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Development of wheat-tetraploid Thinopyrum elongatum 4EL small fragment translocation lines with stripe rust resistance gene Yr4EL. 开发具有条锈病抗性基因 Yr4EL 的小麦四倍体 Thinopyrum elongatum 4EL 小片段易位系。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-10-04 DOI: 10.1007/s00122-024-04756-0
Biran Gong, Jing Gao, Yangqiu Xie, Hao Zhang, Wei Zhu, Lili Xu, Yiran Cheng, Yi Wang, Jian Zeng, Xing Fan, Lina Sha, Haiqin Zhang, Yonghong Zhou, Dandan Wu, Yinghui Li, Houyang Kang

Key message: Two small fragment translocation lines (T4DS·4DL-4EL and T5AS·5AL-4EL) showed high resistance to stripe rust and resistance gene Yr4EL was localized to an about 35 Mb region at the end of chr arm 4EL. Stripe rust, caused by the fungus Puccinia striiformis f. sp. tritici, is a devastating wheat disease worldwide. Deployment of disease resistance (R) genes in wheat cultivars is the most effective way to control the disease. Previously, the all-stage stripe rust R gene Yr4EL from tetraploid Thinopyrum elongatum was introduced into common wheat as 4E(4D) substitution and T4DS·4EL translocation lines. To further map and utilize Yr4EL, Chinese Spring (CS) mutant pairing homoeologous gene ph1b was used in crossing to induce recombination between chromosome (chr) 4EL and wheat chromosomes. Two small fragment translocation lines T4DS·4DL-4EL and T5AS·5AL-4EL with Yr4EL resistance were selected using molecular markers and confirmed by genomic in situ hybridization (GISH), fluorescence in situ hybridization (FISH), and Wheat 660 K SNP array analyses. We mapped Yr4EL to an about 35 Mb region at the end of chr 4EL, corresponding to 577.76-612.97 Mb based on the diploid Th. elongatum reference genome. In addition, two competitive allele-specific PCR (KASP) markers co-segregating with Yr4EL were developed to facilitate molecular marker-assisted selection in breeding. The T4DS·4DL-4EL lines were crossed and backcrossed with wheat cultivars SM482 and CM42, and the resulting pre-breeding lines showed high stripe rust resistance and potential for wheat breeding with good agronomic traits. These lines represent new germplasm for wheat stripe rust resistance breeding, as well as providing a solid foundation for Yr4EL fine mapping and cloning.

关键信息:两个小片段易位系(T4DS-4DL-4EL和T5AS-5AL-4EL)对条锈病表现出高度抗性,抗性基因Yr4EL定位在chr臂4EL末端约35 Mb的区域。由条锈病真菌 Puccinia striiformis f. sp. tritici 引起的条锈病是一种全球性的毁灭性小麦病害。在小麦栽培品种中部署抗病(R)基因是控制该病害的最有效方法。此前,四倍体 Thinopyrum elongatum 的全阶段条锈病 R 基因 Yr4EL 以 4E(4D) 替代系和 T4DS-4EL 易位系的形式被引入普通小麦。为了进一步绘制和利用 Yr4EL,在杂交中使用了中国春(CS)突变体配对同源基因 ph1b,以诱导染色体(chr)4EL 与小麦染色体之间的重组。利用分子标记筛选出了两个具有抗Yr4EL能力的小片段易位系T4DS-4DL-4EL和T5AS-5AL-4EL,并通过基因组原位杂交(GISH)、荧光原位杂交(FISH)和小麦660 K SNP阵列分析进行了确认。我们将 Yr4EL 映射到 chr 4EL 末端约 35 Mb 的区域,根据二倍体 Th. elongatum 的参考基因组,该区域对应于 577.76-612.97 Mb。此外,还开发了两个与 Yr4EL 共分离的竞争性等位基因特异性 PCR(KASP)标记,以促进育种中的分子标记辅助选择。T4DS-4DL-4EL 株系与小麦栽培品种 SM482 和 CM42 进行了杂交和回交,育成的预育种株系表现出较高的条锈病抗性和良好的农艺性状,具有进行小麦育种的潜力。这些品系代表了小麦抗条锈病育种的新种质,同时也为 Yr4EL 的精细作图和克隆奠定了坚实的基础。
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引用次数: 0
Unambiguous chromosome identification reveals the factors impacting irregular chromosome behaviors in allotriploid AAC Brassica. 明确的染色体鉴定揭示了影响异源三倍体芸薹属植物不规则染色体行为的因素。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-10-04 DOI: 10.1007/s00122-024-04734-6
Yao Cao, Junxiong Xu, Minhang Wang, Jing Gao, Zhen Zhao, Kexin Li, Lu Yang, Kanglu Zhao, Meiping Sun, Jing Dong, Getu Chao, Hong Zhang, Yaqingqing Niu, Chunxia Yan, Xiufeng Gong, Lei Wu, Zhiyong Xiong

