Pub Date : 2025-06-16DOI: 10.1016/j.cropd.2025.100109
Yu-Xiao Wang , Jian-Hong Xu
Plants frequently encounter diverse abiotic stresses, including high temperature, low temperature, drought, salinity, and heavy metal contamination during their growth and development. These environmental challenges disrupt cellular homeostasis, impacting cell membrane stability, osmotic regulation, ionic composition, thereby leading to protein misfolding and the over-accumulation of reactive oxygen species (ROS). Heat shock transcription factors (HSFs) play a crucial role in plant stress response and adaptation by regulating the transcription of heat shock protein (HSP) genes and other stress-inducible genes. This process is integral to plant resilience against adverse conditions and other physiological functions. This review synthesizes the structure features, classification, regulatory mechanisms, and functional roles of plant HSFs in response to abiotic stresses such as high and low temperature, drought and salinity. Furthermore, we discuss future research directions, aiming to provide a theoretical guidance and genetic resources for enhancing crop stress tolerance through genetic improvement.
{"title":"The heat shock transcription factors regulate response mechanisms to abiotic stresses in plants","authors":"Yu-Xiao Wang , Jian-Hong Xu","doi":"10.1016/j.cropd.2025.100109","DOIUrl":"10.1016/j.cropd.2025.100109","url":null,"abstract":"<div><div>Plants frequently encounter diverse abiotic stresses, including high temperature, low temperature, drought, salinity, and heavy metal contamination during their growth and development. These environmental challenges disrupt cellular homeostasis, impacting cell membrane stability, osmotic regulation, ionic composition, thereby leading to protein misfolding and the over-accumulation of reactive oxygen species (ROS). Heat shock transcription factors (HSFs) play a crucial role in plant stress response and adaptation by regulating the transcription of heat shock protein (HSP) genes and other stress-inducible genes. This process is integral to plant resilience against adverse conditions and other physiological functions. This review synthesizes the structure features, classification, regulatory mechanisms, and functional roles of plant HSFs in response to abiotic stresses such as high and low temperature, drought and salinity. Furthermore, we discuss future research directions, aiming to provide a theoretical guidance and genetic resources for enhancing crop stress tolerance through genetic improvement.</div></div>","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"4 3","pages":"Article 100109"},"PeriodicalIF":0.0,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144656532","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mutations were induced through chemical mutagens to increase the genetic variability for the development of various mutants in M2 generation from genetic background of Capsicum annuum L. Main objective of this study was to identify mutants and to assess the genetic diversity in EMS, MMS, Cd(NO3)2 and Pb(NO3)2 induced M2 populations of Capsicum annuum L. Mutant phenotypes were categorized into sub-categories on the basis of their plant growth and morphological appearance, including plant habit, leaf, flower, fruit, and root. Mean value and genetic parameters such as genetic coefficient of variance, heritability and genetic gain were evaluated in quantitative traits. Inter-population differences were also carried out through analysis of variance. Enhanced heritability and genetic advance with high genetic coefficient variation in yield attributing traits provide an opportunity for the improvement of Capsicum annuum L. through phenotypic selection. In the present result, enhanced mean value at lower concentrations of mutagens in quantitative traits could endorse the improvement of mutant lines over their parental lines. Numbers of fruit per plant and 1000-seed weight were main priority traits in selection of high-yielding mutants and have a strong association with yield. The cluster analysis revealed that three divergent groups of Capsicum annuum L. with parent genotypes in an independent group showed high efficacy of mutagens. Genetic divergence among the cluster populations provides more opportunities to use chemical mutagens for inducing heritable changes in genetic material of Capsicum annuum L. and for further improvement of desirable traits. Mutants selected from treatments, including EMS1, EMS2, EMS3, MMS1 and MMS2, and Pb1, Pb2, and Cd1 could be used to develop an efficient and fast crop variety with desirable traits, and the mutagen EMS and MMS are more effective than Cd(NO3)2 and Pb(NO3)2.
