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Genome-wide association study reveals genetic loci for ten trace elements in foxtail millet (Setaria italica). 全基因组关联研究揭示了狐尾黍(Setaria italica)中十种微量元素的遗传位点。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-07-17 DOI: 10.1007/s00122-024-04690-1
Hanxiao Liu, Xin Zhang, Yuping Shang, Shaoxing Zhao, Yingjia Li, Xutao Zhou, Xiaoyu Huo, Pengfei Qiao, Xin Wang, Keli Dai, Huixia Li, Jie Guo, Weiping Shi

Key message: One hundred and fifty-five QTL for trace element concentrations in foxtail millet were identified using a genome-wide association study, and a candidate gene associated with Ni-Co-Cr concentrations was detected. Foxtail millet (Setaria italica) is an important regional crop known for its rich mineral nutrient content, which has beneficial effects on human health. We assessed the concentrations of ten trace elements (Ba, Co, Cr, Cu, Fe, Mn, Ni, Pb, Sr, and Zn) in the grain of 408 foxtail millet accessions. Significant differences in the concentrations of five elements (Ba, Co, Ni, Sr, and Zn) were observed between two subpopulations of spring- and summer-sown foxtail millet varieties. Moreover, 84.4% of the element pairs exhibited significant correlations. To identify the genetic factors influencing trace element accumulation, a comprehensive genome-wide association study was conducted, identifying 155 quantitative trait locus (QTL) for the ten trace elements across three different environments. Among them, ten QTL were consistently detected in multiple environments, including qZn2.1, qZn4.4, qCr4.1, qFe6.3, qFe6.5, qCo6.1, qPb7.3, qPb7.5, qBa9.1, and qNi9.1. Thirteen QTL clusters were detected for multiple elements, which partially explained the correlations between elements. Additionally, the different concentrations of five elements between foxtail millet subpopulations were caused by the different frequencies of high-concentration alleles associated with important marker-trait associations. Haplotype analysis identified a candidate gene SETIT_036676mg associated with Ni accumulation, with the GG haplotype significantly increasing Ni-Co-Cr concentrations in foxtail millet. A cleaved amplified polymorphic sequence marker (cNi6676) based on the two haplotypes of SETIT_036676mg was developed and validated. Results of this study provide valuable reference information for the genetic research and improvement of trace element content in foxtail millet.

关键信息通过全基因组关联研究发现了155个狐尾粟微量元素浓度的QTL,并发现了一个与镍-钴-铬浓度相关的候选基因。狐尾黍(Setaria italica)是一种重要的地区性作物,以其丰富的矿物质营养成分而闻名,对人类健康有益。我们评估了 408 个狐尾粟品种谷粒中 10 种微量元素(钡、钴、铬、铜、铁、锰、镍、铅、锶和锌)的浓度。在春播和夏播狐尾黍两个亚群之间,五种元素(钡、钴、镍、锶和锌)的浓度存在显著差异。此外,84.4%的元素对表现出显著的相关性。为了确定影响微量元素积累的遗传因素,研究人员进行了一项全面的全基因组关联研究,在三种不同环境中确定了 155 个十种微量元素的数量性状位点(QTL)。其中,10个QTL在多个环境中被一致检测到,包括qZn2.1、qZn4.4、qCr4.1、qFe6.3、qFe6.5、qCo6.1、qPb7.3、qPb7.5、qBa9.1和qNi9.1。检测到 13 个多元素 QTL 簇,这部分解释了元素之间的相关性。此外,狐尾粟亚群之间五种元素的浓度不同是由于与重要标记-性状关联相关的高浓度等位基因频率不同造成的。单倍型分析发现了一个与镍积累相关的候选基因 SETIT_036676mg,其 GG 单倍型可显著提高狐尾黍中镍-钴-铬的浓度。基于 SETIT_036676mg 的两个单倍型,开发并验证了裂解扩增多态性序列标记(cNi6676)。研究结果为狐尾粟微量元素含量的遗传研究和改良提供了有价值的参考信息。
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引用次数: 0
Nitrogen deficiency tolerance conferred by introgression of a QTL derived from wild emmer into bread wheat. 将源自野生小麦的 QTL 基因导入面包小麦,赋予小麦耐缺氮性。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-07-17 DOI: 10.1007/s00122-024-04692-z
Nikolai Govta, Andrii Fatiukha, Liubov Govta, Curtis Pozniak, Assaf Distelfeld, Tzion Fahima, Diane M Beckles, Tamar Krugman

