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Nguyen HTL, Suetsugu S, Nakamura Y, Demeter Z, Zheng SH, Fujita D. Identification and characterization of stable QTLs for vascular bundle number at the panicle neck in rice ( Oryza sativa L.). BREEDING SCIENCE 2023; 73:365-372. [PMID: 38106512 PMCID: PMC10722095 DOI: 10.1270/jsbbs.23013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 06/11/2023] [Indexed: 12/19/2023]
Abstract
A large vascular bundle number (VBN) in the panicle neck in rice (Oryza sativa L.) is related to the ability to transport assimilates from stem and leaf to reproductive organs during seed maturation. Several quantitative trait loci (QTLs) for VBN have been identified by using segregating populations derived from a cross between indica and japonica rice cultivars. However, the detailed location, effect, and interaction of QTLs for VBN were not understood well. Here, to elucidate the genetic basis of VBN, we identified three stable QTLs for VBN-qVBN5, qVBN6 and qVBN11-by using 71 recombinant inbred lines derived from a cross between indica 'IR24' and japonica 'Asominori'. We confirmed their positions and characterized their effects by using chromosome segment substitution lines (CSSLs) with an 'IR24' genetic background. qVBN6 had the most substantial effect on VBN, followed by qVBN11 and qVBN5. We developed pyramided lines carrying two QTLs for VBN to estimate their interaction. The combination of qVBN6 and qVBN11 accumulated VBN negatively in the pyramided lines owing to the independent actions of each QTL. The QTLs detected for VBN will enhance our understanding of genetic mechanisms of VBN and can be used in rice breeding.
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Affiliation(s)
- Ha Thi Le Nguyen
- The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-8580, Japan
- Forest Science Institute of South Vietnam, 1 Pham Van Hai, Tan Binh District, Ho Chi Minh City, Viet Nam
| | - Shizuka Suetsugu
- Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga 840-8502, Japan
| | - Yuna Nakamura
- Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga 840-8502, Japan
| | - Zita Demeter
- Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga 840-8502, Japan
| | - Shao-Hui Zheng
- Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga 840-8502, Japan
| | - Daisuke Fujita
- Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga 840-8502, Japan
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Kiyosawa A, Yonemaru JI, Mizuno H, Kanamori H, Wu J, Kawahigashi H, Goto K. Fine mapping of Rf5 region for a sorghum fertility restorer gene and microsynteny analysis across grass species. BREEDING SCIENCE 2022; 72:141-149. [PMID: 36275935 PMCID: PMC9522528 DOI: 10.1270/jsbbs.21057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/20/2021] [Indexed: 06/16/2023]
Abstract
Cytoplasmic male sterility (CMS) is widely used to control pollination in the production of commercial F1 hybrid seed in sorghum. So far, 6 major fertility restorer genes, Rf1 to Rf6, have been reported in sorghum. Here, we fine-mapped the Rf5 locus on sorghum chromosome 5 using descendant populations of a 'Nakei MS-3A' × 'JN43' cross. The Rf5 locus was narrowed to a 140-kb region in BTx623 genome (161-kb in JN43) with 16 predicted genes, including 6 homologous to the rice fertility restorer Rf1 (PPR.1 to PPR.6). These 6 homologs have tandem pentatricopeptide repeat (PPR) motifs. Many Rf genes encode PPR proteins, which bind RNA transcripts and modulate gene expression at the RNA level. No PPR genes were detected at the Rf5 locus on the corresponding homologous chromosome of rice, foxtail millet, or maize, so this gene cluster may have originated by chromosome translocation and duplication after the divergence of sorghum from these species. Comparison of the sequences of these genes between fertile and CMS lines identified PPR.4 as the most plausible candidate gene for Rf5.