{"title":"Qualitative and quantitative characterization of mutations and genetic diversity analysis in M2 populations of chilli (Capsicum annuum L.)","authors":"Nazarul Hasan , Sana Choudhary , Neha Naaz , Nidhi Sharma , Megha Budakoti , Dinesh Chandra Joshi , Mahendar Singh Bhinda , Rafiul Amin Laskar","doi":"10.1016/j.cropd.2025.100108","DOIUrl":"10.1016/j.cropd.2025.100108","url":null,"abstract":"<div><div>Mutations were induced through chemical mutagens to increase the genetic variability for the development of various mutants in M<sub>2</sub> generation from genetic background of <em>Capsicum annuum</em> L. Main objective of this study was to identify mutants and to assess the genetic diversity in EMS, MMS, Cd(NO<sub>3</sub>)<sub>2</sub> and Pb(NO<sub>3</sub>)<sub>2</sub> induced M<sub>2</sub> populations of <em>Capsicum annuum</em> L. Mutant phenotypes were categorized into sub-categories on the basis of their plant growth and morphological appearance, including plant habit, leaf, flower, fruit, and root. Mean value and genetic parameters such as genetic coefficient of variance, heritability and genetic gain were evaluated in quantitative traits. Inter-population differences were also carried out through analysis of variance. Enhanced heritability and genetic advance with high genetic coefficient variation in yield attributing traits provide an opportunity for the improvement of <em>Capsicum annuum</em> L. through phenotypic selection. In the present result, enhanced mean value at lower concentrations of mutagens in quantitative traits could endorse the improvement of mutant lines over their parental lines. Numbers of fruit per plant and 1000-seed weight were main priority traits in selection of high-yielding mutants and have a strong association with yield. The cluster analysis revealed that three divergent groups of <em>Capsicum annuum</em> L. with parent genotypes in an independent group showed high efficacy of mutagens. Genetic divergence among the cluster populations provides more opportunities to use chemical mutagens for inducing heritable changes in genetic material of <em>Capsicum annuum</em> L. and for further improvement of desirable traits. Mutants selected from treatments, including EMS1, EMS2, EMS3, MMS1 and MMS2, and Pb1, Pb2, and Cd1 could be used to develop an efficient and fast crop variety with desirable traits, and the mutagen EMS and MMS are more effective than Cd(NO<sub>3</sub>)<sub>2</sub> and Pb(NO<sub>3</sub>)<sub>2</sub>.</div></div>","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"4 3","pages":"Article 100108"},"PeriodicalIF":0.0,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144656531","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-04-17DOI: 10.1016/j.cropd.2025.100103
Qingshuo Gu , Shasha Liu , Zuhua He , Xiangzong Meng , Yiwen Deng
Plants defend against pathogens by employing intracellular NLR (nucleotide-binding leucine-rich repeat) receptors to detect pathogen effectors and initiate immune responses. While some NLRs function independently, increasing evidence reveals that many NLRs act in single, pairs or within immune networks, involving cooperative or antagonistic interactions mediated by domains such as TIR, CC, or integrated decoy domains. Recent structural breakthroughs have shown how NLRs assemble into oligomeric resistosomes, such as ZAR1 and Sr35 forming Ca2+-permeable channels, and TNL resistosomes acting as NADases to generate signaling molecules. These molecules are sensed by EDS1–PAD4 or EDS1–SAG101 complexes, which subsequently activate helper NLRs like ADR1s and NRG1s to mediate defense signaling and cell death. Moreover, novel regulatory mechanisms and negative regulators are being uncovered. These advances offer mechanistic insights into the NLR immune network and provide valuable insight into novel R gene design and molecular breeding for crop disease resistance.