Key message: Genetic dissection of a QTL from wild emmer wheat, QGpc.huj.uh-5B.2, introgressed into bread wheat, identified candidate genes associated with tolerance to nitrogen deficiency, and potentially useful for improving nitrogen-use efficiency. Nitrogen (N) is an important macronutrient critical to wheat growth and development; its deficiency is one of the main factors causing reductions in grain yield and quality. N availability is significantly affected by drought or flooding, that are dependent on additional factors including soil type or duration and severity of stress. In a previous study, we identified a high grain protein content QTL (QGpc.huj.uh-5B.2) derived from the 5B chromosome of wild emmer wheat, that showed a higher proportion of explained variation under water-stress conditions. We hypothesized that this QTL is associated with tolerance to N deficiency as a possible mechanism underlying the higher effect under stress. To validate this hypothesis, we introgressed the QTL into the elite bread wheat var. Ruta, and showed that under N-deficient field conditions the introgression IL99 had a 33% increase in GPC (p < 0.05) compared to the recipient parent. Furthermore, evaluation of IL99 response to severe N deficiency (10% N) for 14 days, applied using a semi-hydroponic system under controlled conditions, confirmed its tolerance to N deficiency. Fine-mapping of the QTL resulted in 26 homozygous near-isogenic lines (BC4F5) segregating to N-deficiency tolerance. The QTL was delimited from - 28.28 to - 1.29 Mb and included 13 candidate genes, most associated with N-stress response, N transport, and abiotic stress responses. These genes may improve N-use efficiency under severely N-deficient environments. Our study demonstrates the importance of WEW as a source of novel candidate genes for sustainable improvement in tolerance to N deficiency in wheat.

关键信息:对野生小麦QGpc.huj.uh-5B.2的一个QTL进行遗传分析,发现了与耐氮缺乏有关的候选基因,这些基因可能有助于提高氮的利用效率。氮(N)是对小麦生长发育至关重要的重要宏量营养元素;缺氮是导致谷物产量和质量下降的主要因素之一。氮的可用性受干旱或洪水的影响很大,而干旱或洪水又取决于其他因素,包括土壤类型或胁迫的持续时间和严重程度。在之前的一项研究中,我们从野生小麦的 5B 染色体中发现了一个高籽粒蛋白含量 QTL(QGpc.huj.uh-5B.2),该 QTL 在水胁迫条件下的解释变异比例较高。我们假设该 QTL 与对氮缺乏的耐受性有关,这可能是胁迫条件下较高效应的一种机制。为了验证这一假设,我们将该 QTL 引种到精英面包小麦变种 Ruta 中,结果表明在缺氮的田间条件下,引种 IL99 的 GPC(p 4F5)增加了 33%,并分离出对缺氮的耐受性。该 QTL 的范围为 - 28.28 到 - 1.29 Mb,包括 13 个候选基因,其中大部分与氮胁迫响应、氮转运和非生物胁迫响应有关。这些基因可能会提高严重缺氮环境下的氮利用效率。我们的研究表明,WEW 是新型候选基因的重要来源,可持续提高小麦对氮缺乏的耐受性。
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引用次数: 0
Association studies of salinity tolerance in sunflower provide robust breeding and selection strategies under climate change. 向日葵耐盐碱性的关联研究为气候变化下的育种和选育提供了有力的策略。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-07-15 DOI: 10.1007/s00122-024-04672-3
James P McNellie, William E May, Loren H Rieseberg, Brent S Hulke

Phytotoxic soil salinity is a global problem, and in the northern Great Plains and western Canada, salt accumulates on the surface of marine sediment soils with high water tables under annual crop cover, particularly near wetlands. Crop production can overcome saline-affected soils using crop species and cultivars with salinity tolerance along with changes in management practices. This research seeks to improve our understanding of sunflower (Helianthus annuus) genetic tolerance to high salinity soils. Genome-wide association was conducted using the Sunflower Association Mapping panel grown for two years in naturally occurring saline soils (2016 and 2017, near Indian Head, Saskatchewan, Canada), and six phenotypes were measured: days to bloom, height, leaf area, leaf mass, oil percentage, and yield. Plot level soil salinity was determined by grid sampling of soil followed by kriging. Three estimates of sunflower performance were calculated: (1) under low soil salinity (< 4 dS/m), (2) under high soil salinity (> 4 dS/m), and (3) plasticity (regression coefficient between phenotype and soil salinity). Fourteen loci were significant, with one instance of co-localization between a leaf area and a leaf mass locus. Some genomic regions identified as significant in this study were also significant in a recent greenhouse salinity experiment using the same panel. Also, some candidate genes underlying significant QTL have been identified in other plant species as having a role in salinity response. This research identifies alleles for cultivar improvement and for genetic studies to further elucidate salinity tolerance pathways.

