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Wang J, Zhao G, Zhao Y, Zhao Z, Yang S, Zhou A, Li P, Zhang S. N 6-methylation in the development, diagnosis, and treatment of gastric cancer. J Transl Int Med 2024; 12:5-21. [PMID: 38525439 PMCID: PMC10956730 DOI: 10.2478/jtim-2023-0103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024] Open
Abstract
Gastric cancer (GC) ranks third among cancers in terms of mortality rate worldwide. A clear understanding of the mechanisms underlying the genesis and progression of GC will contribute to clinical decision making. N6-methyladenosine (m6A) is the most abundant among diverse mRNA modification types and regulates multiple facets of RNA metabolism. In recent years, emerging studies have shown that m6A modifications are involved in gastric carcinoma tumorigenesis and progression and can potentially be valuable new prospects for diagnosis and prognosis. This article reviews the recent progress regarding m6A in GC.
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Affiliation(s)
- Jiaxin Wang
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Guiping Zhao
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Yan Zhao
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Zheng Zhao
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Shuyue Yang
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Anni Zhou
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Peng Li
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Shutian Zhang
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
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Niu Y, Liu Q, He Z, Raman R, Wang H, Long X, Qin H, Raman H, Parkin IAP, Bancroft I, Zou J. A Brassica carinata pan-genome platform for Brassica crop improvement. PLANT COMMUNICATIONS 2024; 5:100725. [PMID: 37803826 PMCID: PMC10811369 DOI: 10.1016/j.xplc.2023.100725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/21/2023] [Accepted: 09/26/2023] [Indexed: 10/08/2023]
Affiliation(s)
- Yan Niu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qingqing Liu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhesi He
- Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Rosy Raman
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW 2650, Australia
| | - Hao Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xinxin Long
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Han Qin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Harsh Raman
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW 2650, Australia
| | - Isobel A P Parkin
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, SK, Canada
| | - Ian Bancroft
- Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.
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Tesfaye M, Feyissa T, Hailesilassie T, Kanagarajan S, Zhu LH. Genetic Diversity and Population Structure in Ethiopian Mustard ( Brassica carinata A. Braun) as Revealed by Single Nucleotide Polymorphism Markers. Genes (Basel) 2023; 14:1757. [PMID: 37761897 PMCID: PMC10530317 DOI: 10.3390/genes14091757] [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: 08/11/2023] [Revised: 08/25/2023] [Accepted: 09/01/2023] [Indexed: 09/29/2023] Open
Abstract
Ethiopian mustard (Brassica carinata A. Braun) is currently one of the potential oilseeds dedicated to the production for biofuel and other bio-industrial applications. The crop is assumed to be native to Ethiopia where a number of diversified B. carinata germplasms are found and conserved ex situ. However, there is very limited information on the genetic diversity and population structure of the species. This study aimed to investigate the genetic diversity and population structure of B. carinata genotypes of different origins using high-throughput single nucleotide polymorphism (SNP) markers. We used Brassica 90K Illumina InfiniumTM SNP array for genotyping 90 B. carinata genotypes, and a total of 11,499 informative SNP markers were used for investigating the population structure and genetic diversity. The structure analysis, principal coordinate analysis (PcoA) and neighbor-joining tree analysis clustered the 90 B. carinata genotypes into two distinct subpopulations (Pop1 and Pop2). The majority of accessions (65%) were clustered in Pop1, mainly obtained from Oromia and South West Ethiopian People (SWEP) regions. Pop2 constituted dominantly of breeding lines and varieties, implying target selection contributed to the formation of distinct populations. Analysis of molecular variance (AMOVA) revealed a higher genetic variation (93%) within populations than between populations (7%), with low genetic differentiation (PhiPT = 0.07) and poor correlation between genetic and geographical distance (R = 0.02). This implies the presence of gene flow (Nm > 1) and weak geographical structure of accessions. Genetic diversity indices showed the presence of moderate genetic diversity in B. carinata populations with an average genetic diversity value (HE = 0.31) and polymorphism information content (PIC = 0.26). The findings of this study provide important and relevant information for future breeding and conservation efforts of B. carinata.
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Affiliation(s)
- Misteru Tesfaye
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 190, 234 22 Lomma, Sweden; (M.T.); (S.K.)
- Institute of Biotechnology, Addis Ababa University, Addis Ababa P.O. Box 1176, Ethiopia; (T.F.); (T.H.)
| | - Tileye Feyissa
- Institute of Biotechnology, Addis Ababa University, Addis Ababa P.O. Box 1176, Ethiopia; (T.F.); (T.H.)
| | | | - Selvaraju Kanagarajan
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 190, 234 22 Lomma, Sweden; (M.T.); (S.K.)
| | - Li-Hua Zhu
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 190, 234 22 Lomma, Sweden; (M.T.); (S.K.)