{"title":"NLRs in plant immunity: Structural insights and molecular mechanisms","authors":"Qingshuo Gu , Shasha Liu , Zuhua He , Xiangzong Meng , Yiwen Deng","doi":"10.1016/j.cropd.2025.100103","DOIUrl":"10.1016/j.cropd.2025.100103","url":null,"abstract":"<div><div>Plants defend against pathogens by employing intracellular NLR (nucleotide-binding leucine-rich repeat) receptors to detect pathogen effectors and initiate immune responses. While some NLRs function independently, increasing evidence reveals that many NLRs act in single, pairs or within immune networks, involving cooperative or antagonistic interactions mediated by domains such as TIR, CC, or integrated decoy domains. Recent structural breakthroughs have shown how NLRs assemble into oligomeric resistosomes, such as ZAR1 and Sr35 forming Ca<sup>2+</sup>-permeable channels, and TNL resistosomes acting as NADases to generate signaling molecules. These molecules are sensed by EDS1–PAD4 or EDS1–SAG101 complexes, which subsequently activate helper NLRs like ADR1s and NRG1s to mediate defense signaling and cell death. Moreover, novel regulatory mechanisms and negative regulators are being uncovered. These advances offer mechanistic insights into the NLR immune network and provide valuable insight into novel <em>R</em> gene design and molecular breeding for crop disease resistance.</div></div>","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"4 2","pages":"Article 100103"},"PeriodicalIF":0.0,"publicationDate":"2025-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143855206","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-03-26DOI: 10.1016/j.cropd.2025.100102
Mengzhu Zhang , Wu Jiao , Xinyu Jiang , Jinhui Wang , Longfei Wang , Wenxue Ye , Yue Wang , Qingshan Chen , Dawei Xin , Qingxin Song
Soybean seeds are a major source of protein and oil for human and animal nutrition. The molecular mechanisms underlying seed weight regulation, especially through epigenetic processes, are still poorly understood in soybean. Here, we reveal that a DNA demethylase gene, GmDMEa, underlies a genetic locus controlling seed weight through genome-wide association studies of 316 soybean accessions. Disruption of GmDMEa by CRISPR/Cas9 significantly increases seed weight and yield per plant accompanied with increased DNA methylation levels in the specific genomic regions which are demethylated in endosperm relative to embryo. GmDMEa is involved in activation of the endosperm-preferred genes that are negatively correlated with seed weight. Furthermore, DNA methylation variations induce significant changes of chromatin accessibility in endosperm. Notably, allelic variations of GmDMEa were artificially selected during soybean domestication. These findings reveal the role of dynamic DNA methylation in regulation of seed weight and provide a valuable gene resource for soybean breeding.
{"title":"Control of seed weight by a DNA demethylase in soybean","authors":"Mengzhu Zhang , Wu Jiao , Xinyu Jiang , Jinhui Wang , Longfei Wang , Wenxue Ye , Yue Wang , Qingshan Chen , Dawei Xin , Qingxin Song","doi":"10.1016/j.cropd.2025.100102","DOIUrl":"10.1016/j.cropd.2025.100102","url":null,"abstract":"<div><div>Soybean seeds are a major source of protein and oil for human and animal nutrition. The molecular mechanisms underlying seed weight regulation, especially through epigenetic processes, are still poorly understood in soybean. Here, we reveal that a DNA demethylase gene, <em>GmDMEa</em>, underlies a genetic locus controlling seed weight through genome-wide association studies of 316 soybean accessions. Disruption of <em>GmDMEa</em> by CRISPR/Cas9 significantly increases seed weight and yield per plant accompanied with increased DNA methylation levels in the specific genomic regions which are demethylated in endosperm relative to embryo. <em>GmDMEa</em> is involved in activation of the endosperm-preferred genes that are negatively correlated with seed weight. Furthermore, DNA methylation variations induce significant changes of chromatin accessibility in endosperm. Notably, allelic variations of <em>GmDMEa</em> were artificially selected during soybean domestication. These findings reveal the role of dynamic DNA methylation in regulation of seed weight and provide a valuable gene resource for soybean breeding.</div></div>","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"4 2","pages":"Article 100102"},"PeriodicalIF":0.0,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143859235","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-03-21DOI: 10.1016/j.cropd.2025.100101
Sivamathini Rajappa , Prakash Kumar
Plant chloride transporters are pivotal for preserving turgor pressure, pH, and cellular ion balance while adapting to salinity stress. We identified a salt-responsive gene, AoCLCf from Avicennia officinalis, which belongs to the chloride channel (CLC) family, and it shares significant sequence similarity with its Arabidopsis counterpart, AtCLCf. Through functional characterization in yeast mutants and Arabidopsis plants, we found that AoCLCf expression was induced primarily in roots under salt stress. Subcellular localization revealed a salt-induced translocation of GFP-AoCLCf from the Golgi apparatus to the plasma membrane. Expression of AoCLCf in the Saccharomyces cerevisiae mutant strain Δgef1 helped to rescue the growth of the mutant at high NaCl concentrations (up to 1.25M). Moreover, constitutive expression of AoCLCf in wild-type Arabidopsis significantly enhanced salt tolerance, as evidenced by increased seed germination rates, and improved seedling growth (greater root and shoot length) under 150 mM NaCl treatment. Spectrofluorimetric assays using liposomes embedded with recombinant AoCLCf protein showed that it functions as a chloride channel. These findings underscore the pivotal role of AoCLCf in improving salt stress tolerance through the maintenance of cellular ion homeostasis.
