Salvatore Esposito, Samuela Palombieri, Paolo Vitale, Giuseppina Angione, Chiara D'Attilia, Francesca Taranto, Francesco Sestili, Pasquale De Vita
{"title":"Correction to: Identification and development of functional markers for purple grain genes in durum wheat (Triticum durum Desf.).","authors":"Salvatore Esposito, Samuela Palombieri, Paolo Vitale, Giuseppina Angione, Chiara D'Attilia, Francesca Taranto, Francesco Sestili, Pasquale De Vita","doi":"10.1007/s00122-024-04755-1","DOIUrl":"10.1007/s00122-024-04755-1","url":null,"abstract":"","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"137 11","pages":"256"},"PeriodicalIF":4.4,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142508493","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}
{"title":"A single-nucleotide insertion in Rxp confers durable resistance to bacterial pustule in soybean.","authors":"Fumio Taguchi-Shiobara, Koji Takahashi, Ryoichi Yano, Rintaro Suzuki, Yuko Yokota, Toshimasa Yamazaki, Tetsuya Yamada, Takashi Sayama, Naohiro Yamada, Nobuhiko Oki, Toyoaki Anai, Akito Kaga, Masao Ishimoto","doi":"10.1007/s00122-024-04743-5","DOIUrl":"10.1007/s00122-024-04743-5","url":null,"abstract":"<p><strong>Key message: </strong>The soybean Rxp gene, encoding a bHLH transcription factor and an ACT-like domain, has an rxp allele producing a truncated protein that confers resistance to pustule-causing Xanthomonas axonopodis pv. glycines. In soybean, bacterial pustules caused by Xanthomonas axonopodis pv. glycines lead to premature defoliation and decreased yield in warm, wet climates. In the USA, approximately 70 years ago, bacterial pustules were eliminated by introducing a recessive resistance allele, rxp, of the Rxp gene, representing the first example of successful soybean breeding for durable disease resistance in North America. In this study, we isolated this historical Rxp gene from resistant soybean varieties using positional cloning. The 1.06 Mb region where Rxp was reported to reside was narrowed down to an 11.1 kb region containing a single gene, Glyma.17g090500. The resistance allele, rxp, contains a T insertion. A complementation test of the Rxp allele in resistant plants confirmed the identification of the Rxp gene. The product of the susceptible wild-type allele, Rxp, is presumed to be a basic helix-loop-helix (bHLH) transcription factor with an aspartate kinase, chorismate mutase, and TyrA (ACT)-like domain. This gene was mainly expressed in extended leaves, and its homologs were identified to be distributed in angiosperms. A total of six alleles were obtained: four from spontaneous variation, including the wild-type and three mutant alleles that encoded truncated proteins, and two from ethyl methanesulfonate mutants, including an allele that encoded a truncated protein and a missense allele. By evaluating the resistance of these six alleles, we found that the loss of function of RXP decreased the bacterial pustule lesions. This study provides important insights into the soybean rxp allele, which confers durable resistance to bacterial pustules.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"137 11","pages":"254"},"PeriodicalIF":4.4,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142508492","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}
{"title":"Genome-wide mapping of quantitative trait loci conferring resistance to stripe rust in spring wheat line PI 660072.","authors":"Xinli Zhou, Yuqi Wang, Yuqi Luo, Jie Shuai, Guoyun Jia, Hongyang Chen, Liangqi Zhang, Hao Chen, Xin Li, Kebing Huang, Suizhuang Yang, Meinan Wang, Yong Ren, Gang Li, Xianming Chen","doi":"10.1007/s00122-024-04760-4","DOIUrl":"10.1007/s00122-024-04760-4","url":null,"abstract":"<p><strong>Key message: </strong>Two major QTL for resistance to stripe rust were mapped on chromosome 2BL and 4BL in spring wheat PI 660072, and their KASP markers were developed. Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most devastating diseases of wheat worldwide. Identifying resistance genes is crucial for developing resistant cultivars to control the disease. Spring wheat PI 660072 (Triticum aestivum) has been identified to possess both adult-plant resistance (APR) and all-stage resistance (ASR) to stripe rust. To elucidate the genetic basis of the resistance in PI 660072, a mapping population consisting of 211 F<sub>5</sub><sup>-</sup>F<sub>7</sub> recombinant-inbred lines (RILs) was developed from a cross of PI 660072 with susceptible spring wheat Avocet S. The mapping population was phenotyped for stripe rust responses across five field environments from 2020 to 2022 and genotyped using the 15 K SNP (single nucleotide polymorphism) array to map stripe rust resistance loci. The mapping population was also tested at the seedling stage with predominant Chinese Pst races CYR31, CYR32, CYR34 and PST-YX1-3-1 in the greenhouse. Stripe rust resistance genes were identified using the quantitative trait locus (QTL) mapping approach. Two QTL were identified with QYrPI660072.swust-2BL mapped on the long arm of chromosome 2B for ASR and QYrPI660072.swust-4BL on the long arm of chromosome 4B for APR. To facilitate marker-assisted selection breeding, Kompetitive allele specific PCR (KASP) markers, KASP-1269 for QYrPI660072.swust-2BL and KASP-3209 for QYrPI660072.swust-4BL, were developed. These markers could be used to introgress the effective resistance QTL into new wheat cultivars.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"137 11","pages":"255"},"PeriodicalIF":4.4,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142508496","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}
