Breeding Science最新文献_第3页

The impact of telomere-to-telomere genome assembly in the plant pan-genomics era. 端粒到端粒基因组组装在植物泛基因组时代的影响。

IF 2 4区农林科学

Breeding Science Pub Date : 2025-03-01 Epub Date: 2025-02-21 DOI: 10.1270/jsbbs.24065

Yuta Aoyagi Blue, Hideaki Iimura, Mitsuhiko P Sato, Kenta Shirasawa

引用次数: 0

Usage of wild Oryza germplasms for breeding in pan-genomics era. 泛基因组时代野生稻种质资源在育种中的应用。

IF 2 4区农林科学

Breeding Science Pub Date : 2025-03-01 Epub Date: 2025-02-21 DOI: 10.1270/jsbbs.24050

Takanori Yoshikawa, Yutaka Sato

{"title":"Usage of wild Oryza germplasms for breeding in pan-genomics era.","authors":"Takanori Yoshikawa, Yutaka Sato","doi":"10.1270/jsbbs.24050","DOIUrl":"10.1270/jsbbs.24050","url":null,"abstract":"One approach to sustainable agricultural production in a changing global environment is the effective utilization of unutilized germplasms. Among these, crop wild relatives (CWRs) represent valuable germplasms that retain the diversity lost during domestication. The genus Oryza has two cultivated species and 22 wild species. One of the cultivated species, Oryza sativa, produces the rice that is the staple food for half of the world's population. We are responsible for the maintenance and distribution of wild Oryza genetic resources held by Japan's National Institute of Genetics (NIG). The NIG has collected the genome sequences of numerous wild Oryza accessions, aiming at understanding and promoting the utilization of Oryza germplasm for both basic and applied sciences, such as breeding. The genome information of many wild Oryza germplasms deciphered by multiple groups is publicly available in databases, allowing for pangenome analysis. This review mainly introduces the wild Oryza genetic resources held by the NIG, discusses the genome diversity revealed through genome sequencing, presents new attempts to utilize wild Oryza germplasm as novel resources enabled by genome sequencing, and discusses the challenges in further effectively utilizing wild Oryza germplasm in breeding.","PeriodicalId":9258,"journal":{"name":"Breeding Science","volume":"75 1","pages":"51-60"},"PeriodicalIF":2.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12203248/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144526491","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Current and future pangenomic research in cucurbit crops. 瓜类作物全基因组研究现状与展望。

IF 2 4区农林科学

Breeding Science Pub Date : 2025-03-01 Epub Date: 2025-02-26 DOI: 10.1270/jsbbs.24048

Gentaro Shigita, Katsunori Tanaka, Kenji Kato

{"title":"Current and future pangenomic research in cucurbit crops.","authors":"Gentaro Shigita, Katsunori Tanaka, Kenji Kato","doi":"10.1270/jsbbs.24048","DOIUrl":"10.1270/jsbbs.24048","url":null,"abstract":"Pangenomics is the exploration and characterization of the full spectrum of genetic variation within a species or a given taxonomic clade. Driven by the accelerating decline in sequencing costs and the widespread adoption of long-read sequencing technologies, the \"wave\" of pangenomics is now hitting various major crops, uncovering substantial intraspecific diversity previously underestimated and neglected. This includes crops belonging to the gourd family (Cucurbitaceae), such as cucumber (Cucumis sativus), melon (Cucumis melo), watermelon (Citrullus lanatus), wax gourd (Benincasa hispida), and bottle gourd (Lagenaria siceraria), all of which are important on a global or regional scale. In this review, we consolidate the findings from all nine pangenomic studies reported as of June 2024, on the five cucurbit crops listed above. This summarizes the current state of pangenomics in the family. We then highlight remaining knowledge gaps for each crop, and propose further research to fill these gaps. Finally, we discuss how pangenomics will shape the future of crop breeding and expand the framework of crop genetic resources in synergy with other technological advances. These insights would apply not only to cucurbits but also to crops across diverse families.","PeriodicalId":9258,"journal":{"name":"Breeding Science","volume":"75 1","pages":"34-50"},"PeriodicalIF":2.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12203251/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144526484","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Novel breeding resources for the underutilised legume, lablab, based on a pangenome approach. 未充分利用的豆科植物的新育种资源，实验室，基于泛基因组方法。

IF 2 4区农林科学

Breeding Science Pub Date : 2025-03-01 Epub Date: 2025-02-05 DOI: 10.1270/jsbbs.24055

