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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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引用次数: 0
A MYB family transcription factor TdRCA1 from wild emmer wheat regulates anthocyanin biosynthesis in coleoptile. 野生珙桐小麦中的 MYB 家族转录因子 TdRCA1 可调控小麦叶柄中花青素的生物合成。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-08-24 DOI: 10.1007/s00122-024-04723-9
Jinlong Li, Chaozhong Zhang, Xiangru Xu, Yuqing Su, Yutian Gao, Jiatian Yang, Chaojie Xie, Jun Ma

As important secondary metabolites in plants, anthocyanins not only contribute to colored plants organs, but also provide protections against various biotic and abiotic stresses. In this study, a MYB transcription factor gene TdRCA1 from wild emmer wheat regulating anthocyanin biosynthesis in wheat coleoptile was identified on the short arm of chromosome 7A in common wheat genetic background. The TdRCA1 overexpression lines showed colored callus, coleoptile, auricle and stem nodes, as well as up regulation of six anthocyanin-related structural genes. The expression of TdRCA1 was activated by light in a temporal manner. While coleoptile color of 48 and 60 h dark-grown seedlings changed from green to red after 24 h light treatment, those grown in dark for 72 and 96 h failed to develop red coleoptiles after light restoration. Interestingly, the over expression of TdRCA1 resulted in increased resistance to Fusarium crown rot, a chronic and severe fungal disease in many cereal growing regions in the world. Our results offer a better understanding of the molecular basis of coleoptile color in bread wheat.

花青素是植物中重要的次生代谢产物,不仅能使植物器官着色,还能抵御各种生物和非生物胁迫。本研究在普通小麦遗传背景的 7A 染色体短臂上发现了一个来自野生小麦的 MYB 转录因子基因 TdRCA1,该基因调控小麦胚叶花青素的生物合成。TdRCA1过表达株系的胼胝体、胚轴、叶耳和茎节均呈彩色,并上调了6个与花青素相关的结构基因。TdRCA1 的表达受光的激活具有时间性。经 24 小时光照处理后,48 小时和 60 小时黑暗生长的幼苗的叶柄颜色由绿色变为红色,而 72 小时和 96 小时黑暗生长的幼苗在光照恢复后未能长出红色叶柄。有趣的是,TdRCA1 的过度表达增强了对镰刀菌冠腐病的抗性。我们的研究结果有助于更好地理解面包小麦胚轴颜色的分子基础。
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引用次数: 0
Integrating RTM-GWAS and meta‑QTL data revealed genomic regions and candidate genes associated with the first fruit branch node and its height in upland cotton. 整合 RTM-GWAS 和元 QTL 数据,揭示了与陆地棉第一果枝节及其高度相关的基因组区域和候选基因。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-08-22 DOI: 10.1007/s00122-024-04703-z
Junji Su, Dandan Li, Wenmin Yuan, Ying Li, Jisheng Ju, Ning Wang, Pingjie Ling, Keyun Feng, Caixiang Wang

Key message: Two genomic regions associated with FFBN and HFFBN and a potential regulatory gene (GhE6) of HFFBN were identified through the integration of RTM-GWAS and meta‑QTL analyses. Abstract The first fruit branch node (FFBN) and the height of the first fruit branch node (HFFBN) are two important traits that are related to plant architecture and early maturation in upland cotton. Several studies have been conducted to elucidate the genetic basis of these traits in cotton using biparental and natural populations. In this study, by using 9,244 SNP linkage disequilibrium block (SNPLDB) loci from 315 upland cotton accessions, we carried out restricted two-stage multilocus and multiallele genome-wide association studies (RTM-GWASs) and identified promising haplotypes/alleles of the four stable and true major SNPLDB loci that were significantly associated with FFBN and HFFBN. Additionally, a meta-quantitative trait locus (MQTL) analysis was conducted on 274 original QTLs that were reported in 27 studies, and 40 MQTLs associated with FFBN and HFFBN were identified. Through the integration of the RTM-GWAS and meta‑QTL analyses, two stable and true major SNPLDBs (LDB_5_15144433 and LDB_16_37952328) that were distributed in the two MQTLs were identified. Ultimately, 142 genes in the two genomic regions were annotated, and three candidate genes associated with FFBN and HFFBN were identified in the genomic region (A05:14.64-15.64 Mb) via RNA-Seq and qRT‒PCR. The results of virus-induced gene silencing (VIGS) experiments indicated that GhE6 was a key gene related to HFFBN and that GhDRM1 and GhGES were important genes associated with early flowering in upland cotton. These findings will aid in the future identification of molecular markers and genetic resources for developing elite early-maturing cultivars with ideal plant characteristics.

