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Khan A, Ahmad M, Shani MY, Khan MKR, Rahimi M, Tan DKY. Identifying the physiological traits associated with DNA marker using genome wide association in wheat under heat stress. Sci Rep 2024; 14:20134. [PMID: 39209932 PMCID: PMC11362520 DOI: 10.1038/s41598-024-70630-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024] Open
Abstract
Heat stress poses a significant environmental challenge that profoundly impacts wheat productivity. It disrupts vital physiological processes such as photosynthesis, by impeding the functionality of the photosynthetic apparatus and compromising plasma membrane stability, thereby detrimentally affecting grain development in wheat. The scarcity of identified marker trait associations pertinent to thermotolerance presents a formidable obstacle in the development of marker-assisted selection strategies against heat stress. To address this, wheat accessions were systematically exposed to both normal and heat stress conditions and phenotypic data were collected on physiological traits including proline content, canopy temperature depression, cell membrane injury, photosynthetic rate, transpiration rate (at vegetative and reproductive stage and 'stay-green'. Principal component analysis elucidated the most significant contributors being proline content, transpiration rate, and canopy temperature depression, which exhibited a synergistic relationship with grain yield. Remarkably, cluster analysis delineated the wheat accessions into four discrete groups based on physiological attributes. Moreover, to explore the relationship between physiological traits and DNA markers, 158 wheat accessions were genotyped with 186 SSRs. Allelic frequency and polymorphic information content value were found to be highest on genome A (4.94 and 0.688), chromosome 1A (5.00 and 0.712), and marker Xgwm44 (13.0 and 0.916). Population structure, principal coordinate analysis and cluster analysis also partitioned the wheat accessions into four subpopulations based on genotypic data, highlighting their genetic homogeneity. Population diversity and presence of linkage disequilibrium established the suitability of population for association mapping. Additionally, linkage disequilibrium decay was most pronounced within a 15-20 cM region on chromosome 1A. Association mapping revealed highly significant marker trait associations at Bonferroni correction P < 0.00027. Markers Xwmc418 (located on chromosome 3D) and Xgwm233 (chromosome 7A) demonstrated associations with transpiration rate, while marker Xgwm494 (chromosome 3A) exhibited an association with photosynthetic rates at both vegetative and reproductive stages under heat stress conditions. Additionally, markers Xwmc201 (chromosome 6A) and Xcfa2129 (chromosome 1A) displayed robust associations with canopy temperature depression, while markers Xbarc163 (chromosome 4B) and Xbarc49 (chromosome 5A) were strongly associated with cell membrane injury at both stages. Notably, marker Xbarc49 (chromosome 5A) exhibited a significant association with the 'stay-green' trait under heat stress conditions. These results offers the potential utility in marker-assisted selection, gene pyramiding and genomic selection models to predict performance of wheat accession under heat stress conditions.
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Affiliation(s)
- Adeel Khan
- Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad, 38950, Pakistan.
- Pakistan Institute of Engineering and Applied Sciences, Islamabad, Pakistan.
- Department of Plant Breeding and Genetics, PMAS-Arid Agriculture University, Rawalpindi, 46300, Pakistan.
| | - Munir Ahmad
- Department of Plant Breeding and Genetics, PMAS-Arid Agriculture University, Rawalpindi, 46300, Pakistan
| | - Muhammad Yousaf Shani
- Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad, 38950, Pakistan
- Pakistan Institute of Engineering and Applied Sciences, Islamabad, Pakistan
| | - Muhammad Kashif Riaz Khan
- Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad, 38950, Pakistan
- Pakistan Institute of Engineering and Applied Sciences, Islamabad, Pakistan
| | - Mehdi Rahimi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran.
