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Bayesian neural networks for genomic prediction: uncertainty quantification and SNP interpretation with SHAP and GWAS. 基因组预测的贝叶斯神经网络:不确定性量化和SNP解释与SHAP和GWAS。
IF 4.2 1区 农林科学 Q1 AGRONOMY Pub Date : 2026-01-10 DOI: 10.1007/s00122-025-05127-z
Jin Sun, Xiaoran Zhang, Xiaowei You, Osval A Montesinos-López, Abelardo Montesinos-López, José Crossa, Mark E Sorrells

Key message: This study presents a Bayesian neural networks framework with LASSO regularization and the GSMeSP interpretability tool, enabling accurate, uncertainty-aware, and biologically interpretable genomic prediction. Deep learning offers significant potential for genomic prediction by modeling complex, nonlinear genotype-phenotype relationships. However, its application in plant breeding has been constrained by limited model interpretability and a lack of uncertainty quantification. To address these challenges, we developed a Bayesian neural networks (BNNs) framework incorporating least absolute shrinkage and selection operator (LASSO) regularization for multi-trait genomic prediction with credible uncertainty estimation. In parallel, we introduce GSMeSP, a novel interpretability framework that integrates SHapley Additive exPlanations (SHAP) with genome-wide association study (GWAS) signals to prioritize trait-associated single nucleotide polymorphisms (SNPs) from both statistical and biological perspectives. We applied this framework to a diverse panel of 1385 upland cotton (Gossypium hirsutum) accessions genotyped with over 12,000 SNPs, evaluating performance across multiple fiber-related traits. The BNNs model consistently outperformed conventional and deep learning benchmarks, achieving 0.46-47.85% improvements in predictive accuracy. Moreover, it generated trait- and sample-specific 95% credible intervals, enabling robust uncertainty quantification and more informed selection decisions. Using GSMeSP, we identified biologically meaningful loci, with a substantial proportion of top-ranked SNPs located in the D-subgenome. Notably, chromosome D05 emerged as a genomic hotspot enriched for SNPs associated with fiber length, lint percentage, and uniformity. By integrating high predictive performance, credible uncertainty estimation, and biologically grounded interpretability, our framework provides a transparent and robust deep learning approach to accelerate genomic selection in crop breeding programs.

本研究提出了一个具有LASSO正则化和GSMeSP可解释性工具的贝叶斯神经网络框架,实现了准确、不确定性感知和生物可解释性的基因组预测。通过建模复杂的非线性基因型-表型关系,深度学习为基因组预测提供了巨大的潜力。然而,其在植物育种中的应用受到模型可解释性有限和缺乏不确定性量化的限制。为了解决这些挑战,我们开发了一个贝叶斯神经网络(BNNs)框架,该框架结合了最小绝对收缩和选择算子(LASSO)正则化,用于具有可靠不确定性估计的多性状基因组预测。同时,我们引入了GSMeSP,这是一个新的可解释性框架,它将SHapley加性解释(SHAP)与全基因组关联研究(GWAS)信号相结合,从统计学和生物学的角度优先考虑性状相关的单核苷酸多态性(snp)。我们将这一框架应用于1385个具有超过12000个snp基因型的陆地棉(Gossypium hirsutum)的不同面板,评估了多个纤维相关性状的性能。BNNs模型始终优于传统和深度学习基准,预测准确率提高了0.46-47.85%。此外,它还生成了性状和样本特定的95%可信区间,从而实现了稳健的不确定性量化和更明智的选择决策。使用GSMeSP,我们确定了具有生物学意义的位点,其中大部分排名靠前的snp位于d -亚基因组中。值得注意的是,染色体D05成为一个基因组热点,富含与纤维长度、衣分率和均匀性相关的snp。通过整合高预测性能、可靠的不确定性估计和生物学基础的可解释性,我们的框架提供了一个透明和强大的深度学习方法来加速作物育种计划中的基因组选择。
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引用次数: 0
Genomic approaches to build de novo elite breeding gene pools from locally adapted landraces. 从当地适应的地方品种中建立从头开始的精英育种基因库的基因组方法。
IF 4.2 1区 农林科学 Q1 AGRONOMY Pub Date : 2026-01-07 DOI: 10.1007/s00122-025-05124-2
Safiétou Tooli Fall, Alexander Kena, Brian R Rice, Ghislain Kanfany, Cyril Diatta, Ndjido A Kane, Allan K Fritz, Geoffrey P Morris