Key message: The major irregular chromosome pairing and mis-segregation were detected during meiosis through unambiguous chromosome identification and found that allotriploid Brassica can undergo meiosis successfully and produce mostly viable aneuploid gametes. Triploids have played a crucial role in the evolution of species by forming polyploids and facilitating interploidy gene transfer. It is widely accepted that triploids cannot undergo meiosis normally and predominantly produce nonfunctional aneuploid gametes, which restricts their role in species evolution. In this study, we demonstrated that natural and synthetic allotriploid Brassica (AAC), produced by crossing natural and synthetic Brassica napus (AACC) with Brassica rapa (AA), exhibits basically normal chromosome pairing and segregation during meiosis. Homologous A chromosomes paired faithfully and generally segregated equally. Monosomic C chromosomes were largely retained as univalents and randomly entered daughter cells. The primary irregular meiotic behaviors included associations of homoeologs and 45S rDNA loci at diakinesis, as well as homoeologous chromosome replacement and premature sister chromatid separation at anaphase I. Preexisting homoeologous arrangements altered meiotic behaviors in both chromosome irregular pairing and mis-segregation by increasing the formation of A-genomic univalents and A-C bivalents, as well as premature sister chromatid separation and homologous chromosome nondisjunction. Meiotic behaviors depended significantly on the genetic background and heterozygous homoeologous rearrangement. AAC triploids mainly generated aneuploid gametes, most of which were viable. These results demonstrate that allotriploid Brassica containing an intact karyotype can proceed through meiosis successfully, broadening our current understanding of the inheritance and role in species evolution of allotriploid.

关键信息:通过对染色体的明确识别,发现了减数分裂过程中主要的不规则染色体配对和错误分离现象,并发现异源三倍体甘蓝能够成功地进行减数分裂,并产生大部分有活力的非整倍体配子。三倍体通过形成多倍体和促进倍性间的基因转移,在物种进化过程中发挥了至关重要的作用。人们普遍认为,三倍体不能正常进行减数分裂,主要产生无功能的非整倍体配子,这限制了它们在物种进化中的作用。在这项研究中,我们证明了天然和人工合成的异源三倍体甘蓝(AAC),由天然和人工合成的甘蓝(AACC)与甘蓝(AA)杂交产生,在减数分裂过程中染色体配对和分离基本正常。同源的 A 染色体忠实地配对,一般都能平等地分离。单体 C 染色体基本上保留为单价体,并随机进入子细胞。主要的不规则减数分裂行为包括同源染色体和 45S rDNA 位点在二分裂期的结合,以及同源染色体的替换和无丝分裂期 I 的过早姐妹染色单体分离。减数分裂行为在很大程度上取决于遗传背景和杂合同源重排。AAC 三倍体主要产生非整倍体配子,其中大部分都能存活。这些结果表明,含有完整核型的甘蓝型异源三倍体可以成功地进行减数分裂,从而拓宽了我们目前对异源三倍体的遗传和在物种进化中的作用的认识。
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引用次数: 0
Integrating targeted genetic markers to genotyping-by-sequencing for an ultimate genotyping tool. 将靶向遗传标记与基因分型测序相结合,打造终极基因分型工具。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-10-04 DOI: 10.1007/s00122-024-04750-6
Maxime de Ronne, Amina Abed, Gaétan Légaré, Jérôme Laroche, Vincent-Thomas Boucher St-Amour, Éric Fortier, Aaron Beattie, Ana Badea, Raja Khanal, Louise O'Donoughue, Istvan Rajcan, François Belzile, Brian Boyle, Davoud Torkamaneh