植物氯离子转运体是维持膨压、pH值和细胞离子平衡的关键，同时适应盐度胁迫。研究人员从拟南芥（Avicennia officinalis）中鉴定了一个盐响应基因AoCLCf，该基因属于氯离子通道（CLC）家族，与拟南芥对应基因AtCLCf具有显著的序列相似性。通过对酵母突变体和拟南芥的功能鉴定，我们发现盐胁迫下AoCLCf主要在根中表达。亚细胞定位显示盐诱导GFP-AoCLCf从高尔基体转移到质膜。AoCLCf在酿酒酵母（Saccharomyces cerevisiae）突变株Δgef1中的表达有助于在高NaCl浓度（高达1.25M）下挽救突变体的生长。此外，在150 mM NaCl处理下，AoCLCf在野生型拟南芥中的组成性表达显著增强了耐盐性，表现为种子发芽率提高，幼苗生长（根和茎长增加）改善。用包埋重组AoCLCf蛋白的脂质体进行荧光光谱分析，发现其具有氯离子通道的功能。这些发现强调了AoCLCf通过维持细胞离子稳态在提高盐胁迫耐受性方面的关键作用。
{"title":"Heterologous expression of a chloride transporter gene AoCLCf from Avicennia officinalis enhances salt tolerance of Arabidopsis plants","authors":"Sivamathini Rajappa , Prakash Kumar","doi":"10.1016/j.cropd.2025.100101","DOIUrl":"10.1016/j.cropd.2025.100101","url":null,"abstract":"<div><div>Plant chloride transporters are pivotal for preserving turgor pressure, pH, and cellular ion balance while adapting to salinity stress. We identified a salt-responsive gene, <em>AoCLCf</em> from <em>Avicennia officinalis</em>, which belongs to the chloride channel (CLC) family, and it shares significant sequence similarity with its <em>Arabidopsis</em> counterpart, <em>AtCLCf</em>. Through functional characterization in yeast mutants and <em>Arabidopsis</em> plants, we found that <em>AoCLCf</em> expression was induced primarily in roots under salt stress. Subcellular localization revealed a salt-induced translocation of GFP-AoCLCf from the Golgi apparatus to the plasma membrane. Expression of <em>AoCLCf</em> in the <em>Saccharomyces cerevisiae</em> mutant strain <em>Δgef1</em> helped to rescue the growth of the mutant at high NaCl concentrations (up to 1.25M). Moreover, constitutive expression of <em>AoCLCf</em> in wild-type <em>Arabidopsis</em> significantly enhanced salt tolerance, as evidenced by increased seed germination rates, and improved seedling growth (greater root and shoot length) under 150 mM NaCl treatment. Spectrofluorimetric assays using liposomes embedded with recombinant AoCLCf protein showed that it functions as a chloride channel. These findings underscore the pivotal role of AoCLCf in improving salt stress tolerance through the maintenance of cellular ion homeostasis.</div></div>","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"4 2","pages":"Article 100101"},"PeriodicalIF":0.0,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143859234","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-28DOI: 10.1016/j.cropd.2025.100100
Aishwarya Ashok Gaude, Siddhi Kashinath Jalmi
Secondary metabolites represnt are diverse array of plant-synthesized compounds that, while not essential for growth and development, play crucial roles in plant defense against biotic and abiotic stresses, attracting pollinators and seed dispersers, and facilating adaptation to environmental challenges The biosynthesis of these secondary metabolites, incuding alkaloids, terpenoids, phenolics, and flavonoids is tightly regulated through multiple pathways, particularly under stress conditions which enables the plant to tolerate the stressful environment. Understanding how environmental stresses modulate secondary metabolite biosynthesis can be harnessed to develop stress-resistant crops and enhance the production of commercially and pharmaceutically valuable compounds by utilizing stress as an elicitor. This review provides a comprehensive overview of the current understanding of the transcriptional regulation of secondary metabolite pathways, with a focus on key classes such as flavonoids, terpenoids, and terpenoid indole alkaloids in response to abiotic stresses (e.g. salinity, drought, light, and temperature) and biotic stress. We highlight the critical roles of transcription factors like MYB, bHLH, and WRKY in regulating these pathways and their contribution to plant stress tolerance. This comprehensive analysis offers insights into improving crop resilience and enabling the sustainable production of high-value phytochemicals through advanced understanding of secondary metabolite regulation.