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Sharma Koirala P, Neff MM. Improving seed size, seed weight and seedling emergence in Camelina sativa by overexpressing the Atsob3-6 gene variant. Transgenic Res 2020; 29:409-418. [PMID: 32748170 DOI: 10.1007/s11248-020-00208-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 06/19/2020] [Indexed: 11/28/2022]
Abstract
Seedling stand establishment is a critical factor affecting crop yield in low-precipitation agricultural regions. This is especially true for small seeded crops, such as Camelina (Camelina sativa) and canola (Brassica napus), that need to be planted shallow. Deeper planting would be desirable so that seeds can access soil moisture and bigger seeds could improve emergence and stand establishment by providing the energy necessary for seedling elongation. AHL (AT-Hook Containing, Nuclear Localized) genes play an important role in seedling growth and development. AHL proteins contain two structural units, the DNA-binding AT-hook motif and the Plant and Prokaryote Conserved (PPC) domain, required for protein-protein interactions. Our previous studies demonstrate that AtAHL29/SOB3 (Suppressor of phytochrome B-4 #3) regulates seedling development in Arabidopsis (Arabidopsis thaliana). Activation-tagged overexpression of AtSOB3 (Atsob3-D) represses the long-hypocotyl phenotype of an Arabidopsis phytochrome B mutant. In contrast, overexpression of the Atsob3-6 variant (Atsob3-6-OX), with a non-functional AT-hook, confers a long-hypocotyl phenotype. In this study, we demonstrate the role of Atsob3-D and Atsob3-6-OX in modulating seed size and hypocotyl length in the brassicas Arabidopsis and Camelina. In Arabidopsis, Atsob3-D reduces seed weight whereas Atsob3-6-OX increases seed weight and size when compared to the wild type. Similarly, Atsob3-6-OX transgenic Camelina seedlings are taller than the wild type, and produce larger and heavier seeds. These larger Atsob3-6-OX Camelina seeds also confer better emergence in deep-soil planting when compared to the wild type. Taken together, Atsob3-6-OX increases seed size, seed weight, seedling hypocotyl length and stand establishment in the oilseed crop Camelina.
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Affiliation(s)
- Pushpa Sharma Koirala
- Department Crop and Soil Sciences, Washington State University, 387 Johnson Hall, PO Box 646420, Pullman, WA, 99164-6420, USA
| | - Michael M Neff
- Department Crop and Soil Sciences, Washington State University, 387 Johnson Hall, PO Box 646420, Pullman, WA, 99164-6420, USA.
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Khedikar Y, Clarke WE, Chen L, Higgins EE, Kagale S, Koh CS, Bennett R, Parkin IAP. Narrow genetic base shapes population structure and linkage disequilibrium in an industrial oilseed crop, Brassica carinata A. Braun. Sci Rep 2020; 10:12629. [PMID: 32724070 PMCID: PMC7387349 DOI: 10.1038/s41598-020-69255-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 07/09/2020] [Indexed: 12/16/2022] Open
Abstract
Ethiopian mustard (Brassica carinata A. Braun) is an emerging sustainable source of vegetable oil, in particular for the biofuel industry. The present study exploited genome assemblies of the Brassica diploids, Brassica nigra and Brassica oleracea, to discover over 10,000 genome-wide SNPs using genotype by sequencing of 620 B. carinata lines. The analyses revealed a SNP frequency of one every 91.7 kb, a heterozygosity level of 0.30, nucleotide diversity levels of 1.31 × 10-05, and the first five principal components captured only 13% molecular variation, indicating low levels of genetic diversity among the B. carinata collection. Genome bias was observed, with greater SNP density found on the B subgenome. The 620 lines clustered into two distinct sub-populations (SP1 and SP2) with the majority of accessions (88%) clustered in SP1 with those from Ethiopia, the presumed centre of origin. SP2 was distinguished by a collection of breeding lines, implicating targeted selection in creating population structure. Two selective sweep regions on B3 and B8 were detected, which harbour genes involved in fatty acid and aliphatic glucosinolate biosynthesis, respectively. The assessment of genetic diversity, population structure, and LD in the global B. carinata collection provides critical information to assist future crop improvement.
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Affiliation(s)
- Yogendra Khedikar
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, Canada
| | - Wayne E Clarke
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, Canada
| | - Lifeng Chen
- Agrisoma Biosciences Inc., 110 Gymnasium Place, Saskatoon, SK, Canada
| | - Erin E Higgins
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, Canada
| | - Sateesh Kagale
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, Canada
| | - Chu Shin Koh
- Global Institute of Food Security, Saskatoon, SK, Canada
| | - Rick Bennett
- Agrisoma Biosciences Inc., 110 Gymnasium Place, Saskatoon, SK, Canada
| | - Isobel A P Parkin
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, Canada.
