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Current status of molecular rice breeding for durable and broad-spectrum resistance to major diseases and insect pests 针对主要病虫害的持久和广谱抗性的分子水稻育种现状
IF 5.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-09-10 DOI: 10.1007/s00122-024-04729-3
Xiaoyan Cheng, Guohua Zhou, Wei Chen, Lin Tan, Qishi Long, Fusheng Cui, Lei Tan, Guoxing Zou, Yong Tan

In the past century, there have been great achievements in identifying resistance (R) genes and quantitative trait loci (QTLs) as well as revealing the corresponding molecular mechanisms for resistance in rice to major diseases and insect pests. The introgression of R genes to develop resistant rice cultivars has become the most effective and eco-friendly method to control pathogens/insects at present. However, little attention has been paid to durable and broad-spectrum resistance, which determines the real applicability of R genes. Here, we summarize all the R genes and QTLs conferring durable and broad-spectrum resistance in rice to fungal blast, bacterial leaf blight (BLB), and the brown planthopper (BPH) in molecular breeding. We discuss the molecular mechanisms and feasible methods of improving durable and broad-spectrum resistance to blast, BLB, and BPH. We will particularly focus on pyramiding multiple R genes or QTLs as the most useful method to improve durability and broaden the disease/insect spectrum in practical breeding regardless of its uncertainty. We believe that this review provides useful information for scientists and breeders in rice breeding for multiple stress resistance in the future.

上个世纪,在鉴定水稻主要病虫害的抗性(R)基因和数量性状位点(QTLs)以及揭示相应的分子机制方面取得了巨大成就。引入 R 基因培育抗性水稻栽培品种已成为目前控制病原体/虫害最有效、最环保的方法。然而,人们很少关注持久和广谱的抗性,这决定了 R 基因的真正适用性。在此,我们总结了分子育种中赋予水稻对真菌稻瘟病、细菌性叶枯病(BLB)和褐斑病(BPH)持久和广谱抗性的所有 R 基因和 QTL。我们将讨论提高对稻瘟病、细菌性叶枯病和褐飞虱的持久和广谱抗性的分子机制和可行方法。我们将特别关注将多个 R 基因或 QTLs 排列成金字塔,作为在实际育种中提高耐久性和扩大病/虫谱的最有用的方法,而不考虑其不确定性。我们相信,本综述将为科学家和育种家今后进行水稻抗多种胁迫育种提供有用的信息。
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引用次数: 0
Fine-mapping of a major QTL controlling plant height by BSA-seq and transcriptome sequencing in cotton. 通过 BSA-seq 和转录组测序精细绘制控制棉花株高的主要 QTL 图谱。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-09-09 DOI: 10.1007/s00122-024-04714-w
Chao Li, Longyu Huang, Yiwen Huang, Meng Kuang, Yuzhen Wu, Zhiying Ma, Xiaoqiong Fu

Key message: GhSOT (GH_D05G3950) plays a negative role in regulating plant height development by modulating the GA signaling. Plant height is an important indicator affecting mechanical harvesting for cotton. Therefore, understanding the genes associated with the plant height is crucial for cotton breeding and production. In this study, we used bulk segregant analysis sequencing to identify a new quantitative trait locu (QTL) called qPH5.1, which is linked to plant height. Local QTL mapping using seven kompetitive allele-specific PCR (KASP) markers and linkage analysis successfully narrowed down qPH5.1 to ~ 0.34 Mb region harbored five candidate genes. Subsequently, RNA sequencing (RNA-seq) analysis and examination of expression patterns revealed that GhSOT exhibited the highest likelihood of being the candidate gene responsible for the plant height at this locus. Seven SNP site variations were identified in the GhSOT promoter between the two parents, and Luciferase experiments confirmed that the promoter of GhSOT from cz3 enhances downstream gene expression more effectively. Additionally, suppression of GhSOT in cz3 resulted in the restoration of plant height, further emphasizing the functional significance of this gene. Application of exogenous gibberellin acid (GA) significantly restored plant height in cz3, as demonstrated by RNA-seq analysis and exogenous hormone treatment, which revealed alterations in genes associated with GA signaling pathways. These results reveal GhSOT is a key gene controlling plant height, which may affect plant height by regulating GA signaling.