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Affiliation(s)
- Atsushi Kiyosawa
- Nagano Animal Industry Experiment Station, 10931-1 Kataoka, Shiojiri, Nagano 399-0711, Japan
| | - Jun-ichi Yonemaru
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Hiroshi Mizuno
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Hiroyuki Kanamori
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Jianzhong Wu
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Hiroyuki Kawahigashi
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Kazumi Goto
- Nagano Animal Industry Experiment Station, 10931-1 Kataoka, Shiojiri, Nagano 399-0711, Japan
- Nagano Agricultural Development Public Corporation, Kami-Ina Branch, 3497 Arai, Ina, Nagano 396-8666, Japan
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Ye W, Yang Y, Wang P, Zhang Y, Zhang L, Tian D, Zhang L, Zhang L, Zhou B. InDel marker development and QTL analysis of agronomic traits in mung bean [ Vigna radiate (L.) Wilczek]. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:66. [PMID: 37309317 PMCID: PMC10236061 DOI: 10.1007/s11032-021-01233-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 05/11/2021] [Indexed: 06/14/2023]
Abstract
The stem color of young mung bean is a very useful tool in germplasm identification. Flowering time and plant height (PH) are known to be strongly correlated with crop adaption and yield. However, few studies have focused on elucidating the genetic mechanisms that regulate these five particular traits: young stem color (YSC), days to first flowering (DFF), days to maturity (DM), PH, and nodes on the main stem (NMS). In this study, a genetic linkage map for the F2 population was constructed using 129 InDel markers that were developed based on the sequence variations between parents. A total of 14 QTLs related to YSC, DFF, DM, PH, and NMS were detected. These QTLs were distributed on six chromosomes (1, 3, 4, 6, 7, and 10), which individually accounted for 1.32 to 90.07% of the total phenotypic variation. Using a short and high-density linkage map for the F3 population, six of the seven QTLs which clustered at two intervals on chromosomes 3 and 10 were detected again. Further analysis found that four QTLs between InDel markers R3-15 and R3-19 controlled DFF, DM, PH, and NMS, and each QTL accounted for a large percent of the total phenotypic variation. Analysis of two separated F2:3 lines also found that the phenotype was highly corresponded to its genotype which was between R3-15 and R3-19. Phenotype and genotype analysis for 30 mung bean accessions showed that the major effect QTL qDFF3 was a key regulator for DFF. Using a map-based cloning method, the major effect QTL qYSC4 for YSC was mapped in a 347 Kb interval on chromosome 4. Candidate gene analysis showed that sequence variations and expression level differences existed in the predicted candidate gene between the parents. These results provide a theoretical basis for cloning these QTLs and marker-assisted selection. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01233-0.
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Affiliation(s)
- Weijun Ye
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230000 Anhui China
- Anhui Province Key Laboratory of Crop Quality Improvement, Hefei, 230000 Anhui China
| | - Yong Yang
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230000 Anhui China
| | - Peiran Wang
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230000 Anhui China
| | - Yin Zhang
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230000 Anhui China
| | - Liya Zhang
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230000 Anhui China
| | - Dongfeng Tian
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230000 Anhui China
| | - Lei Zhang
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230000 Anhui China
| | - Lingling Zhang
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230000 Anhui China
| | - Bin Zhou
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230000 Anhui China
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Munguambe NE, Inoue S, Demeter Z, Yamagata Y, Yasui H, Zheng SH, Fujita D. Substitution Mapping of a Locus Responsible for Hybrid Breakdown in Populations Derived From Interspecific Introgression Line. FRONTIERS IN PLANT SCIENCE 2021; 12:633247. [PMID: 33968097 PMCID: PMC8097182 DOI: 10.3389/fpls.2021.633247] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 03/22/2021] [Indexed: 05/27/2023]
Abstract
Hybrid breakdown, a form of postzygotic reproductive barrier, has been reported to hinder gene flow in many crosses between wild and cultivated rice. Here, the phenomenon of hybrid breakdown was observed as low-tillering (i.e., low tiller number) in some progeny of an interspecific cross produced in an attempt to introduce Oryza meridionalis Ng (W1625) chromosomal segments into Oryza sativa L. ssp. japonica "Taichung 65" (T65). Low-tillering lines were obtained in BC4-derived progeny from a cross between W1625 and "Taichung 65," but the locus for low-tillering could not be mapped in segregating populations. As a second approach to map the locus for low-tillering, we analyzed an F2 population derived from a cross between the low-tillering lines and a high-yielding indica cultivar, "Takanari." A major QTL for low-tillering, qLTN4, was detected between PCR-based markers MS10 and RM307 on the long arm of chromosome 4, with a LOD score of 15.6. The low-tillering phenotype was associated with weak growth and pale yellow phenotype; however, low-tillering plant had less reduction of grain fertility. In an F4 population (4896 plants), 563 recombinant plants were identified and the low-tillering locus was delimited to a 4.6-Mbp region between markers W1 and C5-indel3729. This region could not be further delimited because recombination is restricted in this region of qLTN4, which is near the centromere. Understanding the genetic basis of hybrid breakdown, including the low-tillering habit, will be important for improving varieties in rice breeding.