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Rahman H, Bennett RA, Kebede B. Molecular mapping of QTL alleles of Brassica oleracea affecting days to flowering and photosensitivity in spring Brassica napus. PLoS One 2018; 13:e0189723. [PMID: 29320498 PMCID: PMC5761838 DOI: 10.1371/journal.pone.0189723] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 11/30/2017] [Indexed: 12/29/2022] Open
Abstract
Earliness of flowering and maturity are important traits in spring Brassica napus canola–whether grown under long- or short-day condition. By use of a spring B. napus mapping population carrying the genome content of B. oleracea and testing this population under 10 to 18 h photoperiod and 18 to 20 0C (day) temperature conditions, we identified a major QTL on the chromosome C1 affecting flowering time without being influenced by photoperiod and temperature, and a major QTL on C9 affecting flowering time under a short photoperiod (10 h); in both cases, the QTL alleles reducing the number of days to flowering in B. napus were introgressed from the late flowering species B. oleracea. Additive effect of the C1 QTL allele at 14 to18 h photoperiod was 1.1 to 2.9 days; however, the same QTL allele exerted an additive effect of 6.2 days at 10 h photoperiod. Additive effect of the C9 QTL at 10 h photoperiod was 2.8 days. These two QTL also showed significant interaction in the control of flowering only under a short-day (10 h photoperiod) condition with an effect of 2.3 days. A few additional QTL were also detected on the chromosomes C2 and C8; however, none of these QTL could be detected under all photoperiod and temperature conditions. BLASTn search identified several putative flowering time genes on the chromosomes C1 and C9 and located the physical position of the QTL markers in the Brassica genome; however, only a few of these genes were found within the QTL region. Thus, the molecular markers and the genomic regions identified in this research could potentially be used in breeding for the development of early flowering photoinsensitive B. napus canola cultivars, as well as for identification of candidate genes involved in flowering time variation and photosensitivity.
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Affiliation(s)
- Habibur Rahman
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
- * E-mail:
| | - Rick A. Bennett
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
| | - Berisso Kebede
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
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Melville J, Haines ML, Boysen K, Hodkinson L, Kilian A, Smith Date KL, Potvin DA, Parris KM. Identifying hybridization and admixture using SNPs: application of the DArTseq platform in phylogeographic research on vertebrates. ROYAL SOCIETY OPEN SCIENCE 2017; 4:161061. [PMID: 28791133 PMCID: PMC5541528 DOI: 10.1098/rsos.161061] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 06/14/2017] [Indexed: 05/04/2023]
Abstract
Next-generation sequencing (NGS) approaches are increasingly being used to generate multi-locus data for phylogeographic and evolutionary genetics research. We detail the applicability of a restriction enzyme-mediated genome complexity reduction approach with subsequent NGS (DArTseq) in vertebrate study systems at different evolutionary and geographical scales. We present two case studies using SNP data from the DArTseq molecular marker platform. First, we used DArTseq in a large phylogeographic study of the agamid lizard Ctenophorus caudicinctus, including 91 individuals and spanning the geographical range of this species across arid Australia. A low-density DArTseq assay resulted in 28 960 SNPs, with low density referring to a comparably reduced set of identified and sequenced markers as a cost-effective approach. Second, we applied this approach to an evolutionary genetics study of a classic frog hybrid zone (Litoria ewingii-Litoria paraewingi) across 93 individuals, which resulted in 48 117 and 67 060 SNPs for a low- and high-density assay, respectively. We provide a docker-based workflow to facilitate data preparation and analysis, then analyse SNP data using multiple methods including Bayesian model-based clustering and conditional likelihood approaches. Based on comparison of results from the DArTseq platform and traditional molecular approaches, we conclude that DArTseq can be used successfully in vertebrates and will be of particular interest to researchers working at the interface between population genetics and phylogenetics, exploring species boundaries, gene exchange and hybridization.
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Affiliation(s)
- Jane Melville
- Department of Sciences, Museum Victoria, Carlton, Victoria 3052, Australia
- Author for correspondence: Jane Melville e-mail:
| | - Margaret L. Haines
- Department of Sciences, Museum Victoria, Carlton, Victoria 3052, Australia
| | - Katja Boysen
- Department of Sciences, Museum Victoria, Carlton, Victoria 3052, Australia
| | - Luke Hodkinson
- Department of Sciences, Museum Victoria, Carlton, Victoria 3052, Australia
| | - Andrzej Kilian
- Diversity Arrays Technology, University of Canberra, Bruce, Australian Capital Territory 2617, Australia
| | | | | | - Kirsten M. Parris
- School of Ecosystem and Forest Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
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Yu CY, Dong JG, Hu SW, Xu AX. Exposure to trace amounts of sulfonylurea herbicide tribenuron-methyl causes male sterility in 17 species or subspecies of cruciferous plants. BMC PLANT BIOLOGY 2017; 17:95. [PMID: 28571580 PMCID: PMC5455082 DOI: 10.1186/s12870-017-1019-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 03/27/2017] [Indexed: 05/08/2023]
Abstract
BACKGROUND For most cruciferous plants, which are known as important crops and a number of weeds, hybrid breeding is hampered by the unavailability of a pollination control system. Male sterility induced by a gametocide can be useful for the utilization of plant heterosis. RESULTS The gametocidal effect of sulfonylurea herbicide tribenuron-methyl was tested across seventeen cruciferous species or subspecies including Brassica juncea, B. carinata, B. oleracea ssp. capitata, B. oleracea ssp. acephala, B. rapa ssp. pekinensis, B. rapa ssp. chinensis, B. rapa ssp. parachinensis, B. nigra, Orychophragmus violaceus, Matthiola incana, Raphanus sativa, Sisymbrium altissimum, Eruca sativa, Sinapis alba, Sinapis arvensis, Capsella bursa-pastoris and Camelina sativa. The plants of 23 cultivars in these species or subspecies were foliar sprayed with 10 ml of 0.2 or 0.4 mg/L of tribenuron-methyl before the vacuolated microspore formed in the largest flower buds; the application was repeated ten to twelve days afterwards. Tribenuron-methyl exposure significantly changed the flowering phenology and reproductive function. The treated plants demonstrated a one to four day delay in flowering time and a shortened duration of flowering, as well as other slight phytotoxic effects including a reduction in plant height and floral organ size. Approximately 80% to 100% male sterility, which was estimated by both pollen staining and selfing seed-set rate, was induced in the plants. As a result, plants were rendered functionally able to out-cross, with an average 87% and 54% manually pollinated seed-set rate compared to the corresponding controls at the 0.2 mg/L and 0.4 mg/L doses, respectively. CONCLUSIONS The results suggested that male reproductive function was much more sensitive to tribenuron-methyl exposure than female function. This sulfonylurea herbicide has a promising use as the gametocide for hybrid production in cruciferous plants.
