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Ali F, Arif MAR, Ali A, Nadeem MA, Aksoy E, Bakhsh A, Khan SU, Kurt C, Tekdal D, Ilyas MK, Hameed A, Chung YS, Baloch FS. Genome-wide association studies identifies genetic loci related to fatty acid and branched-chain amino acid metabolism and histone modifications under varying nitrogen treatments in safflower ( Carthamus tinctorius). FUNCTIONAL PLANT BIOLOGY : FPB 2024; 51:FP23310. [PMID: 38683936 DOI: 10.1071/fp23310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 04/09/2024] [Indexed: 05/02/2024]
Abstract
Effective identification and usage of genetic variation are prerequisites for developing nutrient-efficient cultivars. A collection of 94 safflower (Carthamus tinctorius ) genotypes (G) was investigated for important morphological and photosynthetic traits at four nitrogen (N) treatments. We found significant variation for all the studied traits except chlorophyll b (chl b ) among safflower genotypes, nitrogen treatments and G×N interaction. The examined traits showed a 2.82-50.00% increase in response to N application. Biological yield (BY) reflected a significantly positive correlation with fresh shoot weight (FSW), root length (RL), fresh root weight (FRW) and number of leaves (NOL), while a significantly positive correlation was also observed among carotenoids (C), chlorophyll a (chl a ), chl b and total chlorophyll content (CT) under all treatments. Superior genotypes with respect to plant height (PH), FSW, NOL, RL, FRW and BY were clustered into Group 3, while genotypes with better mean performance regarding chl a , chl b C and CT were clustered into Group 2 as observed in principal component analysis. The identified eight best-performing genotypes could be useful to develop improved nitrogen efficient cultivars. Genome-wide association analysis resulted in 32 marker-trait associations (MTAs) under four treatments. Markers namely DArT-45481731 , DArT-17812864 , DArT-15670279 and DArT-45482737 were found consistent. Protein-protein interaction networks of loci associated with MTAs were related to fatty acid and branched-chain amino acid metabolism and histone modifications.
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Affiliation(s)
- Fawad Ali
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry Hainan University, Sanya 572025, Hai-nan, China; and Department of Botany, University of Baltistan Skardu, Gilgil Baltistan, 16100, Pakistan
| | - Mian A R Arif
- Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
| | - Arif Ali
- Department of Plant Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Muhammad A Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas 58140, Turkey
| | - Emre Aksoy
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Allah Bakhsh
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Shahid U Khan
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China; and Women Medical and Dental College, Khyber Medical University, Peshawar, KPK, 22020, Pakistan
| | - Cemal Kurt
- Department of Field Crops, Faculty of Agriculture, University of Çukurova, Adana, Turkey
| | - Dilek Tekdal
- Faculty of Science, Department of Biotechnology, Mersin University, 33343, Yenisehir, Mersin, Turkey
| | - Muhammad K Ilyas
- National Agricultural Research Centre, Park Road, Islamabad 45500, Pakistan
| | - Amjad Hameed
- Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
| | - Yong S Chung
- Department of Plant Resources and Environment, Jeju National University, Jeju 63243, Republic of Korea
| | - Faheem S Baloch
- Faculty of Science, Department of Biotechnology, Mersin University, 33343, Yenisehir, Mersin, Turkey
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Ahmad M, Waraich EA, Skalicky M, Hussain S, Zulfiqar U, Anjum MZ, Habib ur Rahman M, Brestic M, Ratnasekera D, Lamilla-Tamayo L, Al-Ashkar I, EL Sabagh A. Adaptation Strategies to Improve the Resistance of Oilseed Crops to Heat Stress Under a Changing Climate: An Overview. FRONTIERS IN PLANT SCIENCE 2021; 12:767150. [PMID: 34975951 PMCID: PMC8714756 DOI: 10.3389/fpls.2021.767150] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/11/2021] [Indexed: 05/16/2023]
Abstract
Temperature is one of the decisive environmental factors that is projected to increase by 1. 5°C over the next two decades due to climate change that may affect various agronomic characteristics, such as biomass production, phenology and physiology, and yield-contributing traits in oilseed crops. Oilseed crops such as soybean, sunflower, canola, peanut, cottonseed, coconut, palm oil, sesame, safflower, olive etc., are widely grown. Specific importance is the vulnerability of oil synthesis in these crops against the rise in climatic temperature, threatening the stability of yield and quality. The natural defense system in these crops cannot withstand the harmful impacts of heat stress, thus causing a considerable loss in seed and oil yield. Therefore, a proper understanding of underlying mechanisms of genotype-environment interactions that could affect oil synthesis pathways is a prime requirement in developing stable cultivars. Heat stress tolerance is a complex quantitative trait controlled by many genes and is challenging to study and characterize. However, heat tolerance studies to date have pointed to several sophisticated mechanisms to deal with the stress of high temperatures, including hormonal signaling pathways for sensing heat stimuli and acquiring tolerance to heat stress, maintaining membrane integrity, production of heat shock proteins (HSPs), removal of reactive oxygen species (ROS), assembly of antioxidants, accumulation of compatible solutes, modified gene expression to enable changes, intelligent agricultural technologies, and several other agronomic techniques for thriving and surviving. Manipulation of multiple genes responsible for thermo-tolerance and exploring their high expressions greatly impacts their potential application using CRISPR/Cas genome editing and OMICS technology. This review highlights the latest outcomes on the response and tolerance to heat stress at the cellular, organelle, and whole plant levels describing numerous approaches applied to enhance thermos-tolerance in oilseed crops. We are attempting to critically analyze the scattered existing approaches to temperature tolerance used in oilseeds as a whole, work toward extending studies into the field, and provide researchers and related parties with useful information to streamline their breeding programs so that they can seek new avenues and develop guidelines that will greatly enhance ongoing efforts to establish heat stress tolerance in oilseeds.
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Affiliation(s)
- Muhammad Ahmad
- Department of Agronomy, University of Agriculture, Faisalabad, Pakistan
- Horticultural Sciences Department, Tropical Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Homestead, FL, United States
| | | | - Milan Skalicky
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czechia
| | - Saddam Hussain
- Department of Agronomy, University of Agriculture, Faisalabad, Pakistan
| | - Usman Zulfiqar
- Department of Agronomy, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Zohaib Anjum
- Department of Forestry and Range Management, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Habib ur Rahman
- Department of Agronomy, Muhammad Nawaz Shareef University of Agriculture, Multan, Pakistan
- Crop Science Group, Institute of Crop Science and Resource Conservation (INRES), University Bonn, Bonn, Germany
| | - Marian Brestic
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czechia
- Department of Plant Physiology, Slovak University of Agriculture, Nitra, Slovakia
| | - Disna Ratnasekera
- Department of Agricultural Biology, Faculty of Agriculture, University of Ruhuna, Kamburupitiya, Sri Lanka
| | - Laura Lamilla-Tamayo
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czechia
| | - Ibrahim Al-Ashkar
- Department of Plant Production, College of Food and Agriculture, King Saud University, Riyadh, Saudi Arabia
- Agronomy Department, Faculty of Agriculture, Al-Azhar University, Cairo, Egypt
| | - Ayman EL Sabagh
- Department of Field Crops, Faculty of Agriculture, Siirt University, Siirt, Turkey
- Department of Agronomy, Faculty of Agriculture, Kafrelsheikh University, Kafr El-Shaikh, Egypt
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Menendez YC, Sanchez DH, Snowdon RJ, Rondanini DP, Botto JF. Unraveling the impact on agronomic traits of the genetic architecture underlying plant-density responses in canola. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5426-5441. [PMID: 33940608 DOI: 10.1093/jxb/erab191] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 04/28/2021] [Indexed: 06/12/2023]
Abstract
Plant density defines vegetative architecture and the competition for light between individuals. Brassica napus (canola, rapeseed) presents a radically different plant architecture compared to traditional crops commonly cultivated at high density, and can act as a model system of indeterminate growth. Using a panel of 152 spring-type accessions and a double-haploid population of 99 lines from a cross between the cultivars Lynx and Monty, we performed genome-wide association studies (GWAS) and quantitative trait locus (QTL) mapping for 12 growth and yield traits at two contrasting plant densities of 15 and 60 plants m-2. The most significant associations were found for time to flowering, biomass at harvest, plant height, silique and seed numbers, and seed yield. These were generally independent of plant density, but some density-dependent associations were found in low-density populations. RNA-seq transcriptomic analysis revealed distinctive latent gene-regulatory responses to simulated shade between Lynx and Monty. Having identified candidate genes within the canola QTLs, we further examined their influence on density responses in Arabidopsis lines mutated in certain homologous genes. The results suggested that TCP1 might promote growth independently of plant density, while HY5 could increase biomass and seed yield specifically at high plant density. For flowering time, the results suggested that PIN genes might accelerate flowering in plant a density-dependent manner whilst FT, HY5, and TCP1 might accelerate it in a density-independent. This work highlights the advantages of using agronomic field experiments together with genetic and transcriptomic approaches to decipher quantitative complex traits that potentially mediate improved crop productivity.