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Affiliation(s)
- Nilsa Emilia Munguambe
- Tropical Crop Improvement Laboratory, Faculty of Agriculture, Saga University, Saga, Japan
| | - Shouta Inoue
- Tropical Crop Improvement Laboratory, Faculty of Agriculture, Saga University, Saga, Japan
| | - Zita Demeter
- Tropical Crop Improvement Laboratory, Faculty of Agriculture, Saga University, Saga, Japan
| | - Yoshiyuki Yamagata
- Plant Breeding Laboratory, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Hideshi Yasui
- Plant Breeding Laboratory, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Shao-Hui Zheng
- Tropical Crop Improvement Laboratory, Faculty of Agriculture, Saga University, Saga, Japan
| | - Daisuke Fujita
- Tropical Crop Improvement Laboratory, Faculty of Agriculture, Saga University, Saga, Japan
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Vasumathy SK, Peringottillam M, Sundaram KT, Kumar SHK, Alagu M. Genome- wide structural and functional variant discovery of rice landraces using genotyping by sequencing. Mol Biol Rep 2020; 47:7391-7402. [PMID: 32886328 DOI: 10.1007/s11033-020-05794-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 08/28/2020] [Indexed: 12/20/2022]
Abstract
Rice landraces are vital genetic resources for agronomic and quality traits but the undeniable collection of Kerala landraces remains poorly delineated. To effectively conserve, manage, and use these resources, understanding the genomic structure of germplasm is essential. Genotyping by sequencing (GBS) enables identification of an immense number of single nucleotide polymorphism (SNP) and insertion deletion (InDel) from 96 rice germplasm. In the present study, a total of 16.9 × 107 reads were generated, and among that 16.3 × 107 reads were mapped to the indica reference genome. Exploring GBS data unfolded a wide genomic variations including 82,59,639 SNPs and 1,07,140 Indels. Both neighbor-joining tree and principal coordinate analysis with InDel markers revealed the selected germplasm in this study as highly diverse in structure. We assembled unmapped reads which were further employed for gene ontology analysis. These unmapped sequences that are generally expelled from subsequent studies of GBS data analysis may exist as an unexplored resort for several novel significant biological findings. The discovery of SNPs from the haplotyping results of GS3 and GIF1 genes provided insight into marker- assisted selection based on grain size and yield and can be utilized for rice yield improvement. To our knowledge, this is the first report on structural variation analysis using the GBS platform in rice landraces collected from Kerala. Genomic information from this study endows with valuable resources for perceptive rice landrace structure and can also facilitate sequencing-based molecular breeding.
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Affiliation(s)
| | - Maya Peringottillam
- Department of Genomic Science, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Krishna T Sundaram
- South Asia hub, ICRISAT Campus, International Rice Research Institute, Secundarabad, Telangana, India
| | - S Hari Krishna Kumar
- Department of Genomic Science, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Manickavelu Alagu
- Department of Genomic Science, Central University of Kerala, Kasaragod, Kerala, 671316, India.
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6
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Identification and characterization of the stunted sterile (ss) mutant in rice. Genes Genomics 2020; 42:869-882. [PMID: 32506267 DOI: 10.1007/s13258-020-00954-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 05/19/2020] [Indexed: 10/24/2022]
Abstract
BACKGROUND Proper organ development is pivotal for normal rice growth and production. Many genes are involved in this process, and these genes provide a basis for rice breeding. OBJECTIVE To identify a novel mutation causing developmental defects in rice. METHODS The phenotype of a rice mutant, stunted sterile (ss), identified from the japonica rice cultivar Samkwang treated with N-methyl-N-nitrosourea, was characterized, including anatomical and pollen activity analyses. A genetic analysis and fine mapping were performed to identify a candidate locus, followed by a sequence analysis to determine the causal mutation for the phenotype. RESULTS Compared with wild-type plants, the mutant exhibited a 34% reduction in height, 46% reduction in flag leaf width, and complete panicle sterility. Cell proliferation in the leaf and pollen viability were significantly inhibited in the mutant. The mutant phenotypes were controlled by a single recessive gene that was fine-mapped to an 84 kb region between two SNP markers on the short arm of chromosome 5. A candidate gene analysis determined that the mutant carries an 11 bp insertion in the coding region of LOC_Os05g03550, which encodes a protein containing two SANT domains, resulting in a premature termination codon before the conserved domain. CONCLUSIONS We identified a novel rice gene, Stunted sterile, involved in the regulation of various developmental processes. Our findings improve our understanding of the role of chromatin remodeling in organ development and have implications for breeding owing to the broad effects of the gene on plant growth.
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Kiyosawa A, Yonemaru JI, Kawahigashi H, Goto K. Analysis of quantitative trait loci for fertility restoration in seven F 2 populations derived from sorghum F 1 hybrids bred in Japan. BREEDING SCIENCE 2020; 70:379-386. [PMID: 32714061 PMCID: PMC7372026 DOI: 10.1270/jsbbs.19144] [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: 10/16/2019] [Accepted: 02/23/2020] [Indexed: 06/11/2023]
Abstract
To clarify the genetic mechanisms of fertility restoration in sorghum F1 hybrids produced in Japan ('Ryokuryu', 'Hazuki', 'Haretaka', 'Natsuibuki', 'Hanaaoba', 'Akidachi' and 'Kazetachi'), we analyzed QTLs for fertility restoration using seven F2 populations derived from those hybrids. By QTL mapping with a series of SSR markers, we detected three major QTLs for fertility restoration. These data and the results of haplotype analysis of known fertility restorer (Rf) genes showed that qRf5, corresponding to the Rf5 locus, was the most widely used Rf gene for fertility restoration of sorghum F1 hybrids among the lines tested. Other major Rf genes detected were qRf8, corresponding to Rf1, and qRf2, corresponding to Rf2. QTLs for grain weight also corresponded to these Rf loci. A minor QTL, qRf3, may also affect restoration of fertility. Our data show that three major Rfs-Rf1, Rf2, and Rf5-were used in F1 hybrid sorghum production in Japan. This knowledge can be used to improve the efficiency of the F1 sorghum breeding program.