关键信息:通过整合RTM-GWAS和元QTL分析,确定了与FFBN和HFFBN相关的两个基因组区域以及HFFBN的一个潜在调控基因(GhE6)。摘要 第一果枝节(FFBN)和第一果枝节高度(HFFBN)是与陆地棉植株结构和早熟有关的两个重要性状。为了阐明棉花这些性状的遗传基础,已经利用双亲和自然群体开展了多项研究。在本研究中,我们利用来自 315 个陆地棉品种的 9,244 个 SNP 连接不平衡块(SNPLDB)位点,开展了限制性两阶段多焦点和多序列全基因组关联研究(RTM-GWASs),并确定了与 FFBN 和 HFFBN 显著相关的四个稳定且真实的主要 SNPLDB 位点的单倍型/等位基因。此外,还对 27 项研究报告的 274 个原始 QTL 进行了元定量性状位点(MQTL)分析,并确定了 40 个与 FFBN 和 HFFBN 相关的 MQTL。通过整合 RTM-GWAS 和元 QTL 分析,确定了分布在两个 MQTL 中的两个稳定且真实的主要 SNPLDB(LDB_5_15144433 和 LDB_16_37952328)。最终,对两个基因组区域中的 142 个基因进行了注释,并通过 RNA-Seq 和 qRT-PCR 在基因组区域(A05:14.64-15.64 Mb)中确定了三个与 FFBN 和 HFFBN 相关的候选基因。病毒诱导基因沉默(VIGS)实验结果表明,GhE6 是与 HFFBN 相关的关键基因,GhDRM1 和 GhGES 是与陆地棉早花相关的重要基因。这些发现将有助于今后鉴定分子标记和遗传资源,以培育具有理想植株特征的早熟栽培品种。
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引用次数: 0
Fine mapping of stem rust resistance derived from soft red winter wheat cultivar AGS2000 to an NLR gene cluster on chromosome 6D. 将软红冬小麦栽培品种 AGS2000 的茎锈病抗性精细映射到 6D 染色体上的 NLR 基因簇。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-08-19 DOI: 10.1007/s00122-024-04702-0
L Rivera-Burgos, C VanGessel, M Guedira, J Smith, D Marshall, Y Jin, M Rouse, G Brown-Guedira

The Puccinia graminis f. sp. tritici (Pgt) Ug99-emerging virulent races present a major challenge to global wheat production. To meet present and future needs, new sources of resistance must be found. Identification of markers that allow tracking of resistance genes is needed for deployment strategies to combat highly virulent pathogen races. Field evaluation of a DH population located a QTL for stem rust (Sr) resistance, QSr.nc-6D from the breeding line MD01W28-08-11 to the distal region of chromosome arm 6DS where Sr resistance genes Sr42, SrCad, and SrTmp have been identified. A locus for seedling resistance to Pgt race TTKSK was identified in a DH population and an RIL population derived from the cross AGS2000 × LA95135. The resistant cultivar AGS2000 is in the pedigree of MD01W28-08-11 and our results suggest that it is the source of Sr resistance in this breeding line. We exploited published markers and exome capture data to enrich marker density in a 10 Mb region flanking QSr.nc-6D. Our fine mapping in heterozygous inbred families identified three markers co-segregating with resistance and delimited QSr.nc-6D to a 1.3 Mb region. We further exploited information from other genome assemblies and identified collinear regions of 6DS harboring clusters of NLR genes. Evaluation of KASP assays corresponding to our co-segregating SNP suggests that they can be used to track this Sr resistance in breeding programs. However, our results also underscore the challenges posed in identifying genes underlying resistance in such complex regions in the absence of genome sequence from the resistant genotypes.