关键信息:GhSOT (GH_D05G3950)通过调节 GA 信号传导,在调节植株高度发育中起负作用。株高是影响棉花机械收获的一个重要指标。因此,了解与株高相关的基因对棉花育种和生产至关重要。在本研究中,我们利用批量分离分析测序技术鉴定出了一个名为qPH5.1的新数量性状位点(QTL),它与株高有关。利用 7 个竞争性等位基因特异性 PCR(KASP)标记和连锁分析绘制的局部 QTL 图谱成功地将 qPH5.1 缩小到约 0.34 Mb 的区域,其中包含 5 个候选基因。随后的 RNA 测序(RNA-seq)分析和表达模式检查显示,GhSOT 最有可能是该位点上导致植株高度的候选基因。在两个亲本的 GhSOT 启动子中发现了七个 SNP 位点变异,荧光素酶实验证实 cz3 的 GhSOT 启动子能更有效地增强下游基因的表达。此外,抑制 cz3 中的 GhSOT 还能恢复植株高度,这进一步强调了该基因的功能意义。通过 RNA-seq 分析和外源激素处理,发现与 GA 信号通路相关的基因发生了改变,应用外源赤霉素(GA)可显著恢复 cz3 的植株高度。这些结果揭示了 GhSOT 是控制植株高度的关键基因,它可能通过调节 GA 信号转导来影响植株高度。
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引用次数: 0
Map-based cloning of LPD, a major gene positively regulates leaf prickle development in eggplant. 基于图谱克隆茄子叶刺发育的主要正调控基因 LPD。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-09-09 DOI: 10.1007/s00122-024-04726-6
Changjiao Ke, Wenxiang Guan, Jialong Jiang, Likun Huang, Hui Li, Wenjing Li, Yanyu Lin, Lihui Lin, Xiaofang Xie, Weiren Wu, Wenxia Gao, Yan Zheng

Key message: A critical gene for leaf prickle development (LPD) in eggplant was mapped on chromosome E06 and was confirmed to be SmARF10B through RNA interference using a new genetic transformation technique called SACI developed in this study Prickles on eggplant pose challenges for agriculture and are undesirable in cultivated varieties. This study aimed to uncover the genetic mechanisms behind prickle formation in eggplant. Using the F2 and F2:3 populations derived from a cross between the prickly wild eggplant, YQ, and the prickle-free cultivated variety, YZQ, we identified a key genetic locus (LPD, leaf prickle development) on chromosome E06 associated with leaf prickle development through BSA-seq and QTL mapping. An auxin response factor gene, SmARF10B, was predicted as the candidate gene as it exhibited high expression in YQ's mature leaves, while being significantly low in YZQ. Downregulating SmARF10B in YQ through RNAi using a simple and efficient Agrobacterium-mediated genetic transformation method named Seedling Apical Cut Infection (SACI) developed in this study substantially reduced the size and density of leaf prickles, confirming the role of this gene in prickle development. Besides, an effective SNP was identified in SmARF10B, resulting in an amino acid change between YQ and YZQ. However, this SNP did not consistently correlate with prickle formation in eight other eggplant materials examined. This study sheds light on the pivotal role of SmARF10B in eggplant prickle development and introduces a new genetic transformation method for eggplant, paving the way for future research in this field.

关键信息:茄子叶刺发育(LPD)的一个关键基因被绘制在 E06 号染色体上,并通过本研究开发的一种名为 SACI 的新型遗传转化技术进行 RNA 干扰,证实该基因为 SmARF10B。本研究旨在揭示茄子皮刺形成背后的遗传机制。利用多刺野生茄子YQ和无刺栽培品种YZQ杂交产生的F2和F2:3群体,通过BSA-seq和QTL作图,我们在E06染色体上发现了一个与叶刺发育相关的关键遗传位点(LPD,叶刺发育)。一个辅助因子响应因子 SmARF10B 被预测为候选基因,因为它在 YQ 的成熟叶片中表现出较高的表达量,而在 YZQ 中则明显较低。本研究开发了一种名为 "幼苗顶端切口感染(SACI)"的简单高效的农杆菌介导遗传转化方法,通过RNAi技术下调YQ中的SmARF10B,大大降低了叶刺的大小和密度,证实了该基因在叶刺发育过程中的作用。此外,还在 SmARF10B 中发现了一个有效的 SNP,导致 YQ 和 YZQ 之间的氨基酸发生变化。然而,在研究的其他 8 种茄子材料中,该 SNP 与皮刺形成的相关性并不一致。这项研究揭示了 SmARF10B 在茄子皮刺发育过程中的关键作用,并为茄子引入了一种新的遗传转化方法,为该领域的未来研究铺平了道路。
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引用次数: 0
Mapping rust resistance in European winter wheat: many QTLs for yellow rust resistance, but only a few well characterized genes for stem rust resistance. 绘制欧洲冬小麦的抗锈病基因图谱:抗黄锈病的 QTLs 数量众多,但抗茎干锈病的特征基因却寥寥无几。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-09-05 DOI: 10.1007/s00122-024-04731-9
Thomas Miedaner, Wera Eckhoff, Kerstin Flath, Anne-Kristin Schmitt, Philipp Schulz, Johannes Schacht, Philipp Boeven, Wessam Akel, Hubert Kempf, Paul Gruner

