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Candidate gene analysis of rice grain shape based on genome-wide association study. 基于全基因组关联研究的水稻粒形候选基因分析
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-09-29 DOI: 10.1007/s00122-024-04724-8
Wei Xin, Ning Chen, Jiaqi Wang, Yilei Liu, Yifeng Sun, Baojia Han, Xinghua Wang, Zijie Liu, Hualong Liu, Hongliang Zheng, Luomiao Yang, Detang Zou, Jingguo Wang

Key message: Thirteen QTLs associated with rice grain shape were localized by genome-wide association study. LOC_Os01g74020, the putative candidate gene in the co-localized QTL-qGSE1.2 interval, was identified and validated. Grain shape (GS) is a key trait that affects yield and quality of rice. Identifying and analyzing GS-related genes and elucidating the physiological, biochemical and molecular mechanisms are important for rice breeding. In this study, genome-wide association studies (GWAS) were conducted based on 1, 795, 076 single-nucleotide polymorphisms (SNPs) and three GS-related traits, grain length (GL), grain width (GW) and thousand-grain weight (TGW), in a natural population which comprised 374 rice varieties. A total of 13 quantitative trait locus (QTLs) related to GL, GW and TGW were identified, respectively, of which two QTLs (qGSE1.2 and qGSE5.3) were associated with both GL and TGW. A known key GS regulatory gene, GW5, was present in the interval of qGSE5.3. Based on the qRT-PCR results, LOC_Os01g74020 (OsGSE1.2) was identified as a GS candidate gene. Functional analysis of OsGSE1.2 showed that glume cell width and GW were significantly reduced, and that glume cell length, GL, TGW and single-plant yield were significantly increased in OsGSE1.2 knockout lines than those of wild type. OsGSE1.2 affects rice grain length by suppressing the elongation of glume cell and is a novel GS regulatory gene. These findings laid the foundation for molecular breeding to improve rice GS and increase rice yield and profitability.

关键信息:通过全基因组关联研究定位了13个与水稻粒形相关的QTL。鉴定并验证了共定位 QTL-qGSE1.2 区间的推测候选基因 LOC_Os01g74020。粒形(GS)是影响水稻产量和品质的关键性状。鉴定和分析GS相关基因并阐明其生理、生化和分子机制对水稻育种非常重要。本研究在一个由 374 个水稻品种组成的自然群体中,基于 1,795,076 个单核苷酸多态性(SNPs)和三个 GS 相关性状(粒长(GL)、粒宽(GW)和千粒重(TGW))进行了全基因组关联研究(GWAS)。共鉴定出 13 个与 GL、GW 和 TGW 相关的数量性状位点(QTL),其中两个 QTL(qGSE1.2 和 qGSE5.3)与 GL 和 TGW 均相关。在 qGSE5.3 的区间内有一个已知的 GS 关键调控基因 GW5。根据 qRT-PCR 结果,LOC_Os01g74020(OsGSE1.2)被确定为 GS 候选基因。对 OsGSE1.2 的功能分析表明,与野生型相比,OsGSE1.2 基因敲除株的颖壳宽度和 GW 显著减少,而颖壳长度、GL、TGW 和单株产量显著增加。OsGSE1.2通过抑制颖壳细胞的伸长来影响水稻谷粒的长度,是一个新的GS调控基因。这些发现为分子育种改良水稻GS、提高水稻产量和收益奠定了基础。
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引用次数: 0
Deciphering the genetic basis of salinity tolerance in a diverse panel of cultivated and wild soybean accessions by genome-wide association mapping. 通过全基因组关联图谱破解栽培和野生大豆品种耐盐性的遗传基础。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-09-28 DOI: 10.1007/s00122-024-04752-4
Rajat Pruthi, Chanderkant Chaudhary, Sandeep Chapagain, Mostafa Mohamed Elbasuoni Abozaid, Prabhat Rana, Ravi Kiran Reddy Kondi, Roberto Fritsche-Neto, Prasanta K Subudhi