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Affiliation(s)
- Cheng-Yu Yu
- College of Agronomy, Northwest A&F University, 3 Taicheng Road, Yangling, Shaanxi 712100 China
| | - Jun-Gang Dong
- College of Agronomy, Northwest A&F University, 3 Taicheng Road, Yangling, Shaanxi 712100 China
| | - Sheng-Wu Hu
- College of Agronomy, Northwest A&F University, 3 Taicheng Road, Yangling, Shaanxi 712100 China
| | - Ai-Xia Xu
- College of Agronomy, Northwest A&F University, 3 Taicheng Road, Yangling, Shaanxi 712100 China
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Valdisser PAMR, Pereira WJ, Almeida Filho JE, Müller BSF, Coelho GRC, de Menezes IPP, Vianna JPG, Zucchi MI, Lanna AC, Coelho ASG, de Oliveira JP, Moraes ADC, Brondani C, Vianello RP. In-depth genome characterization of a Brazilian common bean core collection using DArTseq high-density SNP genotyping. BMC Genomics 2017; 18:423. [PMID: 28558696 PMCID: PMC5450071 DOI: 10.1186/s12864-017-3805-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 05/17/2017] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Common bean is a legume of social and nutritional importance as a food crop, cultivated worldwide especially in developing countries, accounting for an important source of income for small farmers. The availability of the complete sequences of the two common bean genomes has dramatically accelerated and has enabled new experimental strategies to be applied for genetic research. DArTseq has been widely used as a method of SNP genotyping allowing comprehensive genome coverage with genetic applications in common bean breeding programs. RESULTS Using this technology, 6286 SNPs (1 SNP/86.5 Kbp) were genotyped in genic (43.3%) and non-genic regions (56.7%). Genetic subdivision associated to the common bean gene pools (K = 2) and related to grain types (K = 3 and K = 5) were reported. A total of 83% and 91% of all SNPs were polymorphic within the Andean and Mesoamerican gene pools, respectively, and 26% were able to differentiate the gene pools. Genetic diversity analysis revealed an average H E of 0.442 for the whole collection, 0.102 for Andean and 0.168 for Mesoamerican gene pools (F ST = 0.747 between gene pools), 0.440 for the group of cultivars and lines, and 0.448 for the group of landrace accessions (F ST = 0.002 between cultivar/line and landrace groups). The SNP effects were predicted with predominance of impact on non-coding regions (77.8%). SNPs under selection were identified within gene pools comparing landrace and cultivar/line germplasm groups (Andean: 18; Mesoamerican: 69) and between the gene pools (59 SNPs), predominantly on chromosomes 1 and 9. The LD extension estimate corrected for population structure and relatedness (r2SV) was ~ 88 kbp, while for the Andean gene pool was ~ 395 kbp, and for the Mesoamerican was ~ 130 kbp. CONCLUSIONS For common bean, DArTseq provides an efficient and cost-effective strategy of generating SNPs for large-scale genome-wide studies. The DArTseq resulted in an operational panel of 560 polymorphic SNPs in linkage equilibrium, providing high genome coverage. This SNP set could be used in genotyping platforms with many applications, such as population genetics, phylogeny relation between common bean varieties and support to molecular breeding approaches.