Puccinia graminis f. sp. tritici (Pgt) Ug99-emerging剧毒品系对全球小麦生产构成了重大挑战。为了满足当前和未来的需求,必须找到新的抗性来源。需要鉴定能够追踪抗性基因的标记,以部署抗击高致病性病原物品系的战略。对一个 DH 群体的田间评估发现了一个抗茎锈病(Sr)的 QTL,即来自育种品系 MD01W28-08-11 的 QSr.nc-6D,该 QTL 位于染色体臂 6DS 的远端区域,在该区域已鉴定出 Sr 抗性基因 Sr42、SrCad 和 SrTmp。在 AGS2000 × LA95135 杂交的一个 DH 群体和一个 RIL 群体中发现了幼苗抗 Pgt 杂交种 TTKSK 的基因座。抗性栽培品种 AGS2000 在 MD01W28-08-11 的血统中,我们的研究结果表明它是该育种品系的 Sr 抗性来源。我们利用已发表的标记和外显子组捕获数据,丰富了 QSr.nc-6D 侧翼 10 Mb 区域的标记密度。我们在杂合子近交系中进行了精细作图,发现了三个与抗性共分离的标记,并将 QSr.nc-6D 限定在 1.3 Mb 的区域内。我们进一步利用来自其他基因组组装的信息,确定了 6DS 中携带 NLR 基因簇的共线区域。与我们的共分离 SNP 相对应的 KASP 检测方法的评估表明,它们可用于在育种计划中跟踪这种 Sr 抗性。然而,我们的研究结果也强调了在缺乏抗性基因型基因组序列的情况下,在这种复杂区域中鉴定抗性基因所面临的挑战。
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引用次数: 0
Two dwarfing genes Rht-B1b and Rht-D1b show pleiotropic effects on grain protein content in bread wheat (Triticum aestivum L.). 两个矮化基因Rht-B1b和Rht-D1b对面包小麦(Triticum aestivum L.)谷物蛋白质含量具有多效性。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-08-14 DOI: 10.1007/s00122-024-04713-x
Wenjing Hu, Di Wu, Dongshen Li, Xiaoming Cheng, Zunjie Wang, Die Zhao, Jizeng Jia

Key message: Five QTL for wheat grain protein content were identified, and the effects of two dwarfing genes Rht-B1b and Rht-D1b on grain protein content were validated in multiple populations. Grain protein content (GPC) plays an important role in wheat quality. Here, a recombinant inbred line (RIL) population derived from a cross between Yangmai 12 (YM12) and Yanzhan 1 (YZ1) was used to identify quantitative trait loci (QTL) for GPC. Two hundred and five RILs and their parents were grown in three years in randomized complete blocks each with two replications, and genotyped using the wheat 55 K SNP array. Five QTL were identified for GPC on chromosomes 1A, 1B, 2D, 4B, and 4D. Notably, QGpc.yaas-4B (co-located with Rht-B1) and QGpc.yaas-4D (co-located with Rht-D1) were consistently detected across all experiments and best linear unbiased estimating, accounting for 6.61-8.39% and 6.05-10.21% of the phenotypic variances, respectively. The effects of these two dwarfing alleles Rht-B1b and Rht-D1b on reducing GPC and plant height were validated in two additional RIL populations and one natural population. This study lays a foundation for further investigating the effects of dwarfing genes Rht-B1b and Rht-D1b on wheat GPC.