New selection methods, using trait-specific markers (marker-assisted selection (MAS)) and/or genome-wide markers (genomic selection (GS)), are becoming increasingly widespread in breeding programs. This new era requires innovative and cost-efficient solutions for genotyping. Reduction in sequencing cost has enhanced the use of high-throughput low-cost genotyping methods such as genotyping-by-sequencing (GBS) for genome-wide single-nucleotide polymorphism (SNP) profiling in large breeding populations. However, the major weakness of GBS methodologies is their inability to genotype targeted markers. Conversely, targeted methods, such as amplicon sequencing (AmpSeq), often face cost constraints, hindering genome-wide genotyping across a large cohort. Although GBS and AmpSeq data can be generated from the same sample, an efficient method to achieve this is lacking. In this study, we present the Genome-wide & Targeted Amplicon (GTA) genotyping platform, an innovative way to integrate multiplex targeted amplicons into the GBS library preparation to provide an all-in-one cost-effective genotyping solution to breeders and research communities. Custom primers were designed to target 23 and 36 high-value markers associated with key agronomical traits in soybean and barley, respectively. The resulting multiplex amplicons were compatible with the GBS library preparation enabling both GBS and targeted genotyping data to be produced efficiently and cost-effectively. To facilitate data analysis, we have introduced Fast-GBS.v3, a user-friendly bioinformatic pipeline that generates comprehensive outputs from data obtained following sequencing of GTA libraries. This high-throughput low-cost approach will greatly facilitate the application of DNA markers as it provides required markers for both MAS and GS in a single assay.

在育种计划中,使用性状特异性标记(标记辅助选择(MAS))和/或全基因组标记(基因组选择(GS))的新选择方法正变得越来越广泛。在这个新时代,基因分型需要具有成本效益的创新解决方案。测序成本的降低促进了高通量、低成本基因分型方法的使用,如在大型育种群体中进行全基因组单核苷酸多态性(SNP)分析的基因分型测序法(GBS)。然而,GBS 方法的主要弱点是无法对目标标记进行基因分型。与此相反,扩增子测序(AmpSeq)等靶向方法往往面临成本限制,阻碍了对大型群体进行全基因组基因分型。虽然 GBS 和 AmpSeq 数据可以从同一样本中生成,但目前还缺乏实现这一目标的有效方法。在这项研究中,我们提出了全基因组和靶向扩增子(GTA)基因分型平台,这是一种将多重靶向扩增子整合到 GBS 文库制备中的创新方法,可为育种者和研究团体提供一体化的经济高效的基因分型解决方案。设计的定制引物分别针对与大豆和大麦关键农艺性状相关的 23 个和 36 个高价值标记。由此产生的多重扩增子与 GBS 文库制备兼容,从而能高效、经济地生成 GBS 和定向基因分型数据。为便于数据分析,我们推出了 Fast-GBS.v3,这是一个用户友好型生物信息学管道,可从 GTA 文库测序后获得的数据中生成全面的输出结果。这种高通量、低成本的方法将极大地促进 DNA 标记的应用,因为它能在一次检测中同时提供 MAS 和 GS 所需的标记。
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引用次数: 0
Identification of transcription factor BnHDG4-A08 as a novel candidate associated with the accumulation of oleic, linoleic, linolenic, and erucic acid in Brassica napus. 鉴定转录因子 BnHDG4-A08 为与甘蓝型油菜中油酸、亚油酸、亚麻酸和芥酸积累相关的新型候选因子。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-10-01 DOI: 10.1007/s00122-024-04733-7
Ying Fu, Min Yao, Ping Qiu, Maolin Song, Xiyuan Ni, Erli Niu, Jianghua Shi, Tanliu Wang, Yaofeng Zhang, Huasheng Yu, Lunwen Qian