Key message: In a genome-wide association study involving 269 cultivated and wild soybean accessions, potential salt tolerance donors were identified along with significant markers and candidate genes, such as GmKUP6 and GmWRKY33. Salt stress remains a significant challenge in agricultural systems, notably impacting soybean productivity worldwide. A comprehensive genome-wide association study (GWAS) was conducted to elucidate the genetic underpinnings of salt tolerance and identify novel source of salt tolerance among soybean genotypes. A diverse panel comprising 269 wild and cultivated soybean accessions was subjected to saline stress under controlled greenhouse conditions. Phenotypic data revealed that salt tolerance of soybean germplasm accessions was heavily compromised by the accumulation of sodium and chloride, as indicated by highly significant positive correlations of leaf scorching score with leaf sodium/chloride content. The GWAS analysis, leveraging a dataset of 32,832 SNPs, unveiled 32 significant marker-trait associations (MTAs) across seven traits associated with salt tolerance. These markers explained a substantial portion of the phenotypic variation, ranging from 14 to 52%. Notably, 11 markers surpassed Bonferroni's correction threshold, exhibiting highly significant associations with the respective traits. Gene Ontology enrichment analysis conducted within a 100 Kb range of the identified MTAs highlighted candidate genes such as potassium transporter 6 (GmKUP6), cation hydrogen exchanger (GmCHX15), and GmWRKY33. Expression levels of GmKUP6 and GmWRKY33 significantly varied between salt-tolerant and salt-susceptible soybean accessions under salt stress. The genetic markers and candidate genes identified in this study hold promise for developing soybean varieties resilient to salinity stress, thereby mitigating its adverse effects.

关键信息:在一项涉及 269 个栽培和野生大豆品种的全基因组关联研究中,发现了潜在的耐盐性供体以及重要的标记和候选基因,如 GmKUP6 和 GmWRKY33。盐胁迫仍然是农业系统面临的一个重大挑战,尤其影响着全球大豆的产量。为了阐明大豆耐盐性的遗传基础并确定大豆基因型耐盐性的新来源,我们开展了一项全面的全基因组关联研究(GWAS)。在受控温室条件下,对由 269 个野生和栽培大豆品系组成的多样性面板进行了盐胁迫试验。表型数据显示,大豆种质资源的耐盐性受到钠和氯积累的严重影响,叶片焦枯评分与叶片钠/氯含量呈高度显著的正相关。利用 32,832 个 SNP 数据集进行的 GWAS 分析揭示了与耐盐性相关的七个性状中的 32 个显著标记-性状关联(MTAs)。这些标记解释了很大一部分表型变异,从 14% 到 52% 不等。值得注意的是,有 11 个标记超过了 Bonferroni 校正阈值,显示出与相应性状的高度显著关联。在已确定的 MTA 的 100 Kb 范围内进行的基因本体富集分析突出显示了候选基因,如钾转运体 6(GmKUP6)、阳离子氢交换器(GmCHX15)和 GmWRKY33。在盐胁迫条件下,GmKUP6 和 GmWRKY33 的表达水平在耐盐大豆和感盐大豆之间存在显著差异。本研究发现的遗传标记和候选基因有望培育出耐盐胁迫的大豆品种,从而减轻盐胁迫的不利影响。
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引用次数: 0
Identification and fine mapping of a QTL-rich region for yield- and quality-related traits on chromosome 4BS in common wheat (Triticum aestivum L.). 普通小麦(Triticum aestivum L.)4BS染色体上与产量和品质相关性状的QTL富集区的鉴定和精细绘图。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-09-28 DOI: 10.1007/s00122-024-04722-w
Jinghui Li, Huanhuan Zhao, Minghu Zhang, Chan Bi, Xiaoyuan Yang, Xintian Shi, Chaojie Xie, Baoyun Li, Guangbin Ma, Zhengang Ru, Tiezhu Hu, Mingshan You

Yield and quality are important for plant breeding. To better understand the genetic basis underlying yield- and quality-related traits in wheat (Triticum aestivum L.), we conducted the quantitative trait locus (QTL) analysis using recombinant inbred lines (RILs) and a high-density genetic linkage map with a 90 K array. In this study, a total of 117 QTLs were detected for spike number per area (SNPA), thousand grain weight (TGW), grain number per spike (GNS), plant height (PH), spike length (SL), total spikelet number (TSN), spikelet density (SD), grain protein content (GPC), and grain starch content (GSC). Among these QTLs, 30 environmentally stable QTLs for yield- and quality-related traits were detected. Notably, five QTL-rich regions (Qrr) for yield- and/or quality-related traits were identified, including the QTL-rich region on chromosome 4BS (QQrr.cau-4B) for eight traits (SNPA, GNS, PH, SL, TSN, SD, GPC, and GSC). The stable QTL-rich region QQrr.cau-4B was delimited into a physical interval of approximately 2.47 Mb. Based on the annotation information of the Chinese spring wheat genome v1.0 and parental re-sequencing results, the interval included twelve genes with sequence variations. Taken together, these results contribute to further understanding of the genetic basis of SNPA, GNS, PH, SL, TSN, SD, GPC, and GSC, and fine mapping of QQrr.cau-4B will be beneficial for gene cloning and marker-assisted selection in the genetic improvement of wheat varieties.