关键信息:鉴定了小麦籽粒蛋白质含量的五个 QTL,并在多个群体中验证了两个矮化基因 Rht-B1b 和 Rht-D1b 对籽粒蛋白质含量的影响。谷物蛋白质含量(GPC)对小麦品质起着重要作用。本文利用扬麦12号(YM12)和烟占1号(YZ1)杂交产生的重组近交系(RIL)群体来鉴定谷粒蛋白含量的数量性状位点(QTL)。对 255 个 RIL 及其亲本进行了三年的随机完全区组种植,每个区组两次重复,并使用小麦 55 K SNP 阵列进行了基因分型。在 1A、1B、2D、4B 和 4D 染色体上发现了五个 GPC QTL。值得注意的是,QGpc.yaas-4B(与 Rht-B1 共定位)和 QGpc.yaas-4D(与 Rht-D1 共定位)在所有实验中都被一致检测到,并获得最佳线性无偏估计,分别占表型变异的 6.61%-8.39%和 6.05%-10.21%。这两个矮化等位基因 Rht-B1b 和 Rht-D1b 对降低 GPC 和株高的影响在另外两个 RIL 群体和一个自然群体中得到了验证。这项研究为进一步研究矮化基因 Rht-B1b 和 Rht-D1b 对小麦 GPC 的影响奠定了基础。
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引用次数: 0
Characterization of flag leaf morphology identifies a major genomic region controlling flag leaf angle in the US winter wheat (Triticum aestivum L.). 旗叶形态特征确定了控制美国冬小麦(Triticum aestivum L.)旗叶角度的主要基因组区域。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-08-14 DOI: 10.1007/s00122-024-04701-1
Pradeep Kumar, Harsimardeep S Gill, Mandeep Singh, Karanjot Kaur, Dante Koupal, Shyamal Talukder, Amy Bernardo, Paul St Amand, Guihua Bai, Sunish K Sehgal

Key message: Multi-environmental characterization of flag leaf morphology traits in the US winter wheat revealed nine stable genomic regions for different flag leaf-related traits including a major region governing flag leaf angle. Flag leaf in wheat is the primary contributor to accumulating photosynthetic assimilates. Flag leaf morphology (FLM) traits determine the overall canopy structure and capacity to intercept the light, thus influencing photosynthetic efficiency. Hence, understanding the genetic control of these traits could be useful for breeding desirable ideotypes in wheat. We used a panel of 272 accessions from the hard winter wheat (HWW) region of the USA to investigate the genetic architecture of five FLM traits including flag leaf length (FLL), width (FLW), angle (FLANG), length-width ratio, and area using multilocation field experiments. Multi-environment GWAS using 14,537 single-nucleotide polymorphisms identified 36 marker-trait associations for different traits, with nine being stable across environments. A novel and major stable region for FLANG (qFLANG.1A) was identified on chromosome 1A accounting for 9-13% variation. Analysis of spatial distribution for qFLANG.1A in a set of 2354 breeding lines from the HWW region showed a higher frequency of allele associated with narrow leaf angle. A KASP assay was developed for allelic discrimination of qFLANG.1A and was used for its independent validation in a diverse set of spring wheat accessions. Furthermore, candidate gene analysis for two regions associated with FLANG identified seven putative genes of interest for each of the two regions. The present study enhances our understanding of the genetic control of FLM in wheat, particularly FLANG, and these results will be useful for dissecting the genes underlying canopy architecture in wheat facilitating the development of climate-resilient wheat varieties.