{"title":"Environmental stress induced biosynthesis of plant secondary metabolites- transcriptional regulation as a key","authors":"Aishwarya Ashok Gaude, Siddhi Kashinath Jalmi","doi":"10.1016/j.cropd.2025.100100","DOIUrl":"10.1016/j.cropd.2025.100100","url":null,"abstract":"<div><div>Secondary metabolites represnt are diverse array of plant-synthesized compounds that, while not essential for growth and development, play crucial roles in plant defense against biotic and abiotic stresses, attracting pollinators and seed dispersers, and facilating adaptation to environmental challenges The biosynthesis of these secondary metabolites, incuding alkaloids, terpenoids, phenolics, and flavonoids is tightly regulated through multiple pathways, particularly under stress conditions which enables the plant to tolerate the stressful environment. Understanding how environmental stresses modulate secondary metabolite biosynthesis can be harnessed to develop stress-resistant crops and enhance the production of commercially and pharmaceutically valuable compounds by utilizing stress as an elicitor. This review provides a comprehensive overview of the current understanding of the transcriptional regulation of secondary metabolite pathways, with a focus on key classes such as flavonoids, terpenoids, and terpenoid indole alkaloids in response to abiotic stresses (e.g. salinity, drought, light, and temperature) and biotic stress. We highlight the critical roles of transcription factors like MYB, bHLH, and WRKY in regulating these pathways and their contribution to plant stress tolerance. This comprehensive analysis offers insights into improving crop resilience and enabling the sustainable production of high-value phytochemicals through advanced understanding of secondary metabolite regulation.</div></div>","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"4 2","pages":"Article 100100"},"PeriodicalIF":0.0,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143873895","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-01DOI: 10.1016/j.cropd.2024.100091
Xin Liu , Wenjie Yue , Shiqi Lin, Yuxian Yang, Tong Chen, Xiaowen Shi
Using artificial chromosomes in maize breeding allows for site-specific integration of multigene stacks, effectively overcoming the limitations of conventional transgenic approaches. The maize B chromosome, which is dispensable and highly heterochromatic, has minimal impact on phenotypes at low copy numbers, making it a promising platform for engineering artificial chromosomes. However, recent studies have demonstrated that the maize B chromosome can impact gene expression and recombination on the A chromosome. Understanding the genetic characteristics of the B chromosomes and their impact on gene expression is essential for their application in artificial chromosome construction. Despite advancements in elucidating how the B chromosome affects A chromosome expression, the role of long non-coding RNAs (lncRNAs) in this context remains unclear. In this study, we analyzed the RNA-seq data from leaf tissue of plants with 0–7 B chromosomes, identifying a total of 1614 lncRNAs, including 1516 A chromosome-located and 98 B chromosome-located lncRNAs, 72 of which are specific to the B chromosome. While A-located lncRNAs show greater dependence on the mere presence of the B chromosome, the expression of B-located lncRNAs is significantly affected by the number of B chromosomes present. Regulatory networks constructed in this study suggest that B-located lncRNAs may drive the differential expression of A chromosome-located transcription factors and genes associated with circadian rhythm regulation, indicating their regulatory role in A chromosome gene expression.
