Plant Genome最新文献_第9页

Common signatures of selection reveal target loci for breeding across soybean populations. 选择的共同特征揭示了大豆种群育种的目标位点。

IF 4.2 2区生物学

Plant Genome Pub Date : 2024-03-01 Epub Date: 2024-01-23 DOI: 10.1002/tpg2.20426

João Paulo Gomes Viana, Arián Avalos, Zhihai Zhang, Randall Nelson, Matthew E Hudson

{"title":"Common signatures of selection reveal target loci for breeding across soybean populations.","authors":"João Paulo Gomes Viana, Arián Avalos, Zhihai Zhang, Randall Nelson, Matthew E Hudson","doi":"10.1002/tpg2.20426","DOIUrl":"10.1002/tpg2.20426","url":null,"abstract":"Understanding the underlying genetic bases of yield-related selection and distinguishing these changes from genetic drift are critical for both improved understanding and future success of plant breeding. Soybean [Glycine max (L.) Merr.] is a key species for world food security, yet knowledge of the mechanism of selective breeding in soybean, such as the century-long program of artificial selection in U.S. soybean germplasm, is currently limited to certain genes and loci. Here, we identify genome-wide signatures of selection in separate populations of soybean subjected to artificial selection for increased yield by multiple breeding programs in the United States. We compared the alternative soybean breeding population (AGP) created by USDA-ARS to the conventional public soybean lines (CGP) developed at three different stages of breeding (ancestral, intermediate, and elite) to identify shared signatures of selection and differentiate these from drift. The results showed a strong selection for specific haplotypes identified by single site frequency and haplotype homozygosity methods. A set of common selection signatures was identified in both AGP and CGP that supports the hypothesis that separate breeding programs within similar environments coalesce on the fixation of the same key haplotypes. Signatures unique to each breeding program were observed. These results raise the possibility that selection analysis can allow the identification of favorable alleles to enhance directed breeding approaches.","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":"139543393","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

Long- and short-read sequencing methods discover distinct circular RNA pools in Lotus japonicus. 长短线程测序方法在日本莲中发现了不同的环状 RNA 池。

IF 4.2 2区生物学

Plant Genome Pub Date : 2024-03-01 Epub Date: 2024-01-20 DOI: 10.1002/tpg2.20429

Asa Budnick, Megan J Franklin, Delecia Utley, Brianne Edwards, Melodi Charles, Eli D Hornstein, Heike Sederoff

{"title":"Long- and short-read sequencing methods discover distinct circular RNA pools in Lotus japonicus.","authors":"Asa Budnick, Megan J Franklin, Delecia Utley, Brianne Edwards, Melodi Charles, Eli D Hornstein, Heike Sederoff","doi":"10.1002/tpg2.20429","DOIUrl":"10.1002/tpg2.20429","url":null,"abstract":"Circular RNAs (circRNAs) are covalently closed single-stranded RNAs, generated through a back-splicing process that links a downstream 5' site to an upstream 3' end. The only distinction in the sequence between circRNA and their linear cognate RNA is the back splice junction. Their low abundance and sequence similarity with their linear origin RNA have made the discovery and identification of circRNA challenging. We have identified almost 6000 novel circRNAs from Lotus japonicus leaf tissue using different enrichment, amplification, and sequencing methods as well as alternative bioinformatics pipelines. The different methodologies identified different pools of circRNA with little overlap. We validated circRNA identified by the different methods using reverse transcription polymerase chain reaction and characterized sequence variations using nanopore sequencing. We compared validated circRNA identified in L. japonicus to other plant species and showed conservation of high-confidence circRNA-expressing genes. This is the first identification of L. japonicus circRNA and provides a resource for further characterization of their function in gene regulation. CircRNAs identified in this study originated from genes involved in all biological functions of eukaryotic cells. The comparison of methodologies and technologies to sequence, identify, analyze, and validate circRNA from plant tissues will enable further research to characterize the function and biogenesis of circRNA in L. japonicus.","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":"139502015","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

A view of the pan-genome of domesticated Cowpea (Vigna unguiculata [L.] Walp.). 豇豆（Vigna unguiculata [L.] Walp.）

IF 4.2 2区生物学

Plant Genome Pub Date : 2024-03-01 Epub Date: 2023-03-22 DOI: 10.1002/tpg2.20319

Qihua Liang, María Muñoz-Amatriaín, Shengqiang Shu, Sassoum Lo, Xinyi Wu, Joseph W Carlson, Patrick Davidson, David M Goodstein, Jeremy Phillips, Nadia M Janis, Elaine J Lee, Chenxi Liang, Peter L Morrell, Andrew D Farmer, Pei Xu, Timothy J Close, Stefano Lonardi

