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

Seventy-three QTL related to grain color and tannin content were identified in Chinese sorghum accessions, and a new recessive allelic variant of TAN2 gene was discovered. Sorghum is mainly used for brewing distilled liquors in China. Since grain tannins play an important role in liquor brewing, accurately understanding the relationship between grain color and tannin content can provide basis for selection standards of tannin sorghum. We resequenced a panel of 242 Chinese sorghum accessions and performed population structure and genome-wide association study (GWAS) to identify quantitative trait locus (QTL) affecting pericarp color, testa pigment, and tannin content. Phylogenetic analysis, principal component analysis (PCA), and admixture model were used to infer population structure. Two distinct genetic sub-populations were identified according to their corresponding northern and southern geographic origin. To investigate the genetic basis of natural variation in sorghum grain color, GWAS with 2,760,264 SNPs was conducted in four environments using multiple models (Blink, FarmCPU, GLM, and MLM). Seventy-three QTL were identified to be associated for the color of exocarp, mesocarp, testa, and tannin content on all chromosomes except chromosome 5, of which 47 might be novel QTL. Some important QTL were found to colocalize with orthologous genes in the flavonoid biosynthetic pathway from other plants, including orthologous of Arabidopsis (Arabidopsis thaliana) TT2, TT7, TT12, TT16 and AT5G41220 (GST), as well as orthologous of rice (Oryza sativa) MYB61 and OsbHLH025. Our investigation of the variation in grain color and tannin content in Chinese sorghum germplasm may help guide future sorghum breeding for liquor brewing.

Liyi Zhang

Jianxia Xu

Yanqing Ding

Ning Cao

Xu Gao

Zhou Feng

Kuiying Li

Bing Cheng

Lengbo Zhou

Mingjian Ren

Yuezhi Tao

Guihua Zou

Theoretical and Applied Genetics

GWAS of grain color and tannin content in Chinese sorghum based on whole-genome sequencing

基于全基因组测序的中国高粱籽粒颜色和单宁含量全基因组关联分析

qSB12YSB, a major quantitative sheath blight resistance gene originated from rice variety YSBR1 with good breeding potential, was mapped to a 289-Kb region on chromosome 12. Sheath blight (ShB), caused by Rhizoctonia solani kühn, is one of the most serious global rice diseases. Rice resistance to ShB is a typical of quantitative trait controlled by multiple quantitative trait loci (QTLs). Many QTLs for ShB resistance have been reported while only few of them were fine-mapped. In this study, we identified a QTL on chromosome 12, in which the qSB12YSB resistant allele shows significant ShB resistance, by using 150 BC4 backcross inbred lines employing the resistant rice variety YSBR1 as the donor and the susceptible variety Lemont (LE) as the recurrent parent. We further fine-mapped qSB12YSB to a 289-kb region by generating 34 chromosomal segment substitution lines and identified a total of 18 annotated genes as the most likely candidates for qSB12YSB after analyzing resequencing and transcriptomic data. KEGG analysis suggested that qSB12YSB might activate secondary metabolites biosynthesis and ROS scavenging system to improve ShB resistance. qSB12YSB conferred significantly stable resistance in three commercial rice cultivars (NJ9108, NJ5055 and NJ44) in field trials when introduced through marker assisted selection. Under severe ShB disease conditions, qSB12YSB significantly reduced yield losses by up to 13.5% in the LE background, indicating its great breeding potential. Our results will accelerate the isolation of qSB12YSB and its utilization in rice breeding programs against ShB.

Yu Wang

Quanyi Sun

Jianhua Zhao

Taixuan Liu

Haibo Du

Wenfeng Shan

Keting Wu

Xiang Xue

Chao Yang

Jun Liu

Zongxiang Chen

Keming Hu

Zhiming Feng

Shimin Zuo

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik

Theor Appl Genet

Fine mapping and candidate gene analysis of qSB12YSB, a gene conferring major quantitative resistance to rice sheath blight.

qSB12YSB基因精细定位与候选基因分析：该基因赋予水稻纹枯病主要定量抗性。

J. H. Zou

X. B. Pan

Z. X. Chen

J. Y. Xu

J. F. Lu

W. X. Zhai

L. H. Zhu

Mapping quantitative trait loci controlling sheath blight resistance in two rice cultivars (Oryza sativa L.)