产量和品质对植物育种非常重要。为了更好地了解小麦(Triticum aestivum L.)产量和品质相关性状的遗传基础,我们利用重组近交系(RIL)和 90 K 阵列高密度遗传连锁图谱进行了数量性状位点(QTL)分析。在这项研究中,共检测到 117 个 QTL,包括单位面积穗数 (SNPA)、千粒重 (TGW)、每穗粒数 (GNS)、株高 (PH)、穗长 (SL)、总穗数 (TSN)、小穗密度 (SD)、谷物蛋白质含量 (GPC) 和谷物淀粉含量 (GSC)。在这些 QTLs 中,发现了 30 个与产量和品质相关的环境稳定 QTLs。值得注意的是,发现了五个与产量和/或品质相关性状的 QTL 富集区(Qrr),其中包括染色体 4BS 上与八个性状(SNPA、GNS、PH、SL、TSN、SD、GPC 和 GSC)相关的 QTL 富集区(QQrr.cau-4B)。稳定的 QTL 富集区 QQrr.cau-4B 被划分为一个约 2.47 Mb 的物理区间。根据中国春小麦基因组 v1.0 的注释信息和亲本重测序结果,该区间包括 12 个序列变异的基因。综上所述,这些结果有助于进一步了解SNPA、GNS、PH、SL、TSN、SD、GPC和GSC的遗传基础,QQrr.cau-4B的精细作图将有利于小麦品种遗传改良中的基因克隆和标记辅助选择。
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引用次数: 0
Analysis of a global wheat panel reveals a highly diverse introgression landscape and provides evidence for inter-homoeologue chromosomal recombination. 对全球小麦面板的分析揭示了高度多样化的引种景观,并提供了同源染色体间重组的证据。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-09-28 DOI: 10.1007/s00122-024-04721-x
Matthias Heuberger, Zoe Bernasconi, Mahmoud Said, Esther Jung, Gerhard Herren, Victoria Widrig, Hana Šimková, Beat Keller, Javier Sánchez-Martín, Thomas Wicker

Key message: This study highlights the agronomic potential of rare introgressions, as demonstrated by a major QTL for powdery mildew resistance on chromosome 7D. It further shows evidence for inter-homoeologue recombination in wheat. Agriculturally important genes are often introgressed into crops from closely related donor species or landraces. The gene pool of hexaploid bread wheat (Triticum aestivum) is known to contain numerous such "alien" introgressions. Recently established high-quality reference genome sequences allow prediction of the size, frequency and identity of introgressed chromosome regions. Here, we characterise chromosomal introgressions in bread wheat using exome capture data from the WHEALBI collection. We identified 24,981 putative introgression segments of at least 2 Mb across 434 wheat accessions. Detailed study of the most frequent introgressions identified T. timopheevii or its close relatives as a frequent donor species. Importantly, 118 introgressions of at least 10 Mb were exclusive to single wheat accessions, revealing that large populations need to be studied to assess the total diversity of the wheat pangenome. In one case, a 14 Mb introgression in chromosome 7D, exclusive to cultivar Pamukale, was shown by QTL mapping to harbour a recessive powdery mildew resistance gene. We identified multiple events where distal chromosomal segments of one subgenome were duplicated in the genome and replaced the homoeologous segment in another subgenome. We propose that these examples are the results of inter-homoeologue recombination. Our study produced an extensive catalogue of the wheat introgression landscape, providing a resource for wheat breeding. Of note, the finding that the wheat gene pool contains numerous rare, but potentially important introgressions and chromosomal rearrangements has implications for future breeding.

