Wheat yellow mosaic disease is a soilborne disease caused by wheat yellow mosaic virus (WYMV). Symptoms include yellow mosaic coloring of leaves, stunting, and growth inhibition. Here we conducted a detailed analysis of resistance to this virus in winter wheat 'Hokkai 240' by carrying out inoculation tests of WYMV and conducting field tests. The resistance level observed in 'Hokkai 240' was compared with those in varieties harboring known resistance genes. In the inoculation tests, 'Hokkai 240' showed resistance to WYMV Pathotypes I and II and partial resistance to Pathotype III. This result was contrary to the sensitive responses to the three pathotypes exhibited by the variety harboring resistance gene on chromosome 2DL. In fields infected with WYMV Pathotypes II and III, 'Hokkai 240' plants exhibited few disease symptoms and little proliferation of the virus. By analyzing the quantitative trait loci (QTLs) in recombinant inbred lines from a cross between 'Hokkai 240' and 'Nanbukomugi', a single major QTL, Q.Ymhk, from 'Hokkai 240', which had significant effects on Pathotypes II and III of the virus, was detected in the proximity of snp4212 and snp4215 mapped on chromosome 2AS. These results indicate that Q.Ymhk may be useful for developing broad resistance to WYMV in wheat breeding programs.
小麦黄镶嵌病是一种由小麦黄镶嵌病毒(WYMV)引起的土传病害。症状包括叶片染上黄色马赛克、发育不良和生长受抑制。在此,我们通过进行 WYMV 接种试验和田间试验,详细分析了冬小麦'Hokkai 240'对该病毒的抗性。我们将'Hokkai 240'的抗性水平与含有已知抗性基因的品种进行了比较。在接种试验中,"Hokkai 240 "对 WYMV 病原体 I 型和 II 型表现出抗性,对病原体 III 型表现出部分抗性。这一结果与染色体 2DL 上含有抗性基因的品种对三种病型的敏感反应相反。在感染 WYMV 病型 II 和 III 的田块中,'Hokkai 240'植株表现出的病害症状很少,病毒增殖也很少。通过分析'Hokkai 240'和'Nanbukomugi'杂交重组近交系的数量性状位点(QTL),发现'Hokkai 240'的一个主要 QTL Q.Ymhk,对病毒病型 II 和 III 有显著影响,该 QTL 位于 2AS 染色体上的 snp4212 和 snp4215 附近。这些结果表明,Q.Ymhk 可能有助于在小麦育种计划中开发对 WYMV 的广泛抗性。
{"title":"Identification of a major QTL conferring resistance to <i>wheat yellow mosaic virus</i> derived from the winter wheat 'Hokkai 240' on chromosome 2AS.","authors":"Kenji Kawaguchi, Takehiro Ohki, Goro Ishikawa, Mitsuru Sayama, Yohei Terasawa, Shunsuke Oda, Masaya Fujita, Miwako Ito, Koichi Hatta","doi":"10.1270/jsbbs.23079","DOIUrl":"10.1270/jsbbs.23079","url":null,"abstract":"<p><p>Wheat yellow mosaic disease is a soilborne disease caused by <i>wheat yellow mosaic virus</i> (WYMV). Symptoms include yellow mosaic coloring of leaves, stunting, and growth inhibition. Here we conducted a detailed analysis of resistance to this virus in winter wheat 'Hokkai 240' by carrying out inoculation tests of WYMV and conducting field tests. The resistance level observed in 'Hokkai 240' was compared with those in varieties harboring known resistance genes. In the inoculation tests, 'Hokkai 240' showed resistance to WYMV Pathotypes I and II and partial resistance to Pathotype III. This result was contrary to the sensitive responses to the three pathotypes exhibited by the variety harboring resistance gene on chromosome 2DL. In fields infected with WYMV Pathotypes II and III, 'Hokkai 240' plants exhibited few disease symptoms and little proliferation of the virus. By analyzing the quantitative trait loci (QTLs) in recombinant inbred lines from a cross between 'Hokkai 240' and 'Nanbukomugi', a single major QTL, <i>Q.Ymhk</i>, from 'Hokkai 240', which had significant effects on Pathotypes II and III of the virus, was detected in the proximity of <i>snp4212</i> and <i>snp4215</i> mapped on chromosome 2AS. These results indicate that <i>Q.Ymhk</i> may be useful for developing broad resistance to WYMV in wheat breeding programs.</p>","PeriodicalId":9258,"journal":{"name":"Breeding Science","volume":"74 3","pages":"232-239"},"PeriodicalIF":2.0,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11561412/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142645959","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}
Seed development is an essential phenomenon for all sexual propagative plant species. The functional allele at SEED DEVELOPMENT 1 (SDV1) or SEED DEVELOPMENT 2 (SDV2) loci is essential for seed development for Oryza sativa and Oryza meridionalis. In the present study, we performed fine mapping of SDV1, narrowing down the area of interest to 333kb on chromosome 6. Haplotype analysis around the SDV1 locus of O. meridionalis accessions indicated that they shared the DNA polymorphism, suggesting that they have a common abortive allele at the SDV1 locus. Linkage analysis of the candidate SDV2 gene showed that it was located on chromosome 4. The candidate SDV2 was confirmed using a population in which both the SDV1 and SDV2 genes were segregating. The chromosomal region covering the SDV1 gene was predicted to contain 30 protein-coding genes in O. sativa. Five of these genes have conserved DNA sequences in the chromosomal region of the SDV2 gene on chromosome 4, and not on chromosome 6, of O. meridionalis. These results suggest that these five genes could be candidates for SDV1, and that their orthologous genes located on chromosome 4 of O. meridionalis could be candidates for SDV2.
