Plant Genome最新文献

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Comparative genomics points to tandem duplications of SAD gene clusters as drivers of increased α-linolenic (ω-3) content in S. hispanica seeds. 比较基因组学表明,SAD基因簇的串联重复是导致S. hispanica种子中α-亚麻酸(ω-3)含量增加的驱动因素。
IF 4.2 2区 生物学
Plant Genome Pub Date : 2024-03-01 Epub Date: 2024-02-10 DOI: 10.1002/tpg2.20430
Tannaz Zare, Jeff F Paril, Emma M Barnett, Parwinder Kaur, Rudi Appels, Berit Ebert, Ute Roessner, Alexandre Fournier-Level
{"title":"Comparative genomics points to tandem duplications of SAD gene clusters as drivers of increased α-linolenic (ω-3) content in S. hispanica seeds.","authors":"Tannaz Zare, Jeff F Paril, Emma M Barnett, Parwinder Kaur, Rudi Appels, Berit Ebert, Ute Roessner, Alexandre Fournier-Level","doi":"10.1002/tpg2.20430","DOIUrl":"10.1002/tpg2.20430","url":null,"abstract":"<p><p>Salvia hispanica L. (chia) is a source of abundant ω-3 polyunsaturated fatty acids (ω-3-PUFAs) that are highly beneficial to human health. The genomic basis for this accrued ω-3-PUFA content in this emerging crop was investigated through the assembly and comparative analysis of a chromosome-level reference genome for S. hispanica. The highly contiguous 321.5-Mbp genome assembly covering all six chromosomes enabled the identification of 32,922 protein-coding genes. Two whole-genome duplications (WGD) events were identified in the S. hispanica lineage. However, these WGD events could not be linked to the high α-linolenic acid (ALA, ω-3) accumulation in S. hispanica seeds based on phylogenomics. Instead, our analysis supports the hypothesis that evolutionary expansion through tandem duplications of specific lipid gene families, particularly the stearoyl-acyl carrier protein desaturase (ShSAD) gene family, is the main driver of the abundance of ω-3-PUFAs in S. hispanica seeds. The insights gained from the genomic analysis of S. hispanica will help establish a molecular breeding target that can be leveraged through genome editing techniques to increase ω-3 content in oil crops.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139713221","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Genomic and phenotypic characterization of finger millet indicates a complex diversification history. 谷子的基因组和表型特征表明其具有复杂的多样化历史。
IF 4.2 2区 生物学
Plant Genome Pub Date : 2024-03-01 Epub Date: 2023-11-20 DOI: 10.1002/tpg2.20392
Jon Bančič, Damaris A Odeny, Henry F Ojulong, Samuel M Josiah, Jaap Buntjer, R Chris Gaynor, Stephen P Hoad, Gregor Gorjanc, Ian K Dawson
{"title":"Genomic and phenotypic characterization of finger millet indicates a complex diversification history.","authors":"Jon Bančič, Damaris A Odeny, Henry F Ojulong, Samuel M Josiah, Jaap Buntjer, R Chris Gaynor, Stephen P Hoad, Gregor Gorjanc, Ian K Dawson","doi":"10.1002/tpg2.20392","DOIUrl":"10.1002/tpg2.20392","url":null,"abstract":"<p><p>Advances in sequencing technologies mean that insights into crop diversification can now be explored in crops beyond major staples. We use a genome assembly of finger millet, an allotetraploid orphan crop, to analyze DArTseq single nucleotide polymorphisms (SNPs) at the whole and sub-genome level. A set of 8778 SNPs and 13 agronomic traits was used to characterize a diverse panel of 423 landraces from Africa and Asia. Through principal component analysis (PCA) and discriminant analysis of principal components, four distinct groups of accessions were identified that coincided with the primary geographic regions of finger millet cultivation. Notably, East Africa, presumed to be the crop's origin, exhibited the lowest genetic diversity. The PCA of phenotypic data also revealed geographic differentiation, albeit with differing relationships among geographic areas than indicated with genomic data. Further exploration of the sub-genomes A and B using neighbor-joining trees revealed distinct features that provide supporting evidence for the complex evolutionary history of finger millet. Although genome-wide association study found only a limited number of significant marker-trait associations, a clustering approach based on the distribution of marker effects obtained from a ridge regression genomic model was employed to investigate trait complexity. This analysis uncovered two distinct clusters. Overall, the findings suggest that finger millet has undergone complex and context-specific diversification, indicative of a lengthy domestication history. These analyses provide insights for the future development of finger millet.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138177595","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Integrative multi-omics analyses of date palm (Phoenix dactylifera) roots and leaves reveal how the halophyte land plant copes with sea water. 对枣椰树(Phoenix dactylifera)根系和叶片的多组学综合分析揭示了这种卤素陆生植物如何应对海水。