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Affiliation(s)
- Paula A. M. R. Valdisser
- Embrapa Arroz e Feijão (CNPAF), Santo Antônio de Goiás, Goiânia, GO Brazil
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Estadual de Campinas (UNICAMP), Campinas, SP Brazil
| | - Wendell J. Pereira
- Programa de Pós-Graduação em Biologia Molecular, Universidade de Brasília (UnB), Brasília, DF Brazil
| | - Jâneo E. Almeida Filho
- Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, Rio de Janeiro, RJ Brazil
| | - Bárbara S. F. Müller
- Programa de Pós-Graduação em Biologia Molecular, Universidade de Brasília (UnB), Brasília, DF Brazil
| | | | - Ivandilson P. P. de Menezes
- Laboratório de Genética e Biologia Molecular, Departamento de Biologia, Instituto Federal Goiano (IF Goiano), Urutaí, GO Brazil
| | - João P. G. Vianna
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Estadual de Campinas (UNICAMP), Campinas, SP Brazil
| | - Maria I. Zucchi
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Estadual de Campinas (UNICAMP), Campinas, SP Brazil
| | - Anna C. Lanna
- Embrapa Arroz e Feijão (CNPAF), Santo Antônio de Goiás, Goiânia, GO Brazil
| | | | | | | | - Claudio Brondani
- Embrapa Arroz e Feijão (CNPAF), Santo Antônio de Goiás, Goiânia, GO Brazil
| | - Rosana P. Vianello
- Embrapa Arroz e Feijão (CNPAF), Santo Antônio de Goiás, Goiânia, GO Brazil
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Zhang W, Hu D, Raman R, Guo S, Wei Z, Shen X, Meng J, Raman H, Zou J. Investigation of the Genetic Diversity and Quantitative Trait Loci Accounting for Important Agronomic and Seed Quality Traits in Brassica carinata. FRONTIERS IN PLANT SCIENCE 2017; 8:615. [PMID: 28484482 PMCID: PMC5401912 DOI: 10.3389/fpls.2017.00615] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 04/04/2017] [Indexed: 05/21/2023]
Abstract
Brassica carinata (BBCC) is an allotetraploid in Brassicas with unique alleles for agronomic traits and has huge potential as source for biodiesel production. To investigate the genome-wide molecular diversity, population structure and linkage disequilibrium (LD) pattern in this species, we genotyped a panel of 81 accessions of B. carinata with genotyping by sequencing approach DArTseq, generating a total of 54,510 polymorphic markers. Two subpopulations were exhibited in the B. carinata accessions. The average distance of LD decay (r2 = 0.1) in B subgenome (0.25 Mb) was shorter than that of C subgenome (0.40 Mb). Genome-wide association analysis (GWAS) identified a total of seven markers significantly associated with five seed quality traits in two experiments. To further identify the quantitative trait loci (QTL) for important agronomic and seed quality traits, we phenotyped a doubled haploid (DH) mapping population derived from the "YW" cross between two parents (Y-BcDH64 and W-BcDH76) representing from the two subpopulations. The YW DH population and its parents were grown in three contrasting environments; spring (Hezheng and Xining, China), semi-winter (Wuhan, China), and spring (Wagga Wagga, Australia) across 5 years for QTL mapping. Genetic bases of phenotypic variation in seed yield and its seven related traits, and six seed quality traits were determined. A total of 282 consensus QTL accounting for these traits were identified including nine major QTL for flowering time, oleic acid, linolenic acid, pod number of main inflorescence, and seed weight. Of these, 109 and 134 QTL were specific to spring and semi-winter environment, respectively, while 39 consensus QTL were identified in both contrasting environments. Two QTL identified for linolenic acid (B3) and erucic acid (C7) were validated in the diverse lines used for GWAS. A total of 25 QTL accounting for flowering time, erucic acid, and oleic acid were aligned to the homologous QTL or candidate gene regions in the C genome of B. napus. These results would not only provide insights for genetic improvement of this species, but will also identify useful genetic variation hidden in the Cc subgenome of B. carinata to improve canola cultivars.
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Affiliation(s)
- Wenshan Zhang
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture China, Huazhong Agricultural UniversityWuhan, China
| | - Dandan Hu
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture China, Huazhong Agricultural UniversityWuhan, China
| | - Rosy Raman
- Graham Centre for Agricultural Innovation (an Alliance between the Charles Sturt University and NSW Department of Primary Industries), Wagga Wagga Agricultural InstituteWagga Wagga, NSW, Australia
| | - Shaomin Guo
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture China, Huazhong Agricultural UniversityWuhan, China
| | - Zili Wei
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture China, Huazhong Agricultural UniversityWuhan, China
| | - Xueqi Shen
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture China, Huazhong Agricultural UniversityWuhan, China
| | - Jinling Meng
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture China, Huazhong Agricultural UniversityWuhan, China
| | - Harsh Raman
- Graham Centre for Agricultural Innovation (an Alliance between the Charles Sturt University and NSW Department of Primary Industries), Wagga Wagga Agricultural InstituteWagga Wagga, NSW, Australia
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture China, Huazhong Agricultural UniversityWuhan, China
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Raman R, Qiu Y, Coombes N, Song J, Kilian A, Raman H. Molecular Diversity Analysis and Genetic Mapping of Pod Shatter Resistance Loci in Brassica carinata L. FRONTIERS IN PLANT SCIENCE 2017; 8:1765. [PMID: 29250080 PMCID: PMC5716317 DOI: 10.3389/fpls.2017.01765] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 09/27/2017] [Indexed: 05/05/2023]
Abstract
Seed lost due to easy pod dehiscence at maturity (pod shatter) is a major problem in several members of Brassicaceae family. We investigated the level of pod shatter resistance in Ethiopian mustard (Brassica carinata) and identified quantitative trait loci (QTL) for targeted introgression of this trait in Ethiopian mustard and its close relatives of the genus Brassica. A set of 83 accessions of B. carinata, collected from the Australian Grains Genebank, was evaluated for pod shatter resistance based on pod rupture energy (RE). In comparison to B. napus (RE = 2.16 mJ), B. carinata accessions had higher RE values (2.53 to 20.82 mJ). A genetic linkage map of an F2 population from two contrasting B. carinata selections, BC73526 (shatter resistant with high RE) and BC73524 (shatter prone with low RE) comprising 300 individuals, was constructed using a set of 6,464 high quality DArTseq markers and subsequently used for QTL analysis. Genetic analysis of the F2 and F2:3 derived lines revealed five statistically significant QTL (LOD ≥ 3) that are linked with pod shatter resistance on chromosomes B1, B3, B8, and C5. Herein, we report for the first time, identification of genetic loci associated with pod shatter resistance in B. carinata. These characterized accessions would be useful in Brassica breeding programs for introgression of pod shatter resistance alleles in to elite breeding lines. Molecular markers would assist marker-assisted selection for tracing the introgression of resistant alleles. Our results suggest that the value of the germplasm collections can be harnessed through genetic and genomics tools.