| | - Daniel K Y Tan
- Plant Breeding Institute, Sydney Institute of Agriculture, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
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Mizuno N, Matsunaka H, Yanaka M, Ishikawa G, Kobayashi F, Nakamura K. Natural variations of wheat EARLY FLOWERING 3 highlight their contributions to local adaptation through fine-tuning of heading time. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:139. [PMID: 37233781 DOI: 10.1007/s00122-023-04386-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 05/12/2023] [Indexed: 05/27/2023]
Abstract
KEY MESSAGE We identified a large chromosomal deletion containing TaELF-B3 that confers early flowering in wheat. This allele has been preferred in recent wheat breeding in Japan to adapt to the environment. Heading at the appropriate time in each cultivation region can greatly contribute to stabilizing and maximizing yield. Vrn-1 and Ppd-1 are known as the major genes for vernalization requirement and photoperiod sensitivity in wheat. Genotype combinations of Vrn-1 and Ppd-1 can explain the variation in heading time. However, the genes that can explain the remaining variations in heading time are largely unknown. In this study, we aimed to identify the genes conferring early heading using doubled haploid lines derived from Japanese wheat varieties. Quantitative trait locus (QTL) analysis revealed a significant QTL on the long arm of chromosome 1B in multiple growing seasons. Genome sequencing using Illumina short reads and Pacbio HiFi reads revealed a large deletion of a ~ 500 kb region containing TaELF-B3, an orthologue of Arabidopsis clock gene EARLY FLOWERING 3 (ELF3). Plants with the deleted allele of TaELF-B3 (ΔTaELF-B3 allele) headed earlier only under short-day vernalization conditions. Higher expression levels of clock- and clock-output genes, such as Ppd-1 and TaGI, were observed in plants with the ΔTaELF-B3 allele. These results suggest that the deletion of TaELF-B3 causes early heading. Of the TaELF-3 homoeoalleles conferring early heading, the ΔTaELF-B3 allele showed the greatest effect on the early heading phenotype in Japan. The higher allele frequency of the ΔTaELF-B3 allele in western Japan suggests that the ΔTaELF-B3 allele was preferred during recent breeding to adapt to the environment. TaELF-3 homoeologs will help to expand the cultivated area by fine-tuning the optimal timing of heading in each environment.
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Affiliation(s)
- Nobuyuki Mizuno
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan.
| | - Hitoshi Matsunaka
- Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, 496 Izumi, Chikugo, Fukuoka, 833-0041, Japan
- Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization, 9-4 Shinsei-Minami, Memuro, Kasai, Hokkaido, 082-0081, Japan
| | - Mikiko Yanaka
- Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, 496 Izumi, Chikugo, Fukuoka, 833-0041, Japan
| | - Goro Ishikawa
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Fuminori Kobayashi
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Kazuhiro Nakamura
- Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, 496 Izumi, Chikugo, Fukuoka, 833-0041, Japan
- Headquarters, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8517, Japan
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Esmail SM, Omar GE, Mourad AMI. In-Depth Understanding of the Genetic Control of Stripe Rust Resistance ( Puccinia striiformis f. sp. tritici) Induced in Wheat ( Triticum aestivum) by Trichoderma asperellum T34. PLANT DISEASE 2023; 107:457-472. [PMID: 36449539 DOI: 10.1094/pdis-07-22-1593-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Wheat stripe rust (caused by Puccinia striiformis f. tritici Erikss.) causes severe yield losses worldwide. Due to the continuous appearance of new stripe rust races, resistance has been broken in most of the highly resistant genotypes in Egypt and worldwide. Therefore, looking for new ways to resist such a severe disease is urgently needed. Trichoderma asperellum strain T34 has been known as an effective bioagent against many crop diseases. It exists naturally in Egyptian fields. Therefore, in our study, the effectiveness of strain T34 was tested as a bioagent against wheat stripe rust. For this purpose, 198 spring wheat genotypes were tested for their resistance against two different P. striiformis f. tritici populations collected from the Egyptian fields. The most highly aggressive P. striiformis f. tritici population was used to test the effectiveness of strain T34. Highly significant differences were found between strain T34 and stripe rust, suggesting the effectiveness of strain T34 in stripe rust resistance. A genome-wide association study identified 48 gene models controlling resistance under normal conditions and 46 gene models controlling strain T34-induced resistance. Of these gene models, only one common gene model was found, suggesting the presence of two different genetic systems controlling resistance under each condition. The pathways of the biological processes were investigated under both conditions. This study provided in-depth understanding of genetic control and, hence, will accelerate the future of wheat breeding programs for stripe rust resistance.
