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Mansueto L, Tandayu E, Mieog J, Garcia-de Heer L, Das R, Burn A, Mauleon R, Kretzschmar T. HASCH - A high-throughput amplicon-based SNP-platform for medicinal cannabis and industrial hemp genotyping applications. BMC Genomics 2024; 25:818. [PMID: 39210290 PMCID: PMC11363669 DOI: 10.1186/s12864-024-10734-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 08/22/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND Cannabis sativa is seeing a global resurgence as a food, fiber and medicinal crop for industrial hemp and medicinal Cannabis industries respectively. However, a widespread moratorium on the use and research of C. sativa throughout most of the 20th century has seen the development of improved cultivars for specific end uses lag behind that of conventional crops. While C. sativa research and development has seen significant investments in the recent past, resulting in a suite of publicly available genomic resources and tools, a versatile and cost-effective mid-density genotyping platform for applied purposes in breeding and pre-breeding is lacking. Here we report on a first mid-density fixed-target SNP platform for C. sativa. RESULTS The High-throughput Amplicon-based SNP-platform for medicinal Cannabis and industrial Hemp (HASCH) was designed using a combination of filtering and Integer Linear Programming on publicly available whole-genome sequencing and RNA sequencing data, supplemented with in-house generated genotyping-by-sequencing (GBS) data. HASCH contains 1,504 genome-wide targets of high call rate (97% mean) and even distribution across the genome, designed to be highly informative (> 0.3 minor allele frequency) across both medicinal cannabis and industrial hemp gene pools. Average numbers of mismatch SNP between any two accessions were 251 for medicinal cannabis (N = 116) and 272 for industrial hemp (N = 87). Comparing HASCH data with corresponding GBS data on a collection of diverse C. sativa accessions demonstrated high concordance and resulted in comparable phylogenies and genetic distance matrices. Using HASCH on a segregating F2 population derived from a cross between a tetrahydrocannabinol (THC)-dominant and a cannabidiol (CBD)-dominant accession resulted in a genetic map consisting of 310 markers, comprising 10 linkage groups and a total size of 582.7 cM. Quantitative Trait Locus (QTL) mapping identified a major QTL for CBD content on chromosome 7, consistent with previous findings. CONCLUSION HASCH constitutes a versatile, easy to use and cost-effective genotyping solution for the rapidly growing Cannabis research community. It provides consistent genetic fingerprints of 1504 SNPs with wide applicability genetic resource management, quantitative genetics and breeding.
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Affiliation(s)
- Locedie Mansueto
- Southern Cross Plant Science, Faculty of Science and Engineering, Southern Cross University, 1 Military Road, East Lismore, NSW, 2480, Australia
| | - Erwin Tandayu
- Southern Cross Plant Science, Faculty of Science and Engineering, Southern Cross University, 1 Military Road, East Lismore, NSW, 2480, Australia
| | - Jos Mieog
- Southern Cross Plant Science, Faculty of Science and Engineering, Southern Cross University, 1 Military Road, East Lismore, NSW, 2480, Australia
| | - Lennard Garcia-de Heer
- Southern Cross Plant Science, Faculty of Science and Engineering, Southern Cross University, 1 Military Road, East Lismore, NSW, 2480, Australia
| | - Rekhamani Das
- Southern Cross Plant Science, Faculty of Science and Engineering, Southern Cross University, 1 Military Road, East Lismore, NSW, 2480, Australia
| | - Adam Burn
- Southern Cross Plant Science, Faculty of Science and Engineering, Southern Cross University, 1 Military Road, East Lismore, NSW, 2480, Australia
| | - Ramil Mauleon
- Southern Cross Plant Science, Faculty of Science and Engineering, Southern Cross University, 1 Military Road, East Lismore, NSW, 2480, Australia
- International Rice Research Institute, Pili Drive, Los Banos, Laguna, Philippines
| | - Tobias Kretzschmar
- Southern Cross Plant Science, Faculty of Science and Engineering, Southern Cross University, 1 Military Road, East Lismore, NSW, 2480, Australia.
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Sun N, Chen J, Wang Y, Hussain I, Lei N, Ma X, Li W, Liu K, Yu H, Zhao K, Zhao T, Zhang Y, Yu X. Development and utility of SSR markers based on Brassica sp. whole-genome in triangle of U. FRONTIERS IN PLANT SCIENCE 2024; 14:1259736. [PMID: 38259948 PMCID: PMC10801002 DOI: 10.3389/fpls.2023.1259736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 12/13/2023] [Indexed: 01/24/2024]
Abstract
Introduction Simple sequence repeats (SSR), also known as microsatellites, are crucial molecular markers in both animals and plants. Despite extensive previous research on SSRs, the development of microsatellite markers in Brassica crops remains limited and inefficient. Methods Krait software was used to identify microsatellites by genome-wide and marker development based on three recently sequenced basic species of Brassica crops in the triangle of U (Brassica rapa, B. nigra and B. oleracea), as well as three allotetraploids (B. juncea, B. napus and B. carinata) using public databases. Subsequently, the primers and the characteristics of microsatellites for most of them were accordingly designed on each chromosome of each of the six Brassica species, and their physical locations were identified,and the cross-transferability of primers have been carried out. In addition, a B-genome specific SSR marker was screened out. Results A total of 79341, 92089, 125443, 173964, 173604, and 222160 SSR loci have been identified from the whole genome sequences of Brassica crops within the triangle of U crops, B. rapa (AA), B. nigra (BB), B. oleracea (CC), B. napus (AACC), B. juncea (AABB) and B. carinata (BBCC), respectively. Comparing the number distribution of the three allotetraploid SSR loci in the three subgenomes AA, BB and CC, results indicate that the allotetraploid species have significant reduction in the number of SSR loci in the genome compared with their basic diploid counterparts. Moreover, we compared the basic species with their corresponding varieties, and found that the microsatellite characters between the allotetraploids and their corresponding basic species were very similar or almost identical. Subsequently, each of the 40 SSR primers was employed to investigate the polymorphism potential of B. rapa (85.27%), B. nigra (81.33%) and B. oleracea (73.45%), and B. rapa was found to have a higher cross-transfer rate among the basic species in the triangle of U. Meanwhile, a B-genome specific SSR marker, BniSSR23228 possessing the (AAGGA)3 sequence characteristics was obtained, and it located in chromosome B3 with a total length of 97 bp. Discussion In this study, results suggest that the pattern of distribution may be highly conserved during the differentiation of basic Brassica species and their allotetraploid counterparts. Our data indicated that the allotetraploidization process resulted in a significant reduction in SSR loci in the three subgenomes AA, BB and CC. The reasons may be partial gene dominated chromosomal homologous recombination and rearrangement during the evolution of basic diploid species into allotetraploids. This study provides a basis for future genomics and genetic research on the relatedness of Brassica species.
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Affiliation(s)
- Nairan Sun
- Group of Vegetable Breeding, Hainan Institute of Zhejiang University, Sanya, China
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, China
| | - Jisuan Chen
- Department of Supply Chain, Ningbo Haitong Food Technology Co., Ltd., Ningbo, China
| | - Yuqi Wang
- Group of Vegetable Breeding, Hainan Institute of Zhejiang University, Sanya, China
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, China
| | - Iqbal Hussain
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, China
| | - Na Lei
- Section of Horticulture and Landscape Architecture, Harbin Academy of Agricultural Sciences, Harbin, China
| | - Xinyan Ma
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, China
| | - Weiqiang Li
- Group of Vegetable Breeding, Hainan Institute of Zhejiang University, Sanya, China
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, China
| | - Kaiwen Liu
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, China
| | - Hongrui Yu
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, China
| | - Kun Zhao
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, China
| | - Tong Zhao
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, China
| | - Yi Zhang
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, China
| | - Xiaolin Yu
- Group of Vegetable Breeding, Hainan Institute of Zhejiang University, Sanya, China
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, China
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Ezeah CSA, Shimazu J, Kawanabe T, Shimizu M, Kawashima S, Kaji M, Ezinma CO, Nuruzzaman M, Minato N, Fukai E, Okazaki K. Quantitative trait locus (QTL) analysis and fine-mapping for Fusarium oxysporum disease resistance in Raphanus sativus using GRAS-Di technology. BREEDING SCIENCE 2023; 73:421-434. [PMID: 38737918 PMCID: PMC11082455 DOI: 10.1270/jsbbs.23032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 07/16/2023] [Indexed: 05/14/2024]
Abstract
Fusarium wilt is a significant disease in radish, but the genetic mechanisms controlling yellows resistance (YR) are not well understood. This study aimed to identify YR-QTLs and to fine-map one of them using F2:3 populations developed from resistant and susceptible radish parents. In this study, two high-density genetic maps each containing shared co-dominant markers and either female or male dominant markers that spanned 988.6 and 1127.5 cM with average marker densities of 1.40 and 1.53 cM, respectively, were generated using Genotyping by Random Amplicon Sequencing-Direct (GRAS-Di) technology. We identified two YR-QTLs on chromosome R2 and R7, and designated the latter as ForRs1 as the major QTL. Fine mapping narrowed down the ForRs1 locus to a 195 kb region. Among the 16 predicted genes in the delimited region, 4 genes including two receptor-like protein and -kinase genes (RLP/RLK) were identified as prime candidates for ForRs1 based on the nucleotide sequence comparisons between the parents and their predicted functions. This study is the first to use a GRAS-Di for genetic map construction of cruciferous crops and fine map the YR-QTL on the R7 chromosome of radish. These findings will provide groundbreaking insights into radish YR breeding and understanding the genetics of YR mechanism.
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Affiliation(s)
- Chukwunonso Sylvanus Austin Ezeah
- Laboratory of Plant breeding, Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Nishi-ku, Niigata 950-2181, Japan
- Federal Department of Agriculture, Federal Ministry of Agriculture and Rural Development, Abuja, FCT, Nigeria
| | | | | | - Motoki Shimizu
- Iwate Biotechnology Research Center, Kitakami, Iwate 024-0003, Japan
| | | | - Makoto Kaji
- Watanabe Seed Co., Ltd., Miyagi 987-0003, Japan
| | - Charles Onyemaechi Ezinma
- Federal Department of Agriculture, Federal Ministry of Agriculture and Rural Development, Abuja, FCT, Nigeria
| | - Md Nuruzzaman
- Laboratory of Plant breeding, Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Nishi-ku, Niigata 950-2181, Japan
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Nami Minato
- Laboratory of Plant breeding, Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Nishi-ku, Niigata 950-2181, Japan
| | - Eigo Fukai
- Laboratory of Plant breeding, Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Nishi-ku, Niigata 950-2181, Japan
| | - Keiichi Okazaki
- Laboratory of Plant breeding, Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Nishi-ku, Niigata 950-2181, Japan
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Li J, Wang H, Zhou D, Li C, Ding Q, Yang X, Wang F, Zheng H, Gao J. Genetic and Transcriptome Analysis of Leaf Trichome Development in Chinese Cabbage ( Brassica rapa L. subsp. pekinensis) and Molecular Marker Development. Int J Mol Sci 2022; 23:ijms232112721. [PMID: 36361510 PMCID: PMC9659260 DOI: 10.3390/ijms232112721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 10/13/2022] [Accepted: 10/19/2022] [Indexed: 01/25/2023] Open
Abstract
Chinese cabbage (Brassica rapa L. subsp. pekinensis) is one of the vegetables with the largest cultivated area in China and has been a great addition to the daily diet of Chinese people. A genetic map has been constructed in our previous study using the F2 population of two inbred lines of Chinese cabbage, namely "G291" (a hairy line) and "ZHB" (a hairless line), based on which a candidate gene related to trichome traits was identified on chromosome A06 with a phenotypic variance of 47%. A molecular marker was found to co-segregate with the trichome traits of the F2 population, which is in the 5'-flanking region of BrGL1, and a corresponding patent has been granted (NO. CN 108545775 B). Transcriptome analysis was carried out on the cotyledon, the first true leaf and the leaf closest to each inflorescence of F2 individuals of "G291 × ZHB" with or without trichomes, respectively. Ten pathways, including 189 DEGs, were identified to be involved in the development of trichomes in Chinese cabbage, which may be specifically related to the development of leaf trichomes. Most of the pathways were related to the biosynthesis of the secondary metabolites, which may help plants to adapt to the ever-changing external environment. DEGs also enriched the "plant-pathogen interaction" pathway, which is consistent with the conclusion that trichomes are related to the disease resistance of plants. Our study provides a basis for future research on the occurrence and development of trichomes in Chinese cabbage.
