Plant Genome最新文献_第5页

Local haplotyping reveals insights into the genetic control of flowering time variation in wild and domesticated soybean. 局部单倍型分析揭示了野生大豆和驯化大豆花期变异的遗传控制。

IF 3.9 2区生物学

Plant Genome Pub Date : 2024-12-01 Epub Date: 2024-11-07 DOI: 10.1002/tpg2.20528

Shameela Mohamedikbal, Hawlader A Al-Mamun, Jacob I Marsh, Shriprabha Upadhyaya, Monica F Danilevicz, Henry T Nguyen, Babu Valliyodan, Adam Mahan, Jacqueline Batley, David Edwards

{"title":"Local haplotyping reveals insights into the genetic control of flowering time variation in wild and domesticated soybean.","authors":"Shameela Mohamedikbal, Hawlader A Al-Mamun, Jacob I Marsh, Shriprabha Upadhyaya, Monica F Danilevicz, Henry T Nguyen, Babu Valliyodan, Adam Mahan, Jacqueline Batley, David Edwards","doi":"10.1002/tpg2.20528","DOIUrl":"10.1002/tpg2.20528","url":null,"abstract":"The timing of flowering in soybean [Glycine max (L.) Merr.], a key legume crop, is influenced by many factors, including daylight length or photoperiodic sensitivity, that affect crop yield, productivity, and geographical adaptation. Despite its importance, a comprehensive understanding of the local linkage landscape and allelic diversity within regions of the genome influencing flowering and contributing to phenotypic variation in subpopulations has been limited. This study addresses these gaps by conducting an in-depth trait association and linkage analysis coupled with local haplotyping using advanced bioinformatics tools, including crosshap, to characterize genomic variation using a pangenome dataset representing 915 domesticated and wild-type individuals. The association analysis identified eight significant loci on seven chromosomes. Moving beyond traditional association analysis, local haplotyping of targeted regions on chromosomes 6 and 20 identified distinct haplotype structures, variation patterns, and genomic candidates influencing flowering in subpopulations. These results suggest the action of a network of genomic candidates influencing flowering time and an untapped reservoir of genomic variation for this trait in wild germplasm. Notably, GlymaLee.20G147200 on chromosome 20 was identified as a candidate gene that may cause delayed flowering in soybean, potentially through histone modifications of floral repressor loci as seen in Arabidopsis thaliana (L.) Heynh. These findings support future functional validation of haplotype-based alleles for marker-assisted breeding and genomic selection to enhance latitude adaptability of soybean without compromising yield.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20528"},"PeriodicalIF":3.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11628924/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142606549","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Candidate selective sweeps in US wheat populations. 美国小麦种群中的候选选择性横扫。

IF 3.9 2区生物学

Plant Genome Pub Date : 2024-12-01 Epub Date: 2024-09-25 DOI: 10.1002/tpg2.20513

Sajal R Sthapit, Travis M Ruff, Marcus A Hooker, Bosen Zhang, Xianran Li, Deven R See

{"title":"Candidate selective sweeps in US wheat populations.","authors":"Sajal R Sthapit, Travis M Ruff, Marcus A Hooker, Bosen Zhang, Xianran Li, Deven R See","doi":"10.1002/tpg2.20513","DOIUrl":"10.1002/tpg2.20513","url":null,"abstract":"Exploration of novel alleles from ex situ collection is still limited in modern plant breeding as these alleles exist in genetic backgrounds of landraces that are not adapted to modern production environments. The practice of backcross breeding results in preservation of the adapted background of elite parents but leaves little room for novel alleles from landraces to be incorporated. Selection of adaptation-associated linkage blocks instead of the entire adapted background may allow breeders to incorporate more of the landrace's genetic background and to observe and evaluate novel alleles. Important adaptation-associated linkage blocks would have been selected over multiple cycles of breeding and hence are likely to exhibit signatures of positive selection or selective sweeps. We conducted genome-wide scan for candidate selective sweeps (CSS) using Fst, Rsb, and xpEHH in state, regional, spring, winter, and market-class population pairs and reported 446 CSS in 19 population pairs over time and 1033 CSS in 44 population pairs across geography and class. Further validation of these CSS in specific breeding programs may lead to identification of sets of loci that can be selected to restore population-specific adaptation in pre-breeding germplasms.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20513"},"PeriodicalIF":3.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11628914/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142330654","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Functional analysis of PagERF021 gene in salt stress tolerance in Populus alba × P. glandulosa. PagERF021 基因在白杨×腺叶杨耐盐胁迫中的功能分析

