THEORETICAL AND APPLIED GENETICS 在现代植物遗传学、植物基因组学和植物生物技术的所有关键领域发表原创研究和评论文章。所有工作都需要有明确的遗传成分并对植物育种产生重大影响。只有结合新的实验数据和/或如果它们表明在植物遗传学或育种中的相关应用，理论考虑才被接受。该杂志强调实用性，侧重于对主要作物植物的研究和介绍创新方法的文章。

The journal "Theoretical And Applied Genetics" publishes original research and review articles in all key areas of modern plant genetics, plant genomics, and plant biotechnology. All work must have a clear genetic component and make a significant impact on plant breeding. Theoretical considerations are only accepted when combined with new experimental data and/or when they demonstrate relevant applications in plant genetics or breeding. The journal emphasizes practicality, focusing on research on major crop plants and articles introducing innovative methods.

《Theoretical And Applied Genetics》期刊发表现代植物遗传学、植物基因组学和植物生物技术领域的原创研究和评论文章。所有的研究工作都必须具有明确的遗传成分，并对植物育种产生显著影响。理论性的研究只有在结合新的实验数据，或在植物遗传学或育种中具有相关应用时，才会被接受。该期刊强调实用性，重点关注主要作物植物的研究以及介绍创新方法的文章。

Theoretical And Applied Genetics

Abstract Key Message Lack of function of a D-genome adult plant resistance gene upon introgression into durum wheat. Abstract The wheat Lr34/Yr18/Sr57/Pm38/Ltn1 adult plant resistance gene ( Lr34 ), located on chromosome arm 7DS, provides broad spectrum, partial, adult plant resistance to leaf rust, stripe rust, stem rust and powdery mildew. It has been used extensively in hexaploid bread wheat (AABBDD) and conferred durable resistance for many decades. These same diseases also occur on cultivated tetraploid durum wheat and emmer wheat but transfer of D genome sequences to those subspecies is restricted due to very limited intergenomic recombination. Herein we have introgressed the Lr34 gene into chromosome 7A of durum wheat. Durum chromosome substitution line Langdon 7D(7A) was crossed to Cappelli ph1c , a mutant derivative of durum cultivar Cappelli homozygous for a deletion of the chromosome pairing locus Ph1 . Screening of BC 1 F 2 plants and their progeny by KASP and PCR markers, 90 K SNP genotyping and cytology identified 7A chromosomes containing small chromosome 7D fragments encoding Lr34 . However, in contrast to previous transgenesis experiments in durum wheat, resistance to wheat stripe rust was not observed in either Cappelli/Langdon 7D(7A) or Bansi durum plants carrying this Lr34 encoding segment due to low levels of Lr34 gene expression. Key message

Hongyu Li

Peng Zhang

Ming Luo

Mohammad Hoque

Soma Chakraborty

Brenton Brooks

Jianbo Li

Smriti Singh

Kerrie Forest

Allan Binney

Lianquan Zhang

Diane Mather

Michael Ayliffe

Theoretical and Applied Genetics

Introgression of the bread wheat D genome encoded Lr34/Yr18/Sr57/Pm38/Ltn1 adult plant resistance gene into Triticum turgidum (durum wheat)

We have previously described gene introgression from the wild nightshade Solanum lycopersicoides into tomato (Lycopersicon esculentum) through the use of either diploid or sesquidiploid hybrids (the latter consisting of two genomes of L. esculentum and one genome of S. lycopersicoides). Both types of intergeneric hybrids display pollen sterility, but workable ovule fertility. Unilateral incompatibility prevents their direct hybridization with staminate L. esculentum. Pollen of a self-compattible form of the related wild species L. pennellii is compatible with pistils of L. esculentum x S. lycopersicoides hybrids. This trait was backcrossed from L. pennellii to L. esculentum in order to develop bridging lines that could be used to obtain progeny from the intergeneric hybrids and to study the inheritance of bridging ability. In progeny of L. esculentum x S. lycopersicoides hybrids pollinated with L. pennellii-derived bridging lines, preferential transmission of L. pennellii alleles was observed for certain isozyme and RFLP markers on chromosomes 1, 6 and 10. The skewed segregations suggest linkage to three major pollen-expressed compatibility loci. This was confirmed by observations of pollen tube growth, which indicated that compatibility with pistils of the diploid intergeneric hybrid occurred only in bridging lines at least heterozygous for the L. pennellii markers on chromosomes 1, 6 and 10. Compatibility with the sesquidiploid hybrid required only the chromosome 1 and 6 loci, indicating an apparent effect of gene dosage on expression of incompatibility in the pistil. In an F2 L. esculentum x L. pennellii population, preferential transmission of L. pennellii alleles was observed for the same markers on chromosomes 1 and 10, as well as other markers on chromosomes 3, 11, and 12, but not 6. The chromosome 1 pollen compatibility locus maps to or near the S-locus, which determines S-allele specificity. The results are discussed in relation to existing genetic models for unilateral incompatibility, including the possible involvement of the S-locus.