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Affiliation(s)
- Jingjuan Li
- Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Hongxia Wang
- Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Dandan Zhou
- Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan 250100, China
- College of Life Science, Shandong Normal University, Jinan 250100, China
| | - Cheng Li
- Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Qian Ding
- Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Xiaogang Yang
- Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Fengde Wang
- Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan 250100, China
- College of Life Science, Shandong Normal University, Jinan 250100, China
| | - Han Zheng
- Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan 250100, China
- Correspondence: (H.Z.); (J.G.)
| | - Jianwei Gao
- Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan 250100, China
- College of Life Science, Shandong Normal University, Jinan 250100, China
- Correspondence: (H.Z.); (J.G.)
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Szwarc J, Niemann J, Kaczmarek J, Bocianowski J, Weigt D. Genetic Relationship of Brassicaceae Hybrids with Various Resistance to Blackleg Is Disclosed by the Use of Molecular Markers. Curr Issues Mol Biol 2022; 44:4290-4302. [PMID: 36135207 PMCID: PMC9497795 DOI: 10.3390/cimb44090295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/02/2022] [Accepted: 09/15/2022] [Indexed: 11/17/2022] Open
Abstract
Brassica napus is an important oil source. Its narrow gene pool can be widened by interspecific hybridization with the Brassicaceae species. One of the agronomically important traits, that can be transferred through the hybridization, is the resistance to blackleg, a dangerous disease mainly caused by Leptosphaeria maculans. Hybrid individuals can be analyzed with various molecular markers, including Simple Sequence Repeats (SSR). We investigated the genetic similarity of 32 Brassicaceae hybrids and 19 parental components using SSR markers to reveal their genetic relationship. Furthermore, we compared the field resistance to blackleg of the interspecific progenies. The tested set of 15 SSR markers proved to be useful in revealing the genetic distances in the Brassicaceae hybrids and species. However, genetic similarity of the studied hybrids could not be correlated with the level of field resistance to L. maculans. Moreover, our studies confirmed the usefulness of the Brassicaceae hybrids in terms of blackleg management.
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Affiliation(s)
- Justyna Szwarc
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznan, Poland
| | - Janetta Niemann
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznan, Poland
| | - Joanna Kaczmarek
- Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland
| | - Jan Bocianowski
- Department of Mathematical and Statistical Methods, Poznań University of Life Sciences, Wojska Polskiego 28, 60-637 Poznań, Poland
| | - Dorota Weigt
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznan, Poland
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Sinyavina NG, Kochetov AA, Egorova KV, Kocherina NV, Chesnokov YV. Genetic-Biochemical Studies and Morphobiological Assessment of Small Radish (Raphanus sativus L.) under Artificial Light Culture Conditions. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422060102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Construction of an Intragenic SSR-Based Linkage Map and QTL Mapping for Agronomic Traits in Chinese Cabbage (Brassica rapa L. ssp. pekinensis). HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8020165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Chinese cabbage (Brassica rapa L. ssp. pekinensis) is one of the most widely cultivated and economically important vegetables in China. Constructing an effective genetic linkage map and mapping quantitative trait loci (QTLs) related to yield and leafy head morphology is of great importance for molecular breeding of Chinese cabbage. Using two diverse Chinese cabbage inbred lines, ZHB and G291, as parents, an F2 segregating population consisting of 240 individuals was prepared for genetic map construction and phenotype investigation in this study. The two parents are significantly different in both shape and size. Sixteen important agronomic traits of F2 individuals were investigated. A genetic map of 105 intragenic simple sequence repeat (SSR) markers distributed across 10 linkage groups (LGs) was constructed, which was 2034.1 cM in length and had an average inter-locus distance of 21.75 cM. We identified 48 QTLs for the tested important agronomic traits on the studied LGs, with LOD scores of 2.51–12.49, which explained the phenotypic variance of 3.41–26.66%. The QTLs identified in this study will facilitate further genetic analysis and marker-assisted genetic improvement of Chinese cabbage.
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Ma Y, Chhapekar SS, Lu L, Yu X, Kim S, Lee SM, Gan TH, Choi GJ, Lim YP, Choi SR. QTL mapping for Fusarium wilt resistance based on the whole-genome resequencing and their association with functional genes in Raphanus sativus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3925-3940. [PMID: 34387712 DOI: 10.1007/s00122-021-03937-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 08/03/2021] [Indexed: 06/13/2023]
Abstract
Two major QTL associated with resistance to Fusarium wilt (FW) were identified using whole-genome resequencing. Sequence variations and gene expression level differences suggest that TIR-NBS and LRR-RLK are candidate genes associated with FW-resistance. Fusarium wilt (FW) caused by Fusarium oxysporum f. sp. raphani is an important disease in radish, leading to severe decrease in yield and quality. YR4 as a novel genetic source to resistant to FW was confirmed through screening with five pathogen isolates. We have generated F2 and F2:3 populations segregated with FW resistance using YR4 and YR18 inbred lines. The disease symptom was evaluated in F2:3 population (n = 180) in three independent studies over two years. We identified 4 QTL including the two major QTL (FoRsR7.159A and FoRsR9.359A). FoRsR7.159A and FoRsR9.359A were detected in three replicated experiments. FoRsR7.159A was delimited to the 2.18-Mb physical interval on chromosome R07, with a high LOD value (5.17-12.84) and explained phenotypic variation (9.34%-27.97%). The FoRsR9.359A represented relatively low LOD value (3.38-4.52) and explained phenotypic variation (6.24%-8.82%). On the basis of the re-sequencing data for the parental lines, we identified five putative resistance-related genes and 13 unknown genes with sequence variations at the gene and protein levels. A semi-quantitative RT-PCR analysis revealed that Rs382940 (TIR-NBS) and Rs382200 (RLK) were expressed only in 'YR4' from 0 to 6 days after the inoculation. Moreover, Rs382950 (TIR-NBS-LRR) was more highly expressed in 'YR4' from 3 to 6 days after the inoculation. These three genes might be important for FW-resistance in radish. We identified several markers based on these potential candidate genes. The marker set should be useful for breeding system to introduce the FW resistance loci from 'YR4' to improve tolerance to FW.
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Affiliation(s)
- Yinbo Ma
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daehak-ro, Yuseong-gu, Daejeon, 34134, Republic of Korea
| | - Sushil Satish Chhapekar
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daehak-ro, Yuseong-gu, Daejeon, 34134, Republic of Korea
| | - Lu Lu
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daehak-ro, Yuseong-gu, Daejeon, 34134, Republic of Korea
| | - Xiaona Yu
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daehak-ro, Yuseong-gu, Daejeon, 34134, Republic of Korea
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Shandong Peanut Industry Collaborative Innovation Center, College of Agronomy, Qingdao Agricultural University, Qingdao, 266000, China
| | - Seungho Kim
- Neo Seed Co., 256-45 Jingeonjung-gil, Gongdo-eup, Anseong, Gyeonggi Province, 17565, Republic of Korea
| | - Soo Min Lee
- Center for Eco-Friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea
| | - Tae Hyoung Gan
- JIREH Seed Co., 104 Dongtansunhwan-daero 20-gil, Hwaseong, Gyeonggi Province, 18484, Republic of Korea
| | - Gyung Ja Choi
- Center for Eco-Friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea
| | - Yong Pyo Lim
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daehak-ro, Yuseong-gu, Daejeon, 34134, Republic of Korea.
| | - Su Ryun Choi
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daehak-ro, Yuseong-gu, Daejeon, 34134, Republic of Korea.
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Lee ON, Koo H, Yu JW, Park HY. Genotyping-by-Sequencing-Based Genome-Wide Association Studies of Fusarium Wilt Resistance in Radishes ( Raphanus sativus L.). Genes (Basel) 2021; 12:genes12060858. [PMID: 34205206 PMCID: PMC8228987 DOI: 10.3390/genes12060858] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/27/2021] [Accepted: 06/02/2021] [Indexed: 11/22/2022] Open
Abstract
Fusarium wilt (FW) is a fungal disease that causes severe yield losses in radish production. The most effective method to control the FW is the development and use of resistant varieties in cultivation. The identification of marker loci linked to FW resistance are expected to facilitate the breeding of disease-resistant radishes. In the present study, we applied an integrated framework of genome-wide association studies (GWAS) using genotyping-by-sequencing (GBS) to identify FW resistance loci among a panel of 225 radish accessions, including 58 elite breeding lines. Phenotyping was conducted by manual inoculation of seedlings with the FW pathogen, and scoring for the disease index was conducted three weeks after inoculation during two constitutive years. The GWAS analysis identified 44 single nucleotide polymorphisms (SNPs) and twenty putative candidate genes that were significantly associated with FW resistance. In addition, a total of four QTLs were identified from F2 population derived from a FW resistant line and a susceptible line, one of which was co-located with the SNPs on chromosome 7, detected in GWAS study. These markers will be valuable for molecular breeding programs and marker-assisted selection to develop FW resistant varieties of R. sativus.
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Affiliation(s)
- O New Lee
- College of Life Sciences, Sejong University, Seoul 05006, Korea;
| | - Hyunjin Koo
- Department of Agricultural Biotechnology and Research, Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea;
| | | | - Han Yong Park
- College of Life Sciences, Sejong University, Seoul 05006, Korea;
- Correspondence:
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Yu X, Lu L, Ma Y, Chhapekar SS, Yi SY, Lim YP, Choi SR. Fine-mapping of a major QTL (Fwr1) for fusarium wilt resistance in radish. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:329-340. [PMID: 31686113 DOI: 10.1007/s00122-019-03461-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 10/15/2019] [Indexed: 06/10/2023]
Abstract
A major radish QTL (Fwr1) for fusarium wilt resistance was fine-mapped. Sequence and expression analyses suggest that a gene encoding a serine/arginine-rich protein kinase is a candidate gene for Fwr1. Fusarium wilt resistance locus 1 (Fwr1) is a major quantitative trait locus (QTL) mediating the resistance of radish inbred line 'B2' to Fusarium oxysporum, which is responsible for fusarium wilt. We previously detected Fwr1 on radish linkage group 3 (i.e., chromosome 5). In this study, a high-resolution genetic map of the Fwr1 locus was constructed by analyzing 354 recombinant F2 plants derived from a cross between 'B2' and '835', the latter of which is susceptible to fusarium wilt. The Fwr1 QTL was fine-mapped to a 139.8-kb region between markers FM82 and FM87 in the middle part of chromosome 5. Fifteen candidate genes were predicted in this region based on a sequence comparison with the 'WK10039' radish reference genome. Additionally, we examined the time-course expression patterns of these predicted genes following an infection by the fusarium wilt pathogen. The ORF4 expression level was significantly higher in the resistant 'B2' plants than in the susceptible '835' plants. The ORF4 sequence was predicted to encode a serine/arginine-rich protein kinase and includes SNPs that result in nonsynonymous mutations, which may have important functional consequences. This study reveals a novel gene responsible for fusarium wilt resistance in radish. Further analyses of this gene may elucidate the molecular mechanisms underlying the fusarium wilt resistance of plants.
