Therefore, field studies were conducted at two locations in Mississippi to examine the impact of agronomic practices in mitigating fumonisin accumulation in corn. The experiments were set up in a split-plot design, with nitrogen (N) (0, 112, 224, and 336 kg N ha−1) as main plot factor and combination of plant populations (PPs) (75,000, 87,500, 100,000, and 112,500 plants ha−1) and corn hybrids (H) with and without Bacillus thuringiensis (Bt) traits (DKC70-27 and 70-25, respectively, where DKC is Dekalb corn) as subplot factors. Ten ears per plot were inoculated with F. verticillioides for subsequent post-harvest fumonisin quantification. In 2024, fumonisin accumulation was significantly influenced by H × PP interaction (p < 0.05) and ear rot severity was influenced by N × PP interaction (p < 0.05) in Starkville, whereas in 2023, only the main treatments affected fumonisin accumulation in Starkville and Brooksville. Overall, the Bt hybrid showed significantly lower ear rot severity and fumonisin accumulation. Moreover, fumonisin accumulation decreased with an N rate of 112 kg N ha−1 in Starkville, without any noticeable differences at higher N rates. In summary, this study identified that the best preharvest strategy to mitigate fumonisin includes selecting hybrid with Bt traits for reducing insect injury to the ear, maintaining a planting density between 75,000 and 87,500 plants ha−1, and applying at least 112 kg N ha−1 for minimizing nitrogen deficiency.
伏马菌素是由真菌病原体，黄萎病镰刀菌产生的真菌毒素，它们广泛存在于玉米（Zea mays L.）中，特别是在美国东南部。虽然有几种收获后减少伏马菌素的缓解战略，但测试收获前战略的研究有限。因此，在密西西比州的两个地点进行了实地研究，以检查农艺措施对减轻伏马菌素在玉米中的积累的影响。试验采用分畦设计，以氮肥（0、112、224和336 kg N ha−1）为主要样区因子，植物群体（PPs）（75000、87500、100000和112500株ha−1）和具有和不具有苏云金芽孢杆菌（Bt）性状的玉米杂种(H)（分别为DKC70-27和70-25，其中DKC为Dekalb玉米）为次样区因子。每块10穗接种黄萎病菌，用于收获后的伏马菌素定量。2024年Starkville的伏马菌素积累受H × PP互作的显著影响（p < 0.05），穗腐病严重程度受N × PP互作的影响（p < 0.05），而2023年Starkville和Brooksville的伏马菌素积累仅受主要处理的影响。总体而言，Bt杂交品种表现出较低的穗腐病严重程度和伏马菌素积累。施氮量为112 kg N ha - 1时，伏马菌素积累量下降，在较高施氮量下无显著差异。综上所述，本研究确定了缓解伏马菌素的最佳收获前策略包括选择具有Bt性状的杂交品种以减少虫害，种植密度保持在75,000 ~ 87,500株ha - 1之间，施用至少112 kg N ha - 1以尽量减少氮缺乏。
{"title":"Hybrid, plant population, and nitrogen treatment: Impact on preharvest fumonisin contamination in corn (Zea mays)","authors":"Namita Sinha, Dan Jeffers, Ramandeep Sharma, Raju Bheemanahalli, Vaughn Reed, W. Brien Henry, Ebrahiem Babiker, Dylan Williams, Jagman Dhillon","doi":"10.1002/csc2.70200","DOIUrl":"https://doi.org/10.1002/csc2.70200","url":null,"abstract":"Fumonisins are mycotoxins produced by the fungal pathogen, <i>Fusarium verticillioides</i>, and they are widespread in corn (<i>Zea mays</i> L.), especially in the Southeastern United States. While there are several post-harvest mitigation strategies to reduce fumonisin, there are limited studies testing pre-harvest strategies. Therefore, field studies were conducted at two locations in Mississippi to examine the impact of agronomic practices in mitigating fumonisin accumulation in corn. The experiments were set up in a split-plot design, with nitrogen (N) (0, 112, 224, and 336 kg N ha<sup>−1</sup>) as main plot factor and combination of plant populations (PPs) (75,000, 87,500, 100,000, and 112,500 plants ha<sup>−1</sup>) and corn hybrids (H) with and without <i>Bacillus thuringiensis</i> (<i>Bt</i>) traits (DKC70-27 and 70-25, respectively, where DKC is Dekalb corn) as subplot factors. Ten ears per plot were inoculated with <i>F. verticillioides</i> for subsequent post-harvest fumonisin quantification. In 2024, fumonisin accumulation was significantly influenced by H × PP interaction (<i>p </i>< 0.05) and ear rot severity was influenced by N × PP interaction (<i>p </i>< 0.05) in Starkville, whereas in 2023, only the main treatments affected fumonisin accumulation in Starkville and Brooksville. Overall, the <i>Bt</i> hybrid showed significantly lower ear rot severity and fumonisin accumulation. Moreover, fumonisin accumulation decreased with an N rate of 112 kg N ha<sup>−1</sup> in Starkville, without any noticeable differences at higher N rates. In summary, this study identified that the best preharvest strategy to mitigate fumonisin includes selecting hybrid with <i>Bt</i> traits for reducing insect injury to the ear, maintaining a planting density between 75,000 and 87,500 plants ha<sup>−1</sup>, and applying at least 112 kg N ha<sup>−1</sup> for minimizing nitrogen deficiency.","PeriodicalId":10849,"journal":{"name":"Crop Science","volume":"166 1","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145753166","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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