Key message: Stem rust resistance was mainly based on a few, already known resistance genes; for yellow rust resistance there was a combination of designated genes and minor QTLs. Yellow rust (YR) caused by Puccinia striiformis f. sp. tritici (Pst) and stem rust (SR) caused by Puccinia graminis f. sp. tritici (Pgt) are among the most damaging wheat diseases. Although, yellow rust has occurred regularly in Europe since the advent of the Warrior race in 2011, damaging stem rust epidemics are still unusual. We analyzed the resistance of seven segregating populations at the adult growth stage with the parents being selected for YR and SR resistances across three to six environments (location-year combinations) following inoculation with defined Pst and Pgt races. In total, 600 progenies were phenotyped and 563 were genotyped with a 25k SNP array. For SR resistance, three major resistance genes (Sr24, Sr31, Sr38/Yr17) were detected in different combinations. Additional QTLs provided much smaller effects except for a gene on chromosome 4B that explained much of the genetic variance. For YR resistance, ten loci with highly varying percentages of explained genetic variance (pG, 6-99%) were mapped. Our results imply that introgression of new SR resistances will be necessary for breeding future rust resistant cultivars, whereas YR resistance can be achieved by genomic selection of many of the detected QTLs.

关键信息:茎锈病的抗性主要基于几个已知的抗性基因;黄锈病的抗性则是指定基因和次要 QTLs 的组合。由条锈病菌(Puccinia striiformis f. sp. tritici,Pst)引起的黄锈病(YR)和由禾谷镰孢菌(Puccinia graminis f. sp. tritici,Pgt)引起的茎锈病(SR)是危害最大的小麦病害之一。虽然自 2011 年 Warrior 种族出现以来,黄锈病在欧洲经常发生,但破坏性的茎锈病流行仍不常见。我们分析了七个分离群体在成株生长阶段的抗性,其亲本在接种确定的 Pst 和 Pgt 株系后,在三至六个环境(地点-年份组合)中进行了 YR 和 SR 抗性筛选。总共对 600 个后代进行了表型分析,并用 25k SNP 阵列对 563 个后代进行了基因分型。在 SR 抗性方面,以不同组合检测到三个主要抗性基因(Sr24、Sr31、Sr38/Yr17)。除了 4B 染色体上的一个基因能解释大部分遗传变异外,其他 QTL 的影响要小得多。在抗 YR 方面,绘制了 10 个基因座,其解释的遗传变异百分比(pG,6-99%)差异很大。我们的研究结果表明,要培育未来的抗锈病栽培品种,必须引入新的SR抗性,而YR抗性则可以通过对许多检测到的QTL进行基因组选择来实现。
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引用次数: 0
Genome-wide association study of fiber quality traits in US upland cotton (Gossypium hirsutum L.). 美国陆地棉(Gossypium hirsutum L.)纤维质量性状的全基因组关联研究。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-09-03 DOI: 10.1007/s00122-024-04717-7
S Anjan Gowda, Hui Fang, Priyanka Tyagi, Fred Bourland, Jane Dever, Benjamin Todd Campbell, Jinfa Zhang, Abdelraheem Abdelraheem, Shilpa Sood, Don C Jones, Vasu Kuraparthy

Key message: A GWAS in an elite diversity panel, evaluated across 10 environments, identified genomic regions regulating six fiber quality traits, facilitating genomics-assisted breeding and gene discovery in upland cotton. In this study, an elite diversity panel of 348 upland cotton accessions was evaluated in 10 environments across the US Cotton Belt and genotyped with the cottonSNP63K array, for a genome-wide association study of six fiber quality traits. All fiber quality traits, upper half mean length (UHML: mm), fiber strength (FS: g tex-1), fiber uniformity (FU: %), fiber elongation (FE: %), micronaire (MIC) and short fiber content (SFC: %), showed high broad-sense heritability (> 60%). All traits except FE showed high genomic heritability. UHML, FS and FU were all positively correlated with each other and negatively correlated with FE, MIC and SFC. GWAS of these six traits identified 380 significant marker-trait associations (MTAs) including 143 MTAs on 30 genomic regions. These 30 genomic regions included MTAs identified in at least three environments, and 23 of them were novel associations. Phenotypic variation explained for the MTAs in these 30 genomic regions ranged from 6.68 to 11.42%. Most of the fiber quality-associated genomic regions were mapped in the D-subgenome. Further, this study confirmed the pleiotropic region on chromosome D11 (UHML, FS and FU) and identified novel co-localized regions on D04 (FU, SFC), D05 (UHML, FU, and D06 UHML, FU). Marker haplotype analysis identified superior combinations of fiber quality-associated genomic regions with high trait values (UHML = 32.34 mm; FS = 32.73 g tex-1; FE = 6.75%). Genomic analyses of traits, haplotype combinations and candidate gene information described in the current study could help leverage genetic diversity for targeted genetic improvement and gene discovery for fiber quality traits in cotton.