IF 4.2 2区 生物学
Plant Genome Pub Date : 2024-03-01 Epub Date: 2023-07-30 DOI: 10.1002/tpg2.20372
Heike M Mueller, Bastian L Franzisky, Maxim Messerer, Baoguo Du, Thomas Lux, Philip J White, Sebastien Christian Carpentier, Jana Barbro Winkler, Joerg-Peter Schnitzler, Hamed A El-Serehy, Khaled A S Al-Rasheid, Naif Al-Harbi, Saleh Alfarraj, Jörg Kudla, Jaakko Kangasjärvi, Michael Reichelt, Axel Mithöfer, Klaus F X Mayer, Heinz Rennenberg, Peter Ache, Rainer Hedrich, Christoph-Martin Geilfus
{"title":"Integrative multi-omics analyses of date palm (Phoenix dactylifera) roots and leaves reveal how the halophyte land plant copes with sea water.","authors":"Heike M Mueller, Bastian L Franzisky, Maxim Messerer, Baoguo Du, Thomas Lux, Philip J White, Sebastien Christian Carpentier, Jana Barbro Winkler, Joerg-Peter Schnitzler, Hamed A El-Serehy, Khaled A S Al-Rasheid, Naif Al-Harbi, Saleh Alfarraj, Jörg Kudla, Jaakko Kangasjärvi, Michael Reichelt, Axel Mithöfer, Klaus F X Mayer, Heinz Rennenberg, Peter Ache, Rainer Hedrich, Christoph-Martin Geilfus","doi":"10.1002/tpg2.20372","DOIUrl":"10.1002/tpg2.20372","url":null,"abstract":"<p><p>Date palm (Phoenix dactylifera L.) is able to grow and complete its life cycle while being rooted in highly saline soils. Which of the many well-known salt-tolerance strategies are combined to fine-tune this remarkable resilience is unknown. The precise location, whether in the shoot or the root, where these strategies are employed remains uncertain, leaving us unaware of how the various known salt-tolerance mechanisms are integrated to fine-tune this remarkable resilience. To address this shortcoming, we exposed date palm to a salt stress dose equivalent to seawater for up to 4 weeks and applied integrative multi-omics analyses followed by targeted metabolomics, hormone, and ion analyses. Integration of proteomic into transcriptomic data allowed a view beyond simple correlation, revealing a remarkably high degree of convergence between gene expression and protein abundance. This sheds a clear light on the acclimatization mechanisms employed, which depend on reprogramming of protein biosynthesis. For growth in highly saline habitats, date palm effectively combines various salt-tolerance mechanisms found in both halophytes and glycophytes: \"avoidance\" by efficient sodium and chloride exclusion at the roots, and \"acclimation\" by osmotic adjustment, reactive oxygen species scavenging in leaves, and remodeling of the ribosome-associated proteome in salt-exposed root cells. Combined efficiently as in P. dactylifera L., these sets of mechanisms seem to explain the palm's excellent salt stress tolerance.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10009575","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Transcriptome analysis of iron over-accumulating Arabidopsis genotypes uncover putative novel regulators of systemic and retrograde signaling. 铁过度积累拟南芥基因型的转录组分析揭示了系统和逆行信号的新调节因子。
IF 4.2 2区 生物学
Plant Genome Pub Date : 2024-03-01 Epub Date: 2023-12-06 DOI: 10.1002/tpg2.20411
Louis Grillet, En-Jung Hsieh, Wolfgang Schmidt