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Affiliation(s)
- Samar M Esmail
- Wheat Disease Research Department, Plant Pathology Research Institute, Agricultural Research Center, Giza, Egypt
| | - Ghady E Omar
- Wheat Disease Research Department, Plant Pathology Research Institute, Agricultural Research Center, Giza, Egypt
| | - Amira M I Mourad
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Germany
- Department of Agronomy, Faculty of Agriculture, Assiut University, Assiut, Egypt
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Mizuno N, Matsunaka H, Yanaka M, Nakata M, Nakamura K, Nakamaru A, Kiribuchi-Otobe C, Ishikawa G, Chono M, Hatta K, Fujita M, Kobayashi F. Allelic variations of Vrn-1 and Ppd-1 genes in Japanese wheat varieties reveal the genotype-environment interaction for heading time. BREEDING SCIENCE 2022; 72:343-354. [PMID: 36776445 PMCID: PMC9895800 DOI: 10.1270/jsbbs.22017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 08/07/2022] [Indexed: 05/31/2023]
Abstract
The timing of heading is largely affected by environmental conditions. In wheat, Vrn-1 and Ppd-1 have been identified as the major genes involved in vernalization requirement and photoperiod sensitivity, respectively. To compare the effects of Vrn-1 and Ppd-1 alleles on heading time under different environments, we genotyped Vrn-1 and Ppd-1 homoeologues and measured the heading time at Morioka, Tsukuba and Chikugo in Japan for two growing seasons. A total of 128 Japanese and six foreign varieties, classified into four populations based on the 519 genome-wide SNPs, were used for analysis. Varieties with the spring alleles (Vrn-D1a or Vrn-D1b) at the Vrn-D1 locus and insensitive allele (Hapl-I) at the Ppd-D1 locus were found in earlier heading varieties. The effects of Vrn-D1 and Ppd-D1 on heading time were stronger than those of the other Vrn-1 and Ppd-1 homoeologues. Analysis of variance revealed that heading time was significantly affected by the genotype-environment interactions. Some Vrn-1 and Ppd-1 alleles conferred earlier or later heading in specific environments, indicating that the effect of both alleles on the timing of heading depends on the environment. Information on Vrn-1 and Ppd-1 alleles, together with heading time in various environments, provide useful information for wheat breeding.