植物毒性土壤盐碱化是一个全球性问题,在大平原北部和加拿大西部,盐分积聚在每年作物覆盖下地下水位较高的海洋沉积土壤表面,尤其是在湿地附近。作物生产可以利用具有耐盐性的作物品种和栽培品种以及管理方法的改变来克服受盐碱影响的土壤。本研究旨在加深我们对向日葵(Helianthus annuus)基因对高盐度土壤耐受性的了解。使用向日葵关联图谱面板进行了全基因组关联研究,该面板在自然发生的盐碱土壤中生长了两年(2016 年和 2017 年,加拿大萨斯喀彻温省印第安黑德附近),并测量了六种表型:开花天数、高度、叶面积、叶片质量、油分百分比和产量。通过对土壤进行网格取样,然后进行克里格法计算,确定了地块的土壤盐度。计算了向日葵表现的三个估计值:(1) 低土壤盐度下(4 dS/m);(3) 可塑性(表型与土壤盐度之间的回归系数)。有 14 个基因位点具有显著性,其中有一个叶面积和叶片质量基因位点共定位。本研究中发现的一些重要基因组区域,在最近使用同一小组进行的温室盐度实验中也具有重要意义。此外,在其他植物物种中也发现了一些潜在于重要 QTL 的候选基因在盐度反应中的作用。这项研究为改良栽培品种和进一步阐明耐盐碱途径的遗传研究确定了等位基因。
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引用次数: 0
Phenotypic characterization and gene mapping of hybrid necrosis in Triticum durum-Haynaldia villosa amphiploids. Triticum durum-Haynaldia villosa 两性杂交种杂交坏死的表型特征和基因图谱。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-07-15 DOI: 10.1007/s00122-024-04691-0
Yangqi Liu, Jinhong Liu, Zhenpu Huang, Kaiwen Fan, Xinshuo Guo, Liping Xing, Aizhong Cao

Key message: Phenotypical, physiological and genetic characterization was carried out on the hybrid necrosis gene from Haynaldia villosa, and the related gene Ne-V was mapped to chromosome arm 2VL. Introducing genetic variation from wild relatives into common wheat through wide crosses is a vital strategy for enriching genetic diversity and promoting wheat breeding. However, hybrid necrosis, a genetic autoimmunity syndrome, often occurs in the offspring of interspecific or intraspecific crosses, restricting both the selection of hybrid parents and the pyramiding of beneficial genes. To utilize the germplasms of Haynaldia villosa (2n = 2x = 14, VV), we conducted wide hybridization between durum wheat (2n = 4x = 28, AABB) and multiple H. villosa accessions to synthesize the amphiploids (2n = 6x = 42, AABBVV). This study revealed that 61.5% of amphiploids derived from the above crosses exhibited hybrid necrosis, with some amphiploids even dying before reaching maturity. However, the initiation time and severity of necrosis varied dramatically among the progenies, suggesting that there were multiple genetic loci or multiple alleles in the same genetic locus conferring to hybrid necrosis in H. villosa accessions. Genetic analysis was performed on the F2 and derived F2:3 populations, which were constructed between amphiploid STH59-1 with normal leaves and amphiploid STH59-2 with necrotic leaves. A semidominant hybrid necrosis-related gene, Ne-V, was mapped to an 11.8-cM genetic interval on the long arm of chromosome 2V, representing a novel genetic locus identified in Triticum-related species. In addition, the hybrid necrosis was correlated with enhanced H2O2 accumulation and cell death, and it was influenced by the temperature and light. Our findings provide a foundation for cloning the Ne-V gene and exploring its molecular mechanism.