种子发育是所有有性繁殖植物物种的基本现象。种子发育 1(SDV1)或种子发育 2(SDV2)基因座上的功能等位基因对禾本科植物和经果类植物的种子发育至关重要。在本研究中,我们对 SDV1 进行了精细作图,将感兴趣的区域缩小到 6 号染色体上的 333kb。围绕 SDV1 基因座的单倍型分析表明,O. meridionalis 加入的基因具有共同的 DNA 多态性,这表明它们在 SDV1 基因座上有一个共同的失效等位基因。对候选 SDV2 基因的连锁分析表明,该基因位于第 4 号染色体上。利用 SDV1 和 SDV2 基因均发生分离的群体对候选 SDV2 基因进行了确认。据预测,覆盖 SDV1 基因的染色体区域在 O. sativa 中包含 30 个蛋白质编码基因。其中有五个基因的DNA序列与O. meridionalis的SDV2基因的染色体区域一致,SDV2基因位于4号染色体上,而不在6号染色体上。这些结果表明,这五个基因可能是 SDV1 的候选基因,而它们位于 O. meridionalis 第 4 号染色体上的同源基因可能是 SDV2 的候选基因。
{"title":"Seed abortion caused by the combination of two duplicate genes in the progeny from the cross between <i>Oryza sativa</i> and <i>Oryza meridionalis</i>.","authors":"Daiki Toyomoto, Yukika Shibata, Masato Uemura, Satoru Taura, Tadashi Sato, Robert Henry, Ryuji Ishikawa, Katsuyuki Ichitani","doi":"10.1270/jsbbs.23084","DOIUrl":"10.1270/jsbbs.23084","url":null,"abstract":"<p><p>Seed development is an essential phenomenon for all sexual propagative plant species. The functional allele at <i>SEED DEVELOPMENT 1</i> (<i>SDV1</i>) or <i>SEED DEVELOPMENT 2</i> (<i>SDV2</i>) loci is essential for seed development for <i>Oryza sativa</i> and <i>Oryza meridionalis</i>. In the present study, we performed fine mapping of <i>SDV1</i>, narrowing down the area of interest to 333kb on chromosome 6. Haplotype analysis around the <i>SDV1</i> locus of <i>O. meridionalis</i> accessions indicated that they shared the DNA polymorphism, suggesting that they have a common abortive allele at the <i>SDV1</i> locus. Linkage analysis of the candidate <i>SDV2</i> gene showed that it was located on chromosome 4. The candidate <i>SDV2</i> was confirmed using a population in which both the <i>SDV1</i> and <i>SDV2</i> genes were segregating. The chromosomal region covering the <i>SDV1</i> gene was predicted to contain 30 protein-coding genes in <i>O. sativa</i>. Five of these genes have conserved DNA sequences in the chromosomal region of the <i>SDV2</i> gene on chromosome 4, and not on chromosome 6, of <i>O. meridionalis</i>. These results suggest that these five genes could be candidates for <i>SDV1</i>, and that their orthologous genes located on chromosome 4 of <i>O. meridionalis</i> could be candidates for <i>SDV2</i>.</p>","PeriodicalId":9258,"journal":{"name":"Breeding Science","volume":"74 2","pages":"146-158"},"PeriodicalIF":2.0,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11442109/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142361098","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}
In mechanically harvested soybean, green stem disorder (GSD) is an undesirable trait that causes green-stained seeds, which are graded lower in Japan. To obtain DNA markers for reduced GSD, we conducted a quantitative trait locus (QTL) analysis for 2 years using F4 and F5 lines from a cross between 'Suzuotome' (less GSD) and 'Fukuyutaka' (more GSD). We validated the effect of a detected QTL for GSD by first identifying F4 or F5 plants in which one or more markers in the QTL region were heterozygous. The F5 or F6 progeny of each plant was used to form a pair consisting of two groups in which the QTL region was homozygous for either the 'Suzuotome' or 'Fukuyutaka' allele in a similar genetic background, and the two groups within each pair were compared for GSD. Over 3 years of testing, the 'Suzuotome' allele of a QTL on chromosome 6 was found to reduce the level of GSD. This novel QTL was mapped to the region around DNA marker W06_0130, and was not closely linked to QTLs for important agronomic traits including yield components. Using this marker, the low level of GSD from 'Suzuotome' could be conferred to 'Fukuyutaka' or other high-GSD cultivars.
