Pub Date : 2025-04-30DOI: 10.1016/j.plgene.2025.100516
Sani Muhammad Tajo , Zhaoe Pan , K.M. Yusuf , Salisu Bello Sadau , Guowei Lv , Shoupu He , Xiaoli Geng , Xiongming Du
Cotton is one of the important fiber crops. Drought is the primary abiotic factor that restricts cotton growth and development and lowers its output. Plant LOX (lipoxygenases) genes catalyze the oxidation of polyunsaturated fatty acids into a variety of functional oxylipins. The LOX gene family has been thoroughly investigated under biotic and abiotic stressors; however, knowledge of their functions on callus induction and regeneration in cotton is still scarce. This study identified 34, 38, 23, and 20 LOX genes in the Gossypium hirsutum, Gossypium barbadense, Gossypium arboreum, and Gossypium raimondii, respectively. The LOX genes were found to be divided into three main categories, 9-LOX, 13-LOX Type I, and 13-LOX Type II. Three accessions of G. hirsutum were used to generate callus from hypocotyl, cotyledon, and shoot tip and we observed that the highest expression of the GhLOX genes were in the hypocotyl callus and most of LOX gene expression was up-regulated in one week callus and decreased in two week and four week callus except in the shoot tip induced callus in Jinmian 498. Virus-induced gene silencing of GhLOX5 (Gh_A02G037000) revealed that the growth of the silenced plant was significantly decreased compared to WT. Excised leaf water loss and relative electrolyte leakage levels were increased about 23 % and 12 % in the GhLOX5 silenced plant when compared to the WT. Compared to the WT, the silenced plant had significantly higher antioxidant activity (25 % in MDA content and 45 % in H2O2 content). The importance of LOX genes in drought stress and callus induction is clear, but further research is needed to understand their molecular mechanism.
{"title":"Genome-wide identification of LOX gene in four cotton species and revealed its function in callus induction and drought tolerance","authors":"Sani Muhammad Tajo , Zhaoe Pan , K.M. Yusuf , Salisu Bello Sadau , Guowei Lv , Shoupu He , Xiaoli Geng , Xiongming Du","doi":"10.1016/j.plgene.2025.100516","DOIUrl":"10.1016/j.plgene.2025.100516","url":null,"abstract":"<div><div>Cotton is one of the important fiber crops. Drought is the primary abiotic factor that restricts cotton growth and development and lowers its output. Plant <em>LOX</em> (lipoxygenases) genes catalyze the oxidation of polyunsaturated fatty acids into a variety of functional oxylipins. The LOX gene family has been thoroughly investigated under biotic and abiotic stressors; however, knowledge of their functions on callus induction and regeneration in cotton is still scarce. This study identified 34, 38, 23, and 20 LOX genes in the <em>Gossypium hirsutum</em>, <em>Gossypium barbadense</em>, <em>Gossypium arboreum</em>, and <em>Gossypium raimondii</em>, respectively. The <em>LOX</em> genes were found to be divided into three main categories, 9-LOX, 13-LOX Type I, and 13-LOX Type II. Three accessions of <em>G. hirsutum</em> were used to generate callus from hypocotyl, cotyledon, and shoot tip and we observed that the highest expression of the <em>GhLOX</em> genes were in the hypocotyl callus and most of <em>LOX</em> gene expression was up-regulated in one week callus and decreased in two week and four week callus except in the shoot tip induced callus in Jinmian 498. Virus-induced gene silencing of <em>GhLOX5</em> (Gh_A02G037000) revealed that the growth of the silenced plant was significantly decreased compared to WT. Excised leaf water loss and relative electrolyte leakage levels were increased about 23 % and 12 % in the <em>GhLOX5</em> silenced plant when compared to the WT. Compared to the WT, the silenced plant had significantly higher antioxidant activity (25 % in MDA content and 45 % in H<sub>2</sub>O<sub>2</sub> content). The importance of <em>LOX</em> genes in drought stress and callus induction is clear, but further research is needed to understand their molecular mechanism.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"43 ","pages":"Article 100516"},"PeriodicalIF":2.2,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143908207","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}
Plenty of water is required for cultivation of rice by transplanting that is challenging its cultivation, particularly on erratic rainfall or under drought. Direct-sown rice (DSR) is emerging as an alternative to transplanted rice (TPR) to save water. Performance of rice under DSR conditions varies greatly. While the molecular basis of adaptive plasticity of rice is subtle, tolerance to environmental stresses in crops is important for sustainable food production/security. The present study explores the molecular basis of adaptive/genetic plasticity in rice grown by different methods of planting, emphasising the concept of cumulative transcriptional memory. Our findings of comparative RNA-seq analysis highlighted differential gene expression with ∼6130 genes exclusively upregulated in the leaf of Nagina22 (N22) in contrast to only ∼3540 genes upregulated exclusively in the leaf of IR64 grown by dry/direct-sowing. In addition, our findings revealed that numerous genes showing upregulation in N22 were detected downregulated in IR64 that highlight distinct molecular strategies adopted by the rice cultivars. By activating diverse sets of genes coding for transcription factors, growth-regulating factors, translational machinery, nutrient-reservoirs, chromatin organization/epigenetic modifications, cell cycle/division, carbohydrate metabolism, etc., N22 adapts more effectively/efficiently to direct-sown conditions. Complementarity between these factors emerged to play important roles in adaptability of N22 to fluctuating environmental conditions. This helps adjust physio-biochemical responses of N22 to multiple abiotic/biotic stresses experienced under DSR conditions. Thus, our findings make a foundation for the development of molecular markers to facilitate varietal development of DSR for improved water productivity and sustainable agriculture.