关键信息对Haynaldia villosa的杂交坏死基因进行了表型、生理和遗传鉴定,并将相关基因Ne-V绘制到染色体臂2VL上。通过广泛杂交将野生近缘种的遗传变异引入普通小麦是丰富遗传多样性和促进小麦育种的重要策略。然而,种间杂交或种内杂交的后代往往会出现杂交坏死(一种遗传自体免疫综合征),从而限制了杂交亲本的选择和有益基因的金字塔化。为了利用Haynaldia villosa(2n = 2x = 14,VV)的种质资源,我们在硬质小麦(2n = 4x = 28,AABB)和多个H. villosa登录品之间进行了广泛杂交,合成了两倍体(2n = 6x = 42,AABBVV)。这项研究发现,上述杂交产生的两倍体中有 61.5%出现杂交坏死,有些两倍体甚至在成熟前就已经死亡。然而,不同后代发生坏死的时间和严重程度差异很大,这表明在 H. villosa 品种中存在多个遗传位点或同一遗传位点中的多个等位基因导致杂交坏死。在叶片正常的两倍体 STH59-1 和叶片坏死的两倍体 STH59-2 之间构建的 F2 和衍生的 F2:3 群体中进行了遗传分析。一个半显性杂交坏死相关基因 Ne-V 被映射到 2V 染色体长臂上 11.8 厘米的遗传间隔上,这是在小麦相关物种中发现的一个新的遗传位点。此外,杂交种坏死与 H2O2 积累和细胞死亡的增强有关,并受温度和光照的影响。我们的研究结果为克隆 Ne-V 基因和探索其分子机制奠定了基础。
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引用次数: 0
Polyploidy in maize: from evolution to breeding. 玉米的多倍体:从进化到育种。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-07-13 DOI: 10.1007/s00122-024-04688-9
Grigorii Batiru, Thomas Lübberstedt

Polyploidy played an important role in the evolution of the three most important crops: wheat, maize and rice, each of them providing a unique model for studying allopolyploidy, segmental alloploidy or paleopolyploidy. However, its genetic and evolutionary role is still vague. The undelying mechanisms and consequences of polyploidy remain fundamental objectives in the study of eukaryotes. Maize is one of the underutilized crops at the polyploid level. This species has no stable natural polyploids, the existing ones being artificially obtained. From the experimental polyploid series of maize, only the tetraploid forms (4n = 40) are of interest. They are characterized by some valuable morphological, physiological and biochemical features, superior to the diploid forms from which they originated, but also by some drawbacks such as: reduced fertility, slower development, longer vegetation period, low productivity and adaptedness. Due to these barriers to using tetraploids in field production, maize tetraploids primarily found utility in scientific studies regarding genetic variability, inbreeding, heterosis and gene dosage effect. Since the first mention of a triploid maize plant to present, many scientists and schools, devoted their efforts to capitalize on the use of polyploidy in maize. Despite its common disadvantages as a crop, significant progress in developing tetraploid maize with good agronomic performance was achieved leading to registered tetraploid maize varieties. In this review we summarize and discuss the different aspects of polyploidy in maize, such as evolutionary context, methods of induction, morphology, fertility issue, inheritance patterns, gene expression and potential use.

多倍体在小麦、玉米和水稻这三种最重要农作物的进化过程中发挥了重要作用,为研究异源多倍体、节段异源或古多倍体提供了独特的模型。然而,其遗传和进化作用仍然模糊不清。多倍体的内在机制和后果仍然是研究真核生物的基本目标。玉米是多倍体水平上利用率较低的作物之一。该物种没有稳定的天然多倍体,现有的多倍体都是人工获得的。在玉米的实验多倍体系列中,只有四倍体形式(4n = 40)值得关注。它们在形态学、生理学和生物化学方面具有一些有价值的特征,优于其起源的二倍体形式,但也有一些缺点,如:生育力降低、发育缓慢、植被期延长、生产率低和适应性差。由于在田间生产中使用四倍体存在这些障碍,玉米四倍体主要用于有关遗传变异、近交系、杂交和基因剂量效应的科学研究。自从首次提到三倍体玉米植物以来,许多科学家和学校都致力于利用玉米中的多倍体。尽管四倍体玉米作为一种作物普遍存在缺点,但在开发具有良好农艺表现的四倍体玉米方面仍取得了重大进展,并培育出了注册的四倍体玉米品种。在本综述中,我们总结并讨论了玉米多倍体的不同方面,如进化背景、诱导方法、形态学、肥力问题、遗传模式、基因表达和潜在用途。
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引用次数: 0
Quantitative trait locus analysis of gray leaf spot resistance in the maize IBM Syn10 DH population. 玉米 IBM Syn10 DH 群体灰叶斑病抗性的数量性状位点分析。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-07-13 DOI: 10.1007/s00122-024-04694-x
Lina Cui, Mingfei Sun, Lin Zhang, Hongjie Zhu, Qianqian Kong, Ling Dong, Xianjun Liu, Xing Zeng, Yanjie Sun, Haiyan Zhang, Luyao Duan, Wenyi Li, Chengjia Zou, Zhenyu Zhang, WeiLi Cai, Yulin Ming, Thomas Lübberstedt, Hongjun Liu, Xuerong Yang, Xiao Li