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Affiliation(s)
- Atsushi Kiyosawa
- Nagano Animal Industry Experiment Station, 10931-1 Kataoka, Shiojiri, Nagano 399-0711, Japan
| | - Jun-ichi Yonemaru
- Institute of Crop Science (NICS), National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Hiroyuki Kawahigashi
- Institute of Crop Science (NICS), National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Kazumi Goto
- Nagano Animal Industry Experiment Station, 10931-1 Kataoka, Shiojiri, Nagano 399-0711, Japan
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Kitazawa N, Shomura A, Mizubayashi T, Ando T, Nagata K, Hayashi N, Takahashi A, Yamanouchi U, Fukuoka S. Rapid DNA-genotyping system targeting ten loci for resistance to blast disease in rice. BREEDING SCIENCE 2019; 69:68-83. [PMID: 31086485 PMCID: PMC6507720 DOI: 10.1270/jsbbs.18143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 10/13/2018] [Indexed: 06/09/2023]
Abstract
The fungal pathogen Pyricularia oryzae causes blast, a severe disease of rice (Oryza sativa L.). Improving blast resistance is important in rice breeding programs. Inoculation tests have been used to select for resistance genotypes, with DNA marker-based selection becoming an efficient alternative. No comprehensive DNA marker system for race-specific resistance alleles in the Japanese rice breeding program has been developed because some loci contain multiple resistance alleles. Here, we used the Fluidigm SNP genotyping platform to determine a set of 96 single nucleotide polymorphism (SNP) markers for 10 loci with race-specific resistance. The markers were then used to evaluate the presence or absence of 24 resistance alleles in 369 cultivars; results were 93.5% consistent with reported inoculation test-based genotypes in japonica varieties. The evaluation system was successfully applied to high-yield varieties with indica genetic backgrounds. The system includes polymorphisms that distinguish the resistant alleles at the tightly linked Pita and Pita-2 loci, thereby confirming that all the tested cultivars with Pita-2 allele carry Pita allele. We also developed and validated insertion/deletion (InDel) markers for ten resistance loci. Combining SNP and InDel markers is an accurate and efficient strategy for selection for race-specific resistance to blast in breeding programs.
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Affiliation(s)
- Noriyuki Kitazawa
- Institute of Crop Science, National Agriculture and Food Research Organization,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Ayahiko Shomura
- Institute of Crop Science, National Agriculture and Food Research Organization,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Tatsumi Mizubayashi
- Institute of Crop Science, National Agriculture and Food Research Organization,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Tsuyu Ando
- Institute of Crop Science, National Agriculture and Food Research Organization,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Kazufumi Nagata
- Institute of Crop Science, National Agriculture and Food Research Organization,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Nagao Hayashi
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Akira Takahashi
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Utako Yamanouchi
- Institute of Crop Science, National Agriculture and Food Research Organization,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Shuichi Fukuoka
- Institute of Crop Science, National Agriculture and Food Research Organization,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
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9
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Bakti C, Tanaka J. Detection of dominant QTLs for stigma exsertion ratio in rice derived from Oryza rufipogon accession 'W0120'. BREEDING SCIENCE 2019; 69:143-150. [PMID: 31086492 PMCID: PMC6507721 DOI: 10.1270/jsbbs.18139] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 11/16/2018] [Indexed: 05/25/2023]
Abstract
Stigma exsertion can enhance the outcrossing fertility in rice. Dominant genes for this trait are expected to be essential for the effective application of a novel outcrossing-based breeding system that uses male sterility in rice, which is normally autogamous. Because reduction of stigma exsertion is a domestication trait, we screened wild rice species as possible donors of genes or QTLs for stigma exsertion. We used in silico image-based screening and selected the Oryza rufipogon accession 'W0120'. A single F1 individual derived from a cross between the japonica rice cultivar 'Akidawara' and 'W0120' was used to generate F2 and BC1F1 populations. QTL analysis performed using 114 F2 individuals detected QTLs on chromosomes 2, 3, 4, 8, and 11. Only two major QTLs on chromosomes 3 and 8 showed higher degrees of dominance. On the other hand, there were no QTLs near GS3, which is well known as a gene for stigma exsertion. Validation of these QTLs using 188 BC1F1 individuals provided clear evidence for their dominance. Genotypes of the markers nearest to the two QTLs were also related to grain length. We expect the genes responsible for these QTLs to be promising tools for improving outcrossing-based breeding in rice.