Sheath blight (SB), caused by Rhizoctonia solani kühn, is one of the most serious global rice diseases. No major resistance genes to SB have been identified so far. All discovered loci are quantitative resistance to rice SB. The qSB-11(LE) resistance quantitative trait locus (QTL) has been previously reported on chromosome 11 of Lemont (LE). In this study, we report the precise location of qSB-11 (LE) . We developed a near isogenic line, NIL-qSB11(TQ), by marker-assisted selection that contains susceptible allele(s) from Teqing (TQ) at the qSB-11 locus in the LE genetic background. NIL-qSB11(TQ) shows higher susceptibility to SB than LE in both field and greenhouse tests, suggesting that this region of LE contains a QTL contributing to SB resistance. In order to eliminate the genetic background effects and increase the accuracy of phenotypic evaluation, a total of 112 chromosome segment substitution lines (CSSLs) with the substituted segment specific to the qSB-11 (LE) region were produced as the fine mapping population. The genetic backgrounds and morphological characteristics of these CSSLs are similar to those of the recurrent parent LE. The donor TQ chromosomal segments in these CSSL lines contiguously overlap to bridge the qSB-11 (LE) region. Through artificial inoculation, all CSSLs were evaluated for resistance to SB in the field in 2005. For the recombinant lines, their phenotypes were evaluated in the field for another 3 years and during the final year were also evaluated in a controlled greenhouse environment, showing a consistent phenotype in SB resistance across years and conditions. After comparing the genotypic profile of each CSSL with its phenotype, we are able to localize qSB-11 (LE) to the region defined by two cleaved-amplified polymorphic sequence markers, Z22-27C and Z23-33C covering 78.871 kb, based on the rice reference genome. Eleven putative genes were annotated within this region and three of them were considered the most likely candidates. The results of this study will greatly facilitate the cloning of the genes responsible for qSB-11 (LE) and marker-assisted breeding to incorporate qSB-11 (LE) into other rice cultivars.

Yuejun Yin

Cunhong Pan

Yafang Zhang

Shiliang Gu

Lihuang Zhu

Xuebiao Pan

Fine mapping of qSB-11(LE), the QTL that confers partial resistance to rice sheath blight.

A total of 416 InDels and 112 SNPs were significantly associated with soybean photosynthesis-related traits. GmIWS1 and GmCDC48 might be related to chlorophyll fluorescence and gas-exchange parameters, respectively. Photosynthesis is one of the main factors determining crop yield. A better understanding of the genetic architecture for photosynthesis is of great significance for soybean yield improvement. Our previous studies identified 5,410,112 single nucleotide polymorphisms (SNPs) from the resequencing data of 219 natural soybean accessions. Here, we identified 634,106 insertions and deletions (InDels) from these 219 accessions and used these InDel variations to perform principal component and linkage disequilibrium analysis of this population. The genome-wide association study (GWAS) were conducted on six chlorophyll fluorescence parameters (chlorophyll content, light energy absorbed per reaction center, quantum yield for electron transport, probability that a trapped exciton moves an electron into the electron transport chain beyond primary quinone acceptor, maximum quantum yield of photosystem II primary photochemistry in the dark-adapted state, performance index on absorption basis) and four gas-exchange parameters (intercellular carbon dioxide concentration, stomatal conductance, net photosynthesis rate, transpiration rate) and revealed 416 significant InDels and 112 significant SNPs. Based on GWAS results, GmIWS1 (encoding a transcription elongation factor) and GmCDC48 (encoding a cell division cycle protein) with the highest expression in the mapping region were determined as the candidate genes responsible for chlorophyll fluorescence and gas-exchange parameters, respectively. Further identification of favorable haplotypes with higher photosynthesis, seed weight and seed yield were carried out for GmIWS1 and GmCDC48. Overall, this study revealed the natural variations and candidate genes underlying the photosynthesis-related traits based on abundant phenotypic and genetic data, providing valuable insights into the genetic mechanisms controlling photosynthesis and yield in soybean.