IF 3.9 2区生物学

Plant Genome Pub Date : 2024-12-01 Epub Date: 2024-10-16 DOI: 10.1002/tpg2.20521

Gaofeng Fan, Yuan Gao, Xinyue Wu, Yingying Yu, Wenjing Yao, Jiahui Jiang, Huanzhen Liu, Tingbo Jiang

{"title":"Functional analysis of PagERF021 gene in salt stress tolerance in Populus alba × P. glandulosa.","authors":"Gaofeng Fan, Yuan Gao, Xinyue Wu, Yingying Yu, Wenjing Yao, Jiahui Jiang, Huanzhen Liu, Tingbo Jiang","doi":"10.1002/tpg2.20521","DOIUrl":"10.1002/tpg2.20521","url":null,"abstract":"Poplar trees are crucial for timber and greening, but high levels of salt in the soil have severely limited the yield of poplar. Ethylene response factor (ERF) transcription factors play an important role in growth, development, and stress response in eukaryotes. Our study focused on the PagERF021 gene from Populus alba × P. glandulosa, which was significantly upregulated in various tissues under salt stress [Correction added on October 4, 2024, after first online publication: \"ETS2 reporter factor\" is changed to \"Ethylene response factor\".]. Both the tissue-specific expression pattern and β-glucuronidase (GUS) staining of proPagERF021-GUS plants indicated that this gene was predominantly expressed in the roots and stems. The subcellular localization showed that the protein was only localized in the nucleus. The yeast assay demonstrated that this protein had transcriptional activation activity at its C-terminal and could specifically binding to the MYB-core cis-element. The overexpression of PagERF021 gene could scavenge the accumulation of reactive oxygen species and reduce the degree of cellular membrane damage, indicating that this gene enhanced the salt tolerance of poplars. This finding will provide a feasible insight for future research into the regulatory mechanisms of ERF genes in resisting to abiotic stress and the development of new stress-resistant varieties in plants.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20521"},"PeriodicalIF":3.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11628909/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142478517","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Studies of genetic diversity and genome-wide association for vitamin C content in lettuce (Lactuca sativa L.) using high-throughput SNP arrays. 利用高通量 SNP 阵列研究莴苣（Lactuca sativa L.）中维生素 C 含量的遗传多样性和全基因组关联。

IF 3.9 2区生物学

Plant Genome Pub Date : 2024-12-01 Epub Date: 2024-10-24 DOI: 10.1002/tpg2.20518

Inés Medina-Lozano, Juan Ramón Bertolín, Jörg Plieske, Martin Ganal, Heike Gnad, Aurora Díaz