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Affiliation(s)
- Citra Bakti
- Graduate School of Life and Environmental Science, University of Tsukuba,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
- Universitas Padjadjaran,
Jl Raya Bandung-Sumedang km 21, West Java,
Indonesia
| | - Junichi Tanaka
- Graduate School of Life and Environmental Science, University of Tsukuba,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
- Institute of Crop Science, NARO,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
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10
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Yu H, Shahid MQ, Li R, Li W, Liu W, Ghouri F, Liu X. Genome-Wide Analysis of Genetic Variations and the Detection of Rich Variants of NBS-LRR Encoding Genes in Common Wild Rice Lines. PLANT MOLECULAR BIOLOGY REPORTER 2018; 36:618-630. [PMID: 30363818 PMCID: PMC6182389 DOI: 10.1007/s11105-018-1103-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Common wild rice (Oryza rufipogon Griff.) is invaluable genetic resource for rice resistance breeding. Whole-genome re-sequencing was conducted to systematically analyze the variations in two new inbred lines (Huaye 3 and Huaye 4) developed from a common wild rice. A total of 4,841,127 SNPs, 1,170,479 InDels, 24,080 structural variations (SVs), and 298 copy number variations (CNVs) were identified in three materials. Approximately 16.24 and 5.64% of the total SNPs and InDels of Huaye 3 and Huaye 4 were located in genic regions, respectively. Together, 12,486 and 15,925 large-effect SNPs, and 12,417 and 14,513 large-effect InDels, which affect the integrity of the encoded protein, were identified in Huaye 3 and Huaye 4, respectively. The distribution map of 194 and 245 NBS-LRR encoding homologs was constructed across 12 rice chromosomes. Further, GO enrichment analysis of the homologs with identical genotype variations in Huaye 3 and Huaye 4 revealed 67, 82, and 58 homologs involved in cell death, response to stress, and both terms, respectively. Comparative analysis displayed that 550 out of 652 SNPs and 129 out of 147 InDels were present in a widely used blast-susceptible rice variety (LTH). Protein-protein interaction analysis revealed a strong interaction between NBS-LRR candidates and several known R genes. One homolog of disease resistance protein (RPM1) was involved in the plant-pathogen interaction pathway. Artificial inoculation of disease/insect displayed resistance phenotypes against rice blast and brown planthopper in two lines. The results will provide allele-specific markers for rice molecular breeding.
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Affiliation(s)
- Hang Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
| | - Rongbai Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004 China
| | - Wei Li
- College of Agronomy, Guangdong Ocean University, Zhanjiang, 524000 China
| | - Wen Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
- Department of Tropical Crops, Guangdong Agriculture Industry Business Polytechnic College, Guangzhou, 510507 China
| | - Fozia Ghouri
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
| | - Xiangdong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
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11
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Murakami T, Kazama T, Toriyama K. Genetic analysis of male sterility obtained from a rice cultivar Lebed backcrossed with Taichung 65. RICE (NEW YORK, N.Y.) 2018; 11:30. [PMID: 29725869 PMCID: PMC5934291 DOI: 10.1186/s12284-018-0222-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 04/24/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Male sterility is a useful agronomic trait for breeding of self-pollinating crops and is often observed in the progenies of hybrids of distantly related species, for example, Oryza sativa L. subsp. indica and O. sativa L. subsp. japonica. To explore new male sterile lines in rice, we performed successive backcrosses using a japonica cultivar Taichung 65 (T65) as a recurrent pollen parent and various indica cultivars as the initial female parents. FINDINGS We observed male sterile plants in the backcross progeny from an indica cultivar, Lebed. Both fertile and sterile plants were present in the BC4F1 generation. The sterile plants segregated for fertile and sterile plants when backcrossed with T65 in BC5F1, BC6F1 and BC7F1 with a ratio of 1:1. Conversely, all the backcross progenies from the fertile BC4F1 were consistently fertile. Anthers of the male sterile line were stunted and did not shed pollen; cross-sectional observations revealed defects in sporophytic cells. The male sterility appears to be caused by heterozygous alleles derived from T65 and Lebed. A male sterility gene was mapped between two INDEL markers on the long arm of chromosome 10, which corresponded to a 407 kb region in the Nipponbare genome. CONCLUSIONS Since the heterozygous Lebed allele acts as dominant sporophytic pollen killer, it would be useful for recurrent selection breeding of japonica rice.