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Affiliation(s)
- Yesica C Menendez
- IFEVA (CONICET-UBA), Facultad de Agronomía, Universidad de Buenos Aires, Av. San Martín 4453, C1417DSE, Ciudad Autónoma de Buenos Aires, Argentina
- Facultad de Agronomía, Universidad de Buenos Aires, Av. San Martín 4453, C1417DSE, Ciudad Autónoma de Buenos Aires, Argentina
| | - Diego H Sanchez
- IFEVA (CONICET-UBA), Facultad de Agronomía, Universidad de Buenos Aires, Av. San Martín 4453, C1417DSE, Ciudad Autónoma de Buenos Aires, Argentina
- Facultad de Agronomía, Universidad de Buenos Aires, Av. San Martín 4453, C1417DSE, Ciudad Autónoma de Buenos Aires, Argentina
- CONICET, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Av. Godoy Cruz 2290, C1425FQB, Ciudad Autónoma de Buenos Aires, Argentina
| | - Rod J Snowdon
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Deborah P Rondanini
- Facultad de Agronomía, Universidad de Buenos Aires, Av. San Martín 4453, C1417DSE, Ciudad Autónoma de Buenos Aires, Argentina
- CONICET, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Av. Godoy Cruz 2290, C1425FQB, Ciudad Autónoma de Buenos Aires, Argentina
| | - Javier F Botto
- IFEVA (CONICET-UBA), Facultad de Agronomía, Universidad de Buenos Aires, Av. San Martín 4453, C1417DSE, Ciudad Autónoma de Buenos Aires, Argentina
- Facultad de Agronomía, Universidad de Buenos Aires, Av. San Martín 4453, C1417DSE, Ciudad Autónoma de Buenos Aires, Argentina
- CONICET, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Av. Godoy Cruz 2290, C1425FQB, Ciudad Autónoma de Buenos Aires, Argentina
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Youssef HM, Allam M, Boussora F, Himmelbach A, Milner SG, Mascher M, Schnurbusch T. Dissecting the Genetic Basis of Lateral and Central Spikelet Development and Grain Traits in Intermedium-Spike Barley ( Hordeum vulgare Convar. Intermedium). PLANTS 2020; 9:plants9121655. [PMID: 33256118 PMCID: PMC7760360 DOI: 10.3390/plants9121655] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/19/2020] [Accepted: 11/23/2020] [Indexed: 11/16/2022]
Abstract
Barley (Hordeum vulgare L.) is one of the major grain crops worldwide and considered as a model plant for temperate cereals. One of the barley row-type groups, named intermedium-barley, was used in our previous study where we reported that other genetic loci rather than vrs1 and Int-c could play a role in lateral spikelet development and even in setting grains. To continue this work, we used phenotypic and genotypic data of 254 intermedium-spike barley accessions aimed at dissecting the genetic basis of development and grain traits of lateral and central spikelet using genome wide association (GWAS) analysis. After genotypic data filtering, 8,653 single-nucleotide polymorphism (SNPs) were used for GWAS analysis. A total of 169 significant associations were identified and we focused only on the subset of associations that exceeded the p < 10−4 threshold. Thirty-three highly significant marker-trait-associations (MTAs), represented in 28 different SNPs on all seven chromosomes for the central and/or lateral spikelet traits; such as kernel length, width, area, weight, unfilled spikelet and 1000-kernel weight, were detected. Highly significant associated markers were anchored physically using barley genome sequencing to identify candidate genes to either contain the SNPs or the closest gene to the SNP position. The results showed that 12 MTAs were specific for lateral spikelet traits, nine MTAs were specific for central spikelet traits and seven MTAs for both central and lateral traits. All together, the GWAS and candidate gene results support our hypothesis that lateral spikelet development could be regulated by loci different from those regulating central spikelet development.
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Affiliation(s)
- Helmy M. Youssef
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany; (M.A.); (F.B.); (A.H.); (S.G.M.); (M.M.)
- Faculty of Agriculture, Cairo University, Giza 12613, Egypt
- Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
- Correspondence: (H.M.Y.); (T.S.); Tel.: 49-3455522683 (H.M.Y.)
| | - Mohamed Allam
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany; (M.A.); (F.B.); (A.H.); (S.G.M.); (M.M.)
- Faculty of Agriculture, Assuit University, Assuit 71526, Egypt
| | - Faiza Boussora
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany; (M.A.); (F.B.); (A.H.); (S.G.M.); (M.M.)
- Institute of Arid Lands of Medenine, Route du Djorf km 22.5, Médénine 4100, Tunisia
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany; (M.A.); (F.B.); (A.H.); (S.G.M.); (M.M.)
| | - Sara G. Milner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany; (M.A.); (F.B.); (A.H.); (S.G.M.); (M.M.)
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany; (M.A.); (F.B.); (A.H.); (S.G.M.); (M.M.)
| | - Thorsten Schnurbusch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany; (M.A.); (F.B.); (A.H.); (S.G.M.); (M.M.)
- Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
- Correspondence: (H.M.Y.); (T.S.); Tel.: 49-3455522683 (H.M.Y.)
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Identification of Regulatory SNPs Associated with Vicine and Convicine Content of Vicia faba Based on Genotyping by Sequencing Data Using Deep Learning. Genes (Basel) 2020; 11:genes11060614. [PMID: 32516876 PMCID: PMC7349281 DOI: 10.3390/genes11060614] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/26/2020] [Accepted: 05/28/2020] [Indexed: 12/15/2022] Open
Abstract
Faba bean (Vicia faba) is a grain legume, which is globally grown for both human consumption as well as feed for livestock. Despite its agro-ecological importance the usage of Vicia faba is severely hampered by its anti-nutritive seed-compounds vicine and convicine (V+C). The genes responsible for a low V+C content have not yet been identified. In this study, we aim to computationally identify regulatory SNPs (rSNPs), i.e., SNPs in promoter regions of genes that are deemed to govern the V+C content of Vicia faba. For this purpose we first trained a deep learning model with the gene annotations of seven related species of the Leguminosae family. Applying our model, we predicted putative promoters in a partial genome of Vicia faba that we assembled from genotyping-by-sequencing (GBS) data. Exploiting the synteny between Medicago truncatula and Vicia faba, we identified two rSNPs which are statistically significantly associated with V+C content. In particular, the allele substitutions regarding these rSNPs result in dramatic changes of the binding sites of the transcription factors (TFs) MYB4, MYB61, and SQUA. The knowledge about TFs and their rSNPs may enhance our understanding of the regulatory programs controlling V+C content of Vicia faba and could provide new hypotheses for future breeding programs.
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Dheer P, Rautela I, Sharma V, Dhiman M, Sharma A, Sharma N, Sharma MD. Evolution in crop improvement approaches and future prospects of molecular markers to CRISPR/Cas9 system. Gene 2020; 753:144795. [PMID: 32450202 DOI: 10.1016/j.gene.2020.144795] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/07/2020] [Accepted: 05/19/2020] [Indexed: 01/03/2023]
Abstract
The advent of genetic selection and genome modification method assure about a real novel reformation in biotechnology and genetic engineering. With the extensive capabilities of molecular markers of them being stable, cost-effective and easy to use, they ultimately become a potent tool for variety of applications such a gene targeting, selection, editing, functional genomics; mainly for the improvisation of commercially important crops. Three main benefits of molecular marker in the field of agriculture and crop improvement programmes first, reduction of the duration of breeding programmes, second, they allow creation of new genetic variation and genetic diversity of plants and third most promising benefit is help in production of engineered plant for disease resistance, or resistance from pathogen and herbicides. This review is anticipated to present an outline how the techniques have been evolved from the simple conventional applications of DNA based molecular markers to highly throughput CRISPR technology and geared the crop yield. Techniques like using Zinc Finger Nucleases (ZFNs), Transcription Activator-Like Effector Nucleases (TALENs) and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR/Cas9) systems have revolutionised in the field of genome editing. These have been promptly accepted in both the research and commercial industry. On the whole, the widespread use of molecular markers with their types, their appliance in plant breeding along with the advances in genetic selection and genome editing together being a novel strategy to boost crop yield has been reviewed.
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Affiliation(s)
- Pallavi Dheer
- Department of Life Sciences, Shri Guru Ram Rai Institute of Technology & Science, Patel Nagar, Dehradun, Uttarakhand, India
| | - Indra Rautela
- Department of Biotechnology, SALS, Uttaranchal University, Dehradun, Uttarakhand, India
| | - Vandana Sharma
- Department of Botany, K.L.DAV (PG) College, Roorkee,Uttarakhand, India
| | - Manjul Dhiman
- Department of Botany, K.L.DAV (PG) College, Roorkee,Uttarakhand, India
| | - Aditi Sharma
- Department of Biotechnology, Graphic Era University, Dehradun, Uttarakhand, India
| | - Nishesh Sharma
- Department of Biotechnology, SALS, Uttaranchal University, Dehradun, Uttarakhand, India
| | - Manish Dev Sharma
- Department of Biotechnology, School of Basic and Applied Sciences, Shri Guru Ram Rai University, Patel Nagar, Dehradun, Uttarakhand, India.
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Ali F, Nadeem MA, Barut M, Habyarimana E, Chaudhary HJ, Khalil IH, Alsaleh A, Hatipoğlu R, Karaköy T, Kurt C, Aasim M, Sameeullah M, Ludidi N, Yang SH, Chung G, Baloch FS. Genetic Diversity, Population Structure and Marker-Trait Association for 100-Seed Weight in International Safflower Panel Using SilicoDArT Marker Information. PLANTS (BASEL, SWITZERLAND) 2020; 9:E652. [PMID: 32455816 PMCID: PMC7284372 DOI: 10.3390/plants9050652] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 01/09/2023]
Abstract
Safflower is an important oilseed crop mainly grown in the arid and semi-arid regions of the world. The aim of this study was to explore phenotypic and genetic diversity, population structure, and marker-trait association for 100-seed weight in 94 safflower accessions originating from 26 countries using silicoDArT markers. Analysis of variance revealed statistically significant genotypic effects (p < 0.01), while Turkey samples resulted in higher 100-seed weight compared to Pakistan samples. A Constellation plot divided the studied germplasm into two populations on the basis of their 100-seed weight. Various mean genetic diversity parameters including observed number of alleles (1.99), effective number of alleles (1.54), Shannon's information index (0.48), expected heterozygosity (0.32), and unbiased expected heterozygosity (0.32) for the entire population exhibited sufficient genetic diversity using 12232 silicoDArT markers. Analysis of molecular variance (AMOVA) revealed that most of the variations (91%) in world safflower panel are due to differences within country groups. A model-based structure grouped the 94 safflower accessions into populations A, B, C and an admixture population upon membership coefficient. Neighbor joining analysis grouped the safflower accessions into two populations (A and B). Principal coordinate analysis (PCoA) also clustered the safflower accessions on the basis of geographical origin. Three accessions; Egypt-5, Egypt-2, and India-2 revealed the highest genetic distance and hence might be recommended as candidate parental lines for safflower breeding programs. The mixed linear model i.e., the Q + K model, demonstrated that two DArTseq markers (DArT-45483051 and DArT-15672391) had significant association (p < 0.01) for 100-seed weight. We envisage that identified DArTseq markers associated with 100-seed weight will be helpful to develop high-yielding cultivars of safflower through marker-assisted breeding in the near future.