Mark A Chapman

{"title":"Novel breeding resources for the underutilised legume, lablab, based on a pangenome approach.","authors":"Mark A Chapman","doi":"10.1270/jsbbs.24055","DOIUrl":"10.1270/jsbbs.24055","url":null,"abstract":"Individuals across a species exhibit substantial presence-absence variation, to the extent that a reference genome from a single individual only contains a subset of the species' genome. Cataloguing genome regions absent from a reference genome can therefore reveal novel genome regions, and some of this variation can be adaptive. In this work, existing short sequencing reads for the underutilised crop lablab (Lablab purpureus (L.) Sweet) were used to identify regions of the genome absent from the reference genome. Lablab is made up of two distinct gene pools, each with wild and domesticated types therefore represents an opportunity to identify gene pool-specific variation. Approximately 7.7% of the reads from eight accessions failed to map to the lablab reference genome (cv. Highworth), putatively being novel, and these were assembled and collapsed into between 735 and 12,304 contigs. Four samples were focussed on (one each wild and domesticated from each of the gene pools) and the novel contigs compared, to identify those present only in subsets of samples. Whilst the number of contigs containing sequenced with similarity to known genes in other legumes was low, there were some enriched gene ontology (GO) terms that could relate to adaptive differences between the groups and therefore contain novel genes for future lablab breeding. The approached used here has potential use in any other species.","PeriodicalId":9258,"journal":{"name":"Breeding Science","volume":"75 1","pages":"61-66"},"PeriodicalIF":2.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12203249/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144526487","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Roles of microRNAs and histone modifications in enhancing stress tolerance in soybean and their applications in molecular breeding. microrna和组蛋白修饰在大豆抗逆性中的作用及其在分子育种中的应用。

IF 2 4区农林科学

Breeding Science Pub Date : 2025-03-01 Epub Date: 2025-02-21 DOI: 10.1270/jsbbs.24039

Kejing Fan, Long-Yiu Chan, Sze-Wing Chan, Wai-Shing Yung, Liping Wang, Hui Zhang, Hon-Ming Lam

{"title":"Roles of microRNAs and histone modifications in enhancing stress tolerance in soybean and their applications in molecular breeding.","authors":"Kejing Fan, Long-Yiu Chan, Sze-Wing Chan, Wai-Shing Yung, Liping Wang, Hui Zhang, Hon-Ming Lam","doi":"10.1270/jsbbs.24039","DOIUrl":"10.1270/jsbbs.24039","url":null,"abstract":"Soybean is an ancient crop domesticated from wild soybean (Glycine soja Sied. & Zucc) in East Asia 6,000-9,000 years ago and has been widely grown as human food and livestock feed in China, Korea, Japan, and the rest of the world since. Global climate change has led to a series of challenges in soybean cultivation and breeding. With the development of high-throughput genomic sequencing technologies, genomic information on soybeans is now more readily available and can be useful for molecular breeding. However, epigenetic regulations on crop development are still largely unexplored. In this review, we summarized the recent discoveries in the regulatory mechanisms underlying soybean adaptations to biotic and abiotic stresses, particularly with respect to histone modifications and microRNAs (miRNAs). Finally, we discussed the potential applications of this knowledge on histone modifications and miRNAs in soybean molecular breeding to improve crop performance in the changing environment.","PeriodicalId":9258,"journal":{"name":"Breeding Science","volume":"75 1","pages":"67-78"},"PeriodicalIF":2.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12203253/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144526488","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A genome-wide association study using Myanmar indica diversity panel reveals a significant genomic region associated with heading date in rice. 利用缅甸籼稻多样性面板进行的全基因组关联研究揭示了水稻抽穗日期相关的重要基因组区域。

IF 2 4区农林科学

Breeding Science Pub Date : 2024-12-01 Epub Date: 2024-12-04 DOI: 10.1270/jsbbs.23083

Moe Moe Hlaing, Khin Thanda Win, Hideshi Yasui, Atsushi Yoshimura, Yoshiyuki Yamagata

{"title":"A genome-wide association study using Myanmar indica diversity panel reveals a significant genomic region associated with heading date in rice.","authors":"Moe Moe Hlaing, Khin Thanda Win, Hideshi Yasui, Atsushi Yoshimura, Yoshiyuki Yamagata","doi":"10.1270/jsbbs.23083","DOIUrl":"10.1270/jsbbs.23083","url":null,"abstract":"Heading date is a key agronomic trait for adapting rice varieties to different growing areas and crop seasons. The genetic mechanism of heading date in Myanmar rice accessions was investigated using a genome-wide association study (GWAS) in a 250-variety indica diversity panel collected from different geographical regions. Using the days to heading data collected in 2019 and 2020, a major genomic region associated with the heading date, designated as MTA3, was found on chromosome 3. The linkage disequilibrium block of the MTA3 contained the coding sequence (CDS) of the phytochrome gene PhyC but not in its promoter region. Haplotype analysis of the 2-kb promoter and gene regions of PhyC revealed the six haplotypes, PHYCHapA, B, C, D, E, and F. The most prominent haplotypes, PHYCHapA and PHYCHapC, had different CDS and were associated with late heading and early heading phenotypes in MIDP, respectively. The difference in CDS effects between the PHYCHapB, which has identical CDS to PHYCHapA, and PHYCHapC was validated by QTL analysis using an F2 population. The distribution of PHYCHapA in the southern coastal and delta regions and of PHYCHapC in the northern highlands appears to ensure heading at the appropriate time in each area under the local day-length conditions in Myanmar. The natural variation in PhyC would be a major determinant of heading date in Myanmar accessions.","PeriodicalId":9258,"journal":{"name":"Breeding Science","volume":"74 5","pages":"415-426"},"PeriodicalIF":2.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11780332/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143078334","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Seedless formation of a landrace 'Sanenashi' (Pyrus L.) collected from Northern Tohoku, Japan. 从日本东北北部采集的地方品种“三仁”（Pyrus L.）的无籽形成。