Key message: The exploration and dissection of a set of QTLs and candidate genes for gray leaf spot disease resistance using two fully assembled parental genomes may help expedite maize resistance breeding. The fungal disease of maize known as gray leaf spot (GLS), caused by Cercospora zeae-maydis and Cercospora zeina, is a significant concern in China, Southern Africa, and the USA. Resistance to GLS is governed by multiple genes with an additive effect and is influenced by both genotype and environment. The most effective way to reduce the cost of production is to develop resistant hybrids. In this study, we utilized the IBM Syn 10 Doubled Haploid (IBM Syn10 DH) population to identify quantitative trait loci (QTLs) associated with resistance to gray leaf spot (GLS) in multiple locations. Analysis of seven distinct environments revealed a total of 58 QTLs, 49 of which formed 12 discrete clusters distributed across chromosomes 1, 2, 3, 4, 8 and 10. By comparing these findings with published research, we identified colocalized QTLs or GWAS loci within eleven clustering intervals. By integrating transcriptome data with genomic structural variations between parental individuals, we identified a total of 110 genes that exhibit both robust disparities in gene expression and structural alterations. Further analysis revealed 19 potential candidate genes encoding conserved resistance gene domains, including putative leucine-rich repeat receptors, NLP transcription factors, fucosyltransferases, and putative xyloglucan galactosyltransferases. Our results provide a valuable resource and linked loci for GLS marker resistance selection breeding in maize.

关键信息:利用两个完全组装的亲本基因组探索和剖析一组抗灰叶斑病的QTLs和候选基因可能有助于加快玉米抗病育种。由Cercospora zeae-maydis和Cercospora zeina引起的玉米灰叶斑病(GLS)是中国、南部非洲和美国严重关注的真菌病害。对 GLS 的抗性由多种基因决定,具有叠加效应,并受基因型和环境的影响。降低生产成本的最有效方法是培育抗性杂交种。在本研究中,我们利用 IBM Syn 10 双倍单倍体(IBM Syn10 DH)群体在多个地点鉴定了与灰叶斑病(GLS)抗性相关的数量性状位点(QTL)。对七个不同环境的分析共发现了 58 个 QTL,其中 49 个形成了 12 个离散群,分布在 1、2、3、4、8 和 10 号染色体上。通过将这些发现与已发表的研究结果进行比较,我们在11个聚类区间内发现了共定位的QTL或GWAS基因座。通过整合转录组数据和亲本间的基因组结构变异,我们共发现了 110 个基因,这些基因在基因表达和结构改变方面都表现出强大的差异。进一步分析发现了 19 个编码保守抗性基因域的潜在候选基因,包括假定的富亮氨酸重复受体、NLP 转录因子、岩藻糖基转移酶和假定的木糖半乳糖基转移酶。我们的研究结果为玉米的 GLS 标记抗性选择育种提供了宝贵的资源和相关基因位点。
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引用次数: 0
Accuracy of prediction from multi-environment trials for new locations using pedigree information and environmental covariates: the case of sorghum (Sorghum bicolor (L.) Moench) breeding. 利用血统信息和环境协变量对新地点多环境试验进行预测的准确性:以高粱(Sorghum bicolor (L.) Moench)育种为例。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-07-10 DOI: 10.1007/s00122-024-04684-z
Diriba Tadese, Hans-Peter Piepho, Jens Hartung