{"title":"Adaptability of rice to different planting methods: A proof of cumulative transcriptional memory","authors":"Karishma Seem , Ayantika Ghosh , Rashmi Varshney , Rakesh Pandey , S. Gopala Krishnan , Trilochan Mohapatra , Suresh Kumar","doi":"10.1016/j.plgene.2025.100515","DOIUrl":"10.1016/j.plgene.2025.100515","url":null,"abstract":"<div><div>Plenty of water is required for cultivation of rice by transplanting that is challenging its cultivation, particularly on erratic rainfall or under drought. Direct-sown rice (DSR) is emerging as an alternative to transplanted rice (TPR) to save water. Performance of rice under DSR conditions varies greatly. While the molecular basis of adaptive plasticity of rice is subtle, tolerance to environmental stresses in crops is important for sustainable food production/security. The present study explores the molecular basis of adaptive/genetic plasticity in rice grown by different methods of planting, emphasising the concept of cumulative transcriptional memory. Our findings of comparative RNA-seq analysis highlighted differential gene expression with ∼6130 genes exclusively upregulated in the leaf of Nagina22 (N22) in contrast to only ∼3540 genes upregulated exclusively in the leaf of IR64 grown by dry/direct-sowing. In addition, our findings revealed that numerous genes showing upregulation in N22 were detected downregulated in IR64 that highlight distinct molecular strategies adopted by the rice cultivars. By activating diverse sets of genes coding for transcription factors, growth-regulating factors, translational machinery, nutrient-reservoirs, chromatin organization/epigenetic modifications, cell cycle/division, carbohydrate metabolism, etc., N22 adapts more effectively/efficiently to direct-sown conditions. Complementarity between these factors emerged to play important roles in adaptability of N22 to fluctuating environmental conditions. This helps adjust physio-biochemical responses of N22 to multiple abiotic/biotic stresses experienced under DSR conditions. Thus, our findings make a foundation for the development of molecular markers to facilitate varietal development of DSR for improved water productivity and sustainable agriculture.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"43 ","pages":"Article 100515"},"PeriodicalIF":2.2,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143852107","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 : 2025-04-12DOI: 10.1016/j.plgene.2025.100503
Maxwell Darko Asante , Kirpal Agyemang Ofosu , Felix Frimpong , Deladem Kwami Alphonso , Elizabeth Nartey , Agyei Elvis Obeng , Ralph K. Bam , Daniel D. Gamenyah , Priscilla F. Ribeiro , William Manilal
Grain quality is a crucial factor for rice consumers, and as such, it is a major focus for breeders. Phenotyping for grain quality traits can be a laborious and costly process. In this study, we evaluated the effectiveness of KASP-SNP markers in selecting for grain quality traits, including aroma, gelatinization temperature, grain length, grain width, and grain length: width ratio. We phenotyped 300 diverse rice genotypes for these four traits and genotyped them using their respective KASP-SNP markers. A regression analysis of the phenotype on the genotype was performed. The markers associated with the fgr-1 and GS3 genes explained 97 % and 94 % of the phenotypic variation for aroma and grain length, respectively. Two SNP markers (snpOS00440 and snpOS00441) associated with the GW5/SW5 gene each explained 82 % of the phenotypic variation for grain width, which increased marginally to 85 % when combined. However, two markers, snpOS00036 and snpOS00450, for gelatinization temperature explained only 2 % and 25 % of the phenotypic variation, respectively, indicating that these markers were not efficient in predicting this trait. Our findings suggest that the markers associated with aroma (fgr-1), grain length (GS3), and grain width (GW5/SW5) are highly efficient and reliable for marker-assisted selection.