Many nascent breeding programs aim to achieve genetic gain by crossing locally-elite germplasm, but a lack of systematic approaches to develop elite gene pools from locally adapted varieties hinders their progress. Motivated by the observation of undesirable transgressive segregation in presumed elite crosses in Senegalese cereal breeding programs, we designed approaches for de novo development of elite gene pools from locally adapted landrace-derived germplasm. We first define two types of "elite" germplasm: iso-elite, phenotypically similar and genetically homogeneous for locally adapted traits ("attained traits"); versus allo-elite, phenotypically similar, but genetically heterogeneous for attained traits. Next, we defined two genomic approaches for de novo inference of elite gene pools: population-based genotypic inference (PGI) and QTL-based genotypic inference (QGI), and compared to a family-based phenotypic inference (FPI) approach. Using simulations that trace the evolution from locally adapted landraces to elite breeding lines, we evaluate the effectiveness of these strategies in nascent forward breeding programs. QGI accurately and cost-effectively identifies both iso- and allo-elite pairs, regardless of the underlying trait architecture, while PGI is less sensitive when trait architecture is oligogenic. Over ten cycles of phenotypic recurrent selection, programs based on iso-elite crosses consistently outperformed those based on allo-elite crosses for genetic gain. The findings highlight the value of trait genetic architecture knowledge for elite gene pool development and provide a practical roadmap for elite germplasm development in modernizing breeding programs.

许多新兴的育种计划旨在通过杂交本地优质种质来获得遗传增益,但缺乏从本地适应品种中开发优质基因库的系统方法阻碍了他们的进展。由于观察到塞内加尔谷物育种计划中假定的精英杂交中存在不良的越界分离现象,我们设计了从当地适应的地方品种衍生的种质资源中重新开发精英基因库的方法。我们首先定义了两种类型的“精英”种质:对于本地适应性状(“获得性状”),同种精英、表型相似和遗传同质;与异种精英相比,获得的性状在表型上相似,但在遗传上异质。接下来,我们定义了两种用于精英基因库从头推断的基因组方法:基于群体的基因型推断(PGI)和基于qtl的基因型推断(QGI),并与基于家族的表型推断(FPI)方法进行了比较。通过模拟追踪从本地适应的地方品种到精英育种品系的进化,我们评估了这些策略在新生的正向育种计划中的有效性。无论潜在的性状结构如何,QGI都能准确且经济有效地识别出异精英和异精英对,而PGI在性状结构为寡生时则不那么敏感。在10个表型循环选择周期中,基于同精英杂交的方案在遗传增益方面始终优于基于异精英杂交的方案。这些发现突出了性状遗传结构知识对精英基因库开发的价值,并为现代化育种计划中的精英种质资源开发提供了实用的路线图。
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引用次数: 0
Unveiling stagnant flooding tolerance in lowland NERICAs: genomic insights and breeding prospects. 揭示低地耐洪能力停滞不前:基因组的见解和育种前景。
IF 4.2 1区 农林科学 Q1 AGRONOMY Pub Date : 2026-01-06 DOI: 10.1007/s00122-025-05129-x
Vimal Kumar Semwal, Shittu Afeez, Olatunde A Bhadmus, Okanlawon Jolayemi, Ramaiah Venuprasad