Key message: We screened 47 significantly associated haplotype blocks for oleic, linoleic, linolenic, and erucic acid, with 17 blocks influencing multiple traits. A novel candidate of transcription factor BnHDG4 A08 influencing oleic, linoleic, linolenic, and erucic acid was identified, by a joint strategy of haplotype-based genome-wide association study, genomic resequencing, gene cloning, and co-expression network Fatty acid (FA) composition determines the quality and economic value of rapeseed oil (Brassica napus). However, the molecular network of FAs is unclear. In the current study, multi-strategies of haplotype-based genome-wide association study (GWAS), genomic resequencing, gene cloning, and co-expression network were joint to reveal novel genetic factors influencing FA accumulation in rapeseed. We identified 47 significantly associated haplotype blocks for oleic, linoleic, linolenic, and erucic acid, with 17 blocks influencing multiple traits, using a haplotype-based GWAS with phenotype data from 203 Chinese semi-winter accessions. A total of 61 rapeseed orthologs involved in acyl-lipid metabolism, carbohydrate metabolism, or photosynthesis were identified in these 17 blocks. Among these genes, BnHDG4-A08, encoding a class IV homeodomain leucine-zipper transcription factor, exhibited two single-nucleotide polymorphisms (SNPs) in the exon and intron, with significant associations with oleic, linoleic, linolenic, and erucic acid. Gene cloning further validated two SNPs in the exon of BnHDG4-A08 in a population with 75 accessions, leading to two amino acid changes (T372A and P366L) and significant variation of oleic, linoleic, linolenic, and erucic acid. A competitive allele-specific PCR (KASP) marker based on the SNPs was successfully developed and validated. Moreover, 98 genes exhibiting direct interconnections and high weight values with BnHDG4-A08 were identified through co-expression network analysis using transcriptome data from 13 accessions. Our study identified a novel FA candidate of transcription factor BnHDG4-A08 influencing oleic, linoleic, linolenic, and erucic acid. This gene provides a potential promising gene resource for the novel mechanistic understanding of transcription factors regulating FA accumulation.

关键信息:我们筛选了47个与油酸、亚油酸、亚麻酸和芥酸明显相关的单倍型区块,其中17个区块影响多个性状。通过基于单倍型的全基因组关联研究、基因组重测序、基因克隆和共表达网络的联合策略,发现了影响油酸、亚油酸、亚麻酸和芥酸的转录因子 BnHDG4 A08 的新候选基因 脂肪酸(FA)组成决定了菜籽油的品质和经济价值。然而,脂肪酸的分子网络尚不清楚。本研究采用基于单倍型的全基因组关联研究(GWAS)、基因组重测序、基因克隆和共表达网络等多种策略,揭示了影响油菜籽脂肪酸积累的新的遗传因素。利用基于单倍型的 GWAS 和 203 个中国半冬性品种的表型数据,我们发现了油酸、亚油酸、亚麻酸和芥酸的 47 个明显相关的单倍型区块,其中 17 个区块影响多个性状。在这 17 个区块中,共鉴定出 61 个涉及酰脂代谢、碳水化合物代谢或光合作用的油菜籽直向同源基因。在这些基因中,BnHDG4-A08(编码一种第四类同源结构域亮氨酸-拉链转录因子)的外显子和内含子中出现了两个单核苷酸多态性(SNPs),与油酸、亚油酸、亚麻酸和芥酸有显著关联。基因克隆进一步验证了在一个有 75 个品种的群体中 BnHDG4-A08 外显子上的两个 SNPs,这两个 SNPs 导致了两个氨基酸的变化(T372A 和 P366L)以及油酸、亚油酸、亚麻酸和芥酸的显著变化。成功开发并验证了基于 SNPs 的竞争性等位基因特异性 PCR(KASP)标记。此外,通过使用 13 个品种的转录组数据进行共表达网络分析,发现了 98 个与 BnHDG4-A08 有直接关联且权重值较高的基因。我们的研究发现了一个影响油酸、亚油酸、亚麻酸和芥酸的转录因子BnHDG4-A08的新型FA候选基因。该基因为从新的机制角度理解转录因子调控脂肪酸积累提供了潜在的基因资源。
{"title":"Identification of transcription factor BnHDG4-A08 as a novel candidate associated with the accumulation of oleic, linoleic, linolenic, and erucic acid in Brassica napus.","authors":"Ying Fu, Min Yao, Ping Qiu, Maolin Song, Xiyuan Ni, Erli Niu, Jianghua Shi, Tanliu Wang, Yaofeng Zhang, Huasheng Yu, Lunwen Qian","doi":"10.1007/s00122-024-04733-7","DOIUrl":"10.1007/s00122-024-04733-7","url":null,"abstract":"<p><strong>Key message: </strong>We screened 47 significantly associated haplotype blocks for oleic, linoleic, linolenic, and erucic acid, with 17 blocks influencing multiple traits. A novel candidate of transcription factor BnHDG4 A08 influencing oleic, linoleic, linolenic, and erucic acid was identified, by a joint strategy of haplotype-based genome-wide association study, genomic resequencing, gene cloning, and co-expression network Fatty acid (FA) composition determines the quality and economic value of rapeseed oil (Brassica napus). However, the molecular network of FAs is unclear. In the current study, multi-strategies of haplotype-based genome-wide association study (GWAS), genomic resequencing, gene cloning, and co-expression network were joint to reveal novel genetic factors influencing FA accumulation in rapeseed. We identified 47 significantly associated haplotype blocks for oleic, linoleic, linolenic, and erucic acid, with 17 blocks influencing multiple traits, using a haplotype-based GWAS with phenotype data from 203 Chinese semi-winter accessions. A total of 61 rapeseed orthologs involved in acyl-lipid metabolism, carbohydrate metabolism, or photosynthesis were identified in these 17 blocks. Among these genes, BnHDG4-A08, encoding a class IV homeodomain leucine-zipper transcription factor, exhibited two single-nucleotide polymorphisms (SNPs) in the exon and intron, with significant associations with oleic, linoleic, linolenic, and erucic acid. Gene cloning further validated two SNPs in the exon of BnHDG4-A08 in a population with 75 accessions, leading to two amino acid changes (T372A and P366L) and significant variation of oleic, linoleic, linolenic, and erucic acid. A competitive allele-specific PCR (KASP) marker based on the SNPs was successfully developed and validated. Moreover, 98 genes exhibiting direct interconnections and high weight values with BnHDG4-A08 were identified through co-expression network analysis using transcriptome data from 13 accessions. Our study identified a novel FA candidate of transcription factor BnHDG4-A08 influencing oleic, linoleic, linolenic, and erucic acid. This gene provides a potential promising gene resource for the novel mechanistic understanding of transcription factors regulating FA accumulation.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"137 10","pages":"243"},"PeriodicalIF":4.4,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142354274","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
Genomic selection for agronomical phenotypes using genome-wide SNPs and SVs in pearl millet. 利用珍珠粟的全基因组 SNPs 和 SVs 对农艺表型进行基因组选择。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-10-01 DOI: 10.1007/s00122-024-04754-2
Haidong Yan, Yarong Jin, Haipeng Yu, Chengran Wang, Bingchao Wu, Chris Stephen Jones, Xiaoshan Wang, Zheni Xie, Linkai Huang