{"title":"Detection and validation of QTLs for green stem disorder of soybean (<i>Glycine max</i> (L.) Merr.).","authors":"Daisuke Ogata, Fumio Taguchi-Shiobara, Osamu Uchikawa, Masayuki Miyazaki, Yushi Ishibashi","doi":"10.1270/jsbbs.23042","DOIUrl":"10.1270/jsbbs.23042","url":null,"abstract":"<p><p>In mechanically harvested soybean, green stem disorder (GSD) is an undesirable trait that causes green-stained seeds, which are graded lower in Japan. To obtain DNA markers for reduced GSD, we conducted a quantitative trait locus (QTL) analysis for 2 years using F<sub>4</sub> and F<sub>5</sub> lines from a cross between 'Suzuotome' (less GSD) and 'Fukuyutaka' (more GSD). We validated the effect of a detected QTL for GSD by first identifying F<sub>4</sub> or F<sub>5</sub> plants in which one or more markers in the QTL region were heterozygous. The F<sub>5</sub> or F<sub>6</sub> progeny of each plant was used to form a pair consisting of two groups in which the QTL region was homozygous for either the 'Suzuotome' or 'Fukuyutaka' allele in a similar genetic background, and the two groups within each pair were compared for GSD. Over 3 years of testing, the 'Suzuotome' allele of a QTL on chromosome 6 was found to reduce the level of GSD. This novel QTL was mapped to the region around DNA marker W06_0130, and was not closely linked to QTLs for important agronomic traits including yield components. Using this marker, the low level of GSD from 'Suzuotome' could be conferred to 'Fukuyutaka' or other high-GSD cultivars.</p>","PeriodicalId":9258,"journal":{"name":"Breeding Science","volume":"74 2","pages":"138-145"},"PeriodicalIF":2.0,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11442105/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142361091","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}
Pub Date : 2024-04-01Epub Date: 2024-03-22DOI: 10.1270/jsbbs.23053
Miho Ito, Honami Ohashi, Masahiro Takemoto, Chiaki Muto, Takashi Seiko, Yusaku Noda, Eri Ogiso-Tanaka, Atsushi J Nagano, Yu Takahashi, Jun Furukawa, Yuki Monden, Ken Naito
Salt tolerance has been an important issue as a solution for soil salinization and groundwater depletion. To challenge this issue, genetic diversity of wild plants must be harnessed. Here we report a discovery of a candidate gene for salt tolerance in Vigna nakashimae, one of the coastal species in the genus Vigna. Using intraspecific variation, we performed a forward genetic analysis and identified a strong QTL region harboring ~200 genes. To further narrow down the candidate genes, we performed a comparative transcriptome analysis, using the genome sequence of azuki bean (V. angularis) as a reference. However the detected differentially-expressed genes (DEGs) did not include those related to salt tolerance. As we suspected that the target gene in V. nakashimae is missing in V. angularis, we sequenced the whole genome sequence of V. nakashimae with long-reads. By re-analyzing the transcriptome data with the new reference genome, we successfully identified POCO1 as a candidate gene, which was missing not only in V. angularis but also in the salt-sensitive accession of V. nakashimae. Further comparative analysis revealed that the tolerant genotypes conserved the ancestral form of the locus, while the sensitive genotypes did not. We also emphasize the pitfalls in our study, such as position effect in a growth chamber, missing important genes in the reference genome, and limited reproducibility of RNA-seq experiments.