关键信息:美国冬小麦旗叶形态性状的多环境表征揭示了不同旗叶相关性状的九个稳定基因组区域,包括一个支配旗叶角度的主要区域。小麦的旗叶是光合同化物积累的主要贡献者。旗叶形态(FLM)性状决定了整体冠层结构和截光能力,从而影响光合效率。因此,了解这些性状的遗传控制有助于培育理想的小麦表意型。我们利用来自美国硬冬小麦(HWW)地区的 272 个加入品系,通过多地点田间试验研究了五个 FLM 性状的遗传结构,包括旗叶长度(FLL)、宽度(FLW)、角度(FLANG)、长宽比和面积。利用 14,537 个单核苷酸多态性进行的多环境 GWAS 发现了 36 个不同性状的标记-性状关联,其中 9 个在不同环境中是稳定的。在 1A 染色体上发现了一个新的 FLANG 主要稳定区(qFLANG.1A),其变异率为 9-13%。在一组来自 HWW 地区的 2354 个育种品系中对 qFLANG.1A 的空间分布分析表明,与窄叶角相关的等位基因频率较高。为区分 qFLANG.1A 的等位基因开发了一种 KASP 检测方法,并在一组不同的春小麦品种中进行了独立验证。此外,还对与 FLANG 相关的两个区域进行了候选基因分析,在这两个区域中分别发现了七个潜在的相关基因。本研究加深了我们对小麦 FLM(尤其是 FLANG)遗传控制的了解,这些结果将有助于剖析小麦冠层结构的基础基因,从而促进具有气候适应性的小麦品种的开发。
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引用次数: 0
Exploration and genetic analyses of canopy leaf pigmentation changes in soybean (Glycine max L.): unveiling a novel phenotype. 大豆(Glycine max L.)冠层叶片色素变化的探索和遗传分析:揭示一种新的表型。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-08-13 DOI: 10.1007/s00122-024-04693-y
Hee Jin You, Hyun Jo, Ji-Min Kim, Sung-Taeg Kang, Ngoc Ha Luong, Yeong-Ho Kim, Sungwoo Lee

Key message: Pigmentation changes in canopy leaves were first reported, and subsequent genetic analyses identified a major QTL associated with levels of pigmentation changes, suggesting Glyma.06G202300 as a candidate gene. An unexpected reddish-purple pigmentation in upper canopy leaves was discovered during the late reproductive stages in soybean (Glycine max L.) genotypes. Two sensitive genotypes, 'Uram' and PI 96983, exhibited anomalous canopy leaf pigmentation changes (CLPC), while 'Daepung' did not. The objectives of this study were to: (i) characterize the physiological features of pigmented canopy leaves compared with non-pigmented leaves, (ii) evaluate phenotypic variation in a combined recombinant inbred line (RIL) population (N = 169 RILs) under field conditions, and (iii) genetically identify quantitative trait loci (QTL) for CLPC via joint population linkage analysis. Comparison between pigmented and normal leaves revealed different Fv/Fm of photosystem II, hyperspectral reflectance, and cellular properties, suggesting the pigmentation changes occur in response to an undefined abiotic stress. A highly significant QTL was identified on chromosome 6, explaining ~ 62.8% of phenotypic variance. Based on the QTL result, Glyma.06G202300 encoding flavonoid 3'-hydroxylase (F3'H) was identified as a candidate gene. In both Uram and PI 96983, a 1-bp deletion was confirmed in the third exon of Glyma.06G202300 that results in a premature stop codon in both Uram and PI 96983 and a truncated F3'H protein lacking important domains. Additionally, gene expression analyses uncovered significant differences between pigmented and non-pigmented leaves. This is the first report of a novel symptom and an associated major QTL. These results will provide soybean geneticists and breeders with valuable knowledge regarding physiological changes that may affect soybean production. Further studies are required to elucidate the causal environmental stress and the underlying molecular mechanisms.