Key messages: We investigate a method of extracting and fitting synthetic environmental covariates and pedigree information in multilocation trial data analysis to predict genotype performances in untested locations. Plant breeding trials are usually conducted across multiple testing locations to predict genotype performances in the targeted population of environments. The predictive accuracy can be increased by the use of adequate statistical models. We compared linear mixed models with and without synthetic covariates (SCs) and pedigree information under the identity, the diagonal and the factor-analytic variance-covariance structures of the genotype-by-location interactions. A comparison was made to evaluate the accuracy of different models in predicting genotype performances in untested locations using the mean squared error of predicted differences (MSEPD) and the Spearman rank correlation between predicted and adjusted means. A multi-environmental trial (MET) dataset evaluated for yield performance in the dry lowland sorghum (Sorghum bicolor (L.) Moench) breeding program of Ethiopia was used. For validating our models, we followed a leave-one-location-out cross-validation strategy. A total of 65 environmental covariates (ECs) obtained from the sorghum test locations were considered. The SCs were extracted from the ECs using multivariate partial least squares analysis and subsequently fitted in the linear mixed model. Then, the model was extended accounting for pedigree information. According to the MSEPD, models accounting for SC improve predictive accuracy of genotype performances in the three of the variance-covariance structures compared to others without SC. The rank correlation was also higher for the model with the SC. When the SC was fitted, the rank correlation was 0.58 for the factor analytic, 0.51 for the diagonal and 0.46 for the identity variance-covariance structures. Our approach indicates improvement in predictive accuracy with SC in the context of genotype-by-location interactions of a sorghum breeding in Ethiopia.

关键信息:我们研究了一种在多地点试验数据分析中提取和拟合合成环境协变量和血统信息的方法,以预测基因型在未试验地点的表现。植物育种试验通常在多个试验地点进行,以预测基因型在目标环境群体中的表现。使用适当的统计模型可以提高预测的准确性。我们比较了在基因型-地点交互作用的同一性、对角线和因子分析方差-协方差结构下,有无合成协变量(SC)和血统信息的线性混合模型。利用预测差异的均方误差(MSEPD)和预测均值与调整均值之间的斯皮尔曼等级相关性,比较评估了不同模型预测基因型在未试验地点表现的准确性。我们使用了埃塞俄比亚干旱低地高粱(Sorghum bicolor (L.) Moench)育种计划中的多环境试验(MET)数据集,对其产量表现进行了评估。为了验证我们的模型,我们采用了 "一地一出 "的交叉验证策略。共考虑了 65 个从高粱试验地点获得的环境协变量(ECs)。利用多元偏最小二乘法分析从环境协变量中提取 SCs,然后将其拟合到线性混合模型中。然后,根据血统信息对模型进行扩展。根据 MSEPD,与其他不包含 SC 的模型相比,包含 SC 的模型提高了三个方差-协方差结构中基因型表现的预测准确性。有 SC 的模型的等级相关性也更高。拟合 SC 时,因子分析的等级相关性为 0.58,对角线的等级相关性为 0.51,同一方差-协方差结构的等级相关性为 0.46。我们的方法表明,在埃塞俄比亚高粱育种的基因型-地点交互作用背景下,SC 提高了预测的准确性。
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引用次数: 0
Genotyping-by-sequencing targets genic regions and improves resolution of genome-wide association studies in autotetraploid potato. 通过测序进行基因分型锁定基因区域,提高自交系马铃薯全基因组关联研究的分辨率。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-07-09 DOI: 10.1007/s00122-024-04651-8
Sanjeev Kumar Sharma, Karen McLean, Peter E Hedley, Finlay Dale, Steve Daniels, Glenn J Bryan

Key message: De novo genotyping in potato using methylation-sensitive GBS discovers SNPs largely confined to genic or gene-associated regions and displays enhanced effectiveness in estimating LD decay rates, population structure and detecting GWAS associations over 'fixed' SNP genotyping platform. Study also reports the genetic architectures including robust sequence-tagged marker-trait associations for sixteen important potato traits potentially carrying higher transferability across a wider range of germplasm. This study deploys recent advancements in polyploid analytical approaches to perform complex trait analyses in cultivated tetraploid potato. The study employs a 'fixed' SNP Infinium array platform and a 'flexible and open' genome complexity reduction-based sequencing method (GBS, genotyping-by-sequencing) to perform genome-wide association studies (GWAS) for several key potato traits including the assessment of population structure and linkage disequilibrium (LD) in the studied population. GBS SNPs discovered here were largely confined (~ 90%) to genic or gene-associated regions of the genome demonstrating the utility of using a methylation-sensitive restriction enzyme (PstI) for library construction. As compared to Infinium array SNPs, GBS SNPs displayed enhanced effectiveness in estimating LD decay rates and discriminating population subgroups. GWAS using a combined set of 30,363 SNPs identified 189 unique QTL marker-trait associations (QTL-MTAs) covering all studied traits. The majority of the QTL-MTAs were from GBS SNPs potentially illustrating the effectiveness of marker-dense de novo genotyping platforms in overcoming ascertainment bias and providing a more accurate correction for different levels of relatedness in GWAS models. GWAS also detected QTL 'hotspots' for several traits at previously known as well as newly identified genomic locations. Due to the current study exploiting genome-wide genotyping and de novo SNP discovery simultaneously on a large tetraploid panel representing a greater diversity of the cultivated potato gene pool, the reported sequence-tagged MTAs are likely to have higher transferability across a wider range of potato germplasm and increased utility for expediting genomics-assisted breeding for the several complex traits studied.