耐盐性是解决土壤盐碱化和地下水枯竭的一个重要问题。要解决这一问题,必须利用野生植物的遗传多样性。在此,我们报告了在木樨属沿海物种之一的中岛木樨(Vigna nakashimae)中发现的一个耐盐候选基因。利用种内变异,我们进行了正向遗传分析,发现了一个包含约 200 个基因的强 QTL 区域。为了进一步缩小候选基因的范围,我们以红豆(V. angularis)的基因组序列为参考,进行了转录组比较分析。然而,检测到的差异表达基因(DEG)并不包括与耐盐性相关的基因。由于我们怀疑中山菜豆中的目标基因在角豆中缺失,我们对中山菜豆的全基因组序列进行了长读数测序。通过用新的参考基因组重新分析转录组数据,我们成功地发现 POCO1 是一个候选基因,它不仅在 V. angularis 中缺失,而且在盐敏感的 V. nakashimae 中也缺失。进一步的比较分析表明,耐盐基因型保留了该基因座的祖先形式,而敏感基因型则没有。我们还强调了我们研究中的缺陷,如生长室中的位置效应、参考基因组中重要基因的缺失以及 RNA-seq 实验的可重复性有限。
{"title":"Single candidate gene for salt tolerance of <i>Vigna nakashimae</i> (Ohwi) Ohwi & Ohashi identified by QTL mapping, whole genome sequencing and triplicated RNA-seq analyses.","authors":"Miho Ito, Honami Ohashi, Masahiro Takemoto, Chiaki Muto, Takashi Seiko, Yusaku Noda, Eri Ogiso-Tanaka, Atsushi J Nagano, Yu Takahashi, Jun Furukawa, Yuki Monden, Ken Naito","doi":"10.1270/jsbbs.23053","DOIUrl":"10.1270/jsbbs.23053","url":null,"abstract":"<p><p>Salt tolerance has been an important issue as a solution for soil salinization and groundwater depletion. To challenge this issue, genetic diversity of wild plants must be harnessed. Here we report a discovery of a candidate gene for salt tolerance in <i>Vigna nakashimae</i>, one of the coastal species in the genus <i>Vigna</i>. Using intraspecific variation, we performed a forward genetic analysis and identified a strong QTL region harboring ~200 genes. To further narrow down the candidate genes, we performed a comparative transcriptome analysis, using the genome sequence of azuki bean (<i>V. angularis</i>) as a reference. However the detected differentially-expressed genes (DEGs) did not include those related to salt tolerance. As we suspected that the target gene in <i>V. nakashimae</i> is missing in <i>V. angularis</i>, we sequenced the whole genome sequence of <i>V. nakashimae</i> with long-reads. By re-analyzing the transcriptome data with the new reference genome, we successfully identified <i>POCO1</i> as a candidate gene, which was missing not only in <i>V. angularis</i> but also in the salt-sensitive accession of <i>V. nakashimae</i>. Further comparative analysis revealed that the tolerant genotypes conserved the ancestral form of the locus, while the sensitive genotypes did not. We also emphasize the pitfalls in our study, such as position effect in a growth chamber, missing important genes in the reference genome, and limited reproducibility of RNA-seq experiments.</p>","PeriodicalId":9258,"journal":{"name":"Breeding Science","volume":"74 2","pages":"93-102"},"PeriodicalIF":2.0,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11442111/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142361116","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}
DNA markers serve as essential tools in breeding selection and genetic analysis. However, developing DNA markers can be time-consuming and labor-intensive due to the need to identify polymorphisms between cultivars/lines and to design suitable primers. To address these challenges, we have developed DNAMarkMaker, a tool designed to automate the process of primer design for Amplification Refractory Mutation System (ARMS) and Cleaved Amplified Polymorphic Sequences (CAPS) markers, utilizing resequencing data. One key feature of DNAMarkMaker is its user-friendly graphical user interface (GUI), ensuring its accessibility and ease of use, even for researchers not well-versed in bioinformatics. We confirmed DNAMarkMaker's applicability by developing DNA markers for rice, potato, and turnip-each representing distinct genome structures: homozygous diploid, heterozygous autotetraploid, and heterozygous diploid, respectively. DNAMarkMaker will contribute to the rapid and efficient development of DNA markers, accelerating breeding and genetic analysis in various crops.
DNA 标记是育种选育和遗传分析的重要工具。然而,由于需要识别不同栽培品种/品系之间的多态性并设计合适的引物,DNA 标记的开发耗时耗力。为了应对这些挑战,我们开发了 DNAMarkMaker,这是一种利用重测序数据为难扩增突变系统(ARMS)和裂解扩增多态性序列(CAPS)标记自动设计引物的工具。DNAMarkMaker 的一个主要特点是其友好的图形用户界面 (GUI),确保即使是不精通生物信息学的研究人员也能轻松使用。我们为水稻、马铃薯和萝卜开发了DNA标记,证实了DNAMarkMaker的适用性,这些标记分别代表不同的基因组结构:同卵二倍体、异卵自四倍体和异卵二倍体。DNAMarkMaker 将有助于快速高效地开发 DNA 标记,加速各种作物的育种和遗传分析。
{"title":"DNAMarkMaker: streamlining ARMS and CAPS marker development from resequencing data with NGS short reads.","authors":"Tenta Segawa, Sorachi Saiga, Marina Takata, Riki Kumazawa, Makishi Hara, Hiromoto Yamakawa, Hiroki Takagi","doi":"10.1270/jsbbs.23048","DOIUrl":"10.1270/jsbbs.23048","url":null,"abstract":"<p><p>DNA markers serve as essential tools in breeding selection and genetic analysis. However, developing DNA markers can be time-consuming and labor-intensive due to the need to identify polymorphisms between cultivars/lines and to design suitable primers. To address these challenges, we have developed DNAMarkMaker, a tool designed to automate the process of primer design for Amplification Refractory Mutation System (ARMS) and Cleaved Amplified Polymorphic Sequences (CAPS) markers, utilizing resequencing data. One key feature of DNAMarkMaker is its user-friendly graphical user interface (GUI), ensuring its accessibility and ease of use, even for researchers not well-versed in bioinformatics. We confirmed DNAMarkMaker's applicability by developing DNA markers for rice, potato, and turnip-each representing distinct genome structures: homozygous diploid, heterozygous autotetraploid, and heterozygous diploid, respectively. DNAMarkMaker will contribute to the rapid and efficient development of DNA markers, accelerating breeding and genetic analysis in various crops.</p>","PeriodicalId":9258,"journal":{"name":"Breeding Science","volume":"74 2","pages":"73-82"},"PeriodicalIF":2.0,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11442104/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142361093","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}