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Affiliation(s)
- Fawad Ali
- Department of Plant Sciences, Quaid-I-Azam University, Islamabad 45320, Pakistan; (F.A.); (H.J.C.)
- Department of Field Crops, Faculty of Agriculture and Natural Science, Bolu Abant Izzet Baysal University, 14030 Bolu, Turkey; (M.B.); (M.S.)
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, 58140 Sivas, Turkey; (M.A.N.); (T.K.); (M.A.)
| | - Muzaffer Barut
- Department of Field Crops, Faculty of Agriculture and Natural Science, Bolu Abant Izzet Baysal University, 14030 Bolu, Turkey; (M.B.); (M.S.)
- Department of Field Crops, Faculty of Agriculture, Çukurova University, 1000 Adana, Turkey; (R.H.); (C.K.)
| | - Ephrem Habyarimana
- CREA Research Center for Cereal and Industrial Crops, 40128 Bologna, Italy;
| | - Hassan Javed Chaudhary
- Department of Plant Sciences, Quaid-I-Azam University, Islamabad 45320, Pakistan; (F.A.); (H.J.C.)
| | - Iftikhar Hussain Khalil
- Department of Plant Breeding and Genetics, The University of Agriculture, Peshawar 25130, Pakistan;
| | - Ahmad Alsaleh
- Science and Technology Application and Research Center (BİLTEM), Yozgat Bozok University, 66900 Yozgat, Turkey;
| | - Rüştü Hatipoğlu
- Department of Field Crops, Faculty of Agriculture, Çukurova University, 1000 Adana, Turkey; (R.H.); (C.K.)
| | - Tolga Karaköy
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, 58140 Sivas, Turkey; (M.A.N.); (T.K.); (M.A.)
| | - Cemal Kurt
- Department of Field Crops, Faculty of Agriculture, Çukurova University, 1000 Adana, Turkey; (R.H.); (C.K.)
| | - Muhammad Aasim
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, 58140 Sivas, Turkey; (M.A.N.); (T.K.); (M.A.)
| | - Muhammad Sameeullah
- Department of Field Crops, Faculty of Agriculture and Natural Science, Bolu Abant Izzet Baysal University, 14030 Bolu, Turkey; (M.B.); (M.S.)
| | - Ndiko Ludidi
- Department of Biotechnology and Center of Excellence in Food Security, University of the Western Cape, Robert Sobukwe Road, Bellville 7530, South Africa;
| | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Chonnam 59626, Korea;
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Chonnam 59626, Korea;
| | - Faheem Shehzad Baloch
- Department of Field Crops, Faculty of Agriculture and Natural Science, Bolu Abant Izzet Baysal University, 14030 Bolu, Turkey; (M.B.); (M.S.)
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Muktar MS, Teshome A, Hanson J, Negawo AT, Habte E, Domelevo Entfellner JB, Lee KW, Jones CS. Genotyping by sequencing provides new insights into the diversity of Napier grass (Cenchrus purpureus) and reveals variation in genome-wide LD patterns between collections. Sci Rep 2019; 9:6936. [PMID: 31061417 PMCID: PMC6502793 DOI: 10.1038/s41598-019-43406-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 04/24/2019] [Indexed: 12/12/2022] Open
Abstract
Napier grass is an important tropical forage-grass and of growing potential as an energy crop. One-hundred-five Napier grass accessions, encompassing two independent collections, were subjected to genotyping by sequencing which generated a set of high-density genome-wide markers together with short sequence reads. The reads, averaging 54 nucleotides, were mapped to the pearl millet genome and the closest genes and annotation information were used to select candidate genes linked to key forage traits. 980 highly polymorphic SNP markers, distributed across the genome, were used to assess population structure and diversity with seven-subgroups identified. A few representative accessions were selected with the objective of distributing subsets of a manageable size for further evaluation. Genome-wide linkage disequilibrium (LD) analyses revealed a fast LD-decay, on average 2.54 kbp, in the combined population with a slower LD-decay in the ILRI collection compared with the EMBRAPA collection, the significance of which is discussed. This initiative generated high-density markers with a good distribution across the genome. The diversity analysis revealed the existence of a substantial amount of variation in the ILRI collection and identified some unique materials from the EMBRAPA collection, demonstrating the potential of the overall population for further genetic and marker-trait-association studies.
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Affiliation(s)
- Meki S Muktar
- Feed and Forage Development, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Abel Teshome
- Teagasc
- CELUP Crop Research, Oak Park, Carlow, R93 XE12, Ireland
| | - Jean Hanson
- Feed and Forage Development, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Alemayehu T Negawo
- Feed and Forage Development, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Ermias Habte
- Feed and Forage Development, International Livestock Research Institute, Addis Ababa, Ethiopia
| | | | - Ki-Won Lee
- Grassland and Forages Division, National Institute of Animal Science, Rural Development Administration, Cheonan, 31000, Republic of Korea
| | - Chris S Jones
- Feed and Forage Development, International Livestock Research Institute, Nairobi, Kenya.
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9
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Li B, Zhao W, Li D, Chao H, Zhao X, Ta N, Li Y, Guan Z, Guo L, Zhang L, Li S, Wang H, Li M. Genetic dissection of the mechanism of flowering time based on an environmentally stable and specific QTL in Brassica napus. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 277:296-310. [PMID: 30466595 DOI: 10.1016/j.plantsci.2018.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 10/02/2018] [Accepted: 10/04/2018] [Indexed: 05/02/2023]
Abstract
Flowering time is an important agronomic trait that is highly influenced by the environment. To elucidate the genetic mechanism of flowering time in rapeseed (Brassica napus L.), a genome-wide QTL analysis was performed in a doubled haploid population grown in winter, semi-winter and spring ecological conditions. Fifty-five consensus QTLs were identified after combining phenotype and genomic data, including 12 environment-stable QTLs and 43 environment-specific QTLs. Importantly, six major QTLs for flowering time were identified, of which two were considered environment-specific QTLs in spring ecological condition and four were considered environment-stable QTLs in winter and semi-winter ecological conditions. Through QTL comparison, 18 QTLs were colocalized with QTLs from six other published studies. Combining the candidate genes with their functional annotation, in 49 of 55 consensus QTLs, 151 candidate genes in B. napus corresponding to 95 homologous genes in Arabidopsis thaliana related to flowering were identified, including BnaC03g32910D (CO), BnaA02g12130D (FT) and BnaA03g13630D (FLC). Most of the candidate genes were involved in different flowering regulatory pathways. Based on re-sequencing and differences in sequence annotation between the two parents, we found that regions containing some candidate genes have numerous non-frameshift InDels and many non- synonymous mutations, which might directly lead to gene functional variation. Flowering time was negativly correlated with seed yield and thousand seed weight based on a QTL comparison of flowering time and seed yield traits, which has implications in breeding new early-maturing varieties of B. napus. Moreover, a putative flowering regulatory network was constructed, including the photoperiod, circadian clock, vernalization, autonomous and gibberellin pathways. Multiple copies of genes led to functional difference among the different copies of homologous genes, which also increased the complexity of the flowering regulatory networks. Taken together, the present results not only provide new insights into the genetic regulatory network underlying the control of flowering time but also improve our understanding of flowering time regulatory pathways in rapeseed.
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Affiliation(s)
- Baojun Li
- Hybrid Rape Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China; Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
| | - Weiguo Zhao
- Hybrid Rape Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China; Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
| | - Dianrong Li
- Hybrid Rape Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China.
| | - Hongbo Chao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
| | - Xiaoping Zhao
- Hybrid Rape Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China.
| | - Na Ta
- Hybrid Rape Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China.
| | - Yonghong Li
- Hybrid Rape Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China.
| | - Zhoubo Guan
- Hybrid Rape Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China.
| | - Liangxing Guo
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
| | - Lina Zhang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
| | - Shisheng Li
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, China.
| | - Hao Wang
- Hybrid Rape Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China.
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China; Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, China.
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10
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Abu Zaitoun SY, Jamous RM, Shtaya MJ, Mallah OB, Eid IS, Ali-Shtayeh MS. Characterizing Palestinian snake melon (Cucumis melo var. flexuosus) germplasm diversity and structure using SNP and DArTseq markers. BMC PLANT BIOLOGY 2018; 18:246. [PMID: 30340523 PMCID: PMC6194588 DOI: 10.1186/s12870-018-1475-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Accepted: 10/08/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND Crop landraces embody a source of beneficial genes potentially providing endurance to environmental stress and other agronomic qualities including yield. Our study included 88 snake melon accessions (Cucumis melo var. flexuosus) collected from 9 districts in the Palestinian West-Bank. These accessions represent four landraces of Palestinian snake melon: Green, and White Baladi, and Green, and White Sahouri. RESULTS This is the first report on successful application of genotyping by sequencing in snake melon. Nine thousand seven hundred fifty single-nucleotide polymorphism (SNP) and 7400 DArTseq genetic markers were employed to evaluate genetic biodiversity and population structure of Palestinian snake melon germplasm collection. Clustering based on neighbor-joining-analysis, principle coordinate and Bayesian model implemented in Structure showed that patterns of genetic diversity of snake melon landraces depends on their geographical source and unraveled the presence of two major local landraces (Sahouri, and Baladi) with accessions from each group clustering together. A significant correlation was observed between both types of markers in Mantel correlation test. A significant association between genetic and geographic matrices (P < 0.0001) was also detected. AMOVA indicated that majority of variation (90%) was due to the difference within accessions. CONCLUSION The Palestinian landraces seem to have unique genes that may allow the enhancement of the global snake melon gene pool and developments of the plant production worldwide. Our subsequent objective is to detect genotypes with promising qualities and to conduct association mapping studies concentrating on Fusarium-wilt resistance, yield, and environmental stresses.