{"title":"Studies of genetic diversity and genome-wide association for vitamin C content in lettuce (Lactuca sativa L.) using high-throughput SNP arrays.","authors":"Inés Medina-Lozano, Juan Ramón Bertolín, Jörg Plieske, Martin Ganal, Heike Gnad, Aurora Díaz","doi":"10.1002/tpg2.20518","DOIUrl":"10.1002/tpg2.20518","url":null,"abstract":"Lettuce (Lactuca sativa L.) is a source of beneficial compounds though they are generally present in low quantities. We used 40K Axiom and 9K Infinium SNP (single nucleotide polymorphism) arrays to (i) explore the genetic variability in 21 varieties and (ii) carry out genome-wide association studies (GWAS) of vitamin C content in21 varieties and a population of 205 plants from the richest variety in vitamin C ('Lechuga del Pirineo'). Structure and phylogenetic analyses showed that the group formed mainly by traditional varieties was the most diverse, whereas the red commercial varieties clustered together and very distinguishably apart from the rest. GWAS consistently detected, in a region of chromosome 2, several SNPs related to dehydroascorbic acid (a form of vitamin C) content using three different methods to assess population structure, subpopulation membership coefficients, multidimensional scaling, and principal component analysis. The latter detected the highest number of SNPs (17) and the most significantly associated, 12 of them showing a high linkage disequilibrium with the lead SNP. Among the 84 genes in the region, some have been reported to be related to vitamin C content or antioxidant status in other crops either directly, like those encoding long non-coding RNA, several F-box proteins, and a pectinesterase/pectinesterase inhibitor, or indirectly, like extensin-1-like protein and endoglucanase 2 genes. The involvement of other genes identified within the region in vitamin C levels needs to be further studied. Understanding the genetic control of such an important quality trait in lettuce becomes very relevant from a breeding perspective.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20518"},"PeriodicalIF":3.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11628896/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142511141","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Characterization of a new barley greenbug resistance gene Rsg4 in the Chinese landrace CI 2458. 中国大麦品种 CI 2458 中新的抗大麦青虫基因 Rsg4 的特征。

IF 3.9 2区生物学

Plant Genome Pub Date : 2024-12-01 Epub Date: 2024-11-07 DOI: 10.1002/tpg2.20527

Xiangyang Xu, Dolores Mornhinweg, Guihua Bai, Genqiao Li, Ruolin Bian, Amy Bernardo

{"title":"Characterization of a new barley greenbug resistance gene Rsg4 in the Chinese landrace CI 2458.","authors":"Xiangyang Xu, Dolores Mornhinweg, Guihua Bai, Genqiao Li, Ruolin Bian, Amy Bernardo","doi":"10.1002/tpg2.20527","DOIUrl":"10.1002/tpg2.20527","url":null,"abstract":"Barley (Hordeum vulgare) is a climate-resilient crop widely cultivated in both highly productive and suboptimal agricultural systems, and its ability to adapt to multiple biotic and abiotic stresses has contributed significantly to food security. Greenbug is a destructive insect pest for global barley production, and new greenbug resistance genes are needed to overcome the challenges posed by diverse greenbug biotypes in fields. CI 2458 is a Chinese landrace exhibiting a unique resistance profile to a set of 14 greenbug biotypes, which suggests the presence of a new greenbug resistance gene in CI 2458. A recombinant inbred line population from the cross Weskan × CI 2458 was developed, evaluated for responses to greenbug biotype F, and genotyped using single nucleotide polymorphism (SNP) markers generated by genotyping-by-sequencing. Linkage analysis revealed a single gene, designated Rsg4, conditioning greenbug resistance in CI 2458. Rsg4 was delimited to a 1.14 Mb interval between SNP markers S3H_666512114 and S3H_667651446 in the terminal region of chromosome arm 3HL, with genetic distances of 1.2 cM proximal to S3H_667651446 and 1.1 cM distal to S3H_666512114. Allelism tests confirmed that Rsg4 is a new greenbug resistance gene independent of Rsg1 and Rsg3, which reside in the same chromosome arm. Rsg4 differs from Rsg1 alleles and Rsg3 in its resistance to greenbug biotype TX1, one of the most widely virulent biotypes. The introgression of Rsg4 into locally adapted barley cultivars is of agronomic importance, and kompetitive allele-specific polymerase chain reaction (KASP) markers flanking Rsg4, KASP-Rsg336-1 and KASP-Rsg336-2, enable rapid pyramiding of Rsg4 with other resistance genes to develop durable greenbug-resistant cultivars.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20527"},"PeriodicalIF":3.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11628878/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142606409","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

k-mer genome-wide association study for anthracnose and BCMV resistance in a Phaseolus vulgaris Andean Diversity Panel. 安第斯多樣性小組中炭疽病和 BCMV 抗性的 k-mer 全基因組關聯研究。

