Sucrose transporters (SUTs) are crucial for plant growth, development, and stress responses. Despite sugarcane's importance as a sugar and biofuel crop, genomic data on its SUT genes under abiotic stress are limited. In this study, 37 ShSUT genes were identified through bioinformatic analysis. Phylogenetic classification grouped them into three major clades (I-III), with conserved motifs and gene structures supporting their evolutionary relationships. Promoter analysis revealed 15 key cis-elements related to hormone response, stress, development, and light regulation. All ShSUT genes were mapped on three contig regions and seven chromosomes. Collinearity and gene duplication analysis identified 15 segmentally duplicated gene pairs, indicating evolutionary expansion. Additionally, 7 putative 'sbi-miRNAs' were predicted to target 28 ShSUT genes, with sbi-miR5381 alone targeted 17 ShSUTs. For functional characterization, ShSUT04 was chosen due to its evolutionary significance, crucial role in sucrose transport, and potential involvement in regulating abiotic stress responses. Eighteen potential interactors were identified, with confirmed interactions for ShPsbR, ShRF2a, ShCOPTS.1, and ShSPT, validated through BiFC and Y2H assays. qRT-PCR analysis demonstrated stress-responsive expression patterns. Under cold stress, ShRF2a, ShPsbR, and ShSPT were down-regulated, indicating negative regulatory roles, while ShSUT04 and ShCOPT5.1 were up-regulated at specific time points, and ShSUT01 showed strong induction, suggesting a positive role in defense. Under drought, ShSUT04 and ShPsbR showed significant upregulation, suggesting positive regulatory roles. In salinity stress, while several genes were suppressed, ShSUT01 and ShPsbR were induced, reflecting their potential in stress adaptation. This study reveals the evolutionary and functional roles of sugarcane SUT genes in abiotic stress regulation, with ShSUT04 showing dual roles, positive under drought and negative under salinity and cold stresses.
{"title":"Genome-wide analysis of the sugarcane SUT gene family reveals ShSUT4 as a key regulator of abiotic stress responses.","authors":"Xue-Ting Zhao, Ahmad Ali, Cui-Lian Feng, Ji-Shan Lin, Rui-Jie Wu, Shu-Zhen Zhang, Guang-Run Yu, Hai-Feng Jia, Yu-Qing Gong, Ting-Ting Zhao, Jun-Gang Wang","doi":"10.1007/s00122-025-05138-w","DOIUrl":"10.1007/s00122-025-05138-w","url":null,"abstract":"<p><p>Sucrose transporters (SUTs) are crucial for plant growth, development, and stress responses. Despite sugarcane's importance as a sugar and biofuel crop, genomic data on its SUT genes under abiotic stress are limited. In this study, 37 ShSUT genes were identified through bioinformatic analysis. Phylogenetic classification grouped them into three major clades (I-III), with conserved motifs and gene structures supporting their evolutionary relationships. Promoter analysis revealed 15 key cis-elements related to hormone response, stress, development, and light regulation. All ShSUT genes were mapped on three contig regions and seven chromosomes. Collinearity and gene duplication analysis identified 15 segmentally duplicated gene pairs, indicating evolutionary expansion. Additionally, 7 putative 'sbi-miRNAs' were predicted to target 28 ShSUT genes, with sbi-miR5381 alone targeted 17 ShSUTs. For functional characterization, ShSUT04 was chosen due to its evolutionary significance, crucial role in sucrose transport, and potential involvement in regulating abiotic stress responses. Eighteen potential interactors were identified, with confirmed interactions for ShPsbR, ShRF2a, ShCOPTS.1, and ShSPT, validated through BiFC and Y2H assays. qRT-PCR analysis demonstrated stress-responsive expression patterns. Under cold stress, ShRF2a, ShPsbR, and ShSPT were down-regulated, indicating negative regulatory roles, while ShSUT04 and ShCOPT5.1 were up-regulated at specific time points, and ShSUT01 showed strong induction, suggesting a positive role in defense. Under drought, ShSUT04 and ShPsbR showed significant upregulation, suggesting positive regulatory roles. In salinity stress, while several genes were suppressed, ShSUT01 and ShPsbR were induced, reflecting their potential in stress adaptation. This study reveals the evolutionary and functional roles of sugarcane SUT genes in abiotic stress regulation, with ShSUT04 showing dual roles, positive under drought and negative under salinity and cold stresses.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 1","pages":"26"},"PeriodicalIF":4.2,"publicationDate":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145901065","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-05DOI: 10.1007/s00122-025-05108-2
Bin Zhang, Yunyun Cao, Bin Zhang, Tian Tian, Xiaoman Li, Peirong Li, Xiaoyun Xin, Weihong Wang, Xiuyun Zhao, Deshuang Zhang, Yangjun Yu, Fenglan Zhang, Tongbing Su, Shuancang Yu
Key message: BrRLP1 positively regulates the resistance to downy mildew in Brassica rapa by interacting with the monodehydroascorbate reductase BrMDAR1. Downy mildew is a devastating disease that severely affects the yield and quality in Brassica rapa. Receptor-like protein (RLP) is important for plants disease-resistant response. Here, a new downy mildew resistance gene, BrRLP1, was identified in Brassica rapa through GWAS analysis and QTL mapping. BrRLP1 encodes a membrane-localized receptor-like protein, and its expression level showed significant differences in the resistant and susceptible materials after inoculation with downy mildew. Transient expression and transgenic functional verification revealed that BrRLP1 is a positive regulator for the downy mildew resistance. All the BrRLP1R overexpressed plants exhibited a high-resistance phenotype to downy mildew after inoculation. Haplotype analysis revealed that the SNP309 in the LRR domain of BrRLP1 is a key functional site for the resistance difference to downy mildew. Y2H and LCI assays showed that BrRLP1 can interact with the monodehydroascorbate reductase BrMDAR1, which is involved in the ascorbic acid metabolic pathway. Our results revealed the function of BrRLP1 in regulation of downy mildew resistance by interacting with BrMDAR1, which provides new insight into the molecular mechanism underlying disease resistance immune response in Brassica rapa.