关键信息:在一个精英多样性小组中进行的全球基因组研究对 10 种环境进行了评估,确定了调控六种纤维质量性状的基因组区域,从而促进了基因组学辅助育种和陆地棉基因的发现。本研究在美国棉花带的 10 个环境中评估了由 348 个陆地棉品种组成的精英多样性面板,并使用 cottonSNP63K 阵列对其进行了基因分型,从而对六个纤维品质性状进行了全基因组关联研究。所有纤维质量性状,包括上半部平均长度(UHML:mm)、纤维强度(FS:g tex-1)、纤维均匀度(FU:%)、纤维伸长率(FE:%)、微米值(MIC)和短纤维含量(SFC:%),都显示出较高的广义遗传率(> 60%)。除 FE 外,所有性状都表现出较高的基因组遗传率。UHML、FS和FU之间均呈正相关,而与FE、MIC和SFC呈负相关。这六个性状的 GWAS 发现了 380 个显著的标记-性状关联(MTAs),包括 30 个基因组区域上的 143 个 MTAs。这 30 个基因组区域包括至少在三个环境中发现的 MTAs,其中 23 个是新的关联。这30个基因组区域中的MTA所解释的表型变异从6.68%到11.42%不等。大多数纤维质量相关基因组区域都绘制在D亚基因组中。此外,这项研究还证实了染色体 D11(UHML、FS 和 FU)上的多效应区,并在 D04(FU、SFC)、D05(UHML、FU 和 D06 UHML、FU)上发现了新的共定位区。标记单倍型分析确定了具有高性状值的纤维质量相关基因组区域的优良组合(UHML = 32.34 mm;FS = 32.73 g tex-1;FE = 6.75%)。本研究中描述的性状、单体型组合和候选基因信息的基因组分析有助于利用遗传多样性对棉花纤维品质性状进行有针对性的遗传改良和基因发掘。
{"title":"Genome-wide association study of fiber quality traits in US upland cotton (Gossypium hirsutum L.).","authors":"S Anjan Gowda, Hui Fang, Priyanka Tyagi, Fred Bourland, Jane Dever, Benjamin Todd Campbell, Jinfa Zhang, Abdelraheem Abdelraheem, Shilpa Sood, Don C Jones, Vasu Kuraparthy","doi":"10.1007/s00122-024-04717-7","DOIUrl":"10.1007/s00122-024-04717-7","url":null,"abstract":"<p><strong>Key message: </strong>A GWAS in an elite diversity panel, evaluated across 10 environments, identified genomic regions regulating six fiber quality traits, facilitating genomics-assisted breeding and gene discovery in upland cotton. In this study, an elite diversity panel of 348 upland cotton accessions was evaluated in 10 environments across the US Cotton Belt and genotyped with the cottonSNP63K array, for a genome-wide association study of six fiber quality traits. All fiber quality traits, upper half mean length (UHML: mm), fiber strength (FS: g tex<sup>-1</sup>), fiber uniformity (FU: %), fiber elongation (FE: %), micronaire (MIC) and short fiber content (SFC: %), showed high broad-sense heritability (> 60%). All traits except FE showed high genomic heritability. UHML, FS and FU were all positively correlated with each other and negatively correlated with FE, MIC and SFC. GWAS of these six traits identified 380 significant marker-trait associations (MTAs) including 143 MTAs on 30 genomic regions. These 30 genomic regions included MTAs identified in at least three environments, and 23 of them were novel associations. Phenotypic variation explained for the MTAs in these 30 genomic regions ranged from 6.68 to 11.42%. Most of the fiber quality-associated genomic regions were mapped in the D-subgenome. Further, this study confirmed the pleiotropic region on chromosome D11 (UHML, FS and FU) and identified novel co-localized regions on D04 (FU, SFC), D05 (UHML, FU, and D06 UHML, FU). Marker haplotype analysis identified superior combinations of fiber quality-associated genomic regions with high trait values (UHML = 32.34 mm; FS = 32.73 g tex<sup>-1</sup>; FE = 6.75%). Genomic analyses of traits, haplotype combinations and candidate gene information described in the current study could help leverage genetic diversity for targeted genetic improvement and gene discovery for fiber quality traits in cotton.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"137 9","pages":"214"},"PeriodicalIF":4.4,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142120669","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Dissecting the genetic basis of resistance to Soil-borne cereal mosaic virus (SBCMV) in durum wheat by bi-parental mapping and GWAS. 通过双亲图谱和基因组测序分析,剖析硬粒小麦对土传谷物花叶病毒(SBCMV)抗性的遗传基础。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-09-02 DOI: 10.1007/s00122-024-04709-7
Martina Bruschi, Matteo Bozzoli, Claudio Ratti, Giuseppe Sciara, Ellen Goudemand, Pierre Devaux, Danara Ormanbekova, Cristian Forestan, Simona Corneti, Sandra Stefanelli, Sara Castelletti, Elena Fusari, Jad B Novi, Elisabetta Frascaroli, Silvio Salvi, Dragan Perovic, Agata Gadaleta, Concepcion Rubies-Autonell, Maria Corinna Sanguineti, Roberto Tuberosa, Marco Maccaferri