IF 3.9 2区生物学

Plant Genome Pub Date : 2024-12-01 Epub Date: 2024-10-13 DOI: 10.1002/tpg2.20523

Andrew T Wiersma, John P Hamilton, Brieanne Vaillancourt, Julia Brose, Halima E Awale, Evan M Wright, James D Kelly, C Robin Buell

{"title":"k-mer genome-wide association study for anthracnose and BCMV resistance in a Phaseolus vulgaris Andean Diversity Panel.","authors":"Andrew T Wiersma, John P Hamilton, Brieanne Vaillancourt, Julia Brose, Halima E Awale, Evan M Wright, James D Kelly, C Robin Buell","doi":"10.1002/tpg2.20523","DOIUrl":"10.1002/tpg2.20523","url":null,"abstract":"Access to broad genomic resources and closely linked marker-trait associations for common beans (Phaseolus vulgaris L.) can facilitate development of improved varieties with increased yield, improved market quality traits, and enhanced disease resistance. The emergence of virulent races of anthracnose (caused by Colletotrichum lindemuthianum) and bean common mosaic virus (BCMV) highlight the need for improved methods to identify and incorporate pan-genomic variation in breeding for disease resistance. We sequenced the P. vulgaris Andean Diversity Panel (ADP) and performed a genome-wide association study (GWAS) to identify associations for resistance to BCMV and eight races of anthracnose. Historical single nucleotide polymorphism (SNP)-chip and phenotypic data enabled a three-way comparison between SNP-chip, reference-based whole genome shotgun sequence (WGS)-SNP, and reference-free k-mer (short nucleotide subsequence) GWAS. Across all traits, there was excellent concordance between SNP-chip, WGS-SNP, and k-mer GWAS results-albeit at a much higher marker resolution for the WGS data sets. Significant k-mer haplotype variation revealed selection of the linked I-gene and Co-u traits in North American breeding lines and cultivars. Due to structural variation, only 9.1 to 47.3% of the significantly associated k-mers could be mapped to the reference genome. Thus, to determine the genetic context of cis-associated k-mers, we generated draft whole genome assemblies of four ADP accessions and identified an expanded local repertoire of disease resistance genes associated with resistance to anthracnose and BCMV. With access to variant data in the context of a pan-genome, high resolution mapping of agronomic traits for common bean is now feasible.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20523"},"PeriodicalIF":3.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11628888/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142478528","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Parental assigned chromosomes for cultivated cacao provides insights into genetic architecture underlying resistance to vascular streak dieback. 为栽培可可分配亲本染色体，有助于深入了解抗维管束条纹枯萎病的遗传结构。

IF 3.9 2区生物学

Plant Genome Pub Date : 2024-12-01 Epub Date: 2024-10-15 DOI: 10.1002/tpg2.20524

Peri A Tobias, Jacob Downs, Peter Epaina, Gurpreet Singh, Robert F Park, Richard J Edwards, Eirene Brugman, Andi Zulkifli, Junaid Muhammad, Agus Purwantara, David I Guest

{"title":"Parental assigned chromosomes for cultivated cacao provides insights into genetic architecture underlying resistance to vascular streak dieback.","authors":"Peri A Tobias, Jacob Downs, Peter Epaina, Gurpreet Singh, Robert F Park, Richard J Edwards, Eirene Brugman, Andi Zulkifli, Junaid Muhammad, Agus Purwantara, David I Guest","doi":"10.1002/tpg2.20524","DOIUrl":"10.1002/tpg2.20524","url":null,"abstract":"Diseases of Theobroma cacao L. (Malvaceae) disrupt cocoa bean supply and economically impact growers. Vascular streak dieback (VSD), caused by Ceratobasidium theobromae, is a new encounter disease of cacao currently contained to southeast Asia and Melanesia. Resistance to VSD has been tested with large progeny trials in Sulawesi, Indonesia, and in Papua New Guinea with the identification of informative quantitative trait loci (QTLs). Using a VSD susceptible progeny tree (clone 26), derived from a resistant and susceptible parental cross, we assembled the genome to chromosome-level and discriminated alleles inherited from either resistant or susceptible parents. The parentally phased genomes were annotated for all predicted genes and then specifically for resistance genes of the nucleotide-binding site leucine-rich repeat class (NLR). On investigation, we determined the presence of NLR clusters and other potential disease response gene candidates in proximity to informative QTLs. We identified structural variants within NLRs inherited from parentals. We present the first diploid, fully scaffolded, and parentally phased genome resource for T. cacao L. and provide insights into the genetics underlying resistance and susceptibility to VSD.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20524"},"PeriodicalIF":3.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11628906/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142478529","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genome-wide association study uncovers pea candidate genes and metabolic pathways involved in rust resistance. 全基因组关联研究发现了豌豆抗锈病的候选基因和代谢途径。