{"title":"The BrRLP1-BrMDAR1 module regulates the resistance to downy mildew in Brassica rapa.","authors":"Bin Zhang, Yunyun Cao, Bin Zhang, Tian Tian, Xiaoman Li, Peirong Li, Xiaoyun Xin, Weihong Wang, Xiuyun Zhao, Deshuang Zhang, Yangjun Yu, Fenglan Zhang, Tongbing Su, Shuancang Yu","doi":"10.1007/s00122-025-05108-2","DOIUrl":"10.1007/s00122-025-05108-2","url":null,"abstract":"<p><strong>Key message: </strong>BrRLP1 positively regulates the resistance to downy mildew in Brassica rapa by interacting with the monodehydroascorbate reductase BrMDAR1. Downy mildew is a devastating disease that severely affects the yield and quality in Brassica rapa. Receptor-like protein (RLP) is important for plants disease-resistant response. Here, a new downy mildew resistance gene, BrRLP1, was identified in Brassica rapa through GWAS analysis and QTL mapping. BrRLP1 encodes a membrane-localized receptor-like protein, and its expression level showed significant differences in the resistant and susceptible materials after inoculation with downy mildew. Transient expression and transgenic functional verification revealed that BrRLP1 is a positive regulator for the downy mildew resistance. All the BrRLP1<sup>R</sup> overexpressed plants exhibited a high-resistance phenotype to downy mildew after inoculation. Haplotype analysis revealed that the SNP309 in the LRR domain of BrRLP1 is a key functional site for the resistance difference to downy mildew. Y2H and LCI assays showed that BrRLP1 can interact with the monodehydroascorbate reductase BrMDAR1, which is involved in the ascorbic acid metabolic pathway. Our results revealed the function of BrRLP1 in regulation of downy mildew resistance by interacting with BrMDAR1, which provides new insight into the molecular mechanism underlying disease resistance immune response in Brassica rapa.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 1","pages":"25"},"PeriodicalIF":4.2,"publicationDate":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145901101","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Message: A QTL from rye chromosome 5R confers resistance to root-lesion nematode in triticale.Root-lesion nematode (Pratylenchus neglectus, RLN) poses a significant threat to global wheat production. High levels of RLN resistance are rare in wheat. Triticale, an amphiploid generated by combining wheat and rye genomes that naturally carries rye-derived defense alleles, offers an untapped reservoir of nematode resistance. Here, we evaluated the response to RLN in 137 recombinant inbred lines (RILs) derived from a cross between two triticale cultivars: Siskiyou (susceptible) and Villax St. Jose (resistant). Genotyping-by-sequencing identified 1054 high-quality single-nucleotide polymorphism (SNP) markers, which, along with seven simple sequence repeat (SSR) markers, were assembled into 21 linkage groups covering the triticale genome. A single quantitative trait locus (QTL) on the rye-derived chromosome 5R was identified that explained approximately 20% of the phenotypic variance across experiments. A high-throughput Kompetitive allele-specific PCR (KASP) assay based on the most significant SNP marker was developed, providing a rapid genotyping platform for selecting the resistance allele and reducing reliance on labor-intensive phenotyping for P. neglectus resistance in triticale. This study reports the first mapped RLN-resistance QTL in triticale, laying the fundamental foundation for introgressing the 5R resistance allele into wheat via marker-assisted selection combined with chromosome engineering, thereby broadening the genetic basis for nematode resistance in cereal crops.