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Affiliation(s)
| | - Rana M. Jamous
- Biodiversity and Environmental Research Center, BERC, Til, Nablus, Palestine
| | - Munqez J. Shtaya
- Biodiversity and Environmental Research Center, BERC, Til, Nablus, Palestine
- Department of Plant Production and Protection, Faculty of Agriculture, An-Najah University, Tulkarm, Palestine
| | - Omar B. Mallah
- Biodiversity and Environmental Research Center, BERC, Til, Nablus, Palestine
| | - Imad S. Eid
- Biodiversity and Environmental Research Center, BERC, Til, Nablus, Palestine
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11
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Tao A, Huang L, Wu G, Afshar RK, Qi J, Xu J, Fang P, Lin L, Zhang L, Lin P. High-density genetic map construction and QTLs identification for plant height in white jute (Corchorus capsularis L.) using specific locus amplified fragment (SLAF) sequencing. BMC Genomics 2017; 18:355. [PMID: 28482802 PMCID: PMC5421330 DOI: 10.1186/s12864-017-3712-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 04/20/2017] [Indexed: 01/13/2023] Open
Abstract
Background Genetic mapping and quantitative trait locus (QTL) detection are powerful methodologies in plant improvement and breeding. White jute (Corchorus capsularis L.) is an important industrial raw material fiber crop because of its elite characteristics. However, construction of a high-density genetic map and identification of QTLs has been limited in white jute due to a lack of sufficient molecular markers. The specific locus amplified fragment sequencing (SLAF-seq) strategy combines locus-specific amplification and high-throughput sequencing to carry out de novo single nuclear polymorphism (SNP) discovery and large-scale genotyping. In this study, SLAF-seq was employed to obtain sufficient markers to construct a high-density genetic map for white jute. Moreover, with the development of abundant markers, genetic dissection of fiber yield traits such as plant height was also possible. Here, we present QTLs associated with plant height that were identified using our newly constructed genetic linkage groups. Results An F8 population consisting of 100 lines was developed. In total, 69,446 high-quality SLAFs were detected of which 5,074 SLAFs were polymorphic; 913 polymorphic markers were used for the construction of a genetic map. The average coverage for each SLAF marker was 43-fold in the parents, and 9.8-fold in each F8 individual. A linkage map was constructed that contained 913 SLAFs on 11 linkage groups (LGs) covering 1621.4 cM with an average density of 1.61 cM per locus. Among the 11 LGs, LG1 was the largest with 210 markers, a length of 406.34 cM, and an average distance of 1.93 cM between adjacent markers. LG11 was the smallest with only 25 markers, a length of 29.66 cM, and an average distance of 1.19 cM between adjacent markers. ‘SNP_only’ markers accounted for 85.54% and were the predominant markers on the map. QTL mapping based on the F8 phenotypes detected 11 plant height QTLs including one major effect QTL across two cultivation locations, with each QTL accounting for 4.14–15.63% of the phenotypic variance. Conclusions To our knowledge, the linkage map constructed here is the densest one available to date for white jute. This analysis also identified the first QTL in white jute. The results will provide an important platform for gene/QTL mapping, sequence assembly, genome comparisons, and marker-assisted selection breeding for white jute.
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Affiliation(s)
- Aifen Tao
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops; Key Laboratory of Crops by Design, Fujian Agriculture and Forestry University, Fuzhou, 350028, People's Republic of China
| | - Long Huang
- Biomarker Technologies Corporation, 101300, Beijing, China
| | - Guifen Wu
- Guangxi University, 530000, Nanning, China
| | - Reza Keshavarz Afshar
- Eastern Agricultural Research Center, Montana State University, 59270, Sidney, Montana, USA
| | - Jianmin Qi
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops; Key Laboratory of Crops by Design, Fujian Agriculture and Forestry University, Fuzhou, 350028, People's Republic of China.
| | - Jiantang Xu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops; Key Laboratory of Crops by Design, Fujian Agriculture and Forestry University, Fuzhou, 350028, People's Republic of China
| | - Pingping Fang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops; Key Laboratory of Crops by Design, Fujian Agriculture and Forestry University, Fuzhou, 350028, People's Republic of China
| | - Lihui Lin
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops; Key Laboratory of Crops by Design, Fujian Agriculture and Forestry University, Fuzhou, 350028, People's Republic of China
| | - Liwu Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops; Key Laboratory of Crops by Design, Fujian Agriculture and Forestry University, Fuzhou, 350028, People's Republic of China
| | - Peiqing Lin
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops; Key Laboratory of Crops by Design, Fujian Agriculture and Forestry University, Fuzhou, 350028, People's Republic of China
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12
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Mwadzingeni L, Shimelis H, Rees DJG, Tsilo TJ. Genome-wide association analysis of agronomic traits in wheat under drought-stressed and non-stressed conditions. PLoS One 2017; 12:e0171692. [PMID: 28234945 PMCID: PMC5325217 DOI: 10.1371/journal.pone.0171692] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Accepted: 01/24/2017] [Indexed: 12/03/2022] Open
Abstract
This study determined the population structure and genome-wide marker-trait association of agronomic traits of wheat for drought-tolerance breeding. Ninety-three diverse bread wheat genotypes were genotyped using the Diversity Arrays Technology sequencing (DArTseq) protocol. The number of days-to-heading (DTH), number of days-to-maturity (DTM), plant height (PHT), spike length (SPL), number of kernels per spike (KPS), thousand kernel weight (TKW) and grain yield (GYLD), assessed under drought-stressed and non-stressed conditions, were considered for the study. Population structure analysis and genome-wide association mapping were undertaken based on 16,383 silico DArTs loci with < 10% missing data. The population evaluated was grouped into nine distinct genetic structures. Inter-chromosomal linkage disequilibrium showed the existence of linkage decay as physical distance increased. A total of 62 significant (P < 0.001) marker-trait associations (MTAs) were detected explaining more than 20% of the phenotypic variation observed under both drought-stressed and non-stressed conditions. Significant (P < 0.001) MTA event(s) were observed for DTH, PHT, SPL, SPS, and KPS; under both stressed and non-stressed conditions, while additional significant (P < 0.05) associations were observed for TKW, DTM and GYLD under non-stressed condition. The MTAs reported in this population could be useful to initiate marker-assisted selection (MAS) and targeted trait introgression of wheat under drought-stressed and non-stressed conditions, and for fine mapping and cloning of the underlying genes and QTL.
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Affiliation(s)
- Learnmore Mwadzingeni
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
- Agricultural Research Council-Small Grain Institute (ARC-SGI), Bethlehem, South Africa
| | - Hussein Shimelis
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - D. Jasper G. Rees
- Agricultural Research Council-Biotechnology Platform, Pretoria, South Africa
| | - Toi J. Tsilo
- Agricultural Research Council-Small Grain Institute (ARC-SGI), Bethlehem, South Africa
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13
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Raman H, Raman R, Coombes N, Song J, Diffey S, Kilian A, Lindbeck K, Barbulescu DM, Batley J, Edwards D, Salisbury PA, Marcroft S. Genome-wide Association Study Identifies New Loci for Resistance to Leptosphaeria maculans in Canola. FRONTIERS IN PLANT SCIENCE 2016; 7:1513. [PMID: 27822217 PMCID: PMC5075532 DOI: 10.3389/fpls.2016.01513] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 09/23/2016] [Indexed: 05/18/2023]
Abstract
Key message "We identified both quantitative and quantitative resistance loci to Leptosphaeria maculans, a fungal pathogen, causing blackleg disease in canola. Several genome-wide significant associations were detected at known and new loci for blackleg resistance. We further validated statistically significant associations in four genetic mapping populations, demonstrating that GWAS marker loci are indeed associated with resistance to L. maculans. One of the novel loci identified for the first time, Rlm12, conveys adult plant resistance in canola." Blackleg, caused by Leptosphaeria maculans, is a significant disease which affects the sustainable production of canola (Brassica napus). This study reports a genome-wide association study based on 18,804 polymorphic SNPs to identify loci associated with qualitative and quantitative resistance to L. maculans. Genomic regions delimited with 694 significant SNP markers, that are associated with resistance evaluated using 12 single spore isolates and pathotypes from four canola stubble were identified. Several significant associations were detected at known disease resistance loci including in the vicinity of recently cloned Rlm2/LepR3 genes, and at new loci on chromosomes A01/C01, A02/C02, A03/C03, A05/C05, A06, A08, and A09. In addition, we validated statistically significant associations on A01, A07, and A10 in four genetic mapping populations, demonstrating that GWAS marker loci are indeed associated with resistance to L. maculans. One of the novel loci identified for the first time, Rlm12, conveys adult plant resistance and mapped within 13.2 kb from Arabidopsis R gene of TIR-NBS class. We showed that resistance loci are located in the vicinity of R genes of Arabidopsis thaliana and Brassica napus on the sequenced genome of B. napus cv. Darmor-bzh. Significantly associated SNP markers provide a valuable tool to enrich germplasm for favorable alleles in order to improve the level of resistance to L. maculans in canola.