{"title":"Effectiveness of KASP-SNP markers in selecting for grain quality traits in rice","authors":"Maxwell Darko Asante , Kirpal Agyemang Ofosu , Felix Frimpong , Deladem Kwami Alphonso , Elizabeth Nartey , Agyei Elvis Obeng , Ralph K. Bam , Daniel D. Gamenyah , Priscilla F. Ribeiro , William Manilal","doi":"10.1016/j.plgene.2025.100503","DOIUrl":"10.1016/j.plgene.2025.100503","url":null,"abstract":"<div><div>Grain quality is a crucial factor for rice consumers, and as such, it is a major focus for breeders. Phenotyping for grain quality traits can be a laborious and costly process. In this study, we evaluated the effectiveness of KASP-SNP markers in selecting for grain quality traits, including aroma, gelatinization temperature, grain length, grain width, and grain length: width ratio. We phenotyped 300 diverse rice genotypes for these four traits and genotyped them using their respective KASP-SNP markers. A regression analysis of the phenotype on the genotype was performed. The markers associated with the <em>fgr-1</em> and <em>GS3</em> genes explained 97 % and 94 % of the phenotypic variation for aroma and grain length, respectively. Two SNP markers (snpOS00440 and snpOS00441) associated with the <em>GW5/SW5</em> gene each explained 82 % of the phenotypic variation for grain width, which increased marginally to 85 % when combined. However, two markers, snpOS00036 and snpOS00450, for gelatinization temperature explained only 2 % and 25 % of the phenotypic variation, respectively, indicating that these markers were not efficient in predicting this trait. Our findings suggest that the markers associated with aroma (<em>fgr-1</em>), grain length (<em>GS3)</em>, and grain width (<em>GW5/SW5</em>) are highly efficient and reliable for marker-assisted selection.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"43 ","pages":"Article 100503"},"PeriodicalIF":2.2,"publicationDate":"2025-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143844127","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 : 2025-04-11DOI: 10.1016/j.plgene.2025.100507
Maria Khalid , Zoya Khalid , Zubair Ahmed , Lee Hickey , Awais Rasheed , Alvina Gul , Rabia Amir
A lack of understanding about the variations in root number, root angle, and leaf area contributes to inability of wheat withstand drought stress during seedling stage. This discrepancy hinders the development of drought-tolerant wheat varieties. We aimed to evaluate germplasm at seedling stage to find association between markers and traits. We characterized a collection of synthetic hexaploid wheat for root angle, seminal root numbers, and early vigor and identified loci associated with these traits using a 50 K SNP array and genotyping-by-sequencing (GBS) platforms. In total, 39 marker-trait nucleotides (QTNs) were associated with LA, RA, and RN distributed over 10 wheat chromosomes. Out of these, 11 QTNs were associated with LA, 15 QTNs were associated with RA, and 13 QTNs were associated with RN.LA showed a negative correlation with RN and a poor correlation with RA. The phenotypic values of synthetic hexaploid wheat accessions with a higher frequency of favorable alleles have been found to increase. Therefore, prioritizing the use of these synthetic wheat varieties in wheat breeding programs can be beneficial for improving root system architecture (RSA) and early vigor. These preliminary findings can be useful for pre-breeding efforts aimed at enhancing wheat adaptability to drought stress conditions.