{"title":"Phenotypic characterization and genetic mapping of the semi-dwarf mutant sdw9 in maize.","authors":"Jiawen Zhao, Baiyu Yuan, Hao Zhang, Xiao Guo, Liangfa Wang, Xiaoqian Qiu, QianKun Xie, Liqin Mu, Chenhui Ma, Teng Zhou, Javed Hussain, Xiaoyang Chen, Xuehai Zhang, Dong Ding, Jiong Wan, Jihua Tang","doi":"10.1007/s00122-024-04762-2","DOIUrl":"10.1007/s00122-024-04762-2","url":null,"abstract":"<p><strong>Key message: </strong>In summary, we characterized a maize semi-dwarf mutant, sdw9, and successfully isolated the responsible gene, which encodes a GRAS protein, through a combination of map-based cloning and Re-sequencing (Re-seq). Our findings demonstrate that the candidate gene ZmGRAS42 regulates BR signaling genes, thereby influencing internode development. This regulatory function likely involves processes such as cell division, cell cycle regulation and cell wall synthesis. Favorable variations of ZmGRAS42 identified in this study may hold promise for the development of lodging-resistant maize cultivars suitable for high-density planting, contributing to the improvement of maize breeding programs. Plant height and lateral root angle are crucial determinants of plant architecture in maize (Zea mays) which are closely related to lodging resistance at high planting density. These traits are intricately regulated by various phytohormones. Mutations affecting hormone biosynthesis and signaling often lead to reduced yield alongside diminished plant height, posing challenges in breeding dwarf maize varieties. In this study, the maize mutant sdw9 was characterized, which displays shorter stature and altered lateral root angle compared to WT, while showing potential to increase planting density and improve overall yield despite a slight reduction in single-ear yield. Employing positional cloning coupled with Re-seq techniques, we pinpointed a transposon insertion in the candidate gene ZmGRAS42, which encodes a GRAS transcription factor involved in BR signaling in maize. Transcriptome analysis revealed that ZmGRAS42 orchestrates the expression of several known dwarfing genes such as D8, Br2, and Na2, along with genes associated with cell wall organization, cell division, and cell cycle regulation, notably Cesa4, Cesa7, and Cyc11. Furthermore, identification of favorable ZmGRAS42 haplotypes linked to reduced plant height offers novel avenues for maize breeding strategies. These findings not only hold the potential for enhancing maize lodging resistance but also for optimizing land utilization through high-density planting practices.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"137 11","pages":"253"},"PeriodicalIF":4.4,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142475365","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}
{"title":"GW3, encoding a member of the P450 subfamily, controls grain width by regulating the GA<sub>4</sub> content in spikelets of rice (Oryza sativa L.).","authors":"Xiaojing Dang, Qing Xu, Yulong Li, Shaojie Song, Changmin Hu, Chunyu Jing, Ying Zhang, Dezheng Wang, Delin Hong, Jianhua Jiang","doi":"10.1007/s00122-024-04751-5","DOIUrl":"10.1007/s00122-024-04751-5","url":null,"abstract":"<p><strong>Key message: </strong>A stable QTL, GW3, controlling grain width was identified in two populations. Its causal gene LOC_Os03g04680 was verified by gene-based haplotype analysis, expression analysis, gene knockout and complementation transgenic tests. Grain width (GW) is one of the key traits affecting grain size and determines grain yield and appearance quality in rice. Mining gene loci and elite alleles controlling GW is necessary. The GW phenotypes of the two populations were investigated in three environments, which showed abundant phenotypic variation. GW3, encoding a P450 subfamily protein, was identified and validated as a causal gene by gene-based haplotype analysis, expression analysis, gene knockout and complementation transgenic tests. The accessions with large GW values had high gene expression levels. In addition, the GW of the accessions with the GG allele was significantly greater than that of the accessions with the AA allele. The Hap 1 and Hap 3 were identified as elite haplotypes, which can increase GW. The expression levels of OsKO1, OsGA3ox1, OsGA20ox1 and OsGA20ox2 in the young panicle of A7444 were significantly greater than those in the young panicle of the mutants, indicating that GW3 may be involved in the gibberellins (GA) biosynthesis pathway to regulate GW. GA<sub>4</sub> content detection and electron scanning analysis revealed that GA<sub>4</sub> regulates GW by affecting glume cell size. These results provide new insights for studying the genetic mechanism of rice GW and provide a material basis for breeding high-yield rice varieties.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"137 11","pages":"251"},"PeriodicalIF":4.4,"publicationDate":"2024-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142475352","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}