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Affiliation(s)
- Nobuyuki Mizuno
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Hitoshi Matsunaka
- Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, 496 Izumi, Chikugo, Fukuoka 833-0041, Japan
- Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization, 9-4 Shinsei-minami, Memuro, Kasai, Hokkaido 082-0081, Japan
| | - Mikiko Yanaka
- Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, 496 Izumi, Chikugo, Fukuoka 833-0041, Japan
| | - Masaru Nakata
- Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, 496 Izumi, Chikugo, Fukuoka 833-0041, Japan
| | - Kazuhiro Nakamura
- Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, 496 Izumi, Chikugo, Fukuoka 833-0041, Japan
| | - Akiko Nakamaru
- Tohoku Agricultural Research Center, National Agriculture and Food Research Organization, 4 Akahira, Shimo-kuriyagawa, Morioka, Iwate 020-0198, Japan
| | - Chikako Kiribuchi-Otobe
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Goro Ishikawa
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Makiko Chono
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Koichi Hatta
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
- Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization, 9-4 Shinsei-minami, Memuro, Kasai, Hokkaido 082-0081, Japan
| | - Masaya Fujita
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Fuminori Kobayashi
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
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Sekine D, Oku S, Nunome T, Hirakawa H, Tsujimura M, Terachi T, Toyoda A, Shigyo M, Sato S, Tsukazaki H. Development of a genome-wide marker design workflow for onions and its application in target amplicon sequencing-based genotyping. DNA Res 2022; 29:6675293. [PMID: 36007888 PMCID: PMC9410872 DOI: 10.1093/dnares/dsac020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Indexed: 11/24/2022] Open
Abstract
Onions are one of the most widely cultivated vegetables worldwide; however, the development and utilization of molecular markers have been limited because of the large genome of this plant. We present a genome-wide marker design workflow for onions and its application in a high-throughput genotyping method based on target amplicon sequencing. The efficiency of the method was evaluated by genotyping of F2 populations. In the marker design workflow, unigene and genomic sequence data sets were constructed, and polymorphisms between parental lines were detected through transcriptome sequence analysis. The positions of polymorphisms detected in the unigenes were mapped onto the genome sequence, and primer sets were designed. In total, 480 markers covering the whole genome were selected. By genotyping an F2 population, 329 polymorphic sites were obtained from the estimated positions or the flanking sequences. However, missing or sparse marker regions were observed in the resulting genetic linkage map. We modified the markers to cover these regions by genotyping the other F2 populations. The grouping and order of markers on the linkages were similar across the genetic maps. Our marker design workflow and target amplicon sequencing are useful for genome-wide genotyping of onions owing to their reliability, cost effectiveness, and flexibility.
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Affiliation(s)
- Daisuke Sekine
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO) , Tsu, Mie 514-2392, Japan
| | - Satoshi Oku
- Tohoku Agricultural Research Center, NARO , Morioka, Iwate 020-0198, Japan
| | - Tsukasa Nunome
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO) , Tsu, Mie 514-2392, Japan
| | - Hideki Hirakawa
- Kazusa DNA Research Institute , Kisarazu, Chiba 292-0818, Japan
| | - Mai Tsujimura
- Department of Plant Life Science, Faculty of Agriculture, Ryukoku University , Otsu, Shiga 520-2194, Japan
- Plant Organelle Genome Research Center, Kyoto Sangyo University , Kyoto 603-8555, Japan
| | - Toru Terachi
- Plant Organelle Genome Research Center, Kyoto Sangyo University , Kyoto 603-8555, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics , Mishima, Shizuoka 411-8540, Japan
| | - Masayoshi Shigyo
- Laboratory of Vegetable Crop Science, College of Agriculture, Graduate School of Sciences and Technology for Innovation, Yamaguchi University , Yamaguchi City, Yamaguchi 753-8515, Japan
| | - Shusei Sato
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University , Sendai, Miyagi 980-8577, Japan
| | - Hikaru Tsukazaki
- Tohoku Agricultural Research Center, NARO , Morioka, Iwate 020-0198, Japan
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6
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Mourad AMI, Draz IS, Omar GE, Börner A, Esmail SM. Genome-Wide Screening of Broad-Spectrum Resistance to Leaf Rust ( Puccinia triticina Eriks) in Spring Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:921230. [PMID: 35812968 PMCID: PMC9258335 DOI: 10.3389/fpls.2022.921230] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/30/2022] [Indexed: 06/01/2023]
Abstract
Wheat leaf rust (LR) causes significant yield losses worldwide. In Egypt, resistant cultivars began to lose their efficiency in leaf rust resistance. Therefore, a diverse spring wheat panel was evaluated at the seedling stage to identify new sources of broad-spectrum seedling resistance against the Egyptian Puccinia triticina (Pt) races. In three different experiments, seedling evaluation was done using Pt spores collected from different fields and growing seasons. Highly significant differences were found among experiments confirming the presence of different races population in each experiment. Highly significant differences were found among the tested genotypes confirming the ability to select superior genotypes. Genome-wide association study (GWAS) was conducted for each experiment and a set of 87 markers located within 48 gene models were identified. The identified gene models were associated with disease resistance in wheat. Five gene models were identified to resist all Pt races in at least two experiments and could be identified as stable genes under Egyptian conditions. Ten genotypes from five different countries were stable against all the tested Pt races but showed different degrees of resistance.
