Plant GenomePub Date : 2024-09-01Epub Date: 2024-06-05DOI: 10.1002/tpg2.20480
Tao Chen, Yongping Miao, Fanli Jing, Weidong Gao, Yanyan Zhang, Long Zhang, Peipei Zhang, Lijian Guo, Delong Yang
{"title":"Genomic-wide analysis reveals seven in absentia genes regulating grain development in wheat (Triticum aestivum L.).","authors":"Tao Chen, Yongping Miao, Fanli Jing, Weidong Gao, Yanyan Zhang, Long Zhang, Peipei Zhang, Lijian Guo, Delong Yang","doi":"10.1002/tpg2.20480","DOIUrl":"10.1002/tpg2.20480","url":null,"abstract":"<p><p>Seven in absentia proteins, which contain a conserved SINA domain, are involved in regulating various aspects of wheat (Triticum aestivum L.) growth and development, especially in response to environmental stresses. However, it is unclear whether TaSINA family members are involved in regulating grain development until now. In this study, the expression pattern, genomic polymorphism, and relationship with grain-related traits were analyzed for all TaSINA members. Most of the TaSINA genes identified showed higher expression levels in young wheat spikes or grains than other organs. The genomic polymorphism analysis revealed that at least 62 TaSINA genes had different haplotypes, where the haplotypes of five genes were significantly correlated with grain-related traits. Kompetitive allele-specific PCR markers were developed to confirm the single nucleotide polymorphisms in TaSINA101 and TaSINA109 among the five selected genes in a set of 292 wheat accessions. The TaSINA101-Hap II and TaSINA109-Hap II haplotypes had higher grain weight and width compared to TaSINA101-Hap I and TaSINA109-Hap I in at least three environments, respectively. The qRT-PCR assays revealed that TaSINA101 was highly expressed in the palea shell, seed coat, and embryo in young wheat grains. The TaSINA101 protein was unevenly distributed in the nucleus when transiently expressed in the protoplast of wheat. Three homozygous TaSINA101 transgenic lines in rice (Oryza sativa L.) showed higher grain weight and size compared to the wild type. These findings provide valuable insight into the biological function and elite haplotype of TaSINA family genes in wheat grain development at a genomic-wide level.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20480"},"PeriodicalIF":3.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141263135","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}
Plant GenomePub Date : 2024-09-01Epub Date: 2024-08-27DOI: 10.1002/tpg2.20500
Meseret A Wondifraw, Zachary J Winn, Scott D Haley, John A Stromberger, Emily E Hudson-Arns, R Esten Mason
{"title":"Elucidation of the genetic architecture of water absorption capacity in hard winter wheat through genome wide association study.","authors":"Meseret A Wondifraw, Zachary J Winn, Scott D Haley, John A Stromberger, Emily E Hudson-Arns, R Esten Mason","doi":"10.1002/tpg2.20500","DOIUrl":"10.1002/tpg2.20500","url":null,"abstract":"<p><p>Water absorption capacity (WAC) influences various aspects of bread making, such as loaf volume, bread yield, and shelf life. Despite its importance in the baking process and end-product quality, its genetic determinants are less explored. To address this limitation, a genome-wide association study was conducted on 337 hard wheat (Triticum aestivum L.) genotypes evaluated over 5 years in multi-environmental trials. Phenotyping was done using the solvent retention capacity (SRC) test with water (SRC-water), sucrose (SRC-sucrose), lactic acid (SRC-lactic acid), and sodium carbonate (SRC-carbonate) as solvents. Individuals were genotyped using genotyping-by-sequencing to detect single nucleotide polymorphisms across the wheat genome. To detect the genomic regions that underline the SRCs and gluten performance index (GPI), a genome-wide association study was performed using six multi-locus models using the mrMLM package in R. Adjusted means for SRC-water ranged from 54.1% to 66.5%, while SRC-carbonate exhibited a narrow range from 84.9% to 93.9%. Moderate to high genomic heritability values were observed for SRCs and GPI, ranging from h<sup>2 </sup>= 0.61 to 0.88. The genome-wide association study identified a total of 42 quantitative trait nucleotides (QTNs), of which five explained over 10% of the phenotypic variation (R<sup>2</sup> ≥ 10%). Most of the QTNs were detected on chromosomes 1A, 1B, 3B, and 5B. Few QTNs, such as S1A_5190318, S1B_3282665, S4D_472908721, and S7A_37433960, were located near gliadin, glutenin starch synthesis, and galactosyltransferase genes. Overall, these results show WAC to be under polygenic genetic control, with genes involved in the synthesis of key flour components influencing overall water absorption.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20500"},"PeriodicalIF":3.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142082334","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}
Plant GenomePub Date : 2024-09-01Epub Date: 2024-08-28DOI: 10.1002/tpg2.20504
Youcheng Zhu, Di Wang, Fan Yan, Le Wang, Ying Wang, Jingwen Li, Xuguang Yang, Ziwei Gao, Xu Liu, Yajing Liu, Qingyu Wang