关键信息:本研究强调了稀有引种的农艺学潜力,染色体 7D 上白粉病抗性的主要 QTL 就证明了这一点。它进一步显示了小麦同源染色体间重组的证据。对农业具有重要意义的基因往往是从近缘的供体物种或陆地品系中导入到作物中的。众所周知,六倍体面包小麦(Triticum aestivum)的基因库中含有大量此类 "外来 "导入基因。最近建立的高质量参考基因组序列可以预测外来染色体区域的大小、频率和特征。在这里,我们利用来自 WHEALBI 数据库的外显子组捕获数据描述了面包小麦中染色体外源区的特征。我们在 434 个小麦品种中发现了 24,981 个至少 2 Mb 的假定导入片段。对最常见的导入片段进行的详细研究发现,T. timopheevii 或其近缘种是最常见的供体物种。重要的是,118 个至少 10 Mb 的导入片段是单个小麦品种所独有的,这表明需要对大群体进行研究,以评估小麦泛基因组的总体多样性。在一个案例中,染色体 7D 中的一个 14 Mb 的外显子为栽培品种 Pamukale 所独有,通过 QTL 测绘显示该外显子含有一个隐性白粉病抗性基因。我们确定了多个事件,其中一个亚基因组的远端染色体片段在基因组中被复制,并取代了另一个亚基因组中的同源片段。我们认为这些例子是同源基因间重组的结果。我们的研究编制了一份广泛的小麦引种景观目录,为小麦育种提供了资源。值得注意的是,我们发现小麦基因库中包含大量罕见但潜在重要的引种和染色体重排,这对未来的育种工作具有重要意义。
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引用次数: 0
Tracing post-domestication historical events and screening pre-breeding germplasm from large gene pools in wheat in the absence of phenotype data. 在缺乏表型数据的情况下,追踪小麦驯化后的历史事件并从大型基因库中筛选育种前的种质。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-09-28 DOI: 10.1007/s00122-024-04738-2
Demissew Sertse, Aramde Fetene, Jen Leon, Frank M You, Sylvie Cloutier, Curt A McCartney

Wheat, particularly common wheat (Triticum aestivum L.), is a major crop accounting for 25% of the world cereal production and thriving in diverse ecogeographic regions. Its adaptation to diverse environments arises from its three distinct genomes adapted to different environments and post-domestication anthropogenic interventions. In search of key genomic regions revealing historic events and breeding significance to common wheat, we performed genome scan and genome-environment association (GEA) analyses using high-marker density genotype datasets. Whole-genome scans revealed highly differentiated regions on chromosomes 2A, 3B, and 4A. In-depth analyses corroborated our previous prediction of the 4A differentiated region signifying the separation between Spelt/Macha and other wheat types. Individual chromosome scans captured key introgressions, including one from T. timopheevii and one from Thinopyrum ponticum on 2B and 3D, respectively, as well as known genes such as Vrn-A1 on 5A. GEA highlighted loci linked to latitude-induced environmental variations, influencing traits such as photoperiodism and responses to abiotic stress. Variation at the Vrn-A1 locus on 5A assigned accessions to two haplotypes (6% and 94%). Further analysis on Vrn-A1 coding gene revealed four subgroups of the major haplotype, while the minor haplotype remained undifferentiated. Analyses at differentiated loci mostly dichotomized the population, illustrating the possibility of isolating pre-breeding materials with desirable traits from large gene pools in the absence of phenotype data. Given the current availability of broad genetic data, the genome-scan-GEA hybrid can be an efficient and cost-effective approach for pinpointing environmentally resilient pre-breeding germplasm from vast gene pools, including gene banks regardless of trait characterization.

小麦,特别是普通小麦(Triticum aestivum L.),是一种主要作物,占世界谷物产量的 25%,在不同的生态地理区域中生长茂盛。小麦对不同环境的适应性源于其适应不同环境的三个不同基因组以及驯化后的人为干预。为了寻找揭示普通小麦历史事件和育种意义的关键基因组区域,我们利用高标记密度基因型数据集进行了基因组扫描和基因组-环境关联(GEA)分析。全基因组扫描显示了染色体 2A、3B 和 4A 上的高度分化区域。深入分析证实了我们之前的预测,即 4A 分化区域标志着 Spelt/Macha 与其他小麦类型的分离。单个染色体扫描捕捉到了关键的导入基因,包括 2B 和 3D 上分别来自 T. timopheevii 和 Thinopyrum ponticum 的基因,以及 5A 上的 Vrn-A1 等已知基因。GEA 强调了与纬度引起的环境变异有关的基因位点,这些变异影响着光周期和对非生物胁迫的反应等性状。5A 上 Vrn-A1 基因座的变异将加入的品种归入两个单倍型(6% 和 94%)。对 Vrn-A1 编码基因的进一步分析表明,主要单倍型有四个亚群,而次要单倍型仍未分化。对差异基因位点的分析主要是对群体进行二分,这说明在缺乏表型数据的情况下,从大型基因库中分离出具有理想性状的育种前材料是可能的。鉴于目前可获得广泛的遗传数据,基因组扫描-GEA 杂交方法可以成为一种高效、经济的方法,用于从庞大的基因库(包括基因库)中找出环境适应性强的育种前种质,而无需考虑性状特征。
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引用次数: 0
Allelic variation of TaABI5-A4 significantly affects seed dormancy in bread wheat. TaABI5-A4 的等位基因变异会显著影响面包小麦的种子休眠。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-09-28 DOI: 10.1007/s00122-024-04753-3
Yang Han, Zeng Wang, Bing Han, Yingjun Zhang, Jindong Liu, Yan Yang