由于对根系数量、根角和叶面积的变化缺乏了解，小麦在苗期无法抵御干旱胁迫。这种差异阻碍了耐旱小麦品种的发展。我们的目的是在苗期对种质进行评价，寻找标记与性状之间的关联。研究人员利用50 K SNP阵列和基因分型测序（GBS）平台对合成六倍体小麦的根角、种子根数和早期活力进行了表征，并确定了与这些性状相关的位点。共有39个与LA、RA和RN相关的标记性状核苷酸（QTNs）分布在10条小麦染色体上。其中，11个qtn与LA相关，15个qtn与RA相关，13个qtn与RN相关。LA与RN呈负相关，与RA相关性较差。有利等位基因频率较高的合成六倍体小麦材料的表型值增加。因此，在小麦育种计划中优先使用这些合成小麦品种有利于改善根系结构（RSA）和早期活力。这些初步发现可用于提高小麦对干旱胁迫条件的适应性的育种工作。
{"title":"Genome-wide association of root growth angle, seminal root numbers, and leaf area in the synthetic hexaploid wheat diversity panel","authors":"Maria Khalid , Zoya Khalid , Zubair Ahmed , Lee Hickey , Awais Rasheed , Alvina Gul , Rabia Amir","doi":"10.1016/j.plgene.2025.100507","DOIUrl":"10.1016/j.plgene.2025.100507","url":null,"abstract":"<div><div>A lack of understanding about the variations in root number, root angle, and leaf area contributes to inability of wheat withstand drought stress during seedling stage. This discrepancy hinders the development of drought-tolerant wheat varieties. We aimed to evaluate germplasm at seedling stage to find association between markers and traits. We characterized a collection of synthetic hexaploid wheat for root angle, seminal root numbers, and early vigor and identified loci associated with these traits using a 50 K SNP array and genotyping-by-sequencing (GBS) platforms. In total, 39 marker-trait nucleotides (QTNs) were associated with LA, RA, and RN distributed over 10 wheat chromosomes. Out of these, 11 QTNs were associated with LA, 15 QTNs were associated with RA, and 13 QTNs were associated with RN.LA showed a negative correlation with RN and a poor correlation with RA. The phenotypic values of synthetic hexaploid wheat accessions with a higher frequency of favorable alleles have been found to increase. Therefore, prioritizing the use of these synthetic wheat varieties in wheat breeding programs can be beneficial for improving root system architecture (RSA) and early vigor. These preliminary findings can be useful for pre-breeding efforts aimed at enhancing wheat adaptability to drought stress conditions.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"43 ","pages":"Article 100507"},"PeriodicalIF":2.2,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143838150","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 : 2025-04-10DOI: 10.1016/j.plgene.2025.100505
Mohammad Abdul Latif, Omar Kayess, Rakibul Hasan, Lutfur Rahman
Blast and bacterial blight (BB) pose a significant threat to rice production. To enhance resistance to blast and BB, we employed marker-assisted backcross breeding to introgress the resistance genes into the genetic background of BRRI dhan48. The resistant (R) genes Pi9, Pb1, Xa4, xa13, and Xa21 were introgressed from Pi9-US2, Pb1-US2, and IRBB58, respectively. The Pb1 gene strengthens blast resistance in rice by interacting with WRKY45 transcription factor to modulate salicylic acid and phytoalexin pathways, while the Pi9 gene triggers a signaling cascade involving reactive oxygen species (ROS) production and hormones like jasmonic acid and ethylene activation to enhance defense responses. Xa4 strengthens the cell wall via WAK (cell wall-associated kinase) protein, hindering pathogen invasion, xa13 disrupts SWEET (Sugar Will Eventually be Exported Transporter) protein function to limit sugar availability for Xanthomonas oryzae pv. oryzae (Xoo). Xa21 triggers mitogen-activated protein kinases (MAPKs)-mediated signaling cascades, leading to the activation of WRKY transcription factors that suppress bacterial proliferation. For that, triple cross was made, followed by repeated backcrosses, self-pollinations, and marker-assisted selection to generate BC3F5 progeny. Chi-square analysis of 380 BC3F2 individuals confirmed a monogenic inheritance pattern for blast and BB resistance traits. Finally, we selected 32 advanced lines, and among them nineteen lines possessed all these 5 R genes, i.e., Pi9, Pb1, Xa4, xa13, and Xa21, while eight lines consisted of 4 R genes in different combinations. The disease rating of the advanced lines varied from 0 to 5 for both blast and BB diseases, while BRRI dhan48 had a disease rating ranging from 7 to 9. The lines G10, G25, G16, G31, G9, G2, and G20 demonstrated significantly higher grain yield (7.73, 7.72, 7.70, 7.65, 7.64, 7.59, and 7.58 t ha−1, respectively) than the parent (7.00 t ha−1). Investigation of marker trait association showed that molecular markers were negatively linked with blast and BB diseases. So, gene introgression by marker-assisted backcrossing (MABB) offers a robust and efficient way to identify and validate candidate genes with high precision for the development of durable, resistant rice breeding lines. These multiple disease resistant advanced lines may use as a potential genetic stock or incorporate with other desired genes for ensuring sustainable rice production under changing climatic conditions.