Soil-borne cereal mosaic virus (SBCMV), the causative agent of wheat mosaic, is a Furovirus challenging wheat production all over Europe. Differently from bread wheat, durum wheat shows greater susceptibility and stronger yield penalties, so identification and genetic characterization of resistance sources are major targets for durum genetics and breeding. The Sbm1 locus providing high level of resistance to SBCMV was mapped in bread wheat to the 5DL chromosome arm (Bass in Genome 49:1140-1148, 2006). This excluded the direct use of Sbm1 for durum wheat improvement. Only one major QTL has been mapped in durum wheat, namely QSbm.ubo-2B, on the 2BS chromosome region coincident with Sbm2, already known in bread wheat as reported (Bayles in HGCA Project Report, 2007). Therefore, QSbm.ubo-2B = Sbm2 is considered a pillar for growing durum in SBCMV-affected areas. Herein, we report the fine mapping of Sbm2 based on bi-parental mapping and GWAS, using the Infinium 90 K SNP array and high-throughput KASP®. Fine mapping pointed out a critical haploblock of 3.2 Mb defined by concatenated SNPs successfully converted to high-throughput KASP® markers coded as KUBO. The combination of KUBO-27, wPt-2106-ASO/HRM, KUBO-29, and KUBO-1 allows unequivocal tracing of the Sbm2-resistant haplotype. The interval harbors 52 high- and 41 low-confidence genes, encoding 17 cytochrome p450, three receptor kinases, two defensins, and three NBS-LRR genes. These results pave the way for Sbm2 positional cloning. Importantly, the development of Sbm2 haplotype tagging KASP® provides a valuable case study for improving efficacy of the European variety testing system and, ultimately, the decision-making process related to varietal characterization and choice.

土传谷物花叶病毒(SBCMV)是小麦花叶病的病原体,是一种对整个欧洲的小麦生产构成挑战的呋喃病毒。与面包小麦不同,硬粒小麦的易感性更强,产量损失也更大,因此抗性来源的鉴定和遗传特性分析是硬粒小麦遗传学和育种的主要目标。在面包小麦中,对 SBCMV 具有高水平抗性的 Sbm1 基因座被映射到 5DL 染色体臂上(Bass in Genome 49:1140-1148, 2006)。这就排除了将 Sbm1 直接用于硬粒小麦改良的可能性。在硬质小麦中只绘制了一个主要的 QTL,即 QSbm.ubo-2B,位于 2BS 染色体区域,与 Sbm2 重合,据报道,面包小麦中已经知道 Sbm2(Bayles,载于 HGCA 项目报告,2007 年)。因此,QSbm.ubo-2B = Sbm2 被认为是在受 SBCMV 影响地区种植硬质小麦的支柱。在此,我们利用 Infinium 90 K SNP 阵列和高通量 KASP® 报告了基于双亲图谱和 GWAS 的 Sbm2 精细图谱。精细图谱指出了一个3.2 Mb的关键单倍区块,该单倍区块由成功转换为高通量KASP®标记的SNPs连接而成,编码为KUBO。结合 KUBO-27、wPt-2106-ASO/HRM、KUBO-29 和 KUBO-1 可以明确追踪 Sbm2-抗性单倍型。该区间包含 52 个高置信度基因和 41 个低置信度基因,编码 17 个细胞色素 p450、3 个受体激酶、2 个防御素和 3 个 NBS-LRR 基因。这些结果为 Sbm2 定位克隆铺平了道路。重要的是,Sbm2 单倍型标记 KASP® 的开发为提高欧洲品种测试系统的效率以及最终与品种特征描述和选择相关的决策过程提供了一个有价值的案例研究。
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引用次数: 0
Mutations in starch BRANCHING ENZYME 2a suppress the traits caused by the loss of ISOAMYLASE1 in barley. 淀粉分支酶 2a 的突变抑制了大麦中 ISOAMYLASE1 缺失所导致的性状。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-08-31 DOI: 10.1007/s00122-024-04725-7
Ryo Matsushima, Hiroshi Hisano, June-Sik Kim, Rose McNelly, Naoko F Oitome, David Seung, Naoko Fujita, Kazuhiro Sato

Key message: The hvbe2a mutations restore the starch-deficient phenotype caused by the hvisa1 and hvflo6 mutations in barley endosperm. The genetic interactions among starch biosynthesis genes can be exploited to alter starch properties, but they remain poorly understood due to the various combinations of mutations to be tested. Here, we isolated two novel barley mutants defective in starch BRANCHING ENZYME 2a (hvbe2a-1 and hvbe2a-2) based on the starch granule (SG) morphology. Both hvbe2a mutants showed elongated SGs in the endosperm and increased resistant starch content. hvbe2a-1 had a base change in HvBE2a gene, substituting the amino acid essential for its enzyme activity, while hvbe2a-2 is completely missing HvBE2a due to a chromosomal deletion. Further genetic crosses with barley isoamylase1 mutants (hvisa1) revealed that both hvbe2a mutations could suppress defects in endosperm caused by hvisa1, such as reduction in starch, increase in phytoglycogen, and changes in the glucan chain length distribution. Remarkably, hvbe2a mutations also transformed the endosperm SG morphology from the compound SG caused by hvisa1 to bimodal simple SGs, resembling that of wild-type barley. The suppressive impact was in competition with floury endosperm 6 mutation (hvflo6), which could enhance the phenotype of hvisa1 in the endosperm. In contrast, the compound SG formation induced by the hvflo6 hvisa1 mutation in pollen was not suppressed by hvbe2a mutations. Our findings provide new insights into genetic interactions in the starch biosynthetic pathway, demonstrating how specific genetic alterations can influence starch properties and SG morphology, with potential applications in cereal breeding for desired starch properties.