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Affiliation(s)
- Harsh Raman
- Graham Centre for Agricultural Innovation (an alliance between NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga Agricultural Institute, Wagga WaggaNSW, Australia
| | - Rosy Raman
- Graham Centre for Agricultural Innovation (an alliance between NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga Agricultural Institute, Wagga WaggaNSW, Australia
| | - Neil Coombes
- Graham Centre for Agricultural Innovation (an alliance between NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga Agricultural Institute, Wagga WaggaNSW, Australia
| | - Jie Song
- Diversity Array Technology P/L, University of Canberra, CanberraACT, Australia
| | - Simon Diffey
- Centre for Bioinformatics and Biometrics, University of Wollongong, WollongongNSW, Australia
| | - Andrzej Kilian
- Diversity Array Technology P/L, University of Canberra, CanberraACT, Australia
| | - Kurt Lindbeck
- Graham Centre for Agricultural Innovation (an alliance between NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga Agricultural Institute, Wagga WaggaNSW, Australia
| | - Denise M. Barbulescu
- Department of Economic Development, Jobs, Transport and Resources, HorshamVIC, Australia
| | - Jacqueline Batley
- School of Plant Biology, University of Western Australia, CrawleyWA, Australia
| | - David Edwards
- School of Plant Biology, University of Western Australia, CrawleyWA, Australia
- Institute of Agriculture, University of Western Australia, CrawleyWA, Australia
| | - Phil A. Salisbury
- Department of Economic Development, Jobs, Transport and Resources, HorshamVIC, Australia
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, ParkvilleVIC, Australia
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14
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Larkan NJ, Raman H, Lydiate DJ, Robinson SJ, Yu F, Barbulescu DM, Raman R, Luckett DJ, Burton W, Wratten N, Salisbury PA, Rimmer SR, Borhan MH. Multi-environment QTL studies suggest a role for cysteine-rich protein kinase genes in quantitative resistance to blackleg disease in Brassica napus. BMC PLANT BIOLOGY 2016; 16:183. [PMID: 27553246 PMCID: PMC4995785 DOI: 10.1186/s12870-016-0877-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 08/17/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND Resistance to the blackleg disease of Brassica napus (canola/oilseed rape), caused by the hemibiotrophic fungal pathogen Leptosphaeria maculans, is determined by both race-specific resistance (R) genes and quantitative resistance loci (QTL), or adult-plant resistance (APR). While the introgression of R genes into breeding material is relatively simple, QTL are often detected sporadically, making them harder to capture in breeding programs. For the effective deployment of APR in crop varieties, resistance QTL need to have a reliable influence on phenotype in multiple environments and be well defined genetically to enable marker-assisted selection (MAS). RESULTS Doubled-haploid populations produced from the susceptible B. napus variety Topas and APR varieties AG-Castle and AV-Sapphire were analysed for resistance to blackleg in two locations over 3 and 4 years, respectively. Three stable QTL were detected in each population, with two loci appearing to be common to both APR varieties. Physical delineation of three QTL regions was sufficient to identify candidate defense-related genes, including a cluster of cysteine-rich receptor-like kinases contained within a 49 gene QTL interval on chromosome A01. Individual L. maculans isolates were used to define the physical intervals for the race-specific R genes Rlm3 and Rlm4 and to identify QTL common to both field studies and the cotyledon resistance response. CONCLUSION Through multi-environment QTL analysis we have identified and delineated four significant and stable QTL suitable for MAS of quantitative blackleg resistance in B. napus, and identified candidate genes which potentially play a role in quantitative defense responses to L. maculans.
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Affiliation(s)
- Nicholas J. Larkan
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, SK S7N 0X2 Canada
- Armatus Genetics Inc, Saskatoon, SK S7W 0C9 Canada
| | - Harsh Raman
- Graham Centre for Agricultural Innovation (an alliance between Charles Sturt University and NSW Department of Primary Industries), Wagga Wagga Agricultural Institute, Wagga Wagga, NSW 2650 Australia
| | - Derek J. Lydiate
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, SK S7N 0X2 Canada
| | - Stephen J. Robinson
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, SK S7N 0X2 Canada
| | - Fengqun Yu
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, SK S7N 0X2 Canada
| | - Denise M. Barbulescu
- Department of Economic Development, Jobs, Transport and Resources, Grains Innovation Park, Horsham, VIC 3400 Australia
| | - Rosy Raman
- Graham Centre for Agricultural Innovation (an alliance between Charles Sturt University and NSW Department of Primary Industries), Wagga Wagga Agricultural Institute, Wagga Wagga, NSW 2650 Australia
| | - David J. Luckett
- Graham Centre for Agricultural Innovation (an alliance between Charles Sturt University and NSW Department of Primary Industries), Wagga Wagga Agricultural Institute, Wagga Wagga, NSW 2650 Australia
| | - Wayne Burton
- Department of Economic Development, Jobs, Transport and Resources, Grains Innovation Park, Horsham, VIC 3400 Australia
- Seednet Australia, Golf Course Road, Horsham, VIC 3402 Australia
| | - Neil Wratten
- Graham Centre for Agricultural Innovation (an alliance between Charles Sturt University and NSW Department of Primary Industries), Wagga Wagga Agricultural Institute, Wagga Wagga, NSW 2650 Australia
| | - Philip A. Salisbury
- Department of Economic Development, Jobs, Transport and Resources, Centre for AgriBioscience, La Trobe University, Bundoora, VIC 3083 Australia
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, VIC 3010 Australia
| | - S. Roger Rimmer
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, SK S7N 0X2 Canada
| | - M. Hossein Borhan
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, SK S7N 0X2 Canada
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15
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Raman H, Raman R, Coombes N, Song J, Prangnell R, Bandaranayake C, Tahira R, Sundaramoorthi V, Killian A, Meng J, Dennis ES, Balasubramanian S. Genome-wide association analyses reveal complex genetic architecture underlying natural variation for flowering time in canola. PLANT, CELL & ENVIRONMENT 2016; 39:1228-39. [PMID: 26428711 DOI: 10.1111/pce.12644] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 09/17/2015] [Accepted: 09/20/2015] [Indexed: 05/17/2023]
Abstract
Optimum flowering time is the key to maximize canola production in order to meet global demand of vegetable oil, biodiesel and canola-meal. We reveal extensive variation in flowering time across diverse genotypes of canola under field, glasshouse and controlled environmental conditions. We conduct a genome-wide association study and identify 69 single nucleotide polymorphism (SNP) markers associated with flowering time, which are repeatedly detected across experiments. Several associated SNPs occur in clusters across the canola genome; seven of them were detected within 20 Kb regions of a priori candidate genes; FLOWERING LOCUS T, FRUITFUL, FLOWERING LOCUS C, CONSTANS, FRIGIDA, PHYTOCHROME B and an additional five SNPs were localized within 14 Kb of a previously identified quantitative trait loci for flowering time. Expression analyses showed that among FLC paralogs, BnFLC.A2 accounts for ~23% of natural variation in diverse accessions. Genome-wide association analysis for FLC expression levels mapped not only BnFLC.C2 but also other loci that contribute to variation in FLC expression. In addition to revealing the complex genetic architecture of flowering time variation, we demonstrate that the identified SNPs can be modelled to predict flowering time in diverse canola germplasm accurately and hence are suitable for genomic selection of adaptative traits in canola improvement programmes.
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Affiliation(s)
- H 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, 2650, Australia
| | - R 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, 2650, Australia
| | - N Coombes
- Graham Centre for Agricultural Innovation (an alliance between NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, 2650, Australia
| | - J Song
- Diversity Arrays Technology P/L, University of Canberra, Canberra, ACT, 2601, Australia
| | - R Prangnell
- Graham Centre for Agricultural Innovation (an alliance between NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, 2650, Australia
| | - C Bandaranayake
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - R Tahira
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - V Sundaramoorthi
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - A Killian
- Diversity Arrays Technology P/L, University of Canberra, Canberra, ACT, 2601, Australia
| | - J Meng
- National Key Laboratory of Crop Improvement, Huazhong Agricultural University, Wuhan, China
| | - E S Dennis
- CSIRO Division of Plant Industry, Canberra, ACT, 2601, Australia
| | - S Balasubramanian
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
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16
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Recent advances in molecular marker techniques: Insight into QTL mapping, GWAS and genomic selection in plants. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/s12892-015-0037-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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17
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Genome-wide identification of SSR and SNP markers from the non-heading Chinese cabbage for comparative genomic analyses. BMC Genomics 2015; 16:328. [PMID: 25908429 PMCID: PMC4408590 DOI: 10.1186/s12864-015-1534-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 04/13/2015] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Non-heading Chinese cabbage (NHCC), belonging to Brassica, is an important leaf vegetable in Asia. Although genetic analyses have been performed through conventional selection and breeding efforts, the domestication history of NHCC and the genetics underlying its morphological diversity remain unclear. Thus, the reliable molecular markers representative of the whole genome are required for molecular-assisted selection in NHCC. RESULTS A total of 20,836 simple sequence repeats (SSRs) were detected in NHCC, containing repeat types from mononucleotide to nonanucleotide. The average density was 62.93 SSRs/Mb. In gene regions, 5,435 SSRs were identified in 4,569 genes. A total of 5,008 primer pairs were designed, and 74 were randomly selected for validation. Among these, 60 (81.08%) were polymorphic in 18 Cruciferae. The number of polymorphic bands ranged from two to five, with an average of 2.70 for each primer. The average values of the polymorphism information content, observed heterozygosity, Hardy-Weinberg equilibrium, and Shannon's information index were 0.2970, 0.4136, 0.5706, and 0.5885, respectively. Four clusters were classified according to the unweighted pair-group method with arithmetic average cluster analysis of 18 genotypes. In addition, a total of 1,228,979 single nucleotide polymorphisms (SNPs) were identified in the NHCC through a comparison with the genome of Chinese cabbage, and the average SNP density in the whole genome was 4.33/Kb. The number of SNPs ranged from 341,939 to 591,586 in the 10 accessions, and the average heterozygous SNPs ratio was ~42.53%. All analyses showed these markers were high quality and reliable. Therefore, they could be used in the construction of a linkage map and for genetic diversity studies for NHCC in future. CONCLUSIONS This is the first systematic and comprehensive analysis and identification of SSRs in NHCC and 17 species. The development of a large number of SNP and SSR markers was successfully achieved for NHCC. These novel markers are valuable for constructing genetic linkage maps, comparative genome analysis, quantitative trait locus (QTL) mapping, genome-wide association studies, and marker-assisted selection in NHCC breeding system research.