{"title":"Transcriptome analysis of iron over-accumulating Arabidopsis genotypes uncover putative novel regulators of systemic and retrograde signaling.","authors":"Louis Grillet, En-Jung Hsieh, Wolfgang Schmidt","doi":"10.1002/tpg2.20411","DOIUrl":"10.1002/tpg2.20411","url":null,"abstract":"<p><p>On account of its competence to accept and donate electrons, iron (Fe) is an essential element across all forms of life, including plants. Maintaining Fe homeostasis requires precise orchestration of its uptake, trafficking, and translocation in order to meet the demand for Fe sinks such as plastids. Plants harboring defects in the systemic Fe transporter OPT3 (OLIGOPEPTIDE TRANSPORTER 3) display constitutive Fe deficiency responses and accumulate toxic levels of Fe in their leaves. Similarly, ectopic expression of IRONMAN (IMA) genes, encoding a family of phloem-localized signaling peptides, triggers the uptake and accumulation of Fe by inhibiting the putative Fe sensor BRUTUS. This study aims at elucidating the mechanisms operating between OPT3-mediated systemic Fe transport, activation of IMA genes in the phloem, and activation of Fe uptake in the root epidermis. Transcriptional profiling of opt3-2 mutant and IMA1/IMA3 overexpressing (IMA Ox) lines uncovered a small subset of genes that were consistently differentially expressed across all three genotypes and Fe-deficient control plants, constituting potential novel regulators of cellular Fe homeostasis. In particular, expression of the the F-box protein At1g73120 was robustly induced in all genotypes, suggesting a putative function in the posttranslational regulation of cellular Fe homeostasis. As further constituents of this module, two plastid-encoded loci that putatively produce transfer ribonucleic acid (tRNA)-derived small ribonucleic acids are possibly involved in retrograde control of root Fe uptake.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138488841","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Genomic-assisted breeding for climate-smart coffee. 基因组辅助培育气候智能型咖啡。
IF 4.2 2区 生物学
Plant Genome Pub Date : 2024-03-01 Epub Date: 2023-03-22 DOI: 10.1002/tpg2.20321
Maria Amélia G Ferrão, Aymbire F A da Fonseca, Paulo S Volpi, Lucimara C de Souza, Marcone Comério, Abraão C Verdin Filho, Elaine M Riva-Souza, Patricio R Munoz, Romário G Ferrão, Luís Felipe V Ferrão
{"title":"Genomic-assisted breeding for climate-smart coffee.","authors":"Maria Amélia G Ferrão, Aymbire F A da Fonseca, Paulo S Volpi, Lucimara C de Souza, Marcone Comério, Abraão C Verdin Filho, Elaine M Riva-Souza, Patricio R Munoz, Romário G Ferrão, Luís Felipe V Ferrão","doi":"10.1002/tpg2.20321","DOIUrl":"10.1002/tpg2.20321","url":null,"abstract":"<p><p>Coffee is a universal beverage that drives a multi-industry market on a global basis. Today, the sustainability of coffee production is threatened by accelerated climate changes. In this work, we propose the implementation of genomic-assisted breeding for climate-smart coffee in Coffea canephora. This species is adapted to higher temperatures and is more resilient to biotic and abiotic stresses. After evaluating two populations, over multiple harvests, and under severe drought weather condition, we dissected the genetic architecture of yield, disease resistance, and quality-related traits. By integrating genome-wide association studies and diallel analyses, our contribution is four-fold: (i) we identified a set of molecular markers with major effects associated with disease resistance and post-harvest traits, while yield and plant architecture presented a polygenic background; (ii) we demonstrated the relevance of nonadditive gene actions and projected hybrid vigor when genotypes from different geographically botanical groups are crossed; (iii) we computed medium-to-large heritability values for most of the traits, representing potential for fast genetic progress; and (iv) we provided a first step toward implementing molecular breeding to accelerate improvements in C. canephora. Altogether, this work is a blueprint for how quantitative genetics and genomics can assist coffee breeding and support the supply chain in the face of the current global changes.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9509795","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Genetic factors underlying anaerobic germination in rice: Genome-wide association study and transcriptomic analysis. 水稻厌氧发芽的遗传因素:全基因组关联研究和转录组分析
IF 4.2 2区 生物学
Plant Genome Pub Date : 2024-03-01 Epub Date: 2022-09-28 DOI: 10.1002/tpg2.20261
Ranjita Thapa, Rodante E Tabien, Michael J Thomson, Endang M Septiningsih