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Affiliation(s)
- Amira M. I. Mourad
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- Department of Agronomy, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Ibrahim S. Draz
- Wheat Disease Research Department, Plant Pathology Research Institute, Agricultural Research Center, Giza, Egypt
| | - Ghady E. Omar
- Wheat Disease Research Department, Plant Pathology Research Institute, Agricultural Research Center, Giza, Egypt
| | - Andreas Börner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Samar M. Esmail
- Wheat Disease Research Department, Plant Pathology Research Institute, Agricultural Research Center, Giza, Egypt
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Ishikawa G, Sakai H, Mizuno N, Solovieva E, Tanaka T, Matsubara K. Developing core marker sets for effective genomic-assisted selection in wheat and barley breeding programs. BREEDING SCIENCE 2022; 72:257-266. [PMID: 36408318 PMCID: PMC9653188 DOI: 10.1270/jsbbs.22004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 04/07/2022] [Indexed: 06/16/2023]
Abstract
Wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.) are widely cultivated temperate crops. In breeding programs with these crops in Japan, effective genomic-assisted selection was performed by selecting core marker sets from thousands of genome-wide amplicon sequencing markers. The core sets consist of 768 and 960 markers for barley and wheat, respectively. These markers are distributed evenly across the genomes and effectively detect widely distributed polymorphisms in the chromosomes. The core set utility was assessed using 1,032 barley and 1,798 wheat accessions across the country. Minor allele frequency and chromosomal distributions showed that the core sets could effectively capture polymorphisms across the entire genome, indicating that the core sets are applicable to highly-related advanced breeding materials. Using the core sets, we also assessed the trait value predictability. As observed via fivefold cross-validation, the prediction accuracies of six barley traits ranged from 0.56-0.74 and 0.62 on average, and the corresponding values for eight wheat traits ranged from 0.44-0.83 and 0.65 on average. These data indicate that the established core marker sets enable breeding processes to be accelerated in a cost-effective manner and provide a strong foundation for further research on genomic selection in crops.
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Affiliation(s)
- Goro Ishikawa
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Hiroaki Sakai
- Research Center for Advanced Analysis, Core Technology Research Headquarters, National Agriculture and Food Research Organization, 3-1-1 Kannondai, Tsukuba, Ibaraki 305-8517, Japan
| | - Nobuyuki Mizuno
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Elena Solovieva
- Research Center for Advanced Analysis, Core Technology Research Headquarters, National Agriculture and Food Research Organization, 3-1-1 Kannondai, Tsukuba, Ibaraki 305-8517, Japan
| | - Tsuyoshi Tanaka
- Research Center for Advanced Analysis, Core Technology Research Headquarters, National Agriculture and Food Research Organization, 3-1-1 Kannondai, Tsukuba, Ibaraki 305-8517, Japan
| | - Kazuki Matsubara
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
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Ogiso-Tanaka E, Yabe S, Tanaka T. IonBreeders: bioinformatics plugins toward genomics-assisted breeding. BREEDING SCIENCE 2020; 70:396-401. [PMID: 32714063 PMCID: PMC7372021 DOI: 10.1270/jsbbs.19141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 01/07/2020] [Indexed: 06/11/2023]
Abstract
Polymorphism information generated by next-generation sequencing (NGS) technologies has enabled applications of genome-wide markers assisted breeding. However, handling such large-scale data remains a challenge for experimental researchers and breeders, calling for the urgent development of a flexible and straightforward analysis tool for NGS data. We developed "IonBreeders" as bioinformatics plugins that implement general analysis steps from genotyping to genomic prediction. IonBreeders comprises three plugins, "ABH", "IMPUTATION", and "GENOMIC PREDICTION", for format conversion of genotyping data, preprocessing and imputation of genotyping data, and genomic prediction, respectively. "ABH" converts genotyping data derived from NGS into the ABH format, which is acceptable for our further plugins and with other breeding software tools, R/qtl, MapMaker, and AntMap. "IMPUTATION" filters out non-informative markers and imputes missing marker genotypes. In "GENOMIC PREDICTION", users can use four statistical methods based on their target trait, quantitative trait locus effect, and number of markers, and construct a prediction model for genomic selection. IonBreeders is operated in Torrent Suite, but can also handle genotype data in standard formats, e.g., Variant Call Format (VCF), by format conversion using free software or our provided scripts.