{"title":"Genome-wide analysis of HD-Zip genes in Sophora alopecuroides and their role in salt stress response.","authors":"Youcheng Zhu, Di Wang, Fan Yan, Le Wang, Ying Wang, Jingwen Li, Xuguang Yang, Ziwei Gao, Xu Liu, Yajing Liu, Qingyu Wang","doi":"10.1002/tpg2.20504","DOIUrl":"10.1002/tpg2.20504","url":null,"abstract":"<p><p>We aimed to identify HD-Zip (homologous domain leucine zipper) family genes based on the complete Sophora alopecuroides genome sequence. Eighty-six Sophora alopecuroides HD-Zip family (SaHDZ) genes were identified and categorized into four subclasses using phylogenetic analysis. Chromosome localization analysis revealed that these genes were distributed across 18 chromosomes. Gene structure and conserved motif analysis showed high similarity among members of the SaHDZ genes. Prediction analysis revealed 71 cis-acting elements in SaHDZ genes. Transcriptome and quantitative real-time polymerase chain reaction analyses showed that under salt stress, SaHDZ responded positively in S. alopecuroides, and that SaHDZ22 was significantly upregulated afterward. Functional verification experiments revealed that SaHDZ22 overexpression increased the tolerance of Arabidopsis to salt and osmotic stress. Combined with cis-acting element prediction and expression level analysis, HD-Zip family transcription factors may be involved in regulating the balance between plant growth and stress resistance under salt stress by modulating the expression of auxin and abscisic acid signaling pathway genes. The Sophora alopecuroides adenylate kinase protein (SaAKI) and S. alopecuroides tetrapeptide-like repeat protein (SaTPR; pCAMBIA1300-SaTPR-cLUC) expression levels were consistent with those of SaHDZ22, indicating that SaHDZ22 may coordinate with SaAKI and SaTPR to regulate plant salt tolerance. These results lay a foundation in understanding the salt stress response mechanisms of S. alopecuroides and provide a reference for future studies oriented toward exploring plant stress resistance.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20504"},"PeriodicalIF":3.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142094007","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}
Plant GenomePub Date : 2024-09-01Epub Date: 2024-08-01DOI: 10.1002/tpg2.20488
Paul Adunola, Luis Felipe V Ferrão, Juliana Benevenuto, Camila F Azevedo, Patricio R Munoz
{"title":"Genomic selection optimization in blueberry: Data-driven methods for marker and training population design.","authors":"Paul Adunola, Luis Felipe V Ferrão, Juliana Benevenuto, Camila F Azevedo, Patricio R Munoz","doi":"10.1002/tpg2.20488","DOIUrl":"10.1002/tpg2.20488","url":null,"abstract":"<p><p>Genomic prediction is a modern approach that uses genome-wide markers to predict the genetic merit of unphenotyped individuals. With the potential to reduce the breeding cycles and increase the selection accuracy, this tool has been designed to rank genotypes and maximize genetic gains. Despite this importance, its practical implementation in breeding programs requires critical allocation of resources for its application in a predictive framework. In this study, we integrated genetic and data-driven methods to allocate resources for phenotyping and genotyping tailored to genomic prediction. To this end, we used a historical blueberry (Vaccinium corymbosun L.) breeding dataset containing more than 3000 individuals, genotyped using probe-based target sequencing and phenotyped for three fruit quality traits over several years. Our contribution in this study is threefold: (i) for the genotyping resource allocation, the use of genetic data-driven methods to select an optimal set of markers slightly improved prediction results for all the traits; (ii) for the long-term implication, we carried out a simulation study and emphasized that data-driven method results in a slight improvement in genetic gain over 30 cycles than random marker sampling; and (iii) for the phenotyping resource allocation, we compared different optimization algorithms to select training population, showing that it can be leveraged to increase predictive performances. Altogether, we provided a data-oriented decision-making approach for breeders by demonstrating that critical breeding decisions associated with resource allocation for genomic prediction can be tackled through a combination of statistics and genetic methods.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20488"},"PeriodicalIF":3.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141861364","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}
{"title":"Genome-wide association study of carotenoids in maize kernel.","authors":"Weiwei Chen, Xiangbo Zhang, Chuanli Lu, Hailong Chang, Zaid Chachar, Lina Fan, Yuxing An, Xuhui Li, Yongwen Qi","doi":"10.1002/tpg2.20495","DOIUrl":"10.1002/tpg2.20495","url":null,"abstract":"<p><p>In this study, the contents of four carotenoids in 244 maize inbred lines were detected and about three million single nucleotide polymorphisms (SNPs) for genome-wide association study to preliminarily analyze the genetic mechanism of maize kernel carotenoids. We identified 826 quantitative trait loci (QTLs) were significantly associated with carotenoids contents, and two key candidate genes Zm00001d029526 (CYP18) and Zm00001d023336 (wrky91) were obtained. In addition, we found a germplasm IL78 with higher carotenoids. The results of this study can provide a theoretical basis for screening genes that guide kernel carotenoids selection breeding.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20495"},"PeriodicalIF":3.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141917867","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}