{"title":"Genetic factors underlying anaerobic germination in rice: Genome-wide association study and transcriptomic analysis.","authors":"Ranjita Thapa, Rodante E Tabien, Michael J Thomson, Endang M Septiningsih","doi":"10.1002/tpg2.20261","DOIUrl":"10.1002/tpg2.20261","url":null,"abstract":"<p><p>The success of rice (Oryza sativa L.) germination and survival under submerged conditions is mainly determined by the rapid growth of the coleoptile to reach the water surface. Previous reports have shown the presence of genetic variability within rice accessions in the levels of flooding tolerance during germination or anaerobic germination (AG). Although many studies have focused on the physiological mechanisms of oxygen stress, few studies have explored the breadth of natural variation in AG tolerance-related traits in rice. In this study, we evaluated the coleoptile lengths of a geographically diverse rice panel of 241 accessions, including global accessions along with elite breeding lines and released cultivars from the United States, under the normal and flooded conditions in laboratory and greenhouse environments. A genome-wide association study (GWAS) was performed using a 7K single-nucleotide polymorphism (SNP) array and the phenotypic data of normal coleoptile length, flooded coleoptile length, flooding tolerance index, and survival at 14 d after seeding (DAS). Out of the 30 significant GWAS quantitative trait loci (QTL) regions identified, 14 colocalized with previously identified candidate genes of AG tolerance, whereas 16 were potentially novel. Two rice accessions showing contrasting phenotypic responses to AG stress were selected for the transcriptomics study. The combined approach of GWAS and transcriptomics analysis identified 77 potential candidate genes related to AG tolerance. The findings of our study may assist rice improvement programs in developing rice cultivars with robust tolerance under flooding stress during germination and the early seedling stage.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40379543","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Exploring the genomics of abiotic stress tolerance and crop resilience to climate change. 探索非生物胁迫耐受性和作物抵御气候变化能力的基因组学。
IF 4.2 2区 生物学
Plant Genome Pub Date : 2024-03-01 Epub Date: 2024-03-13 DOI: 10.1002/tpg2.20445
Rajeev K Varshney, Rutwik Barmukh, Alison Bentley, Henry T Nguyen
{"title":"Exploring the genomics of abiotic stress tolerance and crop resilience to climate change.","authors":"Rajeev K Varshney, Rutwik Barmukh, Alison Bentley, Henry T Nguyen","doi":"10.1002/tpg2.20445","DOIUrl":"10.1002/tpg2.20445","url":null,"abstract":"","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140121141","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Genomic-wide identification and expression analysis of AP2/ERF transcription factors in Zanthoxylum armatum reveals the candidate genes for the biosynthesis of terpenoids. Zanthoxylum armatum 中 AP2/ERF 转录因子的全基因组鉴定和表达分析揭示了萜类化合物生物合成的候选基因。
IF 4.2 2区 生物学
Plant Genome Pub Date : 2024-03-01 Epub Date: 2023-12-21 DOI: 10.1002/tpg2.20422
Xiaomeng Liu, Weiwei Zhang, Ning Tang, Zexiong Chen, Shen Rao, Hua Cheng, Chengrong Luo, Jiabao Ye, Shuiyuan Cheng, Feng Xu
{"title":"Genomic-wide identification and expression analysis of AP2/ERF transcription factors in Zanthoxylum armatum reveals the candidate genes for the biosynthesis of terpenoids.","authors":"Xiaomeng Liu, Weiwei Zhang, Ning Tang, Zexiong Chen, Shen Rao, Hua Cheng, Chengrong Luo, Jiabao Ye, Shuiyuan Cheng, Feng Xu","doi":"10.1002/tpg2.20422","DOIUrl":"10.1002/tpg2.20422","url":null,"abstract":"<p><p>Terpenoids are the main active components in the Zanthoxylum armatum leaves, which have extensive medicinal value. The Z. armatum leaf is the main by-product in the Z. armatum industry. However, the transcription factors involved in the biosynthesis of terpenoids are rarely reported. This study was performed to identify and classify the APETALA2/ethylene-responsive factor (AP2/ERF) gene family of Z. armatum. The chromosome distribution, gene structure, conserved motifs, and cis-acting elements of the promoter of the species were also comprehensively analyzed. A total of 214 ZaAP2/ERFs were identified. From the obtained transcriptome and terpenoid content data, four candidate ZaAP2/ERFs involved in the biosynthesis of terpenoids were selected via correlation and weighted gene co-expression network analysis. A phylogenetic tree was constructed using 13 AP2/ERFs related to the biosynthesis of terpenoids in other plants. ZaERF063 and ZaERF166 