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Affiliation(s)
- Eri Ogiso-Tanaka
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Shiori Yabe
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Tsuyoshi Tanaka
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
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9
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Ban Y, Ishikawa G, Ueda H, Ishikawa N, Kato K, Takata K, Matsuyama M, Handa H, Nakamura T, Yanaka M. Novel quantitative trait loci for low grain cadmium concentration in common wheat ( Triticum aestivum L.). BREEDING SCIENCE 2020; 70:331-341. [PMID: 32714055 PMCID: PMC7372025 DOI: 10.1270/jsbbs.19150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 01/07/2020] [Indexed: 05/08/2023]
Abstract
Cadmium (Cd) is as an extremely toxic metal that can contaminate agricultural soils. To reduce the risk of Cd intake in food cereals, the development of cultivars with low grain Cd concentration (GCC) is an effective countermeasure. We analyzed quantitative trait loci (QTLs) for GCC in a doubled haploid (DH) common wheat (Triticum aestivum L.) population derived from 'Chugoku 165' (low GCC) × 'Chukei 10-22' (high GCC). We found novel loci for low GCC on the short arm of chromosome 4B and on the long arm of chromosome 6B. These QTLs accounted for 9.4%-25.4% (4B) and 9.0%-17.8% (6B) of the phenotypic variance in the DH population. An association analysis with 43 cultivars identified 3 loci at these QTLs: QCdc.4B-kita, QCdc.6B-kita1, and QCdc.6B-kita2. In contrast to durum wheat and barley, no QTL was detected on the chromosomes of homeologous group 5 for heavy metal P1B-type ATPase 3. These results will contribute to marker-assisted selection for low GCC in breeding of common wheat.
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Affiliation(s)
- Yusuke Ban
- NARO Western Region Agricultural Research Center, 6-12-1 Nishifukatsu-cho, Fukuyama, Hiroshima 721-8514, Japan
| | - Goro Ishikawa
- NARO Institute of Crop Science, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Hiroaki Ueda
- Graduate School of Science, Hiroshima University, 1-4-3 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Naoyuki Ishikawa
- NARO Western Region Agricultural Research Center, 6-12-1 Nishifukatsu-cho, Fukuyama, Hiroshima 721-8514, Japan
| | - Keita Kato
- NARO Western Region Agricultural Research Center, 6-12-1 Nishifukatsu-cho, Fukuyama, Hiroshima 721-8514, Japan
| | - Kanenori Takata
- NARO Western Region Agricultural Research Center, 6-12-1 Nishifukatsu-cho, Fukuyama, Hiroshima 721-8514, Japan
| | - Minoru Matsuyama
- Hyogo Prefectural Technology Center for Agriculture, Forestry and Fisheries, 1533 Befu-cho, Kasai, Hyogo 679-0198, Japan
| | - Hirokazu Handa
- NARO Institute of Crop Science, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Toshiki Nakamura
- NARO Tohoku Agricultural Research Center, 4 Akahira, Shimo-kuriyagawa, Morioka, Iwate 020-0198, Japan
| | - Mikiko Yanaka
- NARO Western Region Agricultural Research Center, 6-12-1 Nishifukatsu-cho, Fukuyama, Hiroshima 721-8514, Japan
- Corresponding author (e-mail: )
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Rasheed A, Takumi S, Hassan MA, Imtiaz M, Ali M, Morgunov AI, Mahmood T, He Z. Appraisal of wheat genomics for gene discovery and breeding applications: a special emphasis on advances in Asia. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1503-1520. [PMID: 31897516 DOI: 10.1007/s00122-019-03523-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 12/23/2019] [Indexed: 06/10/2023]
Abstract