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Affiliation(s)
- Tetsuya Murakami
- Graduate School of Agricultural Science, Tohoku University, Sendai, 980-8572 Japan
| | - Tomohiko Kazama
- Graduate School of Agricultural Science, Tohoku University, Sendai, 980-8572 Japan
| | - Kinya Toriyama
- Graduate School of Agricultural Science, Tohoku University, Sendai, 980-8572 Japan
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Ogawa D, Yamamoto E, Ohtani T, Kanno N, Tsunematsu H, Nonoue Y, Yano M, Yamamoto T, Yonemaru JI. Haplotype-based allele mining in the Japan-MAGIC rice population. Sci Rep 2018. [PMID: 29531264 PMCID: PMC5847589 DOI: 10.1038/s41598-018-22657-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Multi-parent advanced generation inter-cross (MAGIC) lines have broader genetic variation than bi-parental recombinant inbred lines. Genome-wide association study (GWAS) using high number of DNA polymorphisms such as single-nucleotide polymorphisms (SNPs) is a popular tool for allele mining in MAGIC populations, in which the associations of phenotypes with SNPs are investigated; however, the effects of haplotypes from multiple founders on phenotypes are not considered. Here, we describe an improved method of allele mining using the newly developed Japan-MAGIC (JAM) population, which is derived from eight high-yielding rice cultivars in Japan. To obtain information on the haplotypes in the JAM lines, we predicted the haplotype blocks in the whole chromosomes using 16,345 SNPs identified via genotyping-by-sequencing analysis. Using haplotype-based GWAS, we clearly detected the loci controlling the glutinous endosperm and culm length traits. Information on the alleles of the eight founders, which was based on the effects of mutations revealed by the analysis of next-generation sequencing data, was used to narrow down the candidate genes and reveal the associations between alleles and phenotypes. The haplotype-based allele mining (HAM) proposed in this study is a promising approach to the detection of allelic variation in genes controlling agronomic traits in MAGIC populations.
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Affiliation(s)
- Daisuke Ogawa
- Institute of Crop Science, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan.,Agrogenomics Research Centre, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Japan
| | - Eiji Yamamoto
- Agrogenomics Research Centre, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Japan
| | - Toshikazu Ohtani
- Agrogenomics Research Centre, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Japan
| | - Noriko Kanno
- Institute of Crop Science, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan.,Agrogenomics Research Centre, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Japan
| | - Hiroshi Tsunematsu
- Institute of Crop Science, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan
| | - Yasunori Nonoue
- Institute of Crop Science, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan
| | - Masahiro Yano
- Institute of Crop Science, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan.,Agrogenomics Research Centre, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Japan
| | - Toshio Yamamoto
- Institute of Crop Science, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan. .,Agrogenomics Research Centre, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Japan.
| | - Jun-Ichi Yonemaru
- Institute of Crop Science, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan. .,Agrogenomics Research Centre, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Japan.
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13
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Sahu PK, Mondal S, Sharma D, Vishwakarma G, Kumar V, Das BK. InDel marker based genetic differentiation and genetic diversity in traditional rice (Oryza sativa L.) landraces of Chhattisgarh, India. PLoS One 2017; 12:e0188864. [PMID: 29190790 PMCID: PMC5708757 DOI: 10.1371/journal.pone.0188864] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 11/14/2017] [Indexed: 11/28/2022] Open
Abstract
Rice has been cultivating and utilizing by humans for thousands of years under diverse environmental conditions. Therefore, tremendous genetic differentiation and diversity has occurred at various agro-ecosystems. The significant indica–japonica differentiation in rice provides great opportunities for its genetic improvement. In the present investigation, a total of 42 polymorphic InDel markers were used for differentiating 188 rice landraces and two local varieties of Chhattisgarh, India into indica and japonica related genotypes based on ‘InDel molecular index’. Frequency of japonica alleles varied from 0.11 to 0.89 among landraces. Results revealed that 104 rice landraces have indica type genetic architecture along with three tested indica cultivars Swarna, Mahamaya and Rajeshwari. Another 60 landraces were placed under ‘close to indica’ type. It was found that three rice landraces i.e. Kalajeera, Kapri, Tulsimala were ‘close to japonica’ type and 21 landraces were ‘intermediate’ type. The result from the calculation of ‘InDel molecular index’ was further verified with STRUCTURE, AMOVA, PCA and cluster analysis. Population structure analysis revealed two genetically distinct populations within the 190 rice landraces/genotypes. Based on AMOVA, ‘intermediate’ type, ‘close to japonica’ type and Dongjinbyeo (a japonica cultivar from Republic of Korea) displayed significant genetic differentiation (ɸPT = 0.642, P = 0.000) from ‘indica’ and ‘close to indica’ groups. The PCA scatter plot and dendrogram demonstrated a clear pattern of two major group differentiations. ‘Close to japonica’ type and ‘intermediate’ type landraces/genotypes were grouped with Dongjinbyeo and formed a separate cluster at 30% Jaccard’s similarity level from rest of the landraces/genotypes which were ‘close to indica’ or ‘indica’ type. Such a significant genetic differentiation among the locally adapted landraces could be exploited for the development of rice varieties introgressing higher yield potential and better plant types of japonica type as per the need of consumers and rice traders.