关键信息:hvbe2a突变可恢复大麦胚乳中由hvisa1和hvflo6突变引起的淀粉缺乏表型。淀粉生物合成基因之间的遗传相互作用可被用来改变淀粉特性,但由于需要测试各种突变组合,人们对它们的了解仍然很少。在这里,我们根据淀粉粒(SG)的形态分离出了两个淀粉分支酶 2a 缺陷的新型大麦突变体(hvbe2a-1 和 hvbe2a-2)。hvbe2a-1 基因中的 HvBE2a 碱基发生了改变,取代了其酶活性所必需的氨基酸,而 hvbe2a-2 则由于染色体缺失而完全缺失 HvBE2a。进一步与大麦异淀粉酶1突变体(hvisa1)进行遗传杂交发现,hvbe2a突变体都能抑制hvisa1导致的胚乳缺陷,如淀粉减少、植物糖原增加和葡聚糖链长分布的变化。值得注意的是,hvbe2a 突变也使胚乳 SG 形态从 hvisa1 引起的复合 SG 转变为双峰单 SG,与野生型大麦的 SG 形态相似。这种抑制作用与绒毛状胚乳 6 基因突变(hvflo6)形成了竞争关系,后者可以增强 hvisa1 在胚乳中的表型。相比之下,hvflo6 hvisa1 突变在花粉中诱导的复合 SG 形成并没有受到 hvbe2a 突变的抑制。我们的研究结果为淀粉生物合成途径中的遗传相互作用提供了新的见解,证明了特定的遗传改变是如何影响淀粉特性和SG形态的,并有可能应用于谷物育种以获得所需的淀粉特性。
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引用次数: 0
Identification and development of functional markers for purple grain genes in durum wheat (Triticum durum Desf.). 硬粒小麦(Triticum durum Desf.)
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-08-29 DOI: 10.1007/s00122-024-04710-0
Salvatore Esposito, Samuela Palombieri, Paolo Vitale, Giuseppina Angione, Chiara D'Attilia, Francesca Taranto, Francesco Sestili, Pasquale De Vita

Key message: Two allelic variants of Pp-A3 and Pp-B1 were identified in purple durum wheat. Molecular markers at both loci were developed and validated on an independent panel, offering a breakthrough for wheat improvement. Purple wheats are a class of cereals with pigmented kernels of particular interest for their antioxidant and anti-inflammatory properties. Although two complementary loci (Pp-B1 and Pp-A3), responsible for purple pericarp have been pinpointed in bread wheat (Triticum aestivum L.), in durum wheat (Triticum durum Desf.) the causative genes along with functional and non-functional alleles are still unknown. Here, using a quantitative trait loci (QTL) mapping approach on a RIL population derived from purple and non-purple durum wheat genotypes, we identified three major regions on chromosomes 2A, 3A, and 7B explaining the highest phenotypic variation (> 50%). Taking advantage of the Svevo genome, a MYB was reannotated on chromosome 7B and reported as a candidate for Pp-B1. An insertion of ~ 1.6 kb within the first exon led to a non-functional allele (TdPpm1b), whereas the functional allele (TdPpm1a) was characterized and released for the first time in durum wheat. Pp-A3 was instead identified as a duplicated gene, of which only one was functional. The promoter sequencing of the functional allele (TdPpb1a) revealed six 261-bp tandem repeats in purple durum wheat, whereas one unit (TdPpb1b) was found in the yellow once. Functional molecular markers at both loci were developed to precisely discriminate purple and not purple genotypes, representing a valuable resource for selecting superior purple durum lines at early growth stages. Overall, our results expand the understanding of the function of MYB and bHLH activators in durum wheat, paving new ways to explore cis-regulatory elements at the promoter level.