一个来自黑麦5R染色体的QTL赋予了小黑麦对根病线虫的抗性。根损线虫(Pratylenchus neglect, RLN)对全球小麦生产构成严重威胁。小麦对RLN的高水平抗性是罕见的。小黑麦是一种由小麦和黑麦基因组结合产生的两倍体,天然携带黑麦衍生的防御等位基因,提供了一个尚未开发的线虫抗性库。在这里,我们评估了137个重组自交系(rls)对RLN的反应,这些自交系是由两个小黑麦品种Siskiyou(易感)和Villax St. Jose(抗性)杂交而来。基因分型测序鉴定出1054个高质量的单核苷酸多态性(SNP)标记,与7个简单序列重复(SSR)标记一起组装成覆盖小黑麦基因组的21个连锁群。在黑麦衍生的5R染色体上发现了一个单一的数量性状位点(QTL),该位点解释了实验中约20%的表型变异。建立了一种基于最显著SNP标记的高通量竞争等位基因特异性PCR (KASP)方法,为选择抗性等位基因提供了快速的基因分型平台,减少了对劳动密集型表型的依赖。本研究报道了在小黑麦中首次定位到的rnn抗性QTL,为通过标记辅助选择结合染色体工程将5R抗性等位基因渗入小麦奠定了基础,从而拓宽了谷类作物抗线虫的遗传基础。
{"title":"Genetic analysis of a quantitative trait locus associated with resistance to the root-lesion nematode Pratylenchus neglectus in triticale.","authors":"Gurminder Singh, Krishna Acharya, Bonventure Mumia, Siddant Ranabhat, Ekta Ojha, Jatinder Singh, Upinder Gill, Sean Walkowiak, Harmeet Singh Chawla, Xuehui Li, Justin Faris, Zhaohui Liu, Guiping Yan","doi":"10.1007/s00122-025-05112-6","DOIUrl":"10.1007/s00122-025-05112-6","url":null,"abstract":"<p><strong>Message: </strong>A QTL from rye chromosome 5R confers resistance to root-lesion nematode in triticale.Root-lesion nematode (Pratylenchus neglectus, RLN) poses a significant threat to global wheat production. High levels of RLN resistance are rare in wheat. Triticale, an amphiploid generated by combining wheat and rye genomes that naturally carries rye-derived defense alleles, offers an untapped reservoir of nematode resistance. Here, we evaluated the response to RLN in 137 recombinant inbred lines (RILs) derived from a cross between two triticale cultivars: Siskiyou (susceptible) and Villax St. Jose (resistant). Genotyping-by-sequencing identified 1054 high-quality single-nucleotide polymorphism (SNP) markers, which, along with seven simple sequence repeat (SSR) markers, were assembled into 21 linkage groups covering the triticale genome. A single quantitative trait locus (QTL) on the rye-derived chromosome 5R was identified that explained approximately 20% of the phenotypic variance across experiments. A high-throughput Kompetitive allele-specific PCR (KASP) assay based on the most significant SNP marker was developed, providing a rapid genotyping platform for selecting the resistance allele and reducing reliance on labor-intensive phenotyping for P. neglectus resistance in triticale. This study reports the first mapped RLN-resistance QTL in triticale, laying the fundamental foundation for introgressing the 5R resistance allele into wheat via marker-assisted selection combined with chromosome engineering, thereby broadening the genetic basis for nematode resistance in cereal crops.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 1","pages":"24"},"PeriodicalIF":4.2,"publicationDate":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12769958/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145901073","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-03DOI: 10.1007/s00122-025-05121-5
Rajib Kumbhakar, Mayulika Mondal, Virevol Thakro, Yashwant K Yadava, Uday Chand Jha, Shailesh Tripathi, Swarup K Parida
Key message: Integrated genome-wide and haplotype-based association analyses identified a key genomic locus governing plant growth habit (PGH) traits in chickpea. Identification of molecular markers governing plant growth habit (PGH) traits that enable mechanical harvestability is pivotal for boosting production efficiency of crops under changing climates and increasing global food demand. With a combinatorial integrated genomics-assisted breeding strategy comprising of association mapping, haplotype-based association, molecular haplotyping and gene expression analysis in a 286 association panel of chickpea (Cicer arietinum), we dissected the genetic basis of PGH traits. This study employed 382,171 genome-wide SNPs (single-nucleotide polymorphisms) obtained from whole-genome sequencing (WGS) of 286 desi and kabuli chickpea accessions and delineated a major genomic locus associated with PGH traits variation, particularly between erect (E)/semi-erect (SE) versus spreading (S)/semi-spreading (SS) types. Within this genomic loci, CaPAR1 (Cicer arietinum PAR1) and its derived natural alleles/haplotypes was identified as the candidate gene. These findings can facilitate generation of high-yielding, erect/semi-erect, mechanically harvestable cultivars through translational genomics and molecular breeding for genetic enhancement of chickpea.