Rice cultivation in the rainfed lowland ecosystem during the rainy season is prone to encounter substantial flooding challenges in the form of complete submergence or prolonged stagnant flooding. While the Sub1 gene enables rice plants to survive the momentary complete submergence, stagnant flooding, defined by incomplete submergence for extended periods, necessitates moderate stem elongation for survival. In this study, we characterized 60 lowland NERICA varieties under stagnant flooding (SF) conditions, identify tolerant germplasm and detect genomic regions associated with key traits to aid breeding efforts. Phenotypic evaluations revealed significant genetic variability among the NERICA varieties, with some accessions showing 20-60% yield reduction under SF stress. The derived NERICA L-19/IR64 Sub1 RIL population showed improved grain yield under SF compared to both parents and submergence-tolerant checks. A total 27 QTLs were identified associated with plant height, tiller number, panicle number, days to flowering and grain yield. Stable and major-effect QTLs, such as qPH1.1, qPH3.1 and qDTF3.1, were consistent across environments, explaining up to 48% of the phenotypic variation. Several QTLs co-localized, indicating potential pleiotropy or tight linkage. Positional candidate genes associated with these regions include regulators of gibberellin signaling, flowering time and other developmental processes. This study highlights the potential of lowland NERICAs as a genetic resource and provides QTL, donor lines, molecular resources that form a practical basis for marker-assisted selection and pre-breeding of dual-tolerant rice cultivars adapted to climate-induced flooding scenarios in sub-Saharan Africa.

在雨季,雨养低地生态系统中的水稻种植容易遇到严重的洪水挑战,其形式是完全淹没或长期停滞的洪水。虽然Sub1基因使水稻植株能够在短暂的完全淹没中存活下来,但停滞的洪水(由长时间的不完全淹没定义)需要适度的茎伸长才能存活。在本研究中,我们对60个低地NERICA品种在滞洪(SF)条件下的特性进行了分析,鉴定了耐受性种质,并检测了与关键性状相关的基因组区域,以帮助育种工作。表型分析显示,NERICA品种间存在显著的遗传变异,部分品种在SF胁迫下产量下降20-60%。获得的NERICA L-19/IR64 Sub1 RIL群体在顺水处理下的产量比亲本和耐淹性均有提高。共鉴定出27个与株高、分蘖数、穗数、开花天数和籽粒产量相关的qtl。稳定的和主要效应的qtl,如qPH1.1、qPH3.1和qDTF3.1,在不同的环境中是一致的,解释了高达48%的表型变异。几个qtl共定位,表明潜在的多效性或紧密连锁。与这些区域相关的位置候选基因包括赤霉素信号、开花时间和其他发育过程的调节因子。该研究强调了低地NERICAs作为遗传资源的潜力,并提供了QTL、供体系和分子资源,为适应撒哈拉以南非洲气候诱导洪水情景的双耐水稻品种的标记辅助选择和预育种奠定了实践基础。
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引用次数: 0
Genome-wide analysis of the sugarcane SUT gene family reveals ShSUT4 as a key regulator of abiotic stress responses. 甘蔗SUT基因家族的全基因组分析表明,ShSUT4是非生物胁迫反应的关键调控因子。
IF 4.2 1区 农林科学 Q1 AGRONOMY Pub Date : 2026-01-05 DOI: 10.1007/s00122-025-05138-w
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

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.

蔗糖转运蛋白(SUTs)对植物的生长、发育和逆境反应至关重要。尽管甘蔗作为糖和生物燃料作物具有重要意义,但其SUT基因在非生物胁迫下的基因组数据有限。本研究通过生物信息学分析鉴定了37个ShSUT基因。系统发育分类将它们分为三个主要分支(I-III),保守的基序和基因结构支持它们的进化关系。启动子分析揭示了与激素反应、应激、发育和光调节相关的15个关键顺式元件。所有ShSUT基因被定位在3个连续区和7条染色体上。共线性和基因重复分析鉴定出15对片段重复的基因对,表明进化扩展。此外,预计有7个假定的“sbi- mirna”靶向28个ShSUT基因,其中sbi-miR5381单独靶向17个ShSUT基因。在功能表征方面,选择ShSUT04是因为它具有进化意义,在蔗糖转运中起关键作用,并可能参与调节非生物胁迫反应。共鉴定出18个潜在的相互作用因子,其中确认的相互作用因子为ShPsbR、ShRF2a、ShCOPTS。1和ShSPT,通过BiFC和Y2H试验验证。qRT-PCR分析证实了应激反应的表达模式。在冷胁迫下,ShRF2a、ShPsbR和ShSPT下调,表明其具有负调控作用,而ShSUT04和ShCOPT5.1在特定时间点上调,其中ShSUT01表现出强烈的诱导作用,表明其在防御中具有积极作用。干旱条件下,ShSUT04和ShPsbR表达显著上调,提示其具有正向调控作用。在盐胁迫下,虽然有几个基因被抑制,但ShSUT01和ShPsbR被诱导,这反映了它们在胁迫适应中的潜力。本研究揭示了甘蔗SUT基因在非生物胁迫调控中的进化和功能作用,其中ShSUT04在干旱胁迫下表现为正调控,在盐胁迫和冷胁迫下表现为负调控。
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引用次数: 0
The BrRLP1-BrMDAR1 module regulates the resistance to downy mildew in Brassica rapa. BrRLP1-BrMDAR1模块调控油菜对霜霉病的抗性。
IF 4.2 1区 农林科学 Q1 AGRONOMY Pub Date : 2026-01-05 DOI: 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.