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Abstract
Molecular markers, due to their stability, cost-effectiveness and ease of use provide an immensely popular tool for a variety of applications including genome mapping, gene tagging, genetic diversity diversity, phylogenetic analysis and forensic investigations. In the last three decades, a number of molecular marker techniques have been developed and exploited worldwide in different systems. However, only a handful of these techniques, namely RFLPs, RAPDs, AFLPs, ISSRs, SSRs and SNPs have received global acceptance. A recent revolution in DNA sequencing techniques has taken the discovery and application of molecular markers to high-throughput and ultrahigh-throughput levels. Although, the choice of marker will obviously depend on the targeted use, microsatellites, SNPs and genotyping by sequencing (GBS) largely fulfill most of the user requirements. Further, modern transcriptomic and functional markers will lead the ventures onto high-density genetic map construction, identification of QTLs, breeding and conservation strategies in times to come in combination with other high throughput techniques. This review presents an overview of different marker technologies and their variants with a comparative account of their characteristic features and applications.
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Affiliation(s)
- Atul Grover
- a Biotechnology Division , Defence Institute of Bio Energy Research , Goraparao, P.O. Arjunpur , Haldwani , Uttarakhand , India and
| | - P C Sharma
- b University School of Biotechnology, Guru Gobind Singh Indraprastha University , Dwarka Sec. 16C , New Delhi , India
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Raman H, Dalton-Morgan J, Diffey S, Raman R, Alamery S, Edwards D, Batley J. SNP markers-based map construction and genome-wide linkage analysis in Brassica napus. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:851-60. [PMID: 24698362 DOI: 10.1111/pbi.12186] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 01/29/2014] [Accepted: 02/21/2014] [Indexed: 05/19/2023]
Abstract
An Illumina Infinium array comprising 5306 single nucleotide polymorphism (SNP) markers was used to genotype 175 individuals of a doubled haploid population derived from a cross between Skipton and Ag-Spectrum, two Australian cultivars of rapeseed (Brassica napus L.). A genetic linkage map based on 613 SNP and 228 non-SNP (DArT, SSR, SRAP and candidate gene markers) covering 2514.8 cM was constructed and further utilized to identify loci associated with flowering time and resistance to blackleg, a disease caused by the fungus Leptosphaeria maculans. Comparison between genetic map positions of SNP markers and the sequenced Brassica rapa (A) and Brassica oleracea (C) genome scaffolds showed several genomic rearrangements in the B. napus genome. A major locus controlling resistance to L. maculans was identified at both seedling and adult plant stages on chromosome A07. QTL analyses revealed that up to 40.2% of genetic variation for flowering time was accounted for by loci having quantitative effects. Comparative mapping showed Arabidopsis and Brassica flowering genes such as Phytochrome A/D, Flowering Locus C and agamous-Like MADS box gene AGL1 map within marker intervals associated with flowering time in a DH population from Skipton/Ag-Spectrum. Genomic regions associated with flowering time and resistance to L. maculans had several SNP markers mapped within 10 cM. Our results suggest that SNP markers will be suitable for various applications such as trait introgression, comparative mapping and high-resolution mapping of loci in B. napus.
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Affiliation(s)
- 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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Nelson MN, Rajasekaran R, Smith A, Chen S, Beeck CP, Siddique KHM, Cowling WA. Quantitative trait loci for thermal time to flowering and photoperiod responsiveness discovered in summer annual-type Brassica napus L. PLoS One 2014; 9:e102611. [PMID: 25061822 PMCID: PMC4111298 DOI: 10.1371/journal.pone.0102611] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 06/20/2014] [Indexed: 11/18/2022] Open
Abstract
Time of flowering is a key adaptive trait in plants and is conditioned by the interaction of genes and environmental cues including length of photoperiod, ambient temperature and vernalisation. Here we investigated the photoperiod responsiveness of summer annual-types of Brassica napus (rapeseed, canola). A population of 131 doubled haploid lines derived from a cross between European and Australian parents was evaluated for days to flowering, thermal time to flowering (measured in degree-days) and the number of leaf nodes at flowering in a compact and efficient glasshouse-based experiment with replicated short and long day treatments. All three traits were under strong genetic control with heritability estimates ranging from 0.85–0.93. There was a very strong photoperiod effect with flowering in the population accelerated by 765 degree-days in the long day versus short day treatments. However, there was a strong genetic correlation of line effects (0.91) between the long and short day treatments and relatively low genotype x treatment interaction indicating that photoperiod had a similar effect across the population. Bivariate analysis of thermal time to flowering in short and long days revealed three main effect quantitative trait loci (QTLs) that accounted for 57.7% of the variation in the population and no significant interaction QTLs. These results provided insight into the contrasting adaptations of Australian and European varieties. Both parents responded to photoperiod and their alleles shifted the population to earlier flowering under long days. In addition, segregation of QTLs in the population caused wide transgressive segregation in thermal time to flowering. Potential candidate flowering time homologues located near QTLs were identified with the aid of the Brassica rapa reference genome sequence. We discuss how these results will help to guide the breeding of summer annual types of B. napus adapted to new and changing environments.
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Affiliation(s)
- Matthew N. Nelson
- School of Plant Biology, The University of Western Australia, Crawley, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, Australia
- * E-mail:
| | - Ravikesavan Rajasekaran
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, India
| | - Alison Smith
- National Institute for Applied Statistics Research Australia, University of Wollongong, Wollongong, Australia
| | - Sheng Chen
- School of Plant Biology, The University of Western Australia, Crawley, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, Australia
| | - Cameron P. Beeck
- School of Plant Biology, The University of Western Australia, Crawley, Australia
| | | | - Wallace A. Cowling
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, Australia
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21
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Raman H, Raman R, Kilian A, Detering F, Carling J, Coombes N, Diffey S, Kadkol G, Edwards D, McCully M, Ruperao P, Parkin IAP, Batley J, Luckett DJ, Wratten N. Genome-wide delineation of natural variation for pod shatter resistance in Brassica napus. PLoS One 2014; 9:e101673. [PMID: 25006804 PMCID: PMC4090071 DOI: 10.1371/journal.pone.0101673] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 06/02/2014] [Indexed: 12/18/2022] Open
Abstract
Resistance to pod shattering (shatter resistance) is a target trait for global rapeseed (canola, Brassica napus L.), improvement programs to minimise grain loss in the mature standing crop, and during windrowing and mechanical harvest. We describe the genetic basis of natural variation for shatter resistance in B. napus and show that several quantitative trait loci (QTL) control this trait. To identify loci underlying shatter resistance, we used a novel genotyping-by-sequencing approach DArT-Seq. QTL analysis detected a total of 12 significant QTL on chromosomes A03, A07, A09, C03, C04, C06, and C08; which jointly account for approximately 57% of the genotypic variation in shatter resistance. Through Genome-Wide Association Studies, we show that a large number of loci, including those that are involved in shattering in Arabidopsis, account for variation in shatter resistance in diverse B. napus germplasm. Our results indicate that genetic diversity for shatter resistance genes in B. napus is limited; many of the genes that might control this trait were not included during the natural creation of this species, or were not retained during the domestication and selection process. We speculate that valuable diversity for this trait was lost during the natural creation of B. napus. To improve shatter resistance, breeders will need to target the introduction of useful alleles especially from genotypes of other related species of Brassica, such as those that we have identified.
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Affiliation(s)
- 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
| | - 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
| | - Andrzej Kilian
- Diversity Arrays Technology Pty Ltd, University of Canberra, Bruce, ACT, Australia
| | - Frank Detering
- Diversity Arrays Technology Pty Ltd, University of Canberra, Bruce, ACT, Australia
| | - Jason Carling
- Diversity Arrays Technology Pty Ltd, University of Canberra, Bruce, ACT, Australia
| | - Neil Coombes
- 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
| | - Simon Diffey
- University of Wollongong, Wollongong, NSW, Australia
| | - Gururaj Kadkol
- NSW Department of Primary Industries, Tamworth Agricultural Institute, Tamworth, NSW, Australia
| | - David Edwards
- Australian Centre for Plant Functional Genomic, School of Agriculture and Food Sciences, University of Queensland, St Lucia, QLD, Australia; School of Plant Biology, University of Western Australia, Perth, WA, Australia
| | | | - Pradeep Ruperao
- Australian Centre for Plant Functional Genomic, School of Agriculture and Food Sciences, University of Queensland, St Lucia, QLD, Australia; International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Andhra Pradesh, India
| | | | - Jacqueline Batley
- School of Plant Biology, University of Western Australia, Perth, WA, Australia; School of Agriculture and Food Sciences, University of Queensland, St Lucia, QLD, Australia
| | - David J Luckett
- 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
| | - Neil Wratten
- 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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22
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Zou J, Raman H, Guo S, Hu D, Wei Z, Luo Z, Long Y, Shi W, Fu Z, Du D, Meng J. Constructing a dense genetic linkage map and mapping QTL for the traits of flower development in Brassica carinata. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:1593-605. [PMID: 24824567 DOI: 10.1007/s00122-014-2321-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 04/25/2014] [Indexed: 05/10/2023]
Abstract
An integrated dense genetic linkage map was constructed in a B. carinata population and used for comparative genome analysis and QTL identification for flowering time. An integrated dense linkage map of Brassica carinata (BBCC) was constructed in a doubled haploid population based on DArT-Seq(TM) markers. A total of 4,031 markers corresponding to 1,366 unique loci were mapped including 639 bins, covering a genetic distance of 2,048 cM. We identified 136 blocks and islands conserved in Brassicaceae, which showed a feature of hexaploidisation representing the suggested ancestral crucifer karyotype. The B and C genome of B. carinata shared 85 % of commonly conserved blocks with the B genome of B. nigra/B. juncea and 80 % of commonly conserved blocks with the C genome of B. napus, and shown frequent structural rearrangements such as insertions and inversions. Up to 24 quantitative trait loci (QTL) for flowering and budding time were identified in the DH population. Of these QTL, one consistent QTL (qFT.B4-2) for flowering time was identified in all of the environments in the J block of the B4 linkage group, where a group of genes for flowering time were aligned in A. thaliana. Another major QTL for flowering time under a winter-cropped environment was detected in the E block of C6, where the BnFT-C6 gene was previously localised in B. napus. This high-density map would be useful not only to reveal the genetic variation in the species with QTL analysis and genome sequencing, but also for other applications such as marker-assisted selection and genomic selection, for the African mustard improvement.