{"title":"A genome-wide association analysis identifies a key candidate gene controlling plant growth habit in chickpea.","authors":"Rajib Kumbhakar, Mayulika Mondal, Virevol Thakro, Yashwant K Yadava, Uday Chand Jha, Shailesh Tripathi, Swarup K Parida","doi":"10.1007/s00122-025-05121-5","DOIUrl":"10.1007/s00122-025-05121-5","url":null,"abstract":"<p><strong>Key message: </strong>Integrated genome-wide and haplotype-based association analyses identified a key genomic locus governing plant growth habit (PGH) traits in chickpea. Identification of molecular markers governing plant growth habit (PGH) traits that enable mechanical harvestability is pivotal for boosting production efficiency of crops under changing climates and increasing global food demand. With a combinatorial integrated genomics-assisted breeding strategy comprising of association mapping, haplotype-based association, molecular haplotyping and gene expression analysis in a 286 association panel of chickpea (Cicer arietinum), we dissected the genetic basis of PGH traits. This study employed 382,171 genome-wide SNPs (single-nucleotide polymorphisms) obtained from whole-genome sequencing (WGS) of 286 desi and kabuli chickpea accessions and delineated a major genomic locus associated with PGH traits variation, particularly between erect (E)/semi-erect (SE) versus spreading (S)/semi-spreading (SS) types. Within this genomic loci, CaPAR1 (Cicer arietinum PAR1) and its derived natural alleles/haplotypes was identified as the candidate gene. These findings can facilitate generation of high-yielding, erect/semi-erect, mechanically harvestable cultivars through translational genomics and molecular breeding for genetic enhancement of chickpea.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 1","pages":"22"},"PeriodicalIF":4.2,"publicationDate":"2026-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145893049","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Key message: A core set of sequence tagged microsatellite sites (STMS) markers for Oryza sativa complex were developed, validated and utilized for pre-breding and characterization of Oryza germplasm from different taxa. Development of genome-wide distributed cross-transferable molecular markers applicable to different species can enhance pre-breeding efficiency. Screening of 23.5K primer pairs across nine reference genomes identified 1,008 cross-amplifiable sequence-tagged microsatellite site (STMS) markers, including 520 genic ones, for the Oryza sativa complex. Predicted amplicon lengths of the markers were validated using polymerase chain reaction (PCR). Additionally, 3,628-13,280 markers were identified for individual species. Most cross-amplifiable markers were syntenic across the A-genome. However, substantial intra- and inter-chromosomal translocations were detected in O. longistaminata, O. nivara, and O. meridionalis compared to other A-genome species and subspecies. Notably, four markers exhibited contrasting inter-chromosomal translocations between the three Asiatic A-genome species and the five other species from Africa, South America, and Australia. Among the 1K cross-amplifiable core markers, 629 syntenic STMS loci were considered cross-transferable across the A-genome, within which three markers showed distinct species-specific amplicon lengths. Additionally, 42 markers were predicted to be cross-amplifiable among O. sativa complex, O. punctata, and O. coarctata. PCR-based cross-amplification of the markers in 21 Oryza species revealed hyper-variable amplicon lengths, though their synteny could not be confirmed. The A-genome core markers, along with the species combination-wise markers, provide a reliable genomic resource for developing chromosome segment substitution lines (CSSLs), molecular mapping, and transferring diverse traits from multiple wild species to all types of cultivated rice, including O. sativa, O. glaberrima, and New Rice for Africa (NERICA). Selected cross-transferable markers were used to develop CSSLs by introgressing O. rufipogon genomic segments into the O. sativa background.
摘要:开发了一套核心序列标记微卫星位点(STMS),用于不同分类群的水稻种质资源的预育种和鉴定。开发适用于不同物种的全基因组分布、可交叉转移的分子标记可以提高育种前效率。对9个参考基因组的23.5K引物对进行筛选,鉴定出1008个可交叉扩增的序列标记微卫星位点(STMS)标记,其中520个基因标记。预测的扩增子长度用聚合酶链反应(PCR)验证。此外,单个物种鉴定出3,628 ~ 13,280个标记。大多数可交叉扩增的标记在a基因组中是合成的。然而,与其他a基因组物种和亚种相比,在O. longistaminata, O. nivara和O. meridionalis中检测到大量的染色体内和染色体间易位。值得注意的是,有四个标记显示了三个亚洲a基因组物种与来自非洲、南美洲和澳大利亚的其他五个物种之间的染色体间易位的差异。在1K个可交叉扩增的核心标记中,629个同源STMS位点被认为可跨a基因组交叉转移,其中3个标记具有不同的物种特异性扩增子长度。另外,在苜蓿复合体、斑点花和玉米花中有42个标记可交叉扩增。在21个稻属物种中进行pcr交叉扩增,发现扩增子长度高度可变,但它们的合度无法确定。a -基因组核心标记和物种组合标记为染色体片段代换系(CSSLs)的开发、分子定位以及多种野生物种的不同性状向栽培水稻(包括水稻、光斑水稻和非洲新稻)的转移提供了可靠的基因组资源。利用选择的可交叉转移标记,通过将水稻的基因组片段渗入到水稻的背景中来开发CSSLs。
{"title":"A robust 1K-core marker set for wild germplasm management and targeted pre-breeding of rice: development and applications.","authors":"Debashree Dalai, Dipti Ranjan Pani, Swayamsiddha Aswita Dhal, Motilal Behera, Tapan Kumar Mondal, Muhammad Azaharudheen Tp, Joshitha Vijayan, Deepa Sarkar, Pallavi Ghose, Abhijeet Roy, Kutubuddin A Molla, Anilkumar C, Lotan Kumar Bose, Trilochan Mohapatra, Soham Ray, Meera Kumari Kar, Mridul Chakraborti","doi":"10.1007/s00122-025-05133-1","DOIUrl":"10.1007/s00122-025-05133-1","url":null,"abstract":"<p><strong>Key message: </strong>A core set of sequence tagged microsatellite sites (STMS) markers for Oryza sativa complex were developed, validated and utilized for pre-breding and characterization of Oryza germplasm from different taxa. Development of genome-wide distributed cross-transferable molecular markers applicable to different species can enhance pre-breeding efficiency. Screening of 23.5K primer pairs across nine reference genomes identified 1,008 cross-amplifiable sequence-tagged microsatellite site (STMS) markers, including 520 genic ones, for the Oryza sativa complex. Predicted amplicon lengths of the markers were validated using polymerase chain reaction (PCR). Additionally, 3,628-13,280 markers were identified for individual species. Most cross-amplifiable markers were syntenic across the A-genome. However, substantial intra- and inter-chromosomal translocations were detected in O. longistaminata, O. nivara, and O. meridionalis compared to other A-genome species and subspecies. Notably, four markers exhibited contrasting inter-chromosomal translocations