IF 3.9 2区生物学

Plant Genome Pub Date : 2024-12-01 Epub Date: 2024-10-29 DOI: 10.1002/tpg2.20510

Salvador Osuna-Caballero, Diego Rubiales, Nicolas Rispail

{"title":"Genome-wide association study uncovers pea candidate genes and metabolic pathways involved in rust resistance.","authors":"Salvador Osuna-Caballero, Diego Rubiales, Nicolas Rispail","doi":"10.1002/tpg2.20510","DOIUrl":"10.1002/tpg2.20510","url":null,"abstract":"Pea (Pisum sativum L.) is an important temperate legume crop providing plant-based proteins for food and feed worldwide. Pea yield can be limited by several biotic stresses, among which rust represents a major limiting factor in many temperate and subtropical regions. Some efforts have been made to assess the natural variation in pea resistance to rust, but its efficient exploitation in breeding is limited since the resistance loci identified so far are scarce and their responsible gene(s) unknown. To overcome this knowledge gap, a comprehensive genome-wide association study (GWAS) has been performed on pea rust, caused by Uromyces pisi, to uncover genetic loci associated with resistance. Utilizing a diverse collection of 320 pea accessions, we evaluated phenotypic responses to two rust isolates using both traditional methods and advanced image-based phenotyping. We detected 95 significant trait-marker associations using a set of 26,045 Diversity Arrays Technology-sequencing polymorphic markers. Our in silico analysis identified 62 candidate genes putatively involved in rust resistance, grouped into different functional categories such as gene expression regulation, vesicle trafficking, cell wall biosynthesis, and hormonal signaling. This research highlights the potential of GWAS to identify molecular markers associated with resistance and candidate genes against pea rust, offering new targets for precision breeding. By integrating our findings into current breeding programs, we can facilitate the development of pea varieties with improved resistance to rust, contributing to sustainable agricultural practices and food security. This study sets the stage for future functional genomic analyses and the application of genomic selection approaches to enhance disease resistance in peas.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20510"},"PeriodicalIF":3.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11628884/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142548522","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Development and implementation of nested single-nucleotide polymorphism (SNP) assays for breeding and genetic research applications. 开发和实施用于育种和基因研究的嵌套单核苷酸多态性（SNP）测定。

IF 3.9 2区生物学

Plant Genome Pub Date : 2024-09-01 Epub Date: 2024-07-22 DOI: 10.1002/tpg2.20491

Qijian Song, Charles Quigley, Ruifeng He, Dechun Wang, Henry Nguyen, Carrie Miranda, Zenglu Li