关键信息:与 "固定 "SNP基因分型平台相比,利用甲基化敏感的GBS对马铃薯进行全新基因分型可发现主要局限于基因或基因相关区域的SNP,并在估计LD衰减率、种群结构和检测GWAS关联方面显示出更高的有效性。该研究还报告了遗传结构,包括十六个重要马铃薯性状的稳健序列标记-性状关联,这些性状在更广泛的种质中可能具有更高的可转移性。这项研究利用多倍体分析方法的最新进展,对栽培四倍体马铃薯进行复杂的性状分析。该研究采用了 "固定的 "SNP Infinium 阵列平台和 "灵活开放的 "基于基因组复杂性还原的测序方法(GBS,genotyping-by-sequencing),对马铃薯的几个关键性状进行了全基因组关联研究(GWAS),包括对所研究群体的种群结构和连锁不平衡(LD)进行评估。在此发现的 GBS SNPs 大部分(约 90%)局限于基因组的基因或基因相关区域,这证明了使用甲基化敏感限制酶(PstI)构建文库的实用性。与 Infinium 阵列 SNP 相比,GBS SNP 在估计 LD 衰退率和区分人群亚群方面显示出更强的有效性。使用 30,363 个 SNPs 组合的 GWAS 发现了 189 个独特的 QTL 标记-性状关联(QTL-MTAs),涵盖了所有研究的性状。大多数 QTL-MTAs 都来自 GBS SNPs,这可能说明了标记密集的从头基因分型平台在克服确定偏差方面的有效性,并为 GWAS 模型中不同程度的亲缘关系提供了更准确的校正。GWAS 还在先前已知和新发现的基因组位置检测到了几个性状的 QTL "热点"。由于目前的研究同时利用了代表马铃薯栽培基因库更大多样性的大型四倍体面板上的全基因组基因分型和全新SNP发现,所报告的序列标记MTAs可能在更广泛的马铃薯种质中具有更高的可转移性,并在加快所研究的几个复杂性状的基因组辅助育种方面具有更大的效用。
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引用次数: 0
Genome-wide atlas of rust resistance loci in wheat. 小麦抗锈病基因位点的全基因组图谱。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-07-09 DOI: 10.1007/s00122-024-04689-8
Jingyang Tong, Cong Zhao, Dan Liu, Dilani T Jambuthenne, Mengjing Sun, Eric Dinglasan, Sambasivam K Periyannan, Lee T Hickey, Ben J Hayes

Rust diseases, including leaf rust, stripe/yellow rust, and stem rust, significantly impact wheat (Triticum aestivum L.) yields, causing substantial economic losses every year. Breeding and deployment of cultivars with genetic resistance is the most effective and sustainable approach to control these diseases. The genetic toolkit for wheat breeders to select for rust resistance has rapidly expanded with a multitude of genetic loci identified using the latest advances in genomics, mapping and cloning strategies. The goal of this review was to establish a wheat genome atlas that provides a comprehensive summary of reported loci associated with rust resistance. Our atlas provides a summary of mapped quantitative trait loci (QTL) and characterised genes for the three rusts from 170 publications over the past two decades. A total of 920 QTL or resistance genes were positioned across the 21 chromosomes of wheat based on the latest wheat reference genome (IWGSC RefSeq v2.1). Interestingly, 26 genomic regions contained multiple rust loci suggesting they could have pleiotropic effects on two or more rust diseases. We discuss a range of strategies to exploit this wealth of genetic information to efficiently utilise sources of resistance, including genomic information to stack desirable and multiple QTL to develop wheat cultivars with enhanced resistance to rust disease.