Flowering time is an important agronomic trait that is highly correlated with plant height, maturity time and yield in mungbean. Up to present, however, molecular basis of flowering time in mungbean is poorly understood. Previous studies demonstrated that flowering time in mungbean is largely controlled by a major QTL on linkage group 2 (LG2). In this study, the QTL on the LG2 in mungbean was investigated using F2 and F2:3 populations derived from a cross between mungbean cultivar Kamphaeng Saen 2 (KPS2) and wild mungbean accession ACC41. The QTL was narrowed down to a genome region of 164.87 Kb containing a phytochrome gene, designated VrPHYE, encoding phytochrome E (phyE), a known photoreceptor modulating flowering time. Compared to VrPHYE of the wild ACC41, VrPHYE of KPS2 contained several single nucleotide polymorphisms (SNPs) causing amino acid changes. Those SNPs were also found in other mungbean cultivars. Some amino acid changes were predicted to occur in the regulatory region of phytochromes. Gene expression analysis revealed that VrPHYE in KPS2 was expressed significantly higher than that in ACC41. These results showed that VrPHYE is the candidate gene controlling flowering time in the mungbean.
{"title":"Narrowing down a major QTL region reveals <i>Phytochrome E</i> (<i>PHYE</i>) as the candidate gene controlling flowering time in mungbean (<i>Vigna radiata</i>).","authors":"Kitiya Amkul, Kularb Laosatit, Yun Lin, Tarika Yimram, Jingbin Chen, Xingxing Yuan, Xin Chen, Prakit Somta","doi":"10.1270/jsbbs.23036","DOIUrl":"10.1270/jsbbs.23036","url":null,"abstract":"<p><p>Flowering time is an important agronomic trait that is highly correlated with plant height, maturity time and yield in mungbean. Up to present, however, molecular basis of flowering time in mungbean is poorly understood. Previous studies demonstrated that flowering time in mungbean is largely controlled by a major QTL on linkage group 2 (LG2). In this study, the QTL on the LG2 in mungbean was investigated using F<sub>2</sub> and F<sub>2:3</sub> populations derived from a cross between mungbean cultivar Kamphaeng Saen 2 (KPS2) and wild mungbean accession ACC41. The QTL was narrowed down to a genome region of 164.87 Kb containing a phytochrome gene, designated <i>VrPHYE</i>, encoding phytochrome E (phyE), a known photoreceptor modulating flowering time. Compared to <i>VrPHYE</i> of the wild ACC41, <i>VrPHYE</i> of KPS2 contained several single nucleotide polymorphisms (SNPs) causing amino acid changes. Those SNPs were also found in other mungbean cultivars. Some amino acid changes were predicted to occur in the regulatory region of phytochromes. Gene expression analysis revealed that <i>VrPHYE</i> in KPS2 was expressed significantly higher than that in ACC41. These results showed that <i>VrPHYE</i> is the candidate gene controlling flowering time in the mungbean.</p>","PeriodicalId":9258,"journal":{"name":"Breeding Science","volume":"74 2","pages":"83-92"},"PeriodicalIF":2.0,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11442112/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142361096","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}
Pub Date : 2024-04-01Epub Date: 2024-03-08DOI: 10.1270/jsbbs.23040
Kei Matsushita, Akio Onogi, Jun-Ichi Yonemaru
Data from breeding, including phenotypic information, may improve the efficiency of breeding. Historical data from breeding trials accumulated over a long time are also useful. Here, by organizing data accumulated in the National Agriculture and Food Research Organization (NARO) rice breeding program, we developed a historical phenotype dataset, which includes 6052 records obtained for 667 varieties in yield trials in 1991-2018 at six NARO research stations. The best linear unbiased predictions (BLUPs) and principal component analysis (PCA) were used to determine the relationships with various factors, including the year of cultivar release, for 15 traits, including yield. Yield-related traits such as the number of grains per panicle, plant weight, grain yield, and thousand-grain weight increased significantly with time, whereas the number of panicles decreased significantly. Ripening time significantly increased, whereas the lodging degree and protein content of brown rice significantly decreased. These results suggest that panicle-weight-type high-yielding varieties with excellent lodging resistance have been selected. These trends differed slightly among breeding locations, indicating that the main breeding objectives may differ among them. PCA revealed a higher diversity of traits in newer varieties.