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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
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23
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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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24
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Kroc M, Koczyk G, Święcicki W, Kilian A, Nelson MN. New evidence of ancestral polyploidy in the Genistoid legume Lupinus angustifolius L. (narrow-leafed lupin). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:1237-1249. [PMID: 24633641 DOI: 10.1007/s00122-014-2294-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 02/21/2014] [Indexed: 06/03/2023]
Abstract
This is the first clear evidence of duplication and/or triplication of large chromosomal regions in a genome of a Genistoid legume, the most basal clade of Papilionoid legumes. Lupinus angustifolius L. (narrow-leafed lupin) is the most widely cultivated species of Genistoid legume, grown for its high-protein grain. As a member of this most basal clade of Papilionoid legumes, L. angustifolius serves as a useful model for exploring legume genome evolution. Here, we report an improved reference genetic map of L. angustifolius comprising 1207 loci, including 299 newly developed Diversity Arrays Technology markers and 54 new gene-based PCR markers. A comparison between the L. angustifolius and Medicago truncatula genomes was performed using 394 sequence-tagged site markers acting as bridging points between the two genomes. The improved L. angustifolius genetic map, the updated M. truncatula genome assembly and the increased number of bridging points between the genomes together substantially enhanced the resolution of synteny and chromosomal colinearity between these genomes compared to previous reports. While a high degree of syntenic fragmentation was observed that was consistent with the large evolutionary distance between the L. angustifolius and M. truncatula genomes, there were striking examples of conserved colinearity of loci between these genomes. Compelling evidence was found of large-scale duplication and/or triplication in the L. angustifolius genome, consistent with one or more ancestral polyploidy events.
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Affiliation(s)
- Magdalena Kroc
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, 60-479, Poznan, Poland
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25
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Nelson MN, Rajasekaran R, Smith A, Chen S, Beeck CP, Siddique KHM, Cowling WA. Quantitative trait loci for thermal time to flowering and photoperiod responsiveness discovered in summer annual-type Brassica napus L. PLoS One 2014. [PMID: 25061822 DOI: 10.1371/journalpone.0102611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023] Open
Abstract
Time of flowering is a key adaptive trait in plants and is conditioned by the interaction of genes and environmental cues including length of photoperiod, ambient temperature and vernalisation. Here we investigated the photoperiod responsiveness of summer annual-types of Brassica napus (rapeseed, canola). A population of 131 doubled haploid lines derived from a cross between European and Australian parents was evaluated for days to flowering, thermal time to flowering (measured in degree-days) and the number of leaf nodes at flowering in a compact and efficient glasshouse-based experiment with replicated short and long day treatments. All three traits were under strong genetic control with heritability estimates ranging from 0.85-0.93. There was a very strong photoperiod effect with flowering in the population accelerated by 765 degree-days in the long day versus short day treatments. However, there was a strong genetic correlation of line effects (0.91) between the long and short day treatments and relatively low genotype x treatment interaction indicating that photoperiod had a similar effect across the population. Bivariate analysis of thermal time to flowering in short and long days revealed three main effect quantitative trait loci (QTLs) that accounted for 57.7% of the variation in the population and no significant interaction QTLs. These results provided insight into the contrasting adaptations of Australian and European varieties. Both parents responded to photoperiod and their alleles shifted the population to earlier flowering under long days. In addition, segregation of QTLs in the population caused wide transgressive segregation in thermal time to flowering. Potential candidate flowering time homologues located near QTLs were identified with the aid of the Brassica rapa reference genome sequence. We discuss how these results will help to guide the breeding of summer annual types of B. napus adapted to new and changing environments.
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Affiliation(s)
- Matthew N Nelson
- School of Plant Biology, The University of Western Australia, Crawley, Australia; The UWA Institute of Agriculture, The University of Western Australia, Crawley, Australia
| | - Ravikesavan Rajasekaran
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, India
| | - Alison Smith
- National Institute for Applied Statistics Research Australia, University of Wollongong, Wollongong, Australia
| | - Sheng Chen
- School of Plant Biology, The University of Western Australia, Crawley, Australia; The UWA Institute of Agriculture, The University of Western Australia, Crawley, Australia
| | - Cameron P Beeck
- School of Plant Biology, The University of Western Australia, Crawley, Australia
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, Australia
| | - Wallace A Cowling
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, Australia
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Liu L, Qu C, Wittkop B, Yi B, Xiao Y, He Y, Snowdon RJ, Li J. A high-density SNP map for accurate mapping of seed fibre QTL in Brassica napus L. PLoS One 2013; 8:e83052. [PMID: 24386142 PMCID: PMC3873396 DOI: 10.1371/journal.pone.0083052] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2013] [Accepted: 11/07/2013] [Indexed: 11/18/2022] Open
Abstract
A high density genetic linkage map for the complex allotetraploid crop species Brassica napus (oilseed rape) was constructed in a late-generation recombinant inbred line (RIL) population, using genome-wide single nucleotide polymorphism (SNP) markers assayed by the Brassica 60 K Infinium BeadChip Array. The linkage map contains 9164 SNP markers covering 1832.9 cM. 1232 bins account for 7648 of the markers. A subset of 2795 SNP markers, with an average distance of 0.66 cM between adjacent markers, was applied for QTL mapping of seed colour and the cell wall fiber components acid detergent lignin (ADL), cellulose and hemicellulose. After phenotypic analyses across four different environments a total of 11 QTL were detected for seed colour and fiber traits. The high-density map considerably improved QTL resolution compared to the previous low-density maps. A previously identified major QTL with very high effects on seed colour and ADL was pinpointed to a narrow genome interval on chromosome A09, while a minor QTL explaining 8.1% to 14.1% of variation for ADL was detected on chromosome C05. Five and three QTL accounting for 4.7% to 21.9% and 7.3% to 16.9% of the phenotypic variation for cellulose and hemicellulose, respectively, were also detected. To our knowledge this is the first description of QTL for seed cellulose and hemicellulose in B. napus, representing interesting new targets for improving oil content. The high density SNP genetic map enables navigation from interesting B. napus QTL to Brassica genome sequences, giving useful new information for understanding the genetics of key seed quality traits in rapeseed.
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Affiliation(s)
- Liezhao Liu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, China
| | - Cunmin Qu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, China
| | - Benjamin Wittkop
- Department of Plant Breeding, Interdisciplinary Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, National Subcenter of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, China
| | - Yang Xiao
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, China
| | - Yajun He
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, China
| | - Rod J. Snowdon
- Department of Plant Breeding, Interdisciplinary Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
- * E-mail: (RJS); (JL)
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, China
- * E-mail: (RJS); (JL)
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Vipin CA, Luckett DJ, Harper JD, Ash GJ, Kilian A, Ellwood SR, Phan HT, Raman H. Construction of integrated linkage map of a recombinant inbred line population of white lupin (Lupinus albus L.). BREEDING SCIENCE 2013; 63:292-300. [PMID: 24273424 PMCID: PMC3770556 DOI: 10.1270/jsbbs.63.292] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 05/14/2013] [Indexed: 05/21/2023]
Abstract
We report the development of a Diversity Arrays Technology (DArT) marker panel and its utilisation in the development of an integrated genetic linkage map of white lupin (Lupinus albus L.) using an F8 recombinant inbred line population derived from Kiev Mutant/P27174. One hundred and thirty-six DArT markers were merged into the first genetic linkage map composed of 220 amplified fragment length polymorphisms (AFLPs) and 105 genic markers. The integrated map consists of 38 linkage groups of 441 markers and spans a total length of 2,169 cM, with an average interval size of 4.6 cM. The DArT markers exhibited good genome coverage and were associated with previously identified genic and AFLP markers linked with quantitative trait loci for anthracnose resistance, flowering time and alkaloid content. The improved genetic linkage map of white lupin will aid in the identification of markers for traits of interest and future syntenic studies.