叶锈病、条锈病/黄锈病和茎锈病等锈病严重影响小麦(Triticum aestivum L.)的产量,每年都会造成巨大的经济损失。培育和推广具有遗传抗性的栽培品种是控制这些病害的最有效、最可持续的方法。利用基因组学、制图和克隆策略的最新进展,确定了大量遗传位点,小麦育种者选择抗锈病的遗传工具包迅速扩大。本综述的目的是建立一个小麦基因组图谱,全面总结报告的与锈病抗性相关的基因位点。我们的图集汇总了过去二十年中170篇论文中三种锈病的定量性状位点(QTL)和特征基因。根据最新的小麦参考基因组(IWGSC RefSeq v2.1),在小麦的 21 条染色体上共定位了 920 个 QTL 或抗性基因。有趣的是,26 个基因组区域包含多个锈病基因座,这表明它们可能对两种或多种锈病具有多效作用。我们讨论了利用这些丰富的遗传信息有效利用抗性来源的一系列策略,包括通过基因组信息堆叠理想的多重 QTL 来培育对锈病具有更强抗性的小麦栽培品种。
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引用次数: 0
Cold tolerance SNPs and candidate gene mining in the soybean germination stage based on genome-wide association analysis. 基于全基因组关联分析的大豆发芽期耐寒 SNPs 和候选基因挖掘。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-07-08 DOI: 10.1007/s00122-024-04685-y
Yuehan Chen, Zhi Liu, Dezhi Han, Qing Yang, Chenhui Li, Xiaolei Shi, Mengchen Zhang, Chunyan Yang, Lijuan Qiu, Hongchang Jia, Shu Wang, Wencheng Lu, Qian Ma, Long Yan

Key message: Three QTLs associated with low-temperature tolerance were identified by genome-wide association analysis, and 15 candidate genes were identified by haplotype analysis and gene expression analyses. Low temperature is a critical factor affecting the geographical distribution, growth, development, and yield of soybeans, with cold stress during seed germination leading to substantial productivity loss. In this study, an association panel comprising 260 soybean accessions was evaluated for four germination traits and four cold tolerance index traits, revealing extensive variation in cold tolerance. Genome-wide association study (GWAS) identified 10 quantitative trait nucleotides (QTNs) associated with cold tolerance, utilizing 30,799 single nucleotide polymorphisms (SNPs) and four GWAS models. Linkage disequilibrium (LD) analysis positioned these QTNs within three cold-tolerance quantitative trait loci (QTL) and, with QTL19-1, was positioned by three multi-locus models, underscoring its importance as a key QTL. Integrative haplotype analysis, supplemented by transcriptome analysis, uncovered 15 candidate genes. The haplotypes within the genes Glyma.18G044200, Glyma.18G044300, Glyma.18G044900, Glyma.18G045100, Glyma.19G222500, and Glyma.19G222600 exhibited significant phenotypic variations, with differential expression in materials with varying cold tolerance. The QTNs and candidate genes identified in this study offer substantial potential for marker-assisted selection and gene editing in breeding cold-tolerant soybeans, providing valuable insights into the genetic mechanisms underlying cold tolerance during soybean germination.

关键信息通过全基因组关联分析确定了3个与耐低温相关的QTL,通过单倍型分析和基因表达分析确定了15个候选基因。低温是影响大豆地理分布、生长、发育和产量的关键因素,种子萌发过程中的低温胁迫会导致大量的产量损失。在这项研究中,对由 260 个大豆品种组成的关联面板进行了四种萌发性状和四种耐寒指数性状的评估,结果显示耐寒性存在广泛的变异。全基因组关联研究(GWAS)利用 30,799 个单核苷酸多态性(SNPs)和四个 GWAS 模型确定了与耐寒性相关的 10 个数量性状核苷酸(QTNs)。连锁不平衡(LD)分析将这些 QTNs 定位在三个耐寒数量性状位点(QTL)上,其中 QTL19-1 被三个多焦点模型定位,突出了其作为关键 QTL 的重要性。综合单倍型分析以及转录组分析发现了 15 个候选基因。基因Glyma.18G044200、Glyma.18G044300、Glyma.18G044900、Glyma.18G045100、Glyma.19G222500和Glyma.19G222600中的单倍型表现出显著的表型差异,在不同耐寒性的材料中有不同的表达。本研究鉴定的 QTNs 和候选基因为耐寒大豆育种中的标记辅助选择和基因编辑提供了巨大的潜力,为大豆发芽过程中耐寒性的遗传机制提供了宝贵的见解。
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Theoretical and Applied Genetics
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