{"title":"NARO historical phenotype dataset from rice breeding.","authors":"Kei Matsushita, Akio Onogi, Jun-Ichi Yonemaru","doi":"10.1270/jsbbs.23040","DOIUrl":"10.1270/jsbbs.23040","url":null,"abstract":"<p><p>Data from breeding, including phenotypic information, may improve the efficiency of breeding. Historical data from breeding trials accumulated over a long time are also useful. Here, by organizing data accumulated in the National Agriculture and Food Research Organization (NARO) rice breeding program, we developed a historical phenotype dataset, which includes 6052 records obtained for 667 varieties in yield trials in 1991-2018 at six NARO research stations. The best linear unbiased predictions (BLUPs) and principal component analysis (PCA) were used to determine the relationships with various factors, including the year of cultivar release, for 15 traits, including yield. Yield-related traits such as the number of grains per panicle, plant weight, grain yield, and thousand-grain weight increased significantly with time, whereas the number of panicles decreased significantly. Ripening time significantly increased, whereas the lodging degree and protein content of brown rice significantly decreased. These results suggest that panicle-weight-type high-yielding varieties with excellent lodging resistance have been selected. These trends differed slightly among breeding locations, indicating that the main breeding objectives may differ among them. PCA revealed a higher diversity of traits in newer varieties.</p>","PeriodicalId":9258,"journal":{"name":"Breeding Science","volume":"74 2","pages":"114-123"},"PeriodicalIF":2.0,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11442108/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142361095","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}
Pub Date : 2024-04-01Epub Date: 2024-03-22DOI: 10.1270/jsbbs.23077
Tomoyuki Furuta, Ohm Mar Saw, Sandar Moe, Khin Thanda Win, Moe Moe Hlaing, Aye Lae Lae Hlaing, Min San Thein, Hideshi Yasui, Motoyuki Ashikari, Atsushi Yoshimura, Yoshiyuki Yamagata
To counteract the growing population and climate changes, resilient varieties adapted to regional environmental changes are required. Landraces are valuable genetic resources for achieving this goal. Recent advances in sequencing technology have enabled national seed/gene banks to share genomic and genetic information from their collections including landraces, promoting the more efficient utilization of germplasms. In this study, we developed genomic and genetic resources for Myanmar rice germplasms. First, we assembled a diversity panel consisting of 250 accessions representing the genetic diversity of Myanmar indica varieties, including an elite lowland variety, Inn Ma Yebaw (IMY). Our population genetic analyses illustrated that the diversity panel represented Myanmar indica varieties well without any apparent population structure. Second, de novo genome assembly of IMY was conducted. The IMY assembly was constructed by anchoring 2888 contigs, which were assembled from 30× coverage of long reads, into 12 chromosomes. Although many gaps existed in the IMY genome assembly, our quality assessments indicated high completeness in the gene-coding regions, identical to other near-gap-free assemblies. Together with dense variant information, the diversity panel and IMY genome assembly will facilitate deeper genetic research and breeding projects that utilize the untapped Myanmar rice germplasms.