Key message: We identified a pivotal transcription factor TaABI5-A4 that is significantly associated with pre-harvest sprouting in wheat; its function in regulating seed dormancy was confirmed in transgenic rice. ABI5 is a critical transcription factor in regulation of crop seed maturation, dormancy, germination, and post-germination. Sixteen copies of homologous sequences of ABI5 were identified in Chinese wheat line Zhou 8425B. Cultivars of two haplotypes TaABI5-A4a and TaABI5-A4b showed significantly different seed dormancies. Based on two SNPs between the sequences of TaABI5-A4a and TaABI5-A4b, two complementary dominant sequence-tagged site (STS) markers were developed and validated in a natural population of 103 Chinese wheat cultivars and advanced lines and 200 recombinant inbred lines (RILs) derived from the Yangxiaomai/Zhongyou 9507 cross; the STS markers can be used efficiently and reliably to evaluate the dormancy of wheat seeds. The transcription level of TaABI5-A4b was significantly increased in TaABI5-A4a-GFP transgenic rice lines compared with that in TaABI5-A4b-GFP. The average seed germination index of TaABI5-A4a-GFP transgenic rice lines was significantly lower than those of TaABI5-A4b-GFP. In addition, seeds of TaABI5-A4a-GFP transgenic lines had higher ABA sensitivity and endogenous ABA content, lower endogenous GA content and plant height, and thicker stem internodes than those of TaABI5-A4b-GFP. Allelic variation of TaABI5-A4-affected wheat seed dormancy and the gene function was confirmed in transgenic rice. The transgenic rice lines of TaABI5-A4a and TaABI5-A4b had significantly different sensitivities to ABA and contents of endogenous ABA and GA in mature seeds, thereby influencing the seed dormancy, plant height, and stem internode length and diameter.

关键信息:我们发现了一个关键的转录因子TaABI5-A4,它与小麦收获前萌发显著相关;在转基因水稻中证实了它在调控种子休眠方面的功能。ABI5 是调控农作物种子成熟、休眠、萌发和萌发后的关键转录因子。在中国小麦品系周8425B中发现了16个拷贝的ABI5同源序列。两个单倍型 TaABI5-A4a 和 TaABI5-A4b 的品种表现出显著不同的种子休眠。基于TaABI5-A4a和TaABI5-A4b序列之间的两个SNPs,开发了两个互补的显性序列标记位点(STS)标记,并在103个中国小麦栽培品种和先进品系以及200个杨小麦/中优9507杂交重组近交系(RIL)的自然群体中进行了验证;STS标记可用于高效、可靠地评价小麦种子休眠。与TaABI5-A4b-GFP相比,TaABI5-A4a-GFP转基因水稻株系中TaABI5-A4b的转录水平显著提高。TaABI5-A4a-GFP 转基因水稻株系的平均种子发芽指数明显低于 TaABI5-A4b-GFP。此外,与 TaABI5-A4b-GFP 相比,TaABI5-A4a-GFP 转基因品系种子的 ABA 敏感性和内源 ABA 含量更高,内源 GA 含量和株高更低,茎节间更粗。TaABI5-A4 影响小麦种子休眠的等位基因变异及其基因功能在转基因水稻中得到了证实。TaABI5-A4a和TaABI5-A4b的转基因水稻品系对ABA的敏感性以及成熟种子中内源ABA和GA的含量有显著差异,从而影响了种子休眠、株高、茎节间长度和直径。
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引用次数: 0
Physical map of QTL for eleven agronomic traits across fifteen environments, identification of related candidate genes, and development of KASP markers with emphasis on terminal heat stress tolerance in common wheat. 绘制 15 种环境中 11 种农艺性状的 QTL 物理图谱,鉴定相关候选基因,开发 KASP 标记,重点是普通小麦的末期热胁迫耐受性。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-09-27 DOI: 10.1007/s00122-024-04748-0
Sourabh Kumar, Sachin Kumar, Hemant Sharma, Vivudh Pratap Singh, Kanwardeep Singh Rawale, Kaviraj Singh Kahlon, Vikas Gupta, Sunil Kumar Bhatt, Ramanathan Vairamani, Kulvinder Singh Gill, Harindra Singh Balyan