{"title":"Machine learning for genomic and pedigree prediction in sugarcane.","authors":"Minoru Inamori, Tatsuro Kimura, Masaaki Mori, Yusuke Tarumoto, Taiichiro Hattori, Michiko Hayano, Makoto Umeda, Hiroyoshi Iwata","doi":"10.1002/tpg2.20486","DOIUrl":"10.1002/tpg2.20486","url":null,"abstract":"<p><p>Sugarcane (Saccharum spp.) plays a crucial role in global sugar production; however, the efficiency of breeding programs has been hindered by its heterozygous polyploid genomes. Considering non-additive genetic effects is essential in genome prediction (GP) models of crops with highly heterozygous polyploid genomes. This study incorporates non-additive genetic effects and pedigree information using machine learning methods to track sugarcane breeding lines and enhance the prediction by assessing the degree of association between genotypes. This study measured the stalk biomass and sugar content of 297 clones from 87 families within a breeding population used in the Japanese sugarcane breeding program. Subsequently, we conducted analyses based on the marker genotypes of 33,149 single-nucleotide polymorphisms. To validate the accuracy of GP in the population, we first predicted the prediction accuracy of the best linear unbiased prediction (BLUP) based on a genomic relationship matrix. Prediction accuracy was assessed using two different cross-validation methods: repeated 10-fold cross-validation and leave-one-family-out cross-validation. The accuracy of GP of the first and second methods ranged from 0.36 to 0.74 and 0.15 to 0.63, respectively. Next, we compared the prediction accuracy of BLUP and two machine learning methods: random forests and simulation annealing ensemble (SAE), a newly developed machine learning method that explicitly models the interaction between variables. Both pedigree and genomic information were utilized as input in these methods. Through repeated 10-fold cross-validation, we found that the accuracy of the machine learning methods consistently surpassed that of BLUP in most cases. In leave-one-family-out cross-validation, SAE demonstrated the highest accuracy among the methods. These results underscore the effectiveness of GP in Japanese sugarcane breeding and highlight the significant potential of machine learning methods.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20486"},"PeriodicalIF":3.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141460146","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}
Plant GenomePub Date : 2024-09-01Epub Date: 2024-08-31DOI: 10.1002/tpg2.20502
Yinqiang Zi, Mengjie Zhang, Xiuyao Yang, Ke Zhao, Tuo Yin, Ke Wen, Xulin Li, Xiaozhen Liu, Hanyao Zhang
{"title":"Identification of the sweet orange (Citrus sinensis) bHLH gene family and the role of CsbHLH55 and CsbHLH87 in regulating salt stress.","authors":"Yinqiang Zi, Mengjie Zhang, Xiuyao Yang, Ke Zhao, Tuo Yin, Ke Wen, Xulin Li, Xiaozhen Liu, Hanyao Zhang","doi":"10.1002/tpg2.20502","DOIUrl":"10.1002/tpg2.20502","url":null,"abstract":"<p><p>Salt stress is one of the primary environmental stresses limiting plant growth and production and adversely affecting the growth, development, yield, and fruit quality of Citrus sinensis. bHLH (basic helix-loop-helix) genes are involved in many bioregulatory processes in plants, including growth and development, phytohormone signaling, defense responses, and biosynthesis of specific metabolites. In this study, by bioinformatics methods, 120 CsbHLHgenes were identified, and phylogenetic analysis classified them into 18 subfamilies that were unevenly distributed on nine chromosomes. The cis-acting elements of the CsbHLH genes were mainly hormone-related cis-acting elements. Seventeen CsbHLH genes exhibited significant differences in expression under salt stress. Six CsbHLH genes with significant differences in expression were randomly selected for quantitative real-time polymerase chain reaction (qRT-PCR) validation. The qRT-PCR results showed a strong correlation with the transcriptome data. Phytohormones such as jasmonic acid (JA) are essential for biotic and abiotic stress responses in plants, and CsbHLH55 and CsbHLH87 are considered candidate target genes for sweet orange MYC2 transcription factors involved in the JA signaling pathway. These genes are the main downstream effectors in the JA signaling pathway and can be activated to participate in the JA signaling pathway. Activation of the JA signaling pathway inhibits the production of reactive oxygen species and improves the salt tolerance of sweet orange plants. The CsbHLH55 and CsbHLH87 genes could be candidate genes for breeding new transgenic salt-resistant varieties of sweet orange.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20502"},"PeriodicalIF":3.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142113851","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}