R T Chetelat

J W Deverna

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik

Theor Appl Genet

Expression of unilateral incompatibility in pollen of Lycopersicon pennellii is determined by major loci on chromosomes 1, 6 and 10.

Karyotypes evolve through numerical and structural chromosome rearrangements. We show that Phaseolus leptostachyus, a wild bean, underwent a rapid genome reshuffling associated with the reduction from 11 to 10 chromosome pairs, but without whole genome duplication, the highest chromosome evolution rate known for plants. Plant karyotypes evolve through structural rearrangements often associated with polyploidy or dysploidy. The genus Phaseolus comprises ~ 90 species, five of them domesticated due to their nutritional relevance. Most of the species have 2n = 22 karyotypes and are highly syntenic, except for three dysploid karyotypes of species from the Leptostachyus group (2n = 20) that have accumulated several rearrangements. Here, we investigated the degrees of structural rearrangements among Leptostachyus and other Phaseolus groups by estimating their chromosomal evolution rates (CER). For this, we combined our oligo-FISH barcode system for beans and chromosome-specific painting probes for chromosomes 2 and 3, with rDNA and a centromeric probe to establish chromosome orthologies and identify structural rearrangements across nine Phaseolus species. We also integrated the detected rearrangements with a phylogenomic approach to estimate the CERs for each Phaseolus lineage. Our data allowed us to identify translocations, inversions, duplications and deletions, mostly in species belonging to the Leptostachyus group. Phaseolus leptostachyus showed the highest CER (12.31 rearrangements/My), a tenfold increase in contrast to the 2n = 22 species analysed. This is the highest rate known yet for plants, making it a model species for investigating the mechanisms behind rapid genome reshuffling in early species diversification.

Thiago Nascimento

Andrea Pedrosa-Harand

High rates of structural rearrangements have shaped the chromosome evolution in dysploid Phaseolus beans.

High variability for and candidate loci associated with resistance to southern anthracnose and clover rot in a worldwide collection of red clover provide a first basis for genomics-assisted breeding. Red clover (Trifolium pratense L.) is an important forage legume of temperate regions, particularly valued for its high yield potential and its high forage quality. Despite substantial breeding progress during the last decades, continuous improvement of cultivars is crucial to ensure yield stability in view of newly emerging diseases or changing climatic conditions. The high amount of genetic diversity present in red clover ecotypes, landraces, and cultivars provides an invaluable, but often unexploited resource for the improvement of key traits such as yield, quality, and resistance to biotic and abiotic stresses. A collection of 397 red clover accessions was genotyped using a pooled genotyping-by-sequencing approach with 200 plants per accession. Resistance to the two most pertinent diseases in red clover production, southern anthracnose caused by Colletotrichum trifolii, and clover rot caused by Sclerotinia trifoliorum, was assessed using spray inoculation. The mean survival rate for southern anthracnose was 22.9% and the mean resistance index for clover rot was 34.0%. Genome-wide association analysis revealed several loci significantly associated with resistance to southern anthracnose and clover rot. Most of these loci are in coding regions. One quantitative trait locus (QTL) on chromosome 1 explained 16.8% of the variation in resistance to southern anthracnose. For clover rot resistance we found eight QTL, explaining together 80.2% of the total phenotypic variation. The SNPs associated with these QTL provide a promising resource for marker-assisted selection in existing breeding programs, facilitating the development of novel cultivars with increased resistance against two devastating fungal diseases of red clover.