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Affiliation(s)
- Cina Ann Vipin
- Graham Centre for Agricultural Innovation (an alliance between NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga Agricultural Institute,
Wagga Wagga, NSW 2650,
Australia
| | - David J. Luckett
- Graham Centre for Agricultural Innovation (an alliance between NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga Agricultural Institute,
Wagga Wagga, NSW 2650,
Australia
| | - John D.I. Harper
- Graham Centre for Agricultural Innovation (an alliance between NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga Agricultural Institute,
Wagga Wagga, NSW 2650,
Australia
- School of Agricultural and Wine Sciences, Charles Sturt University,
Wagga Wagga, NSW 2678,
Australia
| | - Gavin J. Ash
- Graham Centre for Agricultural Innovation (an alliance between NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga Agricultural Institute,
Wagga Wagga, NSW 2650,
Australia
- School of Agricultural and Wine Sciences, Charles Sturt University,
Wagga Wagga, NSW 2678,
Australia
| | - Andrzej Kilian
- Diversity Arrays Technology P/L,
1 Wilf Crane Crescent, Yarralumla, Canberra, ACT 2600,
Australia
| | - Simon R. Ellwood
- Department of Environment and Agriculture, Curtin University,
Kent Street, Bentley, Perth, Western Australia 6102,
Australia
| | - Huyen T.T. Phan
- Department of Environment and Agriculture, Curtin University,
Kent Street, Bentley, Perth, Western Australia 6102,
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 2650,
Australia
- Corresponding author (e-mail: )
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Raman H, Raman R, Kilian A, Detering F, Long Y, Edwards D, Parkin IAP, Sharpe AG, Nelson MN, Larkan N, Zou J, Meng J, Aslam MN, Batley J, Cowling WA, Lydiate D. A consensus map of rapeseed (Brassica napus L.) based on diversity array technology markers: applications in genetic dissection of qualitative and quantitative traits. BMC Genomics 2013; 14:277. [PMID: 23617817 PMCID: PMC3641989 DOI: 10.1186/1471-2164-14-277] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Accepted: 04/06/2013] [Indexed: 12/03/2022] Open
Abstract
Background Dense consensus genetic maps based on high-throughput genotyping platforms are valuable for making genetic gains in Brassica napus through quantitative trait locus identification, efficient predictive molecular breeding, and map-based gene cloning. This report describes the construction of the first B. napus consensus map consisting of a 1,359 anchored array based genotyping platform; Diversity Arrays Technology (DArT), and non-DArT markers from six populations originating from Australia, Canada, China and Europe. We aligned the B. napus DArT sequences with genomic scaffolds from Brassica rapa and Brassica oleracea, and identified DArT loci that showed linkage with qualitative and quantitative loci associated with agronomic traits. Results The integrated consensus map covered a total of 1,987.2 cM and represented all 19 chromosomes of the A and C genomes, with an average map density of one marker per 1.46 cM, corresponding to approximately 0.88 Mbp of the haploid genome. Through in silico physical mapping 2,457 out of 3,072 (80%) DArT clones were assigned to the genomic scaffolds of B. rapa (A genome) and B. oleracea (C genome). These were used to orientate the genetic consensus map with the chromosomal sequences. The DArT markers showed linkage with previously identified non-DArT markers associated with qualitative and quantitative trait loci for plant architecture, phenological components, seed and oil quality attributes, boron efficiency, sucrose transport, male sterility, and race-specific resistance to blackleg disease. Conclusions The DArT markers provide increased marker density across the B. napus genome. Most of the DArT markers represented on the current array were sequenced and aligned with the B. rapa and B. oleracea genomes, providing insight into the Brassica A and C genomes. This information can be utilised for comparative genomics and genomic evolution studies. In summary, this consensus map can be used to (i) integrate new generation markers such as SNP arrays and next generation sequencing data; (ii) anchor physical maps to facilitate assembly of B. napus genome sequences; and (iii) identify candidate genes underlying natural genetic variation for traits of interest.
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Affiliation(s)
- Harsh Raman
- EH Graham Centre for Agricultural Innovation (an alliance between NSWDPI and Charles Sturt University), Wagga Wagga Agricultural Institute, Wagga Wagga, NSW 2650, Australia
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Raman H, Raman R, Eckermann P, Coombes N, Manoli S, Zou X, Edwards D, Meng J, Prangnell R, Stiller J, Batley J, Luckett D, Wratten N, Dennis E. Genetic and physical mapping of flowering time loci in canola (Brassica napus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:119-32. [PMID: 22955939 DOI: 10.1007/s00122-012-1966-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2012] [Accepted: 08/10/2012] [Indexed: 05/18/2023]
Abstract
We identified quantitative trait loci (QTL) underlying variation for flowering time in a doubled haploid (DH) population of vernalisation-responsive canola (Brassica napus L.) cultivars Skipton and Ag-Spectrum and aligned them with physical map positions of predicted flowering genes from the Brassica rapa genome. Significant genetic variation in flowering time and response to vernalisation were observed among the DH lines from Skipton/Ag-Spectrum. A molecular linkage map was generated comprising 674 simple sequence repeat, sequence-related amplified polymorphism, sequence characterised amplified region, Diversity Array Technology, and candidate gene based markers loci. QTL analysis indicated that flowering time is a complex trait and is controlled by at least 20 loci, localised on ten different chromosomes. These loci each accounted for between 2.4 and 28.6% of the total genotypic variation for first flowering and response to vernalisation. However, identification of consistent QTL was found to be dependant upon growing environments. We compared the locations of QTL with the physical positions of predicted flowering time genes located on the sequenced genome of B. rapa. Some QTL associated with flowering time on A02, A03, A07, and C06 may represent homologues of known flowering time genes in Arabidopsis; VERNALISATION INSENSITIVE 3, APETALA1, CAULIFLOWER, FLOWERING LOCUS C, FLOWERING LOCUS T, CURLY LEAF, SHORT VEGETATIVE PHASE, GA3 OXIDASE, and LEAFY. Identification of the chromosomal location and effect of the genes influencing flowering time may hasten the development of canola varieties having an optimal time for flowering in target environments such as for low rainfall areas, via marker-assisted selection.
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Affiliation(s)
- Harsh Raman
- EH Graham Centre for Agricultural Innovation (an alliance between NSWDPI and Charles Sturt University), Wagga Wagga, Australia.
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Raman H, Raman R, Eckermann P, Coombes N, Manoli S, Zou X, Edwards D, Meng J, Prangnell R, Stiller J, Batley J, Luckett D, Wratten N, Dennis E. Genetic and physical mapping of flowering time loci in canola (Brassica napus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:119-132. [PMID: 22955939 DOI: 10.1007/s00122-012-1966-1968] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/06/2012] [Accepted: 08/10/2012] [Indexed: 05/24/2023]
Abstract
We identified quantitative trait loci (QTL) underlying variation for flowering time in a doubled haploid (DH) population of vernalisation-responsive canola (Brassica napus L.) cultivars Skipton and Ag-Spectrum and aligned them with physical map positions of predicted flowering genes from the Brassica rapa genome. Significant genetic variation in flowering time and response to vernalisation were observed among the DH lines from Skipton/Ag-Spectrum. A molecular linkage map was generated comprising 674 simple sequence repeat, sequence-related amplified polymorphism, sequence characterised amplified region, Diversity Array Technology, and candidate gene based markers loci. QTL analysis indicated that flowering time is a complex trait and is controlled by at least 20 loci, localised on ten different chromosomes. These loci each accounted for between 2.4 and 28.6% of the total genotypic variation for first flowering and response to vernalisation. However, identification of consistent QTL was found to be dependant upon growing environments. We compared the locations of QTL with the physical positions of predicted flowering time genes located on the sequenced genome of B. rapa. Some QTL associated with flowering time on A02, A03, A07, and C06 may represent homologues of known flowering time genes in Arabidopsis; VERNALISATION INSENSITIVE 3, APETALA1, CAULIFLOWER, FLOWERING LOCUS C, FLOWERING LOCUS T, CURLY LEAF, SHORT VEGETATIVE PHASE, GA3 OXIDASE, and LEAFY. Identification of the chromosomal location and effect of the genes influencing flowering time may hasten the development of canola varieties having an optimal time for flowering in target environments such as for low rainfall areas, via marker-assisted selection.
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Affiliation(s)
- Harsh Raman
- EH Graham Centre for Agricultural Innovation (an alliance between NSWDPI and Charles Sturt University), Wagga Wagga, Australia.
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Guo S, Zou J, Li R, Long Y, Chen S, Meng J. A genetic linkage map of Brassica carinata constructed with a doubled haploid population. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:1113-24. [PMID: 22669300 DOI: 10.1007/s00122-012-1898-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Accepted: 05/11/2012] [Indexed: 05/11/2023]
Abstract
Brassica carinata is an important oilseed crop with unique favourable traits that are desirable for other Brassica crops. However, given the limited research into genetic resources in B. carinata, knowledge of the genetic structure of this species is relatively poor. Nine homozygous, genetically distinct accessions of B. carinata were obtained via microspore culture, from which two divergent doubled haploid (DH) lines were used to develop a DH mapping population that consisted of 183 lines. The mapping population showed segregation of multiple traits of interest. A genetic map was constructed with PCR-based markers, and a total of 212 loci, which covered 1,703 cM, were assigned to eight linkage groups in the B genome and nine linkage groups in the C genome, which allowed comparison with genetic maps of other important Brassica species that contain the B/C genome(s). Loci for two Mendelian-inherited traits related to pigmentation (petal and anther tip colour) and one quantitative trait (seed coat colour) were identified using the linkage map. The significance of the mapping population in the context of genetic improvement of Brassica crops is discussed.
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Affiliation(s)
- Shaomin Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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Zou X, Suppanz I, Raman H, Hou J, Wang J, Long Y, Jung C, Meng J. Comparative analysis of FLC homologues in Brassicaceae provides insight into their role in the evolution of oilseed rape. PLoS One 2012; 7:e45751. [PMID: 23029223 PMCID: PMC3459951 DOI: 10.1371/journal.pone.0045751] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2012] [Accepted: 08/24/2012] [Indexed: 11/18/2022] Open
Abstract
We identified nine FLOWERING LOCUS C homologues (BnFLC) in Brassica napus and found that the coding sequences of all BnFLCs were relatively conserved but the intronic and promoter regions were more divergent. The BnFLC homologues were mapped to six of 19 chromosomes. All of the BnFLC homologues were located in the collinear region of FLC in the Arabidopsis genome except BnFLC.A3b and BnFLC.C3b, which were mapped to noncollinear regions of chromosome A3 and C3, respectively. Four of the homologues were associated significantly with quantitative trait loci for flowering time in two mapping populations. The BnFLC homologues showed distinct expression patterns in vegetative and reproductive organs, and at different developmental stages. BnFLC.A3b was differentially expressed between the winter-type and semi-winter-type cultivars. Microsynteny analysis indicated that BnFLC.A3b might have been translocated to the present segment in a cluster with other flowering-time regulators, such as a homologue of FRIGIDA in Arabidopsis. This cluster of flowering-time genes might have conferred a selective advantage to Brassica species in terms of increased adaptability to diverse environments during their evolution and domestication process.
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Affiliation(s)
- Xiaoxiao Zou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Ida Suppanz
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Harsh Raman
- EH Graham Centre for Agricultural Innovation (an alliance between the Charles Sturt University and New South Wales Department of Primary Industries), Wagga Wagga Agricultural Institute, Wagga Wagga, New South Wales, Australia
| | - Jinna Hou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Jing Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yan Long
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Christian Jung
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Jinling Meng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
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