Key message: Key message This study identified stable QTL, promising candidate genes and developed novel KASP markers for heat tolerance, providing genomic resources to assist breeding for the development of high-yielding and heat-tolerant wheat germplasm and varieties. To understand the genetic architecture of eleven agronomic traits under heat stress, we used a doubled-haploid population (177 lines) derived from a heat-sensitive cultivar (PBW343) and a heat-tolerant genotype (KSG1203). This population was evaluated under timely, late and very late sown conditions over locations and years comprising fifteen environments. Best linear unbiased estimates and a genetic map (5,710 SNPs) developed using sequencing-based genotyping were used for QTL mapping. The identified 66 QTL (20 novel) were integrated into wheat physical map (14,263.4 Mb). These QTL explained 5.3% (QDth.ccsu-4A for days to heading and QDtm.ccsu-5B for days to maturity) to 24.9% (QGfd.ccsu-7D for grain filling duration) phenotypic variation. Thirteen stable QTL explaining high phenotypic variation were recommended for marker-assisted recurrent selection (MARS) for optimum/heat stress environments. Selected QTL were validated by their presence in high-yielding doubled-haploid lines. Some QTL for 1000-grain weight (TaERF3-3B, TaFER-5B, and TaZIM-A1), grain yield (TaCol-B5), and developmental traits (TaVRT-2) were co-localized with known genes. Specific known genes for traits like abiotic/biotic stress, grain quality and yield were co-located with 26 other QTL. Furthermore, 209 differentially expressed candidate genes for heat tolerance in plants that encode 28 different proteins were identified. KASP markers for three major/stable QTL, namely QGfd.ccsu-7A for grain filling duration on chromosome 7A (timely sown), QNgs.ccsu-3A for number of grains per spike on 3A, and QDth.ccsu-7A for days to heading on 7A (late and very late sown) environments were developed for MARS focusing on the development of heat-tolerant wheat varieties/germplasm.

关键信息本研究鉴定了耐热性的稳定 QTL、有希望的候选基因并开发了新型 KASP 标记,为培育高产耐热小麦种质和品种提供了基因组资源。为了了解热胁迫下 11 个农艺性状的遗传结构,我们使用了一个由热敏感栽培品种(PBW343)和耐热基因型(KSG1203)衍生的双倍单倍体群体(177 个品系)。该群体在适时播种、晚播种和超晚播种条件下,在 15 个地点和年份进行了评估。利用基于测序的基因分型技术开发的最佳线性无偏估计值和遗传图谱(5,710 个 SNPs)进行了 QTL 绘图。确定的 66 个 QTL(20 个新的 QTL)被整合到小麦物理图谱(14,263.4 Mb)中。这些 QTL 解释了 5.3% (QDth.ccsu-4A 解释了打顶天数,QDtm.ccsu-5B 解释了成熟天数)到 24.9% (QGfd.ccsu-7D 解释了籽粒灌浆期)的表型变异。13 个解释高表型变异的稳定 QTL 被推荐用于最佳/热胁迫环境下的标记辅助重复选择(MARS)。所选 QTL 通过在高产双倍单倍体系中的存在得到了验证。一些千粒重(TaERF3-3B、TaFER-5B 和 TaZIM-A1)、谷物产量(TaCol-B5)和发育性状(TaVRT-2)的 QTL 与已知基因共定位。非生物/生物胁迫、谷物品质和产量等性状的特定已知基因与其他 26 个 QTL 共定位。此外,还发现了 209 个不同表达的植物耐热候选基因,这些基因编码 28 种不同的蛋白质。为 MARS 开发了三个主要/稳定 QTL 的 KASP 标记,即 QGfd.ccsu-7A,表示染色体 7A(适时播种)上的籽粒灌浆期;QNgs.ccsu-3A,表示 3A 上的每穗粒数;QDth.ccsu-7A,表示 7A(晚播种和极晚播)环境下的抽穗期。
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引用次数: 0
QTL mapping and omics analysis to identify genes controlling kernel dehydration in maize. 通过 QTL 映射和 Omics 分析确定控制玉米籽粒脱水的基因。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-09-26 DOI: 10.1007/s00122-024-04715-9
Xining Jin, Xiaoxiang Zhang, Pingxi Wang, Juan Liu, Huaisheng Zhang, Xiangyuan Wu, Rui Song, Zhiyuan Fu, Shilin Chen