Lea A. Frey

Tim Vleugels

Tom Ruttink

Franz X. Schubiger

Marie Pégard

Leif Skøt

Christoph Grieder

Bruno Studer

Isabel Roldán-Ruiz

Roland Kölliker

Phenotypic variation and quantitative trait loci for resistance to southern anthracnose and clover rot in red clover

Utilizing an innovative GWAS in CSLRP, 44 QTL 199 alleles with 72.2 % contribution to SIFC variation were detected and organized into a QTL-allele matrix for cross design and gene annotation. The seed isoflavone content (SIFC) of soybeans is of great importance to health care. The Chinese soybean landrace population (CSLRP) as a genetic reservoir was studied for its whole-genome quantitative trait loci (QTL) system of the SIFC using an innovative restricted two-stage multi-locus genome-wide association study procedure (RTM-GWAS). A sample of 366 landraces was tested under four environments and sequenced using RAD-seq (restriction-site-associated DNA sequencing) technique to obtain 116,769 single nucleotide polymorphisms (SNPs) then organized into 29,119 SNP linkage disequilibrium blocks (SNPLDBs) for GWAS. The detected 44 QTL 199 alleles on 16 chromosomes (explaining 72.2 % of the total phenotypic variation) with the allele effects (92 positive and 107 negative) of the CSLRP were organized into a QTL-allele matrix showing the SIFC population genetic structure. Additional differentiation among eco-regions due to the SIFC in addition to that of genome-wide markers was found. All accessions comprised both positive and negative alleles, implying a great potential for recombination within the population. The optimal crosses were predicted from the matrices, showing transgressive potentials in the CSLRP. From the detected QTL system, 55 candidate genes related to 11 biological processes were χ (2)-tested as an SIFC candidate gene system. The present study explored the genome-wide SIFC QTL/gene system with the innovative RTM-GWAS and found the potentials of the QTL-allele matrix in optimal cross design and population genetic and genomic studies, which may have provided a solution to match the breeding by design strategy at both QTL and gene levels in breeding programs.

Shan Meng

Jianbo He

Tuanjie Zhao

Guangnan Xing

Yan Li

Shouping Yang

Jiangjie Lu

Yufeng Wang

Junyi Gai

Detecting the QTL-allele system of seed isoflavone content in Chinese soybean landrace population for optimal cross design and gene system exploration.

QTL-seq, linkage mapping, and whole-genome resequencing revealed a new locus (qCLS5.1) controlling Cercospora canescens resistance in mungbean and Receptor-like protein 12 (RLP12) genes as candidate genes for the resistance. Cercospora leaf spot (CLS) disease, caused by Cercospora canescens, is a common disease of mungbean (Vigna radiata). In this study, the genetics of CLS resistance was investigated in a new source of resistance (accession V2817) and the resistance was finely mapped to identify candidate genes. F2 and F2:3 populations of the cross V1197 (susceptible) × V2718 and a BC1F1 population of the cross V1197 × (V1197 × V2817) were used in this study. Segregation analysis suggested that the resistance is controlled by a single dominant gene. QTL-seq using F2 individuals revealed that a single QTL (designated qCLS5.1) on chromosome 5 controlled the resistance. The qCLS5.1 was confirmed in the F2:3 and BC1F1 populations by QTL analysis. Fine mapping using 978 F2 individuals localized qCLS5.1 to a 48.94 Kb region containing three tandemly duplicated Receptor-like protein 12 (RLP12) genes. Whole-genome resequencing and alignment of V1197 and V2817 revealed polymorphisms causing amino acid changes and premature stop codons in the three RLP12 genes. Collectively, these results show that qCLS5.1 is a new locus for CLS resistance in mungbean, and a cluster of RLP12 genes are candidate genes for the resistance. The new locus qCLS5.1 will be useful for molecular breeding of durable CLS-resistant mungbean cultivars.

Makawan Srichan

Kularb Laosatit

Yun Lin

Xingxing Yuan

Xin Chen

Prakit Somta

QTL-seq and QTL mapping identify a new locus for Cercospora leaf spot (Cercospora canescens) resistance in mungbean (Vigna radiata) and a cluster of Receptor-like protein 12 (RLP12) genes as candidate genes for the resistance

QTL-seq和QTL定位在绿豆（Vigna radiata）中鉴定出新的尾孢叶斑病（Cercospora canescens）抗性位点，并将受体样蛋白12（RLP12）基因簇作为抗性候选基因