Dezhou Hu

Yajun Zhao

Lixun Zhu

Xiao Li

Jinyu Zhang

Xuan Cui

Wenlong Li

Derong Hao

Zhongyi Yang

Fei Wu

Shupeng Dong

Xiaoyue Su

Fang Huang

Deyue Yu

Genetic dissection of ten photosynthesis-related traits based on InDel- and SNP-GWAS in soybean.

The dQTG.seq model was utilized to investigate the genetic underpinnings of phenotypic plasticity in soybean isoflavone content, leading to the identification of 100 marker sites associated with phenotypic plasticity, including 27 transcription factors. Overexpression of Glyma.18G091600 (GmERF7) hairy roots under low temperature, salt, and drought stress confirmed the regulatory role of GmERF7 in the phenotypic plasticity of soybean isoflavone content. Phenotypic plasticity is characteristic of organisms that undergo phenotypic changes in response to environmental fluctuations. This phenomenon is pivotal in evolutionary processes and the emergence of new traits. Isoflavones, significant secondary metabolites found in soybeans, have garnered considerable attention owing to their beneficial physiological effects on human health. The variation in isoflavone content among different soybean varieties is influenced by diverse environmental factors, thereby influencing the evaluation of high and low isoflavone varieties. In this study, we measured the phenotypic plasticity of isoflavone content in recombinant inbred lines Hefeng 25 and L-28 in three different environments over two years. Utilizing the dQTG.seq model, 100 statistically significant markers were identified, and 101 potential genes, including 27 transcription factors, were screened. Through qRT-PCR analysis, elevated expression levels of Glyma.18G091600, Glyma.09G196200, and Glyma.05G229500 were observed in various parts of soybean plants. Under low temperature, drought or salt stress conditions, the related enzymes involved in the isoflavone synthesis pathway were notably upregulated in Glyma.18G091600 (GmERF7) overexpressed hairy roots compared to wild-type controls, resulting to higher phenotypic plasticity values for DZ, GC, GT, and TI. These results suggest that GmERF7 influences the phenotypic plasticity of soybean isoflavone content, enhancing adaptation to adverse environments, while also promoting the synthesis and accumulation of soybean isoflavones.

Zhenhong Yang

Yuhang Zhan

Yina Zhu

Hanhan Zhu

Changjun Zhou

Ming Yuan

Haiyan Li

Miao Liu

Weili Teng

Yongguang Li

Xue Zhao

Yuhe Wang

Yingpeng Han

The analysis of the genetic loci affecting phenotypic plasticity of soybean isoflavone content by dQTG.seq model

通过dQTG.seq模型分析影响大豆异黄酮含量表型可塑性的遗传位点

Sunchung Park

Ainong Shi

Beiquan Mou

Correction to: Low frequency of the wild‑type freezing‑tolerance LsCBF7 allele among lettuce population suggests a negative selection during domestication and breeding

更正：生菜群体中野生型耐寒LsCBF7等位基因频率较低表明在驯化和育种过程中存在负选择

Mutations in the CsEMS1 gene result in male sterility and reduced wart number and density. Male sterility and fruit wart formation are two significant agronomic characteristics in cucumber (Cucumis sativus), yet knowledge of our underlying genetics is limited. In this study, we identified an EMS-induced male sterility and few small warts mutant (msfsw). Histological observations revealed defects the absence of tapetum, meiotic aberration and impaired microspore formation in the anthers of the mutant. The mutant also exhibits a reduction in both the size and number of fruit spines and fruit tubercules. Genetic analysis revealed that a single recessive gene is responsible for the mutant phenotypes. BSA-Seq and fine genetic mapping mapped the msfsw locus to a 63.7 kb region with four predicted genes. Multiple lines of evidence support CsEMS1(CsaV3_3G016940) as the candidate for the mutant allele which encodes an LRR receptor-like kinase, and a non-synonymous SNP inside the exon of CsEMS1 is the causal polymorphisms for the mutant phenotypes. This function of CsEMS1 in determination of pollen fertility was confirmed with generation and characterization of multiple knockout mutations with CRISPR/Cas9 based gene editing. In the wild-type (WT) plants, CsEMS1 was highly expressed in male flowers. In the mutant, the expression level of CsEMS1, several tapetum identity-related genes, and trichome-related genes were all significantly reduced as compared with the wild-type. Protein-protein interaction assays revealed physical interactions between CsEMS1 and CsTPD1. Quantitation of endogenous phytohormones revealed a reduction in the ethylene precursor ACC in CsEMS1 knockout lines. This work identified an important role of CsEMS1 in anther and pollen development as well as fruit spine/wart development in cucumber.