IF 2 4区农林科学

Breeding Science Pub Date : 2024-12-01 Epub Date: 2024-11-27 DOI: 10.1270/jsbbs.24003

Shohei Mitsuhashi, Seiji Nakano, Chiyomi Uematsu, Hironori Katayama

{"title":"Seedless formation of a landrace 'Sanenashi' (Pyrus L.) collected from Northern Tohoku, Japan.","authors":"Shohei Mitsuhashi, Seiji Nakano, Chiyomi Uematsu, Hironori Katayama","doi":"10.1270/jsbbs.24003","DOIUrl":"10.1270/jsbbs.24003","url":null,"abstract":"'Sanenashi' is a landrace of Pyrus ussuriensis var. aromatica (Iwateyamanashi) with seedless fruit originating from northern Tohoku, Japan. To determine the mechanism of seedless fruit formation, we compared the number of styles in the pistil, fruit, seed set and the pollen tube growth between 'Sanenashi' and the Japanese pear cultivar 'Kosui'. Morphological variations such as short or browning pistils were observed in 64.2% of 'Sanenashi' and 5.9% of 'Kosui'. The initial fruit set rate of 'Sanenashi' was 48.3% at 4 weeks after cross-pollination with pear, and there were no fruit sets with peach pollen and non-pollinated sections at 8 weeks. Although the seed sets of 'Sanenashi' fruit were much lower than that of 'Kosui', 55.3% of viable 'Sanenashi' seeds germinated. Pollen tube growths were observed in the stigma and style of 'Sanenashi', but whether they reached the ovary could not be confirmed. Single sequence repeat (SSR) alleles of F1 progenies between 'Sanenashi' and pear cultivars were presented by five SSR markers. These results suggest that the seedless fruit formation in 'Sanenashi' corresponds with pseudo-parthenocarpy (stenospermocarpy) because pollination by pear pollen is necessary for the fruit set. However, the results do not fully confirm this hypothesis and require further experiments.","PeriodicalId":9258,"journal":{"name":"Breeding Science","volume":"74 5","pages":"427-434"},"PeriodicalIF":2.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11780337/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143078543","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Polyploid QTL-seq identified QTLs controlling potato flesh color and tuber starch phosphorus content in a plexity-dependent manner. 多倍体QTL-seq鉴定出控制马铃薯果肉颜色和块茎淀粉磷含量的qtl，并呈多样性依赖关系。

IF 2 4区农林科学

Breeding Science Pub Date : 2024-12-01 Epub Date: 2024-11-23 DOI: 10.1270/jsbbs.24028

Hiromoto Yamakawa, Tatsumi Mizubayashi, Noriyuki Kitazawa, Utako Yamanouchi, Tsuyu Ando, Yoshiyuki Mukai, Etsuo Shimosaka, Takahiro Noda, Kenji Asano, Kotaro Akai, Kenji Katayama

{"title":"Polyploid QTL-seq identified QTLs controlling potato flesh color and tuber starch phosphorus content in a plexity-dependent manner.","authors":"Hiromoto Yamakawa, Tatsumi Mizubayashi, Noriyuki Kitazawa, Utako Yamanouchi, Tsuyu Ando, Yoshiyuki Mukai, Etsuo Shimosaka, Takahiro Noda, Kenji Asano, Kotaro Akai, Kenji Katayama","doi":"10.1270/jsbbs.24028","DOIUrl":"10.1270/jsbbs.24028","url":null,"abstract":"The progenies of polyploid crops inherit multiple sets of homoeologous chromosomes through various combinations, which impedes the identification of the quantitative trait loci (QTL) governing agronomic traits and the implementation of DNA marker-assisted breeding. Previously, we developed a whole-genome sequencing-based polyploid QTL-seq method that utilizes comprehensively extracted simplex polymorphisms for QTL mapping. Here, we verified the detection of duplex QTLs by modifying the analytical settings to explore the QTLs governing tuber flesh color and starch phosphorus content using tetraploid potato (Solanum tuberosum L.). The F1 progenies were obtained from a cross between 'Touya' (TY) and 'Benimaru' (BM). A single TY-derived QTL responsible for yellow flesh color was identified around a β-carotene hydroxylase gene on chromosome 3 using simplex polymorphisms, and a BM-derived QTL associated with decreased starch phosphorus content near a starch synthase II gene on chromosome 2 was detected using duplex polymorphisms. Furthermore, linked DNA markers were developed at the QTL sites. For the latter QTL, plexity-distinguishable markers were developed using quantitative PCR, fragment analysis, and amplicon sequencing. These revealed the allele dosage-dependent effect of the reduced starch phosphorus content. Thus, the polyploid QTL-seq pipeline can explore versatile QTLs beyond simplex, facilitating DNA marker-assisted breeding in various polyploid crops.","PeriodicalId":9258,"journal":{"name":"Breeding Science","volume":"74 5","pages":"403-414"},"PeriodicalIF":2.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11780331/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143078541","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