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Affiliation(s)
- Xiaona Yu
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon, Korea
- Agronomy Department, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Lu Lu
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon, Korea
| | - Yinbo Ma
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon, Korea
| | - Sushil Satish Chhapekar
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon, Korea
| | - So Young Yi
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon, Korea
| | - Yong Pyo Lim
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon, Korea
| | - Su Ryun Choi
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon, Korea.
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11
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Hirao T, Matsunaga K, Hirakawa H, Shirasawa K, Isoda K, Mishima K, Tamura M, Watanabe A. Construction of genetic linkage map and identification of a novel major locus for resistance to pine wood nematode in Japanese black pine (Pinus thunbergii). BMC PLANT BIOLOGY 2019; 19:424. [PMID: 31615405 PMCID: PMC6792208 DOI: 10.1186/s12870-019-2045-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 09/20/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Pine wilt disease (PWD), which is caused by the pine wood nematode (PWN) Bursaphelenchus xylophilus, is currently the greatest threat to pine forests in Europe and East Asian countries including Japan. Constructing a detailed linkage map of DNA markers and identifying PWD resistance genes/loci lead to improved resistance in Pinus thunbergii, as well as other Pinus species that are also susceptible to PWD. RESULTS A total F1 mapping population of 188 individuals derived from a cross between the PWD-resistant P. thunbergii varieties 'Tanabe 54' (resistant rank 2 to PWD) and 'Tosashimizu 63' (resistant rank 4 to PWD) was inoculated with PWN, and was evaluated for disease symptoms. To perform linkage analysis for PWN resistance, a set of three maps was constructed; two parental maps generated using the integrated two-way pseudo-testcross method, and a consensus map with population-type cross-pollination. The linkage map of 'Tanabe 54' consisted of 167 loci, and covered 14 linkage groups (LGs), with a total genetic distance of 1214.6 cM. The linkage map of 'Tosashimizu 63' consisted of 252 loci, and covered 14 LGs, with a total genetic distance of 1422.1 cM. The integrated consensus map comprised 12 LGs with the basic chromosome number of P. thunbergii, and a total genetic distance of 1403.6 cM. Results from quantitative trait loci (QTL) analysis using phenotype data and linkage maps indicated that PWN resistance is controlled by a single dominant allele, which was derived from the 'Tanabe 54' female parent. This major QTL was located on linkage group 3 and was designated PWD1 for PINE WILT DISEASE 1. CONCLUSIONS The PWD1 locus is a major resistance QTL located on the Pinus consensus LG03 that acts in a dominant manner to confer pine wood nematode resistance. Information from the present study will be useful for P. thunbergii breeding programs to improve resistance to PWD, and also to help identify susceptibility genes in Pinus species.
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Affiliation(s)
- Tomonori Hirao
- Forest Bio-research Center, Forestry and Forest Products Research Institute, 3809-1 Ishi, Juo, Hitachi, Ibaraki 319-1301 Japan
| | - Koji Matsunaga
- Kyushu Regional Breeding Office, Forest Tree Breeding Center, Forestry and Forest Products Research Institute, 2320-5 Suya, Goshi, Kumamoto, 860-0081 Japan
| | - Hideki Hirakawa
- Department of Frontier Research, Kazusa DNA Research Institute, Chiba, 292-0818 Japan
| | - Kenta Shirasawa
- Department of Frontier Research, Kazusa DNA Research Institute, Chiba, 292-0818 Japan
| | - Keiya Isoda
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, 3809-1 Ishi, Juo, Hitachi, Ibaraki 319-1301 Japan
| | - Kentaro Mishima
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, 3809-1 Ishi, Juo, Hitachi, Ibaraki 319-1301 Japan
| | - Miho Tamura
- Department of Forest Environmental Sciences, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, 812-8581 Japan
| | - Atsushi Watanabe
- Department of Forest Environmental Sciences, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, 812-8581 Japan
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Yu HJ, Baek S, Lee YJ, Cho A, Mun JH. The radish genome database (RadishGD): an integrated information resource for radish genomics. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2019; 2019:5306501. [PMID: 30722041 PMCID: PMC6361821 DOI: 10.1093/database/baz009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 01/11/2019] [Indexed: 11/13/2022]
Abstract
Radish (Raphanus sativus L.) is an important root vegetable crop in the family Brassicaceae, which provides diverse nutrients for human health and is closely related to the Brassica crop species. Recently, we sequenced and assembled the radish genome into nine chromosome pseudomolecules. In addition, we developed diverse genomic resources, including genetic maps, molecular markers, transcriptome, genome-wide methylation and variome data. In this study, we describe the radish genome database (RadishGD), including details of data sets that we generated and the web interface that allows access to these data. RadishGD comprises six major units that enable researchers and general users to search, browse and analyze the radish genomic data in an integrated manner. The Search unit provides gene structures and sequences for gene models through keyword or BLAST searches. The Genome browser displays graphic representations of gene models, mRNAs, repetitive sequences, genome-wide methylation and variomes among various genotypes. The Functional annotation unit offers gene ontology, plant ontology, pathway and gene family information for gene models. The Genetic map unit provides information about markers and their genetic locations using two types of genetic maps. The Expression unit presents transcriptional characteristics and methylation levels for each gene in 18 tissues. All sequence data incorporated into RadishGD can be downloaded from the Data resources unit. RadishGD will be continually updated to serve as a community resource for radish genomics and breeding research.
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Affiliation(s)
- Hee-Ju Yu
- Department of Life Science, The Catholic University of Korea, Bucheon, Korea
| | - Seunghoon Baek
- Department of Bioscience and Bioinformatics, Myongji University, Yongin, Korea
| | - Young-Joon Lee
- Department of Life Science, The Catholic University of Korea, Bucheon, Korea
| | - Ara Cho
- Department of Bioscience and Bioinformatics, Myongji University, Yongin, Korea
| | - Jeong-Hwan Mun
- Department of Bioscience and Bioinformatics, Myongji University, Yongin, Korea
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Kim J, Manivannan A, Kim DS, Lee ES, Lee HE. Transcriptome sequencing assisted discovery and computational analysis of novel SNPs associated with flowering in Raphanus sativus in-bred lines for marker-assisted backcross breeding. HORTICULTURE RESEARCH 2019; 6:120. [PMID: 31700647 PMCID: PMC6823433 DOI: 10.1038/s41438-019-0200-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 08/29/2019] [Accepted: 09/02/2019] [Indexed: 05/08/2023]
Abstract
The sequencing of radish genome aids in the better understanding and tailoring of traits associated with economic importance. In order to accelerate the genomics assisted breeding and genetic selection, transcriptomes of 33 radish inbred lines with diverse traits were sequenced for the development of single nucleotide polymorphic (SNP) markers. The sequence reads ranged from 2,560,543,741 bp to 20,039,688,139 bp with the GC (%) of 47.80-49.34 and phred quality score (Q30) of 96.47-97.54%. A total of 4951 polymorphic SNPs were identified among the accessions after stringent filtering and 298 SNPs with efficient marker assisted backcross breeding (MAB) markers were generated from the polymorphic SNPs. Further, functional annotations of SNPs revealed the effects and importance of the SNPs identified in the flowering process. The SNPs were predominantly associated with the four major flowering related transcription factors such as MYB, MADS box (AG), AP2/EREB, and bHLH. In addition, SNPs in the vital flowering integrator gene (FT) and floral repressors (EMBRYONIC FLOWER 1, 2, and FRIGIDA) were identified among the radish inbred lines. Further, 50 SNPs were randomly selected from 298 SNPs and validated using Kompetitive Allele Specific PCR genotyping system (KASP) in 102 radish inbred lines. The homozygosity of the inbred lines varied from 56 to 96% and the phylogenetic analysis resulted in the clustering of inbred lines into three subgroups. Taken together, the SNP markers identified in the present study can be utilized for the discrimination, seed purity test, and adjusting parental combinations for breeding in radish.
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Affiliation(s)
- Jinhee Kim
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, 55365 Republic of Korea
| | - Abinaya Manivannan
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, 55365 Republic of Korea
| | - Do-Sun Kim
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, 55365 Republic of Korea
| | - Eun-Su Lee
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, 55365 Republic of Korea
| | - Hye-Eun Lee
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, 55365 Republic of Korea
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Gene Introgression in Weeds Depends on Initial Gene Location in the Crop: Brassica napus- Raphanus raphanistrum Model. Genetics 2017; 206:1361-1372. [PMID: 28533439 DOI: 10.1534/genetics.117.201715] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 05/07/2017] [Indexed: 11/18/2022] Open
Abstract
The effect of gene location within a crop genome on its transfer to a weed genome remains an open question for gene flow assessment. To elucidate this question, we analyzed advanced generations of intergeneric hybrids, derived from an initial pollination of known oilseed rape varieties (Brassica napus, AACC, 2n = 38) by a local population of wild radish (Raphanus raphanistrum, RrRr, 2n = 18). After five generations of recurrent pollination, 307 G5 plants with a chromosome number similar to wild radish were genotyped using 105 B. napus specific markers well distributed along the chromosomes. They revealed that 49.8% of G5 plants carried at least one B. napus genomic region. According to the frequency of B. napus markers (0-28%), four classes were defined: Class 1 (near zero frequency), with 75 markers covering ∼70% of oilseed rape genome; Class 2 (low frequency), with 20 markers located on 11 genomic regions; Class 3 (high frequency), with eight markers on three genomic regions; and Class 4 (higher frequency), with two adjacent markers detected on A10. Therefore, some regions of the oilseed rape genome are more prone than others to be introgressed into wild radish. Inheritance and growth of plant progeny revealed that genomic regions of oilseed rape could be stably introduced into wild radish and variably impact the plant fitness (plant height and seed number). Our results pinpoint that novel technologies enabling the targeted insertion of transgenes should select genomic regions that are less likely to be introgressed into the weed genome, thereby reducing gene flow.
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15
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Qi W, Lin F, Liu Y, Huang B, Cheng J, Zhang W, Zhao H. High-throughput development of simple sequence repeat markers for genetic diversity research in Crambe abyssinica. BMC PLANT BIOLOGY 2016; 16:139. [PMID: 27317011 PMCID: PMC4912734 DOI: 10.1186/s12870-016-0828-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 06/08/2016] [Indexed: 05/13/2023]
Abstract
BACKGROUND The allohexaploid Crambe abyssinica (crambe) is an oilseed crop that has been recognized for its potential value in the chemical industry, particularly in terms of producing high-erucic acid content vegetable oil. However, as an understudied crop, improvement of crambe has been hampered by the lack of genetic and genomic information to enhance its yield, oil quality and resistance against biotic and abiotic stress. Development of molecular markers is therefore of great significance to facilitate genetic improvement of crambe. RESULTS In this study, high-throughput sequencing was performed to generate sequences for the transcriptome and genome of a widely planted crambe cultivar, Galactica. A total of 186,778 expressed sequence tag (EST) contigs as 8,130,350 genomic contigs were assembled as well. Altogether, 82,523 pairs of primers were designed in the flanking sequences of the simple sequence repeat (SSR) within these contigs. Virtual PCR analysis showed that a fraction of these primers could be mapped onto the genomes of related species of Brassica, including Brassica rapa, B. oleraceae and B. napus. Genetic diversity analysis using a subset of 166 markers on 30 independent C. abyssinica accessions exhibited that 1) 95 % of the designed SSRs were polymorphic among these accessions; 2) the polymorphism information content (PIC) value of the markers ranged from 0.13 to 0.89; 3) the genetic distances (coefficient NEI72) between accessions varied from 0.06 to 0.36. Cluster analysis subsequent on the accessions demonstrated consistency with crambe breeding history. F-statistics analysis revealed a moderate level of genetic differentiation in C. abyssinica (Gst = 0.3934) and a accordingly low estimated gene flow (Nm = 0.7709). CONCLUSION Application of high-throughput sequencing technology has facilitated SSR marker development, which was successfully employed in evaluating genetic diversity of C. abyssinica as demonstrated in our study. Results showed these molecular markers were robust and provided powerful tools for assessing genetic diversity and estimating crambe breeding history. Moreover, the SSR primers and sequence information developed in the study are freely available to the research community.