{"title":"Development and implementation of nested single-nucleotide polymorphism (SNP) assays for breeding and genetic research applications.","authors":"Qijian Song, Charles Quigley, Ruifeng He, Dechun Wang, Henry Nguyen, Carrie Miranda, Zenglu Li","doi":"10.1002/tpg2.20491","DOIUrl":"10.1002/tpg2.20491","url":null,"abstract":"SoySNP50K and SoySNP6K are commonly used for soybean (Glycine max) genotyping. The SoySNP50K assay has been used to genetically analyze the entire USDA Soybean Germplasm Collection, while the SoySNP6K assay, containing a subset of 6000 single-nucleotide polymorphisms (SNPs) from SoySNP50K, has been used for quantitative trait loci mapping of different traits. To meet the needs for genomic selection, selection of parents for crosses, and characterization of breeding populations, especially early selection of ideal offspring from thousands of lines, we developed two assays, SoySNP3K and SoySNP1K, containing 3072 and 1252 SNPs, respectively, based on SoySNP50K and SoySNP6K mark sets. These two assays also contained the trait markers reported or contributed by soybean breeders. The SNPs in the SoySNP3K are a subset from SoySNP6K, while the SNPs in the SoySNP1K are a subset from SoySNP3K. These SNPs were chosen to reduce the SNP number in the large linkage blocks while capturing as much of the haplotype diversity as possible. They are highly polymorphic and of high quality. The mean minor allele frequencies of the SNPs in the southern and northern US elites were 0.25 and 0.27 for SoySNP3K, respectively, and 0.29 and 0.33 for SoySNP1K. The selected SNPs are a valuable source for developing targeted amplicon sequencing assay or beadchip assay in soybean. SoySNP3K and SoySNP1K assays are commercialized by Illumina Inc. and AgriPlex Genomics, respectively. Together with SoySNP50K and SoySNP6K, a series of nested assays with different marker densities will serve as additional low-cost genomic tools for genetic, genomic, and breeding research.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20491"},"PeriodicalIF":3.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141735380","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 identification of bZIP transcription factors in 12 Rosaceae species and modeling of novel mechanisms of EjbZIPs response to salt stress. 12 种蔷薇科植物中 bZIP 转录因子的全基因组鉴定以及 EjbZIPs 应对盐胁迫的新机制建模。

IF 3.9 2区生物学

Plant Genome Pub Date : 2024-09-01 Epub Date: 2024-06-05 DOI: 10.1002/tpg2.20468

Ling Zhu, Mengjie Zhang, Xiuyao Yang, Yinqiang Zi, Tuo Yin, Xulin Li, Ke Wen, Ke Zhao, Jiaqiong Wan, Huiyun Zhang, Xinping Luo, Hanyao Zhang

{"title":"Genome-wide identification of bZIP transcription factors in 12 Rosaceae species and modeling of novel mechanisms of EjbZIPs response to salt stress.","authors":"Ling Zhu, Mengjie Zhang, Xiuyao Yang, Yinqiang Zi, Tuo Yin, Xulin Li, Ke Wen, Ke Zhao, Jiaqiong Wan, Huiyun Zhang, Xinping Luo, Hanyao Zhang","doi":"10.1002/tpg2.20468","DOIUrl":"10.1002/tpg2.20468","url":null,"abstract":"In plantae, basic leucine zipper (bZIP) transcription factors (TFs) are widespread and regulate a variety of biological processes under abiotic stress. However, it has not been extensively studied in Rosaceae, and the functional effects of bZIP on Eriobotrya japonica under salt stress are still unknown. Therefore, in this study, the bZIP TF family of 12 species of Rosaceae was analyzed by bioinformatics method, and the expression profile and quantitative real-time polymerase chain reaction of E. japonica under salt stress were analyzed. The results showed that a total of 869 bZIP TFs were identified in 12 species of Rosaceae and divided into nine subfamilies. Differences in promoter cis-elements between subfamilies vary depending on their role. Species belonging to the same subfamily have a similar number of chromosomes and the number of genes contained on each chromosome. Gene duplication analysis has found segmental duplication to be a prime force in the evolution of Rosaceae species. In addition, nine EjbZIPs were significantly different, including seven up-regulated and two down-regulated in E. japonica under salt stress. Especially, EjbZIP13 was involved in the expression of SA-responsive proteins by binding to the NPR1 gene. EjbZIP27, EjbZIP30, and EjbZIP38 were highly expressed in E. japonica under salt stress, thus improving the salt tolerance capacity of the plants. These results can provide a theoretical basis for exploring the characteristics and functions of the bZIP TF family in more species and breeding salt-tolerant E. japonica varieties. It also provides a reference for resolving the response mechanism of bZIP TF in 12 Rosaceae species under salt stress.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20468"},"PeriodicalIF":3.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141263133","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