关键信息:冠层叶片的色素变化首次被报道,随后的遗传分析发现了一个与色素变化水平相关的主要 QTL,表明 Glyma.06G202300 是一个候选基因。在大豆(Glycine max L.)基因型的生殖后期,发现冠层上部叶片出现了意想不到的紫红色色素沉着。两个敏感基因型'Uram'和 PI 96983 表现出异常冠层叶片色素变化(CLPC),而'Daepung'则没有。本研究的目的是(i) 与非色素斑叶片相比,描述色素斑冠层叶片的生理特征;(ii) 评估田间条件下重组近交系(RIL)群体(N = 169 RILs)的表型变异;(iii) 通过群体联合连锁分析,从遗传学上鉴定 CLPC 的数量性状位点(QTL)。色素沉着叶片与正常叶片的比较显示了不同的光系统 II Fv/Fm、高光谱反射率和细胞特性,表明色素沉着变化是对未确定的非生物胁迫的响应。在 6 号染色体上发现了一个高度显著的 QTL,解释了约 62.8% 的表型变异。根据 QTL 结果,编码黄酮类化合物 3'-羟化酶(F3'H)的 Glyma.06G202300 被确定为候选基因。在 Uram 和 PI 96983 中,Glyma.06G202300 的第三个外显子上都有一个 1-bp 的缺失,这导致 Uram 和 PI 96983 中都有一个过早的终止密码子,F3'H 蛋白被截短,缺乏重要的结构域。此外,基因表达分析发现色素叶片和非色素叶片之间存在显著差异。这是首次报道一种新的症状和相关的主要 QTL。这些结果将为大豆遗传学家和育种家提供有关可能影响大豆产量的生理变化的宝贵知识。需要进一步的研究来阐明致病的环境胁迫和潜在的分子机制。
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引用次数: 0
Fine-mapping of LrN3B on wheat chromosome arm 3BS, one of the two complementary genes for adult-plant leaf rust resistance. LrN3B 在小麦染色体臂 3BS 上的精细图谱,它是小麦叶锈病成株抗性的两个互补基因之一。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-08-13 DOI: 10.1007/s00122-024-04706-w
Weidong Wang, Huifang Li, Lina Qiu, Huifang Wang, Wei Pan, Zuhuan Yang, Wenxin Wei, Nannan Liu, Junna Sun, Zhaorong Hu, Jun Ma, Zhongfu Ni, Yinghui Li, Qixin Sun, Chaojie Xie

The common wheat line 4N0461 showed adult-plant resistance to leaf rust. 4N0461 was crossed with susceptible cultivars Nongda4503 and Shi4185 to map the causal resistance gene(s). Segregation of leaf rust response in F2 populations from both crosses was 9 resistant:7 susceptible, indicative of two complementary dominant resistance genes. The genes were located on chromosome arms 3BS and 4BL and temporarily named LrN3B and LrN4B, respectively. Subpopulations from 4N0461 × Nongda4503 with LrN3B segregating as a single allele were used to fine-map LrN3B locus. LrN3B was delineated in a genetic interval of 0.07 cM, corresponding to 106 kb based on the Chinese Spring reference genome (IWGSC RefSeq v1.1). Four genes were annotated in this region, among which TraesCS3B02G014800 and TraesCS3B02G014900 differed between resistant and susceptible genotypes, and both were required for LrN3B resistance in virus-induced gene silencing experiments. Diagnostic markers developed for checking the polymorphism of each candidate gene, can be used for marker-assisted selection in wheat breeding programs.

普通小麦品系 4N0461 表现出对叶锈病的成株抗性。4N0461 与易感栽培品种 Nongda4503 和 Shi4185 杂交,以绘制抗病基因图谱。在两个杂交的 F2 群体中,叶锈病反应的分离是 9 抗:7 感,表明有两个互补的显性抗性基因。这两个基因位于染色体臂 3BS 和 4BL 上,暂时分别命名为 LrN3B 和 LrN4B。利用 4N0461 × Nongda4503 中以 LrN3B 为单等位基因分离的亚群对 LrN3B 基因座进行精细图谱绘制。根据中国春参考基因组(IWGSC RefSeq v1.1),LrN3B 被划定在一个 0.07 cM 的遗传间隔内,相当于 106 kb。该区域有四个基因被注释,其中 TraesCS3B02G014800 和 TraesCS3B02G014900 在抗性基因型和易感基因型之间存在差异,在病毒诱导的基因沉默实验中,这两个基因都是 LrN3B 抗性所必需的。为检测每个候选基因的多态性而开发的诊断标记可用于小麦育种计划中的标记辅助选择。
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引用次数: 0
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Theoretical and Applied Genetics
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