{"title":"Molecular marker assisted gene stacking for multiple diseases resistance in an elite rice cultivar, BRRI dhan48","authors":"Mohammad Abdul Latif, Omar Kayess, Rakibul Hasan, Lutfur Rahman","doi":"10.1016/j.plgene.2025.100505","DOIUrl":"10.1016/j.plgene.2025.100505","url":null,"abstract":"<div><div>Blast and bacterial blight (BB) pose a significant threat to rice production. To enhance resistance to blast and BB, we employed marker-assisted backcross breeding to introgress the resistance genes into the genetic background of BRRI dhan48. The resistant (R) genes <em>Pi9</em>, <em>Pb1</em>, <em>Xa4</em>, <em>xa13</em>, and <em>Xa21</em> were introgressed from Pi9-US2, Pb1-US2, and IRBB58, respectively. The <em>Pb1</em> gene strengthens blast resistance in rice by interacting with WRKY45 transcription factor to modulate salicylic acid and phytoalexin pathways, while the <em>Pi9</em> gene triggers a signaling cascade involving reactive oxygen species (ROS) production and hormones like jasmonic acid and ethylene activation to enhance defense responses. <em>Xa4</em> strengthens the cell wall via WAK (cell wall-associated kinase) protein, hindering pathogen invasion, <em>xa13</em> disrupts SWEET (Sugar Will Eventually be Exported Transporter) protein function to limit sugar availability for <em>Xanthomonas oryzae</em> pv. <em>oryzae</em> (Xoo). <em>Xa21</em> triggers mitogen-activated protein kinases (MAPKs)-mediated signaling cascades, leading to the activation of WRKY transcription factors that suppress bacterial proliferation. For that, triple cross was made, followed by repeated backcrosses, self-pollinations, and marker-assisted selection to generate BC<sub>3</sub>F<sub>5</sub> progeny. Chi-square analysis of 380 BC<sub>3</sub>F<sub>2</sub> individuals confirmed a monogenic inheritance pattern for blast and BB resistance traits. Finally, we selected 32 advanced lines, and among them nineteen lines possessed all these 5 R genes, i.e., <em>Pi9</em>, <em>Pb1</em>, <em>Xa4</em>, <em>xa13</em>, and <em>Xa21</em><sub><em>,</em></sub> while eight lines consisted of 4 R genes in different combinations. The disease rating of the advanced lines varied from 0 to 5 for both blast and BB diseases, while BRRI dhan48 had a disease rating ranging from 7 to 9. The lines G10, G25, G16, G31, G9, G2, and G20 demonstrated significantly higher grain yield (7.73, 7.72, 7.70, 7.65, 7.64, 7.59, and 7.58 t ha<sup>−1</sup>, respectively) than the parent (7.00 t ha<sup>−1</sup>). Investigation of marker trait association showed that molecular markers were negatively linked with blast and BB diseases. So, gene introgression by marker-assisted backcrossing (MABB) offers a robust and efficient way to identify and validate candidate genes with high precision for the development of durable, resistant rice breeding lines. These multiple disease resistant advanced lines may use as a potential genetic stock or incorporate with other desired genes for ensuring sustainable rice production under changing climatic conditions.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"42 ","pages":"Article 100505"},"PeriodicalIF":2.2,"publicationDate":"2025-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143808219","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 : 2025-04-08DOI: 10.1016/j.plgene.2025.100508
Zixia Zhang, Yanfang Jiang, Hailong Zhu, Ziyao Chen, Zefa Liu
F2 materials derived from a cross between introgression lines B-5 × A-3 were used as mapping population in C. moschata. Duch. Among the 89 genetic markers (ls, yf, and 87 marker alleles) analyzed, 5 markers (5.6 % P<0.01) and 12 markers (13.5 % P<0.01) showed genetic distortion in the F2 population. Among these segregation distortion genetic markers, 11 genetic markers were skewed to the male parent B-5(64.70 %), 3 genetic markers were skewed to the heterozygote (17.65 %), and 3 genetic markers were skewed to both parents (17.65 %). These segregation distortion genetic markers were in the clusters of tight loci or single markers, which were distributed in 9 different chromosomes with 3 (SDR1, SDR2, and SDR3) hot regions in 3 (LGP2, LGP6, and LGP10) of them. In this research, reasons for segregation distortion were discussed, and the gametophyte selection may be the result of segregation distortion of genetic polymorphic loci.