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Affiliation(s)
- Rosy Raman
- Graham Centre for Agricultural Innovation (an alliance between NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
- Wagga Wagga Agricultural Institute, NSW Department of Primary Industries, Wagga Wagga, NSW, Australia
- *Correspondence: Rosy Raman,
| | - Yu Qiu
- Wagga Wagga Agricultural Institute, NSW Department of Primary Industries, Wagga Wagga, NSW, Australia
| | - Neil Coombes
- Wagga Wagga Agricultural Institute, NSW Department of Primary Industries, Wagga Wagga, NSW, Australia
| | - Jie Song
- Diversity Arrays Technology Pty. Ltd., University of Canberra, Canberra, ACT, Australia
| | - Andrzej Kilian
- Diversity Arrays Technology Pty. Ltd., University of Canberra, Canberra, ACT, Australia
| | - Harsh Raman
- Graham Centre for Agricultural Innovation (an alliance between NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
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Milczarski P, Hanek M, Tyrka M, Stojałowski S. The application of GBS markers for extending the dense genetic map of rye (Secale cereale L.) and the localization of the Rfc1 gene restoring male fertility in plants with the C source of sterility-inducing cytoplasm. J Appl Genet 2016; 57:439-451. [PMID: 27085345 PMCID: PMC5061839 DOI: 10.1007/s13353-016-0347-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/22/2016] [Accepted: 03/27/2016] [Indexed: 11/28/2022]
Abstract
Genotyping by sequencing (GBS) is an efficient method of genotyping in numerous plant species. One of the crucial steps toward the application of GBS markers in crop improvement is anchoring them on particular chromosomes. In rye (Secale cereale L.), chromosomal localization of GBS markers has not yet been reported. In this paper, the application of GBS markers generated by the DArTseq platform for extending the high-density map of rye is presented. Additionally, their application is used for the localization of the Rfc1 gene that restores male fertility in plants with the C source of sterility-inducing cytoplasm. The total number of markers anchored on the current version of the map is 19,081, of which 18,132 were obtained from the DArTseq platform. Numerous markers co-segregated within the studied mapping population, so, finally, only 3397 unique positions were located on the map of all seven rye chromosomes. The total length of the map is 1593 cM and the average distance between markers is 0.47 cM. In spite of the resolution of the map being not very high, it should be a useful tool for further studies of the Secale cereale genome because of the presence on this map of numerous GBS markers anchored for the first time on rye chromosomes. The Rfc1 gene was located on high-density maps of the long arm of the 4R chromosome obtained for two mapping populations. Genetic maps were composed of DArT, DArTseq, and PCR-based markers. Consistent mapping results were obtained and DArTs tightly linked to the Rfc1 gene were successfully applied for the development of six new PCR-based markers useful in marker-assisted selection.
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Affiliation(s)
- Paweł Milczarski
- Department of Plant Genetics, Breeding and Biotechnology, West Pomeranian University of Technology in Szczecin, Słowackiego 17, 71-434, Szczecin, Poland
| | - Monika Hanek
- Department of Plant Genetics, Breeding and Biotechnology, West Pomeranian University of Technology in Szczecin, Słowackiego 17, 71-434, Szczecin, Poland
| | - Mirosław Tyrka
- Department of Biochemistry and Biotechnology, Rzeszów University of Technology, Powstańców Warszawy 6, 35-959, Rzeszów, Poland
| | - Stefan Stojałowski
- Department of Plant Genetics, Breeding and Biotechnology, West Pomeranian University of Technology in Szczecin, Słowackiego 17, 71-434, Szczecin, Poland.