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Affiliation(s)
- Weicong Qi
- />Institute of Biotechnology, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 China
| | - Feng Lin
- />Institute of Biotechnology, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 China
| | - Yuhe Liu
- />Department of Crop Sciences, University of Illinois, Urbana-Champaign, IL 61801 USA
| | - Bangquan Huang
- />College of Life Science, Hubei University, Wuhan, 430062 China
| | - Jihua Cheng
- />College of Life Science, Hubei University, Wuhan, 430062 China
| | - Wei Zhang
- />Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, NJ 08854 USA
| | - Han Zhao
- />Institute of Biotechnology, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 China
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16
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Characterizing the transcriptome and molecular markers information for roach, Rutilus rutilus. J Genet 2016; 95:45-51. [PMID: 27019431 DOI: 10.1007/s12041-015-0597-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Rutilus rutilus (roach) is native to most of Europe and western Asia, and the Irtysh River basin in Sinkiang, northwest China is the marginal area of their natural distribution. The wide distribution and unique characteristic of this species makes it an ideal model for analysing ecological and comparative genomics. However, the limited genome sequences available for this species have hindered these investigations. Transcriptomes from the brains and livers of five individuals collected from the Irtysh River basin were sequenced using Illumina paired-end sequencing technology. A collection of 132,289 unigenes for this species were obtained using a de novo assembly method based on nearly 120 million clean reads encompassing more than 14 Gb data. Approximately 37.5% (49,656), 27.1% (35,867) and 21.2% (27,987) of the transcriptome had homologues deposited in Nt, Nr and Swiss-Prot, respectively; 12.3% (16,328) were assigned to eukaryotic orthologous groups of proteins classifications, and 21.5% (28,429) harboured Interpro domains. On the basis of the assembled transcriptome, we detected 177,493 single-nuc leotide variation resident in 39.3% (52,029) of the sequences and 20.8% (27,497) of the sequences harbouring 36,639 simple sequence repeats. The identified molecular markers are a basis for further ecological analysis, and the transcriptome reported here allows for more extensive evolutionary analyses of the Cyprinidae, the most species-rich family of freshwater fishes.
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17
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Jung WY, Park HJ, Lee A, Lee SS, Kim YS, Cho HS. Identification of Flowering-Related Genes Responsible for Differences in Bolting Time between Two Radish Inbred Lines. FRONTIERS IN PLANT SCIENCE 2016; 7:1844. [PMID: 28018383 PMCID: PMC5145866 DOI: 10.3389/fpls.2016.01844] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 11/22/2016] [Indexed: 05/19/2023]
Abstract
Late bolting after cold exposure is an economically important characteristic of radish (Raphanus sativus L.), an important Brassicaceae root vegetable crop. However, little information is available regarding the genes and pathways that govern flowering time in this species. We performed high-throughput RNA sequencing analysis to elucidate the molecular mechanisms that determine the differences in flowering times between two radish lines, NH-JS1 (late bolting) and NH-JS2 (early bolting). In total, 71,188 unigenes were identified by reference-guided assembly, of which 309, 788, and 980 genes were differentially expressed between the two inbred lines after 0, 15, and 35 days of vernalization, respectively. Among these genes, 218 homologs of Arabidopsis flowering-time (Ft) genes were identified in the radish, and 49 of these genes were differentially expressed between the two radish lines in the presence or absence of vernalization treatment. Most of the Ft genes up-regulated in NH-JS1 vs. NH-JS2 were repressors of flowering, such as RsFLC, consistent with the late-bolting phenotype of NH-JS1. Although, the functions of genes down-regulated in NH-JS1 were less consistent with late-bolting characteristics than the up-regulated Ft genes, several Ft enhancer genes, including RsSOC1, a key floral integrator, showed an appropriate expression to the late-bolting phenotype. In addition, the patterns of gene expression related to the vernalization pathway closely corresponded with the different bolting times of the two inbred lines. These results suggest that the vernalization pathway is conserved between radish and Arabidopsis.
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Affiliation(s)
- Won Yong Jung
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and BiotechnologyDaejeon, Korea
| | - Hyun Ji Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and BiotechnologyDaejeon, Korea
| | - Areum Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and BiotechnologyDaejeon, Korea
- Biosystems and Bioengineering Program, University of Science and TechnologyDaejeon, South Korea
| | - Sang Sook Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and BiotechnologyDaejeon, Korea
| | - Youn-Sung Kim
- Department of Biotechnology, NongHyup SeedAnseong, South Korea
- *Correspondence: Youn-Sung Kim
| | - Hye Sun Cho
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and BiotechnologyDaejeon, Korea
- Biosystems and Bioengineering Program, University of Science and TechnologyDaejeon, South Korea
- Hye Sun Cho
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18
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Yu X, Choi SR, Dhandapani V, Rameneni JJ, Li X, Pang W, Lee JY, Lim YP. Quantitative Trait Loci for Morphological Traits and their Association with Functional Genes in Raphanus sativus. FRONTIERS IN PLANT SCIENCE 2016; 7:255. [PMID: 26973691 PMCID: PMC4777717 DOI: 10.3389/fpls.2016.00255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 02/15/2016] [Indexed: 05/04/2023]
Abstract
Identification of quantitative trait loci (QTLs) governing morphologically important traits enables to comprehend their potential genetic mechanisms in the genetic breeding program. In this study, we used 210 F2 populations derived from a cross between two radish inbred lines (Raphanus sativus) "835" and "B2," including 258 SSR markers were used to detect QTLs for 11 morphological traits that related to whole plant, leaf, and root yield in 3 years of replicated field test. Total 55 QTLs were detected which were distributed on each linkage group of the Raphanus genome. Individual QTLs accounted for 2.69-12.6 of the LOD value, and 0.82-16.25% of phenotypic variation. Several genomic regions have multiple traits that clustered together, suggested the existence of pleiotropy linkage. Synteny analysis of the QTL regions with A. thaliana genome selected orthologous genes in radish. InDels and SNPs in the parental lines were detected in those regions by Illumina genome sequence. Five identified candidate gene-based markers were validated by co-mapping with underlying QTLs affecting different traits. Semi-quantitative reverse transcriptase PCR analysis showed the different expression levels of these five genes in parental lines. In addition, comparative QTL analysis with B. rapa revealed six common QTL regions and four key major evolutionarily conserved crucifer blocks (J, U, R, and W) harboring QTL for morphological traits. The QTL positions identified in this study will provide a valuable resource for identifying more functional genes when whole radish genome sequence is released. Candidate genes identified in this study that co-localized in QTL regions are expected to facilitate in radish breeding programs.
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Affiliation(s)
- Xiaona Yu
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National UniversityDaejeon, South Korea
| | - Su Ryun Choi
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National UniversityDaejeon, South Korea
| | - Vignesh Dhandapani
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National UniversityDaejeon, South Korea
| | - Jana Jeevan Rameneni
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National UniversityDaejeon, South Korea
| | - Xiaonan Li
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National UniversityDaejeon, South Korea
| | - Wenxing Pang
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National UniversityDaejeon, South Korea
| | - Ji-Young Lee
- School of Biological Sciences, College of Natural Science, Seoul National UniversitySeoul, South Korea
| | - Yong Pyo Lim
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National UniversityDaejeon, South Korea
- *Correspondence: Yong Pyo Lim
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Mitsui Y, Shimomura M, Komatsu K, Namiki N, Shibata-Hatta M, Imai M, Katayose Y, Mukai Y, Kanamori H, Kurita K, Kagami T, Wakatsuki A, Ohyanagi H, Ikawa H, Minaka N, Nakagawa K, Shiwa Y, Sasaki T. The radish genome and comprehensive gene expression profile of tuberous root formation and development. Sci Rep 2015; 5:10835. [PMID: 26056784 PMCID: PMC4650646 DOI: 10.1038/srep10835] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 04/08/2015] [Indexed: 12/23/2022] Open
Abstract
Understanding the processes that regulate plant sink formation and development at the molecular level will contribute to the areas of crop breeding, food production and plant evolutionary studies. We report the annotation and analysis of the draft genome sequence of the radish Raphanus sativus var. hortensis (long and thick root radish) and transcriptome analysis during root development. Based on the hybrid assembly approach of next-generation sequencing, a total of 383 Mb (N50 scaffold: 138.17 kb) of sequences of the radish genome was constructed containing 54,357 genes. Syntenic and phylogenetic analyses indicated that divergence between Raphanus and Brassica coincide with the time of whole genome triplication (WGT), suggesting that WGT triggered diversification of Brassiceae crop plants. Further transcriptome analysis showed that the gene functions and pathways related to carbohydrate metabolism were prominently activated in thickening roots, particularly in cell proliferating tissues. Notably, the expression levels of sucrose synthase 1 (SUS1) were correlated with root thickening rates. We also identified the genes involved in pungency synthesis and their transcription factors.