利用B-5 × a -3杂交获得的F2个材料作为莫夏塔的定位群体。杜赫。在分析的89个遗传标记（ls、yf和87个标记等位基因）中，F2群体中有5个标记（5.6% P<0.01）和12个标记（13.5% P<0.01）存在遗传畸变。在这些分离扭曲遗传标记中，有11个遗传标记偏向父本B-5(64.70%)， 3个遗传标记偏向杂合子（17.65%），3个遗传标记偏向双亲（17.65%）。这些分离畸变遗传标记以紧密位点或单标记簇的形式分布在9条不同的染色体上，其中3条（LGP2、LGP6和LGP10）染色体上有3个（SDR1、SDR2和SDR3）热点区。本文讨论了分离扭曲的原因，认为配子体选择可能是遗传多态性位点分离扭曲的结果。
{"title":"Segregation distortion and linkage analysis in F2 populations of pumpkin (C.Moschata Duch)","authors":"Zixia Zhang, Yanfang Jiang, Hailong Zhu, Ziyao Chen, Zefa Liu","doi":"10.1016/j.plgene.2025.100508","DOIUrl":"10.1016/j.plgene.2025.100508","url":null,"abstract":"<div><div>F<sub>2</sub> materials derived from a cross between introgression lines B-5 × A-3 were used as mapping population in <em>C. moschata.</em> Duch. Among the 89 genetic markers (ls, yf, and 87 marker alleles) analyzed, 5 markers (5.6 % P<0.01) and 12 markers (13.5 % P<0.01) showed genetic distortion in the F<sub>2</sub> population. Among these segregation distortion genetic markers, 11 genetic markers were skewed to the male parent B-5(64.70 %), 3 genetic markers were skewed to the heterozygote (17.65 %), and 3 genetic markers were skewed to both parents (17.65 %). These segregation distortion genetic markers were in the clusters of tight loci or single markers, which were distributed in 9 different chromosomes with 3 (SDR1, SDR2, and SDR3) hot regions in 3 (LGP2, LGP6, and LGP10) of them. In this research, reasons for segregation distortion were discussed, and the gametophyte selection may be the result of segregation distortion of genetic polymorphic loci.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"43 ","pages":"Article 100508"},"PeriodicalIF":2.2,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143835254","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}
The changing climatic conditions have led many plants to restrict their growth and suppress their yield. In their struggle for survival, plants employ unique strategies that help them grow under extreme weather conditions and challenging biotic interactions. Plants can enhance their tolerance through a key process called priming, which strengthens their immune system's response to stimuli from pathogens, beneficial microbes, chemicals, and abiotic cues. Priming provides long-term stress resistance to plants and is based on a rapid and robust defence response to environmental stress conditions. A milder form of stress or chemicals, such as sodium selenite, melatonin, β-aminobutyricacid, polyamines, calcium, zinc, hydrogen peroxide, hydrogen sulfide and sodium hydrosulphide, are used to preactivate plant defence mechanisms. These chemicals play crucial role in stabilizing plant growth by empowering plants to activate their own defence mechanisms and combat unforeseen stressors. This review primarily explores the role of priming phenomena and the mechanisms that enable plants to withstand stressful environmental conditions in their natural habitat.
{"title":"Priming-a state of alert against environmental stress challenges in plants","authors":"Divya Chaudhary , Himanshi Aggarwal , Banpreet Kaur , Himani Agarwal , Arghyabrata Das , Ajay Kumar , Vaibhav Mishra , Prashant Kumar Singh , Naveen Chandra Joshi","doi":"10.1016/j.plgene.2025.100513","DOIUrl":"10.1016/j.plgene.2025.100513","url":null,"abstract":"<div><div>The changing climatic conditions have led many plants to restrict their growth and suppress their yield. In their struggle for survival, plants employ unique strategies that help them grow under extreme weather conditions and challenging biotic interactions. Plants can enhance their tolerance through a key process called priming, which strengthens their immune system's response to stimuli from pathogens, beneficial microbes, chemicals, and abiotic cues. Priming provides long-term stress resistance to plants and is based on a rapid and robust defence response to environmental stress conditions. A milder form of stress or chemicals, such as sodium selenite, melatonin, β-aminobutyricacid, polyamines, calcium, zinc, hydrogen peroxide, hydrogen sulfide and sodium hydrosulphide, are used to preactivate plant defence mechanisms. These chemicals play crucial role in stabilizing plant growth by empowering plants to activate their own defence mechanisms and combat unforeseen stressors. This review primarily explores the role of priming phenomena and the mechanisms that enable plants to withstand stressful environmental conditions in their natural habitat.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"43 ","pages":"Article 100513"},"PeriodicalIF":2.2,"publicationDate":"2025-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143830182","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}
O-methyltransferases (OMTs) are group of enzymes involved in the methylation of various secondary metabolites, including anthocyanins. This secondary modification, together with hydroxylation and glycosylation, affects the chromatic properties, stability and reactivity of these pigments. Meanwhile, no detailed identification or genome-wide analysis of the OMT gene family members in potato (Solanum tuberosum) has been reported. We conducted a genome-wide identification and characterization of potato OMTs, identifying 65 OMT family members. These were characterized based on gene structure, evolutionary relationships, and promoter motifs. Analysis of available gene expression profiles from public databases revealed expression patterns indicative of tissue- and temporal-specificity Finally, we further elucidated expression differences among four selected OMT-encoding genes using potato cell cultures, which represent a smart and gainful alternative for anthocyanin production and deep knowledge about these post-biosynthetic modifications.