{"title":"Yr29 combined with QYr.nwafu-4BL.3 confers durable resistance to stripe rust in wheat cultivar Jing 411.","authors":"Mingjie Xiang, Bo Tian, Jianghao Cao, Shengjie Liu, Caie Zhou, Xiaoting Wang, Yibo Zhang, Jiale Li, Xunying Yuan, Jufen Wan, Rui Yu, Weijun Zheng, Jianhui Wu, Qingdong Zeng, Zhensheng Kang, Chunlian Li, Fa Cui, Dejun Han","doi":"10.1007/s00122-024-04758-y","DOIUrl":"10.1007/s00122-024-04758-y","url":null,"abstract":"<p><strong>Key message: </strong>The combination of a QTL on chromosome arm 4BL and Yr29 provides durable resistance with no significant yield penalty. Wheat stripe rust or yellow rust (YR), caused by Puccinia striiformis f. sp. tritici (Pst), causes substantial yield reductions globally, but losses can be minimized by using resistance genes. Chinese wheat cultivar Jing 411 (J411) has continued to display an acceptable level of adult-plant resistance (APR) to YR in varied field conditions since its release in the 1990s. A recombinant inbred line (RIL) population comprising 187 lines developed from a cross of J411 and Kenong 9204 (KN9204) was evaluated in multiple environments to identify genomic regions carrying genes for YR resistance. A total of five quantitative trait loci (QTL) on chromosome arm 1BL, 3BS, 4BL, 6BS, and 7BL from J411 and two QTL on 3DS and 7DL from KN9204 were detected using inclusive composite interval mapping with the wheat 660 K SNP array. QYr.nwafu-1BL.5 and QYr.nwafu-4BL.3 from J411 were robust and showed similar effects in all environments. QYr.nwafu-1BL.5 was likely the pleiotropic gene of Yr29/Lr46. QYr.nwafu-4BL.3 was located within a 1.0 cM interval delimited by KASP markers AX-111609222 and AX-89755491. Based on haplotype analysis, Yr29 and QYr.nwafu-4BL.3 were identified as genetic components of quantitative resistance in a number of wheat cultivars. Moreover, RILs with Yr29 and QYr.nwafu-4BL.3 individually or when combined showed higher resistance to YR in rust nurseries compared with RILs without them, and there was no negative effect of their presence on agronomic traits under rust-free conditions. These results suggest that effective polymerization strategy is important for breeding high yielding and durable resistance cultivars.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"137 11","pages":"252"},"PeriodicalIF":4.4,"publicationDate":"2024-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142475366","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}
Peter E Eckstein, Lindsay J Griffith, Xiang M Zhang, T Kelly Turkington, Mark G Colin, Samuel Holden, Sean Walkowiak, Gurcharn S Brar, Aaron D Beattie
{"title":"An island of receptor-like genes at the Rrs13 locus on barley chromosome 6HS co-locate with three novel sources of scald resistance.","authors":"Peter E Eckstein, Lindsay J Griffith, Xiang M Zhang, T Kelly Turkington, Mark G Colin, Samuel Holden, Sean Walkowiak, Gurcharn S Brar, Aaron D Beattie","doi":"10.1007/s00122-024-04746-2","DOIUrl":"10.1007/s00122-024-04746-2","url":null,"abstract":"<p><p>Three Hordeum spontaneum-derived resistances (referred to as 145L2, 41T1 and 40Y5) have demonstrated long-term effectiveness against barley scald, caused by Rhynchosporium commune, in western Canada. Genetic mapping of these resistances in three populations, and the use of five barley genome assemblies, revealed they co-located to a narrowly defined 0.58-1.2 Mbp region of chromosome 6HS containing the Rrs13 scald resistance gene. Differential disease reactions among the three resistances and a Rrs13 carrier (AB6) to a panel of 24 scald isolates indicated that the four resistances were unique from one another. A marker created to target the 6HS scald locus was screened across a panel of barley germplasm that included H. vulgare, H. spontaneum and H. bulbosum lines. The marker showed specificity to H. vulgare lines known to carry the 6HS scald resistances and to two H. spontaneum lines that trace their origins to Jordan. Within the 0.58-1.2 Mbp region were 2-7 tandemly repeated leucine-rich repeat receptor-like proteins (LRR-RLP) and one lectin receptor-like kinase (Lec-RLK) genes with abundant sequence variation between them. The well-defined role that RLP and RLK genes play in plant defense responses make them logical candidate resistance genes, with one possible hypothesis being that each unique scald resistance may be encoded by a different RLP that interacts with a common RLK. It is suggested the three scald resistances be temporarily named Rrs13<sup>145L2</sup>, Rrs13<sup>41T1</sup> and Rrs13<sup>40Y5</sup> to recognize their co-location to the Rrs13 locus until it is determined whether these resistances represent unique genes or alleles of the same gene.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"137 11","pages":"249"},"PeriodicalIF":4.4,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11481673/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142393553","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}