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Affiliation(s)
- Yuki Mitsui
- Tokyo University of Agriculture, 1-1-1, Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Michihiko Shimomura
- Mitsubishi Space Software Co., Ltd., 1-6-1, Takezono, Tsukuba, Ibaraki 305-0032, Japan
| | - Kenji Komatsu
- Junior College of Tokyo University of Agriculture, 1-1-1, Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Nobukazu Namiki
- Mitsubishi Space Software Co., Ltd., 1-6-1, Takezono, Tsukuba, Ibaraki 305-0032, Japan
| | - Mari Shibata-Hatta
- Tokyo University of Agriculture, 1-1-1, Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Misaki Imai
- Tokyo University of Agriculture, 1-1-1, Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Yuichi Katayose
- National Institute of Agrobiological Sciences, 1-2, Owashi, Tsukuba, Ibaraki, 305-8634, Japan
| | - Yoshiyuki Mukai
- National Institute of Agrobiological Sciences, 1-2, Owashi, Tsukuba, Ibaraki, 305-8634, Japan
| | - Hiroyuki Kanamori
- National Institute of Agrobiological Sciences, 1-2, Owashi, Tsukuba, Ibaraki, 305-8634, Japan
| | - Kanako Kurita
- National Institute of Agrobiological Sciences, 1-2, Owashi, Tsukuba, Ibaraki, 305-8634, Japan
| | - Tsutomu Kagami
- Sakata Seed Corporation, 2-7-1, Nakamachidai, Tuzuki-ku, Yokohama, 224-0041, Japan
| | - Akihito Wakatsuki
- Sakata Seed Corporation, 2-7-1, Nakamachidai, Tuzuki-ku, Yokohama, 224-0041, Japan
| | - Hajime Ohyanagi
- Mitsubishi Space Software Co., Ltd., 1-6-1, Takezono, Tsukuba, Ibaraki 305-0032, Japan
| | - Hiroshi Ikawa
- Mitsubishi Space Software Co., Ltd., 1-6-1, Takezono, Tsukuba, Ibaraki 305-0032, Japan
| | - Nobuhiro Minaka
- 1] Tokyo University of Agriculture, 1-1-1, Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan [2] National Institute for Agro-Environmental Science, 3-1-3, Tukuba, 305-8604, Japan
| | - Kunihiro Nakagawa
- Tokyo University of Agriculture, 1-1-1, Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Yu Shiwa
- Tokyo University of Agriculture, 1-1-1, Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Takuji Sasaki
- 1] Tokyo University of Agriculture, 1-1-1, Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan [2] National Institute of Agrobiological Sciences, 1-2, Owashi, Tsukuba, Ibaraki, 305-8634, Japan
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Mun JH, Chung H, Chung WH, Oh M, Jeong YM, Kim N, Ahn BO, Park BS, Park S, Lim KB, Hwang YJ, Yu HJ. Construction of a reference genetic map of Raphanus sativus based on genotyping by whole-genome resequencing. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:259-272. [PMID: 25403353 DOI: 10.1007/s00122-014-2426-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 11/02/2014] [Indexed: 06/04/2023]
Abstract
This manuscript provides a genetic map of Raphanus sativus that has been used as a reference genetic map for an ongoing genome sequencing project. The map was constructed based on genotyping by whole-genome resequencing of mapping parents and F 2 population. Raphanus sativus is an annual vegetable crop species of the Brassicaceae family and is one of the key plants in the seed industry, especially in East Asia. Assessment of the R. sativus genome provides fundamental resources for crop improvement as well as the study of crop genome structure and evolution. With the goal of anchoring genome sequence assemblies of R. sativus cv. WK10039 whose genome has been sequenced onto the chromosomes, we developed a reference genetic map based on genotyping of two parents (maternal WK10039 and paternal WK10024) and 93 individuals of the F2 mapping population by whole-genome resequencing. To develop high-confidence genetic markers, ~83 Gb of parental lines and ~591 Gb of mapping population data were generated as Illumina 100 bp paired-end reads. High stringent sequence analysis of the reads mapped to the 344 Mb of genome sequence scaffolds identified a total of 16,282 SNPs and 150 PCR-based markers. Using a subset of the markers, a high-density genetic map was constructed from the analysis of 2,637 markers spanning 1,538 cM with 1,000 unique framework loci. The genetic markers integrated 295 Mb of genome sequences to the cytogenetically defined chromosome arms. Comparative analysis of the chromosome-anchored sequences with Arabidopsis thaliana and Brassica rapa revealed that the R. sativus genome has evident triplicated sub-genome blocks and the structure of gene space is highly similar to that of B. rapa. The genetic map developed in this study will serve as fundamental genomic resources for the study of R. sativus.
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Affiliation(s)
- Jeong-Hwan Mun
- Department of Bioscience and Bioinformatics, Myongji University, Yongin, 449-728, Korea
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Yuan F, Yu H, Zuo S, Adams A. Development of EST-SSR for preliminary analysis of genetic diversity of Cordyceps militaris. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2014.11.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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22
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Qin X, Warguchuk R, Arnal N, Gaborieau L, Mireau H, Brown GG. In vivo functional analysis of a nuclear restorer PPR protein. BMC PLANT BIOLOGY 2014; 14:313. [PMID: 25403785 PMCID: PMC4240901 DOI: 10.1186/s12870-014-0313-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 10/30/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND Nuclear restorers of cytoplasmic male fertility (CMS) act to suppress the male sterile phenotype by down-regulating the expression of novel CMS-specifying mitochondrial genes. One such restorer gene is Rfo, which restores fertility to the radish Ogura or ogu CMS. Rfo, like most characterized restorers, encodes a pentatricopeptide repeat (PPR) protein, a family of eukaryotic proteins characterized by tandem repeats of a 35 amino acid motif. While over 400 PPR genes are found in characterized plant genomes and the importance of this gene family in organelle gene expression is widely recognized, few detailed in vivo assessments of primary structure-function relationships in this protein family have been conducted. RESULTS In contrast to earlier studies, which identified 16 or 17 PPR domains in the Rfo protein, we now find, using a more recently developed predictive tool, that Rfo has 18 repeat domains with the additional domain N-terminal to the others. Comparison of transcript sequences from pooled rfo/rfo plants with pooled Rfo/Rfo plants of a mapping population led to the identification of a non-restoring rfo allele with a 12 bp deletion in the fourth domain. Introduction into ogu CMS plants of a genetic construct in which this deletion had been introduced into Rfo led to a partial loss in the capacity to produce viable pollen, as assessed by vital staining, pollen germination and the capacity for seed production following pollination of CMS plants. The degree of viable pollen production among different transgenic plants roughly correlated with the copy number of the introduced gene and with the reduction of the levels of the ORF138 CMS-associated protein. All other constructs tested, including one in which only the C-terminal PPR repeat was deleted and another in which this repeat was replaced by the corresponding domain of the related, non-restoring gene, PPR-A, failed to result in any measure of fertility restoration. CONCLUSIONS The identification of the additional PPR domain in Rfo indicates that the protein, apart from its N-terminal mitochondrial targeting presequence, consists almost entirely of PPR repeats. The newly identified rfo allele carries the same 4 amino acid deletion as that found in the neighboring, related, non-restoring PPR gene, PPR-A. Introduction of this four amino acid deletion into a central domain the Rfo protein, however, only partially reduces its restoration capacity, even though this alteration might be expected to alter the spacing between the adjoining repeats. All other tested alterations, generated by deleting specific PPR repeats or exchanging repeats with corresponding domains of PPR-A, led to a complete loss of restorer function. Overall we demonstrate that introduction of targeted alterations of Rfo into ogu CMS plants provides a sensitive in vivo readout for analysis of the relationship between primary structure and biological function in this important family of plant proteins.
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Affiliation(s)
- Xike Qin
- />Department of Biology, McGill University, 1205 Doctor Penfield Ave., Montreal, QC H3A 1B1 Canada
- />Current address: Lady Davis Institute for Medical research, 3999 Cote Ste-Catherine Rd., Montreal, QC H3T 1E2 Canada
| | - Richard Warguchuk
- />Department of Biology, McGill University, 1205 Doctor Penfield Ave., Montreal, QC H3A 1B1 Canada
- />Current address: Deparment of Pharmacology and Therapeutics, McGill University, 3655 Promenade Sir-William-Osler, Montréal, QC H3G 1Y6 Canada
| | - Nadège Arnal
- />INRA, UMR1318, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France
- />AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France
- />Current address: INRA, Centre National de Ressources Génomiques Végétales, Castanet Tolosan, France
| | - Lydiane Gaborieau
- />Department of Biology, McGill University, 1205 Doctor Penfield Ave., Montreal, QC H3A 1B1 Canada
| | - Hakim Mireau
- />INRA, UMR1318, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France
- />AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France
| | - Gregory G Brown
- />Department of Biology, McGill University, 1205 Doctor Penfield Ave., Montreal, QC H3A 1B1 Canada
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Cai G, Yang Q, Yi B, Fan C, Edwards D, Batley J, Zhou Y. A complex recombination pattern in the genome of allotetraploid Brassica napus as revealed by a high-density genetic map. PLoS One 2014; 9:e109910. [PMID: 25356735 PMCID: PMC4214627 DOI: 10.1371/journal.pone.0109910] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Accepted: 09/13/2014] [Indexed: 12/29/2022] Open
Abstract
Polyploidy plays a crucial role in plant evolution. Brassica napus (2n = 38, AACC), the most important oil crop in the Brassica genus, is an allotetraploid that originated through natural doubling of chromosomes after the hybridization of its progenitor species, B. rapa (2n = 20, AA) and B. oleracea (2n = 18, CC). A better understanding of the evolutionary relationship between B. napus and B. rapa, B. oleracea, as well as Arabidopsis, which has a common ancestor with these three species, will provide valuable information about the generation and evolution of allopolyploidy. Based on a high-density genetic map with single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers, we performed a comparative genomic analysis of B. napus with Arabidopsis and its progenitor species B. rapa and B. oleracea. Based on the collinear relationship of B. rapa and B. oleracea in the B. napus genetic map, the B. napus genome was found to consist of 70.1% of the skeleton components of the chromosomes of B. rapa and B. oleracea, with 17.7% of sequences derived from reciprocal translocation between homoeologous chromosomes between the A- and C-genome and 3.6% of sequences derived from reciprocal translocation between non-homologous chromosomes at both intra- and inter-genomic levels. The current study thus provides insights into the formation and evolution of the allotetraploid B. napus genome, which will allow for more accurate transfer of genomic information from B. rapa, B. oleracea and Arabidopsis to B. napus.
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Affiliation(s)
- Guangqin Cai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Rapeseed Genetics and Breeding of Agriculture Ministry of China, Huazhong Agricultural University, Wuhan, China
| | - Qingyong Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Chuchuan Fan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - David Edwards
- School of Agriculture and Food Sciences, University of Queensland, St Lucia, Queensland, Australia
| | - Jacqueline Batley
- School of Agriculture and Food Sciences, University of Queensland, St Lucia, Queensland, Australia
| | - Yongming Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Rapeseed Genetics and Breeding of Agriculture Ministry of China, Huazhong Agricultural University, Wuhan, China
- * E-mail:
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Shirasawa K, Isobe S, Tabata S, Hirakawa H. Kazusa Marker DataBase: a database for genomics, genetics, and molecular breeding in plants. BREEDING SCIENCE 2014; 64:264-71. [PMID: 25320561 PMCID: PMC4154615 DOI: 10.1270/jsbbs.64.264] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 05/08/2014] [Indexed: 05/06/2023]
Abstract
In order to provide useful genomic information for agronomical plants, we have established a database, the Kazusa Marker DataBase (http://marker.kazusa.or.jp). This database includes information on DNA markers, e.g., SSR and SNP markers, genetic linkage maps, and physical maps, that were developed at the Kazusa DNA Research Institute. Keyword searches for the markers, sequence data used for marker development, and experimental conditions are also available through this database. Currently, 10 plant species have been targeted: tomato (Solanum lycopersicum), pepper (Capsicum annuum), strawberry (Fragaria × ananassa), radish (Raphanus sativus), Lotus japonicus, soybean (Glycine max), peanut (Arachis hypogaea), red clover (Trifolium pratense), white clover (Trifolium repens), and eucalyptus (Eucalyptus camaldulensis). In addition, the number of plant species registered in this database will be increased as our research progresses. The Kazusa Marker DataBase will be a useful tool for both basic and applied sciences, such as genomics, genetics, and molecular breeding in crops.