关键信息:BrRLP1通过与单脱氢抗坏血酸还原酶BrMDAR1相互作用,正向调节油菜对霜霉病的抗性。霜霉病是一种严重影响油菜产量和品质的毁灭性病害。受体样蛋白(Receptor-like protein, RLP)是植物抗病反应的重要组成部分。本研究通过GWAS分析和QTL定位,在油菜中鉴定出一个新的抗霜霉病基因BrRLP1。BrRLP1编码一种膜定位的受体样蛋白,接种霜霉病后其在抗性和易感材料中的表达水平存在显著差异。瞬时表达和转基因功能验证表明BrRLP1是抗性霜霉病的正调控因子。BrRLP1R过表达植株接种后均表现出对霜霉病的高抗性表型。单倍型分析表明,BrRLP1的LRR结构域的SNP309位点是产生霜霉病抗性差异的关键功能位点。Y2H和LCI实验表明,BrRLP1可以与参与抗坏血酸代谢途径的单脱氢抗坏血酸还原酶BrMDAR1相互作用。我们的研究结果揭示了BrRLP1通过与BrMDAR1相互作用调控霜霉病抗性的功能,为油菜抗病免疫应答的分子机制提供了新的认识。
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引用次数: 0
Genetic analysis of a quantitative trait locus associated with resistance to the root-lesion nematode Pratylenchus neglectus in triticale. 小黑麦抗根病线虫数量性状位点的遗传分析。
IF 4.2 1区 农林科学 Q1 AGRONOMY Pub Date : 2026-01-05 DOI: 10.1007/s00122-025-05112-6
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

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。
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引用次数: 0
A genome-wide association analysis identifies a key candidate gene controlling plant growth habit in chickpea. 全基因组关联分析确定了鹰嘴豆控制植物生长习性的关键候选基因。
IF 4.2 1区 农林科学 Q1 AGRONOMY Pub Date : 2026-01-03 DOI: 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.

综合全基因组和基于单倍型的关联分析确定了鹰嘴豆植物生长习性(PGH)性状的关键基因组位点。识别控制植物生长习性(PGH)性状的分子标记,使其能够实现机械收获,对于在气候变化和全球粮食需求增加的情况下提高作物的生产效率至关重要。通过对鹰嘴豆(Cicer arietinum) 286个关联群体进行关联定位、单倍型关联、分子单倍型分型和基因表达分析等组合整合基因组学辅助育种策略,剖析了鹰嘴豆PGH性状的遗传基础。该研究利用286份德西鹰嘴豆和卡布里鹰嘴豆全基因组测序(WGS)获得的382171个全基因组snp(单核苷酸多态性),描绘了一个与PGH性状变异相关的主要基因组位点,特别是在直立(E)/半直立(SE)型与蔓延(S)/半蔓延(SS)型之间。在该基因座中,CaPAR1 (Cicer arietinum PAR1)及其衍生的天然等位基因/单倍型被确定为候选基因。这些发现为通过转化基因组学和分子育种培育鹰嘴豆高产、直立/半直立、可机械收获的品种提供了有利条件。
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引用次数: 0
A robust 1K-core marker set for wild germplasm management and targeted pre-breeding of rice: development and applications. 用于水稻野生种质资源管理和有针对性的预育种的健壮的1k核心标记集:开发和应用。
IF 4.2 1区 农林科学 Q1 AGRONOMY Pub Date : 2026-01-03 DOI: 10.1007/s00122-025-05133-1
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