between the three Asiatic A-genome species and the five other species from Africa, South America, and Australia. Among the 1K cross-amplifiable core markers, 629 syntenic STMS loci were considered cross-transferable across the A-genome, within which three markers showed distinct species-specific amplicon lengths. Additionally, 42 markers were predicted to be cross-amplifiable among O. sativa complex, O. punctata, and O. coarctata. PCR-based cross-amplification of the markers in 21 Oryza species revealed hyper-variable amplicon lengths, though their synteny could not be confirmed. The A-genome core markers, along with the species combination-wise markers, provide a reliable genomic resource for developing chromosome segment substitution lines (CSSLs), molecular mapping, and transferring diverse traits from multiple wild species to all types of cultivated rice, including O. sativa, O. glaberrima, and New Rice for Africa (NERICA). Selected cross-transferable markers were used to develop CSSLs by introgressing O. rufipogon genomic segments into the O. sativa background.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 1","pages":"23"},"PeriodicalIF":4.2,"publicationDate":"2026-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145896890","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
In Japan, rice cultivars with high eating quality such as Koshihikari are often highly susceptible to the fungus Pyricularia oryzae, which causes rice blast, the most serious disease of rice; however, little is known about the genetic factors leading to this high susceptibility to blast. Here, after our initial inoculations with P. oryzae, the expression of the pathogenesis-related protein 1b (PR1b) gene was not detected in Koshihikari using RT-qPCR, but it was detected in Nipponbare, a moderately resistant cultivar. This unexpected result was due to the insertion of the nonautonomous retrotransposon Dasheng in the coding region of PR1b in Koshihikari. We then showed that blast resistance was higher in transgenic Koshihikari lines that overexpressed PR1b, suggesting that the PR1b mutation was one of the causes of high blast susceptibility of Koshihikari. When we checked for this PR1b mutation in the top 10 most widely grown rice cultivars in Japan and the current leading cultivars in Hokkaido Prefecture as examples, at least the top eight cultivars and all current leading cultivars in Hokkaido Prefecture had this mutation. Thus, the deleterious PR1b mutation seems to be fixed in nearly the entire rice population in Japan. Moreover, our survey of genomic sequences of 36 rice cultivars in public databases showed that Dasheng was inserted into the PR1b gene in two japonica cultivars and an indica cultivar, all bred in China, at a site identical to that in Koshihikari.
{"title":"Modern Japanese rice cultivars often carry a nonautonomous retrotransposon-insertion mutation at the pathogenesis-related 1b protein gene locus causing reduced resistance to Pyricularia oryzae.","authors":"Taketo Ishihara, Kotaro Abe, Miyako Kato, Tsuyoshi Inukai","doi":"10.1007/s00122-025-05132-2","DOIUrl":"10.1007/s00122-025-05132-2","url":null,"abstract":"<p><p>In Japan, rice cultivars with high eating quality such as Koshihikari are often highly susceptible to the fungus Pyricularia oryzae, which causes rice blast, the most serious disease of rice; however, little is known about the genetic factors leading to this high susceptibility to blast. Here, after our initial inoculations with P. oryzae, the expression of the pathogenesis-related protein 1b (PR1b) gene was not detected in Koshihikari using RT-qPCR, but it was detected in Nipponbare, a moderately resistant cultivar. This unexpected result was due to the insertion of the nonautonomous retrotransposon Dasheng in the coding region of PR1b in Koshihikari. We then showed that blast resistance was higher in transgenic Koshihikari lines that overexpressed PR1b, suggesting that the PR1b mutation was one of the causes of high blast susceptibility of Koshihikari. When we checked for this PR1b mutation in the top 10 most widely grown rice cultivars in Japan and the current leading cultivars in Hokkaido Prefecture as examples, at least the top eight cultivars and all current leading cultivars in Hokkaido Prefecture had this mutation. Thus, the deleterious PR1b mutation seems to be fixed in nearly the entire rice population in Japan. Moreover, our survey of genomic sequences of 36 rice cultivars in public databases showed that Dasheng was inserted into the PR1b gene in two japonica cultivars and an indica cultivar, all bred in China, at a site identical to that in Koshihikari.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 1","pages":"21"},"PeriodicalIF":4.2,"publicationDate":"2025-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145850988","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The whitefly-transmitted begomovirus can devastate Solanaceae crops worldwide. Despite a strong demand for the genetic introgression of begomovirus resistance, only the begomovirus resistance gene in tomatoes and peppers has been cloned. Here, we aimed to identify a begomovirus resistance gene in eggplant (Solanum melongena). Previously, we identified accession No.820 as a resistance source against tomato yellow leaf curl Kanchanaburi virus (TYLCKaV). A dominant locus, Eggplant yellow leaf curl disease virus resistance 1 (Ey-1), conferring resistance against TYLCKaV was identified on chromosome 1 by genetic mapping using the F2 and F2:3 segregating populations obtained from cross-pollination of No.820 and begomovirus susceptible No.47. From whole-genome and transcriptome sequencing of No.820 and No.47, we selected 5 genes as candidates among 10 genes on the final 113-kb target region. Reverse genetic analysis using virus-induced gene silencing (VIGS) of these five candidate genes in No.820 revealed that silencing of SmNEN3, which encodes a DEDDh family exonuclease protein, resulted in loss of resistance. Comparison of the genomic and transcript sequences of SmNEN3 from No.820 and No.47 revealed a single amino acid deletion and nonsynonymous mutations that most likely contribute to begomovirus resistance. No.820 is a highly valuable genetic resource with dominant resistance to begomovirus, and the new DNA markers will greatly aid marker-assisted breeding.