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25
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Jeong YM, Chung WH, Chung H, Kim N, Park BS, Lim KB, Yu HJ, Mun JH. Comparative analysis of the radish genome based on a conserved ortholog set (COS) of Brassica. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:1975-1989. [PMID: 25056003 DOI: 10.1007/s00122-014-2354-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 07/04/2014] [Indexed: 06/03/2023]
Abstract
This manuscript provides a Brassica conserved ortholog set (COS) that can be used as diagnostic cross-species markers as well as tools for genetic mapping and genome comparison of the Brassicaceae. A conserved ortholog set (COS) is a collection of genes that are conserved in both sequence and copy number between closely related genomes. COS is a useful resource for developing gene-based markers and is suitable for comparative genome mapping. We developed a COS for Brassica based on proteome comparisons of Arabidopsis thaliana, B. rapa, and B. oleracea to establish a basis for comparative genome analysis of crop species in the Brassicaceae. A total of 1,194 conserved orthologous single-copy genes were identified from the genomes based on whole-genome BLASTP analysis. Gene ontology analysis showed that most of them encoded proteins with unknown function and chloroplast-related genes were enriched. In addition, 152 Brassica COS primer sets were applied to 16 crop and wild species of the Brassicaceae and 57.9-92.8 % of them were successfully amplified across the species representing that a Brassica COS can be used as diagnostic cross-species markers of diverse Brassica species. We constructed a genetic map of Raphanus sativus by analyzing the segregation of 322 COS genes in an F2 population (93 individuals) of Korean cultivars (WK10039 × WK10024). Comparative genome analysis based on the COS genes showed conserved genome structures between R. sativus and B. rapa with lineage-specific rearrangement and fractionation of triplicated subgenome blocks indicating close evolutionary relationship and differentiation of the genomes. The Brassica COS developed in this study will play an important role in genetic, genomic, and breeding studies of crop Brassicaceae species.
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Affiliation(s)
- Young-Min Jeong
- Department of Life Science, The Catholic University of Korea, Bucheon, 420-743, Korea
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26
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Kitashiba H, Li F, Hirakawa H, Kawanabe T, Zou Z, Hasegawa Y, Tonosaki K, Shirasawa S, Fukushima A, Yokoi S, Takahata Y, Kakizaki T, Ishida M, Okamoto S, Sakamoto K, Shirasawa K, Tabata S, Nishio T. Draft sequences of the radish (Raphanus sativus L.) genome. DNA Res 2014; 21:481-90. [PMID: 24848699 PMCID: PMC4195494 DOI: 10.1093/dnares/dsu014] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Radish (Raphanus sativus L., n = 9) is one of the major vegetables in Asia. Since the genomes of Brassica and related species including radish underwent genome rearrangement, it is quite difficult to perform functional analysis based on the reported genomic sequence of Brassica rapa. Therefore, we performed genome sequencing of radish. Short reads of genomic sequences of 191.1 Gb were obtained by next-generation sequencing (NGS) for a radish inbred line, and 76,592 scaffolds of ≥300 bp were constructed along with the bacterial artificial chromosome-end sequences. Finally, the whole draft genomic sequence of 402 Mb spanning 75.9% of the estimated genomic size and containing 61,572 predicted genes was obtained. Subsequently, 221 single nucleotide polymorphism markers and 768 PCR-RFLP markers were used together with the 746 markers produced in our previous study for the construction of a linkage map. The map was combined further with another radish linkage map constructed mainly with expressed sequence tag-simple sequence repeat markers into a high-density integrated map of 1,166 cM with 2,553 DNA markers. A total of 1,345 scaffolds were assigned to the linkage map, spanning 116.0 Mb. Bulked PCR products amplified by 2,880 primer pairs were sequenced by NGS, and SNPs in eight inbred lines were identified.
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Affiliation(s)
- Hiroyasu Kitashiba
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan
| | - Feng Li
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Takahiro Kawanabe
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan
| | - Zhongwei Zou
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan
| | - Yoichi Hasegawa
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan
| | - Kaoru Tonosaki
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan
| | - Sachiko Shirasawa
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan
| | - Aki Fukushima
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan
| | - Shuji Yokoi
- Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan
| | - Yoshihito Takahata
- Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan
| | - Tomohiro Kakizaki
- National Institute of Vegetable and Tea Science, 360, Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Masahiko Ishida
- National Institute of Vegetable and Tea Science, 360, Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Shunsuke Okamoto
- Plant Breeding Experimental Station, Takii Seed Co. Ltd, Kohsei, Kohka-gun, Shiga 520-20, Japan
| | - Koji Sakamoto
- Plant Breeding Experimental Station, Takii Seed Co. Ltd, Kohsei, Kohka-gun, Shiga 520-20, Japan
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Satoshi Tabata
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Takeshi Nishio
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan
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Sharma A, Li X, Lim YP. Comparative genomics of Brassicaceae crops. BREEDING SCIENCE 2014; 64:3-13. [PMID: 24987286 PMCID: PMC4031108 DOI: 10.1270/jsbbs.64.3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 02/16/2014] [Indexed: 06/03/2023]
Abstract
The family Brassicaceae is one of the major groups of the plant kingdom and comprises diverse species of great economic, agronomic and scientific importance, including the model plant Arabidopsis. The sequencing of the Arabidopsis genome has revolutionized our knowledge in the field of plant biology and provides a foundation in genomics and comparative biology. Genomic resources have been utilized in Brassica for diversity analyses, construction of genetic maps and identification of agronomic traits. In Brassicaceae, comparative sequence analysis across the species has been utilized to understand genome structure, evolution and the detection of conserved genomic segments. In this review, we focus on the progress made in genetic resource development, genome sequencing and comparative mapping in Brassica and related species. The utilization of genomic resources and next-generation sequencing approaches in improvement of Brassica crops is also discussed.
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Affiliation(s)
- Ashutosh Sharma
- Graduate School of Agricultural Science, Tohoku University,
Aoba, Sendai, Miyagi 981-8555,
Japan
- Present address: Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Xiaonan Li
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University,
Daejeon 305-764,
Republic of Korea
| | - Yong Pyo Lim
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University,
Daejeon 305-764,
Republic of Korea
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Izzah NK, Lee J, Jayakodi M, Perumal S, Jin M, Park BS, Ahn K, Yang TJ. Transcriptome sequencing of two parental lines of cabbage (Brassica oleracea L. var. capitata L.) and construction of an EST-based genetic map. BMC Genomics 2014; 15:149. [PMID: 24559437 PMCID: PMC3936860 DOI: 10.1186/1471-2164-15-149] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 02/17/2014] [Indexed: 12/27/2022] Open
Abstract
Background Expressed sequence tag (EST)-based markers are preferred because they reflect transcribed portions of the genome. We report the development of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers derived from transcriptome sequences in cabbage, and their utility for map construction. Results Transcriptome sequences were obtained from two cabbage parental lines, C1184 and C1234, which are susceptible and resistant to black rot disease, respectively, using the 454 platform. A total of 92,255 and 127,522 reads were generated and clustered into 34,688 and 40,947 unigenes, respectively. We identified 2,405 SSR motifs from the unigenes of the black rot-resistant parent C1234. Trinucleotide motifs were the most abundant (66.15%) among the repeat motifs. In addition, 1,167 SNPs were detected between the two parental lines. A total of 937 EST-based SSR and 97 SNP-based dCAPS markers were designed and used for detection of polymorphism between parents. Using an F2 population, we built a genetic map comprising 265 loci, and consisting of 98 EST-based SSRs, 21 SNP-based dCAPS, 55 IBP markers derived from B. rapa genome sequence and 91 public SSRs, distributed on nine linkage groups spanning a total of 1,331.88 cM with an average distance of 5.03 cM between adjacent loci. The parental lines used in this study are elite breeding lines with little genetic diversity; therefore, the markers that mapped in our genetic map will have broad spectrum utility. Conclusions This genetic map provides additional genetic information to the existing B. oleracea map. Moreover, the new set of EST-based SSR and dCAPS markers developed herein is a valuable resource for genetic studies and will facilitate cabbage breeding. Additionally, this study demonstrates the usefulness of NGS transcriptomes for the development of genetic maps even with little genetic diversity in the mapping population.
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Affiliation(s)
| | | | | | | | | | | | | | - Tae-Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea.
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Asamizu E, Ichihara H, Nakaya A, Nakamura Y, Hirakawa H, Ishii T, Tamura T, Fukami-Kobayashi K, Nakajima Y, Tabata S. Plant Genome DataBase Japan (PGDBj): a portal website for the integration of plant genome-related databases. PLANT & CELL PHYSIOLOGY 2014; 55:e8. [PMID: 24363285 PMCID: PMC3894704 DOI: 10.1093/pcp/pct189] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The Plant Genome DataBase Japan (PGDBj, http://pgdbj.jp/?ln=en) is a portal website that aims to integrate plant genome-related information from databases (DBs) and the literature. The PGDBj is comprised of three component DBs and a cross-search engine, which provides a seamless search over the contents of the DBs. The three DBs are as follows. (i) The Ortholog DB, providing gene cluster information based on the amino acid sequence similarity. Over 500,000 amino acid sequences of 20 Viridiplantae species were subjected to reciprocal BLAST searches and clustered. Sequences from plant genome DBs (e.g. TAIR10 and RAP-DB) were also included in the cluster with a direct link to the original DB. (ii) The Plant Resource DB, integrating the SABRE DB, which provides cDNA and genome sequence resources accumulated and maintained in the RIKEN BioResource Center and National BioResource Projects. (iii) The DNA Marker DB, providing manually or automatically curated information of DNA markers, quantitative trait loci and related linkage maps, from the literature and external DBs. As the PGDBj targets various plant species, including model plants, algae, and crops important as food, fodder and biofuel, researchers in the field of basic biology as well as a wide range of agronomic fields are encouraged to perform searches using DNA sequences, gene names, traits and phenotypes of interest. The PGDBj will return the search results from the component DBs and various types of linked external DBs.
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Affiliation(s)
- Erika Asamizu
- Department of Plant Genome Research, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan
| | - Hisako Ichihara
- Department of Plant Genome Research, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan
| | - Akihiro Nakaya
- Center for Transdisciplinary Research, Niigata University, 1-757 Asahimachi-dori, Chuo-ku, Niigata, 951-8585 Japan
| | - Yasukazu Nakamura
- Department of Plant Genome Research, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan
| | - Hideki Hirakawa
- Department of Plant Genome Research, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan
| | - Takahiro Ishii
- Department of Plant Genome Research, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan
| | - Takuro Tamura
- LINE Co., Ltd., 5-201 Kandamatsunaga-cho, Tokyo, 101-0023 Japan
| | | | - Yukari Nakajima
- Department of Plant Genome Research, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan
| | - Satoshi Tabata
- Department of Plant Genome Research, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan
- *Corresponding author: Fax: +81-438-52-3918; E-mail,
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30
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Comprehensive analysis of expressed sequence tags from cultivated and wild radish (Raphanus spp.). BMC Genomics 2013; 14:721. [PMID: 24144082 PMCID: PMC3816612 DOI: 10.1186/1471-2164-14-721] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 10/18/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Radish (Raphanus sativus L., 2n = 2× = 18) is an economically important vegetable crop worldwide. A large collection of radish expressed sequence tags (ESTs) has been generated but remains largely uncharacterized. RESULTS In this study, approximately 315,000 ESTs derived from 22 Raphanus cDNA libraries from 18 different genotypes were analyzed, for the purpose of gene and marker discovery and to evaluate large-scale genome duplication and phylogenetic relationships among Raphanus spp. The ESTs were assembled into 85,083 unigenes, of which 90%, 65%, 89% and 89% had homologous sequences in the GenBank nr, SwissProt, TrEMBL and Arabidopsis protein databases, respectively. A total of 66,194 (78%) could be assigned at least one gene ontology (GO) term. Comparative analysis identified 5,595 gene families unique to radish that were significantly enriched with genes related to small molecule metabolism, as well as 12,899 specific to the Brassicaceae that were enriched with genes related to seed oil body biogenesis and responses to phytohormones. The analysis further indicated that the divergence of radish and Brassica rapa occurred approximately 8.9-14.9 million years ago (MYA), following a whole-genome duplication event (12.8-21.4 MYA) in their common ancestor. An additional whole-genome duplication event in radish occurred at 5.1-8.4 MYA, after its divergence from B. rapa. A total of 13,570 simple sequence repeats (SSRs) and 28,758 high-quality single nucleotide polymorphisms (SNPs) were also identified. Using a subset of SNPs, the phylogenetic relationships of eight different accessions of Raphanus was inferred. CONCLUSION Comprehensive analysis of radish ESTs provided new insights into radish genome evolution and the phylogenetic relationships of different radish accessions. Moreover, the radish EST sequences and the associated SSR and SNP markers described in this study represent a valuable resource for radish functional genomics studies and breeding.