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Genetics and Molecular Mapping of Black Rot Resistance Locus Xca1bc on Chromosome B-7 in Ethiopian Mustard (Brassica carinata A. Braun). PLoS One 2016; 11:e0152290. [PMID: 27023128 PMCID: PMC4811439 DOI: 10.1371/journal.pone.0152290] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 03/12/2016] [Indexed: 01/19/2023] Open
Abstract
Black rot caused by Xanthomonas campestris pv. campestris (Pam.) Dowson is the most destructive disease of cauliflower causing huge loss to the farmers throughout the world. Since there are limited sources of resistance to black rot in B. oleracea (C genome Brassica), exploration of A and B genomes of Brassica was planned as these were thought to be potential reservoirs of black rot resistance gene(s). In our search for new gene(s) for black rot resistance, F2 mapping population was developed in Brassica carinata (BBCC) by crossing NPC-17, a susceptible genotype with NPC-9, a resistant genotype. Out of 364 Intron length polymorphic markers and microsatellite primers used in this study, 41 distinguished the parental lines. However, resistant and susceptible bulks could be distinguished by three markers At1g70610, SSR Na14-G02 and At1g71865 which were used for genotyping of F2 mapping population. These markers were placed along the resistance gene, according to order, covering a distance of 36.30 cM. Intron length polymorphic markers At1g70610 and At1g71865 were found to be linked to black rot resistance locus (Xca1bc) at 6.2 and 12.8 cM distance, respectively. This is the first report of identification of markers linked to Xca1bc locus in Brassica carinata on B-7 linkage group. Intron length polymorphic markers provided a novel and attractive option for marker assisted selection due to high cross transferability and cost effectiveness for marker assisted alien gene introgression into cauliflower.
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Zou J, Hu D, Liu P, Raman H, Liu Z, Liu X, Parkin IAP, Chalhoub B, Meng J. Co-linearity and divergence of the A subgenome of Brassica juncea compared with other Brassica species carrying different A subgenomes. BMC Genomics 2016; 17:18. [PMID: 26728943 PMCID: PMC4700566 DOI: 10.1186/s12864-015-2343-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Accepted: 12/22/2015] [Indexed: 01/25/2023] Open
Abstract
Background There are three basic Brassica genomes (A, B, and C) and three parallel sets of subgenomes distinguished in the diploid Brassica (i.e.: B. rapa, ArAr; B. nigra, BniBni; B. oleracea, CoCo) and the derived allotetraploid species (i.e.: B. juncea, AjAjBjBj; B. napus, AnAnCnCn; B. carinata, BcBcCcCc). To understand subgenome differentiation in B. juncea in comparison to other A genome-carrying Brassica species (B. rapa and B. napus), we constructed a dense genetic linkage map of B. juncea, and conducted population genetic analysis on diverse lines of the three A-genome carrying Brassica species using a genotyping-by-sequencing approach (DArT-seq). Results A dense genetic linkage map of B. juncea was constructed using an F2 population derived from Sichuan Yellow/Purple Mustard. The map included 3329 DArT-seq markers on 18 linkage groups and covered 1579 cM with an average density of two markers per cM. Based on this map and the alignment of the marker sequences with the physical genome of Arabidopsis thaliana, we observed strong co-linearity of the ancestral blocks among the different A subgenomes but also considerable block variation. Comparative analyses at the level of genome sequences of B. rapa and B. napus, and marker sequence anchored on the genetic map of B. juncea, revealed a total of 30 potential inversion events across large segments and 20 potential translocation events among the three A subgenomes. Population genetic analysis on 26 accessions of the three A genome-carrying Brassica species showed that the highest genetic distance were estimated when comparing Aj-An than between An-Ar and Aj-Ar subgenome pairs. Conclusions The development of the dense genetic linkage map of B. juncea with informative DArT-seq marker sequences and availability of the reference sequences of the Ar, and AnCn genomes allowed us to compare the A subgenome structure of B. juncea (Aj) . Our results suggest that strong co-linearity exists among the three A Brassica genomes (Ar, An and Aj) but with apparent subgenomic variation. Population genetic analysis on three A-genome carrying Brassica species support the idea that B. juncea has distinct genomic diversity, and/or evolved from a different A genome progenitor of B. napus. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2343-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jun Zou
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Dandan Hu
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Peifa Liu
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Harsh Raman
- Graham Centre for Agricultural Innovation (an alliance between the Charles Sturt University and NSW Department of Primary Industries), Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, 2650, Australia.
| | - Zhongsong Liu
- Oilseed Crops Institute, Hunan Agricultural University, Changsha, 410128, China.
| | - Xianjun Liu
- Oilseed Crops Institute, Hunan Agricultural University, Changsha, 410128, China.
| | - Isobel A P Parkin
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada.
| | - Boulos Chalhoub
- Unité de Recherche en Génomique Végétale (Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Université d'Evry Val d'Essonnes), Organization and Evolution of Plant Genomes, 91057, Evry cedex, France.
| | - Jinling Meng
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, 430070, China.