{"title":"Effect of the B chromosome-located long non-coding RNAs on gene expression in maize","authors":"Xin Liu , Wenjie Yue , Shiqi Lin, Yuxian Yang, Tong Chen, Xiaowen Shi","doi":"10.1016/j.cropd.2024.100091","DOIUrl":"10.1016/j.cropd.2024.100091","url":null,"abstract":"<div><div>Using artificial chromosomes in maize breeding allows for site-specific integration of multigene stacks, effectively overcoming the limitations of conventional transgenic approaches. The maize B chromosome, which is dispensable and highly heterochromatic, has minimal impact on phenotypes at low copy numbers, making it a promising platform for engineering artificial chromosomes. However, recent studies have demonstrated that the maize B chromosome can impact gene expression and recombination on the A chromosome. Understanding the genetic characteristics of the B chromosomes and their impact on gene expression is essential for their application in artificial chromosome construction. Despite advancements in elucidating how the B chromosome affects A chromosome expression, the role of long non-coding RNAs (lncRNAs) in this context remains unclear. In this study, we analyzed the RNA-seq data from leaf tissue of plants with 0–7 B chromosomes, identifying a total of 1614 lncRNAs, including 1516 A chromosome-located and 98 B chromosome-located lncRNAs, 72 of which are specific to the B chromosome. While A-located lncRNAs show greater dependence on the mere presence of the B chromosome, the expression of B-located lncRNAs is significantly affected by the number of B chromosomes present. Regulatory networks constructed in this study suggest that B-located lncRNAs may drive the differential expression of A chromosome-located transcription factors and genes associated with circadian rhythm regulation, indicating their regulatory role in A chromosome gene expression.</div></div>","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"4 1","pages":"Article 100091"},"PeriodicalIF":0.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143095653","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-01DOI: 10.1016/j.cropd.2024.100084
Zakaria El Gataa , Alemu Admas , Samira El Hanafi , Zakaria Kehel , Fatima Ezzahra Rachdad , Wuletaw Tadesse
Drought constitutes the main obstacle to agricultural productivity in the Central and West Asia and North Africa (CWANA) region, notably leading to substantial reductions in wheat yields due to terminal water stress. The adoption of drought-resistant wheat varieties appears to be a vital strategy to maintain wheat production in the face of climatic challenges. In this context, a study was conducted utilizing a set of 198 elite bread wheat genotypes developed at the International Center for Agricultural Research in the Dry Areas (ICARDA). This set of elite genotypes was evaluated at the Sidi Al-Aidi station in Morocco over two years (2021–2022), under rain-fed and irrigated conditions. Phenotypic assessments for grain yield and drought indices were performed, alongside genotyping the population using 15k SNP markers. These preparatory steps facilitated a genome-wide association study (GWAS) and genomic prediction, leveraging the Mixed Linear Model (MLM) to pinpoint marker-trait associations (MTAs) and candidate genes pertinent to grain yield and drought indices. The results manifested substantial variations in both grain yield and drought indices among the genotypes tested. Grain yield performance ranged from 0.34 to 2.57 t/ha under rain-fed conditions and 1.12 to 4.57 t/ha under irrigated scenarios. The comprehensive analysis identified 39 significant MTAs (p < 0.001) and 14 putative genes associated with drought indices and grain yield. Noteworthy is the marker “wsnp_Ex_c12127_19394952” on chromosome 5B, which displayed a significant correlation with grain yield in rain-fed environments. Furthermore, the most prominent marker linked to tolerance index (TOL) was “BobWhite_c42349_99”, situated on chromosome 5A and associated with the TraesCS5A02G498000 gene. This gene plays a critical role, encoding for catalase protein crucial for response to hydrogen peroxide. These markers could be used for marker-assisted selection in wheat breeding programs targeting drought tolerance.