showed close evolutionary relationships with the ERFs in other plant species and shared a high AP2-domain sequence similarity with the two closest AP2/ERF proteins, namelySmERF8 from Salvia miltiorrhiza and AaERF4 from Artemisia annua. Further investigation into the effects of methyl jasmonate (MeJA) treatment on the content of terpenoids in Z. armatum leaves revealed that MeJA significantly induced the upregulation of ZaERF166 and led to a significant increase in the terpenoids content in Z. armatum leaves, indicating that ZaERF166 might be involved in the accumulation of terpenoids of Z. armatum. Results will be beneficial for the functional characterization of AP2/ERFs in Z. armatum and establishment of the theoretical foundation to increase the production of terpenoids via the manipulation of the regulatory elements and strengthen the development and utilization of Z. armatum leaves.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138832558","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Erratum to: Fertilization of grapevine based on gene expression. 勘误:基于基因表达的葡萄施肥。
IF 4.2 2区 生物学
Plant Genome Pub Date : 2024-03-01 Epub Date: 2024-02-10 DOI: 10.1002/tpg2.20406
{"title":"Erratum to: Fertilization of grapevine based on gene expression.","authors":"","doi":"10.1002/tpg2.20406","DOIUrl":"10.1002/tpg2.20406","url":null,"abstract":"","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139713222","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Genome-wide SNP discovery and genotyping delineates potential QTLs underlying major yield-attributing traits in buckwheat. 全基因组 SNP 发现和基因分型划定了荞麦主要产量性状的潜在 QTLs。
IF 4.2 2区 生物学
Plant Genome Pub Date : 2024-03-01 Epub Date: 2024-01-18 DOI: 10.1002/tpg2.20427
Samiullah Naik, Jebi Sudan, Uneeb Urwat, Mohammad Maqbool Pakhtoon, Basharat Bhat, Varun Sharma, Parvaze A Sofi, Asif B Shikari, Bilal A Bhat, Najeebul Rehman Sofi, P V Vara Prasad, Sajad Majeed Zargar
{"title":"Genome-wide SNP discovery and genotyping delineates potential QTLs underlying major yield-attributing traits in buckwheat.","authors":"Samiullah Naik, Jebi Sudan, Uneeb Urwat, Mohammad Maqbool Pakhtoon, Basharat Bhat, Varun Sharma, Parvaze A Sofi, Asif B Shikari, Bilal A Bhat, Najeebul Rehman Sofi, P V Vara Prasad, Sajad Majeed Zargar","doi":"10.1002/tpg2.20427","DOIUrl":"10.1002/tpg2.20427","url":null,"abstract":"<p><p>Buckwheat (Fagopyrum spp.) is an important nutritional and nutraceutical-rich pseudo-cereal crop. Despite its obvious potential as a functional food, buckwheat has not been fully harnessed due to its low yield, self-incompatibility, increased seed cracking, limited seed set, lodging, and frost susceptibility. The inadequate availability of genomics resources in buckwheat is one of the major reasons for this. In the present study, genome-wide association mapping (GWAS) was conducted to identify loci associated with various morphological and yield-related traits in buckwheat. High throughput genotyping by sequencing led to the identification of 34,978 single nucleotide polymorphisms that were distributed across eight chromosomes. Population structure analysis grouped the genotypes into three sub-populations. The genotypes were also characterized for various qualitative and quantitative traits at two diverse locations, the analysis of which revealed a significant difference in the mean values. The association analysis revealed a total of 71 significant marker-trait associations across eight chromosomes. The candidate genes were identified near 100 Kb of quantitative trait loci (QTLs), providing insights into several metabolic and biosynthetic pathways. The integration of phenology and GWAS in the present study is useful to uncover the consistent genomic regions, related markers associated with various yield-related traits, and potential candidate genes having implications for being utilized in molecular breeding for the improvement of economically important traits in buckwheat. Moreover, the identified QTLs will assist in tracking the desirable alleles of target genes within the buckwheat breeding populations/germplasm.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139492374","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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