Haiqiang Zhang

Yanjie Luo

Wenlong Zhen

Xin Li

Mengying Liu

Peng Liu

Gaoyuan Zhang

Peng Chen

Yiqun Weng

Hongzhong Yue

Yuhong Li

Mutations in a Leucine-Rich Repeat Receptor-Like Kinase gene result in male sterility and reduction in the number and size of fruit warts in cucumber (Cucumis sativus L.)

白氨酸重复受体样激酶基因突变导致黄瓜雄性不育及果实疣数量和大小减少

Three computationally efficient algorithms of GP including RHBK, RHDK, and RHPK were developed in approximate genome-based kernel model. The drastically growing amount of genomic information contributes to increasing computational burden of genomic prediction (GP). In this study, we developed three computationally efficient algorithms of GP including RHBK, RHDK, and RHPK in approximate genome-based kernel model, which reduces dimension of genomic data via Nyström approximation and decreases the computational cost significantly thereby. According to the simulation study and real datasets, our three methods demonstrated predictive accuracy similar to or better than RHAPY, GBLUP, and rrBLUP in most cases. They also demonstrated a substantial reduction in computational time compared to GBLUP and rrBLUP in simulation. Due to their advanced computing efficiency, our three methods can be used in a wide range of application scenarios in the future.

Hailan Liu

Jinqing Xu

Xuesong Wang

Handong Wang

Lei Wang

Yuhu Shen

Efficient large-scale genomic prediction in approximate genome-based kernel model

基于近似全基因组核模型的高效大规模基因组预测

Restoration of haploid female and haploid male fertility without colchicine is feasible. Three SNPs and eight gene models for HFF, and one SNP and a gene model for HMF were identified. Doubled haploid (DH) breeding accelerates the development of elite inbred lines and facilitates the incorporation of exotic germplasm, offering a powerful tool for maize improvement. Traditional DH breeding relies on colchicine to induce haploid genome doubling. Colchicine is toxic, and its application is labor-intensive, with most genotypes recording low genome doubling rates (10-30%). This study investigates spontaneous haploid genome doubling (SHGD) as a safer and more efficient alternative to colchicine. We evaluated the effectiveness of SHGD in restoring haploid female fertility (HFF) and haploid male fertility (HMF) without colchicine. Using genome-wide association studies (GWAS), we identified genomic regions influencing HFF and HMF. The plant materials included the BS39-haploid isogenic lines (HILs) and BS39-SHGD-haploid isogenic lines (HILs). Our results revealed significant SNP associations for both traits, with candidate genes involved in cell cycle regulation, cytoskeletal organization, and hormonal signaling. Analysis of variance (ANOVA) revealed significant variation in HFF across haploids and two environments. Similarly, HMF showed substantial differences across haploids and between the two environments. Spearman correlation between HFF and HMF showed no correlation (r = -0.03) between the two traits. HFF showed high heritability (0.8), indicating strong genetic control, whereas HMF displayed moderate heritability (0.5), suggesting additional environmental influences. The findings underscore the potential of SHGD to enhance DH breeding efficiency and support the development of new maize varieties tailored to diverse agricultural needs.

Mercy Fakude

Ann Murithi

Ursula K. Frei

Paul M. Scott

Thomas Lübberstedt

Genome-wide association study of haploid female fertility (HFF) and haploid male fertility (HMF) in BS39-derived doubled haploid maize lines

BS39衍生双单倍体玉米系单倍体雌性育性（HFF）和单倍体雄性育性（HMF）的全基因组关联研究

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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