GenoSee: a novel visualization tool for graphical genotypes. GenoSee：一种新的可视化工具，用于图形基因型。

IF 2 4区农林科学

Breeding Science Pub Date : 2024-12-01 Epub Date: 2024-11-23 DOI: 10.1270/jsbbs.24041

Shumpei Hashimoto

{"title":"GenoSee: a novel visualization tool for graphical genotypes.","authors":"Shumpei Hashimoto","doi":"10.1270/jsbbs.24041","DOIUrl":"10.1270/jsbbs.24041","url":null,"abstract":"Visualizing genotypic data is essential in genetic research and breeding programs as it offers clear representations of genomic information, enhancing understanding of genetic architecture. This becomes especially critical with the emergence of next-generation sequencing (NGS) technologies, which generate vast datasets necessitating effective visualization tools. While traditional tools for graphical genotypes have been groundbreaking, they often lack flexibility and universal applicability. These tools encounter limitations such as user-customized visualization and compatibility issues across different operating systems. In this study, I introduce GenoSee, a novel visualization tool designed to address these shortcomings. GenoSee can handle phased and non-phased variant calling data, offering extensive customization to suit diverse research requirements. It operates seamlessly across multiple platforms, ensuring compatibility, and provides high-quality graphical genotypes. GenoSee facilitates deeper insights into genomic structures, thereby advancing genetic and genomic research, and breeding programs by enhancing accessibility to genetic data visualization.","PeriodicalId":9258,"journal":{"name":"Breeding Science","volume":"74 5","pages":"454-461"},"PeriodicalIF":2.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11780333/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143078526","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","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 identification and salt stress expression analysis of the PLATZ transcription factor genes in Betula platyphylla. 白桦PLATZ转录因子基因的全基因组鉴定及盐胁迫表达分析。

IF 2 4区农林科学

Breeding Science Pub Date : 2024-12-01 Epub Date: 2024-11-20 DOI: 10.1270/jsbbs.24023

Yang Li, Mingyu Yu, Yao Chi, Meiqi Zhou, Zihan Wang, Yan Gao, Xu Li, Caiqiu Gao, Chao Wang

{"title":"Genome-wide identification and salt stress expression analysis of the PLATZ transcription factor genes in Betula platyphylla.","authors":"Yang Li, Mingyu Yu, Yao Chi, Meiqi Zhou, Zihan Wang, Yan Gao, Xu Li, Caiqiu Gao, Chao Wang","doi":"10.1270/jsbbs.24023","DOIUrl":"10.1270/jsbbs.24023","url":null,"abstract":"The PLATZ (Plant AT rich protein and zinc binding protein) transcription factor, which is a type of plant specific zinc dependent DNA binding protein, participates in regulating the process of plant growth and environmental stress responses. In order to clarify the characteristics of the PLATZ family genes in birch (Betula platyphylla), the members of the PLATZ family were screened and analyzed in this study. Totals of ten BpPLATZ genes were identified in birch genome and classified into five groups base on phylogenetic relationship, BpPLATZ genes in the same group usually possess a similar motif composition, exon or intron number. These ten genes distributed on eight chromosomes of fourteen chromosomes of birch. In addition, various cis-elements were distributed in the promoter regions of BpPLATZs, especially with abundant MYC, ABRE and MYB, which were reported to be involved in salt stress responses. The RT-qPCR analysis results show that most genes have the higher expression levels in the roots compared to leaves and stems in birch. BpPLATZ3, BpPLATZ5, BpPLATZ6, BpPLATZ7 and BpPLATZ8 are significantly induced expressed response to salt stress. These studies provide a basis for the further functional study of the BpPLATZ genes.","PeriodicalId":9258,"journal":{"name":"Breeding Science","volume":"74 5","pages":"393-402"},"PeriodicalIF":2.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11780336/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143078524","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0