{"title":"Ey-1 encodes a DEDDh exonuclease in eggplant (Solanum melongena), providing a novel pathway for begomovirus resistance.","authors":"Nadya Syafira Pohan, Kyohei Kikkawa, Natsuki Hata, Ryota Saeki, Atsushi J Nagano, Takaaki Mashiko, Sota Koeda","doi":"10.1007/s00122-025-05120-6","DOIUrl":"10.1007/s00122-025-05120-6","url":null,"abstract":"<p><p>The whitefly-transmitted begomovirus can devastate Solanaceae crops worldwide. Despite a strong demand for the genetic introgression of begomovirus resistance, only the begomovirus resistance gene in tomatoes and peppers has been cloned. Here, we aimed to identify a begomovirus resistance gene in eggplant (Solanum melongena). Previously, we identified accession No.820 as a resistance source against tomato yellow leaf curl Kanchanaburi virus (TYLCKaV). A dominant locus, Eggplant yellow leaf curl disease virus resistance 1 (Ey-1), conferring resistance against TYLCKaV was identified on chromosome 1 by genetic mapping using the F<sub>2</sub> and F<sub>2:3</sub> segregating populations obtained from cross-pollination of No.820 and begomovirus susceptible No.47. From whole-genome and transcriptome sequencing of No.820 and No.47, we selected 5 genes as candidates among 10 genes on the final 113-kb target region. Reverse genetic analysis using virus-induced gene silencing (VIGS) of these five candidate genes in No.820 revealed that silencing of SmNEN3, which encodes a DEDDh family exonuclease protein, resulted in loss of resistance. Comparison of the genomic and transcript sequences of SmNEN3 from No.820 and No.47 revealed a single amino acid deletion and nonsynonymous mutations that most likely contribute to begomovirus resistance. No.820 is a highly valuable genetic resource with dominant resistance to begomovirus, and the new DNA markers will greatly aid marker-assisted breeding.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 1","pages":"20"},"PeriodicalIF":4.2,"publicationDate":"2025-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145847078","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Allopolyploidization is a major driver of plant evolution and crop improvement, influencing both adaptation and diversification. MicroRNAs (miRNAs), 20-24 nt endogenous noncoding RNAs, regulate post-transcriptional gene expression and influence diverse biological processes. MiRNAs regulate a variety of agronomic traits and represent an important genetic resource for crop genetic improvement. While prevalent in plant evolution, the short-term (< 10,000 years) impact of allopolyploidization on miRNA evolution remains unclear. This study systematically compared miRNAs in the A genomes of Brassica rapa, Brassica juncea, and Brassica napus to reveal the short-term effects of allopolyploidization on miRNAs. The results showed that allopolyploidization caused loss of over half of the miRNAs in the A genomes of B. juncea and B. napus and accelerated miRNA cluster loss. The subgenome dominance (LF > MF1/MF2) resulting from ancient whole-genome triplication persisted post-allopolyploidization. Following allopolyploidization, the nucleotide divergence of miRNAs did not change significantly, and the maximum nucleotide divergence was only 0.11. Multi-copy miRNA retention rates differ between B. juncea and B. napus, potentially due to the influence of B and C genomes. MiRNA retention was affected by flanking protein-coding genes, with those adjacent to multi-copy protein-coding genes more likely retained as multiple copies post-allopolyploidization. Retained single miRNAs may form miRNA clusters via tandem duplication events. Additionally, homoeologous exchanges may affect the protein-coding genes flanking miRNAs. These findings indicated that short-term allopolyploidization significantly affected miRNA retention in Brassica A genome, providing new insights into allopolyploidization impacts on miRNA evolution.