Key message: This study mapped and screened three candidate genes related to kernel dehydration in maize. The slow development rate of maize kernels during later stages leads to high kernel moisture content at harvest, posing a challenge for mechanized maize harvesting in China. This study utilized a recombinant inbred line population derived from Zheng 58 (slow dehydration) and PH6WC (fast dehydration) as parents. After four years of trait investigation and analysis, 25 quantitative trait loci (QTLs) associated with kernel dehydration rate and moisture content were identified, with six QTLs showing a significant contribution value exceeding 10% in the phenotype. Furthermore, a comparison was made between the QTLs identified in this study and those from previous research on maize kernel moisture content and dehydration rate, followed by screening through the omics analysis of the parental lines. Three candidate genes related to kernel dehydration rate were identified, primarily involving carbohydrate metabolism, energy metabolism processes (Zm00001d014030 and Zm00001d006476), and stimulus resistance (Zm00001d040113). These findings provide valuable insights to assist and guide future breeding efforts for mechanical harvesting of maize.

关键信息本研究绘制并筛选了三个与玉米籽粒脱水有关的候选基因。玉米后期籽粒发育速度慢,导致收获时籽粒含水量高,给中国玉米机械化收获带来挑战。本研究利用郑58(脱水慢)和PH6WC(脱水快)为亲本的重组近交系群体。经过四年的性状调查和分析,确定了 25 个与籽粒脱水率和水分含量相关的数量性状位点(QTL),其中 6 个 QTL 对表型的显著贡献值超过 10%。此外,通过对亲本品系进行omics分析筛选,将本研究确定的QTL与之前玉米籽粒含水率和脱水率研究中确定的QTL进行了比较。确定了三个与籽粒脱水率有关的候选基因,主要涉及碳水化合物代谢、能量代谢过程(Zm00001d014030 和 Zm00001d006476)和抗刺激性(Zm00001d040113)。这些发现为今后玉米机械收获的育种工作提供了宝贵的帮助和指导。
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引用次数: 0
Discovery of a major QTL for resistance to the guava root-knot nematode (Meloidogyne enterolobii) in 'Tanzania', an African landrace sweetpotato (Ipomoea batatas). 在非洲甘薯(Ipomoea batatas)"坦桑尼亚 "中发现抗番石榴根结线虫(Meloidogyne enterolobii)的主要 QTL。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-09-26 DOI: 10.1007/s00122-024-04739-1
Simon Fraher, Tanner Schwarz, Chris Heim, Gabriel De Siqueira Gesteira, Marcelo Mollinari, Guilherme Da Silva Pereira, Zhao-Bang Zeng, Gina Brown-Guedira, Adrienne Gorny, G Craig Yencho

Sweetpotato, Ipomoea batatas (L.) Lam. (2n = 6x = 90), is among the world's most important food crops and is North Carolina's most important vegetable crop. The recent introduction of Meloidogyne enterolobii poses a significant economic threat to North Carolina's sweetpotato industry and breeding resistance into new varieties has become a high priority for the US sweetpotato industry. Previous studies have shown that 'Tanzania', a released African landrace, is resistant to M. enterolobii. We screened the biparental sweetpotato mapping population, 'Tanzania' x 'Beauregard', for resistance to M. enterolobii by inoculating 246 full-sibs with 10,000 eggs each under greenhouse conditions. 'Tanzania', the female parent, was highly resistant, while 'Beauregard' was highly susceptible. Our bioassays exhibited strong skewing toward resistance for three measures of resistance: reproductive factor, eggs per gram of root tissue, and root gall severity ratings. A 1:1 segregation for resistance suggested a major gene conferred M. enterolobii resistance. Using a random-effect multiple interval mapping model, we identified a single major QTL, herein designated as qIbMe-4.1, on linkage group 4 that explained 70% of variation in resistance to M. enterolobii. This study provides a new understanding of the genetic basis of M. enterolobii resistance in sweetpotato and represents a major step towards the identification of selectable markers for nematode resistance breeding.