为了应对不断增长的人口和气候变化,需要有适应地区环境变化的抗逆性强的品种。陆地品种是实现这一目标的宝贵遗传资源。测序技术的最新进展使国家种子/基因库能够共享其收藏的基因组和遗传信息,包括陆地品系,从而促进更有效地利用种质资源。在这项研究中,我们开发了缅甸水稻种质的基因组和遗传资源。首先,我们建立了一个由 250 个代表缅甸籼稻品种(包括低地精英品种 Inn Ma Yebaw (IMY))遗传多样性的参试品种组成的多样性面板。我们的群体遗传分析表明,该多样性小组很好地代表了缅甸籼稻品种,没有任何明显的群体结构。其次,对 IMY 进行了全新基因组组装。IMY 的基因组组装是通过将 30× 覆盖率的长读数组装成的 2888 个等位基因锚定在 12 条染色体上而构建的。尽管 IMY 基因组组装存在许多空白,但我们的质量评估表明基因编码区的完整性很高,与其他接近无空白的组装结果相同。多样性面板和 IMY 基因组组装与密集的变异信息相结合,将有助于利用尚未开发的缅甸水稻种质资源开展更深入的遗传研究和育种项目。
{"title":"Development of genomic and genetic resources facilitating molecular genetic studies on untapped Myanmar rice germplasms.","authors":"Tomoyuki Furuta, Ohm Mar Saw, Sandar Moe, Khin Thanda Win, Moe Moe Hlaing, Aye Lae Lae Hlaing, Min San Thein, Hideshi Yasui, Motoyuki Ashikari, Atsushi Yoshimura, Yoshiyuki Yamagata","doi":"10.1270/jsbbs.23077","DOIUrl":"10.1270/jsbbs.23077","url":null,"abstract":"<p><p>To counteract the growing population and climate changes, resilient varieties adapted to regional environmental changes are required. Landraces are valuable genetic resources for achieving this goal. Recent advances in sequencing technology have enabled national seed/gene banks to share genomic and genetic information from their collections including landraces, promoting the more efficient utilization of germplasms. In this study, we developed genomic and genetic resources for Myanmar rice germplasms. First, we assembled a diversity panel consisting of 250 accessions representing the genetic diversity of Myanmar <i>indica</i> varieties, including an elite lowland variety, Inn Ma Yebaw (IMY). Our population genetic analyses illustrated that the diversity panel represented Myanmar <i>indica</i> varieties well without any apparent population structure. Second, de novo genome assembly of IMY was conducted. The IMY assembly was constructed by anchoring 2888 contigs, which were assembled from 30× coverage of long reads, into 12 chromosomes. Although many gaps existed in the IMY genome assembly, our quality assessments indicated high completeness in the gene-coding regions, identical to other near-gap-free assemblies. Together with dense variant information, the diversity panel and IMY genome assembly will facilitate deeper genetic research and breeding projects that utilize the untapped Myanmar rice germplasms.</p>","PeriodicalId":9258,"journal":{"name":"Breeding Science","volume":"74 2","pages":"124-137"},"PeriodicalIF":2.0,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11442107/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142361092","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}
Pub Date : 2024-04-01Epub Date: 2024-03-22DOI: 10.1270/jsbbs.23087
Tomohito Ikegaya
Starch properties are the major determinants of grain quality and food characteristics in rice (Oryza sativa L.). Understanding the interactions between genetic regions responsible for starch properties will lead to the development of rice cultivars with desirable characteristics. This study investigated the genetic effect and interaction between qAC9.3, a low-amylose quantitative trait locus (QTL), and the genetic region around Starch branching enzyme IIb (SbeIIb). Both these factors are responsible for the starch properties of the Hokkaido breeding population. The amylose content, pasting temperature, and amylopectin chain-length distribution were compared using F5 lines derived from the cross between the lower amylose content and lower pasting temperature strain 'Hokkai332 (qAC9.3, SbeIIb)' and the higher amylose content and higher pasting temperature variety 'Kitagenki (-, SbeIIbsr )'. The qAC9.3 genotype exhibited low amylose content and reduced the hardness of boiled rice but increased the ratio of amylopectin long chains and did not alter the pasting temperature. In contrast, the SbeIIb genotype was associated with pasting temperature but did not affect the amylose content and hardness of boiled rice. It was suggested that appropriately selecting genotypes of these genetic regions and QTL would allow the fine-tuning of starch properties of cooked rice suitable for future demand.
{"title":"Interaction between genetic regions responsible for the starch properties in non-glutinous rice varieties in Hokkaido, Japan.","authors":"Tomohito Ikegaya","doi":"10.1270/jsbbs.23087","DOIUrl":"10.1270/jsbbs.23087","url":null,"abstract":"<p><p>Starch properties are the major determinants of grain quality and food characteristics in rice (<i>Oryza sativa</i> L.). Understanding the interactions between genetic regions responsible for starch properties will lead to the development of rice cultivars with desirable characteristics. This study investigated the genetic effect and interaction between <i>qAC9.3</i>, a low-amylose quantitative trait locus (QTL), and the genetic region around <i>Starch branching enzyme IIb</i> (<i>SbeIIb</i>). Both these factors are responsible for the starch properties of the Hokkaido breeding population. The amylose