{"title":"Allopolyploidization-driven short-term evolution of miRNAs in Brassica A genome.","authors":"Mengyan Zhang, Guojin Yang, Mingli Yan, Zhixiang Liu, Chaozhen Zeng","doi":"10.1007/s00122-025-05128-y","DOIUrl":"10.1007/s00122-025-05128-y","url":null,"abstract":"<p><p>Allopolyploidization is a major driver of plant evolution and crop improvement, influencing both adaptation and diversification. MicroRNAs (miRNAs), 20-24 nt endogenous noncoding RNAs, regulate post-transcriptional gene expression and influence diverse biological processes. MiRNAs regulate a variety of agronomic traits and represent an important genetic resource for crop genetic improvement. While prevalent in plant evolution, the short-term (< 10,000 years) impact of allopolyploidization on miRNA evolution remains unclear. This study systematically compared miRNAs in the A genomes of Brassica rapa, Brassica juncea, and Brassica napus to reveal the short-term effects of allopolyploidization on miRNAs. The results showed that allopolyploidization caused loss of over half of the miRNAs in the A genomes of B. juncea and B. napus and accelerated miRNA cluster loss. The subgenome dominance (LF > MF1/MF2) resulting from ancient whole-genome triplication persisted post-allopolyploidization. Following allopolyploidization, the nucleotide divergence of miRNAs did not change significantly, and the maximum nucleotide divergence was only 0.11. Multi-copy miRNA retention rates differ between B. juncea and B. napus, potentially due to the influence of B and C genomes. MiRNA retention was affected by flanking protein-coding genes, with those adjacent to multi-copy protein-coding genes more likely retained as multiple copies post-allopolyploidization. Retained single miRNAs may form miRNA clusters via tandem duplication events. Additionally, homoeologous exchanges may affect the protein-coding genes flanking miRNAs. These findings indicated that short-term allopolyploidization significantly affected miRNA retention in Brassica A genome, providing new insights into allopolyploidization impacts on miRNA evolution.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 1","pages":"18"},"PeriodicalIF":4.2,"publicationDate":"2025-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145834169","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-26DOI: 10.1007/s00122-025-05123-3
Xing Zhao, Yurong Li, Xiaodong Tang, Sijie Liu, Qiao Su, Pengju Hu, Xinxin Jin, Yahui Song, Jin Wang, Yongqing Yang
Key message: Arachis hypogaea High Antioxidant Activity gene 1 (AhHAA1), likely encoding an anthocyanidin reductase, enhances nutritional quality of testaless peanut seeds. Improving the antioxidant activity of peanut (Arachis hypogaea) seeds is critical for extending their shelf life and enhancing their nutritional quality. Mining of genetic resources to identify loci associated with antioxidant activity could facilitate the breeding of new cultivars with high antioxidant activity in seeds. Here, we developed a population of advanced recombinant inbred lines containing 175 F5:6 families derived from the parents 'JiHua 11' (JH11) and 'JiHuaTian 1' (JHT1). We constructed a high-resolution genetic map covering 2870.3 cM, with an average length of 143.5 cM per linkage group, using 1108 polymorphic single-nucleotide polymorphisms to identify quantitative trait loci (QTLs) associated with antioxidant activity and the contents of antioxidant components. The major QTL qIAA_A03_2 made the greatest contribution to standing genetic variation (53.75%). We mapped qIAA_A03_2 to a physical interval of approximately 80 kb on chromosome A03. Analysis of whole-genome variation between parents uncovered a strong candidate gene encoding an anthocyanin reductase, designated Arachis hypogaea High Antioxidant Activity 1 (AhHAA1). Analysis of the genotypes and phenotypes of near-inbred lines with high and low antioxidant levels as well as 50 peanut accessions suggested that AhHAA1 increases the antioxidant activity of processed testaless seeds, primarily by affecting the contents of antioxidant component_3 (AC3) and AC4. Our results provide insights into the genetic regulation of antioxidant activity in peanut seeds that can survive testa removal during processing. In addition, the polymorphic markers linked to AhHAA1 could facilitate the selection of germplasm and the breeding of peanuts with high nutritional quality via marker-assisted selection.
{"title":"A major qualitative trait locus increases antioxidant activity in testaless peanut seeds.","authors":"Xing Zhao, Yurong Li, Xiaodong Tang, Sijie Liu, Qiao Su, Pengju Hu, Xinxin Jin, Yahui Song, Jin Wang, Yongqing Yang","doi":"10.1007/s00122-025-05123-3","DOIUrl":"10.1007/s00122-025-05123-3","url":null,"abstract":"<p><strong>Key message: </strong>Arachis hypogaea High Antioxidant Activity gene 1 (AhHAA1), likely encoding an anthocyanidin reductase, enhances nutritional quality of testaless peanut seeds. Improving the antioxidant activity of peanut (Arachis hypogaea) seeds is critical for extending their shelf life and enhancing their nutritional quality. Mining of genetic resources to identify loci associated with antioxidant activity could facilitate the breeding of new cultivars with high antioxidant activity in seeds. Here, we developed a population of advanced recombinant inbred lines containing 175 F<sub>5:6</sub> families derived from the parents 'JiHua 11' (JH11) and 'JiHuaTian 1' (JHT1). We constructed a high-resolution genetic map covering 2870.3 cM, with an average length of 143.5 cM per linkage group, using 1108 polymorphic single-nucleotide polymorphisms to identify quantitative trait loci (QTLs) associated with antioxidant activity and the contents of antioxidant components. The major QTL qIAA_A03_2 made the greatest contribution to standing genetic variation (53.75%). We mapped qIAA_A03_2 to a physical interval of approximately 80 kb on chromosome A03. Analysis of whole-genome variation between parents uncovered a strong candidate gene encoding an anthocyanin reductase, designated Arachis hypogaea High Antioxidant Activity 1 (AhHAA1). Analysis of the genotypes and phenotypes of near-inbred lines with high and low antioxidant levels as well as 50 peanut accessions suggested that AhHAA1 increases the antioxidant activity of processed testaless seeds, primarily by affecting the contents of antioxidant component_3 (AC3) and AC4. Our results provide insights into the genetic regulation of antioxidant activity in peanut seeds that can survive testa removal during processing. In addition, the polymorphic markers linked to AhHAA1 could facilitate the selection of germplasm and the breeding of peanuts with high nutritional quality via marker-assisted selection.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 1","pages":"19"},"PeriodicalIF":4.2,"publicationDate":"2025-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145834828","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-24DOI: 10.1007/s00122-025-05126-0
Weiwei Fan, Lindong Wang, Wenxuan Huang, Jia Liu, Bing Li, Jingyu Peng, Ruirui Ma, Ran Xu, Lianjun Sun
Key message: A stable QTL for petiole length, qPL6, was mapped in a RIL population over three consecutive growing seasons, with two candidate genes identified through integrated RNA-seq analysis. Petiole length is a critical determinant of canopy architecture in soybean (Glycine max (L.) Merr.), directly modulating yield potential through its effects on photosynthetic efficiency. Consequently, identifying genes controlling petiole length is essential for developing an ideal plant architecture adapted to high-density planting, ultimately increasing yield per unit area. Here we identified a stable quantitative trait locus (QTL) for petiole length on chromosome 6, designated qPL6, across three consecutive growing seasons, which explained 6.13-19.42% of the phenotypic variance. By comparing the longitudinal anatomical structures of petioles from Qi Huang No34 (QH34) and Ji Dou No17 (JD17), we determined that the difference in petiole length was attributed to variations in parenchyma cell lengths. Through RNA-seq analysis of two near-isogenic lines (NILs), we identified 90 differential expressed genes (DEGs) common to the upper, middle and lower petioles. These DEGs were significantly enriched in GO terms related to hormone signaling pathways and cell wall organization. By integrating analysis of sequence variations with transcriptional profiles, we selected two candidate genes, Glyma.06G258000 and Glyma.06G260800, both implicated in the auxin-responsive pathway. Glyma.06G258000 showed differential expression in the petiole, pulvinus and leaf, and carried a 626-bp InDel located 737 bp upstream of its coding region. Glyma.06G260800 contained two SNPs in its second exon that induced two nonsynonymous mutations. The novel QTL and candidate genes identified in this study offer valuable genetic resources for soybean molecular breeding aimed at optimizing plant architecture and increasing yield.