{"title":"A view of the pan-genome of domesticated Cowpea (Vigna unguiculata [L.] Walp.).","authors":"Qihua Liang, María Muñoz-Amatriaín, Shengqiang Shu, Sassoum Lo, Xinyi Wu, Joseph W Carlson, Patrick Davidson, David M Goodstein, Jeremy Phillips, Nadia M Janis, Elaine J Lee, Chenxi Liang, Peter L Morrell, Andrew D Farmer, Pei Xu, Timothy J Close, Stefano Lonardi","doi":"10.1002/tpg2.20319","DOIUrl":"10.1002/tpg2.20319","url":null,"abstract":"Cowpea, Vigna unguiculata L. Walp., is a diploid warm-season legume of critical importance as both food and fodder in sub-Saharan Africa. This species is also grown in Northern Africa, Europe, Latin America, North America, and East to Southeast Asia. To capture the genomic diversity of domesticates of this important legume, de novo genome assemblies were produced for representatives of six subpopulations of cultivated cowpea identified previously from genotyping of several hundred diverse accessions. In the most complete assembly (IT97K-499-35), 26,026 core and 4963 noncore genes were identified, with 35,436 pan genes when considering all seven accessions. GO terms associated with response to stress and defense response were highly enriched among the noncore genes, while core genes were enriched in terms related to transcription factor activity, and transport and metabolic processes. Over 5 million single nucleotide polymorphisms (SNPs) relative to each assembly and over 40 structural variants >1 Mb in size were identified by comparing genomes. Vu10 was the chromosome with the highest frequency of SNPs, and Vu04 had the most structural variants. Noncore genes harbor a larger proportion of potentially disruptive variants than core genes, including missense, stop gain, and frameshift mutations; this suggests that noncore genes substantially contribute to diversity within domesticated cowpea.","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":"9202358","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 association mapping for field spot blotch resistance in South Asian spring wheat genotypes. 南亚春小麦基因型田间斑点病抗性的全基因组关联图谱。

IF 4.2 2区生物学

Plant Genome Pub Date : 2024-03-01 Epub Date: 2024-01-14 DOI: 10.1002/tpg2.20425

Umesh Kamble, Xinyao He, Sudhir Navathe, Manjeet Kumar, Madhu Patial, Muhammad Rezaul Kabir, Gyanendra Singh, Gyanendra Pratap Singh, Arun Kumar Joshi, Pawan Kumar Singh

{"title":"Genome-wide association mapping for field spot blotch resistance in South Asian spring wheat genotypes.","authors":"Umesh Kamble, Xinyao He, Sudhir Navathe, Manjeet Kumar, Madhu Patial, Muhammad Rezaul Kabir, Gyanendra Singh, Gyanendra Pratap Singh, Arun Kumar Joshi, Pawan Kumar Singh","doi":"10.1002/tpg2.20425","DOIUrl":"10.1002/tpg2.20425","url":null,"abstract":"Spot blotch caused by Bipolaris sorokiniana ((Sacc.) Shoemaker) (teleomorph: Cochliobolus sativus [Ito and Kuribayashi] Drechsler ex Dastur) is an economically important disease of warm and humid regions. The present study focused on identifying resistant genotypes and single-nucleotide polymorphism (SNP) markers associated with spot blotch resistance in a panel of 174 bread spring wheat lines using field screening and genome-wide association mapping strategies. Field experiments were conducted in Agua Fria, Mexico, during the 2019-2020 and 2020-2021 cropping seasons. A wide range of phenotypic variation was observed among genotypes tested during both years. Twenty SNP markers showed significant association with spot blotch resistance on 15 chromosomes, namely, 1A, 1B, 2A, 2B, 2D, 3A, 3B, 4B, 4D, 5A, 5B, 6A, 6B, 7A, and 7B. Of these, two consistently significant SNPs on 5A, TA003225-0566 and TA003225-1427, may represent a new resistance quantitative trait loci. Further, in the proximity of Tsn1 on 5B, AX-94435238 was the most stable and consistent in both years. The identified genomic regions could be deployed to develop spot blotch-resistant genotypes, particularly in the spot blotch-vulnerable wheat growing areas.","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":"139467297","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

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":"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.","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":"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.","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":"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.","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":"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.","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":"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.","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":"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.","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