content, pasting temperature, and amylopectin chain-length distribution were compared using F<sub>5</sub> lines derived from the cross between the lower amylose content and lower pasting temperature strain 'Hokkai332 (<i>qAC9.3</i>, <i>SbeIIb</i>)' and the higher amylose content and higher pasting temperature variety 'Kitagenki (-, <i>SbeIIb<sup>sr</sup></i> )'. The <i>qAC9.3</i> genotype exhibited low amylose content and reduced the hardness of boiled rice but increased the ratio of amylopectin long chains and did not alter the pasting temperature. In contrast, the <i>SbeIIb</i> genotype was associated with pasting temperature but did not affect the amylose content and hardness of boiled rice. It was suggested that appropriately selecting genotypes of these genetic regions and QTL would allow the fine-tuning of starch properties of cooked rice suitable for future demand.</p>","PeriodicalId":9258,"journal":{"name":"Breeding Science","volume":"74 2","pages":"159-165"},"PeriodicalIF":2.0,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11442103/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142361094","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}
Sweetpotato (Ipomoea batatas) includes diverse cultivars with flesh textures ranging from dry to moist. Moist-fleshed cultivars often contain starch with a lower gelatinization temperature (GT). To elucidate the genetic determinants of flesh texture and starch GT, we conducted a QTL analysis using F1 progenies obtained from a cross between dry-fleshed and moist-fleshed cultivars, 'Benikomachi' (BK) and 'Amahazuki' (AH), by using an updated polyploid QTL-seq pipeline. Flesh texture was assessed based on the wet area ratio (WAR) observed on the cut surface of steamed tubers, as progenies with dry and moist flesh exhibited low and high WAR values, respectively, demonstrating a strong correlation. Three QTLs were found to regulate the WAR. Notably, two AH-derived alleles at 4.30 Mb on Itr_chr05 and 21.01 Mb on Itr_chr07, along with a BK-derived allele at 2.89 Mb on Itr_chr15, were associated with increased WAR. Starch GT, which displayed no correlation with either flesh texture or WAR, was distinctly influenced by two QTLs: a GT-increasing BK-derived allele at 1.74 Mb on Itr_chr05 and a GT-decreasing AH-derived allele at 30.16 Mb on Itr_chr12. Consequently, we developed DNA markers linked to WAR, offering a promising avenue for the targeted breeding of sweetpotato with the desired flesh textures.
甘薯(Ipomoea batatas)包括多种栽培品种,其果肉质地从干燥到湿润不等。湿肉栽培品种通常含有糊化温度(GT)较低的淀粉。为了阐明果肉质地和淀粉GT的遗传决定因素,我们利用干肉栽培品种'Benikomachi'(BK)和湿肉栽培品种'Amahazuki'(AH)杂交得到的F1后代,使用更新的多倍体QTL-seq管道进行了QTL分析。果肉质地是根据蒸熟块茎切面上观察到的湿面积比(WAR)来评估的,因为干果肉和湿果肉的后代分别表现出低和高的 WAR 值,显示出很强的相关性。研究发现,有三个 QTLs 可调控 WAR。值得注意的是,Itr_chr05 上 4.30 Mb 和 Itr_chr07 上 21.01 Mb 处的两个 AH 衍生等位基因以及 Itr_chr15 上 2.89 Mb 处的一个 BK 衍生等位基因与 WAR 值的增加有关。淀粉GT与果肉质地或WAR都没有相关性,但它明显受到两个QTL的影响:Itr_chr05上1.74 Mb处的一个GT增加的BK衍生等位基因和Itr_chr12上30.16 Mb处的一个GT减少的AH衍生等位基因。因此,我们开发出了与 WAR 相关联的 DNA 标记,为定向培育具有理想肉质的甘薯提供了一条很有前景的途径。
{"title":"Polyploid QTL-seq revealed multiple QTLs controlling steamed tuber texture and starch gelatinization temperature in sweetpotato.","authors":"Hiromoto Yamakawa, Tatsumi Mizubayashi, Masaru Tanaka","doi":"10.1270/jsbbs.23060","DOIUrl":"10.1270/jsbbs.23060","url":null,"abstract":"<p><p>Sweetpotato (<i>Ipomoea batatas</i>) includes diverse cultivars with flesh textures ranging from dry to moist. Moist-fleshed cultivars often contain starch with a lower gelatinization temperature (GT). To elucidate the genetic determinants of flesh texture and starch GT, we conducted a QTL analysis using F<sub>1</sub> progenies obtained from a cross between dry-fleshed and moist-fleshed cultivars, 'Benikomachi' (BK) and 'Amahazuki' (AH), by using an updated polyploid QTL-seq pipeline. Flesh texture was assessed based on the wet area ratio (WAR) observed on the cut surface of steamed tubers, as progenies with dry and moist flesh exhibited low and high WAR values, respectively, demonstrating a strong correlation. Three QTLs were found to regulate the WAR. Notably, two AH-derived alleles at 4.30 Mb on Itr_chr05 and 21.01 Mb on Itr_chr07, along with a BK-derived allele at 2.89 Mb on Itr_chr15, were associated with increased WAR. Starch GT, which displayed no correlation with either flesh texture or WAR, was distinctly influenced by two QTLs: a GT-increasing BK-derived allele at 1.74 Mb on Itr_chr05 and a GT-decreasing AH-derived allele at 30.16 Mb on Itr_chr12. Consequently, we developed DNA markers linked to WAR, offering a promising avenue for the targeted breeding of sweetpotato with the desired flesh textures.</p>","PeriodicalId":9258,"journal":{"name":"Breeding Science","volume":"74 2","pages":"103-113"},"PeriodicalIF":2.0,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11442106/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142361097","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}