关键信息:在紫色硬粒小麦中发现了 Pp-A3 和 Pp-B1 的两个等位基因变异。这两个位点上的分子标记都已开发出来,并在一个独立的面板上进行了验证,为小麦改良提供了突破性进展。紫小麦是一类具有色素颗粒的谷物,因其抗氧化和抗炎特性而备受关注。虽然在面包小麦(Triticum aestivum L.)中已经确定了两个导致紫色果皮的互补基因座(Pp-B1 和 Pp-A3),但在硬质小麦(Triticum durum Desf.)中,致病基因以及功能性和非功能性等位基因仍然未知。在此,我们利用定量性状位点(QTL)绘图方法,在紫色和非紫色硬质小麦基因型的 RIL 群体中确定了染色体 2A、3A 和 7B 上的三个主要区域,这三个区域解释了最高的表型变异(> 50%)。利用 Svevo 基因组的优势,我们对 7B 染色体上的一个 MYB 进行了重新标注,并将其报告为 Pp-B1 的候选基因。第一个外显子内约 1.6 kb 的插入导致了一个无功能等位基因(TdPpm1b)的出现,而功能等位基因(TdPpm1a)则首次在硬粒小麦中得到表征和释放。Pp-A3 被鉴定为一个重复基因,其中只有一个是功能基因。功能性等位基因(TdPpb1a)的启动子测序在紫色硬粒小麦中发现了六个 261-bp 的串联重复,而在黄色小麦中发现了一个单位(TdPpb1b)。在这两个位点上开发的功能分子标记可精确区分紫色和非紫色基因型,是在早期生长阶段选育紫色硬粒小麦优良品系的宝贵资源。总之,我们的研究结果拓展了人们对硬粒小麦中 MYB 和 bHLH 激活因子功能的认识,为在启动子水平探索顺式调控元件铺平了新的道路。
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引用次数: 0
Identification of candidate genes and genomic prediction of soybean fatty acid components in two soybean populations. 在两个大豆种群中鉴定候选基因并对大豆脂肪酸成分进行基因组预测。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-08-29 DOI: 10.1007/s00122-024-04716-8
Fengmin Wang, Tiantian Zhao, Yan Feng, Zengfa Ji, Qingsong Zhao, Qingmin Meng, Bingqiang Liu, Luping Liu, Qiang Chen, Jin Qi, Zhengge Zhu, Chunyan Yang, Jun Qin
<p><p>Soybean, a source of plant-derived lipids, contains an array of fatty acids essential for health. A comprehensive understanding of the fatty acid profiles in soybean is crucial for enhancing soybean cultivars and augmenting their qualitative attributes. Here, 180 F<sub>10</sub> generation recombinant inbred lines (RILs), derived from the cross-breeding of the cultivated soybean variety 'Jidou 12' and the wild soybean 'Y9,' were used as primary experimental subjects. Using inclusive composite interval mapping (ICIM), this study undertook a quantitative trait locus (QTL) analysis on five distinct fatty acid components in the RIL population from 2019 to 2021. Concurrently, a genome-wide association study (GWAS) was conducted on 290 samples from a genetically diverse natural population to scrutinize the five fatty acid components during the same timeframe, thereby aiming to identify loci closely associated with fatty acid profiles. In addition, haplotype analysis and the Kyoto Encyclopedia of Genes and Genomes pathway analysis were performed to predict candidate genes. The QTL analysis elucidated 23 stable QTLs intricately associated with the five fatty acid components, exhibiting phenotypic contribution rates ranging from 2.78% to 25.37%. In addition, GWAS of the natural population unveiled 102 significant loci associated with these fatty acid components. The haplotype analysis of the colocalized loci revealed that Glyma.06G221400 on chromosome 6 exhibited a significant correlation with stearic acid content, with Hap1 showing a markedly elevated stearic acid level compared with Hap2 and Hap3. Similarly, Glyma.12G075100 on chromosome 12 was significantly associated with the contents of oleic, linoleic, and linolenic acids, suggesting its involvement in fatty acid biosynthesis. In the natural population, candidate genes associated with the contents of palmitic and linolenic acids were predominantly from the fatty acid metabolic pathway, indicating their potential role as pivotal genes in the critical steps of fatty acid metabolism. Furthermore, genomic selection (GS) for fatty acid components was conducted using ridge regression best linear unbiased prediction based on both random single nucleotide polymorphisms (SNPs) and SNPs significantly associated with fatty acid components identified by GWAS. GS accuracy was contingent upon the SNP set used. Notably, GS efficiency was enhanced when using SNPs derived from QTL mapping analysis and GWAS compared with random SNPs, and reached a plateau when the number of SNP markers exceeded 3,000. This study thus indicates that Glyma.06G221400 and Glyma.12G075100 are genes integral to the synthesis and regulatory mechanisms of fatty acids. It provides insights into the complex biosynthesis and regulation of fatty acids, with significant implications for the directed improvement of soybean oil quality and the selection of superior soybean varieties. The SNP markers delineated in this study can be instrumental
大豆是植物源脂类的一种来源,含有一系列对健康至关重要的脂肪酸。全面了解大豆中的脂肪酸谱对于改良大豆品种和提高其品质属性至关重要。本文以栽培大豆品种'吉豆 12'和野生大豆'Y9'杂交产生的 180 个 F10 代重组近交系(RIL)为主要实验对象。本研究利用包容性复合间隔图谱(ICIM),在2019年至2021年期间对RIL群体中的五种不同脂肪酸组分进行了数量性状位点(QTL)分析。与此同时,在同一时间段内,还对来自遗传多样性自然群体的290个样本进行了全基因组关联研究(GWAS),对这五种脂肪酸成分进行了仔细研究,旨在找出与脂肪酸特征密切相关的位点。此外,还进行了单倍型分析和京都基因和基因组百科全书通路分析,以预测候选基因。QTL分析阐明了23个与五种脂肪酸组分密切相关的稳定QTL,其表型贡献率从2.78%到25.37%不等。此外,对自然群体的 GWAS 分析还发现了 102 个与这些脂肪酸成分相关的重要基因位点。对共定位位点的单倍型分析表明,6号染色体上的Glyma.06G221400与硬脂酸含量有显著相关性,与Hap2和Hap3相比,Hap1的硬脂酸含量明显升高。同样,第 12 号染色体上的 Glyma.12G075100 与油酸、亚油酸和亚麻酸的含量显著相关,表明它参与了脂肪酸的生物合成。在自然群体中,与棕榈酸和亚麻酸含量相关的候选基因主要来自脂肪酸代谢途径,表明它们可能是脂肪酸代谢关键步骤中的关键基因。此外,利用基于随机单核苷酸多态性(SNPs)和通过全球基因组研究发现的与脂肪酸成分显著相关的 SNPs 的脊回归最佳线性无偏预测,对脂肪酸成分进行了基因组选择(GS)。GS的准确性取决于所使用的SNP集。值得注意的是,与随机 SNP 相比,当使用 QTL 图谱分析和 GWAS 得出的 SNP 时,GS 效率有所提高,当 SNP 标记的数量超过 3,000 个时,GS 效率达到顶峰。因此,这项研究表明,Glyma.06G221400 和 Glyma.12G075100 是脂肪酸合成和调控机制中不可或缺的基因。该研究深入揭示了脂肪酸复杂的生物合成和调控机制,对定向改善大豆油品质和选育优良大豆品种具有重要意义。本研究中划定的 SNP 标记有助于建立一个有效的标记辅助选择和基因组学管道,以改善大豆的脂肪酸成分。
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引用次数: 0
Genome-wide association study and selective sweep analysis uncover candidate genes controlling curd branch length in cauliflower. 全基因组关联研究和选择性扫描分析发现了控制花椰菜凝乳枝长度的候选基因。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-08-28 DOI: 10.1007/s00122-024-04719-5
Yingxia Yang, Yutong Guo, Jing Wang, Wenjuan Cheng, Mingjie Lyu, Qian Wang, Jianjin Wu, Mingyan Hua, Weihua Zhang, Deling Sun, Xianhong Ge, Xingwei Yao, Rui Chen