甘薯(Ipomoea batatas (L.) Lam.(2n = 6x = 90),是世界上最重要的粮食作物之一,也是北卡罗来纳州最重要的蔬菜作物。最近引入的Meloidogyne enterolobii对北卡罗来纳州的甘薯产业构成了巨大的经济威胁,培育抗性新品种已成为美国甘薯产业的当务之急。之前的研究表明,"坦桑尼亚"(一种已发布的非洲陆地品种)对 M. enterolobii 具有抗性。我们通过在温室条件下给 246 个全株接种 10,000 个卵,筛选了双亲甘薯制图群体'Tanzania' x 'Beauregard'对肠孢霉的抗性。雌性亲本'Tanzania'具有很强的抗性,而'Beauregard'则非常易感。我们的生物测定显示,在生殖系数、每克根组织的虫卵数和根瘿严重程度等级这三个抗性指标上,抗性都有很强的偏向性。1:1 的抗性分离表明,一个主要基因赋予了 M. enterolobii 抗性。利用随机效应多重区间映射模型,我们在第 4 连接组上发现了一个主要 QTL,在此命名为 qIbMe-4.1,该 QTL 解释了对 M. enterolobii 的抗性变异的 70%。这项研究使我们对甘薯肠杆菌抗性的遗传基础有了新的认识,并为鉴定线虫抗性育种的可选择标记迈出了重要一步。
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引用次数: 0
Identification and variation of a new restorer of fertility gene that induces cleavage in orf138 mRNA of Ogura male sterility in radish. 能诱导萝卜小仓雄性不育的 orf138 mRNA 分裂的新生育力恢复基因的鉴定和变异。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-09-25 DOI: 10.1007/s00122-024-04736-4
Hiroshi Yamagishi, Ayako Hashimoto, Asumi Fukunaga, Mizuki Takenaka, Toru Terachi

Key message: A new restorer of fertility gene, Rfs, of Ogura cytoplasmic male sterility (CMS) in radish encodes a pentatricopeptide repeat protein that binds to 15 nucleotides in mRNA of the CMS gene, orf138. Nucleotide substitutions in both Rfs and orf138 determine effectiveness and specificity of restoration. Cytoplasmic male sterility (CMS) in plants caused by the expression of abnormal mitochondrial genes results from impaired pollen production. The manifestation of CMS is suppressed by the restorer of fertility (Rf) genes in the nuclear genome. Thus, the CMS-Rf system is a suitable model for studying the direct interactions of mitochondrial and nuclear genes. At least nine haplotypes, of which Type B is ancestry, have been reported for the Ogura CMS gene, orf138, in radish (Raphanus sativus). We previously observed that Rfo encoding a pentatricopeptide repeat (PPR) protein, ORF687, which inhibits the translation of orf138 is ineffective in one haplotype (i.e., Type H). Here, we carried out map-based cloning of another Rf gene (Rfs) that cleaves the orf138 mRNA of Type H. Rfs produces a PPR protein consisting of 15 PPR motifs that binds to the mRNA, cleaving the mRNA at about 50nt downstream of the binding site. However, Rfs was ineffective for Type A because of a single nucleotide substitution in the binding site. Both Rfo and Rfs suppress orf138 expression in ancestral Type B, but they are rendered ineffective in Type H and Type A, respectively, by a single nucleotide substitution in orf138.

关键信息:萝卜小仓细胞质雄性不育(CMS)的一个新的生育力恢复基因Rfs编码一个五肽重复蛋白,该蛋白与CMS基因orf138的mRNA中的15个核苷酸结合。Rfs 和 orf138 中的核苷酸取代决定了恢复的有效性和特异性。线粒体基因表达异常导致的植物细胞质雄性不育(CMS)会影响花粉的产生。细胞质雄性不育的表现受到核基因组中生育力恢复基因(Rf)的抑制。因此,CMS-Rf 系统是研究线粒体基因与核基因直接相互作用的合适模型。据报道,萝卜(Raphanus sativus)中的小仓 CMS 基因 orf138 至少有九种单倍型,其中 B 型是祖先型。我们之前观察到,编码五肽重复(PPR)蛋白 ORF687 的 Rfo 在一个单倍型(即 H 型)中无效,而 ORF687 能抑制 orf138 的翻译。在此,我们基于图谱克隆了另一个能裂解 H 型 orf138 mRNA 的 Rf 基因(Rfs)。Rfs 产生的 PPR 蛋白由 15 个 PPR 基序组成,能与 mRNA 结合,并在结合位点下游约 50nt 处裂解 mRNA。然而,由于结合位点的单核苷酸置换,Rfs 对 A 型无效。Rfo 和 Rfs 都能抑制 B 型祖先中 orf138 的表达,但在 H 型和 A 型中,由于 orf138 中一个核苷酸的置换,它们分别失效。
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引用次数: 0
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Theoretical and Applied Genetics
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