Pearl millet is an essential crop worldwide, with noteworthy resilience to abiotic stress, yet the advancement of its breeding remains constrained by the underutilization of molecular-assisted breeding techniques. In this study, we collected 1,455,924 single nucleotide polymorphism (SNP) and 124,532 structural variant (SV) markers primarily from a pearl millet inbred germplasm association panel consisting of 242 accessions including 120 observed phenotypes, mostly related to the yield. Our findings revealed that the SV markers had the capacity to capture genetic diversity not discerned by SNP markers. Furthermore, no correlation in heritability was observed between SNP and SV markers associated with the same phenotype. The assessment of the nine genomic prediction models revealed that SV markers performed better than SNP markers. When using the SV markers as the predictor variable, the genomic BLUP model achieved the best performance, while using the SNP markers, Bayesian methods outperformed the others. The integration of these models enabled the identification of eight candidate accessions with high genomic estimated breeding values (GEBV) across nine phenotypes using SNP markers. Four candidate accessions were identified with high GEBV across 22 phenotypes using SV markers. Notably, accession 'P23' emerged as a consistent candidate predicted based on both SNP and SV markers specifically for panicle number. These findings contribute valuable insights into the potential of utilizing both SNP and SV markers for genomic prediction in pearl millet breeding. Moreover, the identification of promising candidate accessions, such as 'P23', underscores the accelerated prospects of molecular breeding initiatives for enhancing pearl millet varieties.