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Yu X, Choi SR, Ramchiary N, Miao X, Lee SH, Sun HJ, Kim S, Ahn CH, Lim YP. Comparative mapping of Raphanus sativus genome using Brassica markers and quantitative trait loci analysis for the Fusarium wilt resistance trait. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:2553-62. [PMID: 23864230 DOI: 10.1007/s00122-013-2154-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 07/05/2013] [Indexed: 05/21/2023]
Abstract
Fusarium wilt (FW), caused by the soil-borne fungal pathogen Fusarium oxysporum is a serious disease in cruciferous plants, including the radish (Raphanus sativus). To identify quantitative trait loci (QTL) or gene(s) conferring resistance to FW, we constructed a genetic map of R. sativus using an F2 mapping population derived by crossing the inbred lines '835' (susceptible) and 'B2' (resistant). A total of 220 markers distributed in 9 linkage groups (LGs) were mapped in the Raphanus genome, covering a distance of 1,041.5 cM with an average distance between adjacent markers of 4.7 cM. Comparative analysis of the R. sativus genome with that of Arabidopsis thaliana and Brassica rapa revealed 21 and 22 conserved syntenic regions, respectively. QTL mapping detected a total of 8 loci conferring FW resistance that were distributed on 4 LGs, namely, 2, 3, 6, and 7 of the Raphanus genome. Of the detected QTL, 3 QTLs (2 on LG 3 and 1 on LG 7) were constitutively detected throughout the 2-year experiment. QTL analysis of LG 3, flanked by ACMP0609 and cnu_mBRPGM0085, showed a comparatively higher logarithm of the odds (LOD) value and percentage of phenotypic variation. Synteny analysis using the linked markers to this QTL showed homology to A. thaliana chromosome 3, which contains disease-resistance gene clusters, suggesting conservation of resistance genes between them.
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Affiliation(s)
- Xiaona Yu
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon, 305-764, Republic of Korea
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Hashida T, Nakatsuji R, Budahn H, Schrader O, Peterka H, Fujimura T, Kubo N, Hirai M. Construction of a chromosome-assigned, sequence-tagged linkage map for the radish, Raphanus sativus L. and QTL analysis of morphological traits. BREEDING SCIENCE 2013; 63:218-26. [PMID: 23853517 PMCID: PMC3688384 DOI: 10.1270/jsbbs.63.218] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 01/27/2013] [Indexed: 05/21/2023]
Abstract
The radish displays great morphological variation but the genetic factors underlying this variability are mostly unknown. To identify quantitative trait loci (QTLs) controlling radish morphological traits, we cultivated 94 F4 and F5 recombinant inbred lines derived from a cross between the rat-tail radish and the Japanese radish cultivar 'Harufuku' inbred lines. Eight morphological traits (ovule and seed numbers per silique, plant shape, pubescence and root formation) were measured for investigation. We constructed a map composed of 322 markers with a total length of 673.6 cM. The linkage groups were assigned to the radish chromosomes using disomic rape-radish chromosome-addition lines. On the map, eight and 10 QTLs were identified in 2008 and 2009, respectively. The chromosome-linkage group correspondence, the sequence-specific markers and the QTLs detected here will provide useful information for further genetic studies and for selection during radish breeding programs.
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Affiliation(s)
- Tomoko Hashida
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Seika, Kyoto 619-0244, Japan
| | - Ryoichi Nakatsuji
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Seika, Kyoto 619-0244, Japan
| | - Holger Budahn
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Horticultural and Fruit Crops, D-06484 Quedlinburg, Germany
| | - Otto Schrader
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Horticultural and Fruit Crops, D-06484 Quedlinburg, Germany
| | - Herbert Peterka
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Horticultural and Fruit Crops, D-06484 Quedlinburg, Germany
| | - Tatsuhito Fujimura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Nakao Kubo
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Seika, Kyoto 619-0244, Japan
- Corresponding author (e-mail: )
| | - Masashi Hirai
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Seika, Kyoto 619-0244, Japan
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Cheng F, Mandáková T, Wu J, Xie Q, Lysak MA, Wang X. Deciphering the diploid ancestral genome of the Mesohexaploid Brassica rapa. THE PLANT CELL 2013; 25:1541-54. [PMID: 23653472 PMCID: PMC3694691 DOI: 10.1105/tpc.113.110486] [Citation(s) in RCA: 242] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 03/23/2013] [Accepted: 04/17/2013] [Indexed: 05/18/2023]
Abstract
The genus Brassica includes several important agricultural and horticultural crops. Their current genome structures were shaped by whole-genome triplication followed by extensive diploidization. The availability of several crucifer genome sequences, especially that of Chinese cabbage (Brassica rapa), enables study of the evolution of the mesohexaploid Brassica genomes from their diploid progenitors. We reconstructed three ancestral subgenomes of B. rapa (n = 10) by comparing its whole-genome sequence to ancestral and extant Brassicaceae genomes. All three B. rapa paleogenomes apparently consisted of seven chromosomes, similar to the ancestral translocation Proto-Calepineae Karyotype (tPCK; n = 7), which is the evolutionarily younger variant of the Proto-Calepineae Karyotype (n = 7). Based on comparative analysis of genome sequences or linkage maps of Brassica oleracea, Brassica nigra, radish (Raphanus sativus), and other closely related species, we propose a two-step merging of three tPCK-like genomes to form the hexaploid ancestor of the tribe Brassiceae with 42 chromosomes. Subsequent diversification of the Brassiceae was marked by extensive genome reshuffling and chromosome number reduction mediated by translocation events and followed by loss and/or inactivation of centromeres. Furthermore, via interspecies genome comparison, we refined intervals for seven of the genomic blocks of the Ancestral Crucifer Karyotype (n = 8), thus revising the key reference genome for evolutionary genomics of crucifers.
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Affiliation(s)
- Feng Cheng
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Terezie Mandáková
- Plant Cytogenomics, Central European Institute of Technology (CEITEC) and Faculty of Science, Masaryk University, CZ-625 00 Brno, Czech Republic
| | - Jian Wu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qi Xie
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Martin A. Lysak
- Plant Cytogenomics, Central European Institute of Technology (CEITEC) and Faculty of Science, Masaryk University, CZ-625 00 Brno, Czech Republic
| | - Xiaowu Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Address correspondence to
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Shen D, Sun H, Huang M, Zheng Y, Li X, Fei Z. RadishBase: a database for genomics and genetics of radish. PLANT & CELL PHYSIOLOGY 2013; 54:e3. [PMID: 23239846 DOI: 10.1093/pcp/pcs176] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Radish is an economically important vegetable crop. During the past several years, large-scale genomics and genetics resources have been accumulated for this species. To store, query, analyze and integrate these radish resources efficiently, we have developed RadishBase (http://bioinfo.bti.cornell.edu/radish), a genomics and genetics database of radish. Currently the database contains radish mitochondrial genome sequences, expressed sequence tag (EST) and unigene sequences and annotations, biochemical pathways, EST-derived single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers, and genetic maps. RadishBase is designed to enable users easily to retrieve and visualize biologically important information through a set of efficient query interfaces and analysis tools, including the BLAST search and unigene annotation query interfaces, and tools to classify unigenes functionally, to identify enriched gene ontology (GO) terms and to visualize genetic maps. A database containing radish pathways predicted from unigene sequences is also included in RadishBase. The tools and interfaces in RadishBase allow efficient mining of recently released and continually expanding large-scale radish genomics and genetics data sets, including the radish genome sequences and RNA-seq data sets.
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Affiliation(s)
- Di Shen
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
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Zou Z, Ishida M, Li F, Kakizaki T, Suzuki S, Kitashiba H, Nishio T. QTL analysis using SNP markers developed by next-generation sequencing for identification of candidate genes controlling 4-methylthio-3-butenyl glucosinolate contents in roots of radish, Raphanus sativus L. PLoS One 2013; 8:e53541. [PMID: 23308250 PMCID: PMC3538544 DOI: 10.1371/journal.pone.0053541] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 11/29/2012] [Indexed: 12/30/2022] Open
Abstract
SNP markers for QTL analysis of 4-MTB-GSL contents in radish roots were developed by determining nucleotide sequences of bulked PCR products using a next-generation sequencer. DNA fragments were amplified from two radish lines by multiplex PCR with six primer pairs, and those amplified by 2,880 primer pairs were mixed and sequenced. By assembling sequence data, 1,953 SNPs in 750 DNA fragments, 437 of which have been previously mapped in a linkage map, were identified. A linkage map of nine linkage groups was constructed with 188 markers, and five QTLs were detected in two F(2) populations, three of them accounting for more than 50% of the total phenotypic variance being repeatedly detected. In the identified QTL regions, nine SNP markers were newly produced. By synteny analysis of the QTLs regions with Arabidopsis thaliana and Brassica rapa genome sequences, three candidate genes were selected, i.e., RsMAM3 for production of aliphatic glucosinolates linked to GSL-QTL-4, RsIPMDH1 for leucine biosynthesis showing strong co-expression with glucosinolate biosynthesis genes linked to GSL-QTL-2, and RsBCAT4 for branched-chain amino acid aminotransferase linked to GSL-QTL-1. Nucleotide sequences and expression of these genes suggested their possible function in 4MTB-GSL biosynthesis in radish roots.