We discussed the most recent efforts in wheat functional genomics to discover new genes and their deployment in breeding with special emphasis on advances in Asian countries. Wheat research community is making significant progress to bridge genotype-to-phenotype gap and then applying this knowledge in genetic improvement. The advances in genomics and phenomics have intrigued wheat researchers in Asia to make best use of this knowledge in gene and trait discovery. These advancements include, but not limited to, map-based gene cloning, translational genomics, gene mapping, association genetics, gene editing and genomic selection. We reviewed more than 57 homeologous genes discovered underpinning important traits and multiple strategies used for their discovery. Further, the complementary advancements in wheat phenomics and analytical approaches to understand the genetics of wheat adaptability, resilience to climate extremes and resistance to pest and diseases were discussed. The challenge to build a gold standard reference genome sequence of bread wheat is now achieved and several de novo reference sequences from the cultivars representing different gene pools will be available soon. New pan-genome sequencing resources of wheat will strengthen the foundation required for accelerated gene discovery and provide more opportunities to practice the knowledge-based breeding.
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Affiliation(s)
- Awais Rasheed
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China.
- International Maize and Wheat Improvement Center (CIMMYT), CAAS, 12 Zhongguancun South Street, Beijing, 100081, China.
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
| | - Shigeo Takumi
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe, 657-8501, Japan
| | - Muhammad Adeel Hassan
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Muhammad Imtiaz
- International Maize and Wheat Improvement Center (CIMMYT) Pakistan office, c/o National Agriculture Research Center (NARC), Islamabad, Pakistan
| | - Mohsin Ali
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Alex I Morgunov
- International Maize and Wheat Improvement Center (CIMMYT), Yenimahalle, Ankara, 06170, Turkey
| | - Tariq Mahmood
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Zhonghu He
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- International Maize and Wheat Improvement Center (CIMMYT), CAAS, 12 Zhongguancun South Street, Beijing, 100081, China
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11
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Ishikawa G, Hayashi T, Nakamura K, Tanaka T, Kobayashi F, Saito M, Ito H, Ikenaga S, Taniguchi Y, Nakamura T. Multifamily QTL analysis and comprehensive design of genotypes for high-quality soft wheat. PLoS One 2020; 15:e0230326. [PMID: 32160264 PMCID: PMC7065826 DOI: 10.1371/journal.pone.0230326] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 02/27/2020] [Indexed: 01/11/2023] Open
Abstract
Milling properties and flour color are essential selection criteria in soft wheat breeding. However, high phenotypic screening costs restrict selection to relatively few breeding lines in late generations. To achieve marker-based selection of these traits in early generations, we performed genetic dissection of quality traits using three doubled haploid populations that shared the high-quality soft wheat variety Kitahonami as the paternal parent. An amplicon sequencing approach allowed effective construction of well-saturated linkage maps of the populations. Marker-based heritability estimates revealed that target quality traits had relatively high values, indicating the possibility of selection in early generations. Taking advantage of Chinese Spring reference sequences, joint linkage maps of the three populations were generated. Based on the maps, multifamily quantitative trait locus (QTL) analysis revealed a total of 86 QTLs for ten traits investigated. In terms of target quality traits, 12 QTLs were detected for flour yield, and 12 were detected for flour redness (a* value). Among these QTLs, six for flour yield and nine for flour a* were segregating in more than two populations. Some relationships among traits were explained by QTL collocations on chromosomes, especially group 7 chromosomes. Ten different ideotypes with various combinations of favorable alleles for the flour yield and flour a* QTLs were generated. Phenotypes of derivatives from these ideotypes were predicted to design ideal genotypes for high-quality wheat. Simulations revealed the possibility of breeding varieties with better quality than Kitahonami.