珍珠粟是世界上一种重要的农作物,对非生物胁迫具有显著的抗逆性,但由于分子辅助育种技术的利用不足,其育种进展仍然受到限制。在这项研究中,我们主要从由 242 个品种组成的珍珠粟近交种质关联面板中收集了 1,455,924 个单核苷酸多态性(SNP)标记和 124,532 个结构变异(SV)标记,其中包括 120 个观察到的表型,这些表型大多与产量有关。我们的研究结果表明,SV 标记能够捕捉 SNP 标记无法识别的遗传多样性。此外,与同一表型相关的 SNP 标记和 SV 标记之间的遗传率没有相关性。对九个基因组预测模型的评估显示,SV 标记的表现优于 SNP 标记。当使用 SV 标记作为预测变量时,基因组 BLUP 模型的表现最佳,而使用 SNP 标记时,贝叶斯方法的表现优于其他方法。通过整合这些模型,利用 SNP 标记在九种表型中鉴定出了八个具有高基因组估计育种值(GEBV)的候选品种。利用 SV 标记,在 22 种表型中鉴定出 4 个具有高 GEBV 的候选品种。值得注意的是,根据 SNP 和 SV 标记预测,"P23 "是一个一致的候选品种,特别是在圆锥花序数量方面。这些发现为利用 SNP 和 SV 标记进行珍珠粟育种基因组预测的潜力提供了宝贵的见解。此外,'P23'等有希望的候选品种的发现,突显了分子育种计划在改良珍珠粟品种方面的加速前景。
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引用次数: 0
A novel SNP within the Rsa10025320 gene is highly associated with hollowness in red-skinned radish fleshy roots. Rsa10025320 基因中的一个新 SNP 与红皮萝卜肉质根的空洞性高度相关。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-09-30 DOI: 10.1007/s00122-024-04747-1
Dayong Wei, Chuanxing Zhang, Maolin Ran, Jie Wu, Xiaomei Li, Hongzhen Wu, Zhimin Wang, Qinglin Tang, Feng Yang

Hollowness is a physiological disorder that frequently occurs during the growth and postharvest storage phases of fleshy radish roots, significantly diminishing quality, yield, and marketability. However, the molecular mechanism for hollowness remains elusive. To identify the QTLs and potential candidate genes for hollowness tolerance in radish, F2 and BC1 populations were constructed from hollowness-tolerant radish (C16) and hollowness-sensitive radish (C17) in the present study. Genetic analysis indicated that hollowness tolerance may be governed by two independent recessive genes. By employing bulked segregant analysis sequencing (BSA-seq), two significant candidate genomic intervals were pinpointed on chromosomes R04 (960 kb, 6.48-7.44 Mb) and R05 (600 kb, 31.44-32.04 Mb), which together harbor 107 annotated genes. Transcriptomic sequencing revealed that the downregulated differentially expressed genes (DEGs) were significantly enriched in biological processes related to cell death and the response to water stress, whereas the upregulated DEGs were significantly associated with the chitin catabolic process and the cell wall macromolecule metabolic process. A total of 46 intersecting genes were identified among these DEGs within the genomic intervals of interest. One gene with high expression (Rsa10025345) and two with low expression (Rsa10025320 and Rsa10018106) were detected in the tolerant variety C16. Furthermore, a SNP within Rsa10025320 resulting in an amino acid change (A188E) was characterized through sequence variation observed in both BSA-seq and RNA-seq data and further developed as a derived cleaved amplified polymorphic sequence (dCAPS) marker. Our study reveals potential target genes for tolerance to hollowness and paves the way for marker-assisted breeding of hollowness tolerance in red-skinned radishes.

空心症是一种生理障碍,经常发生在肉质萝卜根的生长和采后贮藏阶段,会大大降低萝卜的质量、产量和适销性。然而,空心症的分子机理仍然难以捉摸。为了确定萝卜耐空心菜的 QTLs 和潜在候选基因,本研究用耐空心菜萝卜(C16)和对空心菜敏感的萝卜(C17)构建了 F2 和 BC1 群体。遗传分析表明,空心菜耐受性可能由两个独立的隐性基因控制。通过批量分离分析测序(BSA-seq),在染色体 R04(960 kb,6.48-7.44 Mb)和 R05(600 kb,31.44-32.04 Mb)上确定了两个重要的候选基因组区间,共包含 107 个注释基因。转录组测序显示,下调的差异表达基因(DEGs)明显富集于与细胞死亡和对水胁迫反应相关的生物过程,而上调的差异表达基因(DEGs)则明显与几丁质分解过程和细胞壁大分子代谢过程相关。在感兴趣的基因组区间内的这些 DEGs 中,共发现了 46 个交叉基因。在耐受性品种 C16 中发现了一个高表达基因(Rsa10025345)和两个低表达基因(Rsa10025320 和 Rsa10018106)。此外,通过在 BSA-seq 和 RNA-seq 数据中观察到的序列变异,对 Rsa10025320 中一个导致氨基酸变化(A188E)的 SNP 进行了表征,并进一步将其开发为衍生的裂解扩增多态性序列(dCAPS)标记。我们的研究揭示了耐空心菜的潜在靶基因,为红皮萝卜耐空心菜的标记辅助育种铺平了道路。
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引用次数: 0
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
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Theoretical and Applied Genetics
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