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Affiliation(s)
- Zhongwei Zou
- Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, Japan
| | - Masahiko Ishida
- NARO Institute of Vegetable and Tea Science, Tsu, Mie, Japan
| | - Feng Li
- Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, Japan
| | | | - Sho Suzuki
- Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, Japan
| | - Hiroyasu Kitashiba
- Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, Japan
| | - Takeshi Nishio
- Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, Japan
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Shirasawa K, Ishii K, Kim C, Ban T, Suzuki M, Ito T, Muranaka T, Kobayashi M, Nagata N, Isobe S, Tabata S. Development of Capsicum EST-SSR markers for species identification and in silico mapping onto the tomato genome sequence. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2013; 31:101-110. [PMID: 23316112 PMCID: PMC3538017 DOI: 10.1007/s11032-012-9774-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2012] [Accepted: 08/01/2012] [Indexed: 05/04/2023]
Abstract
Capsicum spp. are widely cultivated for use as vegetables and spices. The Kihara Institute for Biological Research, Yokohama City University, Japan, has stocks of approximately 800 lines of Capsicum spp. collected from various regions of Central and South America, the regions of origin for Capsicum spp. In this study, 5,751 primer pairs for simple sequence repeat markers, based on 118,060 publicly available sequences of expressed sequence tags of Capsicum annuum, were designed and subjected to a similarity search against the genomic sequence of tomato, a model Solanaceae species. Nucleotide sequences spanning 2,245 C. annuum markers were successfully mapped onto the tomato genome, and 96 of these, which spanned the entire tomato genome, were selected for further analysis. In genotyping analysis, 60 out of the 77 markers that produced specific DNA amplicons showed polymorphism among the Capsicum lines examined. On the basis of the resulting data, the 192 tested lines were grouped into five main clusters. The additional sequencing analysis of the plastid genes, matK and rbcL, divided the resources into three groups. As a result, 19 marker loci exhibited genotypes specific to species and cluster, suggesting that the DNA markers are useful for species identification. Information on the DNA markers will contribute to Capsicum genetics, genomics, and breeding. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-012-9774-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kenta Shirasawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 291-0818 Japan
| | - Kohei Ishii
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, 244-0813 Japan
| | - Cholgwang Kim
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, 244-0813 Japan
| | - Tomohiro Ban
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, 244-0813 Japan
| | | | - Takashi Ito
- Osaka University, Suita, Osaka, 565-0871 Japan
| | | | | | - Noriko Nagata
- Japan Women’s University, Bunkyo, Tokyo, 112-8681 Japan
| | - Sachiko Isobe
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 291-0818 Japan
| | - Satoshi Tabata
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 291-0818 Japan
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Wang S, Wang X, He Q, Liu X, Xu W, Li L, Gao J, Wang F. Transcriptome analysis of the roots at early and late seedling stages using Illumina paired-end sequencing and development of EST-SSR markers in radish. PLANT CELL REPORTS 2012; 31:1437-1447. [PMID: 22476438 DOI: 10.1007/s00299-012-1259-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2012] [Revised: 03/14/2012] [Accepted: 03/23/2012] [Indexed: 05/31/2023]
Abstract
UNLABELLED The tuberous root of radish is an important vegetable, but insufficient transcriptomic and genomic data are currently available to understand the molecular mechanisms underlying tuberous root formation and development. High-throughput transcriptomic sequencing is essential to generate a large transcript sequence data set for gene discovery and molecular marker development. In this study, a total of 107.3 million clean reads were generated using Illumina paired-end sequencing technology. De novo assembly generated 61,554 unigenes with an average length of 820 bp. Based on a sequence similarity search with known proteins or nucleotides, 85.51 % (52,634), 90.18 % (55,507) and 54 % (33,242) consensus sequences showed homology with sequences in the Nr, Nt and Swiss-Prot databases, respectively. Of these annotated unigenes, 21,109 and 17,343 unigenes were assigned to gene ontology categories and clusters of orthologous groups, respectively. A total of 27,809 unigenes were assigned to 123 pathways in the Kyoto Encyclopedia of Genes and Genomes database. Analysis of transcript differences between libraries from the early and late seedling developmental stages demonstrated that starch and sucrose metabolism and phenylpropanoid biosynthesis may be the dominant metabolic events during tuberous root formation and plant hormones probably play critical roles in regulation of this developmental process. In total, 14,641 potential EST-SSRs were identified among the unigenes, and 12,733 primer pairs for 2,511 SSR were obtained. Summarily, this study gave us a clue to understand the radish tuberous root formation and development, and also provided us with a valuable sequence resource for novel gene discovery and marker-assisted selective breeding in radish. KEY MESSAGE De novo assembled and characterized the radish tuberous root transcriptome; explored the mechanism of radish tuberous root formation; development of EST-SSR markers in radish.
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Affiliation(s)
- Shufen Wang
- Shandong Key Laboratory of Greenhouse Vegetable Biology, Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan 250100, China
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Cho Y, Lee YP, Park BS, Han TH, Kim S. Construction of a high-resolution linkage map of Rfd1, a restorer-of-fertility locus for cytoplasmic male sterility conferred by DCGMS cytoplasm in radish (Raphanus sativus L.) using synteny between radish and Arabidopsis genomes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:467-477. [PMID: 22434503 DOI: 10.1007/s00122-012-1846-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Accepted: 03/05/2012] [Indexed: 05/31/2023]
Abstract
Cytoplasmic male sterility caused by Dongbu cytoplasmic and genic male-sterility (DCGMS) cytoplasm and its nuclear restorer-of-fertility locus (Rfd1) with a linked molecular marker (A137) have been reported in radish (Raphanus sativus L.). To construct a linkage map of the Rfd1 locus, linked amplified fragment length polymorphism (AFLP) markers were screened using bulked segregant analysis. A 220-bp linked AFLP fragment sequence from radish showed homology with an Arabidopsis coding sequence. Using this Arabidopsis gene sequence, a simple PCR marker (A220) was developed. The A137 and A220 markers flanked the Rfd1 locus. Two homologous Arabidopsis genes with both marker sequences were positioned on Arabidopsis chromosome-3 with an interval of 2.4 Mb. To integrate the Rfd1 locus into a previously reported expressed sequence tag (EST)-simple sequence repeat (SSR) linkage map, the radish EST sequences located in three syntenic blocks within the 2.4-Mb interval were used to develop single nucleotide polymorphism (SNP) markers for tagging each block. The SNP marker in linkage group-2 co-segregated with male fertility in an F(2) population. Using radish ESTs positioned in linkage group-2, five intron length polymorphism (ILP) markers and one cleaved amplified polymorphic sequence (CAPS) marker were developed and used to construct a linkage map of the Rfd1 locus. Two closely linked markers delimited the Rfd1 locus within a 985-kb interval of Arabidopsis chromosome-3. Synteny between the radish and Arabidopsis genomes in the 985-kb interval were used to develop three ILP and three CAPS markers. Two ILP markers further delimited the Rfd1 locus to a 220-kb interval of Arabidopsis chromosome-3.
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Affiliation(s)
- Youngcho Cho
- Department of Plant Biotechnology, Biotechnology Research Institute, Chonnam National University, Gwangju, 500-757, Korea
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Xu L, Wang L, Gong Y, Dai W, Wang Y, Zhu X, Wen T, Liu L. Genetic linkage map construction and QTL mapping of cadmium accumulation in radish (Raphanus sativus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:659-70. [PMID: 22491896 DOI: 10.1007/s00122-012-1858-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 03/21/2012] [Indexed: 05/21/2023]
Abstract
Cadmium (Cd) is a widespread soil pollutant and poses a significant threat to human health via the food chain. Large phenotypic variations in Cd concentration of radish roots and shoots have been observed. However, the genetic and molecular mechanisms of Cd accumulation in radish remain to be elucidated. In this study, a genetic linkage map was constructed using an F(2) mapping population derived from a cross between a high Cd-accumulating cultivar NAU-Dysx and a low Cd-accumulating cultivar NAU-Yh. The linkage map consisted of 523 SRAP, RAPD, SSR, ISSR, RAMP, and RGA markers and had a total length of 1,678.2 cM with a mean distance of 3.4 cM between two markers. All mapped markers distributed on nine linkage groups (LGs) having sizes between 134.7 and 236.8 cM. Four quantitative trait loci (QTLs) for root Cd accumulation were mapped on LGs 1, 4, 6, and 9, which accounted for 9.86 to 48.64 % of all phenotypic variance. Two QTLs associated with shoot Cd accumulation were detected on LG1 and 3, which accounted for 17.08 and 29.53 % of phenotypic variance, respectively. A major-effect QTL, qRCd9 (QTL for root Cd accumulation on LG9), was identified on LG 9 flanked by NAUrp011_754 and EM5me6_286 markers with a high LOD value of 23.6, which accounted for 48.64 % of the total phenotypic variance in Cd accumulation of F(2) lines. The results indicated that qRCd9 is a novel QTL responsible for controlling root Cd accumulation in radish, and the identification of specific molecular markers tightly linked to the major QTL could be further applied for marker-assisted selection (MAS) in low-Cd content radish breeding program.
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Affiliation(s)
- Liang Xu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
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Choudhary S, Gaur R, Gupta S. EST-derived genic molecular markers: development and utilization for generating an advanced transcript map of chickpea. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:1449-62. [PMID: 22301907 DOI: 10.1007/s00122-012-1800-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Accepted: 01/05/2012] [Indexed: 05/17/2023]
Abstract
Well-saturated linkage maps especially those based on expressed sequence tag (EST)-derived genic molecular markers (GMMs) are a pre-requisite for molecular breeding. This is especially true in important legumes such as chickpea where few simple sequence repeats (SSR) and even fewer GMM-based maps have been developed. Therefore, in this study, 2,496 ESTs were generated from chickpea seeds and utilized for the development of 487 novel EST-derived functional markers which included 125 EST-SSRs, 151 intron targeted primers (ITPs), 109 expressed sequence tag polymorphisms (ESTPs), and 102 single nucleotide polymorphisms (SNPs). Whereas ESTSSRs, ITPs, and ESTPs were developed by in silico analysis of the developed EST sequences, SNPs were identified by allele resequencing and their genotyping was performedusing the Illumina GoldenGate Assay. Parental polymorphism was analyzed between C. arietinum ICC4958 and C. reticulatum PI489777, parents of the reference chickpea mapping population, using a total of 872 markers: 487 new gene-based markers developed in this study along with 385 previously published markers, of which 318 (36.5%) were found to be polymorphic and were used for genotyping. The genotypic data were integrated with the previously published data of 108 markers and an advanced linkage map was generated that contained 406 loci distributed on eight linkage groups that spanned 1,497.7 cM. The average marker density was 3.68 cM and the average number of markers per LG was 50.8. Among the mapped markers, 303 new genomic locations were defined that included 177 gene-based and 126 gSSRs (genomic SSRs) thereby producing the most advanced gene-rich map of chickpea solely based on co-dominant markers.
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Affiliation(s)
- Shalu Choudhary
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No 10531, New Delhi 110067, India
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Niemelä T, Seppänen M, Badakshi F, Rokka VM, Heslop-Harrison JSP. Size and location of radish chromosome regions carrying the fertility restorer Rfk1 gene in spring turnip rape. Chromosome Res 2012; 20:353-61. [PMID: 22476396 DOI: 10.1007/s10577-012-9280-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Revised: 02/29/2012] [Accepted: 03/08/2012] [Indexed: 11/25/2022]
Abstract
In spring turnip rape (Brassica rapa L. spp. oleifera), the most promising F1 hybrid system would be the Ogu-INRA CMS/Rf system. A Kosena fertility restorer gene Rfk1, homolog of the Ogura restorer gene Rfo, was successfully transferred from oilseed rape into turnip rape and that restored the fertility in female lines carrying Ogura cms. The trait was, however, unstable in subsequent generations. The physical localization of the radish chromosomal region carrying the Rfk1 gene was investigated using genomic in situ hybridization (GISH) and bacterial artificial chromosome-fluorescence in situ hybridization (BAC-FISH) methods. The metaphase chromosomes were hybridized using radish DNA as the genomic probe and BAC64 probe, which is linked with Rfo gene. Both probes showed a signal in the chromosome spreads of the restorer line 4021-2 Rfk of turnip rape but not in the negative control line 4021B. The GISH analyses clearly showed that the turnip rape restorer plants were either monosomic (2n=2x=20+1R) or disomic (2n=2x=20+2R) addition lines with one or two copies of a single alien chromosome region originating from radish. In the BAC-FISH analysis, double dot signals were detected in subterminal parts of the radish chromosome arms showing that the fertility restorer gene Rfk1 was located in this additional radish chromosome. Detected disomic addition lines were found to be unstable for turnip rape hybrid production. Using the BAC-FISH analysis, weak signals were sometimes visible in two chromosomes of turnip rape and a homologous region of Rfk1 in chromosome 9 of the B. rapa A genome was verified with BLAST analysis. In the future, this homologous area in A genome could be substituted with radish chromosome area carrying the Rfk1 gene.
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Affiliation(s)
- Tarja Niemelä
- Department of Agriculture, University of Helsinki, PO Box 27, FI-00014, Helsinki, Finland.
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