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Affiliation(s)
- Goro Ishikawa
- Division of Basic Research, Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
- * E-mail:
| | - Takeshi Hayashi
- Division of Basic Research, Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Kazuhiro Nakamura
- Division of Lowland Farming Research, Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Chikugo, Fukuoka, Japan
| | - Tsuyoshi Tanaka
- Division of Basic Research, Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Fuminori Kobayashi
- Division of Basic Research, Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Mika Saito
- Division of Field Crops and Horticulture Research, Tohoku Agricultural Research Center, National Agriculture and Food Research Organization, Morioka, Iwate, Japan
| | - Hiroyuki Ito
- Division of Field Crops and Horticulture Research, Tohoku Agricultural Research Center, National Agriculture and Food Research Organization, Morioka, Iwate, Japan
| | - Sachiko Ikenaga
- Division of Field Crops and Horticulture Research, Tohoku Agricultural Research Center, National Agriculture and Food Research Organization, Morioka, Iwate, Japan
| | - Yoshinori Taniguchi
- Division of Field Crops and Horticulture Research, Tohoku Agricultural Research Center, National Agriculture and Food Research Organization, Morioka, Iwate, Japan
| | - Toshiki Nakamura
- Division of Field Crops and Horticulture Research, Tohoku Agricultural Research Center, National Agriculture and Food Research Organization, Morioka, Iwate, Japan
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12
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Nishijima R, Yoshida K, Sakaguchi K, Yoshimura SI, Sato K, Takumi S. RNA Sequencing-Based Bulked Segregant Analysis Facilitates Efficient D-genome Marker Development for a Specific Chromosomal Region of Synthetic Hexaploid Wheat. Int J Mol Sci 2018; 19:E3749. [PMID: 30486239 PMCID: PMC6321645 DOI: 10.3390/ijms19123749] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 11/20/2018] [Accepted: 11/22/2018] [Indexed: 11/16/2022] Open
Abstract
Common wheat originated from interspecific hybridization between cultivated tetraploid wheat and its wild diploid relative Aegilops tauschii followed by amphidiploidization. This evolutionary process can be reproduced artificially, resulting in synthetic hexaploid wheat lines. Here we performed RNA sequencing (RNA-seq)-based bulked segregant analysis (BSA) using a bi-parental mapping population of two synthetic hexaploid wheat lines that shared identical A and B genomes but included with D-genomes of distinct origins. This analysis permitted identification of D-genome-specific polymorphisms around the Net2 gene, a causative locus to hybrid necrosis. The resulting single nucleotide polymorphisms (SNPs) were classified into homoeologous polymorphisms and D-genome allelic variations, based on the RNA-seq results of a parental tetraploid and two Ae. tauschii accessions. The difference in allele frequency at the D-genome-specific SNP sites between the contrasting bulks (ΔSNP-index) was higher on the target chromosome than on the other chromosomes. Several SNPs with the highest ΔSNP-indices were converted into molecular markers and assigned to the Net2 chromosomal region. These results indicated that RNA-seq-based BSA can be applied efficiently to a synthetic hexaploid wheat population to permit molecular marker development in a specific chromosomal region of the D genome.
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Affiliation(s)
- Ryo Nishijima
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe 657-8501, Japan.
| | - Kentaro Yoshida
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe 657-8501, Japan.
| | - Kohei Sakaguchi
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe 657-8501, Japan.
| | - Shin-Ichi Yoshimura
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe 657-8501, Japan.
| | - Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan.
| | - Shigeo Takumi
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe 657-8501, Japan.
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