o -甲基转移酶（OMTs）是一组参与各种次生代谢产物甲基化的酶，包括花青素。这种二级修饰，连同羟基化和糖基化，影响这些颜料的着色性能、稳定性和反应性。同时，马铃薯（Solanum tuberosum） OMT基因家族成员的详细鉴定和全基因组分析尚未见报道。我们对马铃薯OMT进行了全基因组鉴定和表征，鉴定了65个OMT家族成员。这些是基于基因结构、进化关系和启动子基序来鉴定的。通过对公共数据库中可用基因表达谱的分析，揭示了组织特异性和时间特异性的表达模式。最后，我们利用马铃薯细胞培养进一步阐明了四个选定的omt编码基因之间的表达差异，这代表了花青素生产的一个聪明而有益的选择，并深入了解了这些生物合成后修饰。
{"title":"Genome-wide characterization of the anthocyanin O-methyltransferases in the cultivated potato","authors":"Annalisa Staiti , Carmine Fruggiero , Domenico Carputo , Vincenzo D’Amelia , Nunzio D’Agostino","doi":"10.1016/j.plgene.2025.100506","DOIUrl":"10.1016/j.plgene.2025.100506","url":null,"abstract":"<div><div><em>O</em>-methyltransferases (OMTs) are group of enzymes involved in the methylation of various secondary metabolites, including anthocyanins. This secondary modification, together with hydroxylation and glycosylation, affects the chromatic properties, stability and reactivity of these pigments. Meanwhile, no detailed identification or genome-wide analysis of the OMT gene family members in potato (<em>Solanum tuberosum</em>) has been reported. We conducted a genome-wide identification and characterization of potato OMTs, identifying 65 OMT family members. These were characterized based on gene structure, evolutionary relationships, and promoter motifs. Analysis of available gene expression profiles from public databases revealed expression patterns indicative of tissue- and temporal-specificity Finally, we further elucidated expression differences among four selected OMT-encoding genes using potato cell cultures, which represent a smart and gainful alternative for anthocyanin production and deep knowledge about these post-biosynthetic modifications.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"42 ","pages":"Article 100506"},"PeriodicalIF":2.2,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143820948","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 : 2025-04-03DOI: 10.1016/j.plgene.2025.100504
Minghua Lv, Ting Deng, Jiahong Cao, Xinyu Zhang, Fangfang Cai, Jun Mei, Dongliang Yu, Yuqiang Sun
Cotton fibers are among the most important natural fibers worldwide. Developing natural colored cotton (NCC) varieties is crucial for cotton fiber utilization due to their eco-friendly properties. Manipulation of anthocyanin synthesis is an effective strategy for creating novel NCCs. Our previous research revealed enhanced anthocyanin accumulation in an empurpled Gossypium hirsutum mutant, HS2, but the regulatory mechanism has not been fully elucidated. In this study, we employed an integrated analysis of RNA sequencing, small RNA (sRNA) sequencing, and degradome sequencing to assess the expression patterns and potential roles of sRNAs in the development of the empurpled phenotype in HS2. Our findings revealed that the expression profiles of sRNAs are highly similar between the wild type and the mutant, with only 11 miRNAs and 761 siRNAs showing significant expression variation. Eight miRNAs and one siRNA exhibited inverse regulation with their targets, which were not directly involved in regulating anthocyanin biosynthesis. Notably, degradome data analysis identified interactions between miR395 and ATP sulfurylase genes (APS1 and APS3). Further assessment determined down-regulation of miR395 and up-regulation of APS genes in HS2, as well as the enhanced biosynthesis of cysteine and glutathione. These results suggest that miRNA mediated post-transcriptional regulation might not be the primary mechanism driving anthocyanin enhancement in HS2. Instead, the miR395-APS modules are possibly involved in modulating cellular processes to cope with the increased anthocyanin levels. Overall, this study deepens our understanding of the molecular mechanisms underlying the empurpled phenotype in HS2 and facilitates its future use in NCC breeding.