Abstract Flowering time synchronizes reproductive development with favorable environmental conditions to optimize yield. Improved understanding of the genetic control of flowering will help optimize varietal adaptation to future agricultural systems under climate change. Here, we investigate the genetic basis of flowering time in winter wheat ( Triticum aestivum L.) using an eight-founder multi-parent advanced generation intercross (MAGIC) population. Flowering time data was collected from field trials across six growing seasons in the United Kingdom, followed by genetic analysis using a combination of linear modelling, simple interval mapping and composite interval mapping, using either single markers or founder haplotype probabilities. We detected 57 quantitative trait loci (QTL) across three growth stages linked to flowering time, of which 17 QTL were identified only when the major photoperiod response locus Ppd-D1 was included as a covariate. Of the 57 loci, ten were identified using all genetic mapping approaches and classified as ‘major’ QTL, including homoeologous loci on chromosomes 1B and 1D, and 4A and 4B. Additional Earliness per se flowering time QTL were identified, along with growth stage- and year-specific effects. Furthermore, six of the main-effect QTL were found to interact epistatically with Ppd-D1 . Finally, we exploited residual heterozygosity in the MAGIC recombinant inbred lines to Mendelize the Earliness per se QTL QFt.niab-5A.03 , which was confirmed to modulate flowering time by at least four days. This work provides detailed understanding of the genetic control of phenological variation within varieties relevant to the north-western European wheat genepool, aiding informed manipulation of flowering time in wheat breeding.

Laure Fourquet

Tobias Barber

Camila Campos-Mantello

Phil Howell

Beata Orman-Ligeza

Lawrence Percival-Alwyn

Gemma A. Rose

Hester Sheehan

Tally I. C. Wright

Friedrich Longin

Tobias Würschum

Dario Novoselovic

Andy J. Greenland

Ian J. Mackay

James Cockram

Alison R. Bentley

An eight-founder wheat MAGIC population allows fine-mapping of flowering time loci and provides novel insights into the genetic control of flowering time

八亲本小麦MAGIC群体实现开花时间位点的精细定位，并提供关于开花时间遗传控制的新见解

A powdery mildew (Pm) resistance locus PmRc1 was identified and transferred from Roegneria ciliaris into wheat. Two compensative translocation lines carrying PmRc1 were developed. Powdery mildew (Pm), caused by the biotrophic fungal pathogen Blumeria graminis f.sp. tritici (Bgt), is a global destructive disease of bread wheat (Triticum aestivum L.). Identifying and utilizing new Pm resistance gene(s) is the most fundamental work for disease control. Roegneria ciliaris (2n = 4 x= 28, genome ScScYcYc) is a wild relative species of cultivated wheat. In this work, we evaluated wheat-R. ciliaris disomic chromosome addition lines for Pm resistance in multiple years. The introduction of R. ciliaris chromosome 1Sc into wheat enhanced resistance. The resistance locus on 1Sc was designated as PmRc1. To cytologically map PmRc1, we induced structural rearrangements using ion irradiation and increasing homoeologous chromosomal recombination. The identified 43 1Sc translocation or deletion lines were used to construct 1Sc cytological bin map by marker analysis using 111 molecular markers. Based on the Pm resistance of the characterized structural rearrangement lines, the PmRc1 locus was cytologically mapped to bin 1ScS-8 of 1Sc short arm, flanked by markers CMH93-2 and CMH114-1. Two compensatory chromosomal translocation lines (T1ScS · 1BL and T1ScS-1AS · 1AL) carrying PmRc1 were developed and assessed for their agronomic traits. Translocation chromosome T1ScS · 1BL had enhanced Pm resistance accompanied by negative effects on grain number and single plant yield. Translocation chromosome T1ScS-1AS · 1AL had enhanced Pm resistance and increased spikelet number per spike, without any obvious negative effect on other tested traits. Thus, T1ScS-1AS · 1AL is recommended preferentially used in wheat breeding for Pm resistance.

Menghao Cheng

Huajian Zhang

Yao Zhang

Xiong Tang

Zongkuan Wang

Xu Zhang

Xinying Song

Xingyue Li

Huimin Cui

Tong Wang

Rongrong Song

Jin Xiao

Haiyan Wang

Xiue Wang

Cytological mapping of a powdery mildew resistance locus PmRc1 based on wheat-Roegneria ciliaris structural rearrangement library