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Affiliation(s)
- Parmeshwar Kumar Sahu
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, India
| | - Suvendu Mondal
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, India
- * E-mail: (SM); (DS)
| | - Deepak Sharma
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, India
- * E-mail: (SM); (DS)
| | - Gautam Vishwakarma
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, India
| | - Vikash Kumar
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, India
| | - Bikram Kishore Das
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, India
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14
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Kinoshita N, Takano S, Shimoda N, Takamure I, Sato T, Kato K. Development of genome-wide PCR-based markers from insertion, deletion and single nucleotide polymorphisms for closely related Japanese rice cultivars and identification of QTLs for the appearance of cooked rice and polished rice. BREEDING SCIENCE 2016; 66:742-751. [PMID: 28163590 PMCID: PMC5282762 DOI: 10.1270/jsbbs.16108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 09/08/2016] [Indexed: 05/17/2023]
Abstract
Appearance of rice grain is an important property, affecting its acceptance by consumers. Moreover, appearance is a complex characteristic involving many components, including glossiness and whiteness. The genetic bases for the glossiness of cooked rice and the whiteness of polished rice (WPR) were determined using 133 recombinant inbred lines (RILs) derived from a cross between two closely related cultivars from Hokkaido, Joiku462, with high glossiness and whiteness, and Yukihikari, an ancestor of Joiku462 with low glossiness and whiteness. Analyses identified 167 genome-wide InDel markers, five cleaved amplified polymorphic sequences (CAPS) and eight derived CAPS markers differentiating the parental lines. The glossiness area (GLA) and glossiness strength (GLS) of cooked rice and WPR were determined for RILs in two locations, Pippu and Sapporo, Hokkaido. Four QTLs were detected. qGLA10 and qGLS9 were detected on chromosomes 10 and 9, respectively, with both being significant at both geographic locations. qWPR1 on chromosome 1 was significant at Pippu, and qWPR4 on chromosome 4 was significant at Sapporo. The Joiku462 alleles at all QTLs increased each trait. The PCR-based markers flanking these four QTLs may be useful for improvement of GLA, GLS and WPR.
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Affiliation(s)
- Noriko Kinoshita
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine,
Nishi 2-11 Inada, Obihiro, Hokkaido 080-8555,
Japan
| | - Sho Takano
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine,
Nishi 2-11 Inada, Obihiro, Hokkaido 080-8555,
Japan
| | - Naomi Shimoda
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine,
Nishi 2-11 Inada, Obihiro, Hokkaido 080-8555,
Japan
| | - Itsuro Takamure
- Graduate School of Agriculture, Hokkaido University,
Kita 9 Nishi 9, Kita-ku, Sapporo, Hokkaido 060-8589,
Japan
| | - Takashi Sato
- Rice Breeding Group, Kamikawa Agricultural Experiment Station, Local Independent Administrative Agency Hokkaido Research Organization,
Minami 1-5, Pippu, Hokkaido 078-0397,
Japan
| | - Kiyoaki Kato
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine,
Nishi 2-11 Inada, Obihiro, Hokkaido 080-8555,
Japan
- Corresponding author (e-mail: )
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15
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Impact of SNPs on Protein Phosphorylation Status in Rice (Oryza sativa L.). Int J Mol Sci 2016; 17:ijms17111738. [PMID: 27845739 PMCID: PMC5133773 DOI: 10.3390/ijms17111738] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 10/04/2016] [Accepted: 10/11/2016] [Indexed: 11/16/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) are widely used in functional genomics and genetics research work. The high-quality sequence of rice genome has provided a genome-wide SNP and proteome resource. However, the impact of SNPs on protein phosphorylation status in rice is not fully understood. In this paper, we firstly updated rice SNP resource based on the new rice genome Ver. 7.0, then systematically analyzed the potential impact of Non-synonymous SNPs (nsSNPs) on the protein phosphorylation status. There were 3,897,312 SNPs in Ver. 7.0 rice genome, among which 9.9% was nsSNPs. Whilst, a total 2,508,261 phosphorylated sites were predicted in rice proteome. Interestingly, we observed that 150,197 (39.1%) nsSNPs could influence protein phosphorylation status, among which 52.2% might induce changes of protein kinase (PK) types for adjacent phosphorylation sites. We constructed a database, SNP_rice, to deposit the updated rice SNP resource and phosSNPs information. It was freely available to academic researchers at http://bioinformatics.fafu.edu.cn. As a case study, we detected five nsSNPs that potentially influenced heterotrimeric G proteins phosphorylation status in rice, indicating that genetic polymorphisms showed impact on the signal transduction by influencing the phosphorylation status of heterotrimeric G proteins. The results in this work could be a useful resource for future experimental identification and provide interesting information for better rice breeding.