关键信息:一个稳定的叶柄长度qPL6在RIL群体中连续三个生长季节被定位,并通过集成RNA-seq分析鉴定出两个候选基因。叶柄长度是大豆冠层结构的关键决定因素(Glycine max (L.))Merr.),通过其对光合效率的影响直接调节产量潜力。因此,确定控制叶柄长度的基因对于培育适合高密度种植的理想植物结构,最终提高单位面积产量至关重要。本研究在6号染色体上发现了一个稳定的叶柄长度数量性状位点(qPL6),该位点跨越3个生长季节,解释了6.13-19.42%的表型变异。通过比较芪黄34号(QH34)和鸡豆17号(JD17)叶柄的纵向解剖结构,认为叶柄长度的差异是由薄壁细胞长度的差异引起的。通过对两个近等基因系(NILs)的RNA-seq分析,我们鉴定出90个差异表达基因(DEGs)共同存在于上、中、下叶柄。这些deg显著富集与激素信号通路和细胞壁组织相关的氧化石墨烯。通过对序列变异和转录谱的综合分析,我们选择了两个候选基因Glyma.06G258000和Glyma.06G260800,这两个基因都与生长素响应途径有关。Glyma.06G258000在叶柄、叶柄和叶中均有差异表达,其编码区上游737 bp处携带一个626 bp的InDel。Glyma.06G260800的第二个外显子包含两个snp,导致两个非同义突变。本研究鉴定的新QTL和候选基因为大豆分子育种优化植株结构和提高产量提供了宝贵的遗传资源。
{"title":"Identification of quantitative trait loci qPL6 for petiole length in soybean.","authors":"Weiwei Fan, Lindong Wang, Wenxuan Huang, Jia Liu, Bing Li, Jingyu Peng, Ruirui Ma, Ran Xu, Lianjun Sun","doi":"10.1007/s00122-025-05126-0","DOIUrl":"10.1007/s00122-025-05126-0","url":null,"abstract":"<p><strong>Key message: </strong>A stable QTL for petiole length, qPL6, was mapped in a RIL population over three consecutive growing seasons, with two candidate genes identified through integrated RNA-seq analysis. Petiole length is a critical determinant of canopy architecture in soybean (Glycine max (L.) Merr.), directly modulating yield potential through its effects on photosynthetic efficiency. Consequently, identifying genes controlling petiole length is essential for developing an ideal plant architecture adapted to high-density planting, ultimately increasing yield per unit area. Here we identified a stable quantitative trait locus (QTL) for petiole length on chromosome 6, designated qPL6, across three consecutive growing seasons, which explained 6.13-19.42% of the phenotypic variance. By comparing the longitudinal anatomical structures of petioles from Qi Huang No34 (QH34) and Ji Dou No17 (JD17), we determined that the difference in petiole length was attributed to variations in parenchyma cell lengths. Through RNA-seq analysis of two near-isogenic lines (NILs), we identified 90 differential expressed genes (DEGs) common to the upper, middle and lower petioles. These DEGs were significantly enriched in GO terms related to hormone signaling pathways and cell wall organization. By integrating analysis of sequence variations with transcriptional profiles, we selected two candidate genes, Glyma.06G258000 and Glyma.06G260800, both implicated in the auxin-responsive pathway. Glyma.06G258000 showed differential expression in the petiole, pulvinus and leaf, and carried a 626-bp InDel located 737 bp upstream of its coding region. Glyma.06G260800 contained two SNPs in its second exon that induced two nonsynonymous mutations. The novel QTL and candidate genes identified in this study offer valuable genetic resources for soybean molecular breeding aimed at optimizing plant architecture and increasing yield.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"139 1","pages":"17"},"PeriodicalIF":4.2,"publicationDate":"2025-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145820783","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}