基于小麦-鹅观草结构重排文库的白粉病抗性位点PmRc1的细胞学定位

The photosynthetic phenotype of trees undergoes changes and interactions that reflect their abilities to exploit light energy. Environmental disturbances and genetic factors have been recognized as influencing these changes and interactions, yet our understanding of the underlying biological mechanisms remains limited, particularly in stochastic environments. Here, we developed a high-dimensional stochastic differential framework (HDSD) for the genome-wide mapping of quantitative trait loci (QTLs) that regulate competition or cooperation in environment-dependent phenotypes. The framework incorporates random disturbances into system mapping, a dynamic model that views multiple traits as a system. Not only does this framework describe how QTLs regulate a single phenotype, but also how they regulate multiple phenotypes and how they interact with each other to influence phenotypic variations. To validate the proposed model, we conducted mapping experiments using chlorophyll fluorescence phenotype data from Populus simonii. Through this analysis, we identified several significant QTLs that may play a crucial role in photosynthesis in stochastic environments, in which 76 significant QTLs have already been reported to encode proteins or enzymes involved in photosynthesis through functional annotation. The constructed genetic regulatory network allows for a more comprehensive analysis of the internal genetic interactions of the photosynthesis process by visualizing the relationships between SNPs. This study shows a new way to understand the genetic mechanisms that govern the photosynthetic phenotype of trees, focusing on how environmental stochasticity and genetic variation interact to shape their light energy utilization strategies.

Junze Jiang

Ziyang Zhou

Kaiyan Lu

Huiying Gong

Deqiang Zhang

Qing Fang

Xiao-Yu Zhang

Yuepeng Song

Exploiting light energy utilization strategies in Populus simonii through multitrait-GWAS: insights from stochastic differential models

利用多性状全基因组关联分析揭示胡杨光能利用策略：随机微分模型的见解

We revealed the neglected genetic relationships of resistance for six major wheat diseases and established a haploblock-based catalogue with novel forms of resistance by multi-trait haplotype characterisation. Genetic potential to improve multiple disease resistance was highlighted through haplotype stacking simulations. Wheat production is threatened by numerous fungal diseases, but the potential to breed for multiple disease resistance (MDR) mechanisms is yet to be explored. Here, significant global genetic correlations and underlying local genomic regions were identified in the Vavilov wheat diversity panel for six major fungal diseases, including biotrophic leaf rust (LR), yellow rust (YR), stem rust (SR), hemibiotrophic crown rot (CR), and necrotrophic tan spot (TS) and Septoria nodorum blotch (SNB). By adopting haplotype-based local genomic estimated breeding values, derived from an integrated set of 34,899 SNP and DArT markers, we established a novel haplotype catalogue for resistance to the six diseases in over 20 field experiments across Australia and Ethiopia. Haploblocks with high variances of haplotype effects in all environments were identified for three rusts, and pleiotropic haploblocks were identified for at least two diseases, with four haploblocks affecting all six diseases. Through simulation, we demonstrated that stacking optimal haplotypes for one disease could improve resistance substantially, but indirectly affected resistance for other five diseases, which varied depending on the genetic correlation with the non-target disease trait. On the other hand, our simulation results combining beneficial haplotypes for all diseases increased resistance to LR, YR, SR, CR, TS, and SNB, by up to 48.1%, 35.2%, 29.1%, 12.8%, 18.8%, and 32.8%, respectively. Overall, our results highlight the genetic potential to improve MDR in wheat. The haploblock-based catalogue with novel forms of resistance provides a useful resource to guide desirable haplotype stacking for breeding future wheat cultivars with MDR.

Jingyang Tong

Zerihun T. Tarekegn

Dilani Jambuthenne

Samir Alahmad

Sambasivam Periyannan

Lee Hickey

Eric Dinglasan

Ben Hayes

Stacking beneficial haplotypes from the Vavilov wheat collection to accelerate breeding for multiple disease resistance

从瓦维洛夫小麦收集品中叠加有益单倍型以加速多病害抗性育种

Abbreviation	Theoret. Appl. Genetics
Journal Impact	4.44
Quartiles(Global)	PLANT SCIENCES(Q1)

ISSN	0040-5752, 1432-2242
h-index	200
Top Journals	Yes

Publication Information	Publisher: Springer Verlag，Publishing cycle: Semimonthly，Journal Type: journal，Open Access Journals: No
Basic data	Year of publication: 1968，Proportion of original research papers: 90.79%，Self Citation Rate:9.10%， Gold OA Rate: 29.91%
Average review cycle	网友分享经验：平均3.0个月
Average recruitment ratio	网友分享经验：约75%

Theoretical And Applied Genetics

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