{"title":"Co-localization of quantitative trait loci for pod and kernel traits and development of molecular marker for kernel weight on chromosome Arahy05 in peanut (Arachis hypogaea L.).","authors":"Yuanjin Fang, Hua Liu, Ziqi Sun, Li Qin, Zheng Zheng, Feiyan Qi, Jihua Wu, Wenzhao Dong, Bingyan Huang, Xinyou Zhang","doi":"10.1007/s00122-024-04749-z","DOIUrl":"10.1007/s00122-024-04749-z","url":null,"abstract":"<p><strong>Key message: </strong>Stable QTL for pod and kernel traits were co-localized on chromosome Arahy05, and an INDEL marker at 106,411,957 on Arahy05 was developed and validated to be useful for marker-assisted selection of kernel weight. Pod and kernel traits, such as hundred pod weight (HPW), and hundred kernel weight (HKW), along with pod and kernel sizes, are pivotal determinants of yield in peanut breeding programs. This study sought to identify quantitative trait loci (QTL) that are associated with these pod and kernel traits in peanuts. To achieve this, a recombinant inbred line (RIL) population, was derived from a cross between Yuhua15, a cultivar known for its high yield, and a germplasm accession W1202. The investigation uncovered stable and major QTL that are significantly associated with both pod and kernel weight and were consistently co-localized on chromosomes Arahy05 and Arahy08. Furthermore, an INDEL marker was identified and characterized in the QTL interval on Arahy05. An extensive re-sequencing analysis comprising 395 germplasm accessions led to the discovery of two principal haplotypes within a 500-kb window flanking the aforementioned INDEL marker. The haplotypes exhibited a significant correlation with the HKW in our diverse panel of germplasm accessions. Notably, the 170 accessions harboring the haplotype associated with an increased HKW primarily represented botanical varieties, specifically Arachis hypogaea var. hypogaea and A. hypogaea var. hirsuta. On the other hand, the 137 accessions associated with the alternative haplotype, which corresponded to a reduced HKW, were predominately identified as belonging to botanical varieties within A. hypogaea subsp. fastigiata. The INDEL marker located on Arahy05, which demonstrates close linkage to the pod and kernel traits, would be an efficient approach for marker-assisted selection (MAS) of pod and kernel weight in breeding programs.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"137 11","pages":"250"},"PeriodicalIF":4.4,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11464562/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142393554","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}
{"title":"Genomic estimated selection criteria and parental contributions in parent selection increase genetic gain of maternal haploid inducers in maize.","authors":"Yu-Ru Chen, Ursula K Frei, Thomas Lübberstedt","doi":"10.1007/s00122-024-04744-4","DOIUrl":"10.1007/s00122-024-04744-4","url":null,"abstract":"<p><strong>Key message: </strong>Parental combinations determined by genomic estimated usefulness and parental contributions of the lines in bridging population can enhance the genetic gain of traits of interest in maternal haploid inducer breeding. Parent selection in crosses aligns well with the quantitative trait performance in the progenies. We herein take advantage of estimated genetic values (EGV) and usefulness criteria (UC) of bi-parental combinations by genomic prediction (GP) to compare the empirical performance of doubled haploid inducer (DHI) progenies of eight elite inducers crosses in a half-diallel. We used parental contribution and discovery of superiors from elite-by-historical bridging populations to enhance genetic gain for long-term selection. In this empirical study, the narrow-sense heritabilities of four traits of interest (Days to flowering, DTF; haploid induction rate, HIR; plant height, PHT; Total primary branch length, PBL) in DHI population were 0.81, 0.71, 0.45 and 0.46, respectively. The genomic estimated EGV_Mid/Mean and EGV/UC_Inferior was significantly correlated with the sample mean of progenies and inferiors in four traits in the breeding and bridging population. EGV/UC_Superior were significantly correlated with the mean of superiors in DTF, PHT, and PBL in breeding and bridging populations. The genomic estimated parent contributions in DH progenies of bridging populations enabled discovery of favorable genome region from historical inducers to improve the genetic gain of HIR for long-term selection.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"137 11","pages":"248"},"PeriodicalIF":4.4,"publicationDate":"2024-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142378333","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}