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15
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Sharma BB, Kalia P, Yadava DK, Singh D, Sharma TR. Genetics and Molecular Mapping of Black Rot Resistance Locus Xca1bc on Chromosome B-7 in Ethiopian Mustard (Brassica carinata A. Braun). PLoS One 2016. [PMID: 27023128 DOI: 10.1371/jo] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023] Open
Abstract
Black rot caused by Xanthomonas campestris pv. campestris (Pam.) Dowson is the most destructive disease of cauliflower causing huge loss to the farmers throughout the world. Since there are limited sources of resistance to black rot in B. oleracea (C genome Brassica), exploration of A and B genomes of Brassica was planned as these were thought to be potential reservoirs of black rot resistance gene(s). In our search for new gene(s) for black rot resistance, F2 mapping population was developed in Brassica carinata (BBCC) by crossing NPC-17, a susceptible genotype with NPC-9, a resistant genotype. Out of 364 Intron length polymorphic markers and microsatellite primers used in this study, 41 distinguished the parental lines. However, resistant and susceptible bulks could be distinguished by three markers At1g70610, SSR Na14-G02 and At1g71865 which were used for genotyping of F2 mapping population. These markers were placed along the resistance gene, according to order, covering a distance of 36.30 cM. Intron length polymorphic markers At1g70610 and At1g71865 were found to be linked to black rot resistance locus (Xca1bc) at 6.2 and 12.8 cM distance, respectively. This is the first report of identification of markers linked to Xca1bc locus in Brassica carinata on B-7 linkage group. Intron length polymorphic markers provided a novel and attractive option for marker assisted selection due to high cross transferability and cost effectiveness for marker assisted alien gene introgression into cauliflower.
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Affiliation(s)
- Brij Bihari Sharma
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Pritam Kalia
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Devendra Kumar Yadava
- Division of Seed Science & Technology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Dinesh Singh
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Tilak Raj Sharma
- ICAR- National Research Centre on Plant Biotechnology, New Delhi, India
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16
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Wei Z, Wang M, Chang S, Wu C, Liu P, Meng J, Zou J. Introgressing Subgenome Components from Brassica rapa and B. carinata to B. juncea for Broadening Its Genetic Base and Exploring Intersubgenomic Heterosis. FRONTIERS IN PLANT SCIENCE 2016; 7:1677. [PMID: 27909440 PMCID: PMC5112257 DOI: 10.3389/fpls.2016.01677] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 10/25/2016] [Indexed: 05/21/2023]
Abstract
Brassica juncea (AjAjBjBj), is an allotetraploid that arose from two diploid species, B. rapa (ArAr) and B. nigra (BnBn). It is an old oilseed crop with unique favorable traits, but the genetic improvement on this species is limited. We developed an approach to broaden its genetic base within several generations by intensive selection. The Ar subgenome from the Asian oil crop B. rapa (ArAr) and the Bc subgenome from the African oil crop B. carinata (BcBcCcCc) were combined in a synthesized allohexaploid (ArArBcBcCcCc), which was crossed with traditional B. juncea to generate pentaploid F1 hybrids (ArAjBcBjCc), with subsequent self-pollination to obtain newly synthesized B. juncea (Ar/jAr/jBc/jBc/j). After intensive cytological screening and phenotypic selection of fertility and agronomic traits, a population of new-type B. juncea was obtained and was found to be genetically stable at the F6 generation. The new-type B. juncea possesses good fertility and rich genetic diversity and is distinctly divergent but not isolated from traditional B. juncea, as revealed by population genetic analysis with molecular markers. More than half of its genome was modified, showing exotic introgression and novel variation. In addition to the improvement in some traits of the new-type B. juncea lines, a considerable potential for heterosis was observed in inter-subgenomic hybrids between new-type B. juncea lines and traditional B. juncea accessions. The new-type B. juncea exhibited a stable chromosome number and a novel genome composition through multiple generations, providing insight into how to significantly broaden the genetic base of crops with subgenome introgression from their related species and the potential of exploring inter-subgenomic heterosis for hybrid breeding.
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Xu L, Hu K, Zhang Z, Guan C, Chen S, Hua W, Li J, Wen J, Yi B, Shen J, Ma C, Tu J, Fu T. Genome-wide association study reveals the genetic architecture of flowering time in rapeseed (Brassica napus L.). DNA Res 2015; 23:43-52. [PMID: 26659471 PMCID: PMC4755526 DOI: 10.1093/dnares/dsv035] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 11/04/2015] [Indexed: 01/06/2023] Open
Abstract
Flowering time adaptation is a major breeding goal in the allopolyploid species Brassica napus. To investigate the genetic architecture of flowering time, a genome-wide association study (GWAS) of flowering time was conducted with a diversity panel comprising 523 B. napus cultivars and inbred lines grown in eight different environments. Genotyping was performed with a Brassica 60K Illumina Infinium SNP array. A total of 41 single-nucleotide polymorphisms (SNPs) distributed on 14 chromosomes were found to be associated with flowering time, and 12 SNPs located in the confidence intervals of quantitative trait loci (QTL) identified in previous researches based on linkage analyses. Twenty-five candidate genes were orthologous to Arabidopsis thaliana flowering genes. To further our understanding of the genetic factors influencing flowering time in different environments, GWAS was performed on two derived traits, environment sensitivity and temperature sensitivity. The most significant SNPs were found near Bn-scaff_16362_1-p380982, just 13 kb away from BnaC09g41990D, which is orthologous to A. thaliana CONSTANS (CO), an important gene in the photoperiod flowering pathway. These results provide new insights into the genetic control of flowering time in B. napus and indicate that GWAS is an effective method by which to reveal natural variations of complex traits in B. napus.
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Affiliation(s)
- Liping Xu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Kaining Hu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhenqian Zhang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Chunyun Guan
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Song Chen
- Jiangsu Academy of Agricultural Science, Nanjing 210014, China
| | - Wei Hua
- The Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Jiana Li
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
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