{"title":"Genetic dissection and genomic prediction of drought indices in bread wheat (Triticum aestivum L.) genotypes","authors":"Zakaria El Gataa , Alemu Admas , Samira El Hanafi , Zakaria Kehel , Fatima Ezzahra Rachdad , Wuletaw Tadesse","doi":"10.1016/j.cropd.2024.100084","DOIUrl":"10.1016/j.cropd.2024.100084","url":null,"abstract":"<div><div>Drought constitutes the main obstacle to agricultural productivity in the Central and West Asia and North Africa (CWANA) region, notably leading to substantial reductions in wheat yields due to terminal water stress. The adoption of drought-resistant wheat varieties appears to be a vital strategy to maintain wheat production in the face of climatic challenges. In this context, a study was conducted utilizing a set of 198 elite bread wheat genotypes developed at the International Center for Agricultural Research in the Dry Areas (ICARDA). This set of elite genotypes was evaluated at the Sidi Al-Aidi station in Morocco over two years (2021–2022), under rain-fed and irrigated conditions. Phenotypic assessments for grain yield and drought indices were performed, alongside genotyping the population using 15k SNP markers. These preparatory steps facilitated a genome-wide association study (GWAS) and genomic prediction, leveraging the Mixed Linear Model (MLM) to pinpoint marker-trait associations (MTAs) and candidate genes pertinent to grain yield and drought indices. The results manifested substantial variations in both grain yield and drought indices among the genotypes tested. Grain yield performance ranged from 0.34 to 2.57 t/ha under rain-fed conditions and 1.12 to 4.57 t/ha under irrigated scenarios. The comprehensive analysis identified 39 significant MTAs (p < 0.001) and 14 putative genes associated with drought indices and grain yield. Noteworthy is the marker “<em>wsnp_Ex_c12127_19394952”</em> on chromosome 5B, which displayed a significant correlation with grain yield in rain-fed environments. Furthermore, the most prominent marker linked to tolerance index (TOL) was “BobWhite<em>_c42349_99”,</em> situated on chromosome 5A and associated with the <em>TraesCS5A02G498000</em> gene. This gene plays a critical role, encoding for catalase protein crucial for response to hydrogen peroxide. These markers could be used for marker-assisted selection in wheat breeding programs targeting drought tolerance.</div></div>","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"4 1","pages":"Article 100084"},"PeriodicalIF":0.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143135731","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-01DOI: 10.1016/j.cropd.2024.100090
Yuhan Zhou, Ziqi Zhou, Qingyao Shu
Synthetic genomics represents a formidable domain, encompassing the intentional design, construction, and manipulation of artificial genetic material to generate novel organisms or modify existing ones. In the context of crop breeding, molecular design breeding has emerged as a transformative force, ushering in notable progress. Nevertheless, the field faces unprecedented challenges, with climate change, population growth, and the scarcity of superior genetic resources exerting significant pressures. Recent strides in DNA synthesis methodologies, exemplified by innovative techniques like SCRaMbLE, have empowered the assembly and engineering of viral and microbial genomes. These advancements open promising avenues for the application of synthetic genomics in multicellular eukaryotic organisms, particularly in the realm of crop improvement. Synthetic genomics, with its capacity to manipulate gene sequences and regulatory elements, holds immense promise for the breeding of crops that meet diverse needs. Despite these advancements, the integration of synthetic genomics into crop breeding encounters hurdles, including the intricacies of complex crop genomes, the unpredictability introduced by epigenetic modification, and the limitations in achieving robust transformation processes. Addressing these challenges is pivotal to unlock the full potential of synthetic genomics in revolutionizing crop breeding. Looking ahead, we envision synthetic genomics in crop breeding not only as a scientific frontier but also as a burgeoning industry.