Plant GenomePub Date : 2024-09-01Epub Date: 2024-08-20DOI: 10.1002/tpg2.20501
Hector Oberti, Juan Gutierrez-Gonzalez, Clara Pritsch
{"title":"A first de novo transcriptome assembly of feijoa (Acca sellowiana [Berg] Burret) reveals key genes involved in flavonoid biosynthesis.","authors":"Hector Oberti, Juan Gutierrez-Gonzalez, Clara Pritsch","doi":"10.1002/tpg2.20501","DOIUrl":"10.1002/tpg2.20501","url":null,"abstract":"<p><p>Acca sellowiana [Berg] Burret, a cultivated fruit tree originating from South America, is gaining the attention of the nutraceutical and pharmaceutical industries due to their high content of flavonoids and other phenolic compounds in fruits, leaves, and flowers. Flavonoids are a diverse group of secondary metabolites with antioxidant, anti-inflammatory, and antimicrobial properties. They also play a crucial role in plant immune response. Despite their importance, the lack of research on A. sellowiana genomics and transcriptomics hinders a deeper understanding of the molecular mechanisms behind flavonoid biosynthesis and its regulation. Here, we de novo assembled and benchmarked 11 A. sellowiana transcriptomes from leaves and floral tissues at three developmental stages using high-throughput sequencing. We selected and annotated the best assembly according to commonly used metrics and databases. This reference transcriptome consisted of 221,649 nonredundant transcripts, of which 107,612 were functionally annotated. We then used this reference transcriptome to explore the expression profiling of key secondary metabolite genes. Transcripts from genes involved in the flavonoid and anthocyanin biosynthesis pathways were identified. We also identified 4068 putative transcription factors, with the most abundant families being bHLH, C2H2, NAC, MYB, and MYB-related. Transcript expression profiling revealed distinct patterns of gene expression during flower development. Particularly, we found 71 differentially expressed transcripts representing 14 enzymes of the flavonoid pathway, suggesting major changes in flavonoid accumulation across floral stages. Our findings will contribute to understanding the genetic basis of flavonoids and provide a foundation for further research and exploitation of the economic potential of this species.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20501"},"PeriodicalIF":3.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142005616","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}
Plant GenomePub Date : 2024-09-01Epub Date: 2024-08-27DOI: 10.1002/tpg2.20494
Julia Brose, John P Hamilton, Nicholas Schlecht, Dongyan Zhao, Paulina M Mejía-Ponce, Arely Cruz-Pérez, Brieanne Vaillancourt, Joshua C Wood, Patrick P Edger, Salvador Montes-Hernandez, Guillermo Orozco de Rosas, Björn Hamberger, Angélica Cibrian-Jaramillo, C Robin Buell
{"title":"Chromosome-scale Salvia hispanica L. (Chia) genome assembly reveals rampant Salvia interspecies introgression.","authors":"Julia Brose, John P Hamilton, Nicholas Schlecht, Dongyan Zhao, Paulina M Mejía-Ponce, Arely Cruz-Pérez, Brieanne Vaillancourt, Joshua C Wood, Patrick P Edger, Salvador Montes-Hernandez, Guillermo Orozco de Rosas, Björn Hamberger, Angélica Cibrian-Jaramillo, C Robin Buell","doi":"10.1002/tpg2.20494","DOIUrl":"10.1002/tpg2.20494","url":null,"abstract":"<p><p>Salvia hispanica L. (Chia), a member of the Lamiaceae, is an economically important crop in Mesoamerica, with health benefits associated with its seed fatty acid composition. Chia varieties are distinguished based on seed color including mixed white and black (Chia pinta) and black (Chia negra). To facilitate research on Chia and expand on comparative analyses within the Lamiaceae, we generated a chromosome-scale assembly of a Chia pinta accession and performed comparative genome analyses with a previously published Chia negra genome assembly. The Chia pinta and Chia negra genome sequences were highly similar as shown by a limited number of single nucleotide polymorphisms and extensive shared orthologous gene membership. However, there is an enrichment of terpene synthases in the Chia pinta genome relative to the Chia negra genome. We sequenced and analyzed the genomes of 20 Chia accessions with differing seed color and geographic origin revealing population structure within S. hispanica and interspecific introgressions of Salvia species. As the genus Salvia is polyphyletic, its evolutionary history remains unclear. Using large-scale synteny analysis within the Lamiaceae and orthologous group membership, we resolved the phylogeny of Salvia species. This study and its collective resources further our understanding of genomic diversity in this food crop and the extent of interspecies hybridizations in Salvia.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20494"},"PeriodicalIF":3.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142082333","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}