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16
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Genome-wide generation and use of informative intron-spanning and intron-length polymorphism markers for high-throughput genetic analysis in rice. Sci Rep 2016; 6:23765. [PMID: 27032371 PMCID: PMC4817136 DOI: 10.1038/srep23765] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 03/11/2016] [Indexed: 12/13/2022] Open
Abstract
We developed genome-wide 84634 ISM (intron-spanning marker) and 16510 InDel-fragment length polymorphism-based ILP (intron-length polymorphism) markers from genes physically mapped on 12 rice chromosomes. These genic markers revealed much higher amplification-efficiency (80%) and polymorphic-potential (66%) among rice accessions even by a cost-effective agarose gel-based assay. A wider level of functional molecular diversity (17-79%) and well-defined precise admixed genetic structure was assayed by 3052 genome-wide markers in a structured population of indica, japonica, aromatic and wild rice. Six major grain weight QTLs (11.9-21.6% phenotypic variation explained) were mapped on five rice chromosomes of a high-density (inter-marker distance: 0.98 cM) genetic linkage map (IR 64 x Sonasal) anchored with 2785 known/candidate gene-derived ISM and ILP markers. The designing of multiple ISM and ILP markers (2 to 4 markers/gene) in an individual gene will broaden the user-preference to select suitable primer combination for efficient assaying of functional allelic variation/diversity and realistic estimation of differential gene expression profiles among rice accessions. The genomic information generated in our study is made publicly accessible through a user-friendly web-resource, "Oryza ISM-ILP marker" database. The known/candidate gene-derived ISM and ILP markers can be enormously deployed to identify functionally relevant trait-associated molecular tags by optimal-resource expenses, leading towards genomics-assisted crop improvement in rice.
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17
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Liu S, Gao P, Zhu Q, Luan F, Davis AR, Wang X. Development of cleaved amplified polymorphic sequence markers and a CAPS-based genetic linkage map in watermelon (Citrullus lanatus [Thunb.] Matsum. and Nakai) constructed using whole-genome re-sequencing data. BREEDING SCIENCE 2016; 66:244-59. [PMID: 27162496 PMCID: PMC4785002 DOI: 10.1270/jsbbs.66.244] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 11/26/2015] [Indexed: 05/06/2023]
Abstract
Cleaved amplified polymorphic sequence (CAPS) markers are useful tools for detecting single nucleotide polymorphisms (SNPs). This study detected and converted SNP sites into CAPS markers based on high-throughput re-sequencing data in watermelon, for linkage map construction and quantitative trait locus (QTL) analysis. Two inbred lines, Cream of Saskatchewan (COS) and LSW-177 had been re-sequenced and analyzed by Perl self-compiled script for CAPS marker development. 88.7% and 78.5% of the assembled sequences of the two parental materials could map to the reference watermelon genome, respectively. Comparative assembled genome data analysis provided 225,693 and 19,268 SNPs and indels between the two materials. 532 pairs of CAPS markers were designed with 16 restriction enzymes, among which 271 pairs of primers gave distinct bands of the expected length and polymorphic bands, via PCR and enzyme digestion, with a polymorphic rate of 50.94%. Using the new CAPS markers, an initial CAPS-based genetic linkage map was constructed with the F2 population, spanning 1836.51 cM with 11 linkage groups and 301 markers. 12 QTLs were detected related to fruit flesh color, length, width, shape index, and brix content. These newly CAPS markers will be a valuable resource for breeding programs and genetic studies of watermelon.
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Affiliation(s)
- Shi Liu
- Horticulture College, Northeast Agricultural University,
No. 59 Mucai Street Harbin, Heilongjiang Province, 150030,
China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture,
No. 59 Mucai Street Harbin, Heilongjiang Province, 150030,
China
| | - Peng Gao
- Horticulture College, Northeast Agricultural University,
No. 59 Mucai Street Harbin, Heilongjiang Province, 150030,
China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture,
No. 59 Mucai Street Harbin, Heilongjiang Province, 150030,
China
| | - Qianglong Zhu
- Horticulture College, Northeast Agricultural University,
No. 59 Mucai Street Harbin, Heilongjiang Province, 150030,
China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture,
No. 59 Mucai Street Harbin, Heilongjiang Province, 150030,
China
| | - Feishi Luan
- Horticulture College, Northeast Agricultural University,
No. 59 Mucai Street Harbin, Heilongjiang Province, 150030,
China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture,
No. 59 Mucai Street Harbin, Heilongjiang Province, 150030,
China
- Corresponding author (e-mail: )
| | - Angela R. Davis
- South Central Agricultural Research Laboratory, Agricultural Research Service, U.S. Department of Agriculture. Currently with HM. Clause,
9241 Mace Blvd, Davis, CA 95618,
USA
| | - Xiaolu Wang
- Horticulture College, Northeast Agricultural University,
No. 59 Mucai Street Harbin, Heilongjiang Province, 150030,
China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture,
No. 59 Mucai Street Harbin, Heilongjiang Province, 150030,
China
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