{"title":"Synthetic genomics in crop breeding: Evidence, opportunities and challenges","authors":"Yuhan Zhou, Ziqi Zhou, Qingyao Shu","doi":"10.1016/j.cropd.2024.100090","DOIUrl":"10.1016/j.cropd.2024.100090","url":null,"abstract":"<div><div>Synthetic genomics represents a formidable domain, encompassing the intentional design, construction, and manipulation of artificial genetic material to generate novel organisms or modify existing ones. In the context of crop breeding, molecular design breeding has emerged as a transformative force, ushering in notable progress. Nevertheless, the field faces unprecedented challenges, with climate change, population growth, and the scarcity of superior genetic resources exerting significant pressures. Recent strides in DNA synthesis methodologies, exemplified by innovative techniques like SCRaMbLE, have empowered the assembly and engineering of viral and microbial genomes. These advancements open promising avenues for the application of synthetic genomics in multicellular eukaryotic organisms, particularly in the realm of crop improvement. Synthetic genomics, with its capacity to manipulate gene sequences and regulatory elements, holds immense promise for the breeding of crops that meet diverse needs. Despite these advancements, the integration of synthetic genomics into crop breeding encounters hurdles, including the intricacies of complex crop genomes, the unpredictability introduced by epigenetic modification, and the limitations in achieving robust transformation processes. Addressing these challenges is pivotal to unlock the full potential of synthetic genomics in revolutionizing crop breeding. Looking ahead, we envision synthetic genomics in crop breeding not only as a scientific frontier but also as a burgeoning industry.</div></div>","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"4 1","pages":"Article 100090"},"PeriodicalIF":0.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143105205","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Innovation in agrotechnologies is urgently needed to fulfill the demand burden on food and agriculture industries. The key challenge in producing a high-quality, high-yielding crop is using quality seed and its identification. Seed quality identification in the seed industry often uses traditional methods based on manual observations, which are cumbersome and time-consuming. Still, there is always the risk of faulty reporting and non-uniformity in test results among different testing agencies. Because of the changing requirements of the seed industry, Artificial Intelligence (AI)-based tools and various methods have been developed to test the quality of seeds. AI-based tools have been extensively applied in different farming applications. This review explores these tools and strategies, including traditional, semi-automatic, or automated ones developed using machine learning. These include non-destructive techniques such as x-ray imaging, remote sensing, multispectral imaging, hyperspectral imaging, and near-infrared (NIR) spectroscopy, which are less expensive and time and/or labor-savings. Furthermore, we discuss the characteristics of AI-based techniques for depth analysis and their application in various aspects of seed quality, including seed vigor, seed health, seed germination, and seed viability. Lastly, we furhter evaluate the challenges of these methods and how they will provide healthy seeds to each farmer in the future and increase the overall production of crops. We propose to leverage AI-based tools to bridge the knowledge gap between traditional screening methods and integration of advanced technologies for better screening of crop seeds.
{"title":"Artificial intelligence-based tools for next-generation seed quality analysis","authors":"Sumeet Kumar Singh , Rashmi Jha , Saurabh Pandey , Chander Mohan , Chetna , Saipayan Ghosh , Satish Kumar Singh , Sarita Kumari , Ashutosh Singh","doi":"10.1016/j.cropd.2024.100094","DOIUrl":"10.1016/j.cropd.2024.100094","url":null,"abstract":"<div><div>Innovation in agrotechnologies is urgently needed to fulfill the demand burden on food and agriculture industries. The key challenge in producing a high-quality, high-yielding crop is using quality seed and its identification. Seed quality identification in the seed industry often uses traditional methods based on manual observations, which are cumbersome and time-consuming. Still, there is always the risk of faulty reporting and non-uniformity in test results among different testing agencies. Because of the changing requirements of the seed industry, Artificial Intelligence (AI)-based tools and various methods have been developed to test the quality of seeds. AI-based tools have been extensively applied in different farming applications. This review explores these tools and strategies, including traditional, semi-automatic, or automated ones developed using machine learning. These include non-destructive techniques such as x-ray imaging, remote sensing, multispectral imaging, hyperspectral imaging, and near-infrared (NIR) spectroscopy, which are less expensive and time and/or labor-savings. Furthermore, we discuss the characteristics of AI-based techniques for depth analysis and their application in various aspects of seed quality, including seed vigor, seed health, seed germination, and seed viability. Lastly, we furhter evaluate the challenges of these methods and how they will provide healthy seeds to each farmer in the future and increase the overall production of crops. We propose to leverage AI-based tools to bridge the knowledge gap between traditional screening methods and integration of advanced technologies for better screening of crop seeds.</div></div>","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"4 1","pages":"Article 100094"},"PeriodicalIF":0.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143135729","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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