Cauliflower is a distinct subspecies of the Brassica oleracea plants due to its specialized and edible floral organ. Cauliflower curd is composed of enlarged inflorescence meristems that developed by a series of precise molecular regulations. Based solely on the curd solidity, cauliflower is generally classified into two groups (compact-curd and loose-curd), where curd branch length acts as a crucial parameter to determine the curd morphological difference. Herein, to understand the genetic basis of curd branch development, we utilized a total of 298 inbred lines representing two groups of cauliflower to comprehensively investigate the causal genes and regulatory mechanisms. Phylogenetic and population structure analyses revealed that two subgroups could be further categorized into the compact-curd and the loose-curd groups, respectively. Integrating the genotype and phenotype data, we conducted a genome-wide association study for the length of the outermost branch (LOB) and secondary branch (LSB) of the curd. Sixty-four significant loci were identified that are highly associated with curd branch development. Evidence from genome-wide selective sweep analysis (FST and XP-EHH) narrowed down the major signal on chromosome 8 into an approximately 79 kb region which encodes eleven protein-coding genes. After further analysis of haplotypes, transcriptome profiling, and gene expression validation, we finally inferred that BOB08G028680, as a homologous counterpart of AtARR9, might be the causal gene for simultaneously regulating LOB and LSB traits in cauliflower. This result provides valuable information for improving curd solidity in future cauliflower breeding.

菜花是芸薹属植物中的一个独特亚种,因为它有专门的可食用花器官。花椰菜的凝乳是由增大的花序分生组织组成的,通过一系列精确的分子调控发育而成。仅根据凝乳的坚固程度,花椰菜一般被分为两类(紧密凝乳和松散凝乳),其中凝乳分枝长度是决定凝乳形态差异的关键参数。为了解凝乳枝发育的遗传基础,我们利用代表花椰菜两个类群的共 298 个近交系,对其致病基因和调控机制进行了全面研究。系统发育和种群结构分析表明,两个亚群可进一步划分为紧密型凝乳枝组和松散型凝乳枝组。综合基因型和表型数据,我们对凝乳最外层分支(LOB)和次生分支(LSB)的长度进行了全基因组关联研究。研究发现了 64 个与凝乳枝条发育高度相关的重要基因位点。全基因组选择性扫描分析(FST 和 XP-EHH)的证据将 8 号染色体上的主要信号缩小到约 79 kb 的区域,该区域编码 11 个蛋白质编码基因。经过进一步的单倍型分析、转录组分析和基因表达验证,我们最终推断,作为 AtARR9 的同源对应基因,BOB08G028680 可能是同时调控花椰菜 LOB 和 LSB 性状的因果基因。这一结果为今后花椰菜育种中改善凝乳坚实性提供了宝贵的信息。
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Theoretical and Applied Genetics
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