{"title":"Deciphering the role of small RNAs in the development of empurpled phenotypes in the Gossypium hirsutum mutant HS2","authors":"Minghua Lv, Ting Deng, Jiahong Cao, Xinyu Zhang, Fangfang Cai, Jun Mei, Dongliang Yu, Yuqiang Sun","doi":"10.1016/j.plgene.2025.100504","DOIUrl":"10.1016/j.plgene.2025.100504","url":null,"abstract":"<div><div>Cotton fibers are among the most important natural fibers worldwide. Developing natural colored cotton (NCC) varieties is crucial for cotton fiber utilization due to their eco-friendly properties. Manipulation of anthocyanin synthesis is an effective strategy for creating novel NCCs. Our previous research revealed enhanced anthocyanin accumulation in an empurpled <em>Gossypium hirsutum</em> mutant, <em>HS2</em>, but the regulatory mechanism has not been fully elucidated. In this study, we employed an integrated analysis of RNA sequencing, small RNA (sRNA) sequencing, and degradome sequencing to assess the expression patterns and potential roles of sRNAs in the development of the empurpled phenotype in <em>HS2</em>. Our findings revealed that the expression profiles of sRNAs are highly similar between the wild type and the mutant, with only 11 miRNAs and 761 siRNAs showing significant expression variation. Eight miRNAs and one siRNA exhibited inverse regulation with their targets, which were not directly involved in regulating anthocyanin biosynthesis. Notably, degradome data analysis identified interactions between miR395 and ATP sulfurylase genes (<em>APS1</em> and <em>APS3</em>). Further assessment determined down-regulation of miR395 and up-regulation of <em>APS</em> genes in <em>HS2</em>, as well as the enhanced biosynthesis of cysteine and glutathione. These results suggest that miRNA mediated post-transcriptional regulation might not be the primary mechanism driving anthocyanin enhancement in <em>HS2</em>. Instead, the miR395-<em>APS</em> modules are possibly involved in modulating cellular processes to cope with the increased anthocyanin levels. Overall, this study deepens our understanding of the molecular mechanisms underlying the empurpled phenotype in <em>HS2</em> and facilitates its future use in NCC breeding.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"42 ","pages":"Article 100504"},"PeriodicalIF":2.2,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143792513","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 : 2025-04-03DOI: 10.1016/j.plgene.2025.100511
Xiaozeng Mi , Dahe Qiao , Yanlin An , Chun Yang , Kaiqin Lin , Congling Peng , Juan Chen
As one of the most important agronomic traits of the tea plant (Camellia sinensis), the timing of bud flush (TBF) affects the sales price of tea beverages. Here, we performed specific-locus amplified fragment (SLAF) sequencing and genome-wide association study (GWAS) analysis on 200 offspring of natural hybridization from the ‘Qianmei 601’. A total of 796,294 SLAF tags and 2,324,211 single-nucleotide polymorphisms (SNPs) were obtained by sequencing. The 200 tea germplasms were clustered into four groups by population structure, principal component analysis (PCA) and phylogenetic tree analysis. GWAS identified twelve SNPs loci that were significantly associated with TBF traits. Seven candidate genes associated with TBF were subsequently identified by scanning in the regions within 1 Mb SNP loci. In addition, we found that two candidate genes (ARP and WRKY) were highly expressed in individuals with early TBF. Interestingly, cloning and sequencing of the ARP gene revealed C-G variants between the early and late TBF individuals. Our results provide a theoretical basis for early TBF breeding and functional gene analysis in tea plants.
{"title":"Genome-wide association study of tea plant based on SLAF-seq revealed SNP variations regulating timing of bud flush","authors":"Xiaozeng Mi , Dahe Qiao , Yanlin An , Chun Yang , Kaiqin Lin , Congling Peng , Juan Chen","doi":"10.1016/j.plgene.2025.100511","DOIUrl":"10.1016/j.plgene.2025.100511","url":null,"abstract":"<div><div>As one of the most important agronomic traits of the tea plant (<em>Camellia sinensis</em>), the timing of bud flush (TBF) affects the sales price of tea beverages. Here, we performed specific-locus amplified fragment (SLAF) sequencing and genome-wide association study (GWAS) analysis on 200 offspring of natural hybridization from the ‘Qianmei 601’. A total of 796,294 SLAF tags and 2,324,211 single-nucleotide polymorphisms (SNPs) were obtained by sequencing. The 200 tea germplasms were clustered into four groups by population structure, principal component analysis (PCA) and phylogenetic tree analysis. GWAS identified twelve SNPs loci that were significantly associated with TBF traits. Seven candidate genes associated with TBF were subsequently identified by scanning in the regions within 1 Mb SNP loci. In addition, we found that two candidate genes (<em>ARP</em> and <em>WRKY</em>) were highly expressed in individuals with early TBF. Interestingly, cloning and sequencing of the <em>ARP</em> gene revealed C-G variants between the early and late TBF individuals. Our results provide a theoretical basis for early TBF breeding and functional gene analysis in tea plants.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"42 ","pages":"Article 100511"},"PeriodicalIF":2.2,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143792514","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}
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