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。
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引用次数: 0
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. 现代日本水稻品种经常在致病相关的1b蛋白基因位点携带非自主的反转录转座子插入突变,导致对稻瘟病的抗性降低。
IF 4.2 1区 农林科学 Q1 AGRONOMY Pub Date : 2025-12-28 DOI: 10.1007/s00122-025-05132-2
Taketo Ishihara, Kotaro Abe, Miyako Kato, Tsuyoshi Inukai

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.

在日本,食用品质高的水稻品种,如“光”,往往极易感染稻瘟病菌,这种真菌会导致稻瘟病,稻瘟病是水稻最严重的疾病;然而,对导致这种高易感性的遗传因素知之甚少。本研究中,在我们初始接种P. oryzae后,使用RT-qPCR未在Koshihikari中检测到致病相关蛋白1b (PR1b)基因的表达,但在中等抗性品种Nipponbare中检测到该基因的表达。这一意想不到的结果是由于在Koshihikari的PR1b编码区插入了非自主反转录转座子Dasheng。结果表明,过表达PR1b的转基因光秃株系对稻瘟病的抗性更高,这表明PR1b突变是光秃株系对稻瘟病高敏感性的原因之一。当我们以日本最广泛种植的前10个水稻品种和北海道目前的主要品种为例检查PR1b突变时,至少前8个品种和北海道目前的所有主要品种都有这种突变。因此,有害的PR1b突变似乎在几乎整个日本水稻种群中都是固定的。此外,我们对公共数据库中36个水稻品种的基因组序列进行了调查,结果表明,大胜在2个粳稻品种和1个籼稻品种中插入了PR1b基因,位点与光光相同。
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引用次数: 0
Ey-1 encodes a DEDDh exonuclease in eggplant (Solanum melongena), providing a novel pathway for begomovirus resistance. Ey-1在茄子(Solanum melongena)中编码一个DEDDh外切酶,为茄子抗begomavirus提供了新的途径。
IF 4.2 1区 农林科学 Q1 AGRONOMY Pub Date : 2025-12-27 DOI: 10.1007/s00122-025-05120-6
Nadya Syafira Pohan, Kyohei Kikkawa, Natsuki Hata, Ryota Saeki, Atsushi J Nagano, Takaaki Mashiko, Sota Koeda

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.

白蛉传播的begomvirus可以在世界范围内破坏茄科作物。尽管人们强烈要求对begomavirus抗性进行遗传渗入,但目前只有番茄和辣椒的begomavirus抗性基因被克隆出来。在这里,我们旨在鉴定茄子(Solanum melongena)的抗begomvirus基因。此前,我们鉴定了820号加入物为番茄黄卷叶病毒(TYLCKaV)的抗性来源。利用820号和47号异花授粉的F2和F2:3分离群体,在1号染色体上鉴定了茄子黄卷叶病病毒抗性1 (y-1)的显性位点。通过对No.820和No.47的全基因组和转录组测序,我们从最终113-kb靶区10个基因中选择了5个基因作为候选基因。利用病毒诱导基因沉默(VIGS)对No.820这5个候选基因进行反向遗传分析发现,编码DEDDh家族外切酶蛋白的SmNEN3基因沉默导致抗性丧失。比较820号和47号SmNEN3的基因组序列和转录序列,发现一个氨基酸缺失和非同义突变很可能导致begomavirus的抗性。820号是一种对begomavirus具有显性抗性的极具价值的遗传资源,新的DNA标记将极大地促